From d64a942a76b240fd7529a708bac97a7d233258cb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 Aug 2021 12:32:26 +0200 Subject: [PATCH 001/159] fixed MappersTest --- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index c121dee2a..c431b4dd8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -726,8 +726,8 @@ public class MappersTest { final Dataset p = (Dataset) list.get(0); assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); - assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0)); + assertEquals(2, p.getOriginalId().size()); + assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); From 370dddb2fa8c27fbd95b618e22a2be9fcc8ebf40 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 7 Sep 2021 11:20:41 +0200 Subject: [PATCH 002/159] fix bug on oai iterator that skip record cleaned --- .../java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index 75dd746ea..4b254c0ef 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -161,7 +161,7 @@ public class OaiIterator implements Iterator { report.put(e.getClass().getName(), e.getMessage()); final String cleaned = XmlCleaner.cleanAllEntities(xml); try { - doc = DocumentHelper.parseText(xml); + doc = DocumentHelper.parseText(cleaned); } catch (final DocumentException e1) { final String resumptionToken = extractResumptionToken(xml); if (resumptionToken == null) { From ec94cc9b939d4cfe92643d0c1d14afe52e403559 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Oct 2021 09:41:27 +0200 Subject: [PATCH 003/159] IndexNotificationsJob test: persist contents on HDFS instead of passing them to ES --- .../dhp/broker/oa/IndexNotificationsJob.java | 29 ++----------------- 1 file changed, 3 insertions(+), 26 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 80549e1ce..7b65c27ab 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -101,33 +101,10 @@ public class IndexNotificationsJob { ngEncoder) .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); - final JavaRDD inputRdd = notifications + notifications .map((MapFunction) n -> prepareForIndexing(n, total), Encoders.STRING()) - .javaRDD(); - - final Map esCfg = new HashMap<>(); - // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); - - esCfg.put("es.index.auto.create", "false"); - esCfg.put("es.nodes", indexHost); - esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); - esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); - esCfg.put("es.batch.size.entries", esBatchSizeEntries); - esCfg.put("es.nodes.wan.only", esNodesWanOnly); - - log.info("*** Start indexing"); - JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); - log.info("*** End indexing"); - - log.info("*** Deleting old notifications"); - final String message = deleteOldNotifications(brokerApiBaseUrl, startTime - 1000); - log.info("*** Deleted notifications: " + message); - - log.info("*** sendNotifications (emails, ...)"); - sendNotifications(brokerApiBaseUrl, startTime - 1000); - log.info("*** ALL done."); - + .javaRDD() + .saveAsTextFile("/tmp/IndexNotificationsJob_test_6504"); } } From b01cd521b0eede2ad6ab8ab95e22f6a3dd14cae1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Oct 2021 11:26:33 +0200 Subject: [PATCH 004/159] removed configuration specifying the limit to 8 for spark.dynamicAllocation.maxExecutors --- .../dhp/broker/oa/notifications_only/oozie_app/workflow.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 248326d57..70ab7d344 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -135,7 +135,6 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} From 31a6ad1d79cea595d85a1ef9a15fc6ea714a97f3 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 4 Oct 2021 12:01:56 +0200 Subject: [PATCH 005/159] optimization of verifySubsriptions() --- .../dhp/broker/oa/IndexNotificationsJob.java | 39 +++++---- .../broker/oa/IndexNotificationsJobTest.java | 84 +++++++++++++++++++ 2 files changed, 105 insertions(+), 18 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 7b65c27ab..c66e5f4f4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -17,7 +17,6 @@ import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -25,7 +24,6 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -46,13 +44,14 @@ public class IndexNotificationsJob { private static final Logger log = LoggerFactory.getLogger(IndexNotificationsJob.class); + private static Map>> conditionsForSubscriptions = new HashMap<>(); + public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString(IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -89,6 +88,8 @@ public class IndexNotificationsJob { final List subscriptions = listSubscriptions(brokerApiBaseUrl); + initConditionsForSubscriptions(subscriptions); + log.info("Number of subscriptions: " + subscriptions.size()); if (subscriptions.size() > 0) { @@ -96,9 +97,7 @@ public class IndexNotificationsJob { final Encoder nEncoder = Encoders.bean(Notification.class); final Dataset notifications = ClusterUtils .readPath(spark, eventsPath, Event.class) - .map( - (MapFunction) e -> generateNotifications(e, subscriptions, startTime), - ngEncoder) + .map((MapFunction) e -> generateNotifications(e, subscriptions, startTime), ngEncoder) .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); notifications @@ -108,20 +107,27 @@ public class IndexNotificationsJob { } } - private static NotificationGroup generateNotifications(final Event e, + protected static void initConditionsForSubscriptions(final List subscriptions) { + subscriptions.forEach(s -> conditionsForSubscriptions.put(s.getSubscriptionId(), s.conditionsAsMap())); + } + + protected static NotificationGroup generateNotifications(final Event e, final List subscriptions, final long date) { final List list = subscriptions .stream() - .filter( - s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) - .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) + .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> verifyConditions(e.getMap(), conditionsAsMap(s))) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); return new NotificationGroup(list); } + private static Map> conditionsAsMap(final Subscription s) { + return conditionsForSubscriptions.get(s.getSubscriptionId()); + } + private static Notification generateNotification(final Subscription s, final Event e, final long date) { final Notification n = new Notification(); n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId())); @@ -145,18 +151,15 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange( - map.getTrust(), conditions.get("trust").get(0).getValue(), - conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch( - c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch(c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java new file mode 100644 index 000000000..ea5dbd5d1 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java @@ -0,0 +1,84 @@ + +package eu.dnetlib.dhp.broker.oa; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.util.Arrays; +import java.util.List; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.model.MappedFields; +import eu.dnetlib.dhp.broker.model.Subscription; +import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; + +class IndexNotificationsJobTest { + + private List subscriptions; + + @BeforeEach + void setUp() throws Exception { + final Subscription s = new Subscription(); + s.setTopic("ENRICH/MISSING/PID"); + s.setConditions("[{\"field\":\"targetDatasourceName\",\"fieldType\":\"STRING\",\"operator\":\"EXACT\",\"listParams\":[{\"value\":\"reposiTUm\"}]},{\"field\":\"trust\",\"fieldType\":\"FLOAT\",\"operator\":\"RANGE\",\"listParams\":[{\"value\":\"0\",\"otherValue\":\"1\"}]}]"); + subscriptions = Arrays.asList(s); + IndexNotificationsJob.initConditionsForSubscriptions(subscriptions); + } + + @Test + void testGenerateNotifications_invalid_topic() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PROJECT"); + + for (int i = 0; i < 10; i++) { + final long start = System.currentTimeMillis(); + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final long end = System.currentTimeMillis(); + + System.out.println("no topic - execution time (ms): " + (end - start)); + + assertEquals(0, res.getData().size()); + } + } + + @Test + void testGenerateNotifications_topic_match() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PID"); + event.setMap(new MappedFields()); + event.getMap().setTargetDatasourceName("reposiTUm"); + event.getMap().setTrust(0.8f); + + for (int i = 0; i < 10; i++) { + final long start = System.currentTimeMillis(); + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final long end = System.currentTimeMillis(); + + System.out.println("topic match - execution time (ms): " + (end - start)); + + assertEquals(1, res.getData().size()); + } + } + + @Test + void testGenerateNotifications_topic_no_match() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PID"); + event.setMap(new MappedFields()); + event.getMap().setTargetDatasourceName("Puma"); + event.getMap().setTrust(0.8f); + + for (int i = 0; i < 10; i++) { + final long start = System.currentTimeMillis(); + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final long end = System.currentTimeMillis(); + + System.out.println("topic no match - execution time (ms): " + (end - start)); + + assertEquals(0, res.getData().size()); + } + } + +} From 0a9ef34b56cdc1fb9783a0efb84dab29b03ebcbb Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 4 Oct 2021 15:46:12 +0200 Subject: [PATCH 006/159] test --- .../broker/oa/IndexNotificationsJobTest.java | 84 +++++++++++++------ 1 file changed, 60 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java index ea5dbd5d1..6010da2c3 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java @@ -18,6 +18,8 @@ class IndexNotificationsJobTest { private List subscriptions; + private static final int N_TIMES = 1_000_000; + @BeforeEach void setUp() throws Exception { final Subscription s = new Subscription(); @@ -32,15 +34,8 @@ class IndexNotificationsJobTest { final Event event = new Event(); event.setTopic("ENRICH/MISSING/PROJECT"); - for (int i = 0; i < 10; i++) { - final long start = System.currentTimeMillis(); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); - final long end = System.currentTimeMillis(); - - System.out.println("no topic - execution time (ms): " + (end - start)); - - assertEquals(0, res.getData().size()); - } + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + assertEquals(0, res.getData().size()); } @Test @@ -51,15 +46,8 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("reposiTUm"); event.getMap().setTrust(0.8f); - for (int i = 0; i < 10; i++) { - final long start = System.currentTimeMillis(); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); - final long end = System.currentTimeMillis(); - - System.out.println("topic match - execution time (ms): " + (end - start)); - - assertEquals(1, res.getData().size()); - } + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + assertEquals(1, res.getData().size()); } @Test @@ -70,15 +58,63 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("Puma"); event.getMap().setTrust(0.8f); - for (int i = 0; i < 10; i++) { - final long start = System.currentTimeMillis(); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); - final long end = System.currentTimeMillis(); + final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + assertEquals(0, res.getData().size()); + } - System.out.println("topic no match - execution time (ms): " + (end - start)); + @Test + void testGenerateNotifications_invalid_topic_repeated() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PROJECT"); - assertEquals(0, res.getData().size()); + // warm up + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + + final long start = System.currentTimeMillis(); + for (int i = 0; i < N_TIMES; i++) { + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); } + final long end = System.currentTimeMillis(); + System.out.println(String.format("no topic - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); + + } + + @Test + void testGenerateNotifications_topic_match_repeated() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PID"); + event.setMap(new MappedFields()); + event.getMap().setTargetDatasourceName("reposiTUm"); + event.getMap().setTrust(0.8f); + + // warm up + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + + final long start = System.currentTimeMillis(); + for (int i = 0; i < N_TIMES; i++) { + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + } + final long end = System.currentTimeMillis(); + System.out.println(String.format("topic match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); + } + + @Test + void testGenerateNotifications_topic_no_match_repeated() { + final Event event = new Event(); + event.setTopic("ENRICH/MISSING/PID"); + event.setMap(new MappedFields()); + event.getMap().setTargetDatasourceName("Puma"); + event.getMap().setTrust(0.8f); + + // warm up + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + + final long start = System.currentTimeMillis(); + for (int i = 0; i < N_TIMES; i++) { + IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + } + final long end = System.currentTimeMillis(); + System.out.println(String.format("topic no match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); } } From 8bbaa173354e99610053c5adfefd3f1f5c78f43f Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 5 Oct 2021 09:20:37 +0200 Subject: [PATCH 007/159] reimplemented of conditions cache as a non static variable --- .../dhp/broker/oa/IndexNotificationsJob.java | 42 +++++++++++-------- .../broker/oa/IndexNotificationsJobTest.java | 41 +++++++++++------- 2 files changed, 51 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index c66e5f4f4..5dc3315c4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -44,14 +44,13 @@ public class IndexNotificationsJob { private static final Logger log = LoggerFactory.getLogger(IndexNotificationsJob.class); - private static Map>> conditionsForSubscriptions = new HashMap<>(); - public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString( + IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -88,16 +87,19 @@ public class IndexNotificationsJob { final List subscriptions = listSubscriptions(brokerApiBaseUrl); - initConditionsForSubscriptions(subscriptions); - log.info("Number of subscriptions: " + subscriptions.size()); if (subscriptions.size() > 0) { + final Map>> conditionsMap = prepareConditionsMap(subscriptions); + final Encoder ngEncoder = Encoders.bean(NotificationGroup.class); final Encoder nEncoder = Encoders.bean(Notification.class); final Dataset notifications = ClusterUtils .readPath(spark, eventsPath, Event.class) - .map((MapFunction) e -> generateNotifications(e, subscriptions, startTime), ngEncoder) + .map( + (MapFunction) e -> generateNotifications( + e, subscriptions, conditionsMap, startTime), + ngEncoder) .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); notifications @@ -107,27 +109,28 @@ public class IndexNotificationsJob { } } - protected static void initConditionsForSubscriptions(final List subscriptions) { - subscriptions.forEach(s -> conditionsForSubscriptions.put(s.getSubscriptionId(), s.conditionsAsMap())); + protected static Map>> prepareConditionsMap( + final List subscriptions) { + final Map>> map = new HashMap<>(); + subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap())); + return map; } protected static NotificationGroup generateNotifications(final Event e, final List subscriptions, + final Map>> conditionsMap, final long date) { final List list = subscriptions .stream() - .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) - .filter(s -> verifyConditions(e.getMap(), conditionsAsMap(s))) + .filter( + s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId()))) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); return new NotificationGroup(list); } - private static Map> conditionsAsMap(final Subscription s) { - return conditionsForSubscriptions.get(s.getSubscriptionId()); - } - private static Notification generateNotification(final Subscription s, final Event e, final long date) { final Notification n = new Notification(); n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId())); @@ -151,15 +154,18 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange( + map.getTrust(), conditions.get("trust").get(0).getValue(), + conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch(c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch( + c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java index 6010da2c3..8ecb3061b 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java @@ -5,10 +5,12 @@ import static org.junit.jupiter.api.Assertions.assertEquals; import java.util.Arrays; import java.util.List; +import java.util.Map; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; +import eu.dnetlib.dhp.broker.model.ConditionParams; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.MappedFields; import eu.dnetlib.dhp.broker.model.Subscription; @@ -18,15 +20,19 @@ class IndexNotificationsJobTest { private List subscriptions; + private Map>> conditionsMap; + private static final int N_TIMES = 1_000_000; @BeforeEach void setUp() throws Exception { final Subscription s = new Subscription(); s.setTopic("ENRICH/MISSING/PID"); - s.setConditions("[{\"field\":\"targetDatasourceName\",\"fieldType\":\"STRING\",\"operator\":\"EXACT\",\"listParams\":[{\"value\":\"reposiTUm\"}]},{\"field\":\"trust\",\"fieldType\":\"FLOAT\",\"operator\":\"RANGE\",\"listParams\":[{\"value\":\"0\",\"otherValue\":\"1\"}]}]"); + s + .setConditions( + "[{\"field\":\"targetDatasourceName\",\"fieldType\":\"STRING\",\"operator\":\"EXACT\",\"listParams\":[{\"value\":\"reposiTUm\"}]},{\"field\":\"trust\",\"fieldType\":\"FLOAT\",\"operator\":\"RANGE\",\"listParams\":[{\"value\":\"0\",\"otherValue\":\"1\"}]}]"); subscriptions = Arrays.asList(s); - IndexNotificationsJob.initConditionsForSubscriptions(subscriptions); + conditionsMap = IndexNotificationsJob.prepareConditionsMap(subscriptions); } @Test @@ -34,7 +40,8 @@ class IndexNotificationsJobTest { final Event event = new Event(); event.setTopic("ENRICH/MISSING/PROJECT"); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final NotificationGroup res = IndexNotificationsJob + .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(0, res.getData().size()); } @@ -46,7 +53,8 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("reposiTUm"); event.getMap().setTrust(0.8f); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final NotificationGroup res = IndexNotificationsJob + .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(1, res.getData().size()); } @@ -58,7 +66,8 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("Puma"); event.getMap().setTrust(0.8f); - final NotificationGroup res = IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + final NotificationGroup res = IndexNotificationsJob + .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(0, res.getData().size()); } @@ -68,14 +77,15 @@ class IndexNotificationsJobTest { event.setTopic("ENRICH/MISSING/PROJECT"); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); - System.out.println(String.format("no topic - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); + System.out + .println(String.format("no topic - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); } @@ -88,14 +98,15 @@ class IndexNotificationsJobTest { event.getMap().setTrust(0.8f); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); - System.out.println(String.format("topic match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); + System.out + .println(String.format("topic match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); } @Test @@ -107,14 +118,16 @@ class IndexNotificationsJobTest { event.getMap().setTrust(0.8f); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, 0); + IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); - System.out.println(String.format("topic no match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); + System.out + .println( + String.format("topic no match - repeated %s times - execution time: %s ms ", N_TIMES, end - start)); } } From 69008e20c2e1c4e6af8f45c8ad4acd17bdf54fe7 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 5 Oct 2021 11:58:20 +0200 Subject: [PATCH 008/159] log and tests --- .../dhp/broker/oa/IndexNotificationsJob.java | 2 + .../oa/samples/SimpleVariableJobTest.java | 132 ++++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/samples/SimpleVariableJobTest.java diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 5dc3315c4..fb2e26ba2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -92,6 +92,8 @@ public class IndexNotificationsJob { if (subscriptions.size() > 0) { final Map>> conditionsMap = prepareConditionsMap(subscriptions); + log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap)); + final Encoder ngEncoder = Encoders.bean(NotificationGroup.class); final Encoder nEncoder = Encoders.bean(Notification.class); final Dataset notifications = ClusterUtils diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/samples/SimpleVariableJobTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/samples/SimpleVariableJobTest.java new file mode 100644 index 000000000..a6d1c89d3 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/samples/SimpleVariableJobTest.java @@ -0,0 +1,132 @@ + +package eu.dnetlib.dhp.broker.oa.samples; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonParseException; +import com.fasterxml.jackson.databind.JsonMappingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.broker.model.ConditionParams; +import eu.dnetlib.dhp.broker.model.MapCondition; +import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils; + +@Disabled +public class SimpleVariableJobTest { + + private static final Logger log = LoggerFactory.getLogger(SimpleVariableJobTest.class); + + private static Path workingDir; + + private static SparkSession spark; + + private final static List inputList = new ArrayList<>(); + + private static final Map>> staticMap = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + + workingDir = Files.createTempDirectory(SimpleVariableJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + final SparkConf conf = new SparkConf(); + conf.setAppName(SimpleVariableJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + // conf.set("spark.sql.warehouse.dir", workingDir.toString()); + // conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SimpleVariableJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + for (int i = 0; i < 1_000_000; i++) { + inputList.add("record " + i); + } + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testSimpleVariableJob() throws Exception { + final Map>> map = fillMap(); + + final long n = spark + .createDataset(inputList, Encoders.STRING()) + .filter(s -> filter(map.get(s))) + .map((MapFunction) s -> s.toLowerCase(), Encoders.STRING()) + .count(); + + System.out.println(n); + } + + @Test + public void testSimpleVariableJob_static() throws Exception { + + staticMap.putAll(fillMap()); + + final long n = spark + .createDataset(inputList, Encoders.STRING()) + .filter(s -> filter(staticMap.get(s))) + .map((MapFunction) s -> s.toLowerCase(), Encoders.STRING()) + .count(); + + System.out.println(n); + } + + private static Map>> fillMap() + throws JsonParseException, JsonMappingException, IOException { + final String s = "[{\"field\":\"targetDatasourceName\",\"fieldType\":\"STRING\",\"operator\":\"EXACT\",\"listParams\":[{\"value\":\"reposiTUm\"}]},{\"field\":\"trust\",\"fieldType\":\"FLOAT\",\"operator\":\"RANGE\",\"listParams\":[{\"value\":\"0\",\"otherValue\":\"1\"}]}]"; + + final ObjectMapper mapper = new ObjectMapper(); + final List list = mapper + .readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, MapCondition.class)); + final Map> conditions = list + .stream() + .filter(mc -> !mc.getListParams().isEmpty()) + .collect(Collectors.toMap(MapCondition::getField, MapCondition::getListParams)); + + final Map>> map = new HashMap<>(); + inputList.forEach(i -> map.put(i, conditions)); + return map; + } + + private static boolean filter(final Map> conditions) { + if (conditions.containsKey("targetDatasourceName") + && !SubscriptionUtils + .verifyExact("reposiTUm", conditions.get("targetDatasourceName").get(0).getValue())) { + return false; + } + return true; + } + +} From 210d6c0e6d002d76ada343ad4f526cc60e70b41d Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 5 Oct 2021 13:57:46 +0200 Subject: [PATCH 009/159] generateNotificationsJob and indexNotificationsJob --- .../broker/oa/GenerateNotificationsJob.java | 184 ++++++++++++++++++ .../dhp/broker/oa/IndexNotificationsJob.java | 168 +++------------- .../oa/generate_all/oozie_app/workflow.xml | 24 +++ .../dhp/broker/oa/generate_notifications.json | 14 ++ .../notifications_only/oozie_app/workflow.xml | 27 ++- 5 files changed, 279 insertions(+), 138 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java create mode 100644 dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_notifications.json diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java new file mode 100644 index 000000000..21c6c64a6 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java @@ -0,0 +1,184 @@ + +package eu.dnetlib.dhp.broker.oa; + +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import org.apache.commons.codec.digest.DigestUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.util.LongAccumulator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.model.ConditionParams; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.model.MappedFields; +import eu.dnetlib.dhp.broker.model.Notification; +import eu.dnetlib.dhp.broker.model.Subscription; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; +import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils; + +public class GenerateNotificationsJob { + + private static final Logger log = LoggerFactory.getLogger(GenerateNotificationsJob.class); + + public static void main(final String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString(GenerateNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_notifications.json"))); + parser.parseArgument(args); + + final SparkConf conf = new SparkConf(); + + final String eventsPath = parser.get("outputDir") + "/events"; + log.info("eventsPath: {}", eventsPath); + + final String notificationsPath = parser.get("outputDir") + "/notifications"; + log.info("notificationsPath: {}", notificationsPath); + + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); + log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); + + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); + + final LongAccumulator total = spark.sparkContext().longAccumulator("total_notifications"); + + final long startTime = new Date().getTime(); + + final List subscriptions = listSubscriptions(brokerApiBaseUrl); + + log.info("Number of subscriptions: " + subscriptions.size()); + + if (subscriptions.size() > 0) { + final Map>> conditionsMap = prepareConditionsMap(subscriptions); + + log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap)); + + final Encoder ngEncoder = Encoders.bean(NotificationGroup.class); + final Encoder nEncoder = Encoders.bean(Notification.class); + final Dataset notifications = ClusterUtils + .readPath(spark, eventsPath, Event.class) + .map((MapFunction) e -> generateNotifications(e, subscriptions, conditionsMap, startTime), ngEncoder) + .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); + + ClusterUtils.save(notifications, notificationsPath, Notification.class, total); + } + } + + protected static Map>> prepareConditionsMap( + final List subscriptions) { + final Map>> map = new HashMap<>(); + subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap())); + return map; + } + + protected static NotificationGroup generateNotifications(final Event e, + final List subscriptions, + final Map>> conditionsMap, + final long date) { + final List list = subscriptions + .stream() + .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId()))) + .map(s -> generateNotification(s, e, date)) + .collect(Collectors.toList()); + + return new NotificationGroup(list); + } + + private static Notification generateNotification(final Subscription s, final Event e, final long date) { + final Notification n = new Notification(); + n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId())); + n.setSubscriptionId(s.getSubscriptionId()); + n.setEventId(e.getEventId()); + n.setProducerId(e.getProducerId()); + n.setTopic(e.getTopic()); + n.setPayload(e.getPayload()); + n.setMap(e.getMap()); + n.setDate(date); + return n; + } + + private static boolean verifyConditions(final MappedFields map, + final Map> conditions) { + if (conditions.containsKey("targetDatasourceName") + && !SubscriptionUtils + .verifyExact(map.getTargetDatasourceName(), conditions.get("targetDatasourceName").get(0).getValue())) { + return false; + } + + if (conditions.containsKey("trust") + && !SubscriptionUtils + .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + return false; + } + + if (conditions.containsKey("targetDateofacceptance") && !conditions + .get("targetDateofacceptance") + .stream() + .anyMatch(c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + return false; + } + + if (conditions.containsKey("targetResultTitle") + && !conditions + .get("targetResultTitle") + .stream() + .anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) { + return false; + } + + if (conditions.containsKey("targetAuthors") + && !conditions + .get("targetAuthors") + .stream() + .allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) { + return false; + } + + return !conditions.containsKey("targetSubjects") + || conditions + .get("targetSubjects") + .stream() + .allMatch(c -> SubscriptionUtils.verifyListExact(map.getTargetSubjects(), c.getValue())); + + } + + private static List listSubscriptions(final String brokerApiBaseUrl) throws Exception { + final String url = brokerApiBaseUrl + "/api/subscriptions"; + final HttpGet req = new HttpGet(url); + + final ObjectMapper mapper = new ObjectMapper(); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + final String s = IOUtils.toString(response.getEntity().getContent()); + return mapper + .readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, Subscription.class)); + } + } + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index fb2e26ba2..55e82446f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -2,28 +2,22 @@ package eu.dnetlib.dhp.broker.oa; import java.io.IOException; -import java.util.Date; import java.util.HashMap; -import java.util.List; import java.util.Map; -import java.util.stream.Collectors; -import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpDelete; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; +import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -31,14 +25,8 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.broker.model.ConditionParams; -import eu.dnetlib.dhp.broker.model.Event; -import eu.dnetlib.dhp.broker.model.MappedFields; import eu.dnetlib.dhp.broker.model.Notification; -import eu.dnetlib.dhp.broker.model.Subscription; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; -import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; -import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils; public class IndexNotificationsJob { @@ -48,15 +36,14 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString(IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); - final String eventsPath = parser.get("outputDir") + "/events"; - log.info("eventsPath: {}", eventsPath); + final String notificationsPath = parser.get("outputDir") + "/notifications"; + log.info("notificationsPath: {}", notificationsPath); final String index = parser.get("index"); log.info("index: {}", index); @@ -83,131 +70,38 @@ public class IndexNotificationsJob { final LongAccumulator total = spark.sparkContext().longAccumulator("total_indexed"); - final long startTime = new Date().getTime(); + final Long date = ClusterUtils + .readPath(spark, notificationsPath, Notification.class) + .first() + .getDate(); - final List subscriptions = listSubscriptions(brokerApiBaseUrl); + final JavaRDD toIndexRdd = ClusterUtils + .readPath(spark, notificationsPath, Notification.class) + .map((MapFunction) n -> prepareForIndexing(n, total), Encoders.STRING()) + .javaRDD(); - log.info("Number of subscriptions: " + subscriptions.size()); + final Map esCfg = new HashMap<>(); - if (subscriptions.size() > 0) { - final Map>> conditionsMap = prepareConditionsMap(subscriptions); + esCfg.put("es.index.auto.create", "false"); + esCfg.put("es.nodes", indexHost); + esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY + esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); + esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); + esCfg.put("es.batch.size.entries", esBatchSizeEntries); + esCfg.put("es.nodes.wan.only", esNodesWanOnly); - log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap)); + log.info("*** Start indexing"); + JavaEsSpark.saveJsonToEs(toIndexRdd, index, esCfg); + log.info("*** End indexing"); - final Encoder ngEncoder = Encoders.bean(NotificationGroup.class); - final Encoder nEncoder = Encoders.bean(Notification.class); - final Dataset notifications = ClusterUtils - .readPath(spark, eventsPath, Event.class) - .map( - (MapFunction) e -> generateNotifications( - e, subscriptions, conditionsMap, startTime), - ngEncoder) - .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); + log.info("*** Deleting old notifications"); + final String message = deleteOldNotifications(brokerApiBaseUrl, date - 1000); + log.info("*** Deleted notifications: {}", message); - notifications - .map((MapFunction) n -> prepareForIndexing(n, total), Encoders.STRING()) - .javaRDD() - .saveAsTextFile("/tmp/IndexNotificationsJob_test_6504"); - } - } + log.info("*** sendNotifications (emails, ...)"); + sendNotifications(brokerApiBaseUrl, date - 1000); + log.info("*** ALL done."); - protected static Map>> prepareConditionsMap( - final List subscriptions) { - final Map>> map = new HashMap<>(); - subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap())); - return map; - } - - protected static NotificationGroup generateNotifications(final Event e, - final List subscriptions, - final Map>> conditionsMap, - final long date) { - final List list = subscriptions - .stream() - .filter( - s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) - .filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId()))) - .map(s -> generateNotification(s, e, date)) - .collect(Collectors.toList()); - - return new NotificationGroup(list); - } - - private static Notification generateNotification(final Subscription s, final Event e, final long date) { - final Notification n = new Notification(); - n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId())); - n.setSubscriptionId(s.getSubscriptionId()); - n.setEventId(e.getEventId()); - n.setProducerId(e.getProducerId()); - n.setTopic(e.getTopic()); - n.setPayload(e.getPayload()); - n.setMap(e.getMap()); - n.setDate(date); - return n; - } - - private static boolean verifyConditions(final MappedFields map, - final Map> conditions) { - if (conditions.containsKey("targetDatasourceName") - && !SubscriptionUtils - .verifyExact(map.getTargetDatasourceName(), conditions.get("targetDatasourceName").get(0).getValue())) { - return false; - } - - if (conditions.containsKey("trust") - && !SubscriptionUtils - .verifyFloatRange( - map.getTrust(), conditions.get("trust").get(0).getValue(), - conditions.get("trust").get(0).getOtherValue())) { - return false; - } - - if (conditions.containsKey("targetDateofacceptance") && !conditions - .get("targetDateofacceptance") - .stream() - .anyMatch( - c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { - return false; - } - - if (conditions.containsKey("targetResultTitle") - && !conditions - .get("targetResultTitle") - .stream() - .anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) { - return false; - } - - if (conditions.containsKey("targetAuthors") - && !conditions - .get("targetAuthors") - .stream() - .allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) { - return false; - } - - return !conditions.containsKey("targetSubjects") - || conditions - .get("targetSubjects") - .stream() - .allMatch(c -> SubscriptionUtils.verifyListExact(map.getTargetSubjects(), c.getValue())); - - } - - private static List listSubscriptions(final String brokerApiBaseUrl) throws Exception { - final String url = brokerApiBaseUrl + "/api/subscriptions"; - final HttpGet req = new HttpGet(url); - - final ObjectMapper mapper = new ObjectMapper(); - - try (final CloseableHttpClient client = HttpClients.createDefault()) { - try (final CloseableHttpResponse response = client.execute(req)) { - final String s = IOUtils.toString(response.getEntity().getContent()); - return mapper - .readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, Subscription.class)); - } - } } private static String deleteOldNotifications(final String brokerApiBaseUrl, final long l) throws Exception { diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index ea80c3acf..1a98a2513 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -542,6 +542,30 @@ --dbPassword${brokerDbPassword} --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + yarn + cluster + GenerateNotificationsJob + eu.dnetlib.dhp.broker.oa.GenerateNotificationsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --brokerApiBaseUrl${brokerApiBaseUrl} + diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_notifications.json new file mode 100644 index 000000000..6e12783b9 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_notifications.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "o", + "paramLongName": "outputDir", + "paramDescription": "the dir that contains the events folder", + "paramRequired": true + }, + { + "paramName": "broker", + "paramLongName": "brokerApiBaseUrl", + "paramDescription": "the url of the broker service api", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 70ab7d344..d2d7b6d11 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -119,12 +119,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + GenerateNotificationsJob + eu.dnetlib.dhp.broker.oa.GenerateNotificationsJob + dhp-broker-events-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --outputDir${outputDir} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + yarn @@ -135,6 +159,7 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors="8" --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} From d6e1f224086380de758d6be2854a13b6fe8809b4 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 5 Oct 2021 15:09:18 +0200 Subject: [PATCH 010/159] max numbers of workers for indexing --- .../dhp/broker/oa/generate_all/oozie_app/workflow.xml | 9 +++++++-- .../broker/oa/notifications_only/oozie_app/workflow.xml | 7 ++++++- .../dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml | 7 ++++++- 3 files changed, 19 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 1a98a2513..bc6778f52 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -115,6 +115,11 @@ spark2EventLogDir spark 2.* event log dir location + + sparkMaxExecutorsForIndexing + 8 + Max number of workers for ElasticSearch indexing + @@ -498,7 +503,7 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} @@ -580,7 +585,7 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index d2d7b6d11..0d226d78e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -98,6 +98,11 @@ spark2EventLogDir spark 2.* event log dir location + + sparkMaxExecutorsForIndexing + 8 + Max number of workers for ElasticSearch indexing + @@ -159,7 +164,7 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml index 9095004ad..87adfffaa 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/reindex/oozie_app/workflow.xml @@ -75,6 +75,11 @@ spark2EventLogDir spark 2.* event log dir location + + sparkMaxExecutorsForIndexing + 8 + Max number of workers for ElasticSearch indexing + @@ -112,7 +117,7 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} From 2f61054cd198ce563fba2149b23c53aafbaf7029 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Oct 2021 18:29:42 +0200 Subject: [PATCH 011/159] code formatting --- .../main/java/eu/dnetlib/dhp/PropagationConstant.java | 11 ++++++++--- .../SparkOrcidToResultFromSemRelJob.java | 7 +++++-- .../SparkResultToCommunityFromOrganizationJob.java | 4 ++-- .../SparkResultToCommunityThroughSemRelJob.java | 4 ++-- .../dhp/oa/provision/IndexRecordTransformerTest.java | 11 ++++++----- 5 files changed, 23 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 0d7c74475..23e97a97a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -69,7 +69,7 @@ public class PropagationConstant { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_COUNTRY_INSTREPO_CLASS_ID, PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS)); + ModelConstants.DNET_PROVENANCE_ACTIONS)); return nc; } @@ -84,7 +84,8 @@ public class PropagationConstant { return di; } - public static Qualifier getQualifier(String inference_class_id, String inference_class_name, String qualifierSchema) { + public static Qualifier getQualifier(String inference_class_id, String inference_class_name, + String qualifierSchema) { Qualifier pa = new Qualifier(); pa.setClassid(inference_class_id); pa.setClassname(inference_class_name); @@ -108,7 +109,11 @@ public class PropagationConstant { r.setRelClass(rel_class); r.setRelType(rel_type); r.setSubRelType(subrel_type); - r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name, ModelConstants.DNET_PROVENANCE_ACTIONS)); + r + .setDataInfo( + getDataInfo( + inference_provenance, inference_class_id, inference_class_name, + ModelConstants.DNET_PROVENANCE_ACTIONS)); return r; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index 68949b900..a38b4da2e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -173,14 +173,17 @@ public class SparkOrcidToResultFromSemRelJob { if (toaddpid) { StructuredProperty p = new StructuredProperty(); p.setValue(autoritative_author.getOrcid()); - p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES)); + p + .setQualifier( + getQualifier( + ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES)); p .setDataInfo( getDataInfo( PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS)); + ModelConstants.DNET_PROVENANCE_ACTIONS)); Optional> authorPid = Optional.ofNullable(author.getPid()); if (authorPid.isPresent()) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 1289ff644..50df08f8c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -10,7 +10,6 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -22,6 +21,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; @@ -130,7 +130,7 @@ public class SparkResultToCommunityFromOrganizationJob { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); + ModelConstants.DNET_PROVENANCE_ACTIONS))); propagatedContexts.add(newContext); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 7f76ead94..f31a26230 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; @@ -126,7 +126,7 @@ public class SparkResultToCommunityThroughSemRelJob { PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); + ModelConstants.DNET_PROVENANCE_ACTIONS))); return newContext; } return null; diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index 1c7dce3f2..64935e79d 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -84,13 +84,15 @@ public class IndexRecordTransformerTest { @Test public void testForEOSCFutureTraining() throws IOException, TransformerException { - final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml")); + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml")); testRecordTransformation(record); } @Test public void testForEOSCFutureAirQualityCopernicus() throws IOException, TransformerException { - final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml")); + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml")); testRecordTransformation(record); } @@ -102,12 +104,11 @@ public class IndexRecordTransformerTest { @Test public void testForEOSCFutureB2SharePlotRelatedORP() throws IOException, TransformerException { - final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml")); + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml")); testRecordTransformation(record); } - - private void testRecordTransformation(final String record) throws IOException, TransformerException { final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")); From 8db39c86e2ad41f0feefa21e94d8700690884608 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 13 Oct 2021 11:34:24 +0200 Subject: [PATCH 012/159] added new parameter in the doiboost process workflow to specify a folder for the process of MAG dataset --- .../dnetlib/dhp/doiboost/process/oozie_app/workflow.xml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index eb82c3a7d..282c06f4e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -48,7 +48,11 @@ inputPathMAG - the MAG working path + the MAG input path + + + workingPathMAG + the MAG working path where to store the intermediate process results @@ -138,7 +142,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${inputPathMAG}/dataset - --workingPath${inputPathMAG}/process_p + --workingPath${workingPathMAG} --targetPath${workingPath} --masteryarn-cluster From 4b1920f008955e429ac20037fa66cb7676633b8f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 13 Oct 2021 15:33:50 +0200 Subject: [PATCH 013/159] changed the working path parameter value as dependant from the dnet-workflow working dir parameter --- .../eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index 282c06f4e..29a12f4df 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -50,10 +50,6 @@ inputPathMAG the MAG input path - - workingPathMAG - the MAG working path where to store the intermediate process results - @@ -142,7 +138,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --sourcePath${inputPathMAG}/dataset - --workingPath${workingPathMAG} + --workingPath${workingPath}/MAG --targetPath${workingPath} --masteryarn-cluster From e15a1969a57726228f487e8b06b467ad5cdbef33 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 14 Oct 2021 14:33:56 +0200 Subject: [PATCH 014/159] applying fix on the DOIBoost construction process that somehow wasn't part of the merge done in 83c90c71809c947adcfc1e70eb9d9fad195d87aa --- .../eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index e501b4823..c08e09f53 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -206,9 +206,9 @@ object SparkGenerateDoiBoost { (r.getSource, r) else if (r.getTarget.startsWith("unresolved")) (r.getTarget,r) - else + else ("resolved", r) - }) + })(Encoders.tuple(Encoders.STRING, mapEncoderRel)) val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2) @@ -221,8 +221,8 @@ object SparkGenerateDoiBoost { currentRels.setSource(currentOrgs._1) else currentRels.setTarget(currentOrgs._1) - currentRels - }.write.save(s"$workingDirPath/doiBoostPublicationAffiliation") + currentRels + }.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation") magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => { val affiliation = item._2 @@ -242,6 +242,6 @@ object SparkGenerateDoiBoost { else null }).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization") - } + } -} +} \ No newline at end of file From e471f12d5e3eebfddc7ece9b804ef998112bd48f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 Oct 2021 12:35:38 +0200 Subject: [PATCH 015/159] hotfix: recovered implementation removing the hardcoded working_dirs --- .../CreateRelatedEntitiesJob_phase1.java | 39 +++++++++---------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index a33a45517..48e5945c0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -52,8 +52,11 @@ public class CreateRelatedEntitiesJob_phase1 { final String jsonConfiguration = IOUtils .toString( - PrepareRelationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json")); + Objects + .requireNonNull( + CreateRelatedEntitiesJob_phase1.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -75,6 +78,7 @@ public class CreateRelatedEntitiesJob_phase1 { final String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); + @SuppressWarnings("unchecked") final Class entityClazz = (Class) Class.forName(graphTableClassName); final SparkConf conf = new SparkConf(); @@ -101,22 +105,12 @@ public class CreateRelatedEntitiesJob_phase1 { Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class))) .cache(); - readPathEntity(spark, inputEntityPath, clazz) + final Dataset> entities = readPathEntity(spark, inputEntityPath, clazz) .filter("dataInfo.invisible == false") .map( (MapFunction>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)), - Encoders - .tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) - .write() - .mode(SaveMode.Overwrite) - .save("/tmp/beta_provision/working_dir/update_solr/join_partial/relatedEntities/" + clazz.getSimpleName()); - - final Dataset> entities = spark - .read() - .load("/tmp/beta_provision/working_dir/update_solr/join_partial/relatedEntities/" + clazz.getSimpleName()) - .as( - Encoders - .tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))); + Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) + .cache(); relsByTarget .joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner") @@ -149,8 +143,10 @@ public class CreateRelatedEntitiesJob_phase1 { re.setId(entity.getId()); re.setType(EntityType.fromClass(clazz).name()); - if (entity.getPid() != null) + // TODO move the max number of PIDs to eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits + if (Objects.nonNull(entity.getPid())) { re.setPid(entity.getPid().stream().limit(400).collect(Collectors.toList())); + } re.setCollectedfrom(entity.getCollectedfrom()); switch (EntityType.fromClass(clazz)) { @@ -212,7 +208,7 @@ public class CreateRelatedEntitiesJob_phase1 { final List> f = p.getFundingtree(); if (!f.isEmpty()) { - re.setFundingtree(f.stream().map(s -> s.getValue()).collect(Collectors.toList())); + re.setFundingtree(f.stream().map(Field::getValue).collect(Collectors.toList())); } break; } @@ -227,15 +223,16 @@ public class CreateRelatedEntitiesJob_phase1 { return Optional .ofNullable(f) .filter(Objects::nonNull) - .map(x -> x.getValue()) + .map(Field::getValue) .orElse(defaultValue); } /** - * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file, + * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text + * file * - * @param spark - * @param relationPath + * @param spark the SparkSession + * @param relationPath the path storing the relation objects * @return the Dataset containing all the relationships */ private static Dataset readPathRelation( From bdffa86c2f5cb8571520c5bfd79c35e56a6950e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 19 Oct 2021 15:39:38 +0200 Subject: [PATCH 016/159] undo last commit --- .../dhp/broker/oa/IndexNotificationsJob.java | 75 +++++++++---------- .../notifications_only/oozie_app/workflow.xml | 1 - 2 files changed, 34 insertions(+), 42 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index e8ef5dd3e..fb2e26ba2 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -17,7 +17,6 @@ import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -25,7 +24,6 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -33,7 +31,11 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.broker.model.*; +import eu.dnetlib.dhp.broker.model.ConditionParams; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.model.MappedFields; +import eu.dnetlib.dhp.broker.model.Notification; +import eu.dnetlib.dhp.broker.model.Subscription; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils; @@ -85,55 +87,46 @@ public class IndexNotificationsJob { final List subscriptions = listSubscriptions(brokerApiBaseUrl); - log.info("Number of subscriptions: {}", subscriptions.size()); + log.info("Number of subscriptions: " + subscriptions.size()); + + if (subscriptions.size() > 0) { + final Map>> conditionsMap = prepareConditionsMap(subscriptions); + + log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap)); - if (!subscriptions.isEmpty()) { final Encoder ngEncoder = Encoders.bean(NotificationGroup.class); final Encoder nEncoder = Encoders.bean(Notification.class); final Dataset notifications = ClusterUtils .readPath(spark, eventsPath, Event.class) .map( - (MapFunction) e -> generateNotifications(e, subscriptions, startTime), + (MapFunction) e -> generateNotifications( + e, subscriptions, conditionsMap, startTime), ngEncoder) .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); - final JavaRDD inputRdd = notifications + notifications .map((MapFunction) n -> prepareForIndexing(n, total), Encoders.STRING()) - .javaRDD(); - - final Map esCfg = new HashMap<>(); - - esCfg.put("es.index.auto.create", "false"); - esCfg.put("es.nodes", indexHost); - esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY - esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount); - esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait); - esCfg.put("es.batch.size.entries", esBatchSizeEntries); - esCfg.put("es.nodes.wan.only", esNodesWanOnly); - - log.info("*** Start indexing"); - JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); - log.info("*** End indexing"); - - log.info("*** Deleting old notifications"); - final String message = deleteOldNotifications(brokerApiBaseUrl, startTime - 1000); - log.info("*** Deleted notifications: {}", message); - - log.info("*** sendNotifications (emails, ...)"); - sendNotifications(brokerApiBaseUrl, startTime - 1000); - log.info("*** ALL done."); - + .javaRDD() + .saveAsTextFile("/tmp/IndexNotificationsJob_test_6504"); } } - private static NotificationGroup generateNotifications(final Event e, + protected static Map>> prepareConditionsMap( + final List subscriptions) { + final Map>> map = new HashMap<>(); + subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap())); + return map; + } + + protected static NotificationGroup generateNotifications(final Event e, final List subscriptions, + final Map>> conditionsMap, final long date) { final List list = subscriptions .stream() .filter( s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) - .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) + .filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId()))) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -169,28 +162,28 @@ public class IndexNotificationsJob { return false; } - if (conditions.containsKey("targetDateofacceptance") && conditions + if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .noneMatch( + .anyMatch( c -> SubscriptionUtils .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } if (conditions.containsKey("targetResultTitle") - && conditions + && !conditions .get("targetResultTitle") .stream() - .noneMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) { + .anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) { return false; } if (conditions.containsKey("targetAuthors") - && conditions + && !conditions .get("targetAuthors") .stream() - .noneMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) { + .allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) { return false; } @@ -202,7 +195,7 @@ public class IndexNotificationsJob { } - private static List listSubscriptions(final String brokerApiBaseUrl) throws IOException { + private static List listSubscriptions(final String brokerApiBaseUrl) throws Exception { final String url = brokerApiBaseUrl + "/api/subscriptions"; final HttpGet req = new HttpGet(url); @@ -217,7 +210,7 @@ public class IndexNotificationsJob { } } - private static String deleteOldNotifications(final String brokerApiBaseUrl, final long l) throws IOException { + private static String deleteOldNotifications(final String brokerApiBaseUrl, final long l) throws Exception { final String url = brokerApiBaseUrl + "/api/notifications/byDate/0/" + l; final HttpDelete req = new HttpDelete(url); diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml index 248326d57..70ab7d344 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml @@ -135,7 +135,6 @@ --executor-memory=${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} - --conf spark.dynamicAllocation.maxExecutors="8" --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} From c4fce785ab623fcce1afaaecbbcefd45dbcf175f Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 19 Oct 2021 16:18:26 +0200 Subject: [PATCH 017/159] fixed a compilation problem of a unit test --- .../broker/oa/GenerateNotificationsJob.java | 22 +++++++++++++------ .../dhp/broker/oa/IndexNotificationsJob.java | 5 +++-- ...java => GenerateNotificationsJobTest.java} | 22 +++++++++---------- 3 files changed, 29 insertions(+), 20 deletions(-) rename dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/{IndexNotificationsJobTest.java => GenerateNotificationsJobTest.java} (81%) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java index 21c6c64a6..6b8d60f40 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java @@ -45,8 +45,9 @@ public class GenerateNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_notifications.json"))); + .toString( + GenerateNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -79,7 +80,10 @@ public class GenerateNotificationsJob { final Encoder nEncoder = Encoders.bean(Notification.class); final Dataset notifications = ClusterUtils .readPath(spark, eventsPath, Event.class) - .map((MapFunction) e -> generateNotifications(e, subscriptions, conditionsMap, startTime), ngEncoder) + .map( + (MapFunction) e -> generateNotifications( + e, subscriptions, conditionsMap, startTime), + ngEncoder) .flatMap((FlatMapFunction) g -> g.getData().iterator(), nEncoder); ClusterUtils.save(notifications, notificationsPath, Notification.class, total); @@ -99,7 +103,8 @@ public class GenerateNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter( + s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId()))) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -130,15 +135,18 @@ public class GenerateNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange( + map.getTrust(), conditions.get("trust").get(0).getValue(), + conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch(c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch( + c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index 55e82446f..a2aa30092 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -36,8 +36,9 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString( + IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJobTest.java similarity index 81% rename from dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java rename to dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJobTest.java index 8ecb3061b..233963e2f 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJobTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJobTest.java @@ -16,7 +16,7 @@ import eu.dnetlib.dhp.broker.model.MappedFields; import eu.dnetlib.dhp.broker.model.Subscription; import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; -class IndexNotificationsJobTest { +class GenerateNotificationsJobTest { private List subscriptions; @@ -32,7 +32,7 @@ class IndexNotificationsJobTest { .setConditions( "[{\"field\":\"targetDatasourceName\",\"fieldType\":\"STRING\",\"operator\":\"EXACT\",\"listParams\":[{\"value\":\"reposiTUm\"}]},{\"field\":\"trust\",\"fieldType\":\"FLOAT\",\"operator\":\"RANGE\",\"listParams\":[{\"value\":\"0\",\"otherValue\":\"1\"}]}]"); subscriptions = Arrays.asList(s); - conditionsMap = IndexNotificationsJob.prepareConditionsMap(subscriptions); + conditionsMap = GenerateNotificationsJob.prepareConditionsMap(subscriptions); } @Test @@ -40,7 +40,7 @@ class IndexNotificationsJobTest { final Event event = new Event(); event.setTopic("ENRICH/MISSING/PROJECT"); - final NotificationGroup res = IndexNotificationsJob + final NotificationGroup res = GenerateNotificationsJob .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(0, res.getData().size()); } @@ -53,7 +53,7 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("reposiTUm"); event.getMap().setTrust(0.8f); - final NotificationGroup res = IndexNotificationsJob + final NotificationGroup res = GenerateNotificationsJob .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(1, res.getData().size()); } @@ -66,7 +66,7 @@ class IndexNotificationsJobTest { event.getMap().setTargetDatasourceName("Puma"); event.getMap().setTrust(0.8f); - final NotificationGroup res = IndexNotificationsJob + final NotificationGroup res = GenerateNotificationsJob .generateNotifications(event, subscriptions, conditionsMap, 0); assertEquals(0, res.getData().size()); } @@ -77,11 +77,11 @@ class IndexNotificationsJobTest { event.setTopic("ENRICH/MISSING/PROJECT"); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); System.out @@ -98,11 +98,11 @@ class IndexNotificationsJobTest { event.getMap().setTrust(0.8f); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); System.out @@ -118,11 +118,11 @@ class IndexNotificationsJobTest { event.getMap().setTrust(0.8f); // warm up - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); final long start = System.currentTimeMillis(); for (int i = 0; i < N_TIMES; i++) { - IndexNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); + GenerateNotificationsJob.generateNotifications(event, subscriptions, conditionsMap, 0); } final long end = System.currentTimeMillis(); System.out From 43f4eb492b1dc8c747fdf8dd90d22e6d2f98dcb1 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 14 Oct 2021 18:53:35 +0300 Subject: [PATCH 018/159] fetching affiliated results for 4 orgs in monitor. fixed affiliated orgs in stats db --- .../oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 2 +- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 9ea50d488..d39af37d5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -17,7 +17,7 @@ create table TARGET.result as union all select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) union all - select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on p.id=rp.project join SOURCE.project_organizations po on po.id=p.id where rp.id=r.id and po.organization in ( + select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( 'openorgs____::759d59f05d77188faee99b7493b46805', 'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index b3cbc9b41..d461bd343 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -126,7 +126,7 @@ FROM ${stats_db_name}.otherresearchproduct_topics; CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'resultOrganization' +WHERE r.reltype = 'resultOrganization' and r.relclass='hasAuthorInstitution' and r.subreltype='affiliation' and r.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.result_projects AS From a7376907c2bc02b363912392cb06fcb177c53a92 Mon Sep 17 00:00:00 2001 From: antleb Date: Fri, 15 Oct 2021 13:42:55 +0300 Subject: [PATCH 019/159] invalidating medatadata before context thingies --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh index 6d42ab13d..2a40eb920 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh @@ -26,6 +26,8 @@ hdfs dfs -copyFromLocal concepts.csv ${TMP} hdfs dfs -chmod -R 777 ${TMP} echo "Creating and populating impala tables" +impala-shell -q "invalidate metadata" +impala-shell -d ${TARGET_DB} -q "invalidate metadata" impala-shell -q "create table ${TARGET_DB}.context (id string, name string) row format delimited fields terminated by ','" impala-shell -q "create table ${TARGET_DB}.category (context string, id string, name string) row format delimited fields terminated by ','" impala-shell -q "create table ${TARGET_DB}.concept (category string, id string, name string) row format delimited fields terminated by ','" From cece432adc0b4c929e768a94359d024f7e59fbef Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 20 Oct 2021 14:14:53 +0200 Subject: [PATCH 020/159] [stats] reducing the step22 wait time --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh index dc19f84b4..03aa535e1 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh @@ -1,4 +1,4 @@ #!/usr/bin/env bash curl --request GET $1/cache/updateCache -sleep 20h \ No newline at end of file +sleep 6h \ No newline at end of file From b97b78f874ee744e87f1bc4d157cbeb6dfb569a9 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Mon, 1 Nov 2021 15:42:29 +0200 Subject: [PATCH 021/159] removed hardcoded reference --- .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index b977302df..e892da0be 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -65,7 +65,7 @@ FROM ${stats_db_name}.project_tmp p UPDATE ${stats_db_name}.publication_tmp SET delayed = 'yes' WHERE publication_tmp.id IN (SELECT distinct r.id - FROM stats_wf_db_obs.result r, + FROM ${stats_db_name}.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id = pr.result @@ -75,7 +75,7 @@ WHERE publication_tmp.id IN (SELECT distinct r.id UPDATE ${stats_db_name}.dataset_tmp SET delayed = 'yes' WHERE dataset_tmp.id IN (SELECT distinct r.id - FROM stats_wf_db_obs.result r, + FROM ${stats_db_name}.result r, ${stats_db_name}.project_results pr, ${stats_db_name}.project_tmp p WHERE r.id = pr.result From b9d4f115ccf8d6bb3d2b033a3ae351be2f575932 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 9 Nov 2021 12:04:45 +0100 Subject: [PATCH 022/159] fixed Crossref mappign for SFI projects --- .../main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 25f0ff381..91d4bd4d3 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -358,7 +358,7 @@ case object Crossref2Oaf { case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) - case "10.13039/501100001602" => generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) + case "10.13039/501100001602" => generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", "")) case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) case "10.13039/501100000038"=> val targetId = getProjectId("nserc_______" , "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) From 6cd91004e33c0eda2fa6f1381a1a65cd21f8e40f Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 9 Nov 2021 12:22:57 +0100 Subject: [PATCH 023/159] fixed DOI for Wellcome Trust in mapping relationships from Crossref --- .../main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 91d4bd4d3..1404469ef 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -382,8 +382,8 @@ case object Crossref2Oaf { case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a) case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snsfRule) case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a) - case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a) - case "10.13039/100004440"=> val targetId = getProjectId("wt__________" , "1e5e62235d094afd01cd56e65112fc63") + case "10.13039/100004440" => generateSimpleRelationFromAward(funder, "wt__________", a =>a) + val targetId = getProjectId("wt__________" , "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId,targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId,sourceId, ModelConstants.PRODUCES) From fc8fceaac3c5c4f70289ed42735d9d1565f7c385 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 10 Nov 2021 14:11:52 +0100 Subject: [PATCH 024/159] create direct link to WT projects as well --- .../main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 1404469ef..0ce55a96b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -402,7 +402,8 @@ case object Crossref2Oaf { case "The French National Research Agency (ANR)" | "The French National Research Agency" => generateSimpleRelationFromAward(funder, "anr_________", a => a) case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) - case "Wellcome Trust Masters Fellowship" => val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") + case "Wellcome Trust Masters Fellowship" => generateSimpleRelationFromAward(funder, "wt__________", a =>a) + val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY ) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES ) case _ => logger.debug("no match for "+funder.name ) From 3f9b2ba8ce7d987e3bb65d1d76bc517636362814 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 22 Nov 2021 16:59:43 +0100 Subject: [PATCH 025/159] [Hosted By Map] fix issue in test --- .../java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index 1bdcb60aa..4613d5636 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -54,7 +54,7 @@ class TestApply extends java.io.Serializable{ assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy")) assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) - assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.gold)) assertTrue(pa.getBestaccessright.getClassid.equals("OPEN")) assertTrue(pa.getBestaccessright.getClassname.equals("Open Access")) From cd9c51fd7a139cb5b410af8f83ce855c6f49aaee Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 9 Dec 2021 13:57:53 +0100 Subject: [PATCH 026/159] vocabulary based cleaning considers also the term label when looking up for a synonym --- .../common/vocabulary/VocabularyGroup.java | 8 ++ .../clean/GraphCleaningFunctionsTest.java | 7 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 86 +++++++++++++++++++ 3 files changed, 99 insertions(+), 2 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index d5f57849c..1c129ff9c 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable { final String syn = arr[2].trim(); vocs.addSynonyms(vocId, termId, syn); + } } + // add the term names as synonyms + vocs.vocs.values().forEach(voc -> { + voc.getTerms().values().forEach(term -> { + voc.addSynonym(term.getName().toLowerCase(), term.getId()); + }); + }); + return vocs; } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index c8a368dd6..f822daa0e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -101,6 +101,9 @@ public class GraphCleaningFunctionsTest { assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); + assertEquals("0033", p_out.getInstance().get(1).getInstancetype().getClassid()); + assertEquals("Audiovisual", p_out.getInstance().get(1).getInstancetype().getClassname()); + assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid()); assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname()); @@ -114,7 +117,7 @@ public class GraphCleaningFunctionsTest { List poi = p_out.getInstance(); assertNotNull(poi); - assertEquals(1, poi.size()); + assertEquals(2, poi.size()); final Instance poii = poi.get(0); assertNotNull(poii); @@ -163,7 +166,7 @@ public class GraphCleaningFunctionsTest { final List pci = p_cleaned.getInstance(); assertNotNull(pci); - assertEquals(1, pci.size()); + assertEquals(2, pci.size()); final Instance pcii = pci.get(0); assertNotNull(pcii); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index b3e302474..5b9e86c65 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -403,6 +403,92 @@ "http://juuli.fi/Record/0275158616", "http://dx.doi.org/10.1007/s109090161569x" ] + }, + { + "pid": [ + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1002/s21010127267xy" + }, + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1008/abcd" + } + ], + "alternateIdentifier": [ + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1007/s109090161569x" + }, + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1009/qwerty" + } + ], + "accessright": { + "classid": "CLOSED", + "classname": "CLOSED", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "collectedfrom": { + "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", + "value": "VIRTA" + }, + "dateofacceptance": { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "value": "2016-01-01" + }, + "distributionlocation": "", + "hostedby": { + "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", + "value": "VIRTA" + }, + "instancetype": { + "classid": "Audiovisual", + "classname": "Audiovisual", + "schemeid": "dnet:publication_resource", + "schemename": "dnet:publication_resource" + }, + "url": [ + "http://dx.doi.org/10.1002/s21010127267xy" + ] } ], "journal": { From c1b6ae47cd4af0bd2db0901b8c1c623ef3800d5d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 9 Dec 2021 16:44:28 +0100 Subject: [PATCH 027/159] cleaning workflow assigns the proper default instance type when a value could not be cleaned using the vocabularies --- .../oaf/utils/GraphCleaningFunctions.java | 36 +++++++- .../oa/graph/clean/CleanGraphSparkJob.java | 2 +- .../clean/GraphCleaningFunctionsTest.java | 20 +++-- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 90 ++++++++++++++++++- 5 files changed, 138 insertions(+), 12 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 592580ab8..f49a47c0a 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; import com.google.common.collect.Sets; +import eu.dnetlib.dhp.common.vocabulary.Vocabulary; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -115,7 +117,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { return true; } - public static T cleanup(T value) { + public static T cleanup(T value, VocabularyGroup vocs) { if (value instanceof Datasource) { // nothing to clean here } else if (value instanceof Project) { @@ -234,6 +236,38 @@ public class GraphCleaningFunctions extends CleaningFunctions { if (Objects.nonNull(r.getInstance())) { for (Instance i : r.getInstance()) { + if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) { + if (r instanceof Publication) { + i + .setInstancetype( + OafMapperUtils + .qualifier( + "0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE, + ModelConstants.DNET_PUBLICATION_RESOURCE)); + } else if (r instanceof Dataset) { + i + .setInstancetype( + OafMapperUtils + .qualifier( + "0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE, + ModelConstants.DNET_PUBLICATION_RESOURCE)); + } else if (r instanceof Software) { + i + .setInstancetype( + OafMapperUtils + .qualifier( + "0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE, + ModelConstants.DNET_PUBLICATION_RESOURCE)); + } else if (r instanceof OtherResearchProduct) { + i + .setInstancetype( + OafMapperUtils + .qualifier( + "0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE, + ModelConstants.DNET_PUBLICATION_RESOURCE)); + } + } + if (Objects.nonNull(i.getPid())) { i.setPid(processPidCleaning(i.getPid())); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index d43d7ce28..2e2ea567a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -88,7 +88,7 @@ public class CleanGraphSparkJob { readTableFromPath(spark, inputPath, clazz) .map((MapFunction) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz)) .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) - .map((MapFunction) GraphCleaningFunctions::cleanup, Encoders.bean(clazz)) + .map((MapFunction) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz)) .filter((FilterFunction) GraphCleaningFunctions::filter) .write() .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index f822daa0e..0e9efed21 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -101,8 +101,11 @@ public class GraphCleaningFunctionsTest { assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); - assertEquals("0033", p_out.getInstance().get(1).getInstancetype().getClassid()); - assertEquals("Audiovisual", p_out.getInstance().get(1).getInstancetype().getClassname()); + assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid()); + assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname()); + + assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname()); assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid()); assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname()); @@ -117,7 +120,7 @@ public class GraphCleaningFunctionsTest { List poi = p_out.getInstance(); assertNotNull(poi); - assertEquals(2, poi.size()); + assertEquals(3, poi.size()); final Instance poii = poi.get(0); assertNotNull(poii); @@ -145,7 +148,7 @@ public class GraphCleaningFunctionsTest { assertEquals(5, p_out.getTitle().size()); - Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out); + Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies); assertEquals(3, p_cleaned.getTitle().size()); @@ -164,9 +167,12 @@ public class GraphCleaningFunctionsTest { assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue()); + assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid()); + assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname()); + final List pci = p_cleaned.getInstance(); assertNotNull(pci); - assertEquals(2, pci.size()); + assertEquals(3, pci.size()); final Instance pcii = pci.get(0); assertNotNull(pcii); @@ -234,7 +240,7 @@ public class GraphCleaningFunctionsTest { .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json")); Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); - Publication cleaned = GraphCleaningFunctions.cleanup(p_out); + Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies); Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); } @@ -245,7 +251,7 @@ public class GraphCleaningFunctionsTest { .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json")); Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); - Publication cleaned = GraphCleaningFunctions.cleanup(p_out); + Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies); Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 27e33bf27..de79b750a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -708,7 +708,7 @@ class MappersTest { assertEquals(1, p.getTitle().size()); assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); - final Publication p_cleaned = cleanup(fixVocabularyNames(p)); + final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs); assertNotNull(p_cleaned.getTitle()); assertFalse(p_cleaned.getTitle().isEmpty()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 5b9e86c65..78fdc4c9d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -481,14 +481,100 @@ "value": "VIRTA" }, "instancetype": { - "classid": "Audiovisual", - "classname": "Audiovisual", + "classid": "Model", + "classname": "Model", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource" }, "url": [ "http://dx.doi.org/10.1002/s21010127267xy" ] + }, + { + "pid": [ + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1002/s21010127267xy" + }, + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1008/abcd" + } + ], + "alternateIdentifier": [ + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1007/s109090161569x" + }, + { + "dataInfo": null, + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "10.1009/qwerty" + } + ], + "accessright": { + "classid": "CLOSED", + "classname": "CLOSED", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "collectedfrom": { + "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", + "value": "VIRTA" + }, + "dateofacceptance": { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "value": "2016-01-01" + }, + "distributionlocation": "", + "hostedby": { + "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", + "value": "VIRTA" + }, + "instancetype": { + "classid": "xyz", + "classname": "xyz", + "schemeid": "dnet:publication_resource", + "schemename": "dnet:publication_resource" + }, + "url": [ + "http://dx.doi.org/10.1002/t32121238378t" + ] } ], "journal": { From f0b523cfa7eb64c6adca18bee27ce6d0f80d7ecd Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Thu, 11 Nov 2021 12:57:19 +0200 Subject: [PATCH 028/159] removed the too restrctive clause. will discuss again --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index d461bd343..b3cbc9b41 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -126,7 +126,7 @@ FROM ${stats_db_name}.otherresearchproduct_topics; CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'resultOrganization' and r.relclass='hasAuthorInstitution' and r.subreltype='affiliation' +WHERE r.reltype = 'resultOrganization' and r.datainfo.deletedbyinference = false; CREATE TABLE ${stats_db_name}.result_projects AS From 9458ee793834c878c1c2d6f2ca12c52f70dc34dc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 3 Jan 2022 17:25:26 +0100 Subject: [PATCH 029/159] serialise records in the OAF-store-graph mdstores in json format. Read them again in the graph construction phase using a tolerant parser to support backward compatible changes in the evolution of the schema --- .../dhp/collection/CollectionUtils.scala | 13 +++++++ .../GenerateDataciteDatasetSpark.scala | 16 ++++----- .../bio/SparkTransformBioDatabaseToOAF.scala | 14 ++++---- .../ebi/SparkCreateBaselineDataFrame.scala | 16 +++++---- .../dhp/sx/bio/ebi/SparkEBILinksToOaf.scala | 10 +++--- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 2 +- .../raw/CopyHdfsOafSparkApplication.scala | 36 +++++++++++++------ 7 files changed, 68 insertions(+), 39 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala index 11ecfd6cb..26fcecbbd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -1,7 +1,9 @@ package eu.dnetlib.dhp.collection +import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.schema.common.ModelSupport import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation} +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode} object CollectionUtils { @@ -46,4 +48,15 @@ object CollectionUtils { List() } + def saveDataset(d: Dataset[Oaf], targetPath: String):Unit = { + implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + val mapper = new ObjectMapper + + d + .flatMap(i => CollectionUtils.fixRelations(i)) + .filter(i => i != null) + .map(r => mapper.writeValueAsString(r))(Encoders.STRING) + .write.mode(SaveMode.Overwrite).save(targetPath) + } + } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala index e1607ee9c..d11c33fb4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala @@ -2,14 +2,14 @@ package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.AbstractScalaApplication -import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations +import eu.dnetlib.dhp.collection.CollectionUtils import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord} import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile import eu.dnetlib.dhp.utils.ISLookupClientFactory -import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.slf4j.{Logger, LoggerFactory} @@ -73,12 +73,12 @@ class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord] implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - spark.read.load(sourcePath).as[DataciteType] - .filter(d => d.isActive) - .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) - .filter(d => d != null) - .flatMap(i => fixRelations(i)).filter(i => i != null) - .write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset( + spark.read.load(sourcePath).as[DataciteType] + .filter(d => d.isActive) + .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) + .filter(d => d != null), + targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index 8ae8285e3..27caa8f36 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -1,12 +1,12 @@ package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.Oaf -import BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.collection.CollectionUtils +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.slf4j.{Logger, LoggerFactory} object SparkTransformBioDatabaseToOAF { @@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF { import spark.implicits._ database.toUpperCase() match { case "UNIPROT" => - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))), targetPath) case "PDB" => - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))), targetPath) case "SCHOLIX" => - spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset(spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)), targetPath) case "CROSSREF_LINKS" => - spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))), targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index 17d21f19c..0fea4ff7f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -1,9 +1,10 @@ package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.collection.CollectionUtils import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup -import eu.dnetlib.dhp.schema.oaf.Result -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} +import eu.dnetlib.dhp.sx.bio.pubmed._ import eu.dnetlib.dhp.utils.ISLookupClientFactory import org.apache.commons.io.IOUtils import org.apache.hadoop.conf.Configuration @@ -177,7 +178,7 @@ object SparkCreateBaselineDataFrame { implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) - implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) if (!"true".equalsIgnoreCase(skipUpdate)) { downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri) @@ -192,9 +193,10 @@ object SparkCreateBaselineDataFrame { } val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle] - exported_dataset - .map(a => PubMedToOaf.convert(a, vocabularies)).as[Result] - .filter(p => p != null) - .write.mode(SaveMode.Overwrite).save(targetPath) + CollectionUtils.saveDataset(exported_dataset + .map(a => PubMedToOaf.convert(a, vocabularies)).as[Oaf] + .filter(p => p != null), + targetPath) + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index 8da617ca0..cd03f004d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -1,11 +1,10 @@ package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.collection.CollectionUtils import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.sx.bio.BioDBToOAF import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem -import BioDBToOAF.EBILinkItem -import eu.dnetlib.dhp.collection.CollectionUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql._ @@ -35,10 +34,9 @@ object SparkEBILinksToOaf { val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{")) - ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) + CollectionUtils.saveDataset(ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) - .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)) - .flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null) - .write.mode(SaveMode.Overwrite).save(targetPath) + .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)), + targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index ecef32202..d09237842 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -111,7 +111,7 @@ object PubMedToOaf { * @param vocabularies the vocabularies * @return The OAF instance if the mapping did not fail */ - def convert(article: PMArticle, vocabularies: VocabularyGroup): Result = { + def convert(article: PMArticle, vocabularies: VocabularyGroup): Oaf = { if (article.getPublicationTypes == null) return null diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala index c7ad1890d..1376c6b35 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala @@ -1,18 +1,15 @@ package eu.dnetlib.dhp.oa.graph.raw -import com.fasterxml.jackson.databind.ObjectMapper +import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper} import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.common.HdfsSupport import eu.dnetlib.dhp.schema.common.ModelSupport -import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.utils.DHPUtils -import org.apache.commons.io.IOUtils -import org.apache.commons.lang3.StringUtils -import org.apache.http.client.methods.HttpGet -import org.apache.http.impl.client.HttpClients import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.{SparkConf, SparkContext} +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse import org.slf4j.LoggerFactory import scala.collection.JavaConverters._ @@ -51,18 +48,21 @@ object CopyHdfsOafSparkApplication { log.info("hdfsPath: {}", hdfsPath) implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + import spark.implicits._ val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList if (validPaths.nonEmpty) { - val oaf = spark.read.load(validPaths: _*).as[Oaf] - val mapper = new ObjectMapper() - val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList + val oaf = spark.read.load(validPaths: _*).as[String] + val mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false) + val l = ModelSupport.oafTypes.entrySet.asScala.toList l.foreach( e => - oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e)) + oaf + .filter(o => isOafType(o, e.getKey)) + .map(j => mapper.readValue(j, e.getValue).asInstanceOf[Oaf]) .map(s => mapper.writeValueAsString(s))(Encoders.STRING) .write .option("compression", "gzip") @@ -71,4 +71,20 @@ object CopyHdfsOafSparkApplication { ) } } + + def isOafType(input: String, oafType: String): Boolean = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: org.json4s.JValue = parse(input) + if (oafType == "relation") { + val hasSource = (json \ "source").extractOrElse[String](null) + val hasTarget = (json \ "target").extractOrElse[String](null) + + hasSource != null && hasTarget != null + } else { + val hasId = (json \ "id").extractOrElse[String](null) + val resultType = (json \ "resulttype" \ "classid").extractOrElse[String](null) + hasId != null && oafType.equalsIgnoreCase(resultType) + } + + } } From 8d13effa311565955a2b625d652f44551baabdab Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Jan 2022 11:26:56 +0100 Subject: [PATCH 030/159] test for the tolerant deserialisation utility method --- .../raw/CopyHdfsOafSparkApplicationTest.java | 65 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/dataset_1.json | 3 + .../dhp/oa/graph/raw/publication_1.json | 1 + .../raw/publication_2_unknownProperty.json | 1 + .../dnetlib/dhp/oa/graph/raw/relation_1.json | 6 ++ 5 files changed, 76 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/publication_1.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/publication_2_unknownProperty.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/relation_1.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java new file mode 100644 index 000000000..85cb551bc --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplicationTest.java @@ -0,0 +1,65 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +public class CopyHdfsOafSparkApplicationTest { + + @Test + void testIsOafType() throws IOException { + assertTrue( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/publication_1.json")), + "publication")); + assertTrue( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json")), + "dataset")); + assertTrue( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/relation_1.json")), + "relation")); + + assertFalse( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/publication_1.json")), + "dataset")); + assertFalse( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json")), + "publication")); + + assertTrue( + CopyHdfsOafSparkApplication + .isOafType( + IOUtils + .toString( + getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/raw/publication_2_unknownProperty.json")), + "publication")); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json new file mode 100644 index 000000000..c22dc94e3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json @@ -0,0 +1,3 @@ +{"author":[{"affiliation":[],"fullname":"Greenough, 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+{"source":"25a","target":"15a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]} \ No newline at end of file From f82db765db357a76fa2421ca4e430eb6e8ef5d67 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Jan 2022 14:23:01 +0100 Subject: [PATCH 031/159] OAF-store-graph mdstores: save them in text format --- .../java/eu/dnetlib/dhp/collection/CollectionUtils.scala | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala index 26fcecbbd..509e464e5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -56,7 +56,10 @@ object CollectionUtils { .flatMap(i => CollectionUtils.fixRelations(i)) .filter(i => i != null) .map(r => mapper.writeValueAsString(r))(Encoders.STRING) - .write.mode(SaveMode.Overwrite).save(targetPath) + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(targetPath) } } From 3dc48c7ab51fcf843c615614db9e5ea9eec6cb4b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Jan 2022 14:40:16 +0100 Subject: [PATCH 032/159] OAF-store-graph mdstores: save them in text format --- .../java/eu/dnetlib/dhp/collection/CollectionUtils.scala | 8 +++----- .../dhp/datacite/GenerateDataciteDatasetSpark.scala | 4 ++-- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala index 509e464e5..e7de60e07 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -48,18 +48,16 @@ object CollectionUtils { List() } - def saveDataset(d: Dataset[Oaf], targetPath: String):Unit = { + def saveDataset(dataset: Dataset[Oaf], targetPath: String): Unit = { implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - val mapper = new ObjectMapper - d + dataset .flatMap(i => CollectionUtils.fixRelations(i)) .filter(i => i != null) - .map(r => mapper.writeValueAsString(r))(Encoders.STRING) .write .mode(SaveMode.Overwrite) .option("compression", "gzip") - .text(targetPath) + .json(targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala index d11c33fb4..a205edcf2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala @@ -38,7 +38,7 @@ class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) val outputBasePath = cleanedMdStoreVersion.getHdfsPath log.info(s"outputBasePath is '$outputBasePath'") - val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH" + val targetPath = s"$outputBasePath$MDSTORE_DATA_PATH" log.info(s"targetPath is '$targetPath'") generateDataciteDataset(sourcePath, exportLinks, vocabularies, targetPath, spark) @@ -54,7 +54,7 @@ class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log * @param outputBasePath */ def reportTotalSize( targetPath: String, outputBasePath: String ):Unit = { - val total_items = spark.read.load(targetPath).count() + val total_items = spark.read.text(targetPath).count() writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH) } From 3bd3653be9e884679c390f8b9f9f36800b657692 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 4 Jan 2022 15:02:09 +0100 Subject: [PATCH 033/159] OAF-store-graph mdstores: save them in text format --- .../main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala index e7de60e07..86a28ac10 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -50,14 +50,16 @@ object CollectionUtils { def saveDataset(dataset: Dataset[Oaf], targetPath: String): Unit = { implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + val mapper = new ObjectMapper dataset .flatMap(i => CollectionUtils.fixRelations(i)) .filter(i => i != null) + .map(r => mapper.writeValueAsString(r))(Encoders.STRING) .write .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(targetPath) + .text(targetPath) } } From 8ae46ca7896d88561417a34394dc502e6e9be6b6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 5 Jan 2022 15:49:05 +0100 Subject: [PATCH 034/159] OAF-store-graph mdstores: firther fix for PR#180 --- .../raw/CopyHdfsOafSparkApplication.scala | 27 ++++++++++--------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala index 1376c6b35..fa13f477c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala @@ -48,26 +48,27 @@ object CopyHdfsOafSparkApplication { log.info("hdfsPath: {}", hdfsPath) implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - import spark.implicits._ val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList + val types = ModelSupport.oafTypes.entrySet + .asScala + .map(e => Tuple2(e.getKey, e.getValue)) + if (validPaths.nonEmpty) { - val oaf = spark.read.load(validPaths: _*).as[String] + val oaf = spark.read.textFile(validPaths: _*) val mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false) - val l = ModelSupport.oafTypes.entrySet.asScala.toList - l.foreach( - e => - oaf - .filter(o => isOafType(o, e.getKey)) - .map(j => mapper.readValue(j, e.getValue).asInstanceOf[Oaf]) - .map(s => mapper.writeValueAsString(s))(Encoders.STRING) - .write - .option("compression", "gzip") - .mode(SaveMode.Append) - .text(s"$hdfsPath/${e}") + + types.foreach(t => oaf + .filter(o => isOafType(o, t._1)) + .map(j => mapper.readValue(j, t._2).asInstanceOf[Oaf]) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .write + .option("compression", "gzip") + .mode(SaveMode.Append) + .text(s"$hdfsPath/${t._1}") ) } } From bb17e070d8de9fadfdff214a5869e360e0a3299c Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Thu, 23 Dec 2021 15:46:17 +0200 Subject: [PATCH 035/159] added result_result relations --- .../oa/graph/stats/oozie_app/scripts/step13.sql | 15 ++++++++++++++- .../oozie_app/scripts/step20-createMonitorDB.sql | 3 +++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index e4e81175c..315d296fc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -67,4 +67,17 @@ from ( LATERAL VIEW explode(author) a as auth LATERAL VIEW explode(auth.pid) ap as auth_pid LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type - WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res \ No newline at end of file + WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res; + +create table ${stats_db_name}.result_result stored as parquet as +select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype +from ${openaire_db_name}.relation rel +join ${openaire_db_name}.result r1 on rel.source=r1.id +join ${openaire_db_name}.result r2 on r2.id=rel.target +where reltype='resultResult' + and r1.resulttype.classname!=r2.resulttype.classname + and r1.datainfo.deletedbyinference=false + and r2.datainfo.deletedbyinference=false + and r1.resulttype.classname != 'other' + and r2.resulttype.classname != 'other' + and rel.datainfo.deletedbyinference=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index fa8e4c6a7..ce7b4bd9c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -79,6 +79,9 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; +create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source or r.id=orig.target); +compute stats TARGET.result_result; + -- datasources create view if not exists TARGET.datasource as select * from SOURCE.datasource; create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; From a4316bafedbc312de48096caa2e9e77b912b8224 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Thu, 23 Dec 2021 15:33:53 +0200 Subject: [PATCH 036/159] fixed a typo --- .../scripts/step20-createMonitorDB.sql | 24 ++++++++++++------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index ce7b4bd9c..2d6ff41d4 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -49,8 +49,10 @@ compute stats TARGET.result_greenoa; create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_languages; -create table TARGET.result_licences stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.result_licences; +create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_licenses; + +create table TARGET.licenses_normalized as select * from SOURCE.licenses_normalized; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; @@ -79,9 +81,6 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source or r.id=orig.target); -compute stats TARGET.result_result; - -- datasources create view if not exists TARGET.datasource as select * from SOURCE.datasource; create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; @@ -103,6 +102,7 @@ create view if not exists TARGET.project as select * from SOURCE.project; create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; +create view if not exists TARGET.project_classification as select * from SOURCE.project_classification; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; compute stats TARGET.project_results; @@ -118,10 +118,10 @@ create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.i compute stats TARGET.indi_pub_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; -create table TARGET.indi_pub_has_cc_licence stored as parquet as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_has_cc_licence; -create table TARGET.indi_pub_has_cc_licence_url stored as parquet as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_has_cc_licence_url; +create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_result_has_cc_licence; +create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_result_has_cc_licence_url; create view TARGET.indi_funder_country_collab stored as select * from SOURCE.indi_funder_country_collab; @@ -138,6 +138,12 @@ compute stats TARGET.indi_pub_in_transformative; create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_closed_other_open; +create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_result_no_of_copies; + +--- Usage statistics +create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); + --denorm alter table TARGET.result rename to TARGET.res_tmp; From 4878d7485c1e1f79a3bdbb83eaed364c5ce4f576 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 22 Dec 2021 02:54:42 +0200 Subject: [PATCH 037/159] added usage stats --- .../oa/graph/stats/oozie_app/scripts/step10.sql | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index fc0162a9c..13a4803a9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -27,6 +27,22 @@ CREATE OR REPLACE VIEW ${stats_db_name}.licenses_normalized AS SELECT * FROM ${external_stats_db_name}.licenses_normalized; +------------------------------------------------------------------------------------------------ +------------------------------------------------------------------------------------------------ +-- Usage statistics +------------------------------------------------------------------------------------------------ +------------------------------------------------------------------------------------------------ +create or replace view ${stats_db_name}.usage_stats as +select * from openaire_prod_usage_stats.usage_stats; + +create or replace view ${stats_db_name}.downloads_stats as +select * from openaire_prod_usage_stats.downloads_stats; + +create or replace view ${stats_db_name}.pageviews_stats as +select * from openaire_prod_usage_stats.pageviews_stats; + +create or replace view ${stats_db_name}.views_stats as +select * from openaire_prod_usage_stats.views_stats; ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ From 3ce1976627f5ea79d3b34dadcd5707aaa8da79c3 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 21 Dec 2021 22:55:04 +0200 Subject: [PATCH 038/159] fixed column names --- .../stats/oozie_app/scripts/step16-createIndicatorsTables.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 926c8825f..3b1a7eeaf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -304,7 +304,7 @@ with tmp as (select funder, project, country from organization_projects op join organization o on o.id=op.id join project p on p.id=op.project where country <> 'UNKNOWN') -select f1.funder, f1.country, f2.country, count(distinct f1.project) as collaborations +select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations from tmp as f1 join tmp as f2 on f1.project=f2.project where f1.country<>f2.country From e91f06f39bf38016c1d8565d53ff5e853afcc76c Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 21 Dec 2021 15:54:38 +0200 Subject: [PATCH 039/159] fixed typos in indicators. Added extra views in monitor --- .../scripts/step16-createIndicatorsTables.sql | 336 ++++-------------- .../scripts/step20-createMonitorDB.sql | 6 +- 2 files changed, 79 insertions(+), 263 deletions(-) mode change 100644 => 100755 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql old mode 100644 new mode 100755 index 3b1a7eeaf..bdd681f8d --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -1,28 +1,29 @@ +---- Sprint 1 ---- create table indi_pub_green_oa stored as parquet as -select distinct p.id, coalesce(green_oa, 0) as green_oa +select distinct p.id, coalesce(green_oa, 0) as green_oa from publication p -left outer join ( -select p.id, 1 as green_oa +left outer join ( +select p.id, 1 as green_oa from publication p join result_instance ri on ri.id = p.id join datasource on datasource.id = ri.hostedby where datasource.type like '%Repository%' -and (ri.accessright = 'Open Access' -or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp +and (ri.accessright = 'Open Access' +or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp on p.id= tmp.id; create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p left outer join ( -select p.id, 1 as grey_lit +select p.id, 1 as grey_lit from publication p join result_classifications rt on rt.id = p.id -where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and +where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; create table indi_pub_doi_from_crossref stored as parquet as -select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref +select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p left outer join (select ri.id, 1 as doi_from_crossref from result_instance ri @@ -33,7 +34,7 @@ on tmp.id=p.id; create table indi_pub_gold_oa stored as parquet as select distinct p.id, coalesce(gold_oa, 0) as gold_oa from publication p -left outer join ( +left outer join ( select p.id, 1 as gold_oa from publication p join result_instance ri on ri.id = p.id @@ -41,255 +42,56 @@ join datasource on datasource.id = ri.hostedby where datasource.id like '%doajarticles%') tmp on p.id= tmp.id; ---create table indi_project_pubs_count stored as parquet as ---select pr.id id, count(p.id) total_pubs from project_results pr ---join publication p on p.id=pr.result ---group by pr.id; - ---create table indi_project_datasets_count stored as parquet as ---select pr.id id, count(d.id) total_datasets from project_results pr ---join dataset d on d.id=pr.result ---group by pr.id; - ---create table indi_project_software_count stored as parquet as ---select pr.id id, count(s.id) total_software from project_results pr ---join software s on s.id=pr.result ---group by pr.id; - ---create table indi_project_otherresearch_count stored as parquet as ---select pr.id id, count(o.id) total_other from project_results pr ---join otherresearchproduct o on o.id=pr.result ---group by pr.id; - ---create table indi_pub_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA - --from - --(SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 - --ELSE 0 - --END) AS OpenAccess, SUM(CASE - --WHEN bestlicence<>'Open Access' THEN 1 - --ELSE 0 - --END) AS NonOpenAccess - --FROM publication p - --join result_organization ro on p.id=ro.id - --join organization o on o.id=ro.organization - --where cast(year as int)>=2003 and cast(year as int)<=2021 - --group by year, country) tmp; - ---create table indi_dataset_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA ---from - --(SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 - --ELSE 0 - --END) AS OpenAccess, SUM(CASE - --WHEN bestlicence<>'Open Access' THEN 1 - --ELSE 0 - --END) AS NonOpenAccess - --FROM dataset d - --join result_organization ro on d.id=ro.id - --join organization o on o.id=ro.organization - --where cast(year as int)>=2003 and cast(year as int)<=2021 - --group by year, country) tmp; - ---create table indi_software_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA ---from --- (SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 --- ELSE 0 ---END) AS OpenAccess, SUM(CASE --- WHEN bestlicence<>'Open Access' THEN 1 --- ELSE 0 --- END) AS NonOpenAccess --- FROM software s --- join result_organization ro on s.id=ro.id --- join organization o on o.id=ro.organization --- where cast(year as int)>=2003 and cast(year as int)<=2021 --- group by year, country) tmp; - - ---create table indi_other_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA --- from --- (SELECT year, country, SUM(CASE --- WHEN bestlicence='Open Access' THEN 1 --- ELSE 0 --- END) AS OpenAccess, SUM(CASE --- WHEN bestlicence<>'Open Access' THEN 1 --- ELSE 0 --- END) AS NonOpenAccess --- FROM otherresearchproduct orp --- join result_organization ro on orp.id=ro.id --- join organization o on o.id=ro.organization --- where cast(year as int)>=2003 and cast(year as int)<=2021 --- group by year, country) tmp; - ---create table indi_pub_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join publication p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofpubs ---from total; - ---create table indi_dataset_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join dataset p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofdataset ---from total; - ---create table indi_software_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join software p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofsoftware ---from total; - ---create table indi_other_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join otherresearchproduct p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofother ---from total; - ---create table indi_other_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from otherresearchproduct_datasources pd ---join datasource d on datasource=d.id ---join otherresearchproduct p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct ---from total; - ---create table indi_software_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from software_datasources pd ---join datasource d on datasource=d.id ---join software p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfSoftware ---from total; - ---create table indi_dataset_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from dataset_datasources pd ---join datasource d on datasource=d.id ---join dataset p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfDatasets ---from total; - ---create table indi_pub_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from publication_datasources pd ---join datasource d on datasource=d.id ---join publication p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfPubs ---from total; - -create table indi_pub_has_cc_licence stored as parquet as -select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license -from publication p -left outer join (select p.id, license.type as lic from publication p -join publication_licenses as license on license.id = p.id +---- Sprint 2 ---- +create table indi_result_has_cc_licence stored as parquet as +select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license +from result r +left outer join (select r.id, license.type as lic from result r +join result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp -on p.id= tmp.id; +on r.id= tmp.id; -create table indi_pub_has_cc_licence_url stored as parquet as -select distinct p.id, (case when lic_host='' or lic_host is null then 0 else 1 end) as has_cc_license_url -from publication p -left outer join (select p.id, lower(parse_url(license.type, "HOST")) as lic_host -from publication p -join publication_licenses as license on license.id = p.id -WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp -on p.id= tmp.id; - --- EOSC-TR1.1-02M: --- ## Indicator: has_cc_license. Creative Commons licensing has become a --- de facto standard in scholarly communication and is promoted by many initiatives --- like Plan S. This indicator might be only useful when applied --- to openly available publications. ---create table indi_pub_has_cc_licence_tr stored as parquet as ---select distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_tr ---from publication p ---left outer join (select p.id, license.type as lic from publication p ---join publication_licenses as license on license.id = p.id ---where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp ---on p.id= tmp.id - --- #EOSC-F2-01M_cc Rich metadata for scholarly publications --- ## Indicator: has_cc_license. Creative Commons licensing has become a --- de facto standard in scholarly communication and is promoted by many initiatives --- like Plan S. This indicator might be only useful when applied --- to openly available publications. - --- Same indicator as EOSC-TR1.1-02M (Najko's instructions) --- create table indi_pub_has_cc_licence_f stored as parquet as --- select --- distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_f --- from publication p --- left outer join (selectp.id,license.type as lic from publication p --- join publication_licenses as license on license.id = p.id --- where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp --- on p.id= tmp.id +create table indi_result_has_cc_licence_url stored as parquet as +select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url +from result r +left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host +from result r +join result_licenses as license on license.id = r.id +WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp +on r.id= tmp.id; create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; -create table indi_result_with_orcid stored as parquet as +create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid -from result r -left outer join (select id, 1 as has_orcid from result_orcid) tmp -on r.id= tmp.id +from result r +left outer join (select id, 1 as has_orcid from result_orcid) tmp +on r.id= tmp.id; -create table indi_funded_result_with_fundref stored as parquet as + +---- Sprint 3 ---- +create table indi_funded_result_with_fundref stored as parquet as select distinct r.id, coalesce(fundref, 0) as fundref -from project_results r +from project_results r left outer join (select distinct id, 1 as fundref from project_results -where provenance='Harvested') tmp -on r.id= tmp.id +where provenance='Harvested') tmp +on r.id= tmp.id; -create table indi_result_org_country_collab stored as parquet as -with tmp as +create table indi_result_org_country_collab stored as parquet as +with tmp as (select o.id as id, o.country , ro.id as result,r.type from organization o join result_organization ro on o.id=ro.organization join result r on r.id=ro.id where o.country <> 'UNKNOWN') select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations from tmp as o1 join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country +where o1.id<>o2.id and o1.country<>o2.country +group by o1.id, o1.type,o2.country; -create table indi_result_org_collab stored as parquet as -with tmp as +create table indi_result_org_collab stored as parquet as +with tmp as (select o.id, ro.id as result,r.type from organization o join result_organization ro on o.id=ro.organization join result r on r.id=ro.id) @@ -297,66 +99,82 @@ select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaboratio from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.id<>o2.id -group by o1.id, o2.id, o1.type +group by o1.id, o2.id, o1.type; -create table indi_funder_country_collab stored as parquet as -with tmp as (select funder, project, country from organization_projects op -join organization o on o.id=op.id -join project p on p.id=op.project +create table indi_funder_country_collab stored as parquet as +with tmp as (select funder, project, country from organization_projects op +join organization o on o.id=op.id +join project p on p.id=op.project where country <> 'UNKNOWN') -select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations +select f1.funder, f1.country, f2.country, count(distinct f1.project) as collaborations from tmp as f1 join tmp as f2 on f1.project=f2.project -where f1.country<>f2.country -group by f1.funder, f2.country, f1.country +where f1.country<>f2.country +group by f1.funder, f2.country, f1.country; +create table indi_result_country_collab stored as parquet as +with tmp as +(select country, ro.id as result,r.type from organization o +join result_organization ro on o.id=ro.organization +join result r on r.id=ro.id) +select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations +from tmp as o1 +join tmp as o2 on o1.result=o2.result +where o1.country<>o2.country +group by o1.country, o2.country, o1.type; + +---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as -select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal +select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from publication_datasources pd left outer join ( select pd.id, 1 as in_diamond_journal from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_pub_hybrid stored as parquet as -select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid +select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd left outer join ( select pd.id, 1 as is_hybrid from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_is_gold_oa stored as parquet as -(select distinct pd.id, coalesce(gold_oa, 0) as gold_oa +(select distinct pd.id, coalesce(gold_oa, 0) as gold_oa from publication_datasources pd left outer join ( select pd.id, 1 as gold_oa from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online) where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp -on pd.id=tmp.id) - +on pd.id=tmp.id); create table indi_pub_in_transformative stored as parquet as -select distinct pd.id, coalesce(is_transformative, 0) as is_transformative +select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd left outer join ( select pd.id, 1 as is_transformative from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and ps.is_transformative_journal=true) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri -left outer join +left outer join (select ri.id, 1 as pub_closed_other_open from result_instance ri join publication p on p.id=ri.id join datasource d on ri.hostedby=d.id where d.type like '%Journal%' and ri.accessright='Closed Access' and -(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp -on tmp.id=ri.id \ No newline at end of file +(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp +on tmp.id=ri.id; + + +---- Sprint 5 ---- +create table indi_result_no_of_copies stored as parquet as +select id, count(id) as number_of_copies from result_instance group by id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 2d6ff41d4..9bd90aa1f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -52,7 +52,8 @@ compute stats TARGET.result_languages; create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_licenses; -create table TARGET.licenses_normalized as select * from SOURCE.licenses_normalized; +create table TARGET.licenses_normalized stored as parquet as select * from SOURCE.licenses_normalized orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.licenses_normalized; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; @@ -141,9 +142,6 @@ compute stats TARGET.indi_pub_closed_other_open; create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_no_of_copies; ---- Usage statistics -create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); - --denorm alter table TARGET.result rename to TARGET.res_tmp; From b6b4bc0df975508763e86d7cc868d5d81f6db176 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 21 Dec 2021 03:35:04 +0200 Subject: [PATCH 040/159] added first indicator of sprint 5 --- .../oozie_app/scripts/step20-createMonitorDB.sql | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 9bd90aa1f..1ae459640 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -49,11 +49,8 @@ compute stats TARGET.result_greenoa; create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_languages; -create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.result_licenses; - -create table TARGET.licenses_normalized stored as parquet as select * from SOURCE.licenses_normalized orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.licenses_normalized; +create table TARGET.result_licences stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_licences; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; @@ -103,7 +100,6 @@ create view if not exists TARGET.project as select * from SOURCE.project; create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; -create view if not exists TARGET.project_classification as select * from SOURCE.project_classification; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; compute stats TARGET.project_results; @@ -119,8 +115,8 @@ create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.i compute stats TARGET.indi_pub_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; -create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_result_has_cc_licence; +create table TARGET.indi_result_has_cc_licence_f stored as parquet as select * from SOURCE.indi_result_has_cc_licence_f orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_result_has_cc_licence_f; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; From b053b0178e0624c3416cb38eaa82014b99e64be2 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Mon, 20 Dec 2021 19:23:57 +0200 Subject: [PATCH 041/159] Sprint 5 and other changes --- .../scripts/step16-createIndicatorsTables.sql | 234 ++++++++++++++++-- 1 file changed, 219 insertions(+), 15 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index bdd681f8d..9c67da883 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -42,8 +42,181 @@ join datasource on datasource.id = ri.hostedby where datasource.id like '%doajarticles%') tmp on p.id= tmp.id; +--create table indi_project_pubs_count stored as parquet as +--select pr.id id, count(p.id) total_pubs from project_results pr +--join publication p on p.id=pr.result +--group by pr.id; + +--create table indi_project_datasets_count stored as parquet as +--select pr.id id, count(d.id) total_datasets from project_results pr +--join dataset d on d.id=pr.result +--group by pr.id; + +--create table indi_project_software_count stored as parquet as +--select pr.id id, count(s.id) total_software from project_results pr +--join software s on s.id=pr.result +--group by pr.id; + +--create table indi_project_otherresearch_count stored as parquet as +--select pr.id id, count(o.id) total_other from project_results pr +--join otherresearchproduct o on o.id=pr.result +--group by pr.id; + +--create table indi_pub_avg_year_country_oa stored as parquet as +--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA + --from + --(SELECT year, country, SUM(CASE + --WHEN bestlicence='Open Access' THEN 1 + --ELSE 0 + --END) AS OpenAccess, SUM(CASE + --WHEN bestlicence<>'Open Access' THEN 1 + --ELSE 0 + --END) AS NonOpenAccess + --FROM publication p + --join result_organization ro on p.id=ro.id + --join organization o on o.id=ro.organization + --where cast(year as int)>=2003 and cast(year as int)<=2021 + --group by year, country) tmp; + +--create table indi_dataset_avg_year_country_oa stored as parquet as +--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA +--from + --(SELECT year, country, SUM(CASE + --WHEN bestlicence='Open Access' THEN 1 + --ELSE 0 + --END) AS OpenAccess, SUM(CASE + --WHEN bestlicence<>'Open Access' THEN 1 + --ELSE 0 + --END) AS NonOpenAccess + --FROM dataset d + --join result_organization ro on d.id=ro.id + --join organization o on o.id=ro.organization + --where cast(year as int)>=2003 and cast(year as int)<=2021 + --group by year, country) tmp; + +--create table indi_software_avg_year_country_oa stored as parquet as +--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA +--from +-- (SELECT year, country, SUM(CASE + --WHEN bestlicence='Open Access' THEN 1 +-- ELSE 0 +--END) AS OpenAccess, SUM(CASE +-- WHEN bestlicence<>'Open Access' THEN 1 +-- ELSE 0 +-- END) AS NonOpenAccess +-- FROM software s +-- join result_organization ro on s.id=ro.id +-- join organization o on o.id=ro.organization +-- where cast(year as int)>=2003 and cast(year as int)<=2021 +-- group by year, country) tmp; + + +--create table indi_other_avg_year_country_oa stored as parquet as +--select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, +--round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA +-- from +-- (SELECT year, country, SUM(CASE +-- WHEN bestlicence='Open Access' THEN 1 +-- ELSE 0 +-- END) AS OpenAccess, SUM(CASE +-- WHEN bestlicence<>'Open Access' THEN 1 +-- ELSE 0 +-- END) AS NonOpenAccess +-- FROM otherresearchproduct orp +-- join result_organization ro on orp.id=ro.id +-- join organization o on o.id=ro.organization +-- where cast(year as int)>=2003 and cast(year as int)<=2021 +-- group by year, country) tmp; + +--create table indi_pub_avg_year_context_oa stored as parquet as +--with total as +--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc +--join context c on pc.concept like concat('%',c.id,'%') +--join publication p on p.id=pc.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by c.name, year ) +--select year, name, round(no_of_pubs/total*100,3) averageofpubs +--from total; + +--create table indi_dataset_avg_year_context_oa stored as parquet as +--with total as +--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc +--join context c on pc.concept like concat('%',c.id,'%') +--join dataset p on p.id=pc.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by c.name, year ) +--select year, name, round(no_of_pubs/total*100,3) averageofdataset +--from total; + +--create table indi_software_avg_year_context_oa stored as parquet as +--with total as +--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc +--join context c on pc.concept like concat('%',c.id,'%') +--join software p on p.id=pc.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by c.name, year ) +--select year, name, round(no_of_pubs/total*100,3) averageofsoftware +--from total; + +--create table indi_other_avg_year_context_oa stored as parquet as +--with total as +--(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc +--join context c on pc.concept like concat('%',c.id,'%') +--join otherresearchproduct p on p.id=pc.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by c.name, year ) +--select year, name, round(no_of_pubs/total*100,3) averageofother +--from total; + +--create table indi_other_avg_year_content_oa stored as parquet as +--with total as +--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +--from otherresearchproduct_datasources pd +--join datasource d on datasource=d.id +--join otherresearchproduct p on p.id=pd.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by d.type, year) +--select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct +--from total; + +--create table indi_software_avg_year_content_oa stored as parquet as +--with total as +--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +--from software_datasources pd +--join datasource d on datasource=d.id +--join software p on p.id=pd.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by d.type, year) +--select year, type, round(no_of_pubs/total*100,3) averageOfSoftware +--from total; + +--create table indi_dataset_avg_year_content_oa stored as parquet as +--with total as +--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +--from dataset_datasources pd +--join datasource d on datasource=d.id +--join dataset p on p.id=pd.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by d.type, year) +--select year, type, round(no_of_pubs/total*100,3) averageOfDatasets +--from total; + +--create table indi_pub_avg_year_content_oa stored as parquet as +--with total as +--(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total +--from publication_datasources pd +--join datasource d on datasource=d.id +--join publication p on p.id=pd.id +--where cast(year as int)>=2003 and cast(year as int)<=2021 +--group by d.type, year) +--select year, type, round(no_of_pubs/total*100,3) averageOfPubs +--from total; + ---- Sprint 2 ---- -create table indi_result_has_cc_licence stored as parquet as +create table indi_result_has_cc_licence_f stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license from result r left outer join (select r.id, license.type as lic from result r @@ -60,6 +233,35 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; +-- EOSC-TR1.1-02M: +-- ## Indicator: has_cc_license. Creative Commons licensing has become a +-- de facto standard in scholarly communication and is promoted by many initiatives +-- like Plan S. This indicator might be only useful when applied +-- to openly available publications. +--create table indi_pub_has_cc_licence_tr stored as parquet as +--select distinct p.id, case when lic='' or lic is null then 0 else 1 end indi_result_org_collabas has_cc_license_tr +--from publication p +--left outer join (select p.id, license.type as lic from publication p +--join publication_licenses as license on license.id = p.id +--where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp +--on p.id= tmp.id + +-- #EOSC-F2-01M_cc Rich metadata for scholarly publications +-- ## Indicator: has_cc_license. Creative Commons licensing has become a +-- de facto standard in scholarly communication and is promoted by many initiatives +-- like Plan S. This indicator might be only useful when applied +-- to openly available publications. + +-- Same indicator as EOSC-TR1.1-02M (Najko's instructions) +-- create table indi_pub_has_cc_licence_f stored as parquet as +-- select +-- distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_f +-- from publication p +-- left outer join (selectp.id,license.type as lic from publication p +-- join publication_licenses as license on license.id = p.id +-- where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp +-- on p.id= tmp.id + create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; @@ -68,16 +270,16 @@ create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp -on r.id= tmp.id; - +on r.id= tmp.id ---- Sprint 3 ---- + create table indi_funded_result_with_fundref stored as parquet as select distinct r.id, coalesce(fundref, 0) as fundref from project_results r left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp -on r.id= tmp.id; +on r.id= tmp.id create table indi_result_org_country_collab stored as parquet as with tmp as @@ -88,7 +290,7 @@ select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as col from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; +group by o1.id, o1.type,o2.country create table indi_result_org_collab stored as parquet as with tmp as @@ -99,7 +301,7 @@ select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaboratio from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.id<>o2.id -group by o1.id, o2.id, o1.type; +group by o1.id, o2.id, o1.type create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op @@ -110,7 +312,7 @@ select f1.funder, f1.country, f2.country, count(distinct f1.project) as collabor from tmp as f1 join tmp as f2 on f1.project=f2.project where f1.country<>f2.country -group by f1.funder, f2.country, f1.country; +group by f1.funder, f2.country, f1.country create table indi_result_country_collab stored as parquet as with tmp as @@ -121,9 +323,10 @@ select o1.country country1, o2.country country2, o1.type, count(distinct o1.resu from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.country<>o2.country -group by o1.country, o2.country, o1.type; +group by o1.country, o2.country, o1.type ---- Sprint 4 ---- + create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from publication_datasources pd @@ -132,7 +335,7 @@ select pd.id, 1 as in_diamond_journal from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id; +on pd.id=tmp.id create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid @@ -142,7 +345,7 @@ select pd.id, 1 as is_hybrid from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp -on pd.id=tmp.id; +on pd.id=tmp.id create table indi_is_gold_oa stored as parquet as (select distinct pd.id, coalesce(gold_oa, 0) as gold_oa @@ -152,7 +355,8 @@ select pd.id, 1 as gold_oa from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online) where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp -on pd.id=tmp.id); +on pd.id=tmp.id) + create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative @@ -162,7 +366,7 @@ select pd.id, 1 as is_transformative from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and ps.is_transformative_journal=true) tmp -on pd.id=tmp.id; +on pd.id=tmp.id create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri @@ -172,9 +376,9 @@ join publication p on p.id=ri.id join datasource d on ri.hostedby=d.id where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp -on tmp.id=ri.id; - +on tmp.id=ri.id ---- Sprint 5 ---- + create table indi_result_no_of_copies stored as parquet as -select id, count(id) as number_of_copies from result_instance group by id; \ No newline at end of file +select id, count(id) as number_of_copies from result_instance group by id \ No newline at end of file From 9acc32faa69ae1d6dae8bc2f9a0e941d130a5fa3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 12 Jan 2022 12:04:31 +0100 Subject: [PATCH 042/159] [stats wf] final touches for the integration of PRs #166, #179 in the master branch --- .../scripts/step16-createIndicatorsTables.sql | 236 ++---------------- .../scripts/step20-createMonitorDB.sql | 17 +- 2 files changed, 29 insertions(+), 224 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 9c67da883..9f11fa49d 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -42,181 +42,8 @@ join datasource on datasource.id = ri.hostedby where datasource.id like '%doajarticles%') tmp on p.id= tmp.id; ---create table indi_project_pubs_count stored as parquet as ---select pr.id id, count(p.id) total_pubs from project_results pr ---join publication p on p.id=pr.result ---group by pr.id; - ---create table indi_project_datasets_count stored as parquet as ---select pr.id id, count(d.id) total_datasets from project_results pr ---join dataset d on d.id=pr.result ---group by pr.id; - ---create table indi_project_software_count stored as parquet as ---select pr.id id, count(s.id) total_software from project_results pr ---join software s on s.id=pr.result ---group by pr.id; - ---create table indi_project_otherresearch_count stored as parquet as ---select pr.id id, count(o.id) total_other from project_results pr ---join otherresearchproduct o on o.id=pr.result ---group by pr.id; - ---create table indi_pub_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA - --from - --(SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 - --ELSE 0 - --END) AS OpenAccess, SUM(CASE - --WHEN bestlicence<>'Open Access' THEN 1 - --ELSE 0 - --END) AS NonOpenAccess - --FROM publication p - --join result_organization ro on p.id=ro.id - --join organization o on o.id=ro.organization - --where cast(year as int)>=2003 and cast(year as int)<=2021 - --group by year, country) tmp; - ---create table indi_dataset_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA ---from - --(SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 - --ELSE 0 - --END) AS OpenAccess, SUM(CASE - --WHEN bestlicence<>'Open Access' THEN 1 - --ELSE 0 - --END) AS NonOpenAccess - --FROM dataset d - --join result_organization ro on d.id=ro.id - --join organization o on o.id=ro.organization - --where cast(year as int)>=2003 and cast(year as int)<=2021 - --group by year, country) tmp; - ---create table indi_software_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA ---from --- (SELECT year, country, SUM(CASE - --WHEN bestlicence='Open Access' THEN 1 --- ELSE 0 ---END) AS OpenAccess, SUM(CASE --- WHEN bestlicence<>'Open Access' THEN 1 --- ELSE 0 --- END) AS NonOpenAccess --- FROM software s --- join result_organization ro on s.id=ro.id --- join organization o on o.id=ro.organization --- where cast(year as int)>=2003 and cast(year as int)<=2021 --- group by year, country) tmp; - - ---create table indi_other_avg_year_country_oa stored as parquet as ---select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA, ---round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA --- from --- (SELECT year, country, SUM(CASE --- WHEN bestlicence='Open Access' THEN 1 --- ELSE 0 --- END) AS OpenAccess, SUM(CASE --- WHEN bestlicence<>'Open Access' THEN 1 --- ELSE 0 --- END) AS NonOpenAccess --- FROM otherresearchproduct orp --- join result_organization ro on orp.id=ro.id --- join organization o on o.id=ro.organization --- where cast(year as int)>=2003 and cast(year as int)<=2021 --- group by year, country) tmp; - ---create table indi_pub_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join publication p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofpubs ---from total; - ---create table indi_dataset_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join dataset p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofdataset ---from total; - ---create table indi_software_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join software p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofsoftware ---from total; - ---create table indi_other_avg_year_context_oa stored as parquet as ---with total as ---(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc ---join context c on pc.concept like concat('%',c.id,'%') ---join otherresearchproduct p on p.id=pc.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by c.name, year ) ---select year, name, round(no_of_pubs/total*100,3) averageofother ---from total; - ---create table indi_other_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from otherresearchproduct_datasources pd ---join datasource d on datasource=d.id ---join otherresearchproduct p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct ---from total; - ---create table indi_software_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from software_datasources pd ---join datasource d on datasource=d.id ---join software p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfSoftware ---from total; - ---create table indi_dataset_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from dataset_datasources pd ---join datasource d on datasource=d.id ---join dataset p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfDatasets ---from total; - ---create table indi_pub_avg_year_content_oa stored as parquet as ---with total as ---(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total ---from publication_datasources pd ---join datasource d on datasource=d.id ---join publication p on p.id=pd.id ---where cast(year as int)>=2003 and cast(year as int)<=2021 ---group by d.type, year) ---select year, type, round(no_of_pubs/total*100,3) averageOfPubs ---from total; - ---- Sprint 2 ---- -create table indi_result_has_cc_licence_f stored as parquet as +create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license from result r left outer join (select r.id, license.type as lic from result r @@ -233,35 +60,6 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; --- EOSC-TR1.1-02M: --- ## Indicator: has_cc_license. Creative Commons licensing has become a --- de facto standard in scholarly communication and is promoted by many initiatives --- like Plan S. This indicator might be only useful when applied --- to openly available publications. ---create table indi_pub_has_cc_licence_tr stored as parquet as ---select distinct p.id, case when lic='' or lic is null then 0 else 1 end indi_result_org_collabas has_cc_license_tr ---from publication p ---left outer join (select p.id, license.type as lic from publication p ---join publication_licenses as license on license.id = p.id ---where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp ---on p.id= tmp.id - --- #EOSC-F2-01M_cc Rich metadata for scholarly publications --- ## Indicator: has_cc_license. Creative Commons licensing has become a --- de facto standard in scholarly communication and is promoted by many initiatives --- like Plan S. This indicator might be only useful when applied --- to openly available publications. - --- Same indicator as EOSC-TR1.1-02M (Najko's instructions) --- create table indi_pub_has_cc_licence_f stored as parquet as --- select --- distinct p.id, case when lic='' or lic is null then 0 else 1 end as has_cc_license_f --- from publication p --- left outer join (selectp.id,license.type as lic from publication p --- join publication_licenses as license on license.id = p.id --- where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp --- on p.id= tmp.id - create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; @@ -270,16 +68,16 @@ create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp -on r.id= tmp.id +on r.id= tmp.id; + ---- Sprint 3 ---- - create table indi_funded_result_with_fundref stored as parquet as select distinct r.id, coalesce(fundref, 0) as fundref from project_results r left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp -on r.id= tmp.id +on r.id= tmp.id; create table indi_result_org_country_collab stored as parquet as with tmp as @@ -290,7 +88,7 @@ select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as col from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country +group by o1.id, o1.type,o2.country; create table indi_result_org_collab stored as parquet as with tmp as @@ -301,18 +99,18 @@ select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaboratio from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.id<>o2.id -group by o1.id, o2.id, o1.type +group by o1.id, o2.id, o1.type; create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op join organization o on o.id=op.id join project p on p.id=op.project where country <> 'UNKNOWN') -select f1.funder, f1.country, f2.country, count(distinct f1.project) as collaborations +select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations from tmp as f1 join tmp as f2 on f1.project=f2.project where f1.country<>f2.country -group by f1.funder, f2.country, f1.country +group by f1.funder, f2.country, f1.country; create table indi_result_country_collab stored as parquet as with tmp as @@ -323,10 +121,9 @@ select o1.country country1, o2.country country2, o1.type, count(distinct o1.resu from tmp as o1 join tmp as o2 on o1.result=o2.result where o1.country<>o2.country -group by o1.country, o2.country, o1.type +group by o1.country, o2.country, o1.type; ---- Sprint 4 ---- - create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from publication_datasources pd @@ -335,7 +132,7 @@ select pd.id, 1 as in_diamond_journal from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid @@ -345,7 +142,7 @@ select pd.id, 1 as is_hybrid from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_is_gold_oa stored as parquet as (select distinct pd.id, coalesce(gold_oa, 0) as gold_oa @@ -355,8 +152,7 @@ select pd.id, 1 as gold_oa from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online) where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp -on pd.id=tmp.id) - +on pd.id=tmp.id); create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative @@ -366,7 +162,7 @@ select pd.id, 1 as is_transformative from publication_datasources pd join datasource d on d.id=pd.datasource join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) and ps.is_transformative_journal=true) tmp -on pd.id=tmp.id +on pd.id=tmp.id; create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri @@ -376,9 +172,9 @@ join publication p on p.id=ri.id join datasource d on ri.hostedby=d.id where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp -on tmp.id=ri.id +on tmp.id=ri.id; + ---- Sprint 5 ---- - create table indi_result_no_of_copies stored as parquet as -select id, count(id) as number_of_copies from result_instance group by id \ No newline at end of file +select id, count(id) as number_of_copies from result_instance group by id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 1ae459640..e72378f56 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -49,8 +49,10 @@ compute stats TARGET.result_greenoa; create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_languages; -create table TARGET.result_licences stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.result_licences; +create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_licenses; + +create table TARGET.licenses_normalized as select * from SOURCE.licenses_normalized; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; @@ -79,6 +81,9 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; +create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source or r.id=orig.target); +compute stats TARGET.result_result; + -- datasources create view if not exists TARGET.datasource as select * from SOURCE.datasource; create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; @@ -100,6 +105,7 @@ create view if not exists TARGET.project as select * from SOURCE.project; create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; +create view if not exists TARGET.project_classification as select * from SOURCE.project_classification; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; compute stats TARGET.project_results; @@ -115,8 +121,8 @@ create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.i compute stats TARGET.indi_pub_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; -create table TARGET.indi_result_has_cc_licence_f stored as parquet as select * from SOURCE.indi_result_has_cc_licence_f orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_result_has_cc_licence_f; +create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; @@ -138,6 +144,9 @@ compute stats TARGET.indi_pub_closed_other_open; create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_no_of_copies; +--- Usage statistics +create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); + --denorm alter table TARGET.result rename to TARGET.res_tmp; From f2fde5566bc9875731911a3717210c691fbbc8e1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 20 Jan 2022 09:19:07 +0100 Subject: [PATCH 043/159] using helper method from ModelSupport to find the inverse relation descriptor --- .../dhp/blacklist/ReadBlacklistFromDB.java | 2 +- .../dhp/blacklist/BlacklistRelationTest.java | 38 +++++++++++++++++++ 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java index 7d0d6b0b8..380991526 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java @@ -90,7 +90,7 @@ public class ReadBlacklistFromDB implements Closeable { inverse.setSource(target_direct); String encoding = rs.getString("relationship"); - RelationInverse ri = ModelSupport.relationInverseMap.get(encoding); + RelationInverse ri = ModelSupport.findInverse(encoding); direct.setRelClass(ri.getRelClass()); inverse.setRelClass(ri.getInverseRelClass()); direct.setRelType(ri.getRelType()); diff --git a/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java new file mode 100644 index 000000000..160658e5b --- /dev/null +++ b/dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.blacklist; + +import java.util.Arrays; +import java.util.List; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; + +public class BlacklistRelationTest { + + @Test + public void testRelationInverseLookup() { + + final List rels = Arrays + .asList( + "resultResult_relationship_IsRelatedTo", + "resultOrganization_affiliation_isAuthorInstitutionOf", + "resultOrganization_affiliation_hasAuthorInstitution", + "datasourceOrganization_provision_isProvidedBy", + "projectOrganization_participation_hasParticipant", + "resultProject_outcome_produces", + "resultProject_outcome_isProducedBy"); + + rels.forEach(r -> { + RelationInverse inverse = ModelSupport.relationInverseMap.get(r); + Assertions.assertNotNull(inverse); + Assertions.assertNotNull(inverse.getRelType()); + Assertions.assertNotNull(inverse.getSubReltype()); + Assertions.assertNotNull(inverse.getRelClass()); + }); + + } + +} From 8de97883083bf2608a084840ab1f3e03f4244e05 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 24 Jan 2022 11:29:22 +0100 Subject: [PATCH 044/159] applied fix for avoiding ruling out the invisible (APC) records during the graph cleaning --- .../oaf/utils/GraphCleaningFunctions.java | 16 + .../clean/GraphCleaningFunctionsTest.java | 47 + .../dhp/oa/graph/clean/result_invisible.json | 958 ++++++++++++++++++ .../graph/clean/result_missing_invisible.json | 922 +++++++++++++++++ 4 files changed, 1943 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index f49a47c0a..48e35a342 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -88,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions { } public static boolean filter(T value) { + if (Boolean.TRUE + .equals( + Optional + .ofNullable(value) + .map( + o -> Optional + .ofNullable(o.getDataInfo()) + .map( + d -> Optional + .ofNullable(d.getInvisible()) + .orElse(true)) + .orElse(true)) + .orElse(true))) { + return true; + } + if (value instanceof Datasource) { // nothing to evaluate here } else if (value instanceof Project) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 0e9efed21..ebd8cb55c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -71,6 +71,53 @@ public class GraphCleaningFunctionsTest { } } + @Test + void testFilter_invisible_true() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_true_nothing_to_filter() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + + @Test + void testFilter_missing_invisible() throws Exception { + + assertNotNull(vocabularies); + assertNotNull(mapping); + + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + assertTrue(p_in instanceof Result); + assertTrue(p_in instanceof Publication); + + assertEquals(true, GraphCleaningFunctions.filter(p_in)); + } + @Test void testCleaning() throws Exception { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json new file mode 100644 index 000000000..ffcb187c1 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json @@ -0,0 +1,958 @@ +{ + "author": [ + { + "affiliation": [ + ], + "fullname": "Brien, Tom", + "name": "Tom", + "pid": [ + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "ORCID12", + "classname": "ORCID12", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "ORCID12", + "classname": "ORCID12", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "https://orcid.org/0000-0001-9613-6639" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "orcid", + "classname": "ORCID12", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "0000-0001-9613-6639" + } + ], + "rank": 1, + "surname": "Brien" + }, + { + "affiliation": [ + ], + "fullname": "Ade, Peter", + "name": "Peter", + "pid": [ + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "xyz", + "classname": "XYZ", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "qwerty" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "ORCID", + "classname": "ORCID", + "schemeid": "", + "schemename": "" + }, + "value": "asdasd" + } + ], + "rank": 2, + "surname": "Ade" + }, + { + "affiliation": [ + ], + "fullname": "Barry, Peter S.", + "name": "Peter S.", + "pid": null, + "rank": 3, + "surname": "Barry" + }, + { + "affiliation": [ + ], + "fullname": "Dunscombe, Chris J.", + "name": "Chris J.", + "pid": [ + ], + "rank": 4, + "surname": "Dunscombe" + }, + { + "affiliation": [ + ], + "fullname": "Leadley, David R.", + "name": "David R.", + "pid": [ + ], + "rank": 5, + "surname": "Leadley" + }, + { + "affiliation": [ + ], + "fullname": "Morozov, Dmitry V.", + "name": "Dmitry V.", + "pid": [ + ], + "rank": 6, + "surname": "Morozov" + }, + { + "affiliation": [ + ], + "fullname": "Myronov, Maksym", + "name": "Maksym", + "pid": [ + ], + "rank": 7, + "surname": "Myronov" + }, + { + "affiliation": [ + ], + "fullname": "Parker, Evan", + "name": "Evan", + "pid": [ + ], + "rank": 8, + "surname": "Parker" + }, + { + "affiliation": [ + ], + "fullname": "Prest, Martin J.", + "name": "Martin J.", + "pid": [ + ], + "rank": 9, + "surname": "Prest" + }, + { + "affiliation": [ + ], + "fullname": "Prunnila, Mika", + "name": "Mika", + "pid": [ + ], + "rank": 10, + "surname": "Prunnila" + }, + { + "affiliation": [ + ], + "fullname": "Sudiwala, Rashmi V.", + "name": "Rashmi V.", + "pid": [ + ], + "rank": 11, + "surname": "Sudiwala" + }, + { + "affiliation": [ + ], + "fullname": "Whall, Terry E.", + "name": "Terry E.", + "pid": [ + ], + "rank": 12, + "surname": "Whall" + }, + { + "affiliation": [ + ], + "fullname": "Mauskopf", + "name": "", + "pid": [ + ], + "rank": 13, + "surname": "" + }, + { + "affiliation": [ + ], + "fullname": " P. D. ", + "name": "", + "pid": [ + ], + "rank": 14, + "surname": "" + } + ], + "bestaccessright": null, + "publisher": { + "value": null + }, + "collectedfrom": [ + { + "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", + "value": "VIRTA" + } + ], + "context": [ + ], + "contributor": [ + ], + "country": [ + { + "classid": "DE", + "classname": "DE", + "schemeid": "dnet:countries", + "schemename": "dnet:countries" + } + ], + "coverage": [ + ], + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": true, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "dateofacceptance": { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": 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"schemename": "dnet:dataCite_title" + }, + "value": "omic" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "value": "｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "value": "-" + } + ] +} \ No newline at end of file From 59a250337c473f6153e3e3a1771f47dd6830690f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 24 Jan 2022 18:02:07 +0100 Subject: [PATCH 045/159] [graph resolution] drop output path at the beginning --- .../dhp/oa/graph/resolution/oozie_app/workflow.xml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml index 3cd08bc9b..74e792f07 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml @@ -19,12 +19,21 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + yarn From 3c60e53a96b68669e64d09aadc05031408d05cb9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 3 Feb 2022 14:47:08 +0100 Subject: [PATCH 046/159] [stats-wf]fixed the result_result creation for monitor PR#190 on beta --- .../graph/stats/oozie_app/scripts/step13.sql | 14 ++++++------- .../graph/stats/oozie_app/scripts/step14.sql | 10 +++++----- .../graph/stats/oozie_app/scripts/step15.sql | 8 ++++---- .../graph/stats/oozie_app/scripts/step2.sql | 20 +++++++++---------- .../scripts/step20-createMonitorDB.sql | 2 +- .../graph/stats/oozie_app/scripts/step3.sql | 20 +++++++++---------- .../graph/stats/oozie_app/scripts/step4.sql | 20 +++++++++---------- .../graph/stats/oozie_app/scripts/step5.sql | 20 +++++++++---------- .../graph/stats/oozie_app/scripts/step6.sql | 12 ++++++----- .../graph/stats/oozie_app/scripts/step7.sql | 2 +- .../graph/stats/oozie_app/scripts/step8.sql | 2 +- .../graph/stats/oozie_app/scripts/step9.sql | 2 +- 12 files changed, 67 insertions(+), 65 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 315d296fc..947c91072 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -14,7 +14,7 @@ LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource @@ -25,7 +25,7 @@ LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource @@ -36,7 +36,7 @@ LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource @@ -47,7 +47,7 @@ LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_sources AS SELECT * FROM ${stats_db_name}.publication_sources @@ -76,8 +76,8 @@ join ${openaire_db_name}.result r1 on rel.source=r1.id join ${openaire_db_name}.result r2 on r2.id=rel.target where reltype='resultResult' and r1.resulttype.classname!=r2.resulttype.classname - and r1.datainfo.deletedbyinference=false - and r2.datainfo.deletedbyinference=false + and r1.datainfo.deletedbyinference=false and r1.datainfo.invisible = FALSE + and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE and r1.resulttype.classname != 'other' and r2.resulttype.classname != 'other' - and rel.datainfo.deletedbyinference=false; \ No newline at end of file + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index 00a6913bc..e3a33a893 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -8,22 +8,22 @@ CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses -where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false; +where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses -where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false; +where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses -where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false; +where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses -where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false; +where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses @@ -46,7 +46,7 @@ FROM ( LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false) d on o.datasource = d.id; + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; -- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; -- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index 8e66e05c0..f46b65171 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -9,22 +9,22 @@ CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst -where r.datainfo.deletedbyinference=false; +where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst -where r.datainfo.deletedbyinference=false; +where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst -where r.datainfo.deletedbyinference=false; +where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst -where r.datainfo.deletedbyinference=false; +where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_refereed as select * from ${stats_db_name}.publication_refereed diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index bb0d0ac6c..468a42045 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -38,13 +38,13 @@ SELECT substr(p.id, 4) as id, case when size(p.description) > 0 then true else false end as abstract, 'publication' as type from ${openaire_db_name}.publication p -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_classifications AS SELECT substr(p.id, 4) as id, instancetype.classname as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.instancetype) instances as instancetype -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_concepts AS SELECT substr(p.id, 4) as id, case @@ -53,45 +53,45 @@ SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept from ${openaire_db_name}.publication p LATERAL VIEW explode(p.context) contexts as context -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_datasources as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource from ${openaire_db_name}.publication p lateral view explode(p.instance) instances as instance - where p.datainfo.deletedbyinference = false) p + where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference = false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; CREATE TABLE ${stats_db_name}.publication_languages AS select substr(p.id, 4) as id, p.language.classname as language FROM ${openaire_db_name}.publication p -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.originalid) oids AS ids -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.pid) pids AS ppid -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_topics as select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.publication_citations AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" - and p.datainfo.deletedbyinference = false; \ No newline at end of file + and p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index e72378f56..2528e904d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -81,7 +81,7 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source or r.id=orig.target); +create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source) or exists (select 1 from TARGET.result r where r.id=orig.target); compute stats TARGET.result_result; -- datasources diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index 953eaad6a..76a5e5a48 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -38,20 +38,20 @@ SELECT substr(d.id, 4) AS id, CASE WHEN SIZE(d.description) > 0 THEN TRUE ELSE FALSE end AS abstract, 'dataset' AS type FROM ${openaire_db_name}.dataset d -WHERE d.datainfo.deletedbyinference = FALSE; +WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_citations AS SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.dataset d LATERAL VIEW explode(d.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" - and d.datainfo.deletedbyinference = false; + and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_concepts AS SELECT substr(p.id, 4) as id, case @@ -60,7 +60,7 @@ SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.context) contexts as context -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_datasources AS SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource @@ -68,31 +68,31 @@ FROM ( SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance) instances AS instance - where p.datainfo.deletedbyinference = false) p + where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p LEFT OUTER JOIN ( SELECT substr(d.id, 4) id FROM ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference = false) d ON p.datasource = d.id; + WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; CREATE TABLE ${stats_db_name}.dataset_languages AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.dataset p -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.originalid) oids AS ids -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.pid) pids AS ppid -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.dataset_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; \ No newline at end of file +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index 0210dc8cb..dc71f41f1 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -38,20 +38,20 @@ SELECT substr(s.id, 4) as id, CASE WHEN SIZE(s.description) > 0 THEN TRUE ELSE FALSE END AS abstract, 'software' as type from ${openaire_db_name}.software s -where s.datainfo.deletedbyinference = false; +where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_citations AS SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.software s LATERAL VIEW explode(s.extrainfo) citations as citation where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" - and s.datainfo.deletedbyinference = false; + and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_concepts AS SELECT substr(p.id, 4) as id, case @@ -60,7 +60,7 @@ SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.context) contexts AS context -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource @@ -68,31 +68,31 @@ FROM ( SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.instance) instances AS instance - where p.datainfo.deletedbyinference = false) p + where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p LEFT OUTER JOIN ( SELECT substr(d.id, 4) id FROM ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference = false) d ON p.datasource = d.id; + WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; CREATE TABLE ${stats_db_name}.software_languages AS select substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.software p -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.originalid) oids AS ids -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.pid) pids AS ppid -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.software_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; \ No newline at end of file +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index f7b302186..353aa98b7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -37,19 +37,19 @@ SELECT substr(o.id, 4) AS id, CASE WHEN SIZE(o.description) > 0 THEN TRUE ELSE FALSE END AS abstract, 'other' AS type FROM ${openaire_db_name}.otherresearchproduct o -WHERE o.datainfo.deletedbyinference = FALSE; +WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; -- Otherresearchproduct_citations CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" - and o.datainfo.deletedbyinference = false; + and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS SELECT substr(p.id, 4) as id, case @@ -57,33 +57,33 @@ SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance - where p.datainfo.deletedbyinference = false) p + where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p LEFT OUTER JOIN(SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference = false) d on p.datasource = d.id; + WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.otherresearchproduct p -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid -where p.datainfo.deletedbyinference = false; +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject -where p.datainfo.deletedbyinference = false; \ No newline at end of file +where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 378e0f17b..b5e2eb37b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -5,24 +5,26 @@ ------------------------------------------------------ CREATE TABLE ${stats_db_name}.project_oids AS SELECT substr(p.id, 4) AS id, oids.ids AS oid -FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids; +FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids +where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; + CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype = 'projectOrganization' - and r.datainfo.deletedbyinference = false; + and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.project_results AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultProject' - and r.datainfo.deletedbyinference = false; + and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; create table ${stats_db_name}.project_classification as select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3 from ${openaire_db_name}.project p lateral view explode(p.h2020classification) classifs as class -where p.datainfo.deletedbyinference=false and class.h2020programme is not null; +where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null; CREATE TABLE ${stats_db_name}.project_tmp ( @@ -72,7 +74,7 @@ SELECT substr(p.id, 4) AS id, p.code.value AS code, p.totalcost AS totalcost FROM ${openaire_db_name}.project p -WHERE p.datainfo.deletedbyinference = false; +WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; create table ${stats_db_name}.funder as select distinct xpath_string(fund, '//funder/id') as id, diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index b3cbc9b41..a57966abf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -127,7 +127,7 @@ CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultOrganization' - and r.datainfo.deletedbyinference = false; + and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 76d31eb5e..4956daf7f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -44,7 +44,7 @@ FROM ${openaire_db_name}.datasource d1 LATERAL VIEW EXPLODE(originalid) temp AS originalidd WHERE originalidd like "piwik:%") AS d2 ON d1.id = d2.id -WHERE d1.datainfo.deletedbyinference = FALSE; +WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table. -- Creating a temporary dual table that will be removed after the following insert diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index a1cb46185..c73aa811c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -9,7 +9,7 @@ SELECT substr(o.id, 4) as id, o.legalshortname.value as legalshortname, o.country.classid as country FROM ${openaire_db_name}.organization o -WHERE o.datainfo.deletedbyinference = FALSE; +WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible = FALSE; CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS SELECT organization AS id, id AS datasource From bcfdf9a0d70d3ebe3b42134c18c50b2f58ea4f9a Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 3 Feb 2022 16:49:31 +0100 Subject: [PATCH 047/159] iis repository with https --- dhp-workflows/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 53d029467..143178560 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -44,7 +44,7 @@ iis-releases iis releases plugin repository - http://maven.ceon.pl/artifactory/iis-releases + https://maven.ceon.pl/artifactory/iis-releases default From 493caef358d37a4f4d32223b0e1923bc7209885a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Feb 2022 14:51:25 +0100 Subject: [PATCH 048/159] [stats-wf]fixed the result_result table related to PR#191 --- .scalafmt.conf | 21 +++++++++++++++++++ dhp-workflows/dhp-aggregation/.scalafmt.conf | 21 +++++++++++++++++++ dhp-workflows/dhp-graph-mapper/.scalafmt.conf | 21 +++++++++++++++++++ .../scripts/step20-createMonitorDB.sql | 6 +++++- 4 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 .scalafmt.conf create mode 100644 dhp-workflows/dhp-aggregation/.scalafmt.conf create mode 100644 dhp-workflows/dhp-graph-mapper/.scalafmt.conf diff --git a/.scalafmt.conf b/.scalafmt.conf new file mode 100644 index 000000000..0b5dbe0b4 --- /dev/null +++ b/.scalafmt.conf @@ -0,0 +1,21 @@ +style = defaultWithAlign + +align.openParenCallSite = false +align.openParenDefnSite = false +align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}] +continuationIndent.callSite = 2 +continuationIndent.defnSite = 2 +danglingParentheses = true +indentOperator = spray +maxColumn = 120 +newlines.alwaysBeforeTopLevelStatements = true +project.excludeFilters = [".*\\.sbt"] +rewrite.rules = [AvoidInfix] +rewrite.rules = [ExpandImportSelectors] +rewrite.rules = [RedundantBraces] +rewrite.rules = [RedundantParens] +rewrite.rules = [SortImports] +rewrite.rules = [SortModifiers] +rewrite.rules = [PreferCurlyFors] +spaces.inImportCurlyBraces = false +unindentTopLevelOperators = true \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/.scalafmt.conf b/dhp-workflows/dhp-aggregation/.scalafmt.conf new file mode 100644 index 000000000..0b5dbe0b4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/.scalafmt.conf @@ -0,0 +1,21 @@ +style = defaultWithAlign + +align.openParenCallSite = false +align.openParenDefnSite = false +align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}] +continuationIndent.callSite = 2 +continuationIndent.defnSite = 2 +danglingParentheses = true +indentOperator = spray +maxColumn = 120 +newlines.alwaysBeforeTopLevelStatements = true +project.excludeFilters = [".*\\.sbt"] +rewrite.rules = [AvoidInfix] +rewrite.rules = [ExpandImportSelectors] +rewrite.rules = [RedundantBraces] +rewrite.rules = [RedundantParens] +rewrite.rules = [SortImports] +rewrite.rules = [SortModifiers] +rewrite.rules = [PreferCurlyFors] +spaces.inImportCurlyBraces = false +unindentTopLevelOperators = true \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/.scalafmt.conf b/dhp-workflows/dhp-graph-mapper/.scalafmt.conf new file mode 100644 index 000000000..0b5dbe0b4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/.scalafmt.conf @@ -0,0 +1,21 @@ +style = defaultWithAlign + +align.openParenCallSite = false +align.openParenDefnSite = false +align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}] +continuationIndent.callSite = 2 +continuationIndent.defnSite = 2 +danglingParentheses = true +indentOperator = spray +maxColumn = 120 +newlines.alwaysBeforeTopLevelStatements = true +project.excludeFilters = [".*\\.sbt"] +rewrite.rules = [AvoidInfix] +rewrite.rules = [ExpandImportSelectors] +rewrite.rules = [RedundantBraces] +rewrite.rules = [RedundantParens] +rewrite.rules = [SortImports] +rewrite.rules = [SortModifiers] +rewrite.rules = [PreferCurlyFors] +spaces.inImportCurlyBraces = false +unindentTopLevelOperators = true \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 2528e904d..4e5f7a373 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -81,7 +81,11 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -create table TARGET.result_result stored as parquet as select * from SOURCE.result_result orig where exists (select 1 from TARGET.result r where r.id=orig.source) or exists (select 1 from TARGET.result r where r.id=orig.target); +create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); +create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); +create table TARGET.result_result as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; +drop view TARGET.foo1; +drop view TARGET.foo2; compute stats TARGET.result_result; -- datasources From 78be2975f0d324bb4e8947f93f2609d77eb84ec2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 7 Feb 2022 11:22:08 +0100 Subject: [PATCH 049/159] [stats-wf]fixed another typo related to PR#193 --- .../oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 4e5f7a373..9e4edb44a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -130,7 +130,7 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; -create view TARGET.indi_funder_country_collab stored as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_funder_country_collab stored as parquet as select * from SOURCE.indi_funder_country_collab; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; From 393a4ee956fdd3ea7dea2ee40eebfa4df4931ce3 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 15 Feb 2022 12:56:50 +0200 Subject: [PATCH 050/159] fixed yet another typo... --- .../oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 9e4edb44a..e75bdffc8 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -130,7 +130,7 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; -create view TARGET.indi_funder_country_collab stored as parquet as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; From 58c59f46eb2273a65f2fe71f4e212dd202b8e097 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 17 Feb 2022 10:21:09 +0200 Subject: [PATCH 051/159] Added Sprint 6 --- .../scripts/step16-createIndicatorsTables.sql | 181 +++++++++++++++++- 1 file changed, 180 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 9f11fa49d..e5bc588be 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -177,4 +177,183 @@ on tmp.id=ri.id; ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as -select id, count(id) as number_of_copies from result_instance group by id; \ No newline at end of file +select id, count(id) as number_of_copies from result_instance group by id; + +---- Sprint 6 ---- +create table indi_pub_gold_oa_new stored as parquet as +WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn +FROM stats_ext.oa_journals +WHERE issn_1 != "" +UNION ALL +SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn +FROM stats_ext.oa_journals +WHERE issn_2 != "" ), +issn AS (SELECT * FROM +(SELECT id, issn_printed as issn +FROM datasource WHERE issn_printed IS NOT NULL +UNION +SELECT id, issn_online as issn +FROM datasource WHERE issn_online IS NOT NULL) as issn +WHERE LENGTH(issn) > 7) +SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +FROM publication_datasources pd +LEFT OUTER JOIN +(SELECT pd.id, 1 as is_gold FROM publication_datasources pd +JOIN issn on issn.id=pd.datasource +JOIN gold_oa on issn.issn = gold_oa.issn) tmp +ON pd.id=tmp.id; + +create table indi_datasets_gold_oa_new stored as parquet as +WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +FROM stats_ext.oa_journals +WHERE issn_1 != "" +UNION +ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +FROM stats_ext.oa_journals +WHERE issn_2 != "" ), +issn AS (SELECT * +FROM (SELECT id,issn_printed as issn +FROM datasource WHERE issn_printed IS NOT NULL +UNION +SELECT id, issn_online as issn +FROM datasource +WHERE issn_online IS NOT NULL ) as issn +WHERE LENGTH(issn) > 7) +SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +FROM dataset_datasources pd +LEFT OUTER JOIN +(SELECT pd.id, 1 as is_gold FROM dataset_datasources pd +JOIN issn on issn.id=pd.datasource +JOIN gold_oa on issn.issn = gold_oa.issn) tmp +ON pd.id=tmp.id; + +create table indi_software_gold_oa_new stored as parquet as +WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +FROM stats_ext.oa_journals +WHERE issn_1 != "" +UNION +ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +FROM stats_ext.oa_journals +WHERE issn_2 != "" ), +issn AS (SELECT * +FROM (SELECT id,issn_printed as issn +FROM datasource WHERE issn_printed IS NOT NULL +UNION +SELECT id, issn_online as issn +FROM datasource +WHERE issn_online IS NOT NULL ) as issn +WHERE LENGTH(issn) > 7) +SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +FROM software_datasources pd +LEFT OUTER JOIN +(SELECT pd.id, 1 as is_gold FROM software_datasources pd +JOIN issn on issn.id=pd.datasource +JOIN gold_oa on issn.issn = gold_oa.issn) tmp +ON pd.id=tmp.id; + +create table indi_org_findable stored as parquet as +with result_with_pid as +(select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro +join result_pids rp on rp.id=ro.id +group by ro.organization), +result_has_abstract as +(select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro +join result rp on rp.id=ro.id where rp.abstract=true +group by ro.organization), +allresults as (select organization, count(distinct id) no_allresults from result_organization +group by organization), +result_with_pid_share as( +select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share +from allresults +join result_with_pid on result_with_pid.organization=allresults.organization), +result_with_abstract_share as( +select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share +from allresults +join result_has_abstract on result_has_abstract.organization=allresults.organization) +select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable +from allresults +join result_with_pid_share on result_with_pid_share.organization=allresults.organization +left outer join ( +select organization, abstract_share from result_with_abstract_share +)tmp +on tmp.organization=allresults.organization; + +create table indi_org_openess stored as parquet as +WITH datasets_oa as ( +SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg +join openaire_prod_stats.result_organization ro on dg.id=ro.id +join openaire_prod_stats.dataset ds on dg.id=ds.id +WHERE dg.is_gold=1 +group by ro.organization), +software_oa as ( +SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg +join openaire_prod_stats.result_organization ro on dg.id=ro.id +join openaire_prod_stats.software ds on dg.id=ds.id +WHERE dg.is_gold=1 +group by ro.organization), +pubs_oa as ( +SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg +join openaire_prod_stats.result_organization ro on dg.id=ro.id +join openaire_prod_stats.publication ds on dg.id=ds.id +where dg.is_gold=1 +group by ro.organization), +allpubs as ( +SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro +join openaire_prod_stats.publication ps on ps.id=ro.id +group by ro.organization), +alldatasets as ( +SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro +join openaire_prod_stats.dataset ps on ps.id=ro.id +group by ro.organization), +allsoftware as ( +SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro +join openaire_prod_stats.software ps on ps.id=ro.id +group by ro.organization), +allpubsshare as ( +select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs +join pubs_oa on allpubs.organization=pubs_oa.organization), +alldatasetssshare as ( +select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c +from alldatasets +join datasets_oa on alldatasets.organization=datasets_oa.organization), +allsoftwaresshare as ( +select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s +from allsoftware +join software_oa on allsoftware.organization=software_oa.organization) +select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess FROM allpubsshare +left outer join (select organization,c from +alldatasetssshare) tmp +on tmp.organization=allpubsshare.organization +left outer join (select organization,s from +allsoftwaresshare) tmp1 +on tmp1.organization=allpubsshare.organization; + +create table indi_pub_hybrid_oa_with_cc stored as parquet as +WITH hybrid_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn +FROM stats_ext.plan_s_jn +WHERE issn_print != "" +UNION ALL +SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn +FROM stats_ext.plan_s_jn +WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), +issn AS (SELECT * FROM +(SELECT id, issn_printed as issn +FROM datasource +WHERE issn_printed IS NOT NULL +UNION +SELECT id,issn_online as issn +FROM datasource +WHERE issn_online IS NOT NULL ) as issn +WHERE LENGTH(issn) > 7) +SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa +FROM publication_datasources pd +LEFT OUTER JOIN ( +SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd +JOIN datasource d on d.id=pd.datasource +JOIN issn on issn.id=pd.datasource +JOIN hybrid_oa ON issn.issn = hybrid_oa.issn +JOIN indi_result_has_cc_licence cc on pd.id=cc.id +where cc.has_cc_license=1) tmp +on pd.id=tmp.id; + + From 0bff45e739c174a0a925f56c4bc847e638f0771f Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 18 Feb 2022 17:11:23 +0200 Subject: [PATCH 052/159] added sprint 6 indicators to monitor db --- .../scripts/step16-createIndicatorsTables.sql | 321 +++++++++--------- .../scripts/step20-createMonitorDB.sql | 9 + 2 files changed, 162 insertions(+), 168 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index e5bc588be..1e2ac69f3 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -31,17 +31,6 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; -create table indi_pub_gold_oa stored as parquet as -select distinct p.id, coalesce(gold_oa, 0) as gold_oa -from publication p -left outer join ( -select p.id, 1 as gold_oa -from publication p -join result_instance ri on ri.id = p.id -join datasource on datasource.id = ri.hostedby -where datasource.id like '%doajarticles%') tmp -on p.id= tmp.id; - ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -144,16 +133,6 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; -create table indi_is_gold_oa stored as parquet as -(select distinct pd.id, coalesce(gold_oa, 0) as gold_oa -from publication_datasources pd -left outer join ( -select pd.id, 1 as gold_oa from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online) -where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp -on pd.id=tmp.id); - create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -180,180 +159,186 @@ create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; ---- Sprint 6 ---- -create table indi_pub_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION ALL -SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * FROM -(SELECT id, issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource WHERE issn_online IS NOT NULL) as issn -WHERE LENGTH(issn) > 7) +create table indi_pub_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * FROM + (SELECT id, issn_printed as issn + FROM datasource WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource WHERE issn_online IS NOT NULL) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM publication_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM publication_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM publication_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -create table indi_datasets_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION -ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * -FROM (SELECT id,issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +create table indi_datasets_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION + ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * + FROM ( + SELECT id,issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM dataset_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM dataset_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM dataset_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -create table indi_software_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION -ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * -FROM (SELECT id,issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +create table indi_software_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION + ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * + FROM ( + SELECT id,issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM software_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM software_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM software_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; create table indi_org_findable stored as parquet as -with result_with_pid as -(select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro -join result_pids rp on rp.id=ro.id -group by ro.organization), -result_has_abstract as -(select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro -join result rp on rp.id=ro.id where rp.abstract=true -group by ro.organization), -allresults as (select organization, count(distinct id) no_allresults from result_organization -group by organization), -result_with_pid_share as( -select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share -from allresults -join result_with_pid on result_with_pid.organization=allresults.organization), -result_with_abstract_share as( -select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share -from allresults -join result_has_abstract on result_has_abstract.organization=allresults.organization) +with result_with_pid as ( + select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + group by ro.organization), +result_has_abstract as ( + select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro + join result rp on rp.id=ro.id where rp.abstract=true + group by ro.organization), +allresults as ( + select organization, count(distinct id) no_allresults from result_organization + group by organization), +result_with_pid_share as ( + select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share + from allresults + join result_with_pid on result_with_pid.organization=allresults.organization), +result_with_abstract_share as ( + select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share + from allresults + join result_has_abstract on result_has_abstract.organization=allresults.organization) select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable from allresults join result_with_pid_share on result_with_pid_share.organization=allresults.organization left outer join ( -select organization, abstract_share from result_with_abstract_share -)tmp -on tmp.organization=allresults.organization; + select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; create table indi_org_openess stored as parquet as WITH datasets_oa as ( -SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.dataset ds on dg.id=ds.id -WHERE dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.dataset ds on dg.id=ds.id + WHERE dg.is_gold=1 + group by ro.organization), software_oa as ( -SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.software ds on dg.id=ds.id -WHERE dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.software ds on dg.id=ds.id + WHERE dg.is_gold=1 + group by ro.organization), pubs_oa as ( -SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.publication ds on dg.id=ds.id -where dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.publication ds on dg.id=ds.id + where dg.is_gold=1 + group by ro.organization), allpubs as ( -SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro -join openaire_prod_stats.publication ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join openaire_prod_stats.publication ps on ps.id=ro.id + group by ro.organization), alldatasets as ( -SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro -join openaire_prod_stats.dataset ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join openaire_prod_stats.dataset ps on ps.id=ro.id + group by ro.organization), allsoftware as ( -SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro -join openaire_prod_stats.software ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join openaire_prod_stats.software ps on ps.id=ro.id + group by ro.organization), allpubsshare as ( -select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs -join pubs_oa on allpubs.organization=pubs_oa.organization), + select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization), alldatasetssshare as ( -select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c -from alldatasets -join datasets_oa on alldatasets.organization=datasets_oa.organization), + select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization), allsoftwaresshare as ( -select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s -from allsoftware -join software_oa on allsoftware.organization=software_oa.organization) -select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess FROM allpubsshare -left outer join (select organization,c from -alldatasetssshare) tmp -on tmp.organization=allpubsshare.organization -left outer join (select organization,s from -allsoftwaresshare) tmp1 -on tmp1.organization=allpubsshare.organization; + select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization) +select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess +FROM allpubsshare +left outer join ( + select organization,c from + alldatasetssshare) tmp on tmp.organization=allpubsshare.organization +left outer join ( + select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; create table indi_pub_hybrid_oa_with_cc stored as parquet as -WITH hybrid_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn -FROM stats_ext.plan_s_jn -WHERE issn_print != "" -UNION ALL -SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn -FROM stats_ext.plan_s_jn -WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), -issn AS (SELECT * FROM -(SELECT id, issn_printed as issn -FROM datasource -WHERE issn_printed IS NOT NULL -UNION -SELECT id,issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +WITH hybrid_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn + FROM stats_ext.plan_s_jn + WHERE issn_print != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn + FROM stats_ext.plan_s_jn + WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), +issn AS ( + SELECT * + FROM ( + SELECT id, issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id,issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa FROM publication_datasources pd LEFT OUTER JOIN ( -SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd -JOIN datasource d on d.id=pd.datasource -JOIN issn on issn.id=pd.datasource -JOIN hybrid_oa ON issn.issn = hybrid_oa.issn -JOIN indi_result_has_cc_licence cc on pd.id=cc.id -where cc.has_cc_license=1) tmp -on pd.id=tmp.id; - - + SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd + JOIN datasource d on d.id=pd.datasource + JOIN issn on issn.id=pd.datasource + JOIN hybrid_oa ON issn.issn = hybrid_oa.issn + JOIN indi_result_has_cc_licence cc on pd.id=cc.id + where cc.has_cc_license=1) tmp on pd.id=tmp.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index e75bdffc8..afd333492 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -123,6 +123,10 @@ create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * fro compute stats TARGET.indi_pub_doi_from_crossref; create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_gold_oa; +create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_datasets_gold_oa; +create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_software_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); @@ -148,6 +152,11 @@ compute stats TARGET.indi_pub_closed_other_open; create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_no_of_copies; +create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; +create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; +create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_hybrid_oa_with_cc; + --- Usage statistics create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); From 87c91f70a26f73ea89a2878f13634f6699d0b945 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 18 Feb 2022 17:11:23 +0200 Subject: [PATCH 053/159] added sprint 6 indicators to monitor db --- .../scripts/step16-createIndicatorsTables.sql | 344 +++++++++--------- .../scripts/step20-createMonitorDB.sql | 9 + 2 files changed, 187 insertions(+), 166 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index e5bc588be..d925b3694 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -31,17 +31,6 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; -create table indi_pub_gold_oa stored as parquet as -select distinct p.id, coalesce(gold_oa, 0) as gold_oa -from publication p -left outer join ( -select p.id, 1 as gold_oa -from publication p -join result_instance ri on ri.id = p.id -join datasource on datasource.id = ri.hostedby -where datasource.id like '%doajarticles%') tmp -on p.id= tmp.id; - ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -144,16 +133,6 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; -create table indi_is_gold_oa stored as parquet as -(select distinct pd.id, coalesce(gold_oa, 0) as gold_oa -from publication_datasources pd -left outer join ( -select pd.id, 1 as gold_oa from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps on (ps.issn_print=d.issn_printed or ps.issn_online=d.issn_online) -where ps.journal_is_in_doaj is true or ps.journal_is_oa is true) tmp -on pd.id=tmp.id); - create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -180,180 +159,213 @@ create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; ---- Sprint 6 ---- -create table indi_pub_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION ALL -SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * FROM -(SELECT id, issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource WHERE issn_online IS NOT NULL) as issn -WHERE LENGTH(issn) > 7) +create table indi_pub_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * FROM + (SELECT id, issn_printed as issn + FROM datasource WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource WHERE issn_online IS NOT NULL) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM publication_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM publication_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM publication_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -create table indi_datasets_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION -ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * -FROM (SELECT id,issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +create table indi_datasets_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION + ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * + FROM ( + SELECT id,issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM dataset_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM dataset_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM dataset_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -create table indi_software_gold_oa_new stored as parquet as -WITH gold_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn -FROM stats_ext.oa_journals -WHERE issn_1 != "" -UNION -ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn -FROM stats_ext.oa_journals -WHERE issn_2 != "" ), -issn AS (SELECT * -FROM (SELECT id,issn_printed as issn -FROM datasource WHERE issn_printed IS NOT NULL -UNION -SELECT id, issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +create table indi_software_gold_oa stored as parquet as +WITH gold_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn + FROM stats_ext.oa_journals + WHERE issn_1 != "" + UNION + ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn + FROM stats_ext.oa_journals + WHERE issn_2 != "" ), +issn AS ( + SELECT * + FROM ( + SELECT id,issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id, issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold FROM software_datasources pd -LEFT OUTER JOIN -(SELECT pd.id, 1 as is_gold FROM software_datasources pd -JOIN issn on issn.id=pd.datasource -JOIN gold_oa on issn.issn = gold_oa.issn) tmp -ON pd.id=tmp.id; +LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_gold FROM software_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; create table indi_org_findable stored as parquet as -with result_with_pid as -(select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro -join result_pids rp on rp.id=ro.id -group by ro.organization), -result_has_abstract as -(select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro -join result rp on rp.id=ro.id where rp.abstract=true -group by ro.organization), -allresults as (select organization, count(distinct id) no_allresults from result_organization -group by organization), -result_with_pid_share as( -select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share -from allresults -join result_with_pid on result_with_pid.organization=allresults.organization), -result_with_abstract_share as( -select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share -from allresults -join result_has_abstract on result_has_abstract.organization=allresults.organization) +with result_with_pid as ( + select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + group by ro.organization), +result_has_abstract as ( + select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro + join result rp on rp.id=ro.id where rp.abstract=true + group by ro.organization), +allresults as ( + select organization, count(distinct id) no_allresults from result_organization + group by organization), +result_with_pid_share as ( + select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share + from allresults + join result_with_pid on result_with_pid.organization=allresults.organization), +result_with_abstract_share as ( + select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share + from allresults + join result_has_abstract on result_has_abstract.organization=allresults.organization) select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable from allresults join result_with_pid_share on result_with_pid_share.organization=allresults.organization left outer join ( -select organization, abstract_share from result_with_abstract_share -)tmp -on tmp.organization=allresults.organization; + select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; create table indi_org_openess stored as parquet as WITH datasets_oa as ( -SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.dataset ds on dg.id=ds.id -WHERE dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.dataset ds on dg.id=ds.id + WHERE dg.is_gold=1 + group by ro.organization), software_oa as ( -SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.software ds on dg.id=ds.id -WHERE dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.software ds on dg.id=ds.id + WHERE dg.is_gold=1 + group by ro.organization), pubs_oa as ( -SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg -join openaire_prod_stats.result_organization ro on dg.id=ro.id -join openaire_prod_stats.publication ds on dg.id=ds.id -where dg.is_gold=1 -group by ro.organization), + SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg + join openaire_prod_stats.result_organization ro on dg.id=ro.id + join openaire_prod_stats.publication ds on dg.id=ds.id + where dg.is_gold=1 + group by ro.organization), allpubs as ( -SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro -join openaire_prod_stats.publication ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join openaire_prod_stats.publication ps on ps.id=ro.id + group by ro.organization), alldatasets as ( -SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro -join openaire_prod_stats.dataset ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join openaire_prod_stats.dataset ps on ps.id=ro.id + group by ro.organization), allsoftware as ( -SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro -join openaire_prod_stats.software ps on ps.id=ro.id -group by ro.organization), + SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join openaire_prod_stats.software ps on ps.id=ro.id + group by ro.organization), allpubsshare as ( -select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs -join pubs_oa on allpubs.organization=pubs_oa.organization), + select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization), alldatasetssshare as ( -select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c -from alldatasets -join datasets_oa on alldatasets.organization=datasets_oa.organization), + select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization), allsoftwaresshare as ( -select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s -from allsoftware -join software_oa on allsoftware.organization=software_oa.organization) -select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess FROM allpubsshare -left outer join (select organization,c from -alldatasetssshare) tmp -on tmp.organization=allpubsshare.organization -left outer join (select organization,s from -allsoftwaresshare) tmp1 -on tmp1.organization=allpubsshare.organization; + select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization) +select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess +FROM allpubsshare +left outer join ( + select organization,c from + alldatasetssshare) tmp on tmp.organization=allpubsshare.organization +left outer join ( + select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; create table indi_pub_hybrid_oa_with_cc stored as parquet as -WITH hybrid_oa AS (SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn -FROM stats_ext.plan_s_jn -WHERE issn_print != "" -UNION ALL -SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn -FROM stats_ext.plan_s_jn -WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), -issn AS (SELECT * FROM -(SELECT id, issn_printed as issn -FROM datasource -WHERE issn_printed IS NOT NULL -UNION -SELECT id,issn_online as issn -FROM datasource -WHERE issn_online IS NOT NULL ) as issn -WHERE LENGTH(issn) > 7) +WITH hybrid_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn + FROM stats_ext.plan_s_jn + WHERE issn_print != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn + FROM stats_ext.plan_s_jn + WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), +issn AS ( + SELECT * + FROM ( + SELECT id, issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id,issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn + WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa FROM publication_datasources pd LEFT OUTER JOIN ( -SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd -JOIN datasource d on d.id=pd.datasource -JOIN issn on issn.id=pd.datasource -JOIN hybrid_oa ON issn.issn = hybrid_oa.issn -JOIN indi_result_has_cc_licence cc on pd.id=cc.id -where cc.has_cc_license=1) tmp -on pd.id=tmp.id; + SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd + JOIN datasource d on d.id=pd.datasource + JOIN issn on issn.id=pd.datasource + JOIN hybrid_oa ON issn.issn = hybrid_oa.issn + JOIN indi_result_has_cc_licence cc on pd.id=cc.id + where cc.has_cc_license=1) tmp on pd.id=tmp.id; +create table indi_pub_downloads stored as parquet as +SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats +join publication on result_id=id +where downloads>0 +GROUP BY result_id +order by no_dowloads desc; +create table indi_pub_downloads_datasource stored as parquet as +SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats +join publication on result_id=id +where downloads>0 +GROUP BY result_id, repository_id +order by result_id; + +create table indi_pub_downloads_year stored as parquet as +SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us +join publication on result_id=id where downloads>0 +GROUP BY result_id, `year` +order by `year` asc; + +create table indi_pub_downloads_datasource_year stored as parquet as +SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us +join publication on result_id=id +where downloads>0 +GROUP BY result_id, repository_id, `year` +order by `year` asc, result_id; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index e75bdffc8..afd333492 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -123,6 +123,10 @@ create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * fro compute stats TARGET.indi_pub_doi_from_crossref; create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_gold_oa; +create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_datasets_gold_oa; +create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_software_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); @@ -148,6 +152,11 @@ compute stats TARGET.indi_pub_closed_other_open; create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_no_of_copies; +create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; +create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; +create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_hybrid_oa_with_cc; + --- Usage statistics create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); From 3b92a2ab9ce28af7bab0ea0e57e7841d0d29c2cf Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 23 Feb 2022 12:05:57 +0200 Subject: [PATCH 054/159] added the rest of spring 6 in monitor db --- .../stats/oozie_app/scripts/step20-createMonitorDB.sql | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index afd333492..b4964d2b3 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -157,8 +157,14 @@ create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_hybrid_oa_with_cc; ---- Usage statistics -create table TARGET.usage_stats stored as parquet as select * from SOURCE.usage_stats orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_downloads; +create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_downloads_datasource; +create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_downloads_year; +create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_downloads_datasource_year; --denorm alter table TARGET.result rename to TARGET.res_tmp; From 9d6203f79b6a9d16764ec9cc68c287b8da7a1fde Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 23 Feb 2022 15:00:53 +0100 Subject: [PATCH 055/159] test mapping datasource --- .../oa/provision/XmlRecordFactoryTest.java | 30 +++++++++++++++++++ .../dnetlib/dhp/oa/provision/datasource.json | 1 + 2 files changed, 31 insertions(+) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 2b5e08e92..501784872 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -8,6 +8,7 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; +import eu.dnetlib.dhp.schema.oaf.Datasource; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -129,4 +130,33 @@ public class XmlRecordFactoryTest { System.out.println(doc.asXML()); assertEquals("", doc.valueOf("//rel/validated")); } + + @Test + public void testDatasource() throws IOException, DocumentException { + final ContextMapper contextMapper = new ContextMapper(); + + final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, + XmlConverterJob.schemaLocation); + + final Datasource d = OBJECT_MAPPER + .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); + + final String xml = xmlRecordFactory.build(new JoinedEntity<>(d)); + + assertNotNull(xml); + + final Document doc = new SAXReader().read(new StringReader(xml)); + + assertNotNull(doc); + + System.out.println(doc.asXML()); + + // TODO add assertions based of values extracted from the XML record + + assertEquals("National", doc.valueOf("//jurisdiction/@classname")); + assertEquals("true", doc.valueOf("//thematic")); + assertEquals("Journal article", doc.valueOf("//contentpolicy/@classname")); + assertEquals("Journal archive", doc.valueOf("//datasourcetypeui/@classname")); + + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json new file mode 100644 index 000000000..ae069b8b5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -0,0 +1 @@ +{"collectedfrom":[{"key":"10|openaire____::13068d7823ea0bd86516ac2cb66e96ba","value":"Jurnal Fakultas Sastra Universitas Ekasakti","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1645012035118,"id":"10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7","originalId":["274269ac6f3b::2579-5449","piwik:13"],"pid":[],"dateofcollection":"2020-01-21","dateoftransformation":null,"extraInfo":[],"oaiprovenance":null,"datasourcetype":{"classid":"pubsrepository::journal","classname":"pubsrepository::journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"datasourcetypeui":{"classid":"pubsrepository::journal","classname":"Journal archive","schemeid":"dnet:datasource_typologies_ui","schemename":"dnet:datasource_typologies_ui"},"openairecompatibility":{"classid":"hostedBy","classname":"hostedBy","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"officialname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"englishname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"websiteurl":{"value":"http://e-journal.sastra-unes.com/index.php/JIPS/index","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"logourl":null,"contactemail":{"value":"test@test.it","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"namespaceprefix":{"value":"ojs_25795449","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"latitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"longitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"dateofvalidation":null,"description":null,"subjects":[],"odnumberofitems":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"odnumberofitemsdate":null,"odpolicies":null,"odlanguages":[],"odcontenttypes":[{"value":"Journal articles","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"accessinfopackage":[],"releasestartdate":null,"releaseenddate":null,"missionstatementurl":null,"dataprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"serviceprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"databaseaccesstype":null,"datauploadtype":null,"databaseaccessrestriction":null,"datauploadrestriction":null,"versioning":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"citationguidelineurl":null,"qualitymanagementkind":null,"pidsystems":null,"certificates":null,"policies":[],"journal":{"name":"Jurnal Ilmiah Pendidikan Scholastic","issnPrinted":"2579-5449","issnOnline":"2579-5448","issnLinking":"2579-5447","ep":null,"iss":null,"sp":null,"vol":null,"edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"providedentitytypes":null,"providedproducttypes":null,"jurisdiction":{"classid":"National","classname":"National","schemeid":"eosc:jurisdictions","schemename":"eosc:jurisdictions"},"thematic":true,"knowledgegraph":true,"contentpolicies":[{"classid":"Journal article","classname":"Journal article","schemeid":"eosc:contentpolicies","schemename":"eosc:contentpolicies"}]} From 86cdb7a38f52209398db510455488c4331d4db08 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Feb 2022 15:54:18 +0100 Subject: [PATCH 056/159] [provision] serialize measures defined on the result level --- .../oa/provision/utils/XmlRecordFactory.java | 23 +++++++- .../utils/XmlSerializationUtils.java | 14 +++++ .../oa/provision/XmlRecordFactoryTest.java | 7 +++ .../dnetlib/dhp/oa/provision/publication.json | 58 +++++++++++++++++++ 4 files changed, 101 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index e51a84e02..cb29dc121 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -23,7 +23,6 @@ import javax.xml.transform.stream.StreamResult; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.Pair; -import org.apache.http.protocol.HTTP; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -50,6 +49,7 @@ import eu.dnetlib.dhp.schema.common.*; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import scala.Tuple2; public class XmlRecordFactory implements Serializable { @@ -209,6 +209,10 @@ public class XmlRecordFactory implements Serializable { if (ModelSupport.isResult(type)) { final Result r = (Result) entity; + if (r.getMeasures() != null) { + metadata.addAll(measuresAsXml(r.getMeasures())); + } + if (r.getContext() != null) { contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList())); /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */ @@ -936,6 +940,23 @@ public class XmlRecordFactory implements Serializable { return metadata; } + private List measuresAsXml(List measures) { + return measures + .stream() + .flatMap( + m -> m + .getUnit() + .stream() + .map( + u -> Lists + .newArrayList( + new Tuple2<>("id", m.getId()), + new Tuple2<>("key", u.getKey()), + new Tuple2<>("value", u.getValue()))) + .map(l -> XmlSerializationUtils.asXmlElement("measure", l))) + .collect(Collectors.toList()); + } + private String getAuthorPidType(final String s) { return XmlSerializationUtils .escapeXml(s) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java index 213a62b32..73667e056 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java @@ -5,7 +5,10 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; +import java.util.List; + import eu.dnetlib.dhp.schema.oaf.*; +import scala.Tuple2; public class XmlSerializationUtils { @@ -147,4 +150,15 @@ public class XmlSerializationUtils { .append(attr("schemename", q.getSchemename())) .toString(); } + + public static String asXmlElement(String name, List> attributes) { + StringBuilder sb = new StringBuilder(); + sb.append("<"); + sb.append(name); + for (Tuple2 attr : attributes) { + sb.append(" ").append(attr(attr._1(), attr._2())); + } + sb.append("/>"); + return sb.toString(); + } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index c1e0567e6..1df980643 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -69,6 +69,13 @@ public class XmlRecordFactoryTest { assertEquals("1721.47", doc.valueOf("//processingchargeamount/text()")); assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); + + assertEquals( + "1.00889953098e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@value")); + assertEquals( + "30.6576853333", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@value")); + assertEquals( + "4.62970429725e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@value")); } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 3b5b54bbf..d0c8ea4ed 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -1,4 +1,33 @@ { + "measures": [ + { + "id": "influence", + "unit": [ + { + "key": "score", + "value": "1.00889953098e-08" + } + ] + }, + { + "id": "popularity_alt", + "unit": [ + { + "key": "score", + "value": "30.6576853333" + } + ] + }, + { + "id": "popularity", + "unit": [ + { + "key": "score", + "value": "4.62970429725e-08" + } + ] + } + ], "author": [ { "affiliation": [], @@ -284,6 +313,35 @@ "id": "50|CSC_________::0000ec4dd9df012feaafa77e71a0fb4c", "instance": [ { + "measures": [ + { + "id": "influence", + "unit": [ + { + "key": "score", + "value": "1.00889953098e-08" + } + ] + }, + { + "id": "popularity_alt", + "unit": [ + { + "key": "score", + "value": "30.6576853333" + } + ] + }, + { + "id": "popularity", + "unit": [ + { + "key": "score", + "value": "4.62970429725e-08" + } + ] + } + ], "pid": [ { "dataInfo": { From ab36154e3e6d6799fb14fc9de860f09c7178c1dd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 24 Feb 2022 12:16:17 +0100 Subject: [PATCH 057/159] added more ignores --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index f4fb46f2e..0a50a4947 100644 --- a/.gitignore +++ b/.gitignore @@ -27,4 +27,4 @@ spark-warehouse /**/job-override.properties /**/*.log /**/.factorypath - +/**/.scalafmt.conf From 66c09b1bc73c73f5421efdc79237a82f8caf8323 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 24 Feb 2022 12:58:07 +0100 Subject: [PATCH 058/159] code formatting --- .../eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 2142737f0..273132bff 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -8,7 +8,6 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.Datasource; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -24,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -146,10 +146,10 @@ public class XmlRecordFactoryTest { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, - XmlConverterJob.schemaLocation); + XmlConverterJob.schemaLocation); final Datasource d = OBJECT_MAPPER - .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); + .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); final String xml = xmlRecordFactory.build(new JoinedEntity<>(d)); From a40b59b7d55f358232ae6e7432bc67db9bfbb269 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 24 Feb 2022 16:05:57 +0100 Subject: [PATCH 059/159] [ResultToOrgFromInstRepoTest] fixed issue in model of the input resources --- .../alreadyLinked/alreadyLinked_20.json.gz | Bin 3160 -> 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zaRmv*_Hc@6P~M36TX-Kwt*zg{g^law)AyxL=wETH^B$*#t{|l$-kg!ukSDFK$h%LG yeEeWCAem~<P^y)YL5 From 859cb7ac9d024c3c8d172ae1c1f8c2a5530cfd96 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 24 Feb 2022 16:55:32 +0100 Subject: [PATCH 060/159] [DoiBoost AR] changed test resource to be sure the result will always have EMBARGO as value for AccessRight --- .../dnetlib/doiboost/crossref/publication_license_embargo.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json index 47ca55f34..788946fea 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -1456,7 +1456,7 @@ "issued": { "date-parts": [ [ -2021, +3021, 2, 22 ] From b0f369dc78a7b2af64c647a8d042c55315e776d7 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 24 Feb 2022 17:08:24 +0100 Subject: [PATCH 061/159] bug fix in the DedupRecordFactory, DataInfo set before merge --- .../dhp/oa/dedup/DedupRecordFactory.java | 3 +- .../dnetlib/dhp/dedup/conf/orp.new.conf.json | 214 ++++++++ .../dnetlib/dhp/dedup/conf/pub.new.conf.json | 475 ++++++++++++++++++ 3 files changed, 691 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.new.conf.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d65853aff..b8ae4ca02 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -77,6 +77,7 @@ public class DedupRecordFactory { throws IllegalAccessException, InstantiationException { T entity = clazz.newInstance(); + entity.setDataInfo(dataInfo); final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); @@ -106,7 +107,7 @@ public class DedupRecordFactory { entity.setId(id); entity.setLastupdatetimestamp(ts); - entity.setDataInfo(dataInfo); + entity.getDataInfo().setDeletedbyinference(false); return entity; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json new file mode 100644 index 000000000..b0cdade5b --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json @@ -0,0 +1,214 @@ +{ + "wf": { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "otherresearchproduct", + "orderField" : "title", + "queueMaxSize" : "100", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "100", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true", + "idPath" : "$.id", + "maxIterations" : 20 + }, + "pace": { + "clustering": [ + { + "name": "wordsStatsSuffixPrefixChain", + "fields": [ + "title" + ], + "params": { + "mod": "10" + } + }, + { + "name": "lowercase", + "fields": [ + "doi", + "altdoi" + ], + "params": { + "collapseOn:pid": "0" + } + } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "MATCH", + "negative": "pidVSaltid", + "undefined": "pidVSaltid", + "ignoreUndefined": "false" + }, + "pidVSaltid": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "crossCompare": "alternateid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "softCheck", + "negative": "earlyExits", + "undefined": "earlyExits", + "ignoreUndefined": "true" + }, + "softCheck": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 0.9, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + }, + "earlyExits": { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "strongCheck", + "negative": "NO_MATCH", + "undefined": "strongCheck", + "ignoreUndefined": "false" + }, + "strongCheck": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "surnames", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + }, + "surnames": { + "fields": [ + { + "field": "authors", + "comparator": "authorsMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "surname_th": 0.75, + "fullname_th": 0.75, + "mode": "surname" + } + } + ], + "threshold": 0.6, + "aggregation": "MAX", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "MATCH", + "ignoreUndefined": "true" + } + }, + "model": [ + { + "name": "doi", + "type": "String", + "path": "$.instance[*].pid[?(@.qualifier.classid == 'doi')].value" + }, + { + "name": "altdoi", + "type": "String", + "path": "$.instance[*].alternateIdentifier[?(@.qualifier.classid == 'doi')].value" + }, + { + "name": "pid", + "type": "JSON", + "path": "$.instance[*].pid[*]", + "overrideMatch": "true" + }, + { + "name": "alternateid", + "type": "JSON", + "path": "$.instance[*].alternateIdentifier[*]", + "overrideMatch": "true" + }, + { + "name": "title", + "type": "String", + "path": "$.title[?(@.qualifier.classid == 'main title')].value", + "length": 250, + "size": 5 + }, + { + "name": "authors", + "type": "List", + "path": "$.author[*].fullname", + "size": 200 + }, + { + "name": "resulttype", + "type": "String", + "path": "$.resulttype.classid" + }, + { + "name": "instance", + "type": "List", + "path": "$.instance[*].instancetype.classname" + } + ], + "blacklists": {}, + "synonyms": {} + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.new.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.new.conf.json new file mode 100644 index 000000000..89e492e39 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.new.conf.json @@ -0,0 +1,475 @@ +{ + "wf": { + "threshold": "0.99", + "dedupRun": "001", + "entityType": "result", + "subEntityType": "resulttype", + "subEntityValue": "publication", + "orderField": "title", + "queueMaxSize": "200", + "groupMaxSize": "100", + "maxChildren": "100", + "slidingWindowSize": "50", + "rootBuilder": [ + "result", + "resultProject_outcome_isProducedBy", + "resultResult_publicationDataset_isRelatedTo", + "resultResult_similarity_isAmongTopNSimilarDocuments", + "resultResult_similarity_hasAmongTopNSimilarDocuments", + "resultOrganization_affiliation_isAffiliatedWith", + "resultResult_part_hasPart", + "resultResult_part_isPartOf", + "resultResult_supplement_isSupplementTo", + "resultResult_supplement_isSupplementedBy", + "resultResult_version_isVersionOf" + ], + "includeChildren": "true", + "maxIterations": 20, + "idPath": "$.id" + }, + "pace": { + "clustering": [ + { + "name": "wordsStatsSuffixPrefixChain", + "fields": [ + "title" + ], + "params": { + "mod": "10" + } + }, + { + "name": "lowercase", + "fields": [ + "doi", + "altdoi" + ], + "params": { + "collapseOn:pid": "0" + } + } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "MATCH", + "negative": "instanceTypeCheck", + "undefined": "instanceTypeCheck", + "ignoreUndefined": "false" + }, + "instanceTypeCheck": { + "fields": [ + { + "field": "instance", + "comparator": "instanceTypeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 0.5, + "aggregation": "MAX", + "positive": "pidVSaltid", + "negative": "NO_MATCH", + "undefined": "pidVSaltid", + "ignoreUndefined": "true" + }, + "pidVSaltid": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "crossCompare": "alternateid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "softCheck", + "negative": "earlyExits", + "undefined": "earlyExits", + "ignoreUndefined": "true" + }, + "softCheck": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 0.9, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + }, + "earlyExits": { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "strongCheck", + "negative": "NO_MATCH", + "undefined": "strongCheck", + "ignoreUndefined": "false" + }, + "strongCheck": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "surnames", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + }, + "surnames": { + "fields": [ + { + "field": "authors", + "comparator": "authorsMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "surname_th": 0.75, + "fullname_th": 0.75, + "mode": "surname" + } + } + ], + "threshold": 0.6, + "aggregation": "MAX", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "MATCH", + "ignoreUndefined": "true" + } + }, + "model": [ + { + "name": "doi", + "type": "String", + "path": "$.instance[*].pid[?(@.qualifier.classid == 'doi')].value" + }, + { + "name": "altdoi", + "type": "String", + "path": "$.instance[*].alternateIdentifier[?(@.qualifier.classid == 'doi')].value" + }, + { + "name": "pid", + "type": "JSON", + "path": "$.instance[*].pid[*]", + "overrideMatch": "true" + }, + { + "name": "alternateid", + "type": "JSON", + "path": "$.instance[*].alternateIdentifier[*]", + "overrideMatch": "true" + }, + { + "name": "title", + "type": "String", + "path": "$.title[?(@.qualifier.classid == 'main title')].value", + "length": 250, + "size": 5 + }, + { + "name": "authors", + "type": "List", + "path": "$.author[*].fullname", + "size": 200 + }, + { + "name": "resulttype", + "type": "String", + "path": "$.resulttype.classid" + }, + { + "name": "instance", + "type": "List", + "path": "$.instance[*].instancetype.classname" + } + ], + "blacklists": { + "title": [ + "(?i)^Data Management Plan", + "^Inside Front Cover$", + "(?i)^Poster presentations$", + "^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$", + "^Problems with perinatal pathology\\.?$", + "(?i)^Cases? of Puerperal Convulsions$", + "(?i)^Operative Gyna?ecology$", + "(?i)^Mind the gap\\!?\\:?$", + "^Chronic fatigue syndrome\\.?$", + "^Cartas? ao editor Letters? to the Editor$", + "^Note from the Editor$", + "^Anesthesia Abstract$", + "^Annual report$", + "(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\\.?”?$", + "(?i)^Graph and Table of Infectious Diseases?$", + "^Presentation$", + "(?i)^Reviews and Information on Publications$", + "(?i)^PUBLIC HEALTH SERVICES?$", + "(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$", + "(?i)^Adrese autora$", + "(?i)^Systematic Part .*\\. Catalogus Fossilium Austriae, Band 2: Echinoidea neogenica$", + "(?i)^Acknowledgement to Referees$", + "(?i)^Behçet's disease\\.?$", + "(?i)^Isolation and identification of restriction endonuclease.*$", + "(?i)^CEREBROVASCULAR DISEASES?.?$", + "(?i)^Screening for abdominal aortic aneurysms?\\.?$", + "^Event management$", + "(?i)^Breakfast and Crohn's disease.*\\.?$", + "^Cálculo de concentraciones en disoluciones acuosas. Ejercicio interactivo\\..*\\.$", + "(?i)^Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of Autism spectrum disorders?\\.?$", + "^Gushi hakubutsugaku$", + "^Starobosanski nadpisi u Bosni i Hercegovini \\(.*\\)$", + "^Intestinal spirocha?etosis$", + "^Treatment of Rodent Ulcer$", + "(?i)^\\W*Cloud Computing\\W*$", + "^Compendio mathematico : en que se contienen todas las materias mas principales de las Ciencias que tratan de la cantidad$", + "^Free Communications, Poster Presentations: Session [A-F]$", + "^“The Historical Aspects? of Quackery\\.?”$", + "^A designated centre for people with disabilities operated by St John of God Community Services (Limited|Ltd), Louth$", + "^P(er|re)-Mile Premiums for Auto Insurance\\.?$", + "(?i)^Case Report$", + "^Boletín Informativo$", + "(?i)^Glioblastoma Multiforme$", + "(?i)^Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 \\(.*\\)$", + "^Zaměstnanecké výhody$", + "(?i)^The Economics of Terrorism and Counter-Terrorism: A Survey \\(Part .*\\)$", + "(?i)^Carotid body tumours?\\.?$", + "(?i)^\\[Españoles en Francia : La condición Emigrante.*\\]$", + "^Avant-propos$", + "(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$", + "(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Bases?$", + "(?i)^PUBLIC HEALTH VERSUS THE STATE$", + "^Viñetas de Cortázar$", + "(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\\.)?$", + "(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\\.?)$", + "(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$", + "(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$", + "(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$", + "^Aus der AGMB$", + "^Znanstveno-stručni prilozi$", + "(?i)^Zhodnocení finanční situace podniku a návrhy na zlepšení$", + "(?i)^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$", + "(?i)^Hodnocení finanční situace podniku a návrhy na její zlepšení$", + "^Finanční analýza podniku$", + "^Financial analysis( of business)?$", + "(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$", + "^Jikken nihon shūshinsho$", + "(?i)^CORONER('|s)(s|') INQUESTS$", + "(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$", + "(?i)^Consultants' contract(s)?$", + "(?i)^Upute autorima$", + "(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$", + "^Joshi shin kokubun$", + "^Kōtō shōgaku dokuhon nōson'yō$", + "^Jinjō shōgaku shōka$", + "^Shōgaku shūjichō$", + "^Nihon joshi dokuhon$", + "^Joshi shin dokuhon$", + "^Chūtō kanbun dokuhon$", + "^Wabun dokuhon$", + "(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$", + "(?i)^cardiac rehabilitation$", + "(?i)^Analytical summary$", + "^Thesaurus resolutionum Sacrae Congregationis Concilii$", + "(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$", + "^Prikazi i osvrti$", + "^Rodinný dům s provozovnou$", + "^Family house with an establishment$", + "^Shinsei chūtō shin kokugun$", + "^Pulmonary alveolar proteinosis(\\.?)$", + "^Shinshū kanbun$", + "^Viñeta(s?) de Rodríguez$", + "(?i)^RUBRIKA UREDNIKA$", + "^A Matching Model of the Academic Publication Market$", + "^Yōgaku kōyō$", + "^Internetový marketing$", + "^Internet marketing$", + "^Chūtō kokugo dokuhon$", + "^Kokugo dokuhon$", + "^Antibiotic Cover for Dental Extraction(s?)$", + "^Strategie podniku$", + "^Strategy of an Enterprise$", + "(?i)^respiratory disease(s?)(\\.?)$", + "^Award(s?) for Gallantry in Civil Defence$", + "^Podniková kultura$", + "^Corporate Culture$", + "^Severe hyponatraemia in hospital inpatient(s?)(\\.?)$", + "^Pracovní motivace$", + "^Work Motivation$", + "^Kaitei kōtō jogaku dokuhon$", + "^Konsolidovaná účetní závěrka$", + "^Consolidated Financial Statements$", + "(?i)^intracranial tumour(s?)$", + "^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$", + "^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$", + "^Housing Market Dynamics(\\:|\\.) On the Contribution of Income Shocks and Credit Constraint(s?)$", + "^\\[Funciones auxiliares de la música en Radio París,.*\\]$", + "^Úroveň motivačního procesu jako způsobu vedení lidí$", + "^The level of motivation process as a leadership$", + "^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$", + "(?i)^news and events$", + "(?i)^NOVOSTI I DOGAĐAJI$", + "^Sansū no gakushū$", + "^Posouzení informačního systému firmy a návrh změn$", + "^Information System Assessment and Proposal for ICT Modification$", + "^Stresové zatížení pracovníků ve vybrané profesi$", + "^Stress load in a specific job$", + "^Sunday: Poster Sessions, Pt.*$", + "^Monday: Poster Sessions, Pt.*$", + "^Wednesday: Poster Sessions, Pt.*", + "^Tuesday: Poster Sessions, Pt.*$", + "^Analýza reklamy$", + "^Analysis of advertising$", + "^Shōgaku shūshinsho$", + "^Shōgaku sansū$", + "^Shintei joshi kokubun$", + "^Taishō joshi kokubun dokuhon$", + "^Joshi kokubun$", + "^Účetní uzávěrka a účetní závěrka v ČR$", + "(?i)^The \"?Causes\"? of Cancer$", + "^Normas para la publicación de artículos$", + "^Editor('|s)(s|') [Rr]eply$", + "^Editor(’|s)(s|’) letter$", + "^Redaktoriaus žodis$", + "^DISCUSSION ON THE PRECEDING PAPER$", + "^Kōtō shōgaku shūshinsho jidōyō$", + "^Shōgaku nihon rekishi$", + "^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$", + "^Préface$", + "^Occupational [Hh]ealth [Ss]ervices.$", + "^In Memoriam Professor Toshiyuki TAKESHIMA$", + "^Účetní závěrka ve vybraném podniku.*$", + "^Financial statements in selected company$", + "^Abdominal [Aa]ortic [Aa]neurysms.*$", + "^Pseudomyxoma peritonei$", + "^Kazalo autora$", + "(?i)^uvodna riječ$", + "^Motivace jako způsob vedení lidí$", + "^Motivation as a leadership$", + "^Polyfunkční dům$", + "^Multi\\-funkcional building$", + "^Podnikatelský plán$", + "(?i)^Podnikatelský záměr$", + "(?i)^Business Plan$", + "^Oceňování nemovitostí$", + "^Marketingová komunikace$", + "^Marketing communication$", + "^Sumario Analítico$", + "^Riječ uredništva$", + "^Savjetovanja i priredbe$", + "^Índice$", + "^(Starobosanski nadpisi).*$", + "^Vzdělávání pracovníků v organizaci$", + "^Staff training in organization$", + "^(Life Histories of North American Geometridae).*$", + "^Strategická analýza podniku$", + "^Strategic Analysis of an Enterprise$", + "^Sadržaj$", + "^Upute suradnicima$", + "^Rodinný dům$", + "(?i)^Fami(l)?ly house$", + "^Upute autorima$", + "^Strategic Analysis$", + "^Finanční analýza vybraného podniku$", + "^Finanční analýza$", + "^Riječ urednika$", + "(?i)^Content(s?)$", + "(?i)^Inhalt$", + "^Jinjō shōgaku shūshinsho jidōyō$", + "(?i)^Index$", + "^Chūgaku kokubun kyōkasho$", + "^Retrato de una mujer$", + "^Retrato de un hombre$", + "^Kōtō shōgaku dokuhon$", + "^Shotōka kokugo$", + "^Shōgaku dokuhon$", + "^Jinjō shōgaku kokugo dokuhon$", + "^Shinsei kokugo dokuhon$", + "^Teikoku dokuhon$", + "^Instructions to Authors$", + "^KİTAP TAHLİLİ$", + "^PRZEGLĄD PIŚMIENNICTWA$", + "(?i)^Presentación$", + "^İçindekiler$", + "(?i)^Tabl?e of contents$", + "^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$", + "^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*", + "^Editorial( Board)?$", + "(?i)^Editorial \\(English\\)$", + "^Editörden$", + "^(Corpus Oral Dialectal \\(COD\\)\\.).*$", + "^(Kiri Karl Morgensternile).*$", + "^(\\[Eksliibris Aleksandr).*\\]$", + "^(\\[Eksliibris Aleksandr).*$", + "^(Eksliibris Aleksandr).*$", + "^(Kiri A\\. de Vignolles).*$", + "^(2 kirja Karl Morgensternile).*$", + "^(Pirita kloostri idaosa arheoloogilised).*$", + "^(Kiri tundmatule).*$", + "^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$", + "^(Eksliibris Nikolai Birukovile).*$", + "^(Eksliibris Nikolai Issakovile).*$", + "^(WHP Cruise Summary Information of section).*$", + "^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$", + "^(Measurement of the spin\\-dependent structure function).*", + "(?i)^.*authors['’′]? reply\\.?$", + "(?i)^.*authors['’′]? response\\.?$", + "^Data [mM]anagement [sS]ervices\\.$", + "Research and Advanced Technology for Digital Libraries" + ] + }, + "synonyms": {} + } +} \ No newline at end of file From 8991d097b466b587a83ad62160798dfaaf20bb7a Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 24 Feb 2022 17:08:24 +0100 Subject: [PATCH 062/159] bug fix in the DedupRecordFactory, DataInfo set before merge --- .../dhp/oa/dedup/DedupRecordFactory.java | 3 +- .../dnetlib/dhp/dedup/conf/orp.new.conf.json | 214 ++++++++ .../dnetlib/dhp/dedup/conf/pub.new.conf.json | 475 ++++++++++++++++++ 3 files changed, 691 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.new.conf.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d65853aff..b8ae4ca02 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -77,6 +77,7 @@ public class DedupRecordFactory { throws IllegalAccessException, InstantiationException { T entity = clazz.newInstance(); + entity.setDataInfo(dataInfo); final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); @@ -106,7 +107,7 @@ public class DedupRecordFactory { entity.setId(id); entity.setLastupdatetimestamp(ts); - entity.setDataInfo(dataInfo); + entity.getDataInfo().setDeletedbyinference(false); return entity; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json new file mode 100644 index 000000000..b0cdade5b --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.new.conf.json @@ -0,0 +1,214 @@ +{ + "wf": { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "result", + "subEntityType" : "resulttype", + "subEntityValue" : "otherresearchproduct", + "orderField" : "title", + "queueMaxSize" : "100", + "groupMaxSize" : "100", + "maxChildren" : "100", + "slidingWindowSize" : "100", + "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], + "includeChildren" : "true", + "idPath" : "$.id", + "maxIterations" : 20 + }, + "pace": { + "clustering": [ + { + "name": "wordsStatsSuffixPrefixChain", + "fields": [ + "title" + ], + "params": { + "mod": "10" + } + }, + { + "name": "lowercase", + "fields": [ + "doi", + "altdoi" + ], + "params": { + "collapseOn:pid": "0" + } + } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "MATCH", + "negative": "pidVSaltid", + "undefined": "pidVSaltid", + "ignoreUndefined": "false" + }, + "pidVSaltid": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid", + "crossCompare": "alternateid", + "mode": "count" + } + } + ], + "threshold": 1.0, + "aggregation": "MAX", + "positive": "softCheck", + 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On the Contribution of Income Shocks and Credit Constraint(s?)$", + "^\\[Funciones auxiliares de la música en Radio París,.*\\]$", + "^Úroveň motivačního procesu jako způsobu vedení lidí$", + "^The level of motivation process as a leadership$", + "^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$", + "(?i)^news and events$", + "(?i)^NOVOSTI I DOGAĐAJI$", + "^Sansū no gakushū$", + "^Posouzení informačního systému firmy a návrh změn$", + "^Information System Assessment and Proposal for ICT Modification$", + "^Stresové zatížení pracovníků ve vybrané profesi$", + "^Stress load in a specific job$", + "^Sunday: Poster Sessions, Pt.*$", + "^Monday: Poster Sessions, Pt.*$", + "^Wednesday: Poster Sessions, Pt.*", + "^Tuesday: Poster Sessions, Pt.*$", + "^Analýza reklamy$", + "^Analysis of advertising$", + "^Shōgaku shūshinsho$", + "^Shōgaku sansū$", + "^Shintei joshi kokubun$", + "^Taishō joshi kokubun dokuhon$", + "^Joshi kokubun$", + "^Účetní uzávěrka a účetní závěrka v ČR$", + "(?i)^The \"?Causes\"? of Cancer$", + "^Normas para la publicación de artículos$", + "^Editor('|s)(s|') [Rr]eply$", + "^Editor(’|s)(s|’) letter$", + "^Redaktoriaus žodis$", + "^DISCUSSION ON THE PRECEDING PAPER$", + "^Kōtō shōgaku shūshinsho jidōyō$", + "^Shōgaku nihon rekishi$", + "^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$", + "^Préface$", + "^Occupational [Hh]ealth [Ss]ervices.$", + "^In Memoriam Professor Toshiyuki TAKESHIMA$", + "^Účetní závěrka ve vybraném podniku.*$", + "^Financial statements in selected company$", + "^Abdominal [Aa]ortic [Aa]neurysms.*$", + "^Pseudomyxoma peritonei$", + "^Kazalo autora$", + "(?i)^uvodna riječ$", + "^Motivace jako způsob vedení lidí$", + "^Motivation as a leadership$", + "^Polyfunkční dům$", + "^Multi\\-funkcional building$", + "^Podnikatelský plán$", + "(?i)^Podnikatelský záměr$", + "(?i)^Business Plan$", + "^Oceňování nemovitostí$", + "^Marketingová komunikace$", + "^Marketing communication$", + "^Sumario Analítico$", + "^Riječ uredništva$", + "^Savjetovanja i priredbe$", + "^Índice$", + "^(Starobosanski nadpisi).*$", + "^Vzdělávání pracovníků v organizaci$", + "^Staff training in organization$", + "^(Life Histories of North American Geometridae).*$", + "^Strategická analýza podniku$", + "^Strategic Analysis of an Enterprise$", + "^Sadržaj$", + "^Upute suradnicima$", + "^Rodinný dům$", + "(?i)^Fami(l)?ly house$", + "^Upute autorima$", + "^Strategic Analysis$", + "^Finanční analýza vybraného podniku$", + "^Finanční analýza$", + "^Riječ urednika$", + "(?i)^Content(s?)$", + "(?i)^Inhalt$", + "^Jinjō shōgaku shūshinsho jidōyō$", + "(?i)^Index$", + "^Chūgaku kokubun kyōkasho$", + "^Retrato de una mujer$", + "^Retrato de un hombre$", + "^Kōtō shōgaku dokuhon$", + "^Shotōka kokugo$", + "^Shōgaku dokuhon$", + "^Jinjō shōgaku kokugo dokuhon$", + "^Shinsei kokugo dokuhon$", + "^Teikoku dokuhon$", + "^Instructions to Authors$", + "^KİTAP TAHLİLİ$", + "^PRZEGLĄD PIŚMIENNICTWA$", + "(?i)^Presentación$", + "^İçindekiler$", + "(?i)^Tabl?e of contents$", + "^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$", + "^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*", + "^Editorial( Board)?$", + "(?i)^Editorial \\(English\\)$", + "^Editörden$", + "^(Corpus Oral Dialectal \\(COD\\)\\.).*$", + "^(Kiri Karl Morgensternile).*$", + "^(\\[Eksliibris Aleksandr).*\\]$", + "^(\\[Eksliibris Aleksandr).*$", + "^(Eksliibris Aleksandr).*$", + "^(Kiri A\\. de Vignolles).*$", + "^(2 kirja Karl Morgensternile).*$", + "^(Pirita kloostri idaosa arheoloogilised).*$", + "^(Kiri tundmatule).*$", + "^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$", + "^(Eksliibris Nikolai Birukovile).*$", + "^(Eksliibris Nikolai Issakovile).*$", + "^(WHP Cruise Summary Information of section).*$", + "^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$", + "^(Measurement of the spin\\-dependent structure function).*", + "(?i)^.*authors['’′]? reply\\.?$", + "(?i)^.*authors['’′]? response\\.?$", + "^Data [mM]anagement [sS]ervices\\.$", + "Research and Advanced Technology for Digital Libraries" + ] + }, + "synonyms": {} + } +} \ No newline at end of file From f5b0a6f89c9e393c566308f7efc76f222f03dafa Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 25 Feb 2022 10:21:57 +0100 Subject: [PATCH 063/159] [master to beta] fixed issues in test files --- .../crossref/publication_license_embargo.json | 2 +- .../alreadyLinked/alreadyLinked_20.json | 20 ++++++++++++++++++ .../alreadyLinked/alreadyLinked_20.json.gz | Bin 3160 -> 0 bytes .../alreadyLinked/alreadyLinked_20.json | 20 ++++++++++++++++++ .../alreadyLinked/alreadyLinked_20.json.gz | Bin 3175 -> 0 bytes .../alreadyLinked/alreadyLinked_20.json | 20 ++++++++++++++++++ .../alreadyLinked/alreadyLinked_20.json.gz | Bin 3160 -> 0 bytes 7 files changed, 61 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked/alreadyLinked_20.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked/alreadyLinked_20.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked/alreadyLinked_20.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked/alreadyLinked_20.json.gz diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json index 47ca55f34..788946fea 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -1456,7 +1456,7 @@ "issued": { "date-parts": [ [ -2021, +3021, 2, 22 ] diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked/alreadyLinked_20.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked/alreadyLinked_20.json new file mode 100644 index 000000000..ee737ce26 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked/alreadyLinked_20.json @@ -0,0 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z+2&0$_h1NU3yL4{bLf_KB~n|&)Fr=Wt@6pa<6Uzl4hKWzCXp8NzX0Q0|GlunK#xFE z9fViT9B~t)30APc(1_#U@V@tQ>c%Hc-tu~)qr_q1c! zUgBWmu@5)#vsHU^GlK*lIDElS;JV>b5&)UA;~t6X1R4k7UnjcfRoo-|_=;genQguv?q*PmqU^X~xnXPE0MH3-Yj?7$(@jea$lp_eV0&i*}Q8_*1PX7LDz`Nl5#*@cm-V z;wSOrr}8ZhVc3b3q9j`1l;x3T?8uBU`NtvRdzbA}(HG(g3jB4_dhv3ty@NYxgV4XH zkiN>9=cb%IE`Q)4%=+F)2zE#`C*V+8OuNw85mS3mmPR3ptsYv21}3Vw(tz46QQ82Z zUK4$FJp9(FTj?-f4}*8wj?F6+^p@nv@{y5EItg-_2zcJJ9B+#FF$vee5i7%^q&P!m zHZ7vzpI*Yp#8`fQ4u8H6E^2?;Dv-3}ATsBD-s*|9tq=@uYLJhp&Wc4KrN`Jvqk7OK zz&8JunqSCYDjVs}8N(+IBP3j|c8se=mzJ+D6c6q5d@}3^8{G|(q%cg_*@V853L)9J zuF{-gMKI8a9p}M824NJ#g1QgXqSR|3biCG@{XBd?=Aog^3<`Vp^I-cxZXx87{sVI~ zT4)IPPDhsfydxs+>rp4{30sSuoy`{{Cq#GX3UN0)xwo5tL3hp<1>WIeVx=r1dzNe& zElMS{+Z!R?QZVls2{4>x+2@rn*X|m311&elO(dj6_IxM6D zKHd*V7_b4aEfs~cCLSHbas8g*q5Hh>ic}eIpH{;4%z@58rkKRaDIuE&o-jzPjBgcN zSjPpO5?BLi!Ejgui}2M3J}=Th`OSiL+%0hotV`S^YTU9=gm5eD?33Ulp@>!75V^-H z;epDL>D{kiL@cuK=u0D{4-advPz!0Hr!WImzVg4(fhZ(vel8<9rPRLK*vgn`xqi8n zaRmv*_Hc@6P~M36TX-Kwt*zg{g^law)AyxL=wETH^B$*#t{|l$-kg!ukSDFK$h%LG yeEeWCAem~<P^y)YL5 From efeeebfee17d1e807d90e38cc9228ee577b180de Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 2 Mar 2022 13:29:25 +0200 Subject: [PATCH 064/159] fixed query after the change in the indicator table --- .../oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql index 6b4d9b1b0..7ad6f3888 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql @@ -17,6 +17,6 @@ left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; -- GOLD OA: create table ${stats_db_name}.result_gold as -select r.id, case when gold.gold_oa=1 then true else false end as gold +select r.id, case when gold.is_gold=1 then true else false end as gold from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; \ No newline at end of file From 3be8737c323c26ef93e0d57f200a9363c0d2e58a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 2 Mar 2022 14:09:05 +0100 Subject: [PATCH 065/159] [graph-stats] fixed query after the change in the indicator table related to PR#200 --- .../oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql index 6b4d9b1b0..7ad6f3888 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql @@ -17,6 +17,6 @@ left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; -- GOLD OA: create table ${stats_db_name}.result_gold as -select r.id, case when gold.gold_oa=1 then true else false end as gold +select r.id, case when gold.is_gold=1 then true else false end as gold from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; \ No newline at end of file From ad78e505da16fbbe8384976eb70ce48ee0f2314f Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 3 Mar 2022 12:28:12 +0200 Subject: [PATCH 066/159] yet another fix --- .../stats/oozie_app/scripts/step20-createMonitorDB.sql | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index b4964d2b3..7c5257edd 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -157,13 +157,13 @@ create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_hybrid_oa_with_cc; -create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads; -create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads_datasource; -create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads_year; -create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads_datasource_year; --denorm From 44b0c03080f8919884f993c659746be14f35ec84 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Mar 2022 10:37:59 +0100 Subject: [PATCH 067/159] [HostedByMap] update to download the json instead of the csv --- .../oa/graph/hostedbymap/model/doaj/APC.java | 35 +++ .../graph/hostedbymap/model/doaj/Admin.java | 25 ++ .../graph/hostedbymap/model/doaj/Article.java | 44 +++ .../graph/hostedbymap/model/doaj/BibJson.java | 253 ++++++++++++++++++ .../hostedbymap/model/doaj/Copyright.java | 25 ++ .../hostedbymap/model/doaj/DOAJEntry.java | 52 ++++ .../hostedbymap/model/doaj/DepositPolicy.java | 35 +++ .../hostedbymap/model/doaj/Editorial.java | 35 +++ .../hostedbymap/model/doaj/Institution.java | 25 ++ .../graph/hostedbymap/model/doaj/License.java | 67 +++++ .../oa/graph/hostedbymap/model/doaj/Max.java | 25 ++ .../hostedbymap/model/doaj/OtherCharges.java | 25 ++ .../hostedbymap/model/doaj/PidScheme.java | 26 ++ .../hostedbymap/model/doaj/Plagiarism.java | 27 ++ .../hostedbymap/model/doaj/Preservation.java | 44 +++ .../hostedbymap/model/doaj/Publisher.java | 25 ++ .../oa/graph/hostedbymap/model/doaj/Ref.java | 52 ++++ .../graph/hostedbymap/model/doaj/Subject.java | 34 +++ .../graph/hostedbymap/model/doaj/Waiver.java | 25 ++ 19 files changed, 879 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java new file mode 100644 index 000000000..3473e0f9d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class APC implements Serializable { + private Boolean has_apc; + private String url; + private List max; + + public List getMax() { + return max; + } + + public void setMax(List max) { + this.max = max; + } + + public Boolean getHas_apc() { + return has_apc; + } + + public void setHas_apc(Boolean has_apc) { + this.has_apc = has_apc; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java new file mode 100644 index 000000000..b823e3450 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Admin implements Serializable { + private Boolean ticked; + private Boolean seal; + + public Boolean getTicked() { + return ticked; + } + + public void setTicked(Boolean ticked) { + this.ticked = ticked; + } + + public Boolean getSeal() { + return seal; + } + + public void setSeal(Boolean seal) { + this.seal = seal; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java new file mode 100644 index 000000000..7e90e24a2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Article implements Serializable { + private String license_display_example_url; + private List license_display; + private Boolean orcid; + private Boolean i4oc_open_citations; + + public String getLicense_display_example_url() { + return license_display_example_url; + } + + public void setLicense_display_example_url(String license_display_example_url) { + this.license_display_example_url = license_display_example_url; + } + + public List getLicense_display() { + return license_display; + } + + public void setLicense_display(List license_display) { + this.license_display = license_display; + } + + public Boolean getOrcid() { + return orcid; + } + + public void setOrcid(Boolean orcid) { + this.orcid = orcid; + } + + public Boolean getI4oc_open_citations() { + return i4oc_open_citations; + } + + public void setI4oc_open_citations(Boolean i4oc_open_citations) { + this.i4oc_open_citations = i4oc_open_citations; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java new file mode 100644 index 000000000..f7c0d501f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java @@ -0,0 +1,253 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +public class BibJson implements Serializable { + private Editorial editorial; + private PidScheme pid_scheme; + private Copyright copyright; + private List keywords; + private Plagiarism plagiarism; + private List subject; + private String eissn; + private String pissn; + private List language; + private String title; + private Article article; + private Institution institution; + private Preservation preservation; + private List license; + private Ref ref; + private Integer oa_start; + private APC apc; + private OtherCharges other_charges; + private Integer publication_time_weeks; + private DepositPolicy deposit_policy; + private Publisher publisher; + private Boolean boai; + private Waiver waiver; + private String alternative_title; + private List is_replaced_by; + private List replaces; + private String discontinued_date; + + public String getDiscontinued_date() { + return discontinued_date; + } + + public void setDiscontinued_date(String discontinued_date) { + this.discontinued_date = discontinued_date; + } + + public List getReplaces() { + return replaces; + } + + public void setReplaces(List replaces) { + this.replaces = replaces; + } + + public List getIs_replaced_by() { + return is_replaced_by; + } + + public void setIs_replaced_by(List is_replaced_by) { + this.is_replaced_by = is_replaced_by; + } + + public String getAlternative_title() { + return alternative_title; + } + + public void setAlternative_title(String alternative_title) { + this.alternative_title = alternative_title; + } + + public String getPissn() { + return pissn; + } + + public void setPissn(String pissn) { + this.pissn = pissn; + } + + public Editorial getEditorial() { + return editorial; + } + + public void setEditorial(Editorial editorial) { + this.editorial = editorial; + } + + public PidScheme getPid_scheme() { + return pid_scheme; + } + + public void setPid_scheme(PidScheme pid_scheme) { + this.pid_scheme = pid_scheme; + } + + public Copyright getCopyright() { + return copyright; + } + + public void setCopyright(Copyright copyright) { + this.copyright = copyright; + } + + public List getKeywords() { + return keywords; + } + + public void setKeywords(List keywords) { + this.keywords = keywords; + } + + public Plagiarism getPlagiarism() { + return plagiarism; + } + + public void setPlagiarism(Plagiarism plagiarism) { + this.plagiarism = plagiarism; + } + + public List getSubject() { + return subject; + } + + public void setSubject(List subject) { + this.subject = subject; + } + + public String getEissn() { + return eissn; + } + + public void setEissn(String eissn) { + this.eissn = eissn; + } + + public List getLanguage() { + return language; + } + + public void setLanguage(List language) { + this.language = language; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public Article getArticle() { + return article; + } + + public void setArticle(Article article) { + this.article = article; + } + + public Institution getInstitution() { + return institution; + } + + public void setInstitution(Institution institution) { + this.institution = institution; + } + + public Preservation getPreservation() { + return preservation; + } + + public void setPreservation(Preservation preservation) { + this.preservation = preservation; + } + + public List getLicense() { + return license; + } + + public void setLicense(List license) { + this.license = license; + } + + public Ref getRef() { + return ref; + } + + public void setRef(Ref ref) { + this.ref = ref; + } + + public Integer getOa_start() { + return oa_start; + } + + public void setOa_start(Integer oa_start) { + this.oa_start = oa_start; + } + + public APC getApc() { + return apc; + } + + public void setApc(APC apc) { + this.apc = apc; + } + + public OtherCharges getOther_charges() { + return other_charges; + } + + public void setOther_charges(OtherCharges other_charges) { + this.other_charges = other_charges; + } + + public Integer getPublication_time_weeks() { + return publication_time_weeks; + } + + public void setPublication_time_weeks(Integer publication_time_weeks) { + this.publication_time_weeks = publication_time_weeks; + } + + public DepositPolicy getDeposit_policy() { + return deposit_policy; + } + + public void setDeposit_policy(DepositPolicy deposit_policy) { + this.deposit_policy = deposit_policy; + } + + public Publisher getPublisher() { + return publisher; + } + + public void setPublisher(Publisher publisher) { + this.publisher = publisher; + } + + public Boolean getBoai() { + return boai; + } + + public void setBoai(Boolean boai) { + this.boai = boai; + } + + public Waiver getWaiver() { + return waiver; + } + + public void setWaiver(Waiver waiver) { + this.waiver = waiver; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java new file mode 100644 index 000000000..c595c4c88 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Copyright implements Serializable { + private Boolean author_retains; + private String url; + + public Boolean getAuthor_retains() { + return author_retains; + } + + public void setAuthor_retains(Boolean author_retains) { + this.author_retains = author_retains; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java new file mode 100644 index 000000000..add5bf8bf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class DOAJEntry implements Serializable { + private String last_updated; + private BibJson bibjson; + private Admin admin; + private String created_date; + private String id; + + public String getLast_updated() { + return last_updated; + } + + public void setLast_updated(String last_updated) { + this.last_updated = last_updated; + } + + public BibJson getBibjson() { + return bibjson; + } + + public void setBibjson(BibJson bibjson) { + this.bibjson = bibjson; + } + + public Admin getAdmin() { + return admin; + } + + public void setAdmin(Admin admin) { + this.admin = admin; + } + + public String getCreated_date() { + return created_date; + } + + public void setCreated_date(String created_date) { + this.created_date = created_date; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java new file mode 100644 index 000000000..d86c97f34 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class DepositPolicy implements Serializable { + private List service; + private String url; + private Boolean has_policy; + + public List getService() { + return service; + } + + public void setService(List service) { + this.service = service; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_policy() { + return has_policy; + } + + public void setHas_policy(Boolean has_policy) { + this.has_policy = has_policy; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java new file mode 100644 index 000000000..35bfba158 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Editorial implements Serializable { + private List review_process; + private String review_url; + private String board_url; + + public List getReview_process() { + return review_process; + } + + public void setReview_process(List review_process) { + this.review_process = review_process; + } + + public String getReview_url() { + return review_url; + } + + public void setReview_url(String review_url) { + this.review_url = review_url; + } + + public String getBoard_url() { + return board_url; + } + + public void setBoard_url(String board_url) { + this.board_url = board_url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java new file mode 100644 index 000000000..3b4d90493 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Institution implements Serializable { + private String country; + private String name; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java new file mode 100644 index 000000000..64c7bc18f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java @@ -0,0 +1,67 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public class License implements Serializable { + private Boolean nc; + private Boolean nd; + private Boolean by; + private String type; + private Boolean sa; + private String url; + + public Boolean getnC() { + return nc; + } + + @JsonProperty("NC") + public void setnC(Boolean NC) { + this.nc = NC; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public Boolean getNd() { + return nd; + } + + @JsonProperty("ND") + public void setNd(Boolean nd) { + this.nd = nd; + } + + public Boolean getBy() { + return by; + } + + @JsonProperty("BY") + public void setBy(Boolean by) { + this.by = by; + } + + public Boolean getSa() { + return sa; + } + + @JsonProperty("SA") + public void setSa(Boolean sa) { + this.sa = sa; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java new file mode 100644 index 000000000..0e292b631 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Max implements Serializable { + private Integer price; + private String currency; + + public Integer getPrice() { + return price; + } + + public void setPrice(Integer price) { + this.price = price; + } + + public String getCurrency() { + return currency; + } + + public void setCurrency(String currency) { + this.currency = currency; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java new file mode 100644 index 000000000..1583481d2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class OtherCharges implements Serializable { + private Boolean has_other_charges; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_other_charges() { + return has_other_charges; + } + + public void setHas_other_charges(Boolean has_other_charges) { + this.has_other_charges = has_other_charges; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java new file mode 100644 index 000000000..bd7e710dd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class PidScheme implements Serializable { + private List scheme; + private Boolean has_pid_scheme; + + public List getScheme() { + return scheme; + } + + public void setScheme(List scheme) { + this.scheme = scheme; + } + + public Boolean getHas_pid_scheme() { + return has_pid_scheme; + } + + public void setHas_pid_scheme(Boolean has_pid_scheme) { + this.has_pid_scheme = has_pid_scheme; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java new file mode 100644 index 000000000..f2230b3ea --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java @@ -0,0 +1,27 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +import javax.sql.rowset.serial.SerialArray; + +public class Plagiarism implements Serializable { + private Boolean detection; + private String url; + + public Boolean getDetection() { + return detection; + } + + public void setDetection(Boolean detection) { + this.detection = detection; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java new file mode 100644 index 000000000..f56ea9953 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Preservation implements Serializable { + private Boolean has_preservation; + private List service; + private List national_library; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_preservation() { + return has_preservation; + } + + public void setHas_preservation(Boolean has_preservation) { + this.has_preservation = has_preservation; + } + + public List getService() { + return service; + } + + public void setService(List service) { + this.service = service; + } + + public List getNational_library() { + return national_library; + } + + public void setNational_library(List national_library) { + this.national_library = national_library; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java new file mode 100644 index 000000000..6d97a7969 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Publisher implements Serializable { + private String country; + private String name; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java new file mode 100644 index 000000000..0f7c7dc95 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Ref implements Serializable { + private String aims_scope; + private String journal; + private String oa_statement; + private String author_instructions; + private String license_terms; + + public String getAims_scope() { + return aims_scope; + } + + public void setAims_scope(String aims_scope) { + this.aims_scope = aims_scope; + } + + public String getJournal() { + return journal; + } + + public void setJournal(String journal) { + this.journal = journal; + } + + public String getOa_statement() { + return oa_statement; + } + + public void setOa_statement(String oa_statement) { + this.oa_statement = oa_statement; + } + + public String getAuthor_instructions() { + return author_instructions; + } + + public void setAuthor_instructions(String author_instructions) { + this.author_instructions = author_instructions; + } + + public String getLicense_terms() { + return license_terms; + } + + public void setLicense_terms(String license_terms) { + this.license_terms = license_terms; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java new file mode 100644 index 000000000..811638e76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Subject implements Serializable { + private String code; + private String scheme; + private String term; + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getScheme() { + return scheme; + } + + public void setScheme(String scheme) { + this.scheme = scheme; + } + + public String getTerm() { + return term; + } + + public void setTerm(String term) { + this.term = term; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java new file mode 100644 index 000000000..ca67dde0c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Waiver implements Serializable { + private Boolean has_waiver; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_waiver() { + return has_waiver; + } + + public void setHas_waiver(Boolean has_waiver) { + this.has_waiver = has_waiver; + } +} From 8a41f63348a7d7f3ea25ed0bafaa75c3e66afdbe Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Mar 2022 10:38:43 +0100 Subject: [PATCH 068/159] [HostedByMap] update to download the json instead of the csv --- .../hostedbymap/ExtractAndMapDoajJson.java | 117 ++++++++++++++++++ 1 file changed, 117 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java new file mode 100644 index 000000000..17a78760e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java @@ -0,0 +1,117 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap; + +import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract; + +import java.io.BufferedOutputStream; +import java.io.IOException; +import java.io.PrintWriter; +import java.util.Arrays; +import java.util.Objects; + +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.CompressionInputStream; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj.DOAJEntry; + +public class ExtractAndMapDoajJson { + + private static final Logger log = LoggerFactory.getLogger(ExtractAndMapDoajJson.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + ExtractAndMapDoajJson.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json")))); + + parser.parseArgument(args); + + final String compressedInput = parser.get("compressedFile"); + log.info("compressedInput {}", compressedInput); + + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode {}", hdfsNameNode); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + final String workingPath = parser.get("workingPath"); + log.info("workingPath {}", workingPath); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fs = FileSystem.get(conf); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); + doExtract(fs, workingPath, compressedInput); + doMap(fs, workingPath, outputPath, codec); + + } + + private static void doMap(FileSystem fs, String workingPath, String outputPath, CompressionCodec codec) + throws IOException { + RemoteIterator fileStatusListIterator = fs + .listFiles( + new Path(workingPath), true); + + Path hdfsWritePath = new Path(outputPath); + if (fs.exists(hdfsWritePath)) { + fs.delete(hdfsWritePath, true); + + } + try ( + + FSDataOutputStream out = fs + .create(hdfsWritePath); + PrintWriter writer = new PrintWriter(new BufferedOutputStream(out))) { + + while (fileStatusListIterator.hasNext()) { + Path path = fileStatusListIterator.next().getPath(); + if (!fs.isDirectory(path)) { + FSDataInputStream is = fs.open(path); + CompressionInputStream compressionInputStream = codec.createInputStream(is); + DOAJEntry[] doajEntries = new ObjectMapper().readValue(compressionInputStream, DOAJEntry[].class); + Arrays.stream(doajEntries).forEach(doaj -> { + try { + writer.println(new ObjectMapper().writeValueAsString(getDoajModel(doaj))); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + } + + } + + } + + } + + @NotNull + public static DOAJModel getDoajModel(DOAJEntry doaj) { + DOAJModel doajModel = new DOAJModel(); + doajModel.setOaStart(doaj.getBibjson().getOa_start()); + doajModel.setEissn(doaj.getBibjson().getEissn()); + doajModel.setIssn(doaj.getBibjson().getPissn()); + doajModel.setJournalTitle(doaj.getBibjson().getTitle()); + doajModel.setReviewProcess(doaj.getBibjson().getEditorial().getReview_process()); + return doajModel; + } + +} From b7c2340952d9af572b97d6d4f774efe89796019b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Mar 2022 11:05:23 +0100 Subject: [PATCH 069/159] [HostedByMap - DOIBoost] changed to use code moved to common since used also from hostedbymap now --- .../common/collection/DecompressTarGz.java | 40 +++++++++++++++++++ .../crossref/ExtractCrossrefRecords.java | 31 +++----------- 2 files changed, 45 insertions(+), 26 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java new file mode 100644 index 000000000..8bcf14ba4 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java @@ -0,0 +1,40 @@ + +package eu.dnetlib.dhp.common.collection; + +import java.io.BufferedOutputStream; +import java.io.IOException; +import java.util.zip.GZIPOutputStream; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +public class DecompressTarGz { + + public static void doExtract(FileSystem fs, String outputPath, String tarGzPath) throws IOException { + + FSDataInputStream inputFileStream = fs.open(new Path(tarGzPath)); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(inputFileStream))) { + TarArchiveEntry entry = null; + while ((entry = tais.getNextTarEntry()) != null) { + if (!entry.isDirectory()) { + try ( + FSDataOutputStream out = fs + .create(new Path(outputPath.concat(entry.getName()).concat(".gz"))); + GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { + + IOUtils.copy(tais, gzipOs); + + } + + } + } + } + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java index d1861ff0a..6060b619e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java @@ -1,19 +1,13 @@ package eu.dnetlib.doiboost.crossref; -import java.io.BufferedOutputStream; -import java.net.URI; -import java.util.zip.GZIPOutputStream; +import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract; + +import java.net.URI; -import org.apache.commons.compress.archivers.tar.TarArchiveEntry; -import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; -import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataInputStream; -import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; import org.mortbay.log.Log; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -33,31 +27,16 @@ public class ExtractCrossrefRecords { final String outputPath = parser.get("outputPath"); final String crossrefFileNameTarGz = parser.get("crossrefFileNameTarGz"); - Path hdfsreadpath = new Path(workingPath.concat("/").concat(crossrefFileNameTarGz)); Configuration conf = new Configuration(); conf.set("fs.defaultFS", workingPath); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); FileSystem fs = FileSystem.get(URI.create(workingPath), conf); - FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath); - try (TarArchiveInputStream tais = new TarArchiveInputStream( - new GzipCompressorInputStream(crossrefFileStream))) { - TarArchiveEntry entry = null; - while ((entry = tais.getNextTarEntry()) != null) { - if (!entry.isDirectory()) { - try ( - FSDataOutputStream out = fs - .create(new Path(outputPath.concat(entry.getName()).concat(".gz"))); - GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { - IOUtils.copy(tais, gzipOs); + doExtract(fs, outputPath, workingPath.concat("/").concat(crossrefFileNameTarGz)); - } - - } - } - } Log.info("Crossref dump reading completed"); } + } From 5d608d62911fb50c41b5bf15455395a5443e707a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Mar 2022 11:06:09 +0100 Subject: [PATCH 070/159] [HostedByMap] changed the model to include also oaStart date and review process that could be possibly used in the future --- .../oa/graph/hostedbymap/model/DOAJModel.java | 17 ++++- .../hostedbymap/SparkProduceHostedByMap.scala | 67 +++++++++++++------ 2 files changed, 62 insertions(+), 22 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java index 4b5dc22a6..c3b6f1f30 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model; import java.io.Serializable; +import java.util.List; import com.opencsv.bean.CsvBindByName; @@ -17,7 +18,17 @@ public class DOAJModel implements Serializable { private String eissn; @CsvBindByName(column = "Review process") - private String reviewProcess; + private List reviewProcess; + + private Integer oaStart; + + public Integer getOaStart() { + return oaStart; + } + + public void setOaStart(Integer oaStart) { + this.oaStart = oaStart; + } public String getJournalTitle() { return journalTitle; @@ -43,11 +54,11 @@ public class DOAJModel implements Serializable { this.eissn = eissn; } - public String getReviewProcess() { + public List getReviewProcess() { return reviewProcess; } - public void setReviewProcess(String reviewProcess) { + public void setReviewProcess(List reviewProcess) { this.reviewProcess = reviewProcess; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index 8d8965866..bdf0861ae 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala @@ -2,9 +2,10 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel} import eu.dnetlib.dhp.schema.oaf.Datasource -import org.apache.commons.io.IOUtils +import org.apache.commons.io.{FileUtils, IOUtils} import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.{FileSystem, Path} import org.apache.hadoop.io.compress.GzipCodec @@ -13,7 +14,8 @@ import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} import org.json4s.DefaultFormats import org.slf4j.{Logger, LoggerFactory} -import java.io.PrintWriter +import java.io.{File, PrintWriter} +import scala.collection.JavaConverters._ object SparkProduceHostedByMap { @@ -34,7 +36,9 @@ object SparkProduceHostedByMap { openaire.journal_id, "", "", - isOpenAccess + isOpenAccess, + -1, + List[String]() ) case Constants.EISSN => HostedByItemType( @@ -43,7 +47,9 @@ object SparkProduceHostedByMap { "", openaire.journal_id, "", - isOpenAccess + isOpenAccess, + -1, + List[String]() ) case Constants.ISSNL => HostedByItemType( @@ -52,7 +58,9 @@ object SparkProduceHostedByMap { "", "", openaire.journal_id, - isOpenAccess + isOpenAccess, + -1, + List[String]() ) // catch the default with a variable so you can print it @@ -77,34 +85,36 @@ object SparkProduceHostedByMap { issn: String, eissn: String, issnl: String, - oa: Boolean + oa: Boolean, + oaDate: Int, + reviewProcess: List[String] ): HostedByItemType = { if (issn != null) { if (eissn != null) { if (issnl != null) { - HostedByItemType(id, officialname, issn, eissn, issnl, oa) + HostedByItemType(id, officialname, issn, eissn, issnl, oa, oaDate, reviewProcess) } else { - HostedByItemType(id, officialname, issn, eissn, "", oa) + HostedByItemType(id, officialname, issn, eissn, "", oa, oaDate, reviewProcess) } } else { if (issnl != null) { - HostedByItemType(id, officialname, issn, "", issnl, oa) + HostedByItemType(id, officialname, issn, "", issnl, oa, oaDate, reviewProcess) } else { - HostedByItemType(id, officialname, issn, "", "", oa) + HostedByItemType(id, officialname, issn, "", "", oa, oaDate, reviewProcess) } } } else { if (eissn != null) { if (issnl != null) { - HostedByItemType(id, officialname, "", eissn, issnl, oa) + HostedByItemType(id, officialname, "", eissn, issnl, oa, oaDate, reviewProcess) } else { - HostedByItemType(id, officialname, "", eissn, "", oa) + HostedByItemType(id, officialname, "", eissn, "", oa, oaDate, reviewProcess) } } else { if (issnl != null) { - HostedByItemType(id, officialname, "", "", issnl, oa) + HostedByItemType(id, officialname, "", "", issnl, oa, oaDate, reviewProcess) } else { - HostedByItemType("", "", "", "", "", oa) + HostedByItemType("", "", "", "", "", oa, oaDate, reviewProcess) } } } @@ -119,10 +129,12 @@ object SparkProduceHostedByMap { dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, - false + false, + -1, + List[String]() ) } - HostedByItemType("", "", "", "", "", false) + HostedByItemType("", "", "", "", "", false, -1, List[String]()) } def oaHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = { @@ -148,7 +160,9 @@ object SparkProduceHostedByMap { gold.getIssn, "", gold.getIssnL, - true + true, + -1, + List[String]() ) } @@ -171,14 +185,27 @@ object SparkProduceHostedByMap { } def doajToHostedbyItemType(doaj: DOAJModel): HostedByItemType = { - + if (doaj.getOaStart == null) { + return getHostedByItemType( + Constants.DOAJ, + doaj.getJournalTitle, + doaj.getIssn, + doaj.getEissn, + "", + true, + -1, + doaj.getReviewProcess.asScala.toList + ) + } return getHostedByItemType( Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", - true + true, + doaj.getOaStart, + doaj.getReviewProcess.asScala.toList ) } @@ -256,6 +283,8 @@ object SparkProduceHostedByMap { logger.info("Getting the Datasources") + HdfsSupport.remove(outputPath, spark.sparkContext.hadoopConfiguration) + Aggregators .explodeHostedByItemType( oaHostedByDataset(spark, datasourcePath) From 2c5087d55a53c745ac81db84edd995b9f6bdb6a7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 4 Mar 2022 15:18:21 +0100 Subject: [PATCH 071/159] [HostedByMap] download of doaj from json, modification of test resources, deletion of class no more needed for the CSV download --- .../dhp/oa/graph/hostedbymap/DownloadCSV.java | 27 +---- .../oa/graph/hostedbymap/DownloadCSV2.java | 84 --------------- .../hostedbymap/ExtractAndMapDoajJson.java | 2 +- .../graph/hostedbymap/oozie_app/workflow.xml | 101 ++++++++++++++---- .../hostedbymap/SparkProduceHostedByMap.scala | 50 +++------ .../oa/graph/hostedbymap/DownloadCsvTest.java | 51 --------- .../graph/hostedbymap/doaj_transformed.json | 50 ++++----- 7 files changed, 129 insertions(+), 236 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java index dff761c34..bbadde524 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java @@ -23,7 +23,7 @@ public class DownloadCSV { private static final Logger log = LoggerFactory.getLogger(DownloadCSV.class); - public static final char DEFAULT_DELIMITER = ';'; + public static final char DEFAULT_DELIMITER = ','; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -40,9 +40,6 @@ public class DownloadCSV { final String fileURL = parser.get("fileURL"); log.info("fileURL {}", fileURL); - final String workingPath = parser.get("workingPath"); - log.info("workingPath {}", workingPath); - final String outputFile = parser.get("outputFile"); log.info("outputFile {}", outputFile); @@ -63,31 +60,15 @@ public class DownloadCSV { FileSystem fileSystem = FileSystem.get(conf); - new DownloadCSV().doDownload(fileURL, workingPath, outputFile, classForName, delimiter, fileSystem); + new DownloadCSV().doDownload(fileURL, outputFile, classForName, delimiter, fileSystem); } - protected void doDownload(String fileURL, String workingPath, String outputFile, String classForName, + protected void doDownload(String fileURL, String outputFile, String classForName, char delimiter, FileSystem fs) throws IOException, ClassNotFoundException, CollectorException { - final HttpConnector2 connector2 = new HttpConnector2(); - - final Path path = new Path(workingPath + "/replaced.csv"); - - try (BufferedReader in = new BufferedReader( - new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) { - - try (PrintWriter writer = new PrintWriter( - new OutputStreamWriter(fs.create(path, true), StandardCharsets.UTF_8))) { - String line; - while ((line = in.readLine()) != null) { - writer.println(line.replace("\\\"", "\"")); - } - } - } - - try (InputStreamReader reader = new InputStreamReader(fs.open(path))) { + try (InputStreamReader reader = new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL))) { GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java deleted file mode 100644 index d82d00862..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java +++ /dev/null @@ -1,84 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.hostedbymap; - -import java.io.*; -import java.util.Objects; -import java.util.Optional; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.collection.GetCSV; -import eu.dnetlib.dhp.common.collection.HttpConnector2; - -public class DownloadCSV2 { - - private static final Logger log = LoggerFactory.getLogger(DownloadCSV2.class); - - public static final char DEFAULT_DELIMITER = ';'; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - Objects - .requireNonNull( - DownloadCSV2.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json")))); - - parser.parseArgument(args); - - final String fileURL = parser.get("fileURL"); - log.info("fileURL {}", fileURL); - - final String tmpFile = parser.get("tmpFile"); - log.info("tmpFile {}", tmpFile); - - final String outputFile = parser.get("outputFile"); - log.info("outputFile {}", outputFile); - - final String hdfsNameNode = parser.get("hdfsNameNode"); - log.info("hdfsNameNode {}", hdfsNameNode); - - final String classForName = parser.get("classForName"); - log.info("classForName {}", classForName); - - final char delimiter = Optional - .ofNullable(parser.get("delimiter")) - .map(s -> s.charAt(0)) - .orElse(DEFAULT_DELIMITER); - log.info("delimiter {}", delimiter); - - HttpConnector2 connector2 = new HttpConnector2(); - - try (BufferedReader in = new BufferedReader( - new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) { - - try (PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(tmpFile)))) { - String line; - while ((line = in.readLine()) != null) { - writer.println(line.replace("\\\"", "\"")); - } - } - } - - try (BufferedReader in = new BufferedReader(new FileReader(tmpFile))) { - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - GetCSV.getCsv(fileSystem, in, outputFile, classForName, delimiter); - } finally { - FileUtils.deleteQuietly(new File(tmpFile)); - } - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java index 17a78760e..5fede3f59 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java @@ -9,7 +9,6 @@ import java.io.PrintWriter; import java.util.Arrays; import java.util.Objects; -import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; @@ -24,6 +23,7 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel; import eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj.DOAJEntry; public class ExtractAndMapDoajJson { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml index 84035fe4e..1a3261ffb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -74,7 +74,9 @@ ${wf:conf('resumeFrom') eq 'ProduceHBM'} - ${wf:conf('resumeFrom') eq 'download_csv'} + ${wf:conf('resumeFrom') eq 'DownloadBoth'} + ${wf:conf('resumeFrom') eq 'DownloadGold'} + ${wf:conf('resumeFrom') eq 'DownloadDoaj'} @@ -83,18 +85,9 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - + - + @@ -103,21 +96,43 @@ --hdfsNameNode${nameNode} --fileURL${unibiFileURL} --tmpFile/tmp/unibi_gold_replaced.csv - --outputFile${workingDir}/unibi_gold.json + --outputFile/user/${wf:user()}/data/unibi_gold.json --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel - + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${doajJsonFileURL} + ${dumpPath} + ${dumpFileName} + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + - eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2 + eu.dnetlib.dhp.oa.graph.hostedbymap.ExtractAndMapDoajJson --hdfsNameNode${nameNode} - --fileURL${doajFileURL} - --tmpFile/tmp/doaj_replaced.csv - --outputFile${workingDir}/doaj.json - --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel + --compressedFile${dumpPath}/${dumpFileName} + --workingPath${workingDir}/DOAJ/ + --outputPath/user/${wf:user()}/data/doaj.json @@ -125,6 +140,54 @@ + + + eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV + --hdfsNameNode${nameNode} + --fileURL${unibiFileURL} + --tmpFile/tmp/unibi_gold_replaced.csv + --outputFile/user/${wf:user()}/data/unibi_gold.json + --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel + + + + + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${doajJsonFileURL} + ${dumpPath} + ${dumpFileName} + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + + + eu.dnetlib.dhp.oa.graph.hostedbymap.ExtractAndMapDoajJson + --hdfsNameNode${nameNode} + --compressedFile${dumpPath}/${dumpFileName} + --workingPath${workingDir}/DOAJ/ + --outputPath/user/${wf:user()}/data/doaj.json + + + + + yarn-cluster diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index bdf0861ae..9e3a451e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala @@ -36,9 +36,7 @@ object SparkProduceHostedByMap { openaire.journal_id, "", "", - isOpenAccess, - -1, - List[String]() + isOpenAccess ) case Constants.EISSN => HostedByItemType( @@ -47,9 +45,7 @@ object SparkProduceHostedByMap { "", openaire.journal_id, "", - isOpenAccess, - -1, - List[String]() + isOpenAccess ) case Constants.ISSNL => HostedByItemType( @@ -58,9 +54,7 @@ object SparkProduceHostedByMap { "", "", openaire.journal_id, - isOpenAccess, - -1, - List[String]() + isOpenAccess ) // catch the default with a variable so you can print it @@ -85,36 +79,34 @@ object SparkProduceHostedByMap { issn: String, eissn: String, issnl: String, - oa: Boolean, - oaDate: Int, - reviewProcess: List[String] + oa: Boolean ): HostedByItemType = { if (issn != null) { if (eissn != null) { if (issnl != null) { - HostedByItemType(id, officialname, issn, eissn, issnl, oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, issn, eissn, issnl, oa) } else { - HostedByItemType(id, officialname, issn, eissn, "", oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, issn, eissn, "", oa) } } else { if (issnl != null) { - HostedByItemType(id, officialname, issn, "", issnl, oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, issn, "", issnl, oa) } else { - HostedByItemType(id, officialname, issn, "", "", oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, issn, "", "", oa) } } } else { if (eissn != null) { if (issnl != null) { - HostedByItemType(id, officialname, "", eissn, issnl, oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, "", eissn, issnl, oa) } else { - HostedByItemType(id, officialname, "", eissn, "", oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, "", eissn, "", oa) } } else { if (issnl != null) { - HostedByItemType(id, officialname, "", "", issnl, oa, oaDate, reviewProcess) + HostedByItemType(id, officialname, "", "", issnl, oa) } else { - HostedByItemType("", "", "", "", "", oa, oaDate, reviewProcess) + HostedByItemType("", "", "", "", "", oa) } } } @@ -129,12 +121,10 @@ object SparkProduceHostedByMap { dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, - false, - -1, - List[String]() + false ) } - HostedByItemType("", "", "", "", "", false, -1, List[String]()) + HostedByItemType("", "", "", "", "", false) } def oaHostedByDataset(spark: SparkSession, datasourcePath: String): Dataset[HostedByItemType] = { @@ -160,9 +150,7 @@ object SparkProduceHostedByMap { gold.getIssn, "", gold.getIssnL, - true, - -1, - List[String]() + true ) } @@ -192,9 +180,7 @@ object SparkProduceHostedByMap { doaj.getIssn, doaj.getEissn, "", - true, - -1, - doaj.getReviewProcess.asScala.toList + true ) } return getHostedByItemType( @@ -203,9 +189,7 @@ object SparkProduceHostedByMap { doaj.getIssn, doaj.getEissn, "", - true, - doaj.getOaStart, - doaj.getReviewProcess.asScala.toList + true ) } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java index edf74fc6a..48f1e0c06 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java @@ -55,7 +55,6 @@ public class DownloadCsvTest { new DownloadCSV() .doDownload( fileURL, - workingDir + "/unibi_gold", outputFile, UnibiGoldModel.class.getName(), ',', @@ -91,56 +90,6 @@ public class DownloadCsvTest { assertEquals(67028, count); } - @Disabled - @Test - void getDoajFileTest() throws CollectorException, IOException, ClassNotFoundException { - - String fileURL = "https://doaj.org/csv"; - - final String outputFile = workingDir + "/doaj.json"; - new DownloadCSV() - .doDownload( - fileURL, - workingDir + "/doaj", - outputFile, - DOAJModel.class.getName(), - ',', - fs); - - BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile)))); - - String line; - int count = 0; - while ((line = in.readLine()) != null) { - DOAJModel doaj = new ObjectMapper().readValue(line, DOAJModel.class); - if (count == 0) { - assertEquals("0001-3765", doaj.getIssn()); - assertEquals("1678-2690", doaj.getEissn()); - assertEquals("Anais da Academia Brasileira de Ciências", doaj.getJournalTitle()); - } - if (count == 22) { - log.info(new ObjectMapper().writeValueAsString(doaj)); - System.out.println(new ObjectMapper().writeValueAsString(doaj)); - } - if (count == 7904) { - // log.info(new ObjectMapper().writeValueAsString(doaj)); - assertEquals("", doaj.getIssn()); - assertEquals("2055-7159", doaj.getEissn()); - assertEquals("BJR|case reports", doaj.getJournalTitle()); - } - if (count == 16707) { - - assertEquals("2783-1043", doaj.getIssn()); - assertEquals("2783-1051", doaj.getEissn()); - assertEquals("فیزیک کاربردی ایران", doaj.getJournalTitle()); - } - - count += 1; - } - - assertEquals(16715, count); - } - @AfterAll public static void cleanup() { FileUtils.deleteQuietly(new File(workingDir)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json index 9cec80eb4..09730f1da 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json @@ -1,25 +1,25 @@ -{"journalTitle":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","reviewProcess":"Double blind peer review"} -{"journalTitle":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","reviewProcess":"Blind peer review"} -{"journalTitle":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","reviewProcess":"Double blind peer review"} -{"journalTitle":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":"","reviewProcess":"Double blind peer review"} -{"journalTitle":"Revue Internationale de Pédagogie de l’Enseignement Supérieur","issn":"","eissn":"2076-8427","reviewProcess":"Double blind peer review"} -{"journalTitle":"Проблемы развития территории","issn":"2076-8915","eissn":"2409-9007","reviewProcess":"Double blind peer review"} -{"journalTitle":"Rambam Maimonides Medical Journal","issn":"","eissn":"2076-9172","reviewProcess":"Peer review"} -{"journalTitle":"Membranes","issn":"2077-0375","eissn":"","reviewProcess":"Blind peer review"} -{"journalTitle":"Journal of Clinical Medicine","issn":"","eissn":"2077-0383","reviewProcess":"Blind peer review"} -{"journalTitle":"Agriculture","issn":"","eissn":"2077-0472","reviewProcess":"Blind peer review"} -{"journalTitle":"Standartnye Obrazcy","issn":"2077-1177","eissn":"","reviewProcess":"Double blind peer review"} -{"journalTitle":"Металл и литье Украины","issn":"2077-1304","eissn":"2706-5529","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Marine Science and Engineering","issn":"","eissn":"2077-1312","reviewProcess":"Blind peer review"} -{"journalTitle":"Religions","issn":"","eissn":"2077-1444","reviewProcess":"Double blind peer review"} -{"journalTitle":"GW-Unterricht","issn":"2077-1517","eissn":"2414-4169","reviewProcess":"Double blind peer review"} -{"journalTitle":"UCV-Scientia","issn":"2077-172X","eissn":"","reviewProcess":"Peer review"} -{"journalTitle":"Sovremennye Issledovaniâ Socialʹnyh Problem","issn":"2077-1770","eissn":"2218-7405","reviewProcess":"Double blind peer review"} -{"journalTitle":"Granì","issn":"2077-1800","eissn":"2413-8738","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Economics Finance and Administrative Science","issn":"2077-1886","eissn":"2218-0648","reviewProcess":"Double blind peer review"} -{"journalTitle":"Science Education International","issn":"","eissn":"2077-2327","reviewProcess":"Double blind peer review"} -{"journalTitle":"Edumecentro","issn":"","eissn":"2077-2874","reviewProcess":"Double blind peer review"} -{"journalTitle":"Monteverdia","issn":"","eissn":"2077-2890","reviewProcess":"Double blind peer review"} -{"journalTitle":"Transformación","issn":"","eissn":"2077-2955","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","reviewProcess":"Double blind peer review"} -{"journalTitle":"Revue de Primatologie","issn":"","eissn":"2077-3757","reviewProcess":"Peer review"} \ No newline at end of file +{"journalTitle":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","reviewProcess":["Double blind peer review"],"oaStart":2015} +{"journalTitle":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","reviewProcess":["Blind peer review"],"oaStart":2009} +{"journalTitle":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":null,"reviewProcess":["Double blind peer review"],"oaStart":2006} +{"journalTitle":"Revue Internationale de Pédagogie de l’Enseignement Supérieur","issn":null,"eissn":"2076-8427","reviewProcess":["Double blind peer review"],"oaStart":2009} +{"journalTitle":"Проблемы развития территории","issn":"2076-8915","eissn":"2409-9007","reviewProcess":["Double blind peer review"],"oaStart":2008} +{"journalTitle":"Rambam Maimonides Medical Journal","issn":null,"eissn":"2076-9172","reviewProcess":["Peer review"],"oaStart":2010} +{"journalTitle":"Membranes","issn":"2077-0375","eissn":null,"reviewProcess":["Blind peer review"],"oaStart":2011} +{"journalTitle":"Journal of Clinical Medicine","issn":null,"eissn":"2077-0383","reviewProcess":["Blind peer review"],"oaStart":2012} +{"journalTitle":"Agriculture","issn":null,"eissn":"2077-0472","reviewProcess":["Blind peer review"],"oaStart":2011} +{"journalTitle":"Standartnye Obrazcy","issn":"2077-1177","eissn":null,"reviewProcess":["Double blind peer review"],"oaStart":2014} +{"journalTitle":"Металл и литье Украины","issn":"2077-1304","eissn":"2706-5529","reviewProcess":["Double blind peer review"],"oaStart":2019} +{"journalTitle":"Journal of Marine Science and Engineering","issn":null,"eissn":"2077-1312","reviewProcess":["Blind peer review"],"oaStart":2013} +{"journalTitle":"Religions","issn":null,"eissn":"2077-1444","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"GW-Unterricht","issn":"2077-1517","eissn":"2414-4169","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"UCV-Scientia","issn":"2077-172X","eissn":null,"reviewProcess":["Peer review"],"oaStart":2009} +{"journalTitle":"Sovremennye Issledovaniâ Socialʹnyh Problem","issn":"2077-1770","eissn":"2218-7405","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Granì","issn":"2077-1800","eissn":"2413-8738","reviewProcess":["Double blind peer review"],"oaStart":2014} +{"journalTitle":"Journal of Economics Finance and Administrative Science","issn":"2077-1886","eissn":"2218-0648","reviewProcess":["Double blind peer review"],"oaStart":2017} +{"journalTitle":"Science Education International","issn":null,"eissn":"2077-2327","reviewProcess":["Double blind peer review"],"oaStart":2017} +{"journalTitle":"Edumecentro","issn":null,"eissn":"2077-2874","reviewProcess":["Double blind peer review"],"oaStart":2013} +{"journalTitle":"Monteverdia","issn":null,"eissn":"2077-2890","reviewProcess":["Double blind peer review"],"oaStart":2008} +{"journalTitle":"Transformación","issn":null,"eissn":"2077-2955","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","reviewProcess":["Double blind peer review"],"oaStart":2011} +{"journalTitle":"Revue de Primatologie","issn":null,"eissn":"2077-3757","reviewProcess":["Peer review"],"oaStart":2009} \ No newline at end of file From f25407bbe24016355e782b1d5d6e7ccb6e23be97 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Mar 2022 09:32:42 +0100 Subject: [PATCH 072/159] added mapping for datasource consent fields to integrate them in the graph --- .../graph/raw/MigrateDbEntitiesApplication.java | 3 +++ .../dnetlib/dhp/oa/graph/sql/queryDatasources.sql | 3 +++ .../raw/MigrateDbEntitiesApplicationTest.java | 3 +++ .../oa/graph/raw/datasources_resultset_entry.json | 15 +++++++++++++++ pom.xml | 2 +- 5 files changed, 25 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index e453f7918..1f8c23ac3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -309,6 +309,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setThematic(rs.getBoolean("thematic")); ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); + ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); + ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); + ds.setConsenttermsofusedate(rs.getDate("consenttermsofusedate").toString()); return Arrays.asList(ds); } catch (final Exception e) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql index 98092e882..2623c65c4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql @@ -89,6 +89,9 @@ SELECT d.issn AS issnPrinted, d.eissn AS issnOnline, d.lissn AS issnLinking, + d.consenttermsofuse AS consenttermsofuse, + d.fulltextdownload AS fulltextdownload, + d.consenttermsofusedate AS consenttermsofusedate, de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, de.thematic AS thematic, de.knowledge_graph AS knowledgegraph, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index b65bd9fd8..05ae5be74 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -100,6 +100,9 @@ public class MigrateDbEntitiesApplicationTest { assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); + assertEquals(true, ds.getConsenttermsofuse()); + assertEquals(true, ds.getFulltextdownload()); + assertEquals("2022-03-11", ds.getConsenttermsofusedate()); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json index 42b140306..11b884cde 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json @@ -268,5 +268,20 @@ "value": [ "Journal article@@@eosc:contentpolicies" ] + }, + { + "field": "consenttermsofuse", + "type": "boolean", + "value": true + }, + { + "field": "fulltextdownload", + "type": "boolean", + "value": true + }, + { + "field": "consenttermsofusedate", + "type": "date", + "value": "2022-03-11" } ] diff --git a/pom.xml b/pom.xml index 603a4cf1e..7a20a1652 100644 --- a/pom.xml +++ b/pom.xml @@ -797,7 +797,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.29] + [2.10.30-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 2b643059fa5627c42cc6d893d6a35afa8e4239cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 11 Mar 2022 13:56:48 +0100 Subject: [PATCH 073/159] [Country Propagation] changed the logic to get the collectedfrom at the result level. To fix issue when no instance is created for a result that should have the country associated. Change the code to use spark instead of hive to prepare the data needed for the propagation step. Added new tests for the intermediate steps and new verification for the propagation itself --- .../dhp/countrypropagation/CountrySbs.java | 7 ++ .../countrypropagation/DatasourceCountry.java | 7 ++ .../countrypropagation/EntityEntityRel.java | 32 +++++ .../PrepareDatasourceCountryAssociation.java | 78 ++++++------ .../PrepareResultCountrySet.java | 100 +++++++++------ .../SparkCountryPropagationJob.java | 44 +++---- .../input_countrypropagation_parameters.json | 6 - .../input_prepareassoc_parameters.json | 6 - ...input_prepareresultcountry_parameters.json | 6 +- .../CountryPropagationJobTest.java | 73 ++++++++++- .../DatasourceCountryPreparationTest.java | 111 +++++++++++++++++ .../ResultCountryPreparationTest.java | 115 ++++++++++++++++++ .../datasourcecountry/datasourcecountry | 3 + .../graph/datasource/datasource.json | 11 ++ .../graph/organization/organization | 8 ++ .../graph/publication/publication | 12 ++ .../graph/relation/relation.json | 24 ++++ .../software/software_10.json.gz | Bin .../preparedInfo/publication/resultCountrySet | 5 + .../{ => software}/preparedInfo.json.gz | Bin .../oa/provision/XmlRecordFactoryTest.java | 6 +- 21 files changed, 532 insertions(+), 122 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/organization/organization create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/publication/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/relation/relation.json rename dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/{sample => graph}/software/software_10.json.gz (100%) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet rename dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/{ => software}/preparedInfo.json.gz (100%) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java index 271cc6bb3..5dbd912cb 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java @@ -22,4 +22,11 @@ public class CountrySbs implements Serializable { public void setClassname(String classname) { this.classname = classname; } + + public static CountrySbs newInstance(String classid, String classname) { + CountrySbs csbs = new CountrySbs(); + csbs.classid = classid; + csbs.classname = classname; + return csbs; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java index 642192f73..4edc0f7a2 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java @@ -22,4 +22,11 @@ public class DatasourceCountry implements Serializable { public void setCountry(CountrySbs country) { this.country = country; } + + public static DatasourceCountry newInstance(String dataSourceId, CountrySbs country) { + DatasourceCountry dsc = new DatasourceCountry(); + dsc.dataSourceId = dataSourceId; + dsc.country = country; + return dsc; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java new file mode 100644 index 000000000..eece5a0b9 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.dhp.countrypropagation; + +import java.io.Serializable; + +public class EntityEntityRel implements Serializable { + private String entity1Id; + private String entity2Id; + + public static EntityEntityRel newInstance(String source, String target) { + EntityEntityRel dso = new EntityEntityRel(); + dso.entity1Id = source; + dso.entity2Id = target; + return dso; + } + + public String getEntity1Id() { + return entity1Id; + } + + public void setEntity1Id(String entity1Id) { + this.entity1Id = entity1Id; + } + + public String getEntity2Id() { + return entity2Id; + } + + public void setEntity2Id(String entity2Id) { + this.entity2Id = entity2Id; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index ddc7f93f7..c02f37015 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -2,14 +2,17 @@ package eu.dnetlib.dhp.countrypropagation; import static eu.dnetlib.dhp.PropagationConstant.*; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -21,7 +24,9 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; /** * For the association of the country to the datasource The association is computed only for datasource of specific type @@ -54,9 +59,8 @@ public class PrepareDatasourceCountryAssociation { log.info("outputPath {}: ", outputPath); SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + runWithSparkSession( conf, isSparkSessionManaged, spark -> { @@ -77,40 +81,46 @@ public class PrepareDatasourceCountryAssociation { String inputPath, String outputPath) { - final String whitelisted = whitelist - .stream() - .map(id -> " d.id = '" + id + "'") - .collect(Collectors.joining(" OR ")); + // filtering of the datasource taking only the non deleted by inference and those with the allowed types or + // whose id is in whitelist + Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class) + .filter( + (FilterFunction) ds -> !ds.getDataInfo().getDeletedbyinference() && + (allowedtypes.contains(ds.getDatasourcetype().getClassid()) || + whitelist.contains(ds.getId()))); - final String allowed = allowedtypes - .stream() - .map(type -> " d.datasourcetype.classid = '" + type + "'") - .collect(Collectors.joining(" OR ")); + // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass + Dataset relation = readPath(spark, inputPath + "/relation", Relation.class) + .filter( + (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && + !rel.getDataInfo().getDeletedbyinference()); - Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class); - Dataset relation = readPath(spark, inputPath + "/relation", Relation.class); - Dataset organization = readPath(spark, inputPath + "/organization", Organization.class); + // filtering of the organization taking only the non deleted by inference and those with information about the + // country + Dataset organization = readPath(spark, inputPath + "/organization", Organization.class) + .filter( + (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && + o.getCountry().getClassid().length() > 0 && + !o.getCountry().getClassid().equals(ModelConstants.UNKNOWN)) ; - datasource.createOrReplaceTempView("datasource"); - relation.createOrReplaceTempView("relation"); - organization.createOrReplaceTempView("organization"); + // associated the datasource id with the id of the organization providing the datasource + Dataset dse = datasource + .joinWith(relation, datasource.col("id").equalTo(relation.col("source"))) + .map( + (MapFunction, EntityEntityRel>) t2 -> EntityEntityRel + .newInstance(t2._2.getSource(), t2._2.getTarget()), + Encoders.bean(EntityEntityRel.class)); - String query = "SELECT source dataSourceId, " + - "named_struct('classid', country.classid, 'classname', country.classname) country " + - "FROM datasource d " + - "JOIN relation rel " + - "ON d.id = rel.source " + - "JOIN organization o " + - "ON o.id = rel.target " + - "WHERE rel.datainfo.deletedbyinference = false " + - "and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" + - "and o.datainfo.deletedbyinference = false " + - "and length(o.country.classid) > 0 " + - "and (" + allowed + " or " + whitelisted + ")"; - - spark - .sql(query) - .as(Encoders.bean(DatasourceCountry.class)) + // joins with the information stored in the organization dataset to associate the country to the datasource id + dse + .joinWith(organization, dse.col("entity2Id").equalTo(organization.col("id"))) + .map((MapFunction, DatasourceCountry>) t2 -> { + Qualifier country = t2._2.getCountry(); + return DatasourceCountry + .newInstance( + t2._1.getEntity1Id(), + CountrySbs.newInstance(country.getClassid(), country.getClassname())); + }, Encoders.bean(DatasourceCountry.class)) .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java index 77f7288f6..8ca87fa21 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java @@ -3,14 +3,21 @@ package eu.dnetlib.dhp.countrypropagation; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; import java.util.Set; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; import org.slf4j.Logger; @@ -23,14 +30,6 @@ import scala.Tuple2; public class PrepareResultCountrySet { private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); - private static final String RESULT_COUNTRYSET_QUERY = "SELECT id resultId, collect_set(country) countrySet " - + "FROM ( SELECT id, country " - + "FROM datasource_country JOIN cfhb ON cf = dataSourceId " - + "UNION ALL " - + "SELECT id, country FROM datasource_country " - + "JOIN cfhb ON hb = dataSourceId ) tmp " - + "GROUP BY id"; - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -45,6 +44,8 @@ public class PrepareResultCountrySet { Boolean isSparkSessionManaged = isSparkSessionManaged(parser); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + String workingPath = parser.get("workingPath"); + String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); @@ -60,9 +61,9 @@ public class PrepareResultCountrySet { Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + //conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + runWithSparkSession( conf, isSparkSessionManaged, spark -> { @@ -72,6 +73,7 @@ public class PrepareResultCountrySet { inputPath, outputPath, datasourcecountrypath, + workingPath, resultClazz); }); } @@ -81,43 +83,63 @@ public class PrepareResultCountrySet { String inputPath, String outputPath, String datasourcecountrypath, + String workingPath, Class resultClazz) { - Dataset result = readPath(spark, inputPath, resultClazz); - result.createOrReplaceTempView("result"); + // selects all the results non deleted by inference and non invisible + Dataset result = readPath(spark, inputPath, resultClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); - createCfHbforResult(spark); + // of the results collects the distinct keys for collected from (at the level of the result) and hosted by + // and produces pairs resultId, key for each distinct key associated to the result + result.flatMap((FlatMapFunction) r -> { + Set cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet()); + cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet())); + return cfhb + .stream() + .map(value -> EntityEntityRel.newInstance(r.getId(), value)) + .collect(Collectors.toList()) + .iterator(); + }, Encoders.bean(EntityEntityRel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/resultCfHb"); Dataset datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class); - datasource_country.createOrReplaceTempView("datasource_country"); - - spark - .sql(RESULT_COUNTRYSET_QUERY) - .as(Encoders.bean(ResultCountrySet.class)) - .toJavaRDD() - .mapToPair(value -> new Tuple2<>(value.getResultId(), value)) - .reduceByKey((a, b) -> { - ArrayList countryList = a.getCountrySet(); - Set countryCodes = countryList - .stream() - .map(CountrySbs::getClassid) - .collect(Collectors.toSet()); - b - .getCountrySet() - .stream() - .forEach(c -> { - if (!countryCodes.contains(c.getClassid())) { - countryList.add(c); - countryCodes.add(c.getClassid()); - } + Dataset cfhb = readPath(spark, workingPath + "/resultCfHb", EntityEntityRel.class); + datasource_country + .joinWith( + cfhb, cfhb + .col("entity2Id") + .equalTo(datasource_country.col("datasourceId"))) + .groupByKey( + (MapFunction, String>) t2 -> t2._2().getEntity1Id(), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, ResultCountrySet>) (k, it) -> { + ResultCountrySet rcs = new ResultCountrySet(); + rcs.setResultId(k); + Set set = new HashSet<>(); + Set countryCodes = new HashSet<>(); + DatasourceCountry first = it.next()._1(); + countryCodes.add(first.getCountry().getClassid()); + set.add(first.getCountry()); + it.forEachRemaining(t2 -> { + if (!countryCodes.contains(t2._1().getCountry().getClassid())) + set.add(t2._1().getCountry()); }); - a.setCountrySet(countryList); - return a; - }) - .map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2())) - .saveAsTextFile(outputPath, GzipCodec.class); + rcs.setCountrySet(new ArrayList<>(set)); + return rcs; + }, Encoders.bean(ResultCountrySet.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 4aa48583f..1bbfbdafd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -56,12 +56,6 @@ public class SparkCountryPropagationJob { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); - Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); @@ -75,8 +69,7 @@ public class SparkCountryPropagationJob { sourcePath, preparedInfoPath, outputPath, - resultClazz, - saveGraph); + resultClazz); }); } @@ -85,27 +78,26 @@ public class SparkCountryPropagationJob { String sourcePath, String preparedInfoPath, String outputPath, - Class resultClazz, - boolean saveGraph) { + Class resultClazz) { - if (saveGraph) { - log.info("Reading Graph table from: {}", sourcePath); - Dataset res = readPath(spark, sourcePath, resultClazz); - log.info("Reading prepared info: {}", preparedInfoPath); - Dataset prepared = spark - .read() - .json(preparedInfoPath) - .as(Encoders.bean(ResultCountrySet.class)); + log.info("Reading Graph table from: {}", sourcePath); + Dataset res = readPath(spark, sourcePath, resultClazz); + + log.info("Reading prepared info: {}", preparedInfoPath); + Dataset prepared = spark + .read() + .json(preparedInfoPath) + .as(Encoders.bean(ResultCountrySet.class)); + + res + .joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer") + .map(getCountryMergeFn(), Encoders.bean(resultClazz)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); - res - .joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer") - .map(getCountryMergeFn(), Encoders.bean(resultClazz)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - } } private static MapFunction, R> getCountryMergeFn() { diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json index 984b40774..e7a6bf5b0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json @@ -11,12 +11,6 @@ "paramDescription": "the hive metastore uris", "paramRequired": false }, - { - "paramName":"sg", - "paramLongName":"saveGraph", - "paramDescription": "true if the new version of the graph must be saved", - "paramRequired": false - }, { "paramName":"tn", "paramLongName":"resultTableName", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json index 95d4c1c60..a00105f2b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json @@ -5,12 +5,6 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", - "paramRequired": true - }, { "paramName": "out", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json index 5efa3dbd6..18163d1f9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json @@ -12,9 +12,9 @@ "paramRequired": true }, { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", + "paramName":"w", + "paramLongName":"workingPath", + "paramDescription": "the working path", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java index 963ee5529..e0688b430 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java @@ -7,6 +7,7 @@ import java.nio.file.Path; import java.util.ArrayList; import java.util.List; +import eu.dnetlib.dhp.schema.oaf.Publication; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -69,17 +70,16 @@ public class CountryPropagationJobTest { @Test void testCountryPropagationSoftware() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software") + .getResource("/eu/dnetlib/dhp/countrypropagation/graph/software") .getPath(); final String preparedInfoPath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo") + .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/software") .getPath(); SparkCountryPropagationJob .main( new String[] { "--isSparkSessionManaged", Boolean.FALSE.toString(), "--sourcePath", sourcePath, - "-saveGraph", "true", "-resultTableName", Software.class.getCanonicalName(), "-outputPath", workingDir.toString() + "/software", "-preparedInfoPath", preparedInfoPath @@ -91,8 +91,6 @@ public class CountryPropagationJobTest { .textFile(workingDir.toString() + "/software") .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); - // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); - Assertions.assertEquals(10, tmp.count()); Dataset verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); @@ -259,4 +257,69 @@ public class CountryPropagationJobTest { 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count()); } + @Test + void testCountryPropagationPublication() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") + .getPath(); + final String preparedInfoPath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication") + .getPath(); + SparkCountryPropagationJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "-resultTableName", Publication.class.getCanonicalName(), + "-outputPath", workingDir.toString() + "/publication", + "-preparedInfoPath", preparedInfoPath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(12, tmp.count()); + + Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count()); + + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid()))); + tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename()))); + + List countries = tmp.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0).getCountry(); + Assertions.assertEquals(1, countries.size()); + Assertions.assertEquals("NL",countries.get(0).getClassid()); + Assertions.assertEquals("Netherlands",countries.get(0).getClassname()); + + countries = tmp.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0).getCountry(); + Assertions.assertEquals(1, countries.size()); + Assertions.assertEquals("NL",countries.get(0).getClassid()); + Assertions.assertEquals("Netherlands",countries.get(0).getClassname()); + + countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0).getCountry(); + Assertions.assertEquals(2, countries.size()); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + + countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0).getCountry(); + Assertions.assertEquals(2, countries.size()); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); + + countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0).getCountry(); + Assertions.assertEquals(2, countries.size()); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + } + } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java new file mode 100644 index 000000000..8560a9d66 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java @@ -0,0 +1,111 @@ +package eu.dnetlib.dhp.countrypropagation; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; + +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + + +public class DatasourceCountryPreparationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName()); + + SparkConf conf = new SparkConf(); + conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DatasourceCountryPreparationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testPrepareDatasourceCountry() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/graph") + .getPath(); + + PrepareDatasourceCountryAssociation + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "--outputPath", workingDir.toString() + "/datasourceCountry", + "--allowedtypes","pubsrepository::institutional" , + "--whitelist","10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/datasourceCountry") + .map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class)); + + Assertions.assertEquals(3, tmp.count()); + Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).count()); + Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).count()); + Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).count()); + + Assertions.assertEquals("NL", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect() + .get(0).getCountry().getClassid()); + Assertions.assertEquals("Netherlands", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect() + .get(0).getCountry().getClassname()); + + Assertions.assertEquals("IT", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect() + .get(0).getCountry().getClassid()); + Assertions.assertEquals("Italy", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect() + .get(0).getCountry().getClassname()); + + Assertions.assertEquals("FR", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect() + .get(0).getCountry().getClassid()); + Assertions.assertEquals("France", tmp.filter(dsc -> dsc.getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect() + .get(0).getCountry().getClassname()); + + tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e))); + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java new file mode 100644 index 000000000..37cc4f342 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java @@ -0,0 +1,115 @@ +package eu.dnetlib.dhp.countrypropagation; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Publication; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged; + +public class ResultCountryPreparationTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName()); + + SparkConf conf = new SparkConf(); + conf.setAppName(ResultCountryPreparationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(ResultCountryPreparationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testPrepareResultCountry() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") + .getPath(); + + final String preparedInfoPath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry") + .getPath(); + + + PrepareResultCountrySet + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--workingPath", workingDir.toString() + "/working", + "--sourcePath", sourcePath, + "--outputPath", workingDir.toString() + "/resultCountry", + "--preparedInfoPath", preparedInfoPath, + "--resultTableName", Publication.class.getCanonicalName() + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/resultCountry") + .map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class)); + + + Assertions.assertEquals(5, tmp.count()); + + ResultCountrySet rc = tmp.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0); + Assertions.assertEquals(1, rc.getCountrySet().size()); + Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid()); + Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname()); + + rc = tmp.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0); + Assertions.assertEquals(1, rc.getCountrySet().size()); + Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid()); + Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname()); + + rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + + rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); + + + rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry new file mode 100644 index 000000000..ac31abfbd --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry @@ -0,0 +1,3 @@ +{"dataSourceId":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","country":{"classid":"NL","classname":"Netherlands"}} +{"dataSourceId":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","country":{"classid":"IT","classname":"Italy"}} +{"dataSourceId":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","country":{"classid":"FR","classname":"France"}} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json new file mode 100644 index 000000000..6b71024fd --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json @@ -0,0 +1,11 @@ +{"accessinfopackage":[],"collectedfrom":[{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"}],"contentpolicies":[{"classid":"Journal 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The work is carried out on a laboratory scale using local geo-materials sorbents, on the one hand the residues from the treatment of natural phosphorite of Hahotoé-Kpogamé and on the other hand the attapulgite clay mineral from the costal basin of Togo. The work carried out concerns the adsorption of fluoride on those sorbents. The following parameters are batch tested on synthetic fluoride solutions: time, solution pH, geo-material dose and fluoride concentration. The fluoride is analyzed by absorption spectrometry. The adsorption yields on the phosphorite treatment residues for aqueous fluoride solutions at an initial concentration of 10 mg/L and an adsorbent concentration of 10 g/L are 49 % at pH 6.5 and 66 % at pH 4.0. In the same experimental conditions, the yields on clay minerals are 28.2 % and 36.3 %. These yields are logically improved by increasing the adsorbent dosage (from 2 to 30 g/L). 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Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.

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Ex situ analyses of the tiles were performed by secondary ion mass spectrometry.
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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/sample/software/software_10.json.gz b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/software/software_10.json.gz similarity index 100% rename from dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/sample/software/software_10.json.gz rename to dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/software/software_10.json.gz diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet new file mode 100644 index 000000000..87ba23aeb --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet @@ -0,0 +1,5 @@ +{"resultId":"50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b","countrySet":[{"classid":"NL","classname":"Netherlands"}]} +{"resultId":"50|355e65625b88::54a1c76f520bb2c8da27d12e42891088","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]} +{"resultId":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","countrySet":[{"classid":"NL","classname":"Netherlands"}]} +{"resultId":"50|355e65625b88::74009c567c81b4aa55c813db658734df","countrySet":[{"classid":"NL","classname":"Netherlands"},{"classid":"IT","classname":"Italy"}]} +{"resultId":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/preparedInfo.json.gz b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/software/preparedInfo.json.gz similarity index 100% rename from dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/preparedInfo.json.gz rename to dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/software/preparedInfo.json.gz diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 2142737f0..273132bff 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -8,7 +8,6 @@ import java.io.IOException; import java.io.StringReader; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.Datasource; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; @@ -24,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -146,10 +146,10 @@ public class XmlRecordFactoryTest { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, - XmlConverterJob.schemaLocation); + XmlConverterJob.schemaLocation); final Datasource d = OBJECT_MAPPER - .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); + .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); final String xml = xmlRecordFactory.build(new JoinedEntity<>(d)); From 4437f9345d2430b0bac9edab129603b90dfd379b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 11 Mar 2022 13:57:47 +0100 Subject: [PATCH 074/159] [Country Propagation] left out from previous commit --- .../dhp/countrypropagation/CountryPropagationJobTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java index e0688b430..50c7f3a69 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java @@ -315,7 +315,7 @@ public class CountryPropagationJobTest { Assertions.assertEquals(2, countries.size()); Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); - + countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0).getCountry(); Assertions.assertEquals(2, countries.size()); Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); From 12de9acb0da61cc83e4178a7d6619722532d97fd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 11 Mar 2022 14:17:02 +0100 Subject: [PATCH 075/159] [Country Propagation] left out from previous commit --- .../PrepareDatasourceCountryAssociation.java | 7 +- .../PrepareResultCountrySet.java | 2 +- .../SparkCountryPropagationJob.java | 1 - .../CountryPropagationJobTest.java | 152 +++++++++--- .../DatasourceCountryPreparationTest.java | 219 ++++++++++++------ .../ResultCountryPreparationTest.java | 201 +++++++++------- 6 files changed, 383 insertions(+), 199 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index c02f37015..42b7804ea 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; -import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -20,6 +19,8 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -100,8 +101,8 @@ public class PrepareDatasourceCountryAssociation { Dataset organization = readPath(spark, inputPath + "/organization", Organization.class) .filter( (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && - o.getCountry().getClassid().length() > 0 && - !o.getCountry().getClassid().equals(ModelConstants.UNKNOWN)) ; + o.getCountry().getClassid().length() > 0 && + !o.getCountry().getClassid().equals(ModelConstants.UNKNOWN)); // associated the datasource id with the id of the organization providing the datasource Dataset dse = datasource diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java index 8ca87fa21..560a22381 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java @@ -61,7 +61,7 @@ public class PrepareResultCountrySet { Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); - //conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + // conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); runWithSparkSession( conf, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 1bbfbdafd..56aa953b4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -80,7 +80,6 @@ public class SparkCountryPropagationJob { String outputPath, Class resultClazz) { - log.info("Reading Graph table from: {}", sourcePath); Dataset res = readPath(spark, sourcePath, resultClazz); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java index 50c7f3a69..c4141b3e8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java @@ -7,7 +7,6 @@ import java.nio.file.Path; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.Publication; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -25,6 +24,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Country; +import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Software; import scala.Tuple2; @@ -260,66 +260,142 @@ public class CountryPropagationJobTest { @Test void testCountryPropagationPublication() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") - .getPath(); + .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") + .getPath(); final String preparedInfoPath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication") - .getPath(); + .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication") + .getPath(); SparkCountryPropagationJob - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--sourcePath", sourcePath, - "-resultTableName", Publication.class.getCanonicalName(), - "-outputPath", workingDir.toString() + "/publication", - "-preparedInfoPath", preparedInfoPath - }); + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "-resultTableName", Publication.class.getCanonicalName(), + "-outputPath", workingDir.toString() + "/publication", + "-preparedInfoPath", preparedInfoPath + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); Assertions.assertEquals(12, tmp.count()); Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count()); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference()))); + tmp + .foreach( + r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference()))); tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible()))); tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid()))); - tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename()))); + tmp + .foreach( + r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach( + c -> Assertions + .assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach( + c -> Assertions + .assertEquals( + "dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid()))); + tmp + .foreach( + r -> r + .getCountry() + .stream() + .forEach( + c -> Assertions + .assertEquals( + "dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename()))); - List countries = tmp.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0).getCountry(); + List countries = tmp + .filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")) + .collect() + .get(0) + .getCountry(); Assertions.assertEquals(1, countries.size()); - Assertions.assertEquals("NL",countries.get(0).getClassid()); - Assertions.assertEquals("Netherlands",countries.get(0).getClassname()); + Assertions.assertEquals("NL", countries.get(0).getClassid()); + Assertions.assertEquals("Netherlands", countries.get(0).getClassname()); - countries = tmp.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0).getCountry(); + countries = tmp + .filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")) + .collect() + .get(0) + .getCountry(); Assertions.assertEquals(1, countries.size()); - Assertions.assertEquals("NL",countries.get(0).getClassid()); - Assertions.assertEquals("Netherlands",countries.get(0).getClassname()); + Assertions.assertEquals("NL", countries.get(0).getClassid()); + Assertions.assertEquals("Netherlands", countries.get(0).getClassname()); - countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0).getCountry(); + countries = tmp + .filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")) + .collect() + .get(0) + .getCountry(); Assertions.assertEquals(2, countries.size()); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + Assertions + .assertTrue( + countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); - countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0).getCountry(); + countries = tmp + .filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")) + .collect() + .get(0) + .getCountry(); Assertions.assertEquals(2, countries.size()); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); + Assertions + .assertTrue( + countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + countries + .stream() + .anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); - countries = tmp.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0).getCountry(); + countries = tmp + .filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")) + .collect() + .get(0) + .getCountry(); Assertions.assertEquals(2, countries.size()); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + Assertions + .assertTrue( + countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java index 8560a9d66..d9b879de8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java @@ -1,111 +1,176 @@ + package eu.dnetlib.dhp.countrypropagation; -import com.fasterxml.jackson.databind.ObjectMapper; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; - import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - +import com.fasterxml.jackson.databind.ObjectMapper; public class DatasourceCountryPreparationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName()); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName()); - SparkConf conf = new SparkConf(); - conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DatasourceCountryPreparationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(DatasourceCountryPreparationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - void testPrepareDatasourceCountry() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/graph") - .getPath(); + @Test + void testPrepareDatasourceCountry() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/graph") + .getPath(); - PrepareDatasourceCountryAssociation - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--sourcePath", sourcePath, - "--outputPath", workingDir.toString() + "/datasourceCountry", - "--allowedtypes","pubsrepository::institutional" , - "--whitelist","10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48" - }); + PrepareDatasourceCountryAssociation + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "--outputPath", workingDir.toString() + "/datasourceCountry", + "--allowedtypes", "pubsrepository::institutional", + "--whitelist", + "10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48" + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/datasourceCountry") - .map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/datasourceCountry") + .map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class)); - Assertions.assertEquals(3, tmp.count()); - Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).count()); - Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).count()); - Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).count()); + Assertions.assertEquals(3, tmp.count()); + Assertions + .assertEquals( + 1, tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")) + .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")) + .count()); + Assertions + .assertEquals( + 1, tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")) + .count()); - Assertions.assertEquals("NL", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect() - .get(0).getCountry().getClassid()); - Assertions.assertEquals("Netherlands", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect() - .get(0).getCountry().getClassname()); + Assertions + .assertEquals( + "NL", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")) + .collect() + .get(0) + .getCountry() + .getClassid()); + Assertions + .assertEquals( + "Netherlands", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")) + .collect() + .get(0) + .getCountry() + .getClassname()); - Assertions.assertEquals("IT", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect() - .get(0).getCountry().getClassid()); - Assertions.assertEquals("Italy", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect() - .get(0).getCountry().getClassname()); + Assertions + .assertEquals( + "IT", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")) + .collect() + .get(0) + .getCountry() + .getClassid()); + Assertions + .assertEquals( + "Italy", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")) + .collect() + .get(0) + .getCountry() + .getClassname()); - Assertions.assertEquals("FR", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect() - .get(0).getCountry().getClassid()); - Assertions.assertEquals("France", tmp.filter(dsc -> dsc.getDataSourceId() - .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect() - .get(0).getCountry().getClassname()); + Assertions + .assertEquals( + "FR", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")) + .collect() + .get(0) + .getCountry() + .getClassid()); + Assertions + .assertEquals( + "France", tmp + .filter( + dsc -> dsc + .getDataSourceId() + .equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")) + .collect() + .get(0) + .getCountry() + .getClassname()); - tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e))); + tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e))); - } + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java index 37cc4f342..797d1c979 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java @@ -1,8 +1,12 @@ + package eu.dnetlib.dhp.countrypropagation; -import com.fasterxml.jackson.databind.ObjectMapper; +import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; -import eu.dnetlib.dhp.schema.oaf.Publication; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -13,103 +17,142 @@ import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged; +import eu.dnetlib.dhp.schema.oaf.Publication; public class ResultCountryPreparationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName()); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName()); - SparkConf conf = new SparkConf(); - conf.setAppName(ResultCountryPreparationTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(ResultCountryPreparationTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(ResultCountryPreparationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(ResultCountryPreparationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - void testPrepareResultCountry() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") - .getPath(); + @Test + void testPrepareResultCountry() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication") + .getPath(); - final String preparedInfoPath = getClass() - .getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry") - .getPath(); + final String preparedInfoPath = getClass() + .getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry") + .getPath(); + PrepareResultCountrySet + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--workingPath", workingDir.toString() + "/working", + "--sourcePath", sourcePath, + "--outputPath", workingDir.toString() + "/resultCountry", + "--preparedInfoPath", preparedInfoPath, + "--resultTableName", Publication.class.getCanonicalName() + }); - PrepareResultCountrySet - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--workingPath", workingDir.toString() + "/working", - "--sourcePath", sourcePath, - "--outputPath", workingDir.toString() + "/resultCountry", - "--preparedInfoPath", preparedInfoPath, - "--resultTableName", Publication.class.getCanonicalName() - }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/resultCountry") + .map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class)); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/resultCountry") - .map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class)); + Assertions.assertEquals(5, tmp.count()); + ResultCountrySet rc = tmp + .filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")) + .collect() + .get(0); + Assertions.assertEquals(1, rc.getCountrySet().size()); + Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid()); + Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname()); - Assertions.assertEquals(5, tmp.count()); + rc = tmp + .filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")) + .collect() + .get(0); + Assertions.assertEquals(1, rc.getCountrySet().size()); + Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid()); + Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname()); - ResultCountrySet rc = tmp.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0); - Assertions.assertEquals(1, rc.getCountrySet().size()); - Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid()); - Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname()); + rc = tmp + .filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")) + .collect() + .get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); - rc = tmp.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0); - Assertions.assertEquals(1, rc.getCountrySet().size()); - Assertions.assertEquals("NL",rc.getCountrySet().get(0).getClassid()); - Assertions.assertEquals("Netherlands",rc.getCountrySet().get(0).getClassname()); + rc = tmp + .filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")) + .collect() + .get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); - rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0); - Assertions.assertEquals(2, rc.getCountrySet().size()); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); + rc = tmp + .filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")) + .collect() + .get(0); + Assertions.assertEquals(2, rc.getCountrySet().size()); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); + Assertions + .assertTrue( + rc + .getCountrySet() + .stream() + .anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); - rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0); - Assertions.assertEquals(2, rc.getCountrySet().size()); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands"))); - - - rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0); - Assertions.assertEquals(2, rc.getCountrySet().size()); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy"))); - Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France"))); - - - } + } } From f430029596f5630461e03bb51719033499345e0e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Mar 2022 14:28:28 +0100 Subject: [PATCH 076/159] cleanup --- .../dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java index 560a22381..28b6f616d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java @@ -61,7 +61,6 @@ public class PrepareResultCountrySet { Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); - // conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); runWithSparkSession( conf, From 0f7d8ca2e0ab06528d68f785894dac936a359e07 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 11 Mar 2022 15:16:02 +0100 Subject: [PATCH 077/159] [HostedByMap] change on master to align to PR 201 on beta merged as 9f3036c847 --- .../common/collection/DecompressTarGz.java | 39 +++ .../crossref/ExtractCrossrefRecords.java | 31 +-- .../dhp/oa/graph/hostedbymap/DownloadCSV.java | 27 +- .../oa/graph/hostedbymap/DownloadCSV2.java | 84 ------ .../hostedbymap/ExtractAndMapDoajJson.java | 116 ++++++++ .../oa/graph/hostedbymap/model/DOAJModel.java | 17 +- .../oa/graph/hostedbymap/model/doaj/APC.java | 35 +++ .../graph/hostedbymap/model/doaj/Admin.java | 25 ++ .../graph/hostedbymap/model/doaj/Article.java | 44 +++ .../graph/hostedbymap/model/doaj/BibJson.java | 253 ++++++++++++++++++ .../hostedbymap/model/doaj/Copyright.java | 25 ++ .../hostedbymap/model/doaj/DOAJEntry.java | 52 ++++ .../hostedbymap/model/doaj/DepositPolicy.java | 35 +++ .../hostedbymap/model/doaj/Editorial.java | 35 +++ .../hostedbymap/model/doaj/Institution.java | 25 ++ .../graph/hostedbymap/model/doaj/License.java | 67 +++++ .../oa/graph/hostedbymap/model/doaj/Max.java | 25 ++ .../hostedbymap/model/doaj/OtherCharges.java | 25 ++ .../hostedbymap/model/doaj/PidScheme.java | 26 ++ .../hostedbymap/model/doaj/Plagiarism.java | 27 ++ .../hostedbymap/model/doaj/Preservation.java | 44 +++ .../hostedbymap/model/doaj/Publisher.java | 25 ++ .../oa/graph/hostedbymap/model/doaj/Ref.java | 52 ++++ .../graph/hostedbymap/model/doaj/Subject.java | 34 +++ .../graph/hostedbymap/model/doaj/Waiver.java | 25 ++ .../graph/hostedbymap/oozie_app/workflow.xml | 101 +++++-- .../hostedbymap/SparkProduceHostedByMap.scala | 8 +- .../oa/graph/hostedbymap/DownloadCsvTest.java | 51 ---- .../graph/hostedbymap/doaj_transformed.json | 50 ++-- 29 files changed, 1170 insertions(+), 233 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java new file mode 100644 index 000000000..49126984c --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java @@ -0,0 +1,39 @@ +package eu.dnetlib.dhp.common.collection; + +import java.io.BufferedOutputStream; +import java.io.IOException; +import java.util.zip.GZIPOutputStream; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +public class DecompressTarGz { + + public static void doExtract(FileSystem fs, String outputPath, String tarGzPath) throws IOException { + + FSDataInputStream inputFileStream = fs.open(new Path(tarGzPath)); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(inputFileStream))) { + TarArchiveEntry entry = null; + while ((entry = tais.getNextTarEntry()) != null) { + if (!entry.isDirectory()) { + try ( + FSDataOutputStream out = fs + .create(new Path(outputPath.concat(entry.getName()).concat(".gz"))); + GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { + + IOUtils.copy(tais, gzipOs); + + } + + } + } + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java index d1861ff0a..6060b619e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ExtractCrossrefRecords.java @@ -1,19 +1,13 @@ package eu.dnetlib.doiboost.crossref; -import java.io.BufferedOutputStream; -import java.net.URI; -import java.util.zip.GZIPOutputStream; +import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract; + +import java.net.URI; -import org.apache.commons.compress.archivers.tar.TarArchiveEntry; -import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; -import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataInputStream; -import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; import org.mortbay.log.Log; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -33,31 +27,16 @@ public class ExtractCrossrefRecords { final String outputPath = parser.get("outputPath"); final String crossrefFileNameTarGz = parser.get("crossrefFileNameTarGz"); - Path hdfsreadpath = new Path(workingPath.concat("/").concat(crossrefFileNameTarGz)); Configuration conf = new Configuration(); conf.set("fs.defaultFS", workingPath); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); FileSystem fs = FileSystem.get(URI.create(workingPath), conf); - FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath); - try (TarArchiveInputStream tais = new TarArchiveInputStream( - new GzipCompressorInputStream(crossrefFileStream))) { - TarArchiveEntry entry = null; - while ((entry = tais.getNextTarEntry()) != null) { - if (!entry.isDirectory()) { - try ( - FSDataOutputStream out = fs - .create(new Path(outputPath.concat(entry.getName()).concat(".gz"))); - GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { - IOUtils.copy(tais, gzipOs); + doExtract(fs, outputPath, workingPath.concat("/").concat(crossrefFileNameTarGz)); - } - - } - } - } Log.info("Crossref dump reading completed"); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java index dff761c34..bbadde524 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java @@ -23,7 +23,7 @@ public class DownloadCSV { private static final Logger log = LoggerFactory.getLogger(DownloadCSV.class); - public static final char DEFAULT_DELIMITER = ';'; + public static final char DEFAULT_DELIMITER = ','; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -40,9 +40,6 @@ public class DownloadCSV { final String fileURL = parser.get("fileURL"); log.info("fileURL {}", fileURL); - final String workingPath = parser.get("workingPath"); - log.info("workingPath {}", workingPath); - final String outputFile = parser.get("outputFile"); log.info("outputFile {}", outputFile); @@ -63,31 +60,15 @@ public class DownloadCSV { FileSystem fileSystem = FileSystem.get(conf); - new DownloadCSV().doDownload(fileURL, workingPath, outputFile, classForName, delimiter, fileSystem); + new DownloadCSV().doDownload(fileURL, outputFile, classForName, delimiter, fileSystem); } - protected void doDownload(String fileURL, String workingPath, String outputFile, String classForName, + protected void doDownload(String fileURL, String outputFile, String classForName, char delimiter, FileSystem fs) throws IOException, ClassNotFoundException, CollectorException { - final HttpConnector2 connector2 = new HttpConnector2(); - - final Path path = new Path(workingPath + "/replaced.csv"); - - try (BufferedReader in = new BufferedReader( - new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) { - - try (PrintWriter writer = new PrintWriter( - new OutputStreamWriter(fs.create(path, true), StandardCharsets.UTF_8))) { - String line; - while ((line = in.readLine()) != null) { - writer.println(line.replace("\\\"", "\"")); - } - } - } - - try (InputStreamReader reader = new InputStreamReader(fs.open(path))) { + try (InputStreamReader reader = new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL))) { GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java deleted file mode 100644 index d82d00862..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV2.java +++ /dev/null @@ -1,84 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.hostedbymap; - -import java.io.*; -import java.util.Objects; -import java.util.Optional; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.collection.GetCSV; -import eu.dnetlib.dhp.common.collection.HttpConnector2; - -public class DownloadCSV2 { - - private static final Logger log = LoggerFactory.getLogger(DownloadCSV2.class); - - public static final char DEFAULT_DELIMITER = ';'; - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - Objects - .requireNonNull( - DownloadCSV2.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json")))); - - parser.parseArgument(args); - - final String fileURL = parser.get("fileURL"); - log.info("fileURL {}", fileURL); - - final String tmpFile = parser.get("tmpFile"); - log.info("tmpFile {}", tmpFile); - - final String outputFile = parser.get("outputFile"); - log.info("outputFile {}", outputFile); - - final String hdfsNameNode = parser.get("hdfsNameNode"); - log.info("hdfsNameNode {}", hdfsNameNode); - - final String classForName = parser.get("classForName"); - log.info("classForName {}", classForName); - - final char delimiter = Optional - .ofNullable(parser.get("delimiter")) - .map(s -> s.charAt(0)) - .orElse(DEFAULT_DELIMITER); - log.info("delimiter {}", delimiter); - - HttpConnector2 connector2 = new HttpConnector2(); - - try (BufferedReader in = new BufferedReader( - new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) { - - try (PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(tmpFile)))) { - String line; - while ((line = in.readLine()) != null) { - writer.println(line.replace("\\\"", "\"")); - } - } - } - - try (BufferedReader in = new BufferedReader(new FileReader(tmpFile))) { - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - GetCSV.getCsv(fileSystem, in, outputFile, classForName, delimiter); - } finally { - FileUtils.deleteQuietly(new File(tmpFile)); - } - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java new file mode 100644 index 000000000..b3a79e147 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java @@ -0,0 +1,116 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap; + +import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract; + +import java.io.BufferedOutputStream; +import java.io.IOException; +import java.io.PrintWriter; +import java.util.Arrays; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.CompressionInputStream; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel; +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj.DOAJEntry; + +public class ExtractAndMapDoajJson { + + private static final Logger log = LoggerFactory.getLogger(ExtractAndMapDoajJson.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + ExtractAndMapDoajJson.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json")))); + + parser.parseArgument(args); + + final String compressedInput = parser.get("compressedFile"); + log.info("compressedInput {}", compressedInput); + + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode {}", hdfsNameNode); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + final String workingPath = parser.get("workingPath"); + log.info("workingPath {}", workingPath); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fs = FileSystem.get(conf); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); + doExtract(fs, workingPath, compressedInput); + doMap(fs, workingPath, outputPath, codec); + + } + + private static void doMap(FileSystem fs, String workingPath, String outputPath, CompressionCodec codec) + throws IOException { + RemoteIterator fileStatusListIterator = fs + .listFiles( + new Path(workingPath), true); + + Path hdfsWritePath = new Path(outputPath); + if (fs.exists(hdfsWritePath)) { + fs.delete(hdfsWritePath, true); + + } + try ( + + FSDataOutputStream out = fs + .create(hdfsWritePath); + PrintWriter writer = new PrintWriter(new BufferedOutputStream(out))) { + + while (fileStatusListIterator.hasNext()) { + Path path = fileStatusListIterator.next().getPath(); + if (!fs.isDirectory(path)) { + FSDataInputStream is = fs.open(path); + CompressionInputStream compressionInputStream = codec.createInputStream(is); + DOAJEntry[] doajEntries = new ObjectMapper().readValue(compressionInputStream, DOAJEntry[].class); + Arrays.stream(doajEntries).forEach(doaj -> { + try { + writer.println(new ObjectMapper().writeValueAsString(getDoajModel(doaj))); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + } + + } + + } + + } + + @NotNull + public static DOAJModel getDoajModel(DOAJEntry doaj) { + DOAJModel doajModel = new DOAJModel(); + doajModel.setOaStart(doaj.getBibjson().getOa_start()); + doajModel.setEissn(doaj.getBibjson().getEissn()); + doajModel.setIssn(doaj.getBibjson().getPissn()); + doajModel.setJournalTitle(doaj.getBibjson().getTitle()); + doajModel.setReviewProcess(doaj.getBibjson().getEditorial().getReview_process()); + return doajModel; + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java index 4b5dc22a6..c3b6f1f30 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model; import java.io.Serializable; +import java.util.List; import com.opencsv.bean.CsvBindByName; @@ -17,7 +18,17 @@ public class DOAJModel implements Serializable { private String eissn; @CsvBindByName(column = "Review process") - private String reviewProcess; + private List reviewProcess; + + private Integer oaStart; + + public Integer getOaStart() { + return oaStart; + } + + public void setOaStart(Integer oaStart) { + this.oaStart = oaStart; + } public String getJournalTitle() { return journalTitle; @@ -43,11 +54,11 @@ public class DOAJModel implements Serializable { this.eissn = eissn; } - public String getReviewProcess() { + public List getReviewProcess() { return reviewProcess; } - public void setReviewProcess(String reviewProcess) { + public void setReviewProcess(List reviewProcess) { this.reviewProcess = reviewProcess; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java new file mode 100644 index 000000000..3473e0f9d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/APC.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class APC implements Serializable { + private Boolean has_apc; + private String url; + private List max; + + public List getMax() { + return max; + } + + public void setMax(List max) { + this.max = max; + } + + public Boolean getHas_apc() { + return has_apc; + } + + public void setHas_apc(Boolean has_apc) { + this.has_apc = has_apc; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java new file mode 100644 index 000000000..b823e3450 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Admin.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Admin implements Serializable { + private Boolean ticked; + private Boolean seal; + + public Boolean getTicked() { + return ticked; + } + + public void setTicked(Boolean ticked) { + this.ticked = ticked; + } + + public Boolean getSeal() { + return seal; + } + + public void setSeal(Boolean seal) { + this.seal = seal; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java new file mode 100644 index 000000000..7e90e24a2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Article.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Article implements Serializable { + private String license_display_example_url; + private List license_display; + private Boolean orcid; + private Boolean i4oc_open_citations; + + public String getLicense_display_example_url() { + return license_display_example_url; + } + + public void setLicense_display_example_url(String license_display_example_url) { + this.license_display_example_url = license_display_example_url; + } + + public List getLicense_display() { + return license_display; + } + + public void setLicense_display(List license_display) { + this.license_display = license_display; + } + + public Boolean getOrcid() { + return orcid; + } + + public void setOrcid(Boolean orcid) { + this.orcid = orcid; + } + + public Boolean getI4oc_open_citations() { + return i4oc_open_citations; + } + + public void setI4oc_open_citations(Boolean i4oc_open_citations) { + this.i4oc_open_citations = i4oc_open_citations; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java new file mode 100644 index 000000000..f7c0d501f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java @@ -0,0 +1,253 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +public class BibJson implements Serializable { + private Editorial editorial; + private PidScheme pid_scheme; + private Copyright copyright; + private List keywords; + private Plagiarism plagiarism; + private List subject; + private String eissn; + private String pissn; + private List language; + private String title; + private Article article; + private Institution institution; + private Preservation preservation; + private List license; + private Ref ref; + private Integer oa_start; + private APC apc; + private OtherCharges other_charges; + private Integer publication_time_weeks; + private DepositPolicy deposit_policy; + private Publisher publisher; + private Boolean boai; + private Waiver waiver; + private String alternative_title; + private List is_replaced_by; + private List replaces; + private String discontinued_date; + + public String getDiscontinued_date() { + return discontinued_date; + } + + public void setDiscontinued_date(String discontinued_date) { + this.discontinued_date = discontinued_date; + } + + public List getReplaces() { + return replaces; + } + + public void setReplaces(List replaces) { + this.replaces = replaces; + } + + public List getIs_replaced_by() { + return is_replaced_by; + } + + public void setIs_replaced_by(List is_replaced_by) { + this.is_replaced_by = is_replaced_by; + } + + public String getAlternative_title() { + return alternative_title; + } + + public void setAlternative_title(String alternative_title) { + this.alternative_title = alternative_title; + } + + public String getPissn() { + return pissn; + } + + public void setPissn(String pissn) { + this.pissn = pissn; + } + + public Editorial getEditorial() { + return editorial; + } + + public void setEditorial(Editorial editorial) { + this.editorial = editorial; + } + + public PidScheme getPid_scheme() { + return pid_scheme; + } + + public void setPid_scheme(PidScheme pid_scheme) { + this.pid_scheme = pid_scheme; + } + + public Copyright getCopyright() { + return copyright; + } + + public void setCopyright(Copyright copyright) { + this.copyright = copyright; + } + + public List getKeywords() { + return keywords; + } + + public void setKeywords(List keywords) { + this.keywords = keywords; + } + + public Plagiarism getPlagiarism() { + return plagiarism; + } + + public void setPlagiarism(Plagiarism plagiarism) { + this.plagiarism = plagiarism; + } + + public List getSubject() { + return subject; + } + + public void setSubject(List subject) { + this.subject = subject; + } + + public String getEissn() { + return eissn; + } + + public void setEissn(String eissn) { + this.eissn = eissn; + } + + public List getLanguage() { + return language; + } + + public void setLanguage(List language) { + this.language = language; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public Article getArticle() { + return article; + } + + public void setArticle(Article article) { + this.article = article; + } + + public Institution getInstitution() { + return institution; + } + + public void setInstitution(Institution institution) { + this.institution = institution; + } + + public Preservation getPreservation() { + return preservation; + } + + public void setPreservation(Preservation preservation) { + this.preservation = preservation; + } + + public List getLicense() { + return license; + } + + public void setLicense(List license) { + this.license = license; + } + + public Ref getRef() { + return ref; + } + + public void setRef(Ref ref) { + this.ref = ref; + } + + public Integer getOa_start() { + return oa_start; + } + + public void setOa_start(Integer oa_start) { + this.oa_start = oa_start; + } + + public APC getApc() { + return apc; + } + + public void setApc(APC apc) { + this.apc = apc; + } + + public OtherCharges getOther_charges() { + return other_charges; + } + + public void setOther_charges(OtherCharges other_charges) { + this.other_charges = other_charges; + } + + public Integer getPublication_time_weeks() { + return publication_time_weeks; + } + + public void setPublication_time_weeks(Integer publication_time_weeks) { + this.publication_time_weeks = publication_time_weeks; + } + + public DepositPolicy getDeposit_policy() { + return deposit_policy; + } + + public void setDeposit_policy(DepositPolicy deposit_policy) { + this.deposit_policy = deposit_policy; + } + + public Publisher getPublisher() { + return publisher; + } + + public void setPublisher(Publisher publisher) { + this.publisher = publisher; + } + + public Boolean getBoai() { + return boai; + } + + public void setBoai(Boolean boai) { + this.boai = boai; + } + + public Waiver getWaiver() { + return waiver; + } + + public void setWaiver(Waiver waiver) { + this.waiver = waiver; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java new file mode 100644 index 000000000..c595c4c88 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Copyright.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Copyright implements Serializable { + private Boolean author_retains; + private String url; + + public Boolean getAuthor_retains() { + return author_retains; + } + + public void setAuthor_retains(Boolean author_retains) { + this.author_retains = author_retains; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java new file mode 100644 index 000000000..add5bf8bf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DOAJEntry.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class DOAJEntry implements Serializable { + private String last_updated; + private BibJson bibjson; + private Admin admin; + private String created_date; + private String id; + + public String getLast_updated() { + return last_updated; + } + + public void setLast_updated(String last_updated) { + this.last_updated = last_updated; + } + + public BibJson getBibjson() { + return bibjson; + } + + public void setBibjson(BibJson bibjson) { + this.bibjson = bibjson; + } + + public Admin getAdmin() { + return admin; + } + + public void setAdmin(Admin admin) { + this.admin = admin; + } + + public String getCreated_date() { + return created_date; + } + + public void setCreated_date(String created_date) { + this.created_date = created_date; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java new file mode 100644 index 000000000..d86c97f34 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/DepositPolicy.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class DepositPolicy implements Serializable { + private List service; + private String url; + private Boolean has_policy; + + public List getService() { + return service; + } + + public void setService(List service) { + this.service = service; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_policy() { + return has_policy; + } + + public void setHas_policy(Boolean has_policy) { + this.has_policy = has_policy; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java new file mode 100644 index 000000000..35bfba158 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Editorial.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Editorial implements Serializable { + private List review_process; + private String review_url; + private String board_url; + + public List getReview_process() { + return review_process; + } + + public void setReview_process(List review_process) { + this.review_process = review_process; + } + + public String getReview_url() { + return review_url; + } + + public void setReview_url(String review_url) { + this.review_url = review_url; + } + + public String getBoard_url() { + return board_url; + } + + public void setBoard_url(String board_url) { + this.board_url = board_url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java new file mode 100644 index 000000000..3b4d90493 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Institution.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Institution implements Serializable { + private String country; + private String name; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java new file mode 100644 index 000000000..64c7bc18f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/License.java @@ -0,0 +1,67 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +import com.fasterxml.jackson.annotation.JsonProperty; + +public class License implements Serializable { + private Boolean nc; + private Boolean nd; + private Boolean by; + private String type; + private Boolean sa; + private String url; + + public Boolean getnC() { + return nc; + } + + @JsonProperty("NC") + public void setnC(Boolean NC) { + this.nc = NC; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public Boolean getNd() { + return nd; + } + + @JsonProperty("ND") + public void setNd(Boolean nd) { + this.nd = nd; + } + + public Boolean getBy() { + return by; + } + + @JsonProperty("BY") + public void setBy(Boolean by) { + this.by = by; + } + + public Boolean getSa() { + return sa; + } + + @JsonProperty("SA") + public void setSa(Boolean sa) { + this.sa = sa; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java new file mode 100644 index 000000000..0e292b631 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Max.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Max implements Serializable { + private Integer price; + private String currency; + + public Integer getPrice() { + return price; + } + + public void setPrice(Integer price) { + this.price = price; + } + + public String getCurrency() { + return currency; + } + + public void setCurrency(String currency) { + this.currency = currency; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java new file mode 100644 index 000000000..1583481d2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/OtherCharges.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class OtherCharges implements Serializable { + private Boolean has_other_charges; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_other_charges() { + return has_other_charges; + } + + public void setHas_other_charges(Boolean has_other_charges) { + this.has_other_charges = has_other_charges; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java new file mode 100644 index 000000000..bd7e710dd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/PidScheme.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class PidScheme implements Serializable { + private List scheme; + private Boolean has_pid_scheme; + + public List getScheme() { + return scheme; + } + + public void setScheme(List scheme) { + this.scheme = scheme; + } + + public Boolean getHas_pid_scheme() { + return has_pid_scheme; + } + + public void setHas_pid_scheme(Boolean has_pid_scheme) { + this.has_pid_scheme = has_pid_scheme; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java new file mode 100644 index 000000000..f2230b3ea --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Plagiarism.java @@ -0,0 +1,27 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +import javax.sql.rowset.serial.SerialArray; + +public class Plagiarism implements Serializable { + private Boolean detection; + private String url; + + public Boolean getDetection() { + return detection; + } + + public void setDetection(Boolean detection) { + this.detection = detection; + } + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java new file mode 100644 index 000000000..f56ea9953 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Preservation.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; +import java.util.List; + +public class Preservation implements Serializable { + private Boolean has_preservation; + private List service; + private List national_library; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_preservation() { + return has_preservation; + } + + public void setHas_preservation(Boolean has_preservation) { + this.has_preservation = has_preservation; + } + + public List getService() { + return service; + } + + public void setService(List service) { + this.service = service; + } + + public List getNational_library() { + return national_library; + } + + public void setNational_library(List national_library) { + this.national_library = national_library; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java new file mode 100644 index 000000000..6d97a7969 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Publisher.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Publisher implements Serializable { + private String country; + private String name; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java new file mode 100644 index 000000000..0f7c7dc95 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Ref.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Ref implements Serializable { + private String aims_scope; + private String journal; + private String oa_statement; + private String author_instructions; + private String license_terms; + + public String getAims_scope() { + return aims_scope; + } + + public void setAims_scope(String aims_scope) { + this.aims_scope = aims_scope; + } + + public String getJournal() { + return journal; + } + + public void setJournal(String journal) { + this.journal = journal; + } + + public String getOa_statement() { + return oa_statement; + } + + public void setOa_statement(String oa_statement) { + this.oa_statement = oa_statement; + } + + public String getAuthor_instructions() { + return author_instructions; + } + + public void setAuthor_instructions(String author_instructions) { + this.author_instructions = author_instructions; + } + + public String getLicense_terms() { + return license_terms; + } + + public void setLicense_terms(String license_terms) { + this.license_terms = license_terms; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java new file mode 100644 index 000000000..811638e76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Subject.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Subject implements Serializable { + private String code; + private String scheme; + private String term; + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getScheme() { + return scheme; + } + + public void setScheme(String scheme) { + this.scheme = scheme; + } + + public String getTerm() { + return term; + } + + public void setTerm(String term) { + this.term = term; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java new file mode 100644 index 000000000..ca67dde0c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/Waiver.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; + +import java.io.Serializable; + +public class Waiver implements Serializable { + private Boolean has_waiver; + private String url; + + public String getUrl() { + return url; + } + + public void setUrl(String url) { + this.url = url; + } + + public Boolean getHas_waiver() { + return has_waiver; + } + + public void setHas_waiver(Boolean has_waiver) { + this.has_waiver = has_waiver; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml index 84035fe4e..1a3261ffb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -74,7 +74,9 @@ ${wf:conf('resumeFrom') eq 'ProduceHBM'} - ${wf:conf('resumeFrom') eq 'download_csv'} + ${wf:conf('resumeFrom') eq 'DownloadBoth'} + ${wf:conf('resumeFrom') eq 'DownloadGold'} + ${wf:conf('resumeFrom') eq 'DownloadDoaj'} @@ -83,18 +85,9 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - + - + @@ -103,21 +96,43 @@ --hdfsNameNode${nameNode} --fileURL${unibiFileURL} --tmpFile/tmp/unibi_gold_replaced.csv - --outputFile${workingDir}/unibi_gold.json + --outputFile/user/${wf:user()}/data/unibi_gold.json --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel - + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${doajJsonFileURL} + ${dumpPath} + ${dumpFileName} + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + - eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2 + eu.dnetlib.dhp.oa.graph.hostedbymap.ExtractAndMapDoajJson --hdfsNameNode${nameNode} - --fileURL${doajFileURL} - --tmpFile/tmp/doaj_replaced.csv - --outputFile${workingDir}/doaj.json - --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel + --compressedFile${dumpPath}/${dumpFileName} + --workingPath${workingDir}/DOAJ/ + --outputPath/user/${wf:user()}/data/doaj.json @@ -125,6 +140,54 @@ + + + eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV + --hdfsNameNode${nameNode} + --fileURL${unibiFileURL} + --tmpFile/tmp/unibi_gold_replaced.csv + --outputFile/user/${wf:user()}/data/unibi_gold.json + --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel + + + + + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${doajJsonFileURL} + ${dumpPath} + ${dumpFileName} + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + + + eu.dnetlib.dhp.oa.graph.hostedbymap.ExtractAndMapDoajJson + --hdfsNameNode${nameNode} + --compressedFile${dumpPath}/${dumpFileName} + --workingPath${workingDir}/DOAJ/ + --outputPath/user/${wf:user()}/data/doaj.json + + + + + yarn-cluster diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index 8d8965866..0188dac28 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala @@ -2,9 +2,10 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel} import eu.dnetlib.dhp.schema.oaf.Datasource -import org.apache.commons.io.IOUtils +import org.apache.commons.io.{FileUtils, IOUtils} import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.{FileSystem, Path} import org.apache.hadoop.io.compress.GzipCodec @@ -13,7 +14,8 @@ import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} import org.json4s.DefaultFormats import org.slf4j.{Logger, LoggerFactory} -import java.io.PrintWriter +import java.io.{File, PrintWriter} +import scala.collection.JavaConverters._ object SparkProduceHostedByMap { @@ -256,6 +258,8 @@ object SparkProduceHostedByMap { logger.info("Getting the Datasources") + HdfsSupport.remove(outputPath, spark.sparkContext.hadoopConfiguration) + Aggregators .explodeHostedByItemType( oaHostedByDataset(spark, datasourcePath) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java index edf74fc6a..48f1e0c06 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java @@ -55,7 +55,6 @@ public class DownloadCsvTest { new DownloadCSV() .doDownload( fileURL, - workingDir + "/unibi_gold", outputFile, UnibiGoldModel.class.getName(), ',', @@ -91,56 +90,6 @@ public class DownloadCsvTest { assertEquals(67028, count); } - @Disabled - @Test - void getDoajFileTest() throws CollectorException, IOException, ClassNotFoundException { - - String fileURL = "https://doaj.org/csv"; - - final String outputFile = workingDir + "/doaj.json"; - new DownloadCSV() - .doDownload( - fileURL, - workingDir + "/doaj", - outputFile, - DOAJModel.class.getName(), - ',', - fs); - - BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile)))); - - String line; - int count = 0; - while ((line = in.readLine()) != null) { - DOAJModel doaj = new ObjectMapper().readValue(line, DOAJModel.class); - if (count == 0) { - assertEquals("0001-3765", doaj.getIssn()); - assertEquals("1678-2690", doaj.getEissn()); - assertEquals("Anais da Academia Brasileira de Ciências", doaj.getJournalTitle()); - } - if (count == 22) { - log.info(new ObjectMapper().writeValueAsString(doaj)); - System.out.println(new ObjectMapper().writeValueAsString(doaj)); - } - if (count == 7904) { - // log.info(new ObjectMapper().writeValueAsString(doaj)); - assertEquals("", doaj.getIssn()); - assertEquals("2055-7159", doaj.getEissn()); - assertEquals("BJR|case reports", doaj.getJournalTitle()); - } - if (count == 16707) { - - assertEquals("2783-1043", doaj.getIssn()); - assertEquals("2783-1051", doaj.getEissn()); - assertEquals("فیزیک کاربردی ایران", doaj.getJournalTitle()); - } - - count += 1; - } - - assertEquals(16715, count); - } - @AfterAll public static void cleanup() { FileUtils.deleteQuietly(new File(workingDir)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json index 9cec80eb4..09730f1da 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json @@ -1,25 +1,25 @@ -{"journalTitle":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","reviewProcess":"Double blind peer review"} -{"journalTitle":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","reviewProcess":"Blind peer review"} -{"journalTitle":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","reviewProcess":"Double blind peer review"} -{"journalTitle":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":"","reviewProcess":"Double blind peer review"} -{"journalTitle":"Revue Internationale de Pédagogie de l’Enseignement Supérieur","issn":"","eissn":"2076-8427","reviewProcess":"Double blind peer review"} -{"journalTitle":"Проблемы развития территории","issn":"2076-8915","eissn":"2409-9007","reviewProcess":"Double blind peer review"} -{"journalTitle":"Rambam Maimonides Medical Journal","issn":"","eissn":"2076-9172","reviewProcess":"Peer review"} -{"journalTitle":"Membranes","issn":"2077-0375","eissn":"","reviewProcess":"Blind peer review"} -{"journalTitle":"Journal of Clinical Medicine","issn":"","eissn":"2077-0383","reviewProcess":"Blind peer review"} -{"journalTitle":"Agriculture","issn":"","eissn":"2077-0472","reviewProcess":"Blind peer review"} -{"journalTitle":"Standartnye Obrazcy","issn":"2077-1177","eissn":"","reviewProcess":"Double blind peer review"} -{"journalTitle":"Металл и литье Украины","issn":"2077-1304","eissn":"2706-5529","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Marine Science and Engineering","issn":"","eissn":"2077-1312","reviewProcess":"Blind peer review"} -{"journalTitle":"Religions","issn":"","eissn":"2077-1444","reviewProcess":"Double blind peer review"} -{"journalTitle":"GW-Unterricht","issn":"2077-1517","eissn":"2414-4169","reviewProcess":"Double blind peer review"} -{"journalTitle":"UCV-Scientia","issn":"2077-172X","eissn":"","reviewProcess":"Peer review"} -{"journalTitle":"Sovremennye Issledovaniâ Socialʹnyh Problem","issn":"2077-1770","eissn":"2218-7405","reviewProcess":"Double blind peer review"} -{"journalTitle":"Granì","issn":"2077-1800","eissn":"2413-8738","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Economics Finance and Administrative Science","issn":"2077-1886","eissn":"2218-0648","reviewProcess":"Double blind peer review"} -{"journalTitle":"Science Education International","issn":"","eissn":"2077-2327","reviewProcess":"Double blind peer review"} -{"journalTitle":"Edumecentro","issn":"","eissn":"2077-2874","reviewProcess":"Double blind peer review"} -{"journalTitle":"Monteverdia","issn":"","eissn":"2077-2890","reviewProcess":"Double blind peer review"} -{"journalTitle":"Transformación","issn":"","eissn":"2077-2955","reviewProcess":"Double blind peer review"} -{"journalTitle":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","reviewProcess":"Double blind peer review"} -{"journalTitle":"Revue de Primatologie","issn":"","eissn":"2077-3757","reviewProcess":"Peer review"} \ No newline at end of file +{"journalTitle":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","reviewProcess":["Double blind peer review"],"oaStart":2015} +{"journalTitle":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","reviewProcess":["Blind peer review"],"oaStart":2009} +{"journalTitle":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":null,"reviewProcess":["Double blind peer review"],"oaStart":2006} +{"journalTitle":"Revue Internationale de Pédagogie de l’Enseignement Supérieur","issn":null,"eissn":"2076-8427","reviewProcess":["Double blind peer review"],"oaStart":2009} +{"journalTitle":"Проблемы развития территории","issn":"2076-8915","eissn":"2409-9007","reviewProcess":["Double blind peer review"],"oaStart":2008} +{"journalTitle":"Rambam Maimonides Medical Journal","issn":null,"eissn":"2076-9172","reviewProcess":["Peer review"],"oaStart":2010} +{"journalTitle":"Membranes","issn":"2077-0375","eissn":null,"reviewProcess":["Blind peer review"],"oaStart":2011} +{"journalTitle":"Journal of Clinical Medicine","issn":null,"eissn":"2077-0383","reviewProcess":["Blind peer review"],"oaStart":2012} +{"journalTitle":"Agriculture","issn":null,"eissn":"2077-0472","reviewProcess":["Blind peer review"],"oaStart":2011} +{"journalTitle":"Standartnye Obrazcy","issn":"2077-1177","eissn":null,"reviewProcess":["Double blind peer review"],"oaStart":2014} +{"journalTitle":"Металл и литье Украины","issn":"2077-1304","eissn":"2706-5529","reviewProcess":["Double blind peer review"],"oaStart":2019} +{"journalTitle":"Journal of Marine Science and Engineering","issn":null,"eissn":"2077-1312","reviewProcess":["Blind peer review"],"oaStart":2013} +{"journalTitle":"Religions","issn":null,"eissn":"2077-1444","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"GW-Unterricht","issn":"2077-1517","eissn":"2414-4169","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"UCV-Scientia","issn":"2077-172X","eissn":null,"reviewProcess":["Peer review"],"oaStart":2009} +{"journalTitle":"Sovremennye Issledovaniâ Socialʹnyh Problem","issn":"2077-1770","eissn":"2218-7405","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Granì","issn":"2077-1800","eissn":"2413-8738","reviewProcess":["Double blind peer review"],"oaStart":2014} +{"journalTitle":"Journal of Economics Finance and Administrative Science","issn":"2077-1886","eissn":"2218-0648","reviewProcess":["Double blind peer review"],"oaStart":2017} +{"journalTitle":"Science Education International","issn":null,"eissn":"2077-2327","reviewProcess":["Double blind peer review"],"oaStart":2017} +{"journalTitle":"Edumecentro","issn":null,"eissn":"2077-2874","reviewProcess":["Double blind peer review"],"oaStart":2013} +{"journalTitle":"Monteverdia","issn":null,"eissn":"2077-2890","reviewProcess":["Double blind peer review"],"oaStart":2008} +{"journalTitle":"Transformación","issn":null,"eissn":"2077-2955","reviewProcess":["Double blind peer review"],"oaStart":2010} +{"journalTitle":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","reviewProcess":["Double blind peer review"],"oaStart":2011} +{"journalTitle":"Revue de Primatologie","issn":null,"eissn":"2077-3757","reviewProcess":["Peer review"],"oaStart":2009} \ No newline at end of file From c959639bd56a8fc20a90d38df21da83b8b7bfd95 Mon Sep 17 00:00:00 2001 From: miconis Date: Tue, 15 Mar 2022 16:33:03 +0100 Subject: [PATCH 078/159] dependency updated to the new pace-core version --- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 62 ++++++++++++++----- pom.xml | 2 +- 2 files changed, 47 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 549988767..9c9ec43d5 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -206,11 +206,16 @@ public class SparkDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) .count(); - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); + assertEquals(3076, orgs_simrel); + assertEquals(7040, pubs_simrel); assertEquals(336, sw_simrel); assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); + assertEquals(6784, orp_simrel); +// System.out.println("orgs_simrel = " + orgs_simrel); +// System.out.println("pubs_simrel = " + pubs_simrel); +// System.out.println("sw_simrel = " + sw_simrel); +// System.out.println("ds_simrel = " + ds_simrel); +// System.out.println("orp_simrel = " + orp_simrel); } @Test @@ -258,10 +263,14 @@ public class SparkDedupTest implements Serializable { .count(); // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); + assertEquals(3076, orgs_simrel); + assertEquals(7040, pubs_simrel); assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); + assertEquals(6784, orp_simrel); +// System.out.println("orgs_simrel = " + orgs_simrel); +// System.out.println("pubs_simrel = " + pubs_simrel); +// System.out.println("ds_simrel = " + ds_simrel); +// System.out.println("orp_simrel = " + orp_simrel); // entities simrels to be different from the number of previous step (new simrels in the whitelist) Dataset sw_simrel = spark @@ -288,6 +297,7 @@ public class SparkDedupTest implements Serializable { .count() > 0); assertEquals(338, sw_simrel.count()); +// System.out.println("sw_simrel = " + sw_simrel.count()); } @@ -435,11 +445,16 @@ public class SparkDedupTest implements Serializable { .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .count(); - assertEquals(1272, orgs_mergerel); - assertEquals(1438, pubs_mergerel); + assertEquals(1268, orgs_mergerel); + assertEquals(1444, pubs_mergerel); assertEquals(286, sw_mergerel); assertEquals(472, ds_mergerel); - assertEquals(718, orp_mergerel); + assertEquals(738, orp_mergerel); +// System.out.println("orgs_mergerel = " + orgs_mergerel); +// System.out.println("pubs_mergerel = " + pubs_mergerel); +// System.out.println("sw_mergerel = " + sw_mergerel); +// System.out.println("ds_mergerel = " + ds_mergerel); +// System.out.println("orp_mergerel = " + orp_mergerel); } @@ -483,11 +498,17 @@ public class SparkDedupTest implements Serializable { testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord") .count(); - assertEquals(85, orgs_deduprecord); - assertEquals(65, pubs_deduprecord); + assertEquals(86, orgs_deduprecord); + assertEquals(67, pubs_deduprecord); assertEquals(49, sw_deduprecord); assertEquals(97, ds_deduprecord); - assertEquals(89, orp_deduprecord); + assertEquals(92, orp_deduprecord); + +// System.out.println("orgs_deduprecord = " + orgs_deduprecord); +// System.out.println("pubs_deduprecord = " + pubs_deduprecord); +// System.out.println("sw_deduprecord = " + sw_deduprecord); +// System.out.println("ds_deduprecord = " + ds_deduprecord); +// System.out.println("orp_deduprecord = " + orp_deduprecord); } @Test @@ -566,13 +587,21 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); - assertEquals(896, publications); - assertEquals(838, organizations); + assertEquals(898, publications); + assertEquals(839, organizations); assertEquals(100, projects); assertEquals(100, datasource); assertEquals(198, softwares); assertEquals(389, dataset); - assertEquals(517, otherresearchproduct); + assertEquals(520, otherresearchproduct); + +// System.out.println("publications = " + publications); +// System.out.println("organizations = " + organizations); +// System.out.println("projects = " + projects); +// System.out.println("datasource = " + datasource); +// System.out.println("software = " + softwares); +// System.out.println("dataset = " + dataset); +// System.out.println("otherresearchproduct = " + otherresearchproduct); long deletedOrgs = jsc .textFile(testDedupGraphBasePath + "/organization") @@ -626,7 +655,8 @@ public class SparkDedupTest implements Serializable { long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); - assertEquals(4860, relations); +// assertEquals(4860, relations); + System.out.println("relations = " + relations); // check deletedbyinference final Dataset mergeRels = spark diff --git a/pom.xml b/pom.xml index 603a4cf1e..86adee902 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ [4.0.3] [6.0.5] [3.1.6] - [4.1.7] + [4.1.12] [2.6.1] 7.5.0 4.7.2 From c763aded70c9f087c91c28467a695fa41dc383ff Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 16 Mar 2022 16:41:50 +0100 Subject: [PATCH 079/159] dependency updated to the new pace-core version --- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 57 ++++++++++++++----- pom.xml | 2 +- 2 files changed, 43 insertions(+), 16 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 549988767..2b9559867 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -206,11 +206,16 @@ public class SparkDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) .count(); - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); + assertEquals(3076, orgs_simrel); + assertEquals(7040, pubs_simrel); assertEquals(336, sw_simrel); assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); + assertEquals(6784, orp_simrel); +// System.out.println("org_simrel = " + orgs_simrel); +// System.out.println("pub_simrel = " + pubs_simrel); +// System.out.println("sw_simrel = " + sw_simrel); +// System.out.println("ds_simrel = " + ds_simrel); +// System.out.println("orp_simrel = " + orp_simrel); } @Test @@ -258,10 +263,14 @@ public class SparkDedupTest implements Serializable { .count(); // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) - assertEquals(3082, orgs_simrel); - assertEquals(7036, pubs_simrel); + assertEquals(3076, orgs_simrel); + assertEquals(7040, pubs_simrel); assertEquals(442, ds_simrel); - assertEquals(6750, orp_simrel); + assertEquals(6784, orp_simrel); +// System.out.println("org_simrel = " + orgs_simrel); +// System.out.println("pub_simrel = " + pubs_simrel); +// System.out.println("ds_simrel = " + ds_simrel); +// System.out.println("orp_simrel = " + orp_simrel); // entities simrels to be different from the number of previous step (new simrels in the whitelist) Dataset sw_simrel = spark @@ -288,6 +297,7 @@ public class SparkDedupTest implements Serializable { .count() > 0); assertEquals(338, sw_simrel.count()); +// System.out.println("sw_simrel_count = " + sw_simrel.count()); } @@ -435,11 +445,16 @@ public class SparkDedupTest implements Serializable { .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .count(); - assertEquals(1272, orgs_mergerel); - assertEquals(1438, pubs_mergerel); + assertEquals(1268, orgs_mergerel); + assertEquals(1444, pubs_mergerel); assertEquals(286, sw_mergerel); assertEquals(472, ds_mergerel); - assertEquals(718, orp_mergerel); + assertEquals(738, orp_mergerel); +// System.out.println("org_simrel = " + orgs_mergerel); +// System.out.println("pub_simrel = " + pubs_mergerel); +// System.out.println("sw_simrel = " + sw_mergerel); +// System.out.println("ds_simrel = " + ds_mergerel); +// System.out.println("orp_simrel = " + orp_mergerel); } @@ -483,11 +498,16 @@ public class SparkDedupTest implements Serializable { testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord") .count(); - assertEquals(85, orgs_deduprecord); - assertEquals(65, pubs_deduprecord); + assertEquals(86, orgs_deduprecord); + assertEquals(67, pubs_deduprecord); assertEquals(49, sw_deduprecord); assertEquals(97, ds_deduprecord); - assertEquals(89, orp_deduprecord); + assertEquals(92, orp_deduprecord); +// System.out.println("org_simrel = " + orgs_deduprecord); +// System.out.println("pub_simrel = " + pubs_deduprecord); +// System.out.println("sw_simrel = " + sw_deduprecord); +// System.out.println("ds_simrel = " + ds_deduprecord); +// System.out.println("orp_simrel = " + orp_deduprecord); } @Test @@ -566,13 +586,18 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); - assertEquals(896, publications); - assertEquals(838, organizations); + assertEquals(898, publications); + assertEquals(839, organizations); assertEquals(100, projects); assertEquals(100, datasource); assertEquals(198, softwares); assertEquals(389, dataset); - assertEquals(517, otherresearchproduct); + assertEquals(520, otherresearchproduct); +// System.out.println("publications = " + publications); +// System.out.println("organizations = " + organizations); +// System.out.println("softwares = " + softwares); +// System.out.println("dataset = " + dataset); +// System.out.println("orp = " + otherresearchproduct); long deletedOrgs = jsc .textFile(testDedupGraphBasePath + "/organization") @@ -627,6 +652,8 @@ public class SparkDedupTest implements Serializable { long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); assertEquals(4860, relations); +// System.out.println("relations = " + relations); + // check deletedbyinference final Dataset mergeRels = spark diff --git a/pom.xml b/pom.xml index 603a4cf1e..86adee902 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ [4.0.3] [6.0.5] [3.1.6] - [4.1.7] + [4.1.12] [2.6.1] 7.5.0 4.7.2 From 89fd27548077586def45bbe9f9e893ed6862ac84 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 21 Mar 2022 09:54:45 +0100 Subject: [PATCH 080/159] [HostedByMap] added left over from PR and fixed issue on workflow --- .../hostedbymap/download_json_parameters.json | 27 +++++++++++++++++++ .../graph/hostedbymap/oozie_app/download.sh | 3 +++ .../graph/hostedbymap/oozie_app/workflow.xml | 2 +- 3 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json new file mode 100644 index 000000000..72498c4e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json @@ -0,0 +1,27 @@ +[ + + { + "paramName":"op", + "paramLongName":"outputPath", + "paramDescription": "the output json file produced by the CSV downlaod procedure", + "paramRequired": true + }, + + { + "paramName": "hnn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true + },{ + "paramName": "cf", + "paramLongName": "compressedFile", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true +},{ + "paramName":"wp", + "paramLongName":"workingPath", + "paramDescription": "the output json file produced by the CSV downlaod procedure", + "paramRequired": true +} +] + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh new file mode 100644 index 000000000..35220bd8c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh @@ -0,0 +1,3 @@ +#!/bin/bash +curl -LSs $1 | hdfs dfs -put - $2/$3 +curl -LSs http://api.crossref.org/works/10.1099/jgv.0.001453 > prova.txt \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml index 1a3261ffb..c7fffed5b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -92,7 +92,7 @@ - eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2 + eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV --hdfsNameNode${nameNode} --fileURL${unibiFileURL} --tmpFile/tmp/unibi_gold_replaced.csv From dcfbeb8142e91379ae4003be1f789a527895c574 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Mon, 21 Mar 2022 12:36:03 +0200 Subject: [PATCH 081/159] yet more typos --- .../oozie_app/scripts/step16-createIndicatorsTables.sql | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index d925b3694..a95ee74d8 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -265,19 +265,19 @@ left outer join ( create table indi_org_openess stored as parquet as WITH datasets_oa as ( - SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg + SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.dataset ds on dg.id=ds.id WHERE dg.is_gold=1 group by ro.organization), software_oa as ( - SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg + SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.software ds on dg.id=ds.id WHERE dg.is_gold=1 group by ro.organization), pubs_oa as ( - SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg + SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.publication ds on dg.id=ds.id where dg.is_gold=1 From 2e8394ecf8c0df33e047e04191df68251763a0c5 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 22 Mar 2022 16:16:08 +0200 Subject: [PATCH 082/159] creating aaall tables as parquet --- .../oa/graph/stats/oozie_app/scripts/step10.sql | 2 +- .../oa/graph/stats/oozie_app/scripts/step13.sql | 10 +++++----- .../oa/graph/stats/oozie_app/scripts/step14.sql | 12 ++++++------ .../oa/graph/stats/oozie_app/scripts/step15.sql | 8 ++++---- .../graph/stats/oozie_app/scripts/step15_5.sql | 6 +++--- .../oozie_app/scripts/step16_1-definitions.sql | 6 +++--- .../oa/graph/stats/oozie_app/scripts/step2.sql | 16 ++++++++-------- .../oozie_app/scripts/step20-createMonitorDB.sql | 4 ++-- .../oa/graph/stats/oozie_app/scripts/step3.sql | 16 ++++++++-------- .../oa/graph/stats/oozie_app/scripts/step4.sql | 16 ++++++++-------- .../oa/graph/stats/oozie_app/scripts/step5.sql | 16 ++++++++-------- .../oa/graph/stats/oozie_app/scripts/step6.sql | 10 +++++----- .../oa/graph/stats/oozie_app/scripts/step7.sql | 4 ++-- .../oa/graph/stats/oozie_app/scripts/step8.sql | 8 ++++---- .../oa/graph/stats/oozie_app/scripts/step9.sql | 6 +++--- 15 files changed, 70 insertions(+), 70 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index 13a4803a9..f1e1ceedd 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -49,7 +49,7 @@ select * from openaire_prod_usage_stats.views_stats; -- Creation date of the database ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -create table ${stats_db_name}.creation_date as +create table ${stats_db_name}.creation_date STORED AS PARQUET as select date_format(current_date(), 'dd-MM-yyyy') as date; -- -- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index 947c91072..a5839da11 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -5,7 +5,7 @@ -- Sources related tables/views ------------------------------------------------------ ------------------------------------------------------ -CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource @@ -16,7 +16,7 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource @@ -27,7 +27,7 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource @@ -38,7 +38,7 @@ LEFT OUTER JOIN from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource @@ -59,7 +59,7 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; -create table ${stats_db_name}.result_orcid as +create table ${stats_db_name}.result_orcid STORED AS PARQUET as select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid from ( SELECT substr(res.id, 4) as id, auth_pid.value as orcid diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index e3a33a893..e8e29ff11 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -5,22 +5,22 @@ -- Licences related tables/views ------------------------------------------------------ ------------------------------------------------------ -CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses STORED AS PARQUET AS SELECT substr(p.id, 4) as id, licenses.value as type from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; @@ -34,11 +34,11 @@ SELECT * FROM ${stats_db_name}.software_licenses UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids STORED AS PARQUET AS select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources STORED AS PARQUET as SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource FROM ( SELECT substr(o.id, 4) as id, substr(instances.instance.key, 4) as datasource diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql index f46b65171..cec22cd3e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql @@ -6,22 +6,22 @@ ------------------------------------------------------ ------------------------------------------------------ -CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; -CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed STORED AS PARQUET as select substr(r.id, 4) as id, inst.refereed.classname as refereed from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql index 3a7d9f455..04c7f83b9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql @@ -1,21 +1,21 @@ ------------------------------------------- --- Extra tables, mostly used by indicators -create table ${stats_db_name}.result_projectcount as +create table ${stats_db_name}.result_projectcount STORED AS PARQUET as select r.id, count(distinct p.id) as count from ${stats_db_name}.result r left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.project p on p.id=rp.project group by r.id; -create table ${stats_db_name}.result_fundercount as +create table ${stats_db_name}.result_fundercount STORED AS PARQUET as select r.id, count(distinct p.funder) as count from ${stats_db_name}.result r left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.project p on p.id=rp.project group by r.id; -create table ${stats_db_name}.project_resultcount as +create table ${stats_db_name}.project_resultcount STORED AS PARQUET as with rcount as ( select p.id as pid, count(distinct r.id) as `count`, r.type as type from ${stats_db_name}.project p diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql index 7ad6f3888..88c1ece78 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql @@ -3,20 +3,20 @@ ---------------------------------------------------- -- Peer reviewed: -create table ${stats_db_name}.result_peerreviewed as +create table ${stats_db_name}.result_peerreviewed STORED AS PARQUET as select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; -- Green OA: -create table ${stats_db_name}.result_greenoa as +create table ${stats_db_name}.result_greenoa STORED AS PARQUET as select r.id, case when green.green_oa=1 then true else false end as green from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; -- GOLD OA: -create table ${stats_db_name}.result_gold as +create table ${stats_db_name}.result_gold STORED AS PARQUET as select r.id, case when gold.is_gold=1 then true else false end as gold from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql index 468a42045..4ffbd384b 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql @@ -40,13 +40,13 @@ SELECT substr(p.id, 4) as id, from ${openaire_db_name}.publication p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_classifications AS +CREATE TABLE ${stats_db_name}.publication_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) as id, instancetype.classname as type from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.instancetype) instances as instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_concepts AS +CREATE TABLE ${stats_db_name}.publication_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') @@ -55,7 +55,7 @@ from ${openaire_db_name}.publication p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_datasources as +CREATE TABLE ${stats_db_name}.publication_datasources STORED AS PARQUET as SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource FROM ( SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource @@ -66,30 +66,30 @@ FROM ( from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; -CREATE TABLE ${stats_db_name}.publication_languages AS +CREATE TABLE ${stats_db_name}.publication_languages STORED AS PARQUET AS select substr(p.id, 4) as id, p.language.classname as language FROM ${openaire_db_name}.publication p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_oids AS +CREATE TABLE ${stats_db_name}.publication_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_pids AS +CREATE TABLE ${stats_db_name}.publication_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_topics as +CREATE TABLE ${stats_db_name}.publication_topics STORED AS PARQUET as select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic FROM ${openaire_db_name}.publication p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.publication_citations AS +CREATE TABLE ${stats_db_name}.publication_citations STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.publication p lateral view explode(p.extrainfo) citations AS citation diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 7c5257edd..f34e3fabb 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -52,7 +52,7 @@ compute stats TARGET.result_languages; create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_licenses; -create table TARGET.licenses_normalized as select * from SOURCE.licenses_normalized; +create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; @@ -83,7 +83,7 @@ compute stats TARGET.result_topics; create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); -create table TARGET.result_result as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; +create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; drop view TARGET.foo1; drop view TARGET.foo2; compute stats TARGET.result_result; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql index 76a5e5a48..eb97263a7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql @@ -40,20 +40,20 @@ SELECT substr(d.id, 4) AS id, FROM ${openaire_db_name}.dataset d WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_citations AS +CREATE TABLE ${stats_db_name}.dataset_citations STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.dataset d LATERAL VIEW explode(d.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_classifications AS +CREATE TABLE ${stats_db_name}.dataset_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_concepts AS +CREATE TABLE ${stats_db_name}.dataset_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') @@ -62,7 +62,7 @@ from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.context) contexts as context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_datasources AS +CREATE TABLE ${stats_db_name}.dataset_datasources STORED AS PARQUET AS SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM ( SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource @@ -74,24 +74,24 @@ FROM ( FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; -CREATE TABLE ${stats_db_name}.dataset_languages AS +CREATE TABLE ${stats_db_name}.dataset_languages STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.dataset p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_oids AS +CREATE TABLE ${stats_db_name}.dataset_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_pids AS +CREATE TABLE ${stats_db_name}.dataset_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.dataset_topics AS +CREATE TABLE ${stats_db_name}.dataset_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.dataset p LATERAL VIEW explode(p.subject) subjects AS subject diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql index dc71f41f1..0d1f6323e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql @@ -40,20 +40,20 @@ SELECT substr(s.id, 4) as id, from ${openaire_db_name}.software s where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_citations AS +CREATE TABLE ${stats_db_name}.software_citations STORED AS PARQUET AS SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.software s LATERAL VIEW explode(s.extrainfo) citations as citation where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_classifications AS +CREATE TABLE ${stats_db_name}.software_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_concepts AS +CREATE TABLE ${stats_db_name}.software_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') @@ -62,7 +62,7 @@ FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_datasources AS +CREATE TABLE ${stats_db_name}.software_datasources STORED AS PARQUET AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource FROM ( SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource @@ -74,24 +74,24 @@ FROM ( FROM ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; -CREATE TABLE ${stats_db_name}.software_languages AS +CREATE TABLE ${stats_db_name}.software_languages STORED AS PARQUET AS select substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.software p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_oids AS +CREATE TABLE ${stats_db_name}.software_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_pids AS +CREATE TABLE ${stats_db_name}.software_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.software_topics AS +CREATE TABLE ${stats_db_name}.software_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.software p LATERAL VIEW explode(p.subject) subjects AS subject diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql index 353aa98b7..06b616d6a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql @@ -40,18 +40,18 @@ FROM ${openaire_db_name}.otherresearchproduct o WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; -- Otherresearchproduct_citations -CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_citations STORED AS PARQUET AS SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, instancetype.classname AS type FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts STORED AS PARQUET AS SELECT substr(p.id, 4) as id, case when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') @@ -59,7 +59,7 @@ SELECT substr(p.id, 4) as id, case FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources STORED AS PARQUET AS SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance @@ -68,22 +68,22 @@ FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) A from ${openaire_db_name}.datasource d WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; -CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_languages STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, p.language.classname AS language FROM ${openaire_db_name}.otherresearchproduct p where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_pids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS +CREATE TABLE ${stats_db_name}.otherresearchproduct_topics STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index b5e2eb37b..dc7c01046 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -3,24 +3,24 @@ -- Project table/view and Project related tables/views ------------------------------------------------------ ------------------------------------------------------ -CREATE TABLE ${stats_db_name}.project_oids AS +CREATE TABLE ${stats_db_name}.project_oids STORED AS PARQUET AS SELECT substr(p.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.project_organizations AS +CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype = 'projectOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.project_results AS +CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultProject' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; -create table ${stats_db_name}.project_classification as +create table ${stats_db_name}.project_classification STORED AS PARQUET as select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3 from ${openaire_db_name}.project p lateral view explode(p.h2020classification) classifs as class @@ -76,7 +76,7 @@ SELECT substr(p.id, 4) AS id, FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; -create table ${stats_db_name}.funder as +create table ${stats_db_name}.funder STORED AS PARQUET as select distinct xpath_string(fund, '//funder/id') as id, xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/shortname') as shortname diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index a57966abf..e1c36cbc0 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -123,13 +123,13 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; -CREATE TABLE ${stats_db_name}.result_organization AS +CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.result_projects AS +CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id = pr.result diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index d3935fd4a..fa3eca1a9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -80,24 +80,24 @@ UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; -CREATE TABLE ${stats_db_name}.datasource_languages AS +CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, langs.languages AS language FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.datasource_oids AS +CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -CREATE TABLE ${stats_db_name}.datasource_organizations AS +CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. -create table if not exists ${stats_db_name}.datasource_sources AS +create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS select substr(d.id, 4) as id, substr(cf.key, 4) as datasource from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index c73aa811c..02b0aaca7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -3,7 +3,7 @@ -- Organization table/view and Organization related tables/views ---------------------------------------------------------------- ---------------------------------------------------------------- -CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization AS +CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization STORED AS PARQUET AS SELECT substr(o.id, 4) as id, o.legalname.value as name, o.legalshortname.value as legalshortname, @@ -11,11 +11,11 @@ SELECT substr(o.id, 4) as id, FROM ${openaire_db_name}.organization o WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible = FALSE; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS +CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources STORED AS PARQUET AS SELECT organization AS id, id AS datasource FROM ${stats_db_name}.datasource_organizations; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS +CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects STORED AS PARQUET AS SELECT id AS project, organization as id FROM ${stats_db_name}.project_organizations; From 62f91b0869d3014310c4062019c36579d4a507d3 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 22 Mar 2022 16:17:49 +0200 Subject: [PATCH 083/159] cleanup --- .../oa/graph/stats/oozie_app/scripts/step10.sql | 3 --- .../oa/graph/stats/oozie_app/scripts/step11.sql | 5 +---- .../oa/graph/stats/oozie_app/scripts/step14.sql | 15 +-------------- .../oa/graph/stats/oozie_app/scripts/step9.sql | 5 +---- 4 files changed, 3 insertions(+), 25 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql index f1e1ceedd..92dedf243 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql @@ -51,6 +51,3 @@ select * from openaire_prod_usage_stats.views_stats; ------------------------------------------------------------------------------------------------ create table ${stats_db_name}.creation_date STORED AS PARQUET as select date_format(current_date(), 'dd-MM-yyyy') as date; --- --- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index e892da0be..d699b68c3 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -113,7 +113,4 @@ FROM ${stats_db_name}.result_projects, ${stats_db_name}.project WHERE result_projects.id = result.id AND result.type = 'publication' - AND project.id = result_projects.project; - --- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file + AND project.id = result_projects.project; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index e8e29ff11..47a6f84c2 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -46,17 +46,4 @@ FROM ( LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; - --- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS FOR COLUMNS; --- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file + WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index 02b0aaca7..b42640e10 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -17,7 +17,4 @@ FROM ${stats_db_name}.datasource_organizations; CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects STORED AS PARQUET AS SELECT id AS project, organization as id -FROM ${stats_db_name}.project_organizations; - --- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS; --- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS; \ No newline at end of file +FROM ${stats_db_name}.project_organizations; \ No newline at end of file From f10066547bb467dd9eff8e78ed4d538802cdaa10 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Mar 2022 12:22:26 +0100 Subject: [PATCH 084/159] increased spark.sql.shuffle.partitions in affiliation_from_semrel_propagation --- .../dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml index 3f0530aaf..5ce2f5c06 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml @@ -173,6 +173,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + --conf spark.sql.shuffle.partitions=3840 --relationPath${workingDir}/preparedInfo/relation --outputPath${outputPath}/relation From 48d32466e4c4ee5b3ef39a23f04073487b2979da Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 23 Mar 2022 14:52:03 +0100 Subject: [PATCH 085/159] instances grouped by URL expose only one refereed --- .../dhp/oa/provision/model/XmlInstance.java | 13 +++++++--- .../oa/provision/utils/XmlRecordFactory.java | 20 +++++++------- .../oa/provision/XmlRecordFactoryTest.java | 2 +- .../dnetlib/dhp/oa/provision/publication.json | 26 ++++++++++++++++++- pom.xml | 2 +- 5 files changed, 48 insertions(+), 15 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java index a38329750..930eab4c3 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java @@ -12,6 +12,7 @@ import scala.Serializable; public class XmlInstance implements Serializable { public static final AccessRight UNKNOWN_ACCESS_RIGHT; + public static final Qualifier UNKNOWN_REVIEW_LEVEL; static { UNKNOWN_ACCESS_RIGHT = new AccessRight(); @@ -19,6 +20,12 @@ public class XmlInstance implements Serializable { UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN); UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES); UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES); + + UNKNOWN_REVIEW_LEVEL = new Qualifier(); + UNKNOWN_REVIEW_LEVEL.setClassid("0000"); + UNKNOWN_REVIEW_LEVEL.setClassname(ModelConstants.UNKNOWN); + UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_REVIEW_LEVELS); + UNKNOWN_REVIEW_LEVEL.setSchemename(ModelConstants.DNET_REVIEW_LEVELS); } private String url; @@ -50,7 +57,7 @@ public class XmlInstance implements Serializable { // typed results private String processingchargecurrency; - private Set refereed = Sets.newHashSet();; // peer-review status + private Qualifier refereed; // peer-review status public String getUrl() { return url; @@ -148,11 +155,11 @@ public class XmlInstance implements Serializable { this.processingchargecurrency = processingchargecurrency; } - public Set getRefereed() { + public Qualifier getRefereed() { return refereed; } - public void setRefereed(Set refereed) { + public void setRefereed(Qualifier refereed) { this.refereed = refereed; } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index cb29dc121..5d4a831c0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -31,6 +31,7 @@ import org.dom4j.Node; import org.dom4j.io.OutputFormat; import org.dom4j.io.SAXReader; import org.dom4j.io.XMLWriter; +import org.json4s.Xml; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.base.Joiner; @@ -1208,14 +1209,8 @@ public class XmlRecordFactory implements Serializable { if (instance.getRefereed() != null) { fields - .addAll( - instance - .getRefereed() - .stream() - .filter(Objects::nonNull) - .filter(r -> !r.isBlank()) - .map(r -> XmlSerializationUtils.mapQualifier("refereed", r)) - .collect(Collectors.toList())); + .add( + XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed())); } if (instance.getProcessingchargeamount() != null && isNotBlank(instance.getProcessingchargeamount())) { @@ -1359,13 +1354,20 @@ public class XmlRecordFactory implements Serializable { .map(Instance::getAccessright) .min(new AccessRightComparator()) .orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT)); + instance + .setRefereed( + instances + .stream() + .map(Pair::getValue) + .map(i -> Optional.ofNullable(i.getRefereed()).orElse(XmlInstance.UNKNOWN_REVIEW_LEVEL)) + .min(new RefereedComparator()) + .orElse(XmlInstance.UNKNOWN_REVIEW_LEVEL)); instances.forEach(p -> { final Instance i = p.getRight(); instance.getCollectedfrom().add(i.getCollectedfrom()); instance.getHostedby().add(i.getHostedby()); instance.getInstancetype().add(i.getInstancetype()); - instance.getRefereed().add(i.getRefereed()); instance .setProcessingchargeamount( Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null)); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 273132bff..c32d868e8 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -66,7 +66,7 @@ public class XmlRecordFactoryTest { assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid")); assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()")); - assertEquals(3, doc.selectNodes("//instance").size()); + assertEquals(2, doc.selectNodes("//instance").size()); assertEquals("1721.47", doc.valueOf("//processingchargeamount/text()")); assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index d0c8ea4ed..2c52ce269 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -453,6 +453,12 @@ "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource" }, + "refereed": { + "classid": "0001", + "classname": "peerReviewed", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + }, "license": { "dataInfo": { "deletedbyinference": false, @@ -585,6 +591,12 @@ "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource" }, + "refereed": { + "classid": "0000", + "classname": "UNKNOWN", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + }, "license": { "dataInfo": { "deletedbyinference": false, @@ -717,6 +729,12 @@ "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource" }, + "refereed": { + "classid": "0002", + "classname": "nonPeerReviewed", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + }, "license": { "dataInfo": { "deletedbyinference": false, @@ -849,6 +867,12 @@ "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource" }, + "refereed": { + "classid": "0001", + "classname": "peerReviewed", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + }, "license": { "dataInfo": { "deletedbyinference": false, @@ -866,7 +890,7 @@ "value": "" }, "url": [ - "http://dx.doi.org/10.1109/TED.2018.2853552", + "http://dx.doi.org/10.1109/TED.2018.2853551", "http://dx.doi.org/10.1109/TED.2018.2853554" ] }, diff --git a/pom.xml b/pom.xml index 86adee902..0f0aa711e 100644 --- a/pom.xml +++ b/pom.xml @@ -797,7 +797,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.29] + [2.10.30] [4.0.3] [6.0.5] [3.1.6] From 7b8f85692e990abdc30e0f70e77f63bc95fbbe31 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 23 Mar 2022 17:20:23 +0100 Subject: [PATCH 086/159] [Enrichment country] fixed issues with parameters and workflow args --- .../input_countrypropagation_parameters.json | 6 ------ .../dhp/countrypropagation/oozie_app/workflow.xml | 9 ++++----- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json index e7a6bf5b0..f217e2458 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json @@ -5,12 +5,6 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", - "paramRequired": false - }, { "paramName":"tn", "paramLongName":"resultTableName", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index 85116e4cc..202c86a6d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -110,7 +110,6 @@ --sourcePath${sourcePath} --whitelist${whitelist} --allowedtypes${allowedtypes} - --hive_metastore_uris${hive_metastore_uris} --outputPath${workingDir}/preparedInfo @@ -146,7 +145,7 @@ --sourcePath${sourcePath}/publication --outputPath${workingDir}/publication - --hive_metastore_uris${hive_metastore_uris} + --workingPath${workingDir}/workingP --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --preparedInfoPath${workingDir}/preparedInfo @@ -176,7 +175,7 @@ --sourcePath${sourcePath}/dataset --outputPath${workingDir}/dataset - --hive_metastore_uris${hive_metastore_uris} + --workingPath${workingDir}/workingD --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --preparedInfoPath${workingDir}/preparedInfo @@ -206,7 +205,7 @@ --sourcePath${sourcePath}/otherresearchproduct --outputPath${workingDir}/otherresearchproduct - --hive_metastore_uris${hive_metastore_uris} + --workingPath${workingDir}/workingO --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --preparedInfoPath${workingDir}/preparedInfo @@ -236,7 +235,7 @@ --sourcePath${sourcePath}/software --outputPath${workingDir}/software - --hive_metastore_uris${hive_metastore_uris} + --workingPath${workingDir}/workingS --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --preparedInfoPath${workingDir}/preparedInfo From d8503cd19144f64d77b88b9e68c4242b978d017f Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 24 Mar 2022 14:02:36 +0200 Subject: [PATCH 087/159] added moooar organizations --- .../oozie_app/scripts/step20-createMonitorDB.sql | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index f34e3fabb..76674b227 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -22,7 +22,16 @@ create table TARGET.result stored as parquet as 'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', - 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2') )) foo; + 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', + 'openorgs____::d169c7407dd417152596908d48c11460', + 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', + 'openorgs____::2fb1e47b4612688d9de9169d579939a7', + 'openorgs____::759d59f05d77188faee99b7493b46805', + 'openorgs____::cad284878801b9465fa51a95b1d779db', + 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', + 'openorgs____::c0286313e36479eff8676dba9b724b40' + -- ,'openorgs____::c80a8243a5e5c620d7931c88d93bf17a' -- Paris Diderot + ) )) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); From 61319b2e8324d73620ed3618acd527333fbceef6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 25 Mar 2022 16:38:33 +0100 Subject: [PATCH 088/159] updated dhp-schema version; set entity-level dataInfo before & after merging the fields from the group of duplicates --- .../eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java | 2 +- .../eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java | 11 ++++++++++- pom.xml | 2 +- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index b8ae4ca02..d345cf98f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -107,7 +107,7 @@ public class DedupRecordFactory { entity.setId(id); entity.setLastupdatetimestamp(ts); - entity.getDataInfo().setDeletedbyinference(false); + entity.setDataInfo(dataInfo); return entity; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index e86f91f99..aa3722ce5 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -77,7 +77,16 @@ class EntityMergerTest implements Serializable { // verify id assertEquals(dedupId, pub_merged.getId()); - assertEquals(pub_top.getJournal(), pub_merged.getJournal()); + assertEquals(pub_top.getJournal().getName(), pub_merged.getJournal().getName()); + assertEquals(pub_top.getJournal().getIssnOnline(), pub_merged.getJournal().getIssnOnline()); + assertEquals(pub_top.getJournal().getIssnLinking(), pub_merged.getJournal().getIssnLinking()); + assertEquals(pub_top.getJournal().getIssnPrinted(), pub_merged.getJournal().getIssnPrinted()); + assertEquals(pub_top.getJournal().getIss(), pub_merged.getJournal().getIss()); + assertEquals(pub_top.getJournal().getEp(), pub_merged.getJournal().getEp()); + assertEquals(pub_top.getJournal().getSp(), pub_merged.getJournal().getSp()); + assertEquals(pub_top.getJournal().getVol(), pub_merged.getJournal().getVol()); + assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate()); + assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace()); assertEquals("OPEN", pub_merged.getBestaccessright().getClassid()); assertEquals(pub_top.getResulttype(), pub_merged.getResulttype()); assertEquals(pub_top.getLanguage(), pub_merged.getLanguage()); diff --git a/pom.xml b/pom.xml index 86adee902..45265d5ba 100644 --- a/pom.xml +++ b/pom.xml @@ -797,7 +797,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.29] + [2.10.31] [4.0.3] [6.0.5] [3.1.6] From 3610f1749ab7896cc72f131236a3455635200c65 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 28 Mar 2022 09:20:27 +0200 Subject: [PATCH 089/159] merged pom.xml from beta branch --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 7a20a1652..45265d5ba 100644 --- a/pom.xml +++ b/pom.xml @@ -797,11 +797,11 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.30-SNAPSHOT] + [2.10.31] [4.0.3] [6.0.5] [3.1.6] - [4.1.7] + [4.1.12] [2.6.1] 7.5.0 4.7.2 From 395ac6ececc1ac72947fb9efffd3e49e25708ba6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 28 Mar 2022 09:23:42 +0200 Subject: [PATCH 090/159] merged pom.xml from beta branch --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 0f0aa711e..45265d5ba 100644 --- a/pom.xml +++ b/pom.xml @@ -797,7 +797,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.30] + [2.10.31] [4.0.3] [6.0.5] [3.1.6] From eca82e30c9b986be0a7049fbbaa477d91536c677 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 29 Mar 2022 09:46:49 +0200 Subject: [PATCH 091/159] updated dhp-schema version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 45265d5ba..6a14954e5 100644 --- a/pom.xml +++ b/pom.xml @@ -797,7 +797,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.31] + [2.10.32] [4.0.3] [6.0.5] [3.1.6] From 0a0ae84c2232d8ed7fa08ee8f8e77349fd14a90a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 29 Mar 2022 10:52:58 +0200 Subject: [PATCH 092/159] [graph raw] DOI based instance URLs on https --- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 639c1ab30..1bbeac9fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -25,7 +25,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { - public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; + public static final String HTTP_DX_DOI_PREIFX = "https://dx.doi.org/"; public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, final boolean forceOrginalId) { From 1b1101016944ee921da8b49dbeff9106c05a6220 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 29 Mar 2022 10:59:14 +0200 Subject: [PATCH 093/159] minor fix --- .../test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index ca1dbc665..136b0fb93 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -70,6 +70,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) + spark.read.load(targetPath).printSchema(); + + val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result From ee24f3eb2c8fd92f43a49a3358d7a083365995b5 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 29 Mar 2022 13:47:48 +0300 Subject: [PATCH 094/159] views cannot be stored as parquet... --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index b42640e10..eec037a54 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -15,6 +15,6 @@ CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources STORED AS PARQU SELECT organization AS id, id AS datasource FROM ${stats_db_name}.datasource_organizations; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects STORED AS PARQUET AS +CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS SELECT id AS project, organization as id FROM ${stats_db_name}.project_organizations; \ No newline at end of file From fff0b3cc199ae5fc5da302895d229fac776e3bfc Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 29 Mar 2022 14:15:31 +0300 Subject: [PATCH 095/159] added apcs in monitor db --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 76674b227..bcc9f0b5d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -90,6 +90,11 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; +create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_apc; + + + create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; From 7112806a735013f438463c64847321d025be41e6 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 29 Mar 2022 16:37:29 +0300 Subject: [PATCH 096/159] views cannot be stored as parquet... --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql index eec037a54..3da36dfe5 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql @@ -11,7 +11,7 @@ SELECT substr(o.id, 4) as id, FROM ${openaire_db_name}.organization o WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible = FALSE; -CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources STORED AS PARQUET AS +CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS SELECT organization AS id, id AS datasource FROM ${stats_db_name}.datasource_organizations; From 79336d46c5f7575619992e5d004d561166751c36 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 4 Apr 2022 15:52:31 +0200 Subject: [PATCH 097/159] [Clean Context] first naive implementation of a functionality to clean not wanted contextes from one result. This implementation simply verifies the main title of the results start with a given string --- .../oa/graph/clean/CleanContextSparkJob.java | 113 +++++++++++++ .../graph/input_clean_context_parameters.json | 37 ++++ .../dhp/oa/graph/clean/CleanContextTest.java | 159 ++++++++++++++++++ .../clean/publication_clean_context.json | 7 + 4 files changed, 316 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java new file mode 100644 index 000000000..b20dcb67b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -0,0 +1,113 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class CleanContextSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } + + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); + + res.map((MapFunction) r -> { + if(!r.getTitle() + .stream() + .filter(t -> t.getQualifier().getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ + return r; + } + r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)).collect(Collectors.toList())); + return r; + } ,Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath); + + spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json new file mode 100644 index 000000000..9b1588283 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -0,0 +1,37 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + },{ + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true +} +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java new file mode 100644 index 000000000..bba814346 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -0,0 +1,159 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + +public class CleanContextTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + + + spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) + .write().json(workingDir.toString() + "/publication"); + + + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId","sobigdata", + "-verifyParam","gCube " + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(7, tmp.count()); + + //original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions.assertEquals(0, + tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + + //original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + + //original result with sobigdata context with gcube as starting string in the subtitle + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); + List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata context with gcube not as starting string in the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata in context and also other contexts with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + + + //original result without sobigdata in context with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); + + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json new file mode 100644 index 000000000..b7c51d810 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json @@ -0,0 +1,7 @@ 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Nach Pausanias"},{"dataInfo":null,"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"gcube xiv die worter άγαλμα eίχών ξόανον ανδρuις und verwandte in ihren verschiedenen beziehungen nach pausanias"}],"journal":{"conferencedate":null,"conferenceplace":null,"dataInfo":null,"edition":null,"ep":null,"iss":null,"issnLinking":null,"issnOnline":"2196-7008","issnPrinted":"0031-7985","name":"Philologus","sp":null,"vol":"24"}} \ No newline at end of file From e77d1049511170f954f9122e54083dd491392387 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 5 Apr 2022 15:07:11 +0200 Subject: [PATCH 098/159] [OC] added / to workflow path --- .../dhp/actionmanager/opencitations/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml index aee2559ee..0f01039f7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml @@ -83,7 +83,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --workingPath${workingPath}/COCI - --outputPath${workingPath}/COCI_JSON + --outputPath${workingPath}/COCI_JSON/ --delimiter${delimiter} --inputFile${inputFileCoci} From c442c91f8951d42f89d1270797b833d270f9217b Mon Sep 17 00:00:00 2001 From: antleb Date: Wed, 6 Apr 2022 12:40:02 +0300 Subject: [PATCH 099/159] computing stats in each step --- .../scripts/step16-createIndicatorsTables.sql | 51 ++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index a95ee74d8..24e6bff7e 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -12,6 +12,8 @@ and (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp on p.id= tmp.id; +compute stats indi_pub_green_oa; + create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p @@ -22,6 +24,8 @@ join result_classifications rt on rt.id = p.id where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; +compute stats indi_pub_grey_lit; + create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p @@ -31,6 +35,7 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; +compute stats indi_pub_doi_from_crossref; ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -40,6 +45,8 @@ join result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence; + create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r @@ -49,16 +56,21 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence_url; + create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; +compute stats indi_pub_has_abstract; + create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp on r.id= tmp.id; +compute stats indi_result_with_orcid; ---- Sprint 3 ---- create table indi_funded_result_with_fundref stored as parquet as @@ -68,6 +80,8 @@ left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp on r.id= tmp.id; +compute stats indi_funded_result_with_fundref; + create table indi_result_org_country_collab stored as parquet as with tmp as (select o.id as id, o.country , ro.id as result,r.type from organization o @@ -79,6 +93,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id and o1.country<>o2.country group by o1.id, o1.type,o2.country; +compute stats indi_result_org_country_collab; + create table indi_result_org_collab stored as parquet as with tmp as (select o.id, ro.id as result,r.type from organization o @@ -90,6 +106,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id group by o1.id, o2.id, o1.type; +compute stats indi_result_org_collab; + create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op join organization o on o.id=op.id @@ -101,6 +119,8 @@ join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; +compute stats indi_funder_country_collab; + create table indi_result_country_collab stored as parquet as with tmp as (select country, ro.id as result,r.type from organization o @@ -112,6 +132,8 @@ join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; +compute stats indi_result_country_collab; + ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal @@ -123,6 +145,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp on pd.id=tmp.id; +compute stats indi_pub_diamond; + create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd @@ -133,6 +157,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid; + create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -143,6 +169,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and ps.is_transformative_journal=true) tmp on pd.id=tmp.id; +compute stats indi_pub_in_transformative; + create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri left outer join @@ -153,11 +181,12 @@ where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp on tmp.id=ri.id; - +compute stats indi_pub_closed_other_open; ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; +compute stats indi_result_no_of_copies; ---- Sprint 6 ---- create table indi_pub_gold_oa stored as parquet as WITH gold_oa AS ( @@ -183,6 +212,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_pub_gold_oa; + create table indi_datasets_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -210,6 +241,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_datasets_gold_oa; + create table indi_software_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -237,6 +270,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_software_gold_oa; + create table indi_org_findable stored as parquet as with result_with_pid as ( select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro @@ -263,6 +298,8 @@ join result_with_pid_share on result_with_pid_share.organization=allresults.orga left outer join ( select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +compute stats indi_org_findable; + create table indi_org_openess stored as parquet as WITH datasets_oa as ( SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg @@ -313,6 +350,8 @@ left outer join ( left outer join ( select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +compute stats indi_org_openess; + create table indi_pub_hybrid_oa_with_cc stored as parquet as WITH hybrid_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn @@ -343,6 +382,8 @@ LEFT OUTER JOIN ( JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid_oa_with_cc; + create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -350,6 +391,8 @@ where downloads>0 GROUP BY result_id order by no_dowloads desc; +compute stats indi_pub_downloads; + create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -357,15 +400,21 @@ where downloads>0 GROUP BY result_id, repository_id order by result_id; +compute stats indi_pub_downloads_datasource; + create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; +compute stats indi_pub_downloads_year; + create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; + +compute stats indi_pub_downloads_datasource_year; \ No newline at end of file From 05fafa14082fd7dbedc70c19505026a9fea60d72 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 6 Apr 2022 15:23:50 +0200 Subject: [PATCH 100/159] [graph raw] avoid NPEs importing datasource consent fields --- .../oa/graph/raw/MigrateDbEntitiesApplication.java | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 1f8c23ac3..b5801ca5c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -42,10 +42,7 @@ import java.io.IOException; import java.sql.Array; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.List; +import java.util.*; import java.util.function.Consumer; import java.util.function.Function; import java.util.function.Predicate; @@ -311,7 +308,13 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); - ds.setConsenttermsofusedate(rs.getDate("consenttermsofusedate").toString()); + ds + .setConsenttermsofusedate( + Optional + .ofNullable( + rs.getDate("consenttermsofusedate")) + .map(c -> c.toString()) + .orElse(null)); return Arrays.asList(ds); } catch (final Exception e) { From 4190c9f6bc2db772e0ea788c85a94c165d0f4cfa Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 6 Apr 2022 15:23:50 +0200 Subject: [PATCH 101/159] [graph raw] avoid NPEs importing datasource consent fields --- .../oa/graph/raw/MigrateDbEntitiesApplication.java | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 1f8c23ac3..b5801ca5c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -42,10 +42,7 @@ import java.io.IOException; import java.sql.Array; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.List; +import java.util.*; import java.util.function.Consumer; import java.util.function.Function; import java.util.function.Predicate; @@ -311,7 +308,13 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); - ds.setConsenttermsofusedate(rs.getDate("consenttermsofusedate").toString()); + ds + .setConsenttermsofusedate( + Optional + .ofNullable( + rs.getDate("consenttermsofusedate")) + .map(c -> c.toString()) + .orElse(null)); return Arrays.asList(ds); } catch (final Exception e) { From 66e718981ec4001bc7ddee5eace375b14e472a90 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 11:34:02 +0200 Subject: [PATCH 102/159] [maven-release-plugin] prepare release dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++---- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 25 insertions(+), 27 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..a4ab512a8 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..5efa96c43 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index db0097d64..05830a5c1 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.4 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..a193dd893 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..901e1b26f 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..559bc3125 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..f1a7b08f0 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..8f07db5be 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..3b8a09d16 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..5cb9283ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..e4685d7ff 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..f33b8c4c5 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..122362196 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.4 compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..fd60cafb2 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index e402d0600..518f8f565 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index c64c2f58e..ee52031e8 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 52f35ff07..3c1b2ec6e 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..b39a7a9a0 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..a9152062d 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..a4dbade09 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..47bda3d00 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/pom.xml b/pom.xml index 6a14954e5..44bef5516 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD + dhp-1.2.4 This module is the root descriptor for the dnet-hadoop project From 505420fd61e530dfbab5e689f3352280f08a1074 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 11:34:06 +0200 Subject: [PATCH 103/159] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 24 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index a4ab512a8..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 5efa96c43..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 05830a5c1..9d592943a 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4 + 1.2.5-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a193dd893..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 901e1b26f..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 559bc3125..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index f1a7b08f0..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 8f07db5be..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 3b8a09d16..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 5cb9283ce..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index e4685d7ff..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f33b8c4c5..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 122362196..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4 + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index fd60cafb2..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 518f8f565..ae8f3b53a 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ee52031e8..ce3e739a5 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 3c1b2ec6e..2bc610c42 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index b39a7a9a0..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index a9152062d..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index a4dbade09..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 47bda3d00..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 44bef5516..be58842a1 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - dhp-1.2.4 + HEAD This module is the root descriptor for the dnet-hadoop project From bc05b6168aa5cda8c4e014af385e01ed77e3c43d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 11:49:06 +0200 Subject: [PATCH 104/159] [maven-release-plugin] rollback the release of dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++++-- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 2 +- 22 files changed, 26 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 44165995d..012ff89a3 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 7579bdf45..256017e2c 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 9d592943a..db0097d64 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 9040ea94e..97fbdf45b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 6df11f4ea..7b18f0105 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 29e1fab1f..f63f3aa01 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 53d349d2a..c89cc9d1d 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 479a9e8c6..047767d33 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 5a41a0090..afbd93dcb 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,9 +1,11 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index a14076a78..f47f8ba6e 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index c3d3a7375..8c10538c0 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 37accbc4f..f496ea9a2 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 591cad252..0b4269acd 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 687f0de66..17146903a 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index ae8f3b53a..e402d0600 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ce3e739a5..c64c2f58e 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 2bc610c42..52f35ff07 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index 954c8bd39..a78f92d41 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 54e18580b..20d2f5b76 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index 8c71a5ca1..b1c51c497 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 541d59007..143178560 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index be58842a1..6a14954e5 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT pom From 85bc722ff49ff86d379c1c6b07c4229fe7da8bb4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 12:18:43 +0200 Subject: [PATCH 105/159] [maven-release-plugin] prepare release dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++---- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 25 insertions(+), 27 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..a4ab512a8 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..5efa96c43 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index db0097d64..05830a5c1 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.4 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..a193dd893 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..901e1b26f 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..559bc3125 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..f1a7b08f0 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..8f07db5be 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..3b8a09d16 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..5cb9283ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..e4685d7ff 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..f33b8c4c5 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..122362196 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.4 compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..fd60cafb2 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index e402d0600..518f8f565 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index c64c2f58e..ee52031e8 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 52f35ff07..3c1b2ec6e 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..b39a7a9a0 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..a9152062d 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..a4dbade09 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..47bda3d00 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/pom.xml b/pom.xml index 6a14954e5..44bef5516 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD + dhp-1.2.4 This module is the root descriptor for the dnet-hadoop project From 2ac2d928bd7b450753cfff1130ff3180da76052a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 12:18:47 +0200 Subject: [PATCH 106/159] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 24 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index a4ab512a8..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 5efa96c43..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 05830a5c1..9d592943a 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4 + 1.2.5-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a193dd893..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 901e1b26f..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 559bc3125..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index f1a7b08f0..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 8f07db5be..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 3b8a09d16..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 5cb9283ce..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index e4685d7ff..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f33b8c4c5..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 122362196..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4 + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index fd60cafb2..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 518f8f565..ae8f3b53a 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ee52031e8..ce3e739a5 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 3c1b2ec6e..2bc610c42 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index b39a7a9a0..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index a9152062d..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index a4dbade09..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 47bda3d00..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 44bef5516..be58842a1 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - dhp-1.2.4 + HEAD This module is the root descriptor for the dnet-hadoop project From 3bba6d6e384074014b5d5a9d97ca5633ddd2a4a6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 12:23:17 +0200 Subject: [PATCH 107/159] [maven-release-plugin] rollback the release of dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++++-- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 2 +- 22 files changed, 26 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 44165995d..012ff89a3 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 7579bdf45..256017e2c 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 9d592943a..db0097d64 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 9040ea94e..97fbdf45b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 6df11f4ea..7b18f0105 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 29e1fab1f..f63f3aa01 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 53d349d2a..c89cc9d1d 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 479a9e8c6..047767d33 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 5a41a0090..afbd93dcb 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,9 +1,11 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index a14076a78..f47f8ba6e 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index c3d3a7375..8c10538c0 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 37accbc4f..f496ea9a2 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 591cad252..0b4269acd 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 687f0de66..17146903a 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index ae8f3b53a..e402d0600 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ce3e739a5..c64c2f58e 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 2bc610c42..52f35ff07 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index 954c8bd39..a78f92d41 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 54e18580b..20d2f5b76 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index 8c71a5ca1..b1c51c497 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 541d59007..143178560 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index be58842a1..6a14954e5 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT pom From f03dea4f4993ac0b6c41d33bcfef2c4a0aa7f579 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:22:55 +0200 Subject: [PATCH 108/159] allow to skip maven site --- dhp-build/dhp-code-style/pom.xml | 4 ++++ pom.xml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index db0097d64..a7a67ff77 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -47,12 +47,16 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + true + + UTF-8 sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop diff --git a/pom.xml b/pom.xml index 6a14954e5..010dd56fe 100644 --- a/pom.xml +++ b/pom.xml @@ -551,6 +551,9 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + ${dhp.site.skip} + @@ -791,6 +794,7 @@ 2.4.0.cloudera2 2.9.6 3.5 + true 11.0.2 2.11.12 5.6.1 From db3d9877a55eb97abecf4936737465210d3c21c2 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:26:58 +0200 Subject: [PATCH 109/159] [maven-release-plugin] prepare release dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++---- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 25 insertions(+), 27 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..a4ab512a8 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..5efa96c43 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index a7a67ff77..ab942d9ac 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.4 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..a193dd893 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..901e1b26f 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..559bc3125 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..f1a7b08f0 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..8f07db5be 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..3b8a09d16 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..5cb9283ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..e4685d7ff 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..f33b8c4c5 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..122362196 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.4 compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..fd60cafb2 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index e402d0600..518f8f565 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index c64c2f58e..ee52031e8 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 52f35ff07..3c1b2ec6e 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..b39a7a9a0 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..a9152062d 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..a4dbade09 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..47bda3d00 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/pom.xml b/pom.xml index 010dd56fe..2a807e3d0 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD + dhp-1.2.4 This module is the root descriptor for the dnet-hadoop project From 598e11dfd77edfd56457b620810f7aff26c82bb0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:27:02 +0200 Subject: [PATCH 110/159] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 24 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index a4ab512a8..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 5efa96c43..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index ab942d9ac..5a86efe17 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4 + 1.2.5-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a193dd893..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 901e1b26f..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 559bc3125..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index f1a7b08f0..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 8f07db5be..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 3b8a09d16..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 5cb9283ce..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index e4685d7ff..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f33b8c4c5..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 122362196..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4 + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index fd60cafb2..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 518f8f565..ae8f3b53a 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ee52031e8..ce3e739a5 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 3c1b2ec6e..2bc610c42 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index b39a7a9a0..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index a9152062d..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index a4dbade09..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 47bda3d00..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 2a807e3d0..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - dhp-1.2.4 + HEAD This module is the root descriptor for the dnet-hadoop project From ad85d88eafbd14fc1a7ef7a53fe8c3e180c6b4af Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:28:35 +0200 Subject: [PATCH 111/159] [maven-release-plugin] rollback the release of dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++++-- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 2 +- 22 files changed, 26 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 44165995d..012ff89a3 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 7579bdf45..256017e2c 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 5a86efe17..a7a67ff77 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 9040ea94e..97fbdf45b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 6df11f4ea..7b18f0105 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 29e1fab1f..f63f3aa01 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 53d349d2a..c89cc9d1d 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 479a9e8c6..047767d33 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 5a41a0090..afbd93dcb 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,9 +1,11 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index a14076a78..f47f8ba6e 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index c3d3a7375..8c10538c0 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 37accbc4f..f496ea9a2 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 591cad252..0b4269acd 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 687f0de66..17146903a 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index ae8f3b53a..e402d0600 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ce3e739a5..c64c2f58e 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 2bc610c42..52f35ff07 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index 954c8bd39..a78f92d41 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 54e18580b..20d2f5b76 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index 8c71a5ca1..b1c51c497 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 541d59007..143178560 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 136b9b867..010dd56fe 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.5-SNAPSHOT + 1.2.4-SNAPSHOT pom From 86585a6b274ad8e0beaa9e7f43d123b7320739be Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:32:19 +0200 Subject: [PATCH 112/159] [maven-release-plugin] prepare release dhp-1.2.4 --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 6 ++---- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 25 insertions(+), 27 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..a4ab512a8 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..5efa96c43 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.4 dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index a7a67ff77..ab942d9ac 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.4 jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..a193dd893 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..901e1b26f 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..559bc3125 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..f1a7b08f0 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.4 dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..8f07db5be 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..3b8a09d16 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..5cb9283ce 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..e4685d7ff 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..f33b8c4c5 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..122362196 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.4 compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..fd60cafb2 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index e402d0600..518f8f565 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index c64c2f58e..ee52031e8 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 52f35ff07..3c1b2ec6e 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..b39a7a9a0 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..a9152062d 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..a4dbade09 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.4 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..47bda3d00 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 ../pom.xml diff --git a/pom.xml b/pom.xml index 010dd56fe..2a807e3d0 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.4 pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD + dhp-1.2.4 This module is the root descriptor for the dnet-hadoop project From c26222623fbd81dee46040acddab4fa9cd644296 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 7 Apr 2022 13:32:22 +0200 Subject: [PATCH 113/159] [maven-release-plugin] prepare for next development iteration --- dhp-build/dhp-build-assembly-resources/pom.xml | 2 +- dhp-build/dhp-build-properties-maven-plugin/pom.xml | 2 +- dhp-build/dhp-code-style/pom.xml | 2 +- dhp-build/pom.xml | 2 +- dhp-common/pom.xml | 2 +- dhp-workflows/dhp-actionmanager/pom.xml | 2 +- dhp-workflows/dhp-aggregation/pom.xml | 2 +- dhp-workflows/dhp-blacklist/pom.xml | 2 +- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-dedup-openaire/pom.xml | 2 +- dhp-workflows/dhp-distcp/pom.xml | 2 +- dhp-workflows/dhp-doiboost/pom.xml | 2 +- dhp-workflows/dhp-enrichment/pom.xml | 4 ++-- dhp-workflows/dhp-graph-mapper/pom.xml | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 2 +- dhp-workflows/dhp-stats-promote/pom.xml | 2 +- dhp-workflows/dhp-stats-update/pom.xml | 2 +- dhp-workflows/dhp-usage-raw-data-update/pom.xml | 2 +- dhp-workflows/dhp-usage-stats-build/pom.xml | 2 +- dhp-workflows/dhp-workflow-profiles/pom.xml | 2 +- dhp-workflows/pom.xml | 2 +- pom.xml | 4 ++-- 22 files changed, 24 insertions(+), 24 deletions(-) diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index a4ab512a8..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 5efa96c43..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4 + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index ab942d9ac..5a86efe17 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4 + 1.2.5-SNAPSHOT jar diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index a193dd893..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 901e1b26f..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index 559bc3125..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index f1a7b08f0..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4 + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 8f07db5be..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index 3b8a09d16..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index 5cb9283ce..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index e4685d7ff..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f33b8c4c5..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 122362196..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4 + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index fd60cafb2..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index 518f8f565..ae8f3b53a 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index ee52031e8..ce3e739a5 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 3c1b2ec6e..2bc610c42 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index b39a7a9a0..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index a9152062d..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index a4dbade09..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4 + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 47bda3d00..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 2a807e3d0..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4 + 1.2.5-SNAPSHOT pom @@ -37,7 +37,7 @@ scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git https://code-repo.d4science.org/D-Net/dnet-hadoop/ - dhp-1.2.4 + HEAD This module is the root descriptor for the dnet-hadoop project From 21f32b83c68f75fcf7122454f0f66cd16a5e0f2f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Apr 2022 08:52:12 +0200 Subject: [PATCH 114/159] [graph enrichment] fixed country_propagation oozie workflow definition, parameter saveGraph is not needed anymore by the SparkCountryPropagationJob --- .../eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index 202c86a6d..271ccbf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -274,7 +274,6 @@ --sourcePath${sourcePath}/publication --preparedInfoPath${workingDir}/publication - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -304,7 +303,6 @@ --sourcePath${sourcePath}/dataset --preparedInfoPath${workingDir}/dataset - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -334,7 +332,6 @@ --sourcePath${sourcePath}/otherresearchproduct --preparedInfoPath${workingDir}/otherresearchproduct - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -364,7 +361,6 @@ --sourcePath${sourcePath}/software --preparedInfoPath${workingDir}/software - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software From 48b580b45cc2e36ca08d73e2b111ffed019dfce1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Apr 2022 08:52:12 +0200 Subject: [PATCH 115/159] [graph enrichment] fixed country_propagation oozie workflow definition, parameter saveGraph is not needed anymore by the SparkCountryPropagationJob --- .../eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index 202c86a6d..271ccbf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -274,7 +274,6 @@ --sourcePath${sourcePath}/publication --preparedInfoPath${workingDir}/publication - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -304,7 +303,6 @@ --sourcePath${sourcePath}/dataset --preparedInfoPath${workingDir}/dataset - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -334,7 +332,6 @@ --sourcePath${sourcePath}/otherresearchproduct --preparedInfoPath${workingDir}/otherresearchproduct - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -364,7 +361,6 @@ --sourcePath${sourcePath}/software --preparedInfoPath${workingDir}/software - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software From 73c172926a03447119b2fa4dccdd9765e736b2a5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 12 Apr 2022 10:25:42 +0200 Subject: [PATCH 116/159] [Doiboost] fixed fundingReference extraction from the Crossref records --- .../doiboost/crossref/Crossref2Oaf.scala | 39 +++++++------------ 1 file changed, 14 insertions(+), 25 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0cb08ea94..b4d6d67e2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -446,16 +446,12 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) - case "10.13039/100000001" => - generateSimpleRelationFromAward(funder, "nsf_________", a => a) - case "10.13039/501100001665" => - generateSimpleRelationFromAward(funder, "anr_________", a => a) - case "10.13039/501100002341" => - generateSimpleRelationFromAward(funder, "aka_________", a => a) + case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) + case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) case "10.13039/501100001602" => - generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) - case "10.13039/501100000923" => - generateSimpleRelationFromAward(funder, "arc_________", a => a) + generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", "")) + case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) case "10.13039/501100000038" => val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) @@ -468,14 +464,10 @@ case object Crossref2Oaf { val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) - case "10.13039/501100002848" => - generateSimpleRelationFromAward(funder, "conicytf____", a => a) - case "10.13039/501100003448" => - generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) - case "10.13039/501100010198" => - generateSimpleRelationFromAward(funder, "sgov________", a => a) - case "10.13039/501100004564" => - generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) + case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a) + case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) + case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a) + case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a => a) val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63") @@ -487,15 +479,11 @@ case object Crossref2Oaf { "irb_hr______", a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "") ) - case "10.13039/501100006769" => - generateSimpleRelationFromAward(funder, "rsf_________", a => a) - case "10.13039/501100001711" => - generateSimpleRelationFromAward(funder, "snsf________", snsfRule) - case "10.13039/501100004410" => - generateSimpleRelationFromAward(funder, "tubitakf____", a => a) - case "10.10.13039/100004440" => - generateSimpleRelationFromAward(funder, "wt__________", a => a) + case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a) + case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule) + case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a) case "10.13039/100004440" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) @@ -516,6 +504,7 @@ case object Crossref2Oaf { case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) case "Wellcome Trust Masters Fellowship" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) From b93a141d6c76aa4e89413868f87a9b6604046ba1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 12 Apr 2022 10:25:42 +0200 Subject: [PATCH 117/159] [Doiboost] fixed fundingReference extraction from the Crossref records --- .../doiboost/crossref/Crossref2Oaf.scala | 39 +++++++------------ 1 file changed, 14 insertions(+), 25 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0cb08ea94..b4d6d67e2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -446,16 +446,12 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) - case "10.13039/100000001" => - generateSimpleRelationFromAward(funder, "nsf_________", a => a) - case "10.13039/501100001665" => - generateSimpleRelationFromAward(funder, "anr_________", a => a) - case "10.13039/501100002341" => - generateSimpleRelationFromAward(funder, "aka_________", a => a) + case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) + case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) case "10.13039/501100001602" => - generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) - case "10.13039/501100000923" => - generateSimpleRelationFromAward(funder, "arc_________", a => a) + generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", "")) + case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) case "10.13039/501100000038" => val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) @@ -468,14 +464,10 @@ case object Crossref2Oaf { val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) - case "10.13039/501100002848" => - generateSimpleRelationFromAward(funder, "conicytf____", a => a) - case "10.13039/501100003448" => - generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) - case "10.13039/501100010198" => - generateSimpleRelationFromAward(funder, "sgov________", a => a) - case "10.13039/501100004564" => - generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) + case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a) + case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) + case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a) + case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a => a) val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63") @@ -487,15 +479,11 @@ case object Crossref2Oaf { "irb_hr______", a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "") ) - case "10.13039/501100006769" => - generateSimpleRelationFromAward(funder, "rsf_________", a => a) - case "10.13039/501100001711" => - generateSimpleRelationFromAward(funder, "snsf________", snsfRule) - case "10.13039/501100004410" => - generateSimpleRelationFromAward(funder, "tubitakf____", a => a) - case "10.10.13039/100004440" => - generateSimpleRelationFromAward(funder, "wt__________", a => a) + case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a) + case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule) + case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a) case "10.13039/100004440" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) @@ -516,6 +504,7 @@ case object Crossref2Oaf { case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) case "Wellcome Trust Masters Fellowship" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) From d5b29d96a7c7b8d77e2b31599a65e4bd48164382 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Apr 2022 11:07:04 +0200 Subject: [PATCH 118/159] fix merging in crossrefAggregator which creates dataInfo null --- .../main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9323c994c..79b9e8183 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -71,6 +71,7 @@ object SparkGenerateDoiBoost { } } else { if (a != null && a._2 != null) { + b.mergeOAFDataInfo(a._2) b.mergeFrom(a._2) b.setId(a._1) val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor) @@ -87,6 +88,7 @@ object SparkGenerateDoiBoost { return b2 } else { if (b2 != null) { + b1.mergeOAFDataInfo(b2) b1.mergeFrom(b2) val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) b1.setAuthor(authors) From 4314db55c8bf94150cabe07d7b2342fc18ec1001 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 19 Apr 2022 15:05:02 +0200 Subject: [PATCH 119/159] migration to services: update sql queries --- ...eryDatasourceOrganization.sql => queryServiceOrganization.sql} | 0 .../dhp/oa/graph/sql/{queryDatasources.sql => queryServices.sql} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/{queryDatasourceOrganization.sql => queryServiceOrganization.sql} (100%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/{queryDatasources.sql => queryServices.sql} (100%) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql From c96a8613f8152311480aec93b65a627d4f6421f3 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 20 Apr 2022 12:07:49 +0200 Subject: [PATCH 120/159] update SQL queries --- .../dhp/oa/graph/sql/queryOrganizations.sql | 2 +- .../oa/graph/sql/queryProjectOrganization.sql | 2 +- .../dhp/oa/graph/sql/queryProjects.sql | 2 +- .../oa/graph/sql/queryProjects_production.sql | 2 +- .../oa/graph/sql/queryServiceOrganization.sql | 8 +-- .../dhp/oa/graph/sql/queryServices.sql | 57 +++++++++++-------- 6 files changed, 40 insertions(+), 33 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index 11a8c50af..3451333c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -27,7 +27,7 @@ SELECT 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid FROM dsm_organizations o - LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) + LEFT OUTER JOIN dsm_services d ON (d.id = o.collectedfrom) LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = p.pid) GROUP BY diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index bcdef8221..d9a77427d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -16,4 +16,4 @@ SELECT FROM project_organization po LEFT OUTER JOIN projects p ON (p.id = po.project) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom); \ No newline at end of file + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql index db0da83f7..af5913e75 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql @@ -42,7 +42,7 @@ SELECT LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql index 234bb7c3e..80cbda4b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql @@ -40,7 +40,7 @@ SELECT LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql index f72e72105..02bed4b65 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql @@ -1,5 +1,5 @@ SELECT - dor.datasource AS datasource, + dor.service AS service, dor.organization AS organization, NULL AS startdate, NULL AS enddate, @@ -11,6 +11,6 @@ SELECT dc.officialname AS collectedfromname, 'providedBy@@@dnet:datasources_organizations_typologies' AS semantics, d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction -FROM dsm_datasource_organization dor - LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom); \ No newline at end of file +FROM dsm_service_organization dor + LEFT OUTER JOIN dsm_services d ON (dor.service = d.id) + LEFT OUTER JOIN dsm_services dc ON (dc.id = d.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 2623c65c4..81be79420 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -57,8 +57,12 @@ SELECT NULL AS odpolicies, ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + + -- Term provided only by OpenDOAR: + -- probably updating the TR it could be replaced by research_entity_types[] + -- But a study on the vocabulary terms is needed + -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + false AS inferred, false AS deletedbyinference, 0.9 AS trust, @@ -69,22 +73,25 @@ SELECT d.releasestartdate AS releasestartdate, d.releaseenddate AS releaseenddate, d.missionstatementurl AS missionstatementurl, - d.dataprovider AS dataprovider, - d.serviceprovider AS serviceprovider, + -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[] + -- VALUE 'Research Data' : d.dataprovider AS dataprovider, + -- VALUE 'Services' : d.serviceprovider AS serviceprovider, d.databaseaccesstype AS databaseaccesstype, d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, - d.versioning AS versioning, + -- REPLACED BY version_control : d.versioning AS versioning, + d.version_control AS versioning, d.citationguidelineurl AS citationguidelineurl, - d.qualitymanagementkind AS qualitymanagementkind, + -- REMOVED (it was provided only by re3data: yes, no, unknown): d.qualitymanagementkind AS qualitymanagementkind, d.pidsystems AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - d.typology||'@@@dnet:datasource_typologies' AS datasourcetype, - d.typology||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, + d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, + d.eosc_type||'@@@dnet:eosc_types' AS eosc_type, + d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eosc_datasoorce_type, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, @@ -92,16 +99,15 @@ SELECT d.consenttermsofuse AS consenttermsofuse, d.fulltextdownload AS fulltextdownload, d.consenttermsofusedate AS consenttermsofusedate, - de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, - de.thematic AS thematic, - de.knowledge_graph AS knowledgegraph, - array(select unnest(de.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies + d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, + d.thematic AS thematic, + -- REMOVED ???: d.knowledge_graph AS knowledgegraph, + array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies -FROM dsm_datasources d -LEFT OUTER JOIN dsm_datasources_eosc de on (d.id = de.id) -LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id) -LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource) -LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource) +FROM dsm_services d +LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) +LEFT OUTER JOIN dsm_api a ON (d.id = a.service) +LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) GROUP BY d.id, @@ -119,15 +125,16 @@ GROUP BY d.releasestartdate, d.releaseenddate, d.missionstatementurl, - d.dataprovider, - d.serviceprovider, + -- TODO REMOVED ???: d.dataprovider, + -- TODO REMOVED ???: d.serviceprovider, d.databaseaccesstype, d.datauploadtype, d.databaseaccessrestriction, d.datauploadrestriction, - d.versioning, + -- REPLACED BY version_control : d.versioning, + d.version_control d.citationguidelineurl, - d.qualitymanagementkind, + -- REMOVED: d.qualitymanagementkind, d.pidsystems, d.certificates, dc.id, @@ -135,7 +142,7 @@ GROUP BY d.issn, d.eissn, d.lissn, - de.jurisdiction, - de.thematic, - de.knowledge_graph, - de.content_policies + d.jurisdiction, + d.thematic, + -- REMOVED ???: de.knowledge_graph, + d.content_policies From 869407c6e202e765ba26d15b684ad47c516eff12 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 14:02:05 +0200 Subject: [PATCH 121/159] [Measures] added new measure (usagecounts) as action set. Measure added at the level of the result. Ref #7587 --- .../dnetlib/dhp/actionmanager/Constants.java | 2 + .../usagestats/SparkAtomicActionUsageJob.java | 165 ++++++++++++++++++ .../usagestats/UsageStatsModel.java | 34 ++++ .../usagestats/input_actionset_parameter.json | 26 +++ .../usagestats/oozie_app/config-default.xml | 30 ++++ .../usagestats/oozie_app/workflow.xml | 98 +++++++++++ .../SparkAtomicActionCountJobTest.java | 133 ++++++++++++++ .../dhp/actionmanager/usagestats/usagestatsdb | 12 ++ pom.xml | 2 +- 9 files changed, 501 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index b790d90cb..aa25ca633 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -27,6 +27,8 @@ public class Constants { public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE"; public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip"; public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg"; + public static final String UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID = "measure:usage_counts"; + public static final String UPDATE_KEY_USAGE_COUNTS = "count"; public static final String FOS_CLASS_ID = "FOS"; public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java new file mode 100644 index 000000000..04f861df5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static eu.dnetlib.dhp.actionmanager.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.cxf.wsdl.service.factory.MethodNameSoapActionServiceConfiguration; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; +import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Measure; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import lombok.val; +import scala.Tuple2; + +/** + * created the Atomic Action for each tipe of results + */ +public class SparkAtomicActionUsageJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionUsageJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionUsageJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + + final String dbname = parser.get("statsdb"); + + final String workingPath = parser.get("workingPath"); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(dbname, spark, outputPath); + prepareActionSet(spark, workingPath, outputPath); + }); + } + + public static void prepareResults(String db, SparkSession spark, String workingPath) { + spark + .sql( + "Select result_id, downloads, views " + + "from " + db + ".usage_stats") + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + } + + public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath){ + readPath(spark, inputPath, UsageStatsModel.class) + .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + UsageStatsModel first = it.next(); + it.forEachRemaining(us -> { + first.setDownloads(first.getDownloads() + us.getDownloads()); + first.setViews(first.getViews() + us.getViews()); + }); + + Result res = new Result(); + res.setId("50|" + k); + + + res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); + return res; + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static List getMeasure(Long downloads, Long views) { + DataInfo dataInfo = OafMapperUtils + .dataInfo( + false, + UPDATE_DATA_INFO_TYPE, + true, + false, + OafMapperUtils + .qualifier( + UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID, + UPDATE_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + ""); + + return Arrays + .asList( + Measure + .newInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + Measure.newInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java new file mode 100644 index 000000000..df8a77eb6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import java.io.Serializable; + +public class UsageStatsModel implements Serializable { + private String result_id; + private Long downloads; + private Long views; + + public String getResult_id() { + return result_id; + } + + public void setResult_id(String result_id) { + this.result_id = result_id; + } + + public Long getDownloads() { + return downloads; + } + + public void setDownloads(Long downloads) { + this.downloads = downloads; + } + + public Long getViews() { + return views; + } + + public void setViews(Long views) { + this.views = views; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json new file mode 100644 index 000000000..b8ae24e12 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "hmu", + "paramLongName": "hive_metastore_uris", + "paramDescription": "the URI for the hive metastore", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "sdb", + "paramLongName": "statsdb", + "paramDescription": "the name of the db to be used", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml new file mode 100644 index 000000000..781efb475 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -0,0 +1,98 @@ + + + + outputPath + the path where to store the actionset + + + statsdb + the path where to store the actionset + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn + cluster + Produces the atomic action with the usage stats count for results + eu.dnetlib.dhp.actionmanager.usagestats.SparkAtomicActionUsageJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --hive_metastore_uris${hiveMetastoreUris} + --outputPath${outputPath} + --statsdb${statsdb} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java new file mode 100644 index 000000000..33d76893d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -0,0 +1,133 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkAtomicActionCountJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionCountJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionCountJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionCountJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkAtomicActionCountJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testMatch() { + String usageScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); + + SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/actionSet") + .map(usm -> OBJECT_MAPPER.readValue(usm, Result.class)); + + Assertions.assertEquals(9, tmp.count()); + + tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); + + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("measure:usage_counts", + u.getDataInfo().getProvenanceaction().getClassid())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("Inferred by OpenAIRE", + u.getDataInfo().getProvenanceaction().getClassname())))); + + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("count", + u.getKey())))); + + Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + + Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("5", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + + Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("1", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + + Assertions.assertEquals("2", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("6", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + } + + + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb new file mode 100644 index 000000000..fee74f697 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb @@ -0,0 +1,12 @@ +{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4} +{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1} +{"result_id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"result_id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"result_id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3} +{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3} +{"result_id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"result_id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8} +{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2} +{"result_id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/pom.xml b/pom.xml index 136b9b867..b0957393a 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.32] + [2.11.34-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 5feae77937df688e43f8c17988424dcf04259722 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 15:13:09 +0200 Subject: [PATCH 122/159] [Measures] last changes to accomodate tests --- .../usagestats/SparkAtomicActionUsageJob.java | 23 +- .../usagestats/input_actionset_parameter.json | 6 + .../usagestats/oozie_app/workflow.xml | 1 + .../SparkAtomicActionCountJobTest.java | 200 ++++++++++++++---- 4 files changed, 181 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 04f861df5..012261c39 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -94,19 +94,19 @@ public class SparkAtomicActionUsageJob implements Serializable { public static void prepareResults(String db, SparkSession spark, String workingPath) { spark - .sql( - "Select result_id, downloads, views " + - "from " + db + ".usage_stats") - .as(Encoders.bean(UsageStatsModel.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath); + .sql( + "Select result_id, downloads, views " + + "from " + db + ".usage_stats") + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); } - public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath){ - readPath(spark, inputPath, UsageStatsModel.class) - .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) + public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath) { + readPath(spark, inputPath, UsageStatsModel.class) + .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { UsageStatsModel first = it.next(); it.forEachRemaining(us -> { @@ -117,7 +117,6 @@ public class SparkAtomicActionUsageJob implements Serializable { Result res = new Result(); res.setId("50|" + k); - res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json index b8ae24e12..821905da4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -22,5 +22,11 @@ "paramLongName": "statsdb", "paramDescription": "the name of the db to be used", "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the workingPath where to save the content of the usage_stats table", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml index 781efb475..5b552ca4b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -89,6 +89,7 @@ --hive_metastore_uris${hiveMetastoreUris} --outputPath${outputPath} --statsdb${statsdb} + --workingPath${workingDir}/usageDb diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 33d76893d..7cc9eb326 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -75,7 +75,7 @@ public class SparkAtomicActionCountJobTest { .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") .getPath(); - SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); @@ -86,48 +86,174 @@ public class SparkAtomicActionCountJobTest { Assertions.assertEquals(9, tmp.count()); tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("measure:usage_counts", - u.getDataInfo().getProvenanceaction().getClassid())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("Inferred by OpenAIRE", - u.getDataInfo().getProvenanceaction().getClassname())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "measure:usage_counts", + u.getDataInfo().getProvenanceaction().getClassid())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "Inferred by OpenAIRE", + u.getDataInfo().getProvenanceaction().getClassname())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("count", - u.getKey())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "count", + u.getKey())))); - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + Assertions + .assertEquals( + 1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); - Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("5", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "5", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); - Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("1", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "1", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); - Assertions.assertEquals("2", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("6", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "2", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "6", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); } - - } From dbfbe8841a8ec3335ed479111cc96b48f2a6b30b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 15:41:03 +0200 Subject: [PATCH 123/159] [Clean Context] changed the description in input parameters --- .../dnetlib/dhp/oa/graph/input_clean_context_parameters.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json index 9b1588283..e3d31d69f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -20,7 +20,7 @@ { "paramName": "ci", "paramLongName": "contextId", - "paramDescription": "url to the ISLookup Service", + "paramDescription": "the id of the context to be removed", "paramRequired": true }, { @@ -31,7 +31,7 @@ },{ "paramName": "vf", "paramLongName": "verifyParam", - "paramDescription": "url to the ISLookup Service", + "paramDescription": "the parameter to be verified to remove the context", "paramRequired": true } ] From 5295effc9664fea8f92e148019d36469091484fd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 16:20:40 +0200 Subject: [PATCH 124/159] [Measures] fixed issue --- .../dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 012261c39..261794598 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -87,7 +87,7 @@ public class SparkAtomicActionUsageJob implements Serializable { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareResults(dbname, spark, outputPath); + prepareResults(dbname, spark, workingPath); prepareActionSet(spark, workingPath, outputPath); }); } From c304657d9195b334c44bce4a11649a68c60a3299 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 11:27:26 +0200 Subject: [PATCH 125/159] [Measures] put the logic in common, no need to change the schema --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 15 +++++++++++++ .../usagestats/SparkAtomicActionUsageJob.java | 22 ++++--------------- pom.xml | 2 +- 3 files changed, 20 insertions(+), 19 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 0a51e8600..8d67ce804 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -391,4 +391,19 @@ public class OafMapperUtils { } return null; } + + public static KeyValue newKeyValueInstance (String key, String value, DataInfo dataInfo){ + KeyValue kv = new KeyValue(); + kv.setDataInfo(dataInfo); + kv.setKey(key); + kv.setValue(value); + return kv; + } + + public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) { + Measure m = new Measure(); + m.setId(id); + m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo))); + return m; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 261794598..790170ccc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -3,23 +3,14 @@ package eu.dnetlib.dhp.actionmanager.usagestats; import static eu.dnetlib.dhp.actionmanager.Constants.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; -import org.apache.cxf.wsdl.service.factory.MethodNameSoapActionServiceConfiguration; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -31,19 +22,15 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; -import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import lombok.val; -import scala.Tuple2; + /** * created the Atomic Action for each tipe of results @@ -143,9 +130,8 @@ public class SparkAtomicActionUsageJob implements Serializable { return Arrays .asList( - Measure - .newInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), - Measure.newInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + OafMapperUtils.newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); } diff --git a/pom.xml b/pom.xml index b0957393a..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.11.34-SNAPSHOT] + [2.10.32] [4.0.3] [6.0.5] [3.1.6] From d012d125d7b5c75a5d492353a0e387f05cf0934e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:02:09 +0200 Subject: [PATCH 126/159] [EOSCTag] - --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java new file mode 100644 index 000000000..2b44275cd --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -0,0 +1,67 @@ +package eu.dnetlib.dhp.bulktag; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; +import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; +import eu.dnetlib.dhp.bulktag.community.ProtoMap; +import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Optional; + +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class SparkEoscTag { + private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosctag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + execEoscTag(spark, inputPath); + + }); + } + + private static void execEoscTag(SparkSession spark, String inputPath) { + //search for notebook + //subject contiene jupyter. + //esistono python e notebook nei subject non necessariamente nello stesso + //si cerca fra i prodotto di tipo software + Dataset sw = readPath(spark, inputPath + "/software", Software.class) + + } +} From b61efd613b5ba5e324f2a1e4a40f549baf52b4dc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:09:37 +0200 Subject: [PATCH 127/159] [Measures] addressed comments in the PR --- .../eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java | 2 +- .../usagestats/SparkAtomicActionUsageJob.java | 9 ++++----- .../usagestats/input_actionset_parameter.json | 2 +- .../dhp/actionmanager/usagestats/oozie_app/workflow.xml | 6 +++--- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 8d67ce804..9ee359cd5 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -392,7 +392,7 @@ public class OafMapperUtils { return null; } - public static KeyValue newKeyValueInstance (String key, String value, DataInfo dataInfo){ + public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) { KeyValue kv = new KeyValue(); kv.setDataInfo(dataInfo); kv.setKey(key); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 790170ccc..04533aa53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -22,7 +22,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; @@ -31,7 +30,6 @@ import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; - /** * created the Atomic Action for each tipe of results */ @@ -65,7 +63,7 @@ public class SparkAtomicActionUsageJob implements Serializable { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String dbname = parser.get("statsdb"); + final String dbname = parser.get("usagestatsdb"); final String workingPath = parser.get("workingPath"); @@ -130,8 +128,9 @@ public class SparkAtomicActionUsageJob implements Serializable { return Arrays .asList( - OafMapperUtils.newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), - OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + OafMapperUtils + .newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json index 821905da4..e9200d3ad 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -19,7 +19,7 @@ }, { "paramName": "sdb", - "paramLongName": "statsdb", + "paramLongName": "usagestatsdb", "paramDescription": "the name of the db to be used", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml index 5b552ca4b..d94cf7d53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -5,8 +5,8 @@ the path where to store the actionset - statsdb - the path where to store the actionset + usagestatsdb + the name of the db to be used sparkDriverMemory @@ -88,7 +88,7 @@ --hive_metastore_uris${hiveMetastoreUris} --outputPath${outputPath} - --statsdb${statsdb} + --usagestatsdb${usagestatsdb} --workingPath${workingDir}/usageDb From 20de75ca64cb0237dcc6a19caa0fc1308d60f7d5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:14:03 +0200 Subject: [PATCH 128/159] [Measures] removed typo --- .../dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 04533aa53..c284ad8bd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -31,7 +31,7 @@ import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** - * created the Atomic Action for each tipe of results + * created the Atomic Action for each type of results */ public class SparkAtomicActionUsageJob implements Serializable { From ccba1a3db1f5dfd99743e4aee957a2e5553f4a83 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 13:00:06 +0200 Subject: [PATCH 129/159] [Clean Context] added logic to cleaning workflow to accomodate also context cleaning --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index dc0529012..58ad6f1f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -13,6 +13,10 @@ isLookupUrl the address of the lookUp service + + shouldCleanContext + false + sparkDriverMemory @@ -275,7 +279,23 @@ - + + + + + ${wf:conf('shouldCleanContext') eq true} + + + + + + + + + + + + \ No newline at end of file From 5b7d9e741c2a77d408cc0db3ef9d357c4c27fe96 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 13:02:14 +0200 Subject: [PATCH 130/159] [Clean Context] added logic to cleaning workflow to accomodate also context cleaning --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 108 ++++++++++++++++++ 1 file changed, 108 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 58ad6f1f5..12ba3e5a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -295,7 +295,115 @@ + + + yarn + cluster + Clean publications context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${inputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + yarn + cluster + Clean datasets Context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + yarn + cluster + Clean otherresearchproducts context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + + yarn + cluster + Clean softwares context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + \ No newline at end of file From 29150a5d0c69a540b546ffcfbc91114e68c40301 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 Apr 2022 13:31:56 +0200 Subject: [PATCH 131/159] code formatting --- .../oa/graph/clean/CleanContextSparkJob.java | 181 +++++---- .../dhp/oa/graph/clean/CleanContextTest.java | 375 ++++++++++++------ 2 files changed, 357 insertions(+), 199 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index b20dcb67b..3e9b17f3f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -1,16 +1,13 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,93 +18,113 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + Class entityClazz = (Class) Class.forName(graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, + String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); - }); - } + res.map((MapFunction) r -> { + if (!r + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return r; + } + r + .setContext( + r + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if(!r.getTitle() - .stream() - .filter(t -> t.getQualifier().getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ - return r; - } - r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)).collect(Collectors.toList())); - return r; - } ,Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath); - } + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index bba814346..472d3781d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -1,18 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,133 +21,280 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.Locale; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); - spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) - .write().json(workingDir.toString() + "/publication"); + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId", "sobigdata", + "-verifyParam", "gCube " + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-contextId","sobigdata", - "-verifyParam","gCube " - }); + Assertions.assertEquals(7, tmp.count()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + // original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getContext() + .size()); - Assertions.assertEquals(7, tmp.count()); + // original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); - //original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions.assertEquals(0, - tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + // original result with sobigdata context with gcube as starting string in the subtitle + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + List titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + // original result with sobigdata context with gcube not as starting string in the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::1", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube as starting string in the subtitle - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); - List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube not as starting string in the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - //original result with sobigdata in context and also other contexts with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result without sobigdata in context with gcube as starting string for the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); - //original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - - //original result without sobigdata in context with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); - - - } + } } From 9a961a0092d2de554c197934cb317beb5bb0335f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 15:12:24 +0200 Subject: [PATCH 132/159] [Clean Context] fixed issue in param name --- .../oa/graph/clean/CleanContextSparkJob.java | 181 +++++---- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 20 +- .../dhp/oa/graph/clean/CleanContextTest.java | 375 ++++++++++++------ 3 files changed, 367 insertions(+), 209 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index b20dcb67b..3e9b17f3f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -1,16 +1,13 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,93 +18,113 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + Class entityClazz = (Class) Class.forName(graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, + String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); - }); - } + res.map((MapFunction) r -> { + if (!r + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return r; + } + r + .setContext( + r + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if(!r.getTitle() - .stream() - .filter(t -> t.getQualifier().getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ - return r; - } - r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)).collect(Collectors.toList())); - return r; - } ,Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath); - } + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 12ba3e5a7..3d4d60d73 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -15,7 +15,7 @@ shouldCleanContext - false + true if the context have to be cleaned @@ -312,9 +312,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${inputPath}/publication + --inputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingPath${workingDir}/working + --workingPath${workingDir}/working/publication --contextId${contextId} --verifyParam${verifyParam} @@ -339,9 +339,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/dataset + --inputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingPath${workingDir}/working + --workingPath${workingDir}/working/dataset --contextId${contextId} --verifyParam${verifyParam} @@ -366,9 +366,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/otherresearchproduct + --inputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingPath${workingDir}/working + --workingPath${workingDir}/working/otherresearchproduct --contextId${contextId} --verifyParam${verifyParam} @@ -393,9 +393,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/software + --inputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingPath${workingDir}/working + --workingPath${workingDir}/working/software --contextId${contextId} --verifyParam${verifyParam} @@ -404,6 +404,6 @@ - + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index bba814346..472d3781d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -1,18 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,133 +21,280 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.Locale; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); - spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) - .write().json(workingDir.toString() + "/publication"); + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId", "sobigdata", + "-verifyParam", "gCube " + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-contextId","sobigdata", - "-verifyParam","gCube " - }); + Assertions.assertEquals(7, tmp.count()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + // original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getContext() + .size()); - Assertions.assertEquals(7, tmp.count()); + // original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); - //original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions.assertEquals(0, - tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + // original result with sobigdata context with gcube as starting string in the subtitle + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + List titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + // original result with sobigdata context with gcube not as starting string in the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::1", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube as starting string in the subtitle - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); - List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube not as starting string in the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - //original result with sobigdata in context and also other contexts with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result without sobigdata in context with gcube as starting string for the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); - //original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - - //original result without sobigdata in context with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); - - - } + } } From 6dc68c48e0d8720b875173692eab09d9e46e77cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 16:19:04 +0200 Subject: [PATCH 133/159] [EOSCTag] - --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 61 +++++++++++++++++-- 1 file changed, 57 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 2b44275cd..7dc3b5878 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -7,11 +7,18 @@ import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; import eu.dnetlib.dhp.bulktag.community.ProtoMap; import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -25,6 +32,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( + "EOSC::Jupyter Notebook", OafMapperUtils.qualifier("eosc","European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES) + ,OafMapperUtils.dataInfo(false, "propagation", true, false, + OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9")); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -45,23 +58,63 @@ public class SparkEoscTag { final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { - execEoscTag(spark, inputPath); + execEoscTag(spark, inputPath, workingPath); }); } - private static void execEoscTag(SparkSession spark, String inputPath) { + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { //search for notebook //subject contiene jupyter. //esistono python e notebook nei subject non necessariamente nello stesso - //si cerca fra i prodotto di tipo software - Dataset sw = readPath(spark, inputPath + "/software", Software.class) + //si cerca fra i prodotti di tipo software + + + readPath(spark, inputPath + "/software", Software.class) + .map((MapFunction) s -> { + if(containsSubjectNotebook(s)){ + s.getSubject().add(EOSC_NOTEBOOK); + } + return s; + }, Encoders.bean(Software.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/software"); + + readPath(spark, workingPath + "/software" , Software.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/software"); } + + private static boolean containsSubjectNotebook(Software s) { + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) + return true; + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && + s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } + + private static boolean containsTitleNotebook(Software s) { + if (s.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("jupyter") && + t.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } } From e0915061c234447edbeb898a4cb726f62b89eb29 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 16:32:40 +0200 Subject: [PATCH 134/159] [Clean Context] fixed issue in param name --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 3d4d60d73..45e492387 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -17,6 +17,14 @@ shouldCleanContext true if the context have to be cleaned + + contextId + sobigdata + + + verifyParam + gcube + sparkDriverMemory From 7cb70664721e57c0bd9a8d9b0aaafaf87257b508 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 10:44:17 +0200 Subject: [PATCH 135/159] [EoscTag] first "rough" implementation --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 109 ++++++++++++++---- .../dhp/bulktag/input_eoscTag_parameters.json | 21 ++++ .../dhp/bulktag/oozie_app/workflow.xml | 26 ++++- 3 files changed, 131 insertions(+), 25 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 7dc3b5878..ea7e77e39 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -1,22 +1,13 @@ package eu.dnetlib.dhp.bulktag; import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; -import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; -import eu.dnetlib.dhp.bulktag.community.ProtoMap; -import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -26,25 +17,30 @@ import org.slf4j.LoggerFactory; import java.util.Optional; import static eu.dnetlib.dhp.PropagationConstant.readPath; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final Qualifier EOSC_QUALIFIER = OafMapperUtils.qualifier("eosc", + "European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES); + public static final DataInfo EOSC_DATAINFO = OafMapperUtils.dataInfo(false, "propagation", true, false, + OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9"); public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( - "EOSC::Jupyter Notebook", OafMapperUtils.qualifier("eosc","European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES) - ,OafMapperUtils.dataInfo(false, "propagation", true, false, - OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9")); + "EOSC::Jupyter Notebook", EOSC_QUALIFIER,EOSC_DATAINFO); + public final static StructuredProperty EOSC_GALAXY = OafMapperUtils.structuredProperty( + "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_TWITTER = OafMapperUtils.structuredProperty( + "EOSC::Twitter Data", EOSC_QUALIFIER,EOSC_DATAINFO); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkEoscTag.class .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_eosctag_parameters.json")); + "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -73,17 +69,15 @@ public class SparkEoscTag { } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { - //search for notebook - //subject contiene jupyter. - //esistono python e notebook nei subject non necessariamente nello stesso - //si cerca fra i prodotti di tipo software - readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - if(containsSubjectNotebook(s)){ + if(containsCriteriaNotebook(s)){ s.getSubject().add(EOSC_NOTEBOOK); } + if(containsCriteriaGalaxy(s)){ + s.getSubject().add(EOSC_GALAXY); + } return s; }, Encoders.bean(Software.class) ) .write() @@ -97,9 +91,75 @@ public class SparkEoscTag { .option("compression","gzip") .json(inputPath + "/software"); + readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) + .map((MapFunction) orp -> + { + if(containsCriteriaGalaxy(orp)){ + orp.getSubject().add(EOSC_GALAXY); + } + if(containscriteriaTwitter(orp)){ + orp.getSubject().add(EOSC_TWITTER); + } + return orp; + }, Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/otherresearchproduct"); + + readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/otherresearchproduct"); + + readPath(spark, inputPath + "/dataset", Dataset.class) + .map((MapFunction) d -> { + if(containscriteriaTwitter(d)){ + d.getSubject().add(EOSC_TWITTER); + } + return d; + } , Encoders.bean(Dataset.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/dataset"); + + readPath(spark, workingPath + "/dataset" , Dataset.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/dataset"); } - private static boolean containsSubjectNotebook(Software s) { + private static boolean containscriteriaTwitter(Result r) { + if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("twitter") && + t.getValue().toLowerCase().contains("data"))) + return true; + if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("twitter") && + d.getValue().toLowerCase().contains("data") )) + return true; + if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + return true; + return false; + } + + private static boolean containsCriteriaGalaxy(Result r) { + if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("galaxy") && + (t.getValue().toLowerCase().contains("workflow") || t.getValue().toLowerCase().contains("software")))) + return true; + if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("galaxy") && + (d.getValue().toLowerCase().contains("workflow") || d.getValue().toLowerCase().contains("software")))) + return true; + if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + return true; + return false; + } + + private static boolean containsCriteriaNotebook(Software s) { if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && @@ -117,4 +177,5 @@ public class SparkEoscTag { return true; return false; } + } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json new file mode 100644 index 000000000..4c25fea01 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json @@ -0,0 +1,21 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f019f8413..91fca7d61 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -204,7 +204,31 @@ - + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.SparkEoscTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath} + --workingPath${workingDir}/eoscTag + + + + From aa12429f500e563a114b39650b3d8c13c361d3fa Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Apr 2022 11:05:08 +0200 Subject: [PATCH 136/159] Modified last intersection since we lost many titles. --- .../doiboost/SparkGenerateDoiBoost.scala | 83 ++++++++----------- 1 file changed, 34 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9323c994c..10a5be969 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -59,52 +59,6 @@ object SparkGenerateDoiBoost { val workingDirPath = parser.get("workingPath") val openaireOrganizationPath = parser.get("openaireOrganizationPath") - val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = new Publication - - override def reduce(b: Publication, a: (String, Publication)): Publication = { - - if (b == null) { - if (a != null && a._2 != null) { - a._2.setId(a._1) - return a._2 - } - } else { - if (a != null && a._2 != null) { - b.mergeFrom(a._2) - b.setId(a._1) - val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor) - b.setAuthor(authors) - return b - } - } - new Publication - } - - override def merge(b1: Publication, b2: Publication): Publication = { - if (b1 == null) { - if (b2 != null) - return b2 - } else { - if (b2 != null) { - b1.mergeFrom(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - return b1 - } - } - new Publication - } - - override def finish(reduction: Publication): Publication = reduction - - override def bufferEncoder: Encoder[Publication] = Encoders.kryo[Publication] - - override def outputEncoder: Encoder[Publication] = Encoders.kryo[Publication] - } - implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] @@ -175,12 +129,43 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .agg(crossrefAggregator.toColumn) - .map(p => p._2) + .reduceGroups((left, right) => + { + //Check left is not null + if (left != null && left._1 != null) + { + //If right is null then return left + if (right == null || right._2 == null) + left + else { + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) + } + } + else { + // Left is Null so we return right + right + } + } + + ) + .filter(s => s!= null && s._2!=null) + .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") + val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") @@ -305,4 +290,4 @@ object SparkGenerateDoiBoost { .save(s"$workingDirPath/doiBoostOrganization") } -} +} \ No newline at end of file From a82ec3aaaf60ea77918f3ff1cfab20538ef6fe7e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Apr 2022 11:08:13 +0200 Subject: [PATCH 137/159] code formatter --- .../doiboost/SparkGenerateDoiBoost.scala | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 10a5be969..2cbd53097 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -129,11 +129,9 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .reduceGroups((left, right) => - { + .reduceGroups((left, right) => { //Check left is not null - if (left != null && left._1 != null) - { + if (left != null && left._1 != null) { //If right is null then return left if (right == null || right._2 == null) left @@ -151,21 +149,17 @@ object SparkGenerateDoiBoost { //Return publication Merged (b1.getId, b1) } - } - else { + } else { // Left is Null so we return right right } - } - - ) - .filter(s => s!= null && s._2!=null) + }) + .filter(s => s != null && s._2 != null) .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") - val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") @@ -290,4 +284,4 @@ object SparkGenerateDoiBoost { .save(s"$workingDirPath/doiBoostOrganization") } -} \ No newline at end of file +} From bbb77052d321498f1148ac7371036789b09146fd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 11:32:57 +0200 Subject: [PATCH 138/159] [EOSCTag] first test --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 770 ++++++++++++++++++ 1 file changed, 770 insertions(+) create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java new file mode 100644 index 000000000..2141e1eac --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -0,0 +1,770 @@ + +package eu.dnetlib.dhp.bulktag; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; + +public class EOSCTagJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; + + public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," + + " \"title\" : \"$['title'][*]['value']\"," + + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + + " \"contributor\" : \"$['contributor'][*]['value']\"," + + " \"description\" : \"$['description'][*]['value']\"}"; + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); + + private static String taggingConf = ""; + + static { + try { + taggingConf = IOUtils + .toString( + EOSCTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml")); + } catch (IOException e) { + e.printStackTrace(); + } + } + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCTagJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void noUpdatesTest() throws Exception { + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + Assertions.assertEquals(0, spark.sql(query).count()); + } + + @Test + void bulktagBySubjectNoPreviousContextTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") + .getPath(); + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + Assertions.assertEquals(5, spark.sql(query).count()); + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 5, + idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count()); + + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); + + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") + .count()); + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") + .count()); + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") + .count()); + } + + @Test + void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") + .getPath(); + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyT.id = 'covid-19' "; + + Assertions.assertEquals(3, spark.sql(query).count()); + + org.apache.spark.sql.Dataset communityContext = spark.sql(query); + + Assertions + .assertEquals( + 2, + communityContext + .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + Assertions + .assertEquals( + 1, + communityContext + .filter( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'") + .count()); + Assertions + .assertEquals( + 1, + communityContext + .filter( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from dataset " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + Assertions + .assertEquals( + 2, + spark + .sql(query) + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a" + + "nd community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagByDatasourceTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/publication", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + + verificationDataset.createOrReplaceTempView("publication"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from publication " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + Assertions.assertEquals(5, idExplodeCommunity.count()); + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions + .assertEquals( + 5, + idExplodeCommunity + .filter("name = 'Bulktagging for Community - Datasource'") + .count()); + + Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); + + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' " + + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' " + + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' " + + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") + .count()); + } + + @Test + void bulktagByZenodoCommunityTest() throws Exception { + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", + "-outputPath", workingDir.toString() + "/orp", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/orp") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class)); + + verificationDataset.createOrReplaceTempView("orp"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from orp " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(8, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + Assertions + .assertEquals( + 8, + idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count()); + + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count()); + + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' " + + "and community = 'covid-19'") + .count()); + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and " + + "(community = 'aginfra' or community = 'mes' or community = 'fam')") + .count()); + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' " + + "and community = 'beopen'") + .count()); + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and " + + "(community = 'beopen' or community = 'fam' or community = 'mes')") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from orp " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + Assertions + .assertEquals( + 2, + spark + .sql(query) + .select("datainfosize") + .where( + "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a" + + "nd community = 'beopen'") + .collectAsList() + .get(0) + .getInt(0)); + + // verify the zenodo community context is not present anymore in the records + query = "select id, MyT.id community " + + "from orp " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD "; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 0, + tmp2 + .select("community") + .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR)) + .count()); + } + + @Test + void bulktagBySubjectDatasourceTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(7, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from dataset " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " + + "community = 'aginfra'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " + + "community = 'fam'") + .collectAsList() + .get(0) + .getInt(0)); + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " + + "community = 'fam'") + .collectAsList() + .get(0) + .getInt(0)); + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " + + "community = 'mes'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception { + + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", + "-outputPath", workingDir.toString() + "/software", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Software.class)); + + verificationDataset.createOrReplaceTempView("software"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from software " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(10, idExplodeCommunity.count()); + + idExplodeCommunity.show(false); + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions + .assertEquals( + 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + + Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count()); + Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "provenance = 'community:zenodocommunity' and " + + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and (" + + "community = 'dh-ch' or community = 'dariah')") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from software " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 3, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and " + + "community = 'aginfra'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagDatasourcewithConstraintsTest() throws Exception { + + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + idExplodeCommunity.show(false); + Assertions.assertEquals(3, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + } +} From 19d90658fc74006408d76269dc332d7205aaeedd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 15:41:23 +0200 Subject: [PATCH 139/159] [Clean Context] added description to parameters --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 45e492387..0cf6cdd05 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -20,10 +20,15 @@ contextId sobigdata + It is the context id that should be removed from the result if the condition is matched. + Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json + where to specify also the constraints that should be verified to remove the context from the result verifyParam gcube + It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in + the title. If title starts with gcube than the context sobigdata will be removed by the result if present From 27c85e901a9162a1c171f521f989f8f77c7c1395 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 17:38:10 +0200 Subject: [PATCH 140/159] [EOSCTag] added resources and finalized test for Jupyter Notebook tagging --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 751 ++---------------- .../eosctag/galaxy/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/galaxy/software/software_10.json | 10 + .../eosctag/jupyter/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/jupyter/software/software_10.json | 10 + .../eosctag/twitter/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/twitter/software/software_10.json | 10 + 10 files changed, 165 insertions(+), 676 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/software/software_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/software/software_10.json diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 2141e1eac..82ac9f751 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -2,15 +2,13 @@ package eu.dnetlib.dhp.bulktag; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -24,6 +22,7 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.List; import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; @@ -31,13 +30,7 @@ public class EOSCTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," - + " \"title\" : \"$['title'][*]['value']\"," - + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," - + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\"}"; private static SparkSession spark; @@ -45,19 +38,6 @@ public class EOSCTagJobTest { private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); - private static String taggingConf = ""; - - static { - try { - taggingConf = IOUtils - .toString( - EOSCTagJobTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml")); - } catch (IOException e) { - e.printStackTrace(); - } - } @BeforeAll public static void beforeAll() throws IOException { @@ -88,683 +68,102 @@ public class EOSCTagJobTest { } @Test - void noUpdatesTest() throws Exception { - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob + void jupyterUpdatesTest() throws Exception { + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/software"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag .main( new String[] { - "-isTest", Boolean.TRUE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - Assertions.assertEquals(0, spark.sql(query).count()); - } - - @Test - void bulktagBySubjectNoPreviousContextTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") - .getPath(); - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - Assertions.assertEquals(5, spark.sql(query).count()); - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 5, - idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count()); - - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); - - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") - .count()); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") - .count()); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") - .count()); - } - - @Test - void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") - .getPath(); - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyT.id = 'covid-19' "; - - Assertions.assertEquals(3, spark.sql(query).count()); - - org.apache.spark.sql.Dataset communityContext = spark.sql(query); - - Assertions - .assertEquals( - 2, - communityContext - .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - Assertions - .assertEquals( - 1, - communityContext - .filter( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'") - .count()); - Assertions - .assertEquals( - 1, - communityContext - .filter( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'") - .count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from dataset " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - Assertions - .assertEquals( - 2, - spark - .sql(query) - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a" - + "nd community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - } - - @Test - void bulktagByDatasourceTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/publication", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - verificationDataset.createOrReplaceTempView("publication"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from publication " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - - Assertions.assertEquals(5, idExplodeCommunity.count()); - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions - .assertEquals( - 5, - idExplodeCommunity - .filter("name = 'Bulktagging for Community - Datasource'") - .count()); - - Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); - - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' " - + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' " - + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' " - + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") - .count()); - } - - @Test - void bulktagByZenodoCommunityTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/orp", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/orp") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class)); - - verificationDataset.createOrReplaceTempView("orp"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from orp " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(8, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); - Assertions - .assertEquals( - 8, - idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count()); - - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count()); - - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' " - + "and community = 'covid-19'") - .count()); - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and " - + "(community = 'aginfra' or community = 'mes' or community = 'fam')") - .count()); - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' " - + "and community = 'beopen'") - .count()); - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and " - + "(community = 'beopen' or community = 'fam' or community = 'mes')") - .count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from orp " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - Assertions - .assertEquals( - 2, - spark - .sql(query) - .select("datainfosize") - .where( - "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a" - + "nd community = 'beopen'") - .collectAsList() - .get(0) - .getInt(0)); - - // verify the zenodo community context is not present anymore in the records - query = "select id, MyT.id community " - + "from orp " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD "; - - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); - - Assertions - .assertEquals( - 0, - tmp2 - .select("community") - .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR)) - .count()); - } - - @Test - void bulktagBySubjectDatasourceTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(7, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from dataset " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); - - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " - + "community = 'aginfra'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " - + "community = 'fam'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " - + "community = 'fam'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " - + "community = 'mes'") - .collectAsList() - .get(0) - .getInt(0)); - } - - @Test - void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception { - - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/software") + .textFile(workingDir.toString() + "/input/software") .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Software.class)); - verificationDataset.createOrReplaceTempView("software"); + Assertions.assertEquals(4, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from software " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; + Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(10, idExplodeCommunity.count()); - idExplodeCommunity.show(false); - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions - .assertEquals( - 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count()); - Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "provenance = 'community:zenodocommunity' and " - + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and (" - + "community = 'dh-ch' or community = 'dariah')") - .count()); + Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from software " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; + Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + List subjects = tmp.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")).collect() + .get(0).getSubject(); + Assertions.assertEquals(8, subjects.size()); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide"))); - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 3, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and " - + "community = 'aginfra'") - .collectAsList() - .get(0) - .getInt(0)); + Assertions.assertEquals(10, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count()); + + Assertions.assertEquals(0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + + + Assertions.assertEquals(10, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).count()); + + Assertions.assertEquals(0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); } - @Test - void bulktagDatasourcewithConstraintsTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - - idExplodeCommunity.show(false); - Assertions.assertEquals(3, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json new file mode 100644 index 000000000..0243a4e3d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json @@ -0,0 +1,10 @@ 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json @@ -0,0 +1,10 @@ +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055422336,"id":"50|od______2017::0750a4d0782265873d669520f5e33c07","originalId":["od______2017::0750a4d0782265873d669520f5e33c07"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct/otherresearchproduct_10.json @@ -0,0 +1,10 @@ +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055422336,"id":"50|od______2017::0750a4d0782265873d669520f5e33c07","originalId":["od______2017::0750a4d0782265873d669520f5e33c07"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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(2017) to estimate a stochastic frontier with technical inefficiency effects when one input is endogenous.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":{"value":"https://creativecommons.org/licenses/by-sa/3.0/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0029","classname":"Software","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"url":["http://prodinra.inra.fr/record/407676"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"documentationUrl":[],"license":[],"codeRepositoryUrl":null,"programmingLanguage":null} From dfbd2bcbea332606b82968136eb98316a47359e7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 18:34:03 +0200 Subject: [PATCH 141/159] [EOSC TAG] added logic in case subject is null --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 27 +++++++++++++++---- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index ea7e77e39..16baf70a6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -14,6 +14,9 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import java.util.Optional; import static eu.dnetlib.dhp.PropagationConstant.readPath; @@ -72,11 +75,17 @@ public class SparkEoscTag { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { + List sbject; + if (!Optional.ofNullable(s.getSubject()).isPresent()) + s.setSubject(new ArrayList<>()); + sbject = s.getSubject(); + if(containsCriteriaNotebook(s)){ - s.getSubject().add(EOSC_NOTEBOOK); + sbject.add(EOSC_NOTEBOOK); + } if(containsCriteriaGalaxy(s)){ - s.getSubject().add(EOSC_GALAXY); + sbject.add(EOSC_GALAXY); } return s; }, Encoders.bean(Software.class) ) @@ -94,11 +103,15 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { + List sbject; + if (!Optional.ofNullable(orp.getSubject()).isPresent()) + orp.setSubject(new ArrayList<>()); + sbject = orp.getSubject(); if(containsCriteriaGalaxy(orp)){ - orp.getSubject().add(EOSC_GALAXY); + sbject.add(EOSC_GALAXY); } if(containscriteriaTwitter(orp)){ - orp.getSubject().add(EOSC_TWITTER); + sbject.add(EOSC_TWITTER); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -115,8 +128,12 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { + List sbject; + if (!Optional.ofNullable(d.getSubject()).isPresent()) + d.setSubject(new ArrayList<>()); + sbject = d.getSubject(); if(containscriteriaTwitter(d)){ - d.getSubject().add(EOSC_TWITTER); + sbject.add(EOSC_TWITTER); } return d; } , Encoders.bean(Dataset.class) ) From 88562c0930dd65eef55e026ae2a299b56eeddeb5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 18:35:03 +0200 Subject: [PATCH 142/159] [EOSC TAG] added test for galaxy for title and description criterias --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 82ac9f751..2c2334a6c 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -166,4 +166,84 @@ public class EOSCTagJobTest { } + @Test + void galaxyUpdatesTest() throws Exception { + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/software"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions.assertEquals(2, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + + Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + + Assertions.assertEquals(6, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(8, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + JavaRDD orp = sc.textFile(workingDir.toString() + "/input/otherresearchproduct").map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions.assertEquals(2, orp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + + + Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(2, orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + } + } From e342ec93f00e7ff5a042c700ce6a5e20ec364c30 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 18:35:37 +0200 Subject: [PATCH 143/159] [EOSCTag] prepared resources for test --- .../otherresearchproduct/otherresearchproduct_10.json | 6 +++--- .../dnetlib/dhp/eosctag/galaxy/software/software_10.json | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json index ae580eab9..d6b4603d5 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json @@ -1,6 +1,6 @@ -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055422336,"id":"50|od______2017::0750a4d0782265873d669520f5e33c07","originalId":["od______2017::0750a4d0782265873d669520f5e33c07"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2018-05-08T17:28:57.843Z","dateoftransformation":"2019-11-30T04:19:48.897Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2018-05-08T17:28:57.843Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/4572","datestamp":"2017-05-05T02:01:39Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Godinho, Maria do Céu","name":"Maria Do Céu","surname":"Godinho","rank":1,"pid":null,"affiliation":null},{"fullname":"Costa, Cristina Amaro","name":"Cristina Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção integrada","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"O uso dos pesticidas em Portugal. Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das culturas.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2016-07-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Quercus","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/chicago-covid-19"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/4572"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.994Z","dateoftransformation":"2019-11-30T04:19:58.463Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.994Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5415","datestamp":"2019-02-23T03:01:23Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Duarte, Natália","name":"Natália","surname":"Duarte","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Alves, Sara","name":"Sara","surname":"Alves","rank":4,"pid":null,"affiliation":null},{"fullname":"Teixeira, Laetitia","name":"Laetitia","surname":"Teixeira","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The interest of the scienti􏰀c community to study the centenarian population has been growing due to the signi􏰀cant expansion of life expectancy and human longevity. Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are required.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2016-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"propagation:community:productsthroughsemrel","classname":" 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Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2018-05-08T17:28:57.843Z","dateoftransformation":"2019-11-30T04:19:48.897Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2018-05-08T17:28:57.843Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/4572","datestamp":"2017-05-05T02:01:39Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Godinho, Maria do Céu","name":"Maria Do Céu","surname":"Godinho","rank":1,"pid":null,"affiliation":null},{"fullname":"Costa, Cristina Amaro","name":"Cristina Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção integrada","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"O uso dos pesticidas em Portugal. Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"This galaxy workflow is for , onde estão incluídos onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das culturas.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2016-07-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Quercus","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/chicago-covid-19"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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+{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423621,"id":"50|od______2017::1bd97baef19dbd2db3203b112bb83bc5","originalId":["od______2017::1bd97baef19dbd2db3203b112bb83bc5"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"galaxy framwork and software is itself aging, and achieving an adva an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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expected heterozygosity, or by R, the allelic richness). This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two means.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2006-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/covid_19_senacyt_abc_panama"},{"id":"covid-19"}],"externalReference":[],"instance":[{"license":{"value":"https://creativecommons.org/licenses/by-sa/3.0/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. I usually go for a one-sided test (i.e. I test if Rst>Gst, and not 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the expected heterozygosity, or by R, the allelic richness). This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. 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return dt + return GraphCleaningFunctions.cleanDate(dt) if (datePart != null && datePart.size == 1) { val res = datePart.head if (res.size == 3) { val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d" if (dp.length == 10) { - return dp + return GraphCleaningFunctions.cleanDate(dp) } } + else if (res.size ==2) { + val dp = f"${res.head}-${res(1)}%02d-01" + return GraphCleaningFunctions.cleanDate(dp) + } + else if (res.size ==1) { + return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") + } } null diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json new file mode 100644 index 000000000..d74b2c167 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json @@ -0,0 +1,330 @@ +{ + "indexed":{ + "date-parts":[ + [ + 2022, + 4, + 14 + ] + ], + "date-time":"2022-04-14T11:27:30Z", + "timestamp":1649935650109 + }, + "reference-count":22, + "publisher":"SAGE Publications", + "issue":"2", + "license":[ + { + "start":{ + "date-parts":[ + [ + 1980, + 4, + 1 + ] + ], + "date-time":"1980-04-01T00:00:00Z", + "timestamp":323395200000 + }, + "content-version":"tdm", + "delay-in-days":0, + "URL":"http:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license" + } + ], + "content-domain":{ + "domain":[ + + ], + "crossmark-restriction":false + }, + "short-container-title":[ + "Perception" + ], + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "abstract":" To answer the question \u2018What is suppressed during binocular rivalry?\u2019 a series of three experiments was performed. In the first experiment observers viewed binocular rivalry between orthogonally oriented patterns. When the dominant and suppressed patterns were interchanged between the eyes observers continued seeing with the dominant eye, indicating that an eye, not a pattern, is suppressed during rivalry. In a second experiment it was found that a suppressed eye was able to contribute to stereopsis. A third experiment demonstrated that the predominance of an eye could be influenced by prior adaptation of the other eye, indicating that binocular mechanisms participate in the rivalry process. <\/jats:p>", + "DOI":"10.1068\/p090223", + "type":"journal-article", + "created":{ + "date-parts":[ + [ + 2007, + 1, + 23 + ] + ], + "date-time":"2007-01-23T15:21:36Z", + "timestamp":1169565696000 + }, + "page":"223-231", + "source":"Crossref", + "is-referenced-by-count":123, + "title":[ + "What is Suppressed during Binocular Rivalry?" + ], + "prefix":"10.1177", + "volume":"9", + "author":[ + { + "given":"Randolph", + "family":"Blake", + "sequence":"first", + "affiliation":[ + { + "name":"Cresap Neuroscience Laboratory, Northwestern University, Evanston, Illinois 60201, USA" + } + ] + }, + { + "given":"David H", + "family":"Westendorf", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, University of Arkansas, Fayetteville, Arkansas 72701, USA" + } + ] + }, + { + "given":"Randall", + "family":"Overton", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, Illinois State University, Normal, Illinois 61761, USA" + } + ] + } + ], + "member":"179", + "published-online":{ + "date-parts":[ + [ + 2016, + 6, + 25 + ] + ] + }, + "reference":[ + { + "key":"bibr1-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1136\/bjo.37.1.37" + }, + { + "key":"bibr2-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0096-1523.5.2.315" + }, + { + "key":"bibr3-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(74)90065-0" + }, + { + "key":"bibr4-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p080143" + }, + { + "key":"bibr5-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(70)90036-2" + }, + { + "key":"bibr6-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1969.sp008862" + }, + { + "key":"bibr7-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1972.sp010006" + }, + { + "key":"bibr8-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1146\/annurev.ps.23.020172.002213" + }, + { + "key":"bibr9-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1126\/science.166.3902.245" + }, + { + "key":"bibr10-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0075805" + }, + { + "key":"bibr11-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1968.sp008552" + }, + { + "key":"bibr12-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1965.sp007784" + }, + { + "key":"bibr13-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0032455" + }, + { + "key":"bibr14-p090223", + "volume-title":"Treatise on Physiological Optics", + "volume":"3", + "author":"von Helmholtz H", + "year":"1866", + "edition":"3" + }, + { + "key":"bibr15-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p040125" + }, + { + "key":"bibr16-p090223", + "volume-title":"On Binocular Rivalry", + "author":"Levelt W J M", + "year":"1965" + }, + { + "key":"bibr17-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1001\/archopht.1935.00840020011001" + }, + { + "key":"bibr18-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03205796" + }, + { + "key":"bibr19-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210180" + }, + { + "key":"bibr20-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0033-2909.85.2.376" + }, + { + "key":"bibr21-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(79)90169-X" + }, + { + "key":"bibr22-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210465" + } + ], + "container-title":[ + "Perception" + ], + "original-title":[ + + ], + "language":"en", + "link":[ + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"application\/pdf", + "content-version":"vor", + "intended-application":"text-mining" + }, + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"unspecified", + "content-version":"vor", + "intended-application":"similarity-checking" + } + ], + "deposited":{ + "date-parts":[ + [ + 2021, + 12, + 3 + ] + ], + "date-time":"2021-12-03T11:49:48Z", + "timestamp":1638532188000 + }, + "score":1, + "resource":{ + "primary":{ + "URL":"http:\/\/journals.sagepub.com\/doi\/10.1068\/p090223" + } + }, + "subtitle":[ + + ], + "short-title":[ + + ], + "issued":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "references-count":22, + "journal-issue":{ + "issue":"2", + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } + }, + "alternative-id":[ + "10.1068\/p090223" + ], + "URL":"http:\/\/dx.doi.org\/10.1068\/p090223", + "relation":{ + + }, + "ISSN":[ + "0301-0066", + "1468-4233" + ], + "issn-type":[ + { + "value":"0301-0066", + "type":"print" + }, + { + "value":"1468-4233", + "type":"electronic" + } + ], + "subject":[ + "Artificial Intelligence", + "Sensory Systems", + "Experimental and Cognitive Psychology", + "Ophthalmology" + ], + "published":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 8124a5aae..9025cd6d2 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -73,6 +73,20 @@ class CrossrefMappingTest { } + + @Test + def crossrefIssueDateTest(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString + assertNotNull(json) + assertFalse(json.isEmpty) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + println(mapper.writeValueAsString(items.head)) + } + @Test def testOrcidID(): Unit = { val json = Source @@ -82,7 +96,7 @@ class CrossrefMappingTest { .mkString assertNotNull(json) - assertFalse(json.isEmpty); + assertFalse(json.isEmpty) val resultList: List[Oaf] = Crossref2Oaf.convert(json) From 5ffc24d1baead98eea96bb50bcef12488fcda3f1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 26 Apr 2022 16:18:41 +0200 Subject: [PATCH 145/159] EOSC Services - ongoing update --- .../raw/MigrateDbEntitiesApplication.java | 6 +-- .../dhp/oa/graph/sql/queryServices.sql | 51 +++++++++++++------ .../raw/MigrateDbEntitiesApplicationTest.java | 4 +- 3 files changed, 40 insertions(+), 21 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b5801ca5c..b1be7f10a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -143,8 +143,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i smdbe.execute("queryClaims.sql", smdbe::processClaims); break; case openaire: - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix); + log.info("Processing services..."); + smdbe.execute("queryServices.sql", smdbe::processService, verifyNamespacePrefix); log.info("Processing projects..."); if (dbSchema.equalsIgnoreCase("beta")) { @@ -235,7 +235,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i dbClient.processResults(sql, consumer); } - public List processDatasource(final ResultSet rs) { + public List processService(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 81be79420..603b1e9b2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,6 +1,6 @@ SELECT d.id AS datasourceid, - d.id || array_agg(distinct di.pid) AS identities, + array_remove(d.id || array_agg(distinct di.pid) filter (where di.pid like 'piwik%') || array_agg(distinct dds.duplicate), NULL) AS identities, d.officialname AS officialname, d.englishname AS englishname, d.contactemail AS contactemail, @@ -57,7 +57,8 @@ SELECT NULL AS odpolicies, ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - + ARRAY(SELECT trim(s) + FROM unnest(string_to_array(d.languages, ',')) AS s) AS languages, -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed @@ -74,40 +75,54 @@ SELECT d.releaseenddate AS releaseenddate, d.missionstatementurl AS missionstatementurl, -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[] - -- VALUE 'Research Data' : d.dataprovider AS dataprovider, - -- VALUE 'Services' : d.serviceprovider AS serviceprovider, + -- VALUE 'Research Data' : d.dataprovider AS dataprovider, + -- VALUE 'Services' : d.serviceprovider AS serviceprovider, d.databaseaccesstype AS databaseaccesstype, d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, -- REPLACED BY version_control : d.versioning AS versioning, - d.version_control AS versioning, + d.version_control AS versioning, + d.version_control AS versioncontrol, d.citationguidelineurl AS citationguidelineurl, - -- REMOVED (it was provided only by re3data: yes, no, unknown): d.qualitymanagementkind AS qualitymanagementkind, + d.pidsystems AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, - dc.id AS collectedfromid, - dc.officialname AS collectedfromname, + array_remove(dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname), NULL) AS collectedfrom, + d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, - d.eosc_type||'@@@dnet:eosc_types' AS eosc_type, - d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eosc_datasoorce_type, + d.eosc_type||'@@@dnet:eosc_types' AS eosctype, + d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eoscdatasourcetype, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, d.lissn AS issnLinking, + d.research_entity_types AS researchentitytypes, d.consenttermsofuse AS consenttermsofuse, d.fulltextdownload AS fulltextdownload, d.consenttermsofusedate AS consenttermsofusedate, - d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, - d.thematic AS thematic, - -- REMOVED ???: d.knowledge_graph AS knowledgegraph, - array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies + d.lastconsenttermsofusedate AS lastconsenttermsofusedate, + d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, + d.thematic AS thematic, + -- REMOVED ???: d.knowledge_graph AS knowledgegraph, + array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, + d.submission_policy_url AS submissionpolicyurl, + d.preservation_policy_url AS preservationpolicyurl, + d.research_product_access_policies AS researchproductaccesspolicies, + d.research_product_metadata_access_policies AS researchproductmetadataaccesspolicies FROM dsm_services d LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) LEFT OUTER JOIN dsm_api a ON (d.id = a.service) LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) +LEFT OUTER JOIN dsm_dedup_services dds ON (d.id = dds.id) +LEFT OUTER JOIN dsm_services dds_dup ON (dds.duplicate = dds_dup.id) +LEFT OUTER JOIN dsm_services dds_cf ON (dds_dup.collectedfrom = dds_cf.id) + + +WHERE + d.dedup_main_service = true GROUP BY d.id, @@ -132,7 +147,7 @@ GROUP BY d.databaseaccessrestriction, d.datauploadrestriction, -- REPLACED BY version_control : d.versioning, - d.version_control + d.version_control, d.citationguidelineurl, -- REMOVED: d.qualitymanagementkind, d.pidsystems, @@ -145,4 +160,8 @@ GROUP BY d.jurisdiction, d.thematic, -- REMOVED ???: de.knowledge_graph, - d.content_policies + d.content_policies, + d.submission_policy_url, + d.preservation_policy_url, + d.research_product_access_policies, + d.research_product_metadata_access_policies \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 05ae5be74..488a1f70b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -63,10 +63,10 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessDatasource() throws Exception { + public void testProcessService() throws Exception { final List fields = prepareMocks("datasources_resultset_entry.json"); - final List list = app.processDatasource(rs); + final List list = app.processService(rs); assertEquals(1, list.size()); verifyMocks(fields); From f5f532d134159c1e14f72811cef1aba36f80d980 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Apr 2022 12:25:24 +0200 Subject: [PATCH 146/159] EOSC Services - ongoing update --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 13 + .../schema/oaf/utils/OafMapperUtilsTest.java | 185 +++++++------- .../raw/MigrateDbEntitiesApplication.java | 75 ++++-- .../dhp/oa/graph/sql/queryServices.sql | 52 ++-- .../raw/MigrateDbEntitiesApplicationTest.java | 137 +++++++++-- ...try.json => services_resultset_entry.json} | 229 ++++++++++++------ .../oa/provision/utils/XmlRecordFactory.java | 6 - pom.xml | 2 +- 8 files changed, 459 insertions(+), 240 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/{datasources_resultset_entry.json => services_resultset_entry.json} (68%) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 0a51e8600..aac2a7801 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import java.sql.Array; +import java.sql.SQLException; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.function.Function; @@ -118,6 +120,17 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static List listValues(Array values) throws SQLException { + if (Objects.isNull(values)) { + return null; + } + return Arrays + .stream((T[]) values.getArray()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + public static List> listFields(final DataInfo info, final List values) { return values .stream() diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index 79629a171..9111ac2df 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -44,105 +44,104 @@ class OafMapperUtilsTest { @Test void testDateValidation() { - assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate(" 2016-04-05").isPresent()); + assertNotNull(GraphCleaningFunctions.cleanDate("2016-05-07T12:41:19.202Z ")); + assertNotNull(GraphCleaningFunctions.cleanDate("2020-09-10 11:08:52 ")); + assertNotNull(GraphCleaningFunctions.cleanDate(" 2016-04-05")); - assertEquals("2016-04-05", GraphCleaningFunctions.doCleanDate("2016 Apr 05").get()); + assertEquals("2016-04-05", GraphCleaningFunctions.cleanDate("2016 Apr 05")); - assertEquals("2009-05-08", GraphCleaningFunctions.doCleanDate("May 8, 2009 5:57:51 PM").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, '70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 70").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 MST 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 02 15:04:05 -0700 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Monday, 02-Jan-06 15:04:05 MST").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 MST").get()); - assertEquals("2017-07-11", GraphCleaningFunctions.doCleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 -0700").get()); - assertEquals("2018-01-04", GraphCleaningFunctions.doCleanDate("Thu, 4 Jan 2018 17:53:36 +0000").get()); - assertEquals("2015-08-10", GraphCleaningFunctions.doCleanDate("Mon Aug 10 15:44:11 UTC+0100 2015").get()); + assertEquals("2009-05-08", GraphCleaningFunctions.cleanDate("May 8, 2009 5:57:51 PM")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, '70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 70")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 MST 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 02 15:04:05 -0700 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Monday, 02-Jan-06 15:04:05 MST")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 MST")); + assertEquals("2017-07-11", GraphCleaningFunctions.cleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 -0700")); + assertEquals("2018-01-04", GraphCleaningFunctions.cleanDate("Thu, 4 Jan 2018 17:53:36 +0000")); + assertEquals("2015-08-10", GraphCleaningFunctions.cleanDate("Mon Aug 10 15:44:11 UTC+0100 2015")); assertEquals( "2015-07-03", - GraphCleaningFunctions.doCleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 10:09am").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 at 10:09am PST-08").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012, 10:10:09").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7th, 1970").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006, 19:17").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006 19:17").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 1970").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("03 February 2013").get()); - assertEquals("2013-07-01", GraphCleaningFunctions.doCleanDate("1 July 2013").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("2013-Feb-03").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3/31/2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03/31/2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08/21/71").get()); - assertEquals("1971-01-08", GraphCleaningFunctions.doCleanDate("8/1/71").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("04/08/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/14 22:05").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("04/2/2014 03:00:51").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00:00 AM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00:01 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 1:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00 AM").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("4/02/2014 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59.3186369").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/3/31").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/03/31").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/4/8 22:05").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/04/08 22:05").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/04/2 03:00:51").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/4/02 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59.3186369").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014年04月08日").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get()); - assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43:22").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 UTC").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 GMT").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 05:24:37 PM").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800 +08").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:44 +09:00").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000 +0000 UTC").get()); - assertEquals("2015-09-30", GraphCleaningFunctions.doCleanDate("2015-09-30 18:48:56.35272715 +0000 UTC").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 GMT").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 UTC").get()); + GraphCleaningFunctions.cleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 10:09am")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 at 10:09am PST-08")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012, 10:10:09")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7th, 1970")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006, 19:17")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006 19:17")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 1970")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("03 February 2013")); + assertEquals("2013-07-01", GraphCleaningFunctions.cleanDate("1 July 2013")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("2013-Feb-03")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3/31/2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03/31/2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08/21/71")); + assertEquals("1971-01-08", GraphCleaningFunctions.cleanDate("8/1/71")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("04/08/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/14 22:05")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("04/2/2014 03:00:51")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00:00 AM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00:01 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 1:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00 AM")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("4/02/2014 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59.3186369")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/3/31")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/03/31")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/4/8 22:05")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/04/08 22:05")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/04/2 03:00:51")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/4/02 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59.3186369")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014年04月08日")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("2006-01-02T15:04:05+0000")); + assertEquals("2009-08-13", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09-07:00")); + assertEquals("2009-08-12", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.3186369")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.123")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43:22")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 UTC")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 GMT")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 05:24:37 PM")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800 +08")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:44 +09:00")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000 +0000 UTC")); + assertEquals("2015-09-30", GraphCleaningFunctions.cleanDate("2015-09-30 18:48:56.35272715 +0000 UTC")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 GMT")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 UTC")); assertEquals( - "2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001").get()); + "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001")); assertEquals( - "2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001").get()); - assertEquals("2017-07-19", GraphCleaningFunctions.doCleanDate("2017-07-19 03:21:51+00:00").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26").get()); - assertEquals("2014-04-01", GraphCleaningFunctions.doCleanDate("2014-04").get()); - assertEquals("2014-01-01", GraphCleaningFunctions.doCleanDate("2014").get()); - assertEquals("2014-05-11", GraphCleaningFunctions.doCleanDate("2014-05-11 08:20:13,787").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3.31.2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03.31.2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08.21.71").get()); - assertEquals("2014-03-01", GraphCleaningFunctions.doCleanDate("2014.03").get()); - assertEquals("2014-03-30", GraphCleaningFunctions.doCleanDate("2014.03.30").get()); - assertEquals("2014-06-01", GraphCleaningFunctions.doCleanDate("20140601").get()); - assertEquals("2014-07-22", GraphCleaningFunctions.doCleanDate("20140722105203").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("1332151919").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367189").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222333").get()); + "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001")); + assertEquals("2017-07-19", GraphCleaningFunctions.cleanDate("2017-07-19 03:21:51+00:00")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26")); + assertEquals("2014-04-01", GraphCleaningFunctions.cleanDate("2014-04")); + assertEquals("2014-01-01", GraphCleaningFunctions.cleanDate("2014")); + assertEquals("2014-05-11", GraphCleaningFunctions.cleanDate("2014-05-11 08:20:13,787")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3.31.2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03.31.2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08.21.71")); + assertEquals("2014-03-01", GraphCleaningFunctions.cleanDate("2014.03")); + assertEquals("2014-03-30", GraphCleaningFunctions.cleanDate("2014.03.30")); + assertEquals("2014-06-01", GraphCleaningFunctions.cleanDate("20140601")); + assertEquals("2014-07-22", GraphCleaningFunctions.cleanDate("20140722105203")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("1332151919")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367189")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222333")); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b1be7f10a..924d53593 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -27,15 +27,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.asString; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.io.Closeable; import java.io.IOException; @@ -245,22 +237,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds .setOriginalId( Arrays - .asList((String[]) rs.getArray("identities").getArray()) + .asList((String[]) rs.getArray("originalid").getArray()) .stream() .filter(StringUtils::isNotBlank) .collect(Collectors.toList())); - ds - .setCollectedfrom( - listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); - ds.setPid(new ArrayList<>()); + ds.setCollectedfrom(prepareCollectedfrom(rs.getArray("collectedfrom"))); + ds.setPid(prepareListOfStructProps(rs.getArray("pid"), info)); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB ds.setOaiprovenance(null); // Values not present in the DB ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); ds.setDatasourcetypeui(prepareQualifierSplitting(rs.getString("datasourcetypeui"))); + ds.setEosctype(prepareQualifierSplitting(rs.getString("eosctype"))); + ds.setEoscdatasourcetype(prepareQualifierSplitting(rs.getString("eoscdatasourcetype"))); ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); ds.setOfficialname(field(rs.getString("officialname"), info)); ds.setEnglishname(field(rs.getString("englishname"), info)); @@ -277,6 +267,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); ds.setOdpolicies(field(rs.getString("odpolicies"), info)); ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setLanguages(listValues(rs.getArray("languages"))); ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); @@ -289,8 +280,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setVersioncontrol(rs.getBoolean("versioncontrol")); ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); ds.setCertificates(field(rs.getString("certificates"), info)); ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array @@ -299,13 +291,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i journal( rs.getString("officialname"), rs.getString("issnPrinted"), rs.getString("issnOnline"), rs.getString("issnLinking"), info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); + ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes"))); + ds.setProvidedproducttypes(listValues(rs.getArray("providedproducttypes"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setThematic(rs.getBoolean("thematic")); ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); + ds.setSubmissionpolicyurl(rs.getString("submissionpolicyurl")); + ds.setPreservationpolicyurl(rs.getString("preservationpolicyurl")); + ds.setResearchproductaccesspolicies(listValues(rs.getArray("researchproductaccesspolicies"))); + ds + .setResearchproductmetadataaccesspolicies( + listValues(rs.getArray("researchproductmetadataaccesspolicies"))); + ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); ds @@ -313,8 +312,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i Optional .ofNullable( rs.getDate("consenttermsofusedate")) - .map(c -> c.toString()) + .map(java.sql.Date::toString) .orElse(null)); + ds + .setLastconsenttermsofusedate( + Optional + .ofNullable( + rs.getDate("lastconsenttermsofusedate")) + .map(java.sql.Date::toString) + .orElse(null)); + + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); return Arrays.asList(ds); } catch (final Exception e) { @@ -603,6 +612,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i String.format("%.3f", trust)); } + private List prepareCollectedfrom(Array values) throws SQLException { + if (Objects.isNull(values)) { + return null; + } + return Arrays + .stream((String[]) values.getArray()) + .filter(Objects::nonNull) + .distinct() + .map(s -> keyValueSplitting(s, "@@@")) + .collect(Collectors.toList()); + } + + public static KeyValue keyValueSplitting(final String s, String separator) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] arr = s.split(separator); + if (arr.length != 2) { + return null; + } + KeyValue kv = new KeyValue(); + kv.setKey(createOpenaireId(10, arr[0], true)); + kv.setValue(arr[1]); + return kv; + } + private Qualifier prepareQualifierSplitting(final String s) { if (StringUtils.isBlank(s)) { return null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 603b1e9b2..3dbb46eaa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,6 +1,7 @@ SELECT d.id AS datasourceid, - array_remove(d.id || array_agg(distinct di.pid) filter (where di.pid like 'piwik%') || array_agg(distinct dds.duplicate), NULL) AS identities, + array_remove(d.id || array_agg(distinct CASE WHEN dp.pid like 'piwik%' THEN di.pid ELSE NULL END) || array_agg(distinct dds.duplicate), NULL) AS originalid, + array_remove(array_agg(distinct CASE WHEN di.pid NOT LIKE 'piwik%' THEN di.pid||'###'||di.issuertype||'@@@'||'dnet:pid_types' ELSE NULL END), NULL) as pid, d.officialname AS officialname, d.englishname AS englishname, d.contactemail AS contactemail, @@ -9,8 +10,8 @@ SELECT THEN 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) - THEN - 'openaire4.0@@@dnet:datasourceCompatibilityLevel' + THEN + 'openaire4.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' @@ -40,29 +41,28 @@ SELECT END AS openairecompatibility, d.websiteurl AS websiteurl, d.logourl AS logourl, - array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END) AS accessinfopackage, + array_remove(array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END), NULL) AS accessinfopackage, d.latitude AS latitude, d.longitude AS longitude, d.namespaceprefix AS namespaceprefix, NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( SELECT trim(s) - FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, + FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, d.description AS description, NULL AS odpolicies, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.languages, ',')) AS s) AS languages, + array_remove(ARRAY(SELECT trim(s) + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS odlanguages, + array_remove(ARRAY(SELECT trim(s) + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS languages, -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed - -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, false AS inferred, false AS deletedbyinference, @@ -81,20 +81,24 @@ SELECT d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, - -- REPLACED BY version_control : d.versioning AS versioning, + -- REPLACED BY version_control : d.versioning AS versioning, d.version_control AS versioning, d.version_control AS versioncontrol, d.citationguidelineurl AS citationguidelineurl, - - d.pidsystems AS pidsystems, + array_to_string(array_agg(distinct dps.scheme), ' ') AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, - array_remove(dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname), NULL) AS collectedfrom, - + array_remove( + array( + select distinct cf + from unnest( + dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname) + ) as cf), + NULL) AS collectedfrom, d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, + d._typology_to_remove_||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, d.eosc_type||'@@@dnet:eosc_types' AS eosctype, d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eoscdatasourcetype, - 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, d.lissn AS issnLinking, @@ -107,19 +111,20 @@ SELECT d.thematic AS thematic, -- REMOVED ???: d.knowledge_graph AS knowledgegraph, array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, - d.submission_policy_url AS submissionpolicyurl, - d.preservation_policy_url AS preservationpolicyurl, - d.research_product_access_policies AS researchproductaccesspolicies, - d.research_product_metadata_access_policies AS researchproductmetadataaccesspolicies + nullif(trim(d.submission_policy_url), '') AS submissionpolicyurl, + nullif(trim(d.preservation_policy_url), '') AS preservationpolicyurl, + array_remove(d.research_product_access_policies, '') AS researchproductaccesspolicies, + array_remove(d.research_product_metadata_access_policies, '') AS researchproductmetadataaccesspolicies FROM dsm_services d LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) LEFT OUTER JOIN dsm_api a ON (d.id = a.service) -LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) +LEFT OUTER JOIN dsm_servicepids dp ON (d.id = dp.service) +LEFT OUTER JOIN dsm_identities di ON (dp.pid = di.pid) LEFT OUTER JOIN dsm_dedup_services dds ON (d.id = dds.id) LEFT OUTER JOIN dsm_services dds_dup ON (dds.duplicate = dds_dup.id) LEFT OUTER JOIN dsm_services dds_cf ON (dds_dup.collectedfrom = dds_cf.id) - +LEFT OUTER JOIN dsm_pid_systems dps ON (d.id = dps.service) WHERE d.dedup_main_service = true @@ -150,7 +155,6 @@ GROUP BY d.version_control, d.citationguidelineurl, -- REMOVED: d.qualitymanagementkind, - d.pidsystems, d.certificates, dc.id, dc.officialname, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 488a1f70b..390db0e4e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -12,8 +12,11 @@ import java.sql.Array; import java.sql.Date; import java.sql.ResultSet; import java.sql.SQLException; +import java.util.HashSet; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -28,12 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @ExtendWith(MockitoExtension.class) @@ -64,7 +62,7 @@ public class MigrateDbEntitiesApplicationTest { @Test public void testProcessService() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + final List fields = prepareMocks("services_resultset_entry.json"); final List list = app.processService(rs); assertEquals(1, list.size()); @@ -72,13 +70,17 @@ public class MigrateDbEntitiesApplicationTest { final Datasource ds = (Datasource) list.get(0); assertValidId(ds.getId()); - assertValidId(ds.getCollectedfrom().get(0).getKey()); + ds + .getCollectedfrom() + .stream() + .map(KeyValue::getKey) + .forEach(dsId -> assertValidId(dsId)); assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue()); assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue()); - assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue()); assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue()); + assertEquals(getValueAsString("logourl", fields), ds.getLogourl()); + assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue()); assertEquals(getValueAsString("namespaceprefix", fields), ds.getNamespaceprefix().getValue()); - assertEquals(getValueAsString("collectedfromname", fields), ds.getCollectedfrom().get(0).getValue()); assertEquals(getValueAsString("officialname", fields), ds.getJournal().getName()); assertEquals(getValueAsString("issnPrinted", fields), ds.getJournal().getIssnPrinted()); assertEquals(getValueAsString("issnOnline", fields), ds.getJournal().getIssnOnline()); @@ -90,19 +92,103 @@ public class MigrateDbEntitiesApplicationTest { assertEquals("pubsrepository::journal", ds.getDatasourcetypeui().getClassid()); assertEquals("dnet:datasource_typologies_ui", ds.getDatasourcetypeui().getSchemeid()); + assertEquals("Data Source", ds.getEosctype().getClassid()); + assertEquals("Data Source", ds.getEosctype().getClassname()); + assertEquals("dnet:eosc_types", ds.getEosctype().getSchemeid()); + assertEquals("dnet:eosc_types", ds.getEosctype().getSchemename()); + + assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassid()); + assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassname()); + assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemeid()); + assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemename()); + + assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassid()); + assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassname()); + assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemeid()); + assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemename()); + + assertEquals(getValueAsDouble("latitude", fields).toString(), ds.getLatitude().getValue()); + assertEquals(getValueAsDouble("longitude", fields).toString(), ds.getLongitude().getValue()); + assertEquals(getValueAsString("dateofvalidation", fields), ds.getDateofvalidation()); + + assertEquals(getValueAsString("description", fields), ds.getDescription().getValue()); + + // TODO assertEquals(getValueAsString("subjects", fields), ds.getSubjects()); + + assertEquals("0.0", ds.getOdnumberofitems().getValue()); + assertEquals(getValueAsString("odnumberofitemsdate", fields), ds.getOdnumberofitemsdate()); + assertEquals(getValueAsString("odpolicies", fields), ds.getOdpolicies()); + + assertEquals( + getValueAsList("odlanguages", fields), + ds.getOdlanguages().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals(getValueAsList("languages", fields), ds.getLanguages()); + assertEquals( + getValueAsList("odcontenttypes", fields), + ds.getOdcontenttypes().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals( + getValueAsList("accessinfopackage", fields), + ds.getAccessinfopackage().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals(getValueAsString("releasestartdate", fields), ds.getReleasestartdate()); + assertEquals(getValueAsString("releaseenddate", fields), ds.getReleasestartdate()); + assertEquals(getValueAsString("missionstatementurl", fields), ds.getMissionstatementurl()); + + assertEquals(false, ds.getDataprovider().getValue()); + assertEquals(false, ds.getServiceprovider().getValue()); + + assertEquals(getValueAsString("databaseaccesstype", fields), ds.getDatabaseaccesstype()); + assertEquals(getValueAsString("datauploadtype", fields), ds.getDatauploadtype()); + assertEquals(getValueAsString("databaseaccessrestriction", fields), ds.getDatabaseaccessrestriction()); + assertEquals(getValueAsString("datauploadrestriction", fields), ds.getDatauploadrestriction()); + + assertEquals(false, ds.getVersioning().getValue()); + assertEquals(false, ds.getVersioncontrol()); + + assertEquals(getValueAsString("citationguidelineurl", fields), ds.getCitationguidelineurl()); + assertEquals(getValueAsString("pidsystems", fields), ds.getPidsystems()); + assertEquals(getValueAsString("certificates", fields), ds.getCertificates()); + + assertEquals(getValueAsList("researchentitytypes", fields), ds.getResearchentitytypes()); + assertEquals(getValueAsList("providedproducttypes", fields), ds.getProvidedproducttypes()); + assertEquals("National", ds.getJurisdiction().getClassid()); assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertTrue(ds.getThematic()); assertTrue(ds.getKnowledgegraph()); - assertEquals(1, ds.getContentpolicies().size()); - assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); - assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); + HashSet cpSchemeId = ds + .getContentpolicies() + .stream() + .map(Qualifier::getSchemeid) + .collect(Collectors.toCollection(HashSet::new)); + assertTrue(cpSchemeId.size() == 1); + assertTrue(cpSchemeId.contains("eosc:contentpolicies")); + HashSet cpSchemeName = ds + .getContentpolicies() + .stream() + .map(Qualifier::getSchemename) + .collect(Collectors.toCollection(HashSet::new)); + assertTrue(cpSchemeName.size() == 1); + assertTrue(cpSchemeName.contains("eosc:contentpolicies")); + assertEquals(2, ds.getContentpolicies().size()); + assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid()); + assertEquals("Resource collection", ds.getContentpolicies().get(1).getClassid()); + + assertEquals(getValueAsString("submissionpolicyurl", fields), ds.getSubmissionpolicyurl()); + assertEquals(getValueAsString("preservationpolicyurl", fields), ds.getPreservationpolicyurl()); + + assertEquals( + getValueAsList("researchproductaccesspolicies", fields), + ds.getResearchproductaccesspolicies()); + assertEquals( + getValueAsList("researchproductmetadataaccesspolicies", fields), + ds.getResearchproductmetadataaccesspolicies()); assertEquals(true, ds.getConsenttermsofuse()); assertEquals(true, ds.getFulltextdownload()); assertEquals("2022-03-11", ds.getConsenttermsofusedate()); + assertEquals("2022-03-11", ds.getLastconsenttermsofusedate()); } @Test @@ -356,18 +442,31 @@ public class MigrateDbEntitiesApplicationTest { } private Float getValueAsFloat(final String name, final List fields) { - return new Float(getValueAs(name, fields).toString()); + final Object value = getValueAs(name, fields); + return value != null ? new Float(value.toString()) : null; + } + + private Double getValueAsDouble(final String name, final List fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Double(value.toString()) : null; + } + + private Integer getValueAsInt(final String name, final List fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Integer(value.toString()) : null; } private T getValueAs(final String name, final List fields) { - return fields + final Optional field = fields .stream() .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> (T) o) .findFirst() - .get(); + .map(TypedField::getValue) + .map(o -> (T) o); + if (!field.isPresent()) { + return null; + } + return field.get(); } private List getValueAsList(final String name, final List fields) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json similarity index 68% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 11b884cde..70fad3323 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -5,14 +5,47 @@ "value": "274269ac6f3b::2579-5449" }, { - "field": "identities", + "field": "originalid", "type": "array", "value": [ - "274269ac6f3b::2579-5449", + "fairsharing_::1562", "piwik:13", - null + null, + "re3data_____::r3d100010213" ] }, + { + "field": "pid", + "type": "array", + "value": [ + "r3d100010218###re3data@@@dnet:pid_types" + ] + }, + { + "field": "datasourcetype", + "type": "string", + "value": "pubsrepository::journal@@@dnet:datasource_typologies" + }, + { + "field": "datasourcetypeui", + "type": "string", + "value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" + }, + { + "field": "eosctype", + "type": "string", + "value": "Data Source@@@dnet:eosc_types" + }, + { + "field": "eoscdatasourcetype", + "type": "string", + "value": "Journal archive@@@dnet:eosc_datasource_types" + }, + { + "field": "openairecompatibility", + "type": "string", + "value": "openaire4.0@@@dnet:datasourceCompatibilityLevel" + }, { "field": "officialname", "type": "string", @@ -23,16 +56,6 @@ "type": "string", "value": "Jurnal Ilmiah Pendidikan Scholastic" }, - { - "field": "contactemail", - "type": "string", - "value": "test@test.it" - }, - { - "field": "openairecompatibility", - "type": "string", - "value": "hostedBy@@@dnet:datasourceCompatibilityLevel" - }, { "field": "websiteurl", "type": "string", @@ -44,11 +67,14 @@ "value": null }, { - "field": "accessinfopackage", - "type": "array", - "value": [ - null - ] + "field": "contactemail", + "type": "string", + "value": "test@test.it" + }, + { + "field": "namespaceprefix", + "type": "string", + "value": "ojs_25795449" }, { "field": "latitude", @@ -61,9 +87,19 @@ "value": 0 }, { - "field": "namespaceprefix", + "field": "dateofvalidation", + "type": "date", + "value": null + }, + { + "field": "description", "type": "string", - "value": "ojs_25795449" + "value": "veterinary medicine" + }, + { + "field": "subjects", + "type": "array", + "value": [] }, { "field": "odnumberofitems", @@ -75,16 +111,6 @@ "type": "date", "value": null }, - { - "field": "subjects", - "type": "array", - "value": null - }, - { - "field": "description", - "type": "string", - "value": null - }, { "field": "odpolicies", "type": "string", @@ -93,7 +119,26 @@ { "field": "odlanguages", "type": "array", - "value": [] + "value": [ + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" + ] + }, + { + "field": "languages", + "type": "array", + "value": [ + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" + ] }, { "field": "odcontenttypes", @@ -103,34 +148,11 @@ ] }, { - "field": "inferred", - "type": "boolean", - "value": false - }, - { - "field": "deletedbyinference", - "type": "boolean", - "value": false - }, - { - "field": "trust", - "type": "double", - "value": 0.9 - }, - { - "field": "inferenceprovenance", - "type": "string", - "value": null - }, - { - "field": "dateofcollection", - "type": "date", - "value": "2020-01-21" - }, - { - "field": "dateofvalidation", - "type": "date", - "value": null + "field": "accessinfopackage", + "type": "array", + "value": [ + "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai" + ] }, { "field": "releasestartdate", @@ -183,12 +205,12 @@ "value": null }, { - "field": "citationguidelineurl", - "type": "string", + "field": "versioncontrol", + "type": "boolean", "value": null }, { - "field": "qualitymanagementkind", + "field": "citationguidelineurl", "type": "string", "value": null }, @@ -208,29 +230,38 @@ "value": [] }, { - "field": "collectedfromid", - "type": "string", - "value": "openaire____::SnVybmFsIEZha3VsdGFzIFNhc3RyYSBVbml2ZXJzaXRhcyBFa2FzYWt0aQ==" + "field": "inferred", + "type": "boolean", + "value": false }, { - "field": "collectedfromname", - "type": "string", - "value": "Jurnal Fakultas Sastra Universitas Ekasakti" + "field": "deletedbyinference", + "type": "boolean", + "value": false }, { - "field": "datasourcetype", - "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies" + "field": "trust", + "type": "double", + "value": 0.9 }, { - "field": "datasourcetypeui", + "field": "inferenceprovenance", "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" + "value": null }, { - "field": "provenanceaction", - "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" + "field": "dateofcollection", + "type": "date", + "value": "2020-01-21" + }, + { + "field": "collectedfrom", + "type": "array", + "value": [ + "openaire____::fairsharing@@@FAIRsharing.org", + "openaire____::opendoar@@@OpenDOAR", + "openaire____::re3data@@@Registry of Research Data Repository" + ] }, { "field": "issnPrinted", @@ -247,6 +278,20 @@ "type": "string", "value": "2579-5447" }, + { + "field": "researchentitytypes", + "type": "array", + "value": [ + "Research Data" + ] + }, + { + "field": "providedproducttypes", + "type": "array", + "value": [ + + ] + }, { "field": "jurisdiction", "type": "string", @@ -266,7 +311,32 @@ "field": "contentpolicies", "type": "array", "value": [ - "Journal article@@@eosc:contentpolicies" + "Taxonomic classification@@@eosc:contentpolicies", + "Resource collection@@@eosc:contentpolicies" + ] + }, + { + "field": "submissionpolicyurl", + "type": "string", + "value": null + }, + { + "field": "preservationpolicyurl", + "type": "string", + "value": "Permanent Archiving https://datadryad.org/stash/faq" + }, + { + "field": "researchproductaccesspolicies", + "type": "array", + "value": [ + "https://100percentit.com/legal/" + ] + }, + { + "field": "researchproductmetadataaccesspolicies", + "type": "array", + "value": [ + "https://wenmr.science.uu.nl/conditions" ] }, { @@ -283,5 +353,10 @@ "field": "consenttermsofusedate", "type": "date", "value": "2022-03-11" + }, + { + "field": "lastconsenttermsofusedate", + "type": "date", + "value": "2022-03-11" } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 5d4a831c0..0daf1c085 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -695,12 +695,6 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); } - if (ds.getQualitymanagementkind() != null) { - metadata - .add( - XmlSerializationUtils - .asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue())); - } if (ds.getPidsystems() != null) { metadata .add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue())); diff --git a/pom.xml b/pom.xml index 136b9b867..03a4496d7 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.32] + [2.11.34-eosc-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 05c1ea92e967185012087f3829aa11bb4a340d1e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Apr 2022 15:56:55 +0200 Subject: [PATCH 147/159] EOSC Services - added Service-specific fields in the XML record serialization --- .../raw/MigrateDbEntitiesApplicationTest.java | 6 + .../oa/provision/utils/XmlRecordFactory.java | 78 +++- .../oa/provision/XmlRecordFactoryTest.java | 11 +- .../dnetlib/dhp/oa/provision/datasource.json | 408 +++++++++++++++++- 4 files changed, 495 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 390db0e4e..69552c4dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -75,6 +75,12 @@ public class MigrateDbEntitiesApplicationTest { .stream() .map(KeyValue::getKey) .forEach(dsId -> assertValidId(dsId)); + + assertEquals(1, ds.getPid().size()); + assertEquals("r3d100010218", ds.getPid().get(0).getValue()); + assertEquals("re3data", ds.getPid().get(0).getQualifier().getClassid()); + assertEquals("dnet:pid_types", ds.getPid().get(0).getQualifier().getSchemeid()); + assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue()); assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue()); assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue()); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 0daf1c085..b811a7a0f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -535,6 +535,12 @@ public class XmlRecordFactory implements Serializable { if (ds.getDatasourcetypeui() != null) { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", ds.getDatasourcetypeui())); } + if (ds.getEosctype() != null) { + metadata.add(XmlSerializationUtils.mapQualifier("eosctype", ds.getEosctype())); + } + if (ds.getEoscdatasourcetype() != null) { + metadata.add(XmlSerializationUtils.mapQualifier("eoscdatasourcetype", ds.getEoscdatasourcetype())); + } if (ds.getOpenairecompatibility() != null) { metadata .add( @@ -583,6 +589,16 @@ public class XmlRecordFactory implements Serializable { metadata .add(XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue())); } + if (ds.getSubjects() != null) { + metadata + .addAll( + ds + .getSubjects() + .stream() + .filter(Objects::nonNull) + .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) + .collect(Collectors.toList())); + } if (ds.getOdnumberofitems() != null) { metadata .add( @@ -609,6 +625,16 @@ public class XmlRecordFactory implements Serializable { .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) .collect(Collectors.toList())); } + if (ds.getLanguages() != null) { + metadata + .addAll( + ds + .getLanguages() + .stream() + .filter(Objects::nonNull) + .map(c -> XmlSerializationUtils.asXmlElement("languages", c)) + .collect(Collectors.toList())); + } if (ds.getOdcontenttypes() != null) { metadata .addAll( @@ -689,6 +715,12 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("versioning", ds.getVersioning().getValue().toString())); } + if (ds.getVersioncontrol() != null) { + metadata + .add( + XmlSerializationUtils + .asXmlElement("versioncontrol", ds.getVersioncontrol().toString())); + } if (ds.getCitationguidelineurl() != null) { metadata .add( @@ -716,17 +748,24 @@ public class XmlRecordFactory implements Serializable { if (ds.getJournal() != null) { metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal())); } - if (ds.getSubjects() != null) { + if (ds.getResearchentitytypes() != null) { metadata .addAll( ds - .getSubjects() + .getResearchentitytypes() .stream() - .filter(Objects::nonNull) - .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) + .map(c -> XmlSerializationUtils.asXmlElement("researchentitytypes", c)) + .collect(Collectors.toList())); + } + if (ds.getProvidedproducttypes() != null) { + metadata + .addAll( + ds + .getProvidedproducttypes() + .stream() + .map(c -> XmlSerializationUtils.asXmlElement("providedproducttypes", c)) .collect(Collectors.toList())); } - if (ds.getJurisdiction() != null) { metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction())); } @@ -750,7 +789,34 @@ public class XmlRecordFactory implements Serializable { .map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q)) .collect(Collectors.toList())); } - + if (ds.getSubmissionpolicyurl() != null) { + metadata + .add(XmlSerializationUtils.asXmlElement("submissionpolicyurl", ds.getSubmissionpolicyurl())); + } + if (ds.getPreservationpolicyurl() != null) { + metadata + .add( + XmlSerializationUtils.asXmlElement("preservationpolicyurl", ds.getPreservationpolicyurl())); + } + if (ds.getResearchproductaccesspolicies() != null) { + metadata + .addAll( + ds + .getResearchproductaccesspolicies() + .stream() + .map(c -> XmlSerializationUtils.asXmlElement("researchproductaccesspolicies", c)) + .collect(Collectors.toList())); + } + if (ds.getResearchproductmetadataaccesspolicies() != null) { + metadata + .addAll( + ds + .getResearchproductmetadataaccesspolicies() + .stream() + .map( + c -> XmlSerializationUtils.asXmlElement("researchproductmetadataaccesspolicies", c)) + .collect(Collectors.toList())); + } break; case organization: final Organization o = (Organization) entity; diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index c32d868e8..f4763618b 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -11,6 +11,7 @@ import java.util.List; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; +import org.dom4j.Element; import org.dom4j.io.SAXReader; import org.junit.jupiter.api.Test; @@ -142,7 +143,7 @@ public class XmlRecordFactoryTest { } @Test - public void testDatasource() throws IOException, DocumentException { + public void testService() throws IOException, DocumentException { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, @@ -167,6 +168,14 @@ public class XmlRecordFactoryTest { assertEquals("true", doc.valueOf("//thematic")); assertEquals("Journal article", doc.valueOf("//contentpolicy/@classname")); assertEquals("Journal archive", doc.valueOf("//datasourcetypeui/@classname")); + assertEquals("Data Source", doc.valueOf("//eosctype/@classname")); + final List pids = doc.selectNodes("//pid"); + assertEquals(1, pids.size()); + assertEquals("re3data", ((Element) pids.get(0)).attribute("classid").getValue()); + assertEquals( + "Registry of research data repositories", ((Element) pids.get(0)).attribute("classname").getValue()); + assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemeid").getValue()); + assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemename").getValue()); } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json index ae069b8b5..8a23b4e6a 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -1 +1,407 @@ -{"collectedfrom":[{"key":"10|openaire____::13068d7823ea0bd86516ac2cb66e96ba","value":"Jurnal Fakultas Sastra Universitas Ekasakti","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1645012035118,"id":"10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7","originalId":["274269ac6f3b::2579-5449","piwik:13"],"pid":[],"dateofcollection":"2020-01-21","dateoftransformation":null,"extraInfo":[],"oaiprovenance":null,"datasourcetype":{"classid":"pubsrepository::journal","classname":"pubsrepository::journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"datasourcetypeui":{"classid":"pubsrepository::journal","classname":"Journal archive","schemeid":"dnet:datasource_typologies_ui","schemename":"dnet:datasource_typologies_ui"},"openairecompatibility":{"classid":"hostedBy","classname":"hostedBy","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"officialname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"englishname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"websiteurl":{"value":"http://e-journal.sastra-unes.com/index.php/JIPS/index","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"logourl":null,"contactemail":{"value":"test@test.it","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"namespaceprefix":{"value":"ojs_25795449","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"latitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"longitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"dateofvalidation":null,"description":null,"subjects":[],"odnumberofitems":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"odnumberofitemsdate":null,"odpolicies":null,"odlanguages":[],"odcontenttypes":[{"value":"Journal articles","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"accessinfopackage":[],"releasestartdate":null,"releaseenddate":null,"missionstatementurl":null,"dataprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"serviceprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"databaseaccesstype":null,"datauploadtype":null,"databaseaccessrestriction":null,"datauploadrestriction":null,"versioning":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"citationguidelineurl":null,"qualitymanagementkind":null,"pidsystems":null,"certificates":null,"policies":[],"journal":{"name":"Jurnal Ilmiah Pendidikan Scholastic","issnPrinted":"2579-5449","issnOnline":"2579-5448","issnLinking":"2579-5447","ep":null,"iss":null,"sp":null,"vol":null,"edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"providedentitytypes":null,"providedproducttypes":null,"jurisdiction":{"classid":"National","classname":"National","schemeid":"eosc:jurisdictions","schemename":"eosc:jurisdictions"},"thematic":true,"knowledgegraph":true,"contentpolicies":[{"classid":"Journal article","classname":"Journal article","schemeid":"eosc:contentpolicies","schemename":"eosc:contentpolicies"}]} +{ + "collectedfrom": [ + { + "key": "10|openaire____::13068d7823ea0bd86516ac2cb66e96ba", + "value": "Jurnal Fakultas Sastra Universitas Ekasakti", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1645012035118, + "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", + "originalId": [ + "274269ac6f3b::2579-5449", + "piwik:13" + ], + "dateofcollection": "2020-01-21", + "dateoftransformation": null, + "extraInfo": [], + "oaiprovenance": null, + "datasourcetype": { + "classid": "pubsrepository::journal", + "classname": "Journal", + "schemeid": "dnet:datasource_typologies", + "schemename": "dnet:datasource_typologies" + }, + "datasourcetypeui": { + "classid": "pubsrepository::journal", + "classname": "Journal archive", + "schemeid": "dnet:datasource_typologies_ui", + "schemename": "dnet:datasource_typologies_ui" + }, + "pid": [ + { + "value": "r3d100010218", + "qualifier": { + "classid": "re3data", + "classname": "Registry of research data repositories", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + } + } + ], + "eosctype": { + "classid": "Data Source", + "classname": "Data Source", + "schemeid": "dnet:eosc_types", + "schemename": "dnet:eosc_types" + }, + "eoscdatasourcetype": { + "classid": "Journal archive", + "classname": "Journal archive", + "schemeid": "dnet:eosc_datasource_types", + "schemename": "dnet:eosc_datasource_types" + }, + "openairecompatibility": { + "classid": "hostedBy", + "classname": "hostedBy", + "schemeid": "dnet:datasourceCompatibilityLevel", + "schemename": "dnet:datasourceCompatibilityLevel" + }, + "officialname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "englishname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "websiteurl": { + "value": "http://e-journal.sastra-unes.com/index.php/JIPS/index", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "logourl": null, + "contactemail": { + "value": "test@test.it", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "namespaceprefix": { + "value": "ojs_25795449", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "latitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "longitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "dateofvalidation": null, + "description": { + "value": "veterinary medicine", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "subjects": [], + "odnumberofitems": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "odnumberofitemsdate": null, + "odpolicies": null, + "odlanguages": [ + { + "value": "English", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "German", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "languages" : [ "English", "German" ], + "odcontenttypes": [ + { + "value": "Journal articles", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "accessinfopackage": [ + { + "value": "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "releasestartdate": null, + "releaseenddate": null, + "missionstatementurl": null, + "dataprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "serviceprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "databaseaccesstype": null, + "datauploadtype": null, + "databaseaccessrestriction": null, + "datauploadrestriction": null, + "versioning": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "versioncontrol": false, + "citationguidelineurl": null, + "qualitymanagementkind": null, + "pidsystems": null, + "certificates": null, + "policies": [], + "journal": { + "name": "Jurnal Ilmiah Pendidikan Scholastic", + "issnPrinted": "2579-5449", + "issnOnline": "2579-5448", + "issnLinking": "2579-5447", + "ep": null, + "iss": null, + "sp": null, + "vol": null, + "edition": null, + "conferenceplace": null, + "conferencedate": null, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "researchentitytypes":[ "Research Data" ], + "providedentitytypes": null, + "providedproducttypes": null, + "jurisdiction": { + "classid": "National", + "classname": "National", + "schemeid": "eosc:jurisdictions", + "schemename": "eosc:jurisdictions" + }, + "thematic": true, + "knowledgegraph": true, + "contentpolicies": [ + { + "classid": "Journal article", + "classname": "Journal article", + "schemeid": "eosc:contentpolicies", + "schemename": "eosc:contentpolicies" + } + ], + "submissionpolicyurl": null, + "preservationpolicyurl" : "Permanent Archiving https://datadryad.org/stash/faq", + "researchproductaccesspolicies": [ + "https://100percentit.com/legal/" + ], + "researchproductmetadataaccesspolicies": [ + "https://wenmr.science.uu.nl/conditions" + ] +} From a8c51f6f1627b357679a6f0a3efc396b2a82f2e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 11:09:03 +0200 Subject: [PATCH 148/159] EOSC Services - fixed query and testing preparation --- .../eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml | 1 + .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 29d4269ef..52462adb4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -102,6 +102,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} --isLookupUrl${isLookupUrl} + --actionopenaire --dbschema${dbSchema} --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 3dbb46eaa..f83e077a3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -56,10 +56,10 @@ SELECT d.description AS description, NULL AS odpolicies, array_remove(ARRAY(SELECT trim(s) - FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS odlanguages, + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS odlanguages, array_remove(ARRAY(SELECT trim(s) - FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS languages, - -- Term provided only by OpenDOAR: + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS languages, + -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, From b6a7ff3a99e0688f64e24e5f69c887245cece7bb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 15:52:33 +0200 Subject: [PATCH 149/159] EOSC Services - removed fields from mapping, testing preparation --- .../raw/MigrateDbEntitiesApplication.java | 13 ++-- .../oa/graph/raw_db/oozie_app/workflow.xml | 64 ++++++++++++++++++- .../dhp/oa/graph/sql/queryServices.sql | 1 - .../raw/MigrateDbEntitiesApplicationTest.java | 7 +- .../graph/raw/services_resultset_entry.json | 17 ----- .../dnetlib/dhp/oa/provision/datasource.json | 19 ------ 6 files changed, 68 insertions(+), 53 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 924d53593..c40f9b392 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -148,10 +148,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i log.info("Processing Organizations..."); smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix); - log.info("Processing relationsNoRemoval ds <-> orgs ..."); + log.info("Processing relations services <-> orgs ..."); smdbe .execute( - "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, + "queryServiceOrganization.sql", smdbe::processServiceOrganization, verifyNamespacePrefix); log.info("Processing projects <-> orgs ..."); @@ -268,13 +268,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setOdpolicies(field(rs.getString("odpolicies"), info)); ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); ds.setLanguages(listValues(rs.getArray("languages"))); - ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); - ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); - ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); @@ -293,10 +290,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i rs.getString("issnLinking"), info)); // Journal ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes"))); - ds.setProvidedproducttypes(listValues(rs.getArray("providedproducttypes"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setThematic(rs.getBoolean("thematic")); - ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setSubmissionpolicyurl(rs.getString("submissionpolicyurl")); ds.setPreservationpolicyurl(rs.getString("preservationpolicyurl")); @@ -434,11 +429,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } - public List processDatasourceOrganization(final ResultSet rs) { + public List processServiceOrganization(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); final String orgId = createOpenaireId(20, rs.getString("organization"), true); - final String dsId = createOpenaireId(10, rs.getString("datasource"), true); + final String dsId = createOpenaireId(10, rs.getString("service"), true); final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 52462adb4..31b726f39 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -30,6 +30,11 @@ a blacklist of nsprefixes (comma separeted) + + reuseContent + false + reuse content in the aggregator database + sparkDriverMemory memory for driver process @@ -85,12 +90,20 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + ${wf:conf('reuseContent') eq false} + ${wf:conf('reuseContent') eq true} + + + + @@ -125,6 +138,55 @@ --actionclaims --nsPrefixBlacklist${nsPrefixBlacklist} + + + + + + + yarn + cluster + GenerateEntities + eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_records,${contentPath}/db_claims + --targetPath${workingDir}/entities + --isLookupUrl${isLookupUrl} + --shouldHashIdtrue + + + + + + + + yarn + cluster + GenerateGraph + eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --sourcePath${workingDir}/entities + --graphRawPath${workingDir}/graph_aggregator + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index f83e077a3..eb70d39e0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -109,7 +109,6 @@ SELECT d.lastconsenttermsofusedate AS lastconsenttermsofusedate, d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, d.thematic AS thematic, - -- REMOVED ???: d.knowledge_graph AS knowledgegraph, array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, nullif(trim(d.submission_policy_url), '') AS submissionpolicyurl, nullif(trim(d.preservation_policy_url), '') AS preservationpolicyurl, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 69552c4dc..948dbfa50 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -129,9 +129,6 @@ public class MigrateDbEntitiesApplicationTest { getValueAsList("odlanguages", fields), ds.getOdlanguages().stream().map(Field::getValue).collect(Collectors.toList())); assertEquals(getValueAsList("languages", fields), ds.getLanguages()); - assertEquals( - getValueAsList("odcontenttypes", fields), - ds.getOdcontenttypes().stream().map(Field::getValue).collect(Collectors.toList())); assertEquals( getValueAsList("accessinfopackage", fields), ds.getAccessinfopackage().stream().map(Field::getValue).collect(Collectors.toList())); @@ -155,13 +152,11 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(getValueAsString("certificates", fields), ds.getCertificates()); assertEquals(getValueAsList("researchentitytypes", fields), ds.getResearchentitytypes()); - assertEquals(getValueAsList("providedproducttypes", fields), ds.getProvidedproducttypes()); assertEquals("National", ds.getJurisdiction().getClassid()); assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertTrue(ds.getThematic()); - assertTrue(ds.getKnowledgegraph()); HashSet cpSchemeId = ds .getContentpolicies() @@ -246,7 +241,7 @@ public class MigrateDbEntitiesApplicationTest { public void testProcessDatasourceOrganization() throws Exception { final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - final List list = app.processDatasourceOrganization(rs); + final List list = app.processServiceOrganization(rs); assertEquals(2, list.size()); verifyMocks(fields); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 70fad3323..445334de5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -140,13 +140,6 @@ "Swedish" ] }, - { - "field": "odcontenttypes", - "type": "array", - "value": [ - "Journal articles" - ] - }, { "field": "accessinfopackage", "type": "array", @@ -169,16 +162,6 @@ "type": "string", "value": null }, - { - "field": "dataprovider", - "type": "boolean", - "value": null - }, - { - "field": "serviceprovider", - "type": "boolean", - "value": null - }, { "field": "databaseaccesstype", "type": "string", diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json index 8a23b4e6a..ce6b10826 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -254,24 +254,6 @@ } ], "languages" : [ "English", "German" ], - "odcontenttypes": [ - { - "value": "Journal articles", - "dataInfo": { - "invisible": false, - "inferred": false, - "deletedbyinference": false, - "trust": "0.900", - "inferenceprovenance": null, - "provenanceaction": { - "classid": "sysimport:crosswalk:entityregistry", - "classname": "sysimport:crosswalk:entityregistry", - "schemeid": "dnet:provenanceActions", - "schemename": "dnet:provenanceActions" - } - } - } - ], "accessinfopackage": [ { "value": "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai", @@ -387,7 +369,6 @@ "schemename": "eosc:jurisdictions" }, "thematic": true, - "knowledgegraph": true, "contentpolicies": [ { "classid": "Journal article", From 2ade69dea694a6d57ce51a5d7da53bc43ac8a22e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 17:03:31 +0200 Subject: [PATCH 150/159] EOSC Services - minor --- .../dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 2 +- .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index c40f9b392..552125307 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -233,7 +233,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Datasource ds = new Datasource(); - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setId(createOpenaireId(10, rs.getString("id"), true)); ds .setOriginalId( Arrays diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index eb70d39e0..81eab8163 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,5 +1,5 @@ SELECT - d.id AS datasourceid, + d.id AS id, array_remove(d.id || array_agg(distinct CASE WHEN dp.pid like 'piwik%' THEN di.pid ELSE NULL END) || array_agg(distinct dds.duplicate), NULL) AS originalid, array_remove(array_agg(distinct CASE WHEN di.pid NOT LIKE 'piwik%' THEN di.pid||'###'||di.issuertype||'@@@'||'dnet:pid_types' ELSE NULL END), NULL) as pid, d.officialname AS officialname, From a21fe310e57c5463eafb50205e1b35ab29759cf5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 May 2022 17:43:20 +0200 Subject: [PATCH 151/159] [EOSCTag] last test and change in the implementation to search in title and descriptio --- .../doiboost/crossref/Crossref2Oaf.scala | 6 +- .../crossref/CrossrefMappingTest.scala | 4 +- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 355 ++++++------ .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 530 ++++++++++++++---- .../eosctag/twitter/dataset/dataset_10.json | 4 +- .../otherresearchproduct_10.json | 10 +- .../eosctag/twitter/software/software_10.json | 2 +- 7 files changed, 620 insertions(+), 291 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0ba77ca84..f2d1dde3d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -584,12 +584,10 @@ case object Crossref2Oaf { if (dp.length == 10) { return GraphCleaningFunctions.cleanDate(dp) } - } - else if (res.size ==2) { + } else if (res.size == 2) { val dp = f"${res.head}-${res(1)}%02d-01" return GraphCleaningFunctions.cleanDate(dp) - } - else if (res.size ==1) { + } else if (res.size == 1) { return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") } } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 9025cd6d2..78ed375c6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -73,10 +73,10 @@ class CrossrefMappingTest { } - @Test def crossrefIssueDateTest(): Unit = { - val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString + val json = + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString assertNotNull(json) assertFalse(json.isEmpty) val resultList: List[Oaf] = Crossref2Oaf.convert(json) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 16baf70a6..1d0aaa631 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.bulktag; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,185 +18,214 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.PropagationConstant.readPath; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { - private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils.qualifier("eosc", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils.dataInfo(false, "propagation", true, false, - OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER,EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils.structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils.structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER,EOSC_DATAINFO); + private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final Qualifier EOSC_QUALIFIER = OafMapperUtils + .qualifier( + "eosc", + "European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); + public static final DataInfo EOSC_DATAINFO = OafMapperUtils + .dataInfo( + false, "propagation", true, false, + OafMapperUtils + .qualifier( + "propagation:subject", "Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"); + public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils + .structuredProperty( + "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_GALAXY = OafMapperUtils + .structuredProperty( + "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_TWITTER = OafMapperUtils + .structuredProperty( + "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - SparkConf conf = new SparkConf(); + SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - execEoscTag(spark, inputPath, workingPath); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + execEoscTag(spark, inputPath, workingPath); - }); - } + }); + } - private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { - readPath(spark, inputPath + "/software", Software.class) - .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); + readPath(spark, inputPath + "/software", Software.class) + .map((MapFunction) s -> { + List sbject; + if (!Optional.ofNullable(s.getSubject()).isPresent()) + s.setSubject(new ArrayList<>()); + sbject = s.getSubject(); - if(containsCriteriaNotebook(s)){ - sbject.add(EOSC_NOTEBOOK); + if (containsCriteriaNotebook(s)) { + sbject.add(EOSC_NOTEBOOK); - } - if(containsCriteriaGalaxy(s)){ - sbject.add(EOSC_GALAXY); - } - return s; - }, Encoders.bean(Software.class) ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/software"); + } + if (containsCriteriaGalaxy(s)) { + sbject.add(EOSC_GALAXY); + } + return s; + }, Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/software"); - readPath(spark, workingPath + "/software" , Software.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/software"); + readPath(spark, workingPath + "/software", Software.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/software"); - readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) - .map((MapFunction) orp -> - { - List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); - if(containsCriteriaGalaxy(orp)){ - sbject.add(EOSC_GALAXY); - } - if(containscriteriaTwitter(orp)){ - sbject.add(EOSC_TWITTER); - } - return orp; - }, Encoders.bean(OtherResearchProduct.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/otherresearchproduct"); + readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) + .map((MapFunction) orp -> { + List sbject; + if (!Optional.ofNullable(orp.getSubject()).isPresent()) + orp.setSubject(new ArrayList<>()); + sbject = orp.getSubject(); + if (containsCriteriaGalaxy(orp)) { + sbject.add(EOSC_GALAXY); + } + if (containscriteriaTwitter(orp)) { + sbject.add(EOSC_TWITTER); + } + return orp; + }, Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/otherresearchproduct"); - readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/otherresearchproduct"); + readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/otherresearchproduct"); - readPath(spark, inputPath + "/dataset", Dataset.class) - .map((MapFunction) d -> { - List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); - if(containscriteriaTwitter(d)){ - sbject.add(EOSC_TWITTER); - } - return d; - } , Encoders.bean(Dataset.class) ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/dataset"); + readPath(spark, inputPath + "/dataset", Dataset.class) + .map((MapFunction) d -> { + List sbject; + if (!Optional.ofNullable(d.getSubject()).isPresent()) + d.setSubject(new ArrayList<>()); + sbject = d.getSubject(); + if (containscriteriaTwitter(d)) { + sbject.add(EOSC_TWITTER); + } + return d; + }, Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/dataset"); - readPath(spark, workingPath + "/dataset" , Dataset.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/dataset"); - } + readPath(spark, workingPath + "/dataset", Dataset.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/dataset"); + } - private static boolean containscriteriaTwitter(Result r) { - if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("twitter") && - t.getValue().toLowerCase().contains("data"))) - return true; - if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("twitter") && - d.getValue().toLowerCase().contains("data") )) - return true; - if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) - return true; - return false; - } + private static boolean containscriteriaTwitter(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); - private static boolean containsCriteriaGalaxy(Result r) { - if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("galaxy") && - (t.getValue().toLowerCase().contains("workflow") || t.getValue().toLowerCase().contains("software")))) - return true; - if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("galaxy") && - (d.getValue().toLowerCase().contains("workflow") || d.getValue().toLowerCase().contains("software")))) - return true; - if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) - return true; - return false; - } + if (words.contains("twitter") && + (words.contains("data") || words.contains("dataset"))) + return true; - private static boolean containsCriteriaNotebook(Software s) { - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) - return true; - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && - sbj.getValue().toLowerCase().contains("notebook"))) - return true; - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && - s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) - return true; - return false; - } + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + return true; + return false; + } - private static boolean containsTitleNotebook(Software s) { - if (s.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("jupyter") && - t.getValue().toLowerCase().contains("notebook"))) - return true; - return false; - } + private static boolean containsCriteriaGalaxy(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); + if (words.contains("galaxy") && + (words.contains("workflow") || words.contains("software"))) + return true; + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + return true; + return false; + } + + private static boolean containsCriteriaNotebook(Software s) { + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) + return true; + if (s + .getSubject() + .stream() + .anyMatch( + sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && + s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } + + private static Set getSubjects(List s) { + Set subjects = new HashSet<>(); + s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); + s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); + return subjects; + } + + private static Set getWordsSP(List elem) { + Set words = new HashSet<>(); + elem + .forEach( + t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; + } + + private static Set getWordsF(List> elem) { + Set words = new HashSet<>(); + elem + .forEach( + t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; + + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 2c2334a6c..d96dc7f6c 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,8 +1,13 @@ package eu.dnetlib.dhp.bulktag; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -11,6 +16,7 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -19,26 +25,20 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; +import eu.dnetlib.dhp.schema.oaf.*; public class EOSCTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; private static Path workingDir; private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName()); @@ -70,23 +70,39 @@ public class EOSCTagJobTest { @Test void jupyterUpdatesTest() throws Exception { - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/software"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/otherresearchproduct"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); SparkEoscTag .main( @@ -106,36 +122,109 @@ public class EOSCTagJobTest { Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(4, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 2, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - - List subjects = tmp.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")).collect() - .get(0).getSubject(); + List subjects = tmp + .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) + .collect() + .get(0) + .getSubject(); Assertions.assertEquals(8, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); @@ -146,104 +235,313 @@ public class EOSCTagJobTest { Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide"))); + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .count()); - Assertions.assertEquals(10, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(0, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(10, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).count()); - - Assertions.assertEquals(0, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + // spark.stop(); } - @Test void galaxyUpdatesTest() throws Exception { - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/software"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/otherresearchproduct"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); SparkEoscTag - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - workingDir.toString() + "/input", - "-workingPath", workingDir.toString() + "/working" + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" - }); + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/input/software") - .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(2, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 2, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); - Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 2, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 6, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(6, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 8, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(8, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - - JavaRDD orp = sc.textFile(workingDir.toString() + "/input/otherresearchproduct").map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); Assertions.assertEquals(10, orp.count()); - Assertions.assertEquals(2, orp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 2, + orp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); + Assertions + .assertEquals( + 3, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 2, orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(2, orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - - Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 3, orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); } + @Test + void twitterUpdatesTest() throws Exception { + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 0, + tmp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD dats = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, dats.count()); + + Assertions + .assertEquals( + 2, + dats + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json index 0243a4e3d..b441bc423 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json @@ -1,5 +1,5 @@ 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"TWITTER","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Constança","name":"Constança","surname":"Paul","rank":5,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Twitter data","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians in Europe","qualifier":{"classid":"main title","classname":"main 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and Asia.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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Oscar","name":"Oscar","surname":"Ribeiro","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"100 years 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this population.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055427049,"id":"50|od______2017::4a1bcdd965b879fbac86a7d3b947a6cc","originalId":["od______2017::4a1bcdd965b879fbac86a7d3b947a6cc"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Porto","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0010","classname":"Lecture","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. I usually go for a one-sided test (i.e. I test if Rst>Gst, and not 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17 00:00:00 2001 From: Claudio Atzori Date: Tue, 3 May 2022 11:55:45 +0200 Subject: [PATCH 152/159] EOSC Services - removed field knowledgegraph; depending on the released schema module --- .../eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 5 ----- pom.xml | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index b811a7a0f..27128138c 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -774,11 +774,6 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString())); } - if (ds.getKnowledgegraph() != null) { - metadata - .add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString())); - } - if (ds.getContentpolicies() != null) { metadata .addAll( diff --git a/pom.xml b/pom.xml index 03a4496d7..54070f654 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.11.34-eosc-SNAPSHOT] + [2.12.0] [4.0.3] [6.0.5] [3.1.6] From 3aeedd931a055dca66d0ef4aabed23a0608770f2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 May 2022 10:06:38 +0200 Subject: [PATCH 153/159] [EOSCTag] fixed issue in case description is null. Modified test resources and classes --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 30 +++++++++++++------ .../dhp/bulktag/oozie_app/workflow.xml | 4 +-- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 6 ++-- .../eosctag/galaxy/dataset/dataset_10.json | 2 +- .../eosctag/galaxy/software/software_10.json | 3 +- .../eosctag/twitter/dataset/dataset_10.json | 1 + 6 files changed, 30 insertions(+), 16 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 1d0aaa631..561e1d57e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -179,12 +179,11 @@ public class SparkEoscTag { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); if (words.contains("galaxy") && - (words.contains("workflow") || words.contains("software"))) + words.contains("workflow")) return true; if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) return true; return false; } @@ -214,17 +213,30 @@ public class SparkEoscTag { private static Set getWordsSP(List elem) { Set words = new HashSet<>(); - elem - .forEach( - t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; } private static Set getWordsF(List> elem) { Set words = new HashSet<>(); - elem - .forEach( - t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); +// elem +// .forEach( +// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); return words; } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 91fca7d61..4c34886e6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -29,7 +29,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,7 +226,7 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag - + diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index d96dc7f6c..55d3939e1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -322,7 +322,7 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/software") .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); - Assertions.assertEquals(10, tmp.count()); + Assertions.assertEquals(11, tmp.count()); Assertions .assertEquals( @@ -534,11 +534,11 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/dataset") .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - Assertions.assertEquals(10, dats.count()); + Assertions.assertEquals(11, dats.count()); Assertions .assertEquals( - 2, + 3, dats .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json index 0243a4e3d..645a7522f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json @@ -7,4 +7,4 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055870582,"id":"50|od______3989::752fd0b2bbac1ea1cc50e52fd46eb663","originalId":["od______3989::752fd0b2bbac1ea1cc50e52fd46eb663"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital e-UCJC","dataInfo":null}],"pid":[],"dateofcollection":"2020-03-03T13:05:34.561Z","dateoftransformation":"2020-03-03T13:06:55.716Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2020-03-03T13:05:34.561Z","altered":true,"baseURL":"http%3A%2F%2Frepositorio.ucjc.edu%2Foai%2Frequest","identifier":"oai:repositorio.ucjc.edu:20.500.12020/798","datestamp":"2018-11-14T12:57:26Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Universidad Camilo José Cela, Vicerrectorado de Innovación","name":"Vicerrectorado Innovación","surname":"Universidad Camilo José Cela","rank":1,"pid":null,"affiliation":null}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"esl/spa","classname":"Spanish","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Psicología","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Alcohol","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Dependencia","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proyectos de investigación","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Alcoholismo","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Realidad virtual","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Psicología conductual","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Investigación - 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La fase final del tratamiento se enfoca en que el paciente \"sea capaz de reconstruir su vida\" a través de programas de entrenamiento de habilidades sociales, asertividad, familias... \"Juntando todas las áreas de intervención, la abstinencia se mantiene mucho más tiempo y las recaídas 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+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -29,7 +29,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] From 846975c8866d341112d3b6f10c1f533a75abf8cc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 5 May 2022 11:37:58 +0200 Subject: [PATCH 155/159] [eosc_services] using the correct 'keyword' subject type, as declared in the dnet:subject_classification_typologies vocabulary --- .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 81eab8163..c4096f90d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -47,7 +47,7 @@ SELECT d.namespaceprefix AS namespaceprefix, NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') + (SELECT array_agg(s|| '###keyword@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( SELECT trim(s) From a056f59c6e3839986120ecbb4847f96851c73f78 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 May 2022 12:51:35 +0200 Subject: [PATCH 156/159] [UsageCount] make it as an action set as it should be, plus changed the test to make them work as well now --- .../usagestats/SparkAtomicActionUsageJob.java | 19 +++++++++++++------ .../SparkAtomicActionCountJobTest.java | 19 ++++++++----------- 2 files changed, 21 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index c284ad8bd..9428f5c59 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -9,7 +9,10 @@ import java.util.Arrays; import java.util.List; import java.util.Optional; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; @@ -29,6 +32,7 @@ import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import scala.Tuple2; /** * created the Atomic Action for each type of results @@ -73,7 +77,7 @@ public class SparkAtomicActionUsageJob implements Serializable { spark -> { removeOutputDir(spark, outputPath); prepareResults(dbname, spark, workingPath); - prepareActionSet(spark, workingPath, outputPath); + writeActionSet(spark, workingPath, outputPath); }); } @@ -89,7 +93,7 @@ public class SparkAtomicActionUsageJob implements Serializable { .json(workingPath); } - public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath) { + public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) { readPath(spark, inputPath, UsageStatsModel.class) .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { @@ -105,10 +109,13 @@ public class SparkAtomicActionUsageJob implements Serializable { res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + } private static List getMeasure(Long downloads, Long views) { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 7cc9eb326..1af408629 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -8,14 +8,12 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -26,8 +24,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob; -import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Result; public class SparkAtomicActionCountJobTest { @@ -72,19 +68,20 @@ public class SparkAtomicActionCountJobTest { @Test void testMatch() { String usageScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") - .getPath(); + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); - SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/actionSet") - .map(usm -> OBJECT_MAPPER.readValue(usm, Result.class)); + JavaRDD tmp = sc.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) + .map(aa -> (Result) aa.getPayload()); Assertions.assertEquals(9, tmp.count()); + tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); tmp .foreach( From 89657a0b78d214017e11613ee4e34b0af805330f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 May 2022 14:43:27 +0200 Subject: [PATCH 157/159] [UsageCount] refactoring --- .../usagestats/SparkAtomicActionUsageJob.java | 14 +++++++------- .../usagestats/SparkAtomicActionCountJobTest.java | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 9428f5c59..5f099b8f2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -9,7 +9,6 @@ import java.util.Arrays; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -27,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Measure; @@ -109,12 +109,12 @@ public class SparkAtomicActionUsageJob implements Serializable { res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) - .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p)) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 1af408629..8aa718bae 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -8,7 +8,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -24,6 +23,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Result; public class SparkAtomicActionCountJobTest { @@ -68,20 +68,20 @@ public class SparkAtomicActionCountJobTest { @Test void testMatch() { String usageScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") - .getPath(); + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) - .map(aa -> (Result) aa.getPayload()); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) + .map(aa -> (Result) aa.getPayload()); Assertions.assertEquals(9, tmp.count()); - tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); tmp .foreach( From 378020e30af91206126377b0d7716452f0fb6f22 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:05:06 +0200 Subject: [PATCH 158/159] [eosc_services] unit test adaptation --- .../raw/MigrateDbEntitiesApplicationTest.java | 4 ++-- .../dhp/oa/graph/hostedbymap/datasource.json | 2 +- ...atasourceorganization_resultset_entry.json | 2 +- .../graph/raw/services_resultset_entry.json | 14 +------------- .../sample/datasource/datasource_10.json.gz | Bin 2227 -> 2211 bytes 5 files changed, 5 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 948dbfa50..9048a22ea 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -136,8 +136,8 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(getValueAsString("releaseenddate", fields), ds.getReleasestartdate()); assertEquals(getValueAsString("missionstatementurl", fields), ds.getMissionstatementurl()); - assertEquals(false, ds.getDataprovider().getValue()); - assertEquals(false, ds.getServiceprovider().getValue()); + assertEquals(null, ds.getDataprovider()); + assertEquals(null, ds.getServiceprovider()); assertEquals(getValueAsString("databaseaccesstype", fields), ds.getDatabaseaccesstype()); assertEquals(getValueAsString("datauploadtype", fields), ds.getDatauploadtype()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json index 5eb41bff5..3bf560135 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json @@ -7,4 +7,4 @@ 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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json @@ -1,6 +1,6 @@ [ { - "field": "datasource", + "field": "service", "type": "string", "value": "openaire____::revistasunicauca" }, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 445334de5..3614c5266 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -1,6 +1,6 @@ [ { - "field": "datasourceid", + "field": "id", "type": "string", "value": "274269ac6f3b::2579-5449" }, @@ -268,13 +268,6 @@ "Research Data" ] }, - { - "field": "providedproducttypes", - "type": "array", - "value": [ - - ] - }, { "field": "jurisdiction", "type": "string", @@ -285,11 +278,6 @@ "type": "boolean", "value": true }, - { - "field": "knowledgegraph", - "type": "boolean", - "value": true - }, { "field": "contentpolicies", "type": "array", diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz index 130dd4c36f3e824c6da8aba020b31729b26935c6..10a4ec591660e1ac2d455beaebc86e9918c92f8a 100644 GIT binary patch literal 2211 zcmV;U2we9ciwFqW8F^v=17u-zVRLVFa${v*F)%J_b8l_{?VVk3D1XVBOt&#C$2Q)%n88w{M7=M? zbNDPRJy!!}*{uqbYX7+^)l?ceibS;^vdD-JR1ylUMX)XiL?o;TM)UlLP<&I@>de?` zzv_Fv>awLfp6X;O6w7O>EQ&rG+n`a)T0 z=UR-Vv3gEt&#NmIi~qNQ;S&*y`~razw!i7a!=e*rU1@pR?^XNy^+T1eZnKo66IRB; 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zz>H7dv$rwh&!f@M+^Rcsqjz}?!FF@(5C$`T^@C!gQDrD-PS<=|ahBv(ZB)c_zDGz5 zx!;2dXCGspS&NTgmA-SB!dhIPiZGmz6j#u^EF4*k?$8%F@;LMajs%W8XFuL+>u@1~ zY0OQ77EG`ZyMxcp9gtp-Uib&nd-|Tejr4wD+OYY(l3(seJCNS(=7;;>Sg+=FL3&Sx z^wQv{{6urQ+m!k@70*NAPw+$fJ@Z|NeAvCd$-FN7w4Q_wG9;Np>2m3=7D@c?g{AP5 zMpxs>Mt%stf5cl1>(Cd7_c-(f;sxS8XFuKx@w(7jNM~rJL@RX};2UE=zUS-?kS~xg z`~&hmeb3&8e6vo`l5hD&hw(*=Gj`c(a<41e{ebr_JN=;3?l&)*or_EV8|1s)d^8nb zq*C#mrq6Pz?`6$vmrs3@bZlHcWTcJtVlYV66WyG8;qX7xap(rM+des5*M2t|>}&VK z|L-B-pO}%n^25)=+t0rYE1#}^d`}ciDZTRitNF13W2`BzQ>^_urILhIs1VZ4PX?2MS?}bzawLj{{=-lef9_000885 Bh;RS^ From 77bc9863e95ac55fcd5f12039e623d8686ae65b9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:06:04 +0200 Subject: [PATCH 159/159] [openorgs] mapping parent/child relations without massaging the semantic labels --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 552125307..63fa8b7e0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -741,10 +741,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r - .setRelClass( - rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF - : ModelConstants.IS_CHILD_OF); + r.setRelClass(rs.getString("type")); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom);