From 65cc736e2fb2848bef81f47715370b0f6a9064a4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Jul 2022 17:05:56 +0200 Subject: [PATCH 1/6] [Clean Country] first implementation to remove country NL from results collected from NARCIS when doi starts with mendely prefix --- .../oa/graph/clean/CleanCountrySparkJob.java | 128 +++++++++++++++++ .../graph/input_clean_country_parameters.json | 43 ++++++ .../dhp/oa/graph/clean/CleanCountryTest.java | 135 ++++++++++++++++++ .../clean/publication_clean_country.json | 7 + 4 files changed, 313 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java new file mode 100644 index 0000000000..ec82d385cd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java @@ -0,0 +1,128 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +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; + +import java.io.Serializable; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + + +public class CleanCountrySparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.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_country_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 country = parser.get("country"); + log.info("country: {}", country); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom); + }); + } + + private static void cleanCountry(SparkSession spark, String country, String verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + ; + + res.map((MapFunction) r -> { + for(StructuredProperty p: r.getPid()){ + if (p.getQualifier().getClassid().equalsIgnoreCase("doi") && + p.getValue().startsWith(verifyParam) && r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equalsIgnoreCase(collectedfrom))) { + + r + .setCountry( + r + .getCountry() + .stream() + .filter( + c -> !c.getClassid() + .equalsIgnoreCase(country)) + .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_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json new file mode 100644 index 0000000000..e46f7b6da2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json @@ -0,0 +1,43 @@ +[ + { + "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": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + },{ + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "the parameter to be verified to remove the country", + "paramRequired": true +}, + { + "paramName": "cf", + "paramLongName": "collectedfrom", + "paramDescription": "the collectedfrom value for which we should apply the cleaning", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java new file mode 100644 index 0000000000..f9dad9fcf6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -0,0 +1,135 @@ +package eu.dnetlib.dhp.oa.graph.clean; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.schema.oaf.Publication; +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; + + +public class CleanCountryTest { + 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_country.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"); + + CleanCountrySparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS" + }); + + 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 NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and pid not starting with Mendely prefix + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getCountry() + .size()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json new file mode 100644 index 0000000000..ebceecff9c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json @@ -0,0 +1,7 @@ +{"author":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked 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Die wörter άγαλμα, είχών, ξόανον, ανδρuις und verwandte, in ihren verschiedenen beziehungen. 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 a12d28c6444616ac914d79b43e5360c4e92d714b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 16:23:12 +0200 Subject: [PATCH 2/6] [Clean Country] added logic not to remove country from result if it exist a hosting datasource with that country. Moreover the country will be removed only if added with propagation --- .../{ => country}/CleanCountrySparkJob.java | 40 ++++++-- .../country/GetDatasourceFromCountry.java | 99 +++++++++++++++++++ .../dhp/oa/graph/clean/CleanCountryTest.java | 3 +- 3 files changed, 130 insertions(+), 12 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/{ => country}/CleanCountrySparkJob.java (75%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java similarity index 75% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index ec82d385cd..1af1aafc0d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.oa.graph.clean; +package eu.dnetlib.dhp.oa.graph.clean.country; /** * @author miriam.baglioni @@ -7,6 +7,7 @@ package eu.dnetlib.dhp.oa.graph.clean; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import org.apache.commons.io.IOUtils; @@ -21,6 +22,7 @@ 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; @@ -54,10 +56,13 @@ public class CleanCountrySparkJob implements Serializable { String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); + String datasourcePath = parser.get("datasourcePath"); + log.info("datasourcePath: {}", datasourcePath); + String country = parser.get("country"); log.info("country: {}", country); - String verifyParam = parser.get("verifyParam"); + String[] verifyParam = parser.get("verifyParam").split(";"); log.info("verifyParam: {}", verifyParam); String collectedfrom = parser.get("collectedfrom"); @@ -74,12 +79,17 @@ public class CleanCountrySparkJob implements Serializable { isSparkSessionManaged, spark -> { - cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom); + cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom, datasourcePath); }); } - private static void cleanCountry(SparkSession spark, String country, String verifyParam, - String inputPath, Class entityClazz, String workingPath, String collectedfrom) { + private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { + + List hostedBy = spark.read().textFile(datasourcePath) + // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) + .collectAsList(); + Dataset res = spark .read() .textFile(inputPath) @@ -89,11 +99,14 @@ public class CleanCountrySparkJob implements Serializable { ; res.map((MapFunction) r -> { - for(StructuredProperty p: r.getPid()){ - if (p.getQualifier().getClassid().equalsIgnoreCase("doi") && - p.getValue().startsWith(verifyParam) && r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equalsIgnoreCase(collectedfrom))) { + if(r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))){ + return r; + } - r + if(r.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam)) + && r.getCountry().stream().anyMatch(c -> c.getClassid().equals(country) && c.getDataInfo().getInferenceprovenance().equals("propagation"))) + { r .setCountry( r .getCountry() @@ -102,7 +115,7 @@ public class CleanCountrySparkJob implements Serializable { c -> !c.getClassid() .equalsIgnoreCase(country)) .collect(Collectors.toList())); - } + } return r; @@ -124,5 +137,12 @@ public class CleanCountrySparkJob implements Serializable { .json(inputPath); } + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam ) + if (value.startsWith(s)) + return true; + return false; + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java new file mode 100644 index 0000000000..cdca961074 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -0,0 +1,99 @@ +package eu.dnetlib.dhp.oa.graph.clean.country; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +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; +import scala.Tuple2; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +public class GetDatasourceFromCountry implements Serializable { + private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + GetDatasourceFromCountry.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_country_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 country = parser.get("country"); + log.info("country: {}", country); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + getDatasourceFromCountry(spark, country, inputPath, workingPath); + }); + } + + private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, String workingPath) { + + Dataset organization = spark.read().textFile(inputPath + "/organization") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), + Encoders.bean(Organization.class)) + .filter( + (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && + o.getCountry().getClassid().length() > 0 && + o.getCountry().getClassid().equals(country));; + + + // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass + Dataset relation = spark.read().textFile( inputPath + "/relation") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), + Encoders.bean(Relation.class)) + .filter( + (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && + !rel.getDataInfo().getDeletedbyinference()); + + organization.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING() ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index f9dad9fcf6..a72093156f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -5,9 +5,9 @@ package eu.dnetlib.dhp.oa.graph.clean; */ import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; import eu.dnetlib.dhp.schema.oaf.Publication; -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; @@ -25,7 +25,6 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.List; public class CleanCountryTest { From 5968ec018db3e9292d8be92552199483791d4ed5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 16:48:38 +0200 Subject: [PATCH 3/6] [Clean Country] modified workflow and added param file --- .../country/GetDatasourceFromCountry.java | 2 +- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 175 +++++++++++++++++- .../graph/input_clean_country_parameters.json | 6 + .../input_datasource_country_parameters.json | 26 +++ 4 files changed, 204 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index cdca961074..c255c445fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -38,7 +38,7 @@ public class GetDatasourceFromCountry implements Serializable { .toString( GetDatasourceFromCountry.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); 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 0cf6cdd05e..2ba0a7ad7d 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 @@ -14,8 +14,8 @@ the address of the lookUp service - shouldCleanContext - true if the context have to be cleaned + shouldClean + true if the operation of deletion of not needed values from the results have to be performed contextId @@ -30,6 +30,22 @@ 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 + + verifyCountryParam + 10.17632;10.5061 + It is the constraints to be verified. This time is hardcoded as the starting doi from mendeley and dryad and it is searched for in + the pid value. If the pid value starts with one of the two prefixes, then the country may be removed + + + country + NL + It is the country to be removed from the set of countries if it is present with provenance propagation. The country will not be removed if in one of the isntances there is a datasource with country `country` + + + collectedfrom + NARCIS + the only datasource for which the country NL will be removed from the country list + sparkDriverMemory @@ -296,7 +312,7 @@ - ${wf:conf('shouldCleanContext') eq true} + ${wf:conf('shouldClean') eq true} @@ -416,7 +432,158 @@ - + + + + + + yarn + cluster + Clean publications context + eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry + dhp-graph-mapper-${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${graphOutputPath} + --workingPath${workingDir}/working/hostedby + --country${country} + + + + + + + + + + + + + + + yarn + cluster + Clean publications counmtry + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${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${graphOutputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --workingPath${workingDir}/working/publication + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean datasets Country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + 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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --workingPath${workingDir}/working/dataset + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean otherresearchproducts country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${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${graphOutputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --workingPath${workingDir}/working/otherresearchproduct + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean softwares country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + 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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --workingPath${workingDir}/working/software + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json index e46f7b6da2..318fb22f80 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json @@ -39,5 +39,11 @@ "paramLongName": "collectedfrom", "paramDescription": "the collectedfrom value for which we should apply the cleaning", "paramRequired": true + }, + { + "paramName": "hb", + "paramLongName": "hostedBy", + "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json new file mode 100644 index 0000000000..e0aa60328d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json @@ -0,0 +1,26 @@ +[ + { + "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": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + } +] From 62d2138806a9740085174e819b361ee19640366f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 8 Aug 2022 14:10:47 +0200 Subject: [PATCH 4/6] [Clean Context] changed a bit the logic. Added the check not to have result hosted by a datasource of type institutional repository from NL. Added also the check that the country should have been included in the result via propagation for it to be removed --- .../clean/country/CleanCountrySparkJob.java | 231 ++++++++++-------- .../country/GetDatasourceFromCountry.java | 139 ++++++----- .../dhp/oa/graph/clean/CleanCountryTest.java | 212 ++++++++-------- .../eu/dnetlib/dhp/oa/graph/clean/hostedBy | 0 .../clean/publication_clean_country.json | 3 +- 5 files changed, 315 insertions(+), 270 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index 1af1aafc0d..3ba84a3177 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -1,15 +1,15 @@ + package eu.dnetlib.dhp.oa.graph.clean.country; -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ +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 javax.swing.text.html.Option; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -21,128 +21,147 @@ 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; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.oaf.Country; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanCountrySparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.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_country_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_country_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 datasourcePath = parser.get("datasourcePath"); - log.info("datasourcePath: {}", datasourcePath); + String datasourcePath = parser.get("hostedBy"); + log.info("datasourcePath: {}", datasourcePath); - String country = parser.get("country"); - log.info("country: {}", country); + String country = parser.get("country"); + log.info("country: {}", country); - String[] verifyParam = parser.get("verifyParam").split(";"); - log.info("verifyParam: {}", verifyParam); + String[] verifyParam = parser.get("verifyParam").split(";"); + log.info("verifyParam: {}", verifyParam); - String collectedfrom = parser.get("collectedfrom"); - log.info("collectedfrom: {}", collectedfrom); + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); - 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 -> { + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { - cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom, datasourcePath); - }); - } + cleanCountry( + spark, country, verifyParam, inputPath, entityClazz, workingPath, collectedfrom, datasourcePath); + }); + } - private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, - String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { + private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { - List hostedBy = spark.read().textFile(datasourcePath) - // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) - .collectAsList(); + List hostedBy = spark + .read() + .textFile(datasourcePath) + // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) + .collectAsList(); - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - ; + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - res.map((MapFunction) r -> { - if(r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || - !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))){ - return r; - } + res.map((MapFunction) r -> { + if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { + return r; + } - if(r.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam)) - && r.getCountry().stream().anyMatch(c -> c.getClassid().equals(country) && c.getDataInfo().getInferenceprovenance().equals("propagation"))) - { r - .setCountry( - r - .getCountry() - .stream() - .filter( - c -> !c.getClassid() - .equalsIgnoreCase(country)) - .collect(Collectors.toList())); + if (r + .getPid() + .stream() + .anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))) { + r + .setCountry( + r + .getCountry() + .stream() + .filter( + c -> toTakeCountry(c, country)) + .collect(Collectors.toList())); - } + } - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath); + 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); + } - private static boolean pidInParam(String value, String[] verifyParam) { - for (String s : verifyParam ) - if (value.startsWith(s)) - return true; - return false; - } + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam) + if (value.startsWith(s)) + return true; + return false; + } + + private static boolean toTakeCountry(Country c, String country) { + // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be + // inserted via propagation + if (!Optional.ofNullable(c.getDataInfo()).isPresent()) + return true; + if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) + return true; + return !(c + .getClassid() + .equalsIgnoreCase(country) && + c.getDataInfo().getInferenceprovenance().equals("propagation")); + } } - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index c255c445fb..dd5af6998a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -1,10 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean.country; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -15,85 +17,92 @@ 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.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** * @author miriam.baglioni * @Date 22/07/22 */ public class GetDatasourceFromCountry implements Serializable { - private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); + private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.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( - GetDatasourceFromCountry.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + GetDatasourceFromCountry.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_datasource_country_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 country = parser.get("country"); - log.info("country: {}", country); + String country = parser.get("country"); + log.info("country: {}", country); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { - getDatasourceFromCountry(spark, country, inputPath, workingPath); - }); - } + getDatasourceFromCountry(spark, country, inputPath, workingPath); + }); + } - private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, String workingPath) { + private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, + String workingPath) { - Dataset organization = spark.read().textFile(inputPath + "/organization") - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), - Encoders.bean(Organization.class)) - .filter( - (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && - o.getCountry().getClassid().length() > 0 && - o.getCountry().getClassid().equals(country));; + Dataset organization = spark + .read() + .textFile(inputPath + "/organization") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), + Encoders.bean(Organization.class)) + .filter( + (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && + o.getCountry().getClassid().length() > 0 && + o.getCountry().getClassid().equals(country)); + ; + // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass + Dataset relation = spark + .read() + .textFile(inputPath + "/relation") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), + Encoders.bean(Relation.class)) + .filter( + (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && + !rel.getDataInfo().getDeletedbyinference()); - // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass - Dataset relation = spark.read().textFile( inputPath + "/relation") - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), - Encoders.bean(Relation.class)) - .filter( - (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && - !rel.getDataInfo().getDeletedbyinference()); + organization + .joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - organization.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") - .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING() ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - } + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index a72093156f..c9f8465708 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.oa.graph.clean; -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.schema.oaf.Publication; +package eu.dnetlib.dhp.oa.graph.clean; + +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; @@ -22,113 +19,132 @@ 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; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; +import eu.dnetlib.dhp.schema.oaf.Publication; public class CleanCountryTest { - 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(CleanCountryTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(CleanCountryTest.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(CleanCountryTest.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_country.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_country.json") + .getPath(); - 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"); - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS" - }); + CleanCountrySparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS", + "-hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + 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()); + Assertions.assertEquals(8, tmp.count()); - // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getCountry() - .size()); + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getCountry() + .size()); - // original result with NL country and pid not starting with Mendely prefix - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getCountry() - .size()); + // original result with NL country and pid not starting with Mendely prefix + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getCountry() + .size()); - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getCountry() - .size()); - } + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not + // inserted with propagation + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with + // propagation + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag")) + .collect() + .get(0) + .getCountry() + .size()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json index ebceecff9c..4916eee734 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json @@ -4,4 +4,5 @@ {"author":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging 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"miriam.baglioni" Date: Wed, 10 Aug 2022 15:13:10 +0200 Subject: [PATCH 5/6] [Clean Country]changes related to https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/241#issuecomment-6766 --- .../dhp/oa/graph/clean/country/CleanCountrySparkJob.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index 3ba84a3177..30991e9d7a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import javax.swing.text.html.Option; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -94,7 +95,6 @@ public class CleanCountrySparkJob implements Serializable { List hostedBy = spark .read() .textFile(datasourcePath) - // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) .collectAsList(); Dataset res = spark @@ -113,7 +113,8 @@ public class CleanCountrySparkJob implements Serializable { if (r .getPid() .stream() - .anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))) { + .anyMatch(p -> p.getQualifier().getClassid() + .equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) { r .setCountry( r From dcd85f8cd79ab8342e03eca6ef9530f35dd242ab Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 22 Sep 2022 13:33:07 +0300 Subject: [PATCH 6/6] - Synchronize indicators in stats-db with monitor-db - added new openorg id for Nanyang Technological University - changed openorg id for University of Helsinki #8088 ticket --- .../scripts/step16-createIndicatorsTables.sql | 35 +++++++++++ .../scripts/step20-createMonitorDB.sql | 61 ++++++++++++------- 2 files changed, 74 insertions(+), 22 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 b8792ae615..417ed6e4e7 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 @@ -92,6 +92,17 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_collab; -- +create table indi_result_org_collab stored as parquet as +with tmp as ( +select distinct ro.organization organization, ro.id from result_organization ro +join organization o on o.id=ro.organization where o.name is not null) +select o1.organization org1, o2.organization org2, count(o1.id) as collaborations +from tmp as o1 +join tmp as o2 on o1.id=o2.id and o1.organization!=o2.organization +group by org1, org2; + +compute stats indi_result_org_collab; + -- 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 @@ -105,6 +116,17 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_country_collab; -- +create table indi_result_org_country_collab stored as parquet as +with tmp as +(select distinct ro.organization organization, ro.id, o.country from result_organization ro +join organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null) +select o1.organization org1,o2.country country2, count(o1.id) as collaborations +from tmp as o1 join tmp as o2 on o1.id=o2.id +where o1.id=o2.id and o1.country!=o2.country +group by o1.organization, o1.id, 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 @@ -166,6 +188,19 @@ compute stats indi_funder_country_collab; -- -- compute stats indi_result_country_collab; +create table indi_result_country_collab stored as parquet as +with tmp as + (select distinct country, ro.id as result from organization o + join result_organization ro on o.id=ro.organization + where country <> 'UNKNOWN' and o.name is not null) +select o1.country country1, o2.country country2, count(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; + +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 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 5af2e9edd5..290acbf9fc 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 @@ -23,7 +23,7 @@ create table TARGET.result stored as parquet as 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ?? 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade - 'openorgs____::2fb1e47b4612688d9de9169d579939a7', --University of Helsinki + 'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen @@ -48,7 +48,8 @@ create table TARGET.result stored as parquet as 'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank - 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3' -- École des Ponts ParisTech + 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech + 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a' -- Nanyang Technological University ) )) foo; compute stats TARGET.result; @@ -154,50 +155,44 @@ create table TARGET.project_results stored as parquet as select id as result, pr compute stats TARGET.project_results; -- indicators +-- Sprint 1 ---- create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_green_oa; create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_grey_lit; create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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; +-- Sprint 2 ---- 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 as select * from SOURCE.indi_funder_country_collab; -create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; -create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; - +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_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; +---- Sprint 3 ---- create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_funded_result_with_fundref; +create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; +create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; +create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; +create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; +---- Sprint 4 ---- create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_diamond; -create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_hybrid; create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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; - +---- Sprint 5 ---- 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; +---- Sprint 6 ---- 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.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.result_id); @@ -206,6 +201,28 @@ create table TARGET.indi_pub_downloads_year stored as parquet as select * from S 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.result_id); compute stats TARGET.indi_pub_downloads_datasource_year; +---- Sprint 7 ---- +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_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_hybrid; +create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; +create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; +create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; +create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub; +create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year; +create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year; +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 view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; +create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); + +--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; --denorm alter table TARGET.result rename to TARGET.res_tmp;