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 5f099b8f2..d7ca00708 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 @@ -8,13 +8,13 @@ import java.io.Serializable; import java.util.Arrays; import java.util.List; import java.util.Optional; - +import eu.dnetlib.dhp.schema.oaf.*; 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; + import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -28,9 +28,6 @@ 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; -import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import scala.Tuple2; @@ -76,41 +73,38 @@ public class SparkAtomicActionUsageJob implements Serializable { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareResults(dbname, spark, workingPath); + prepareData(dbname, spark, workingPath + "/usageDb", "usage_stats", "result_id"); + prepareData(dbname, spark, workingPath + "/projectDb", "project_stats", "id"); + prepareData(dbname, spark, workingPath + "/datasourceDb", "datasource_stats", "repositor_id"); writeActionSet(spark, workingPath, outputPath); }); } - public static void prepareResults(String db, SparkSession spark, String workingPath) { + private static void prepareData(String dbname, SparkSession spark, String workingPath, String tableName, String attribute_name) { 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 " + attribute_name + " as id, sum(downloads) as downloads, sum(views) as views " + + "from " + dbname + "." + tableName + + "group by " + attribute_name) + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); } + + 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) -> { - 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)) - .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p)) + getFinalIndicatorsResult(spark, inputPath+ "/usageDb"). + toJavaRDD(). + map(p -> new AtomicAction(p.getClass(),p)) + .union(getFinalIndicatorsProject(spark, inputPath + "/projectDb") + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p ))) + .union(getFinalIndicatorsDatasource(spark, inputPath + "/datasourceDb") + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p))) .mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), new Text(OBJECT_MAPPER.writeValueAsString(aa)))) @@ -118,6 +112,41 @@ public class SparkAtomicActionUsageJob implements Serializable { } + private static Dataset getFinalIndicatorsResult(SparkSession spark, String inputPath) { + + return readPath(spark, inputPath, UsageStatsModel.class) + .map((MapFunction) usm -> { + Result r = new Result(); + r.setId("50|" + usm.getId()); + r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews())); + return r; + }, Encoders.bean(Result.class)); + } + + private static Dataset getFinalIndicatorsProject(SparkSession spark, String inputPath) { + + return readPath(spark, inputPath, UsageStatsModel.class) + .map((MapFunction) usm -> { + Project r = new Project(); + r.setId("40|" + usm.getId()); + r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews())); + return r; + }, Encoders.bean(Project.class)); + } + + private static Dataset getFinalIndicatorsDatasource(SparkSession spark, String inputPath) { + + return readPath(spark, inputPath, UsageStatsModel.class) + .map((MapFunction) usm -> { + Datasource r = new Datasource(); + r.setId("10|" + usm.getId()); + r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews())); + return r; + }, Encoders.bean(Datasource.class)); + } + + + private static List getMeasure(Long downloads, Long views) { DataInfo dataInfo = OafMapperUtils .dataInfo( 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 index df8a77eb6..07f69b0bb 100644 --- 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 @@ -4,16 +4,16 @@ package eu.dnetlib.dhp.actionmanager.usagestats; import java.io.Serializable; public class UsageStatsModel implements Serializable { - private String result_id; + private String id; private Long downloads; private Long views; - public String getResult_id() { - return result_id; + public String getId() { + return id; } - public void setResult_id(String result_id) { - this.result_id = result_id; + public void setId(String id) { + this.id = id; } public Long getDownloads() { 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 d94cf7d53..de188718a 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 @@ -89,7 +89,7 @@ --hive_metastore_uris${hiveMetastoreUris} --outputPath${outputPath} --usagestatsdb${usagestatsdb} - --workingPath${workingDir}/usageDb + --workingPath${workingDir} 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 8aa718bae..1512f9cf8 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 @@ -8,6 +8,7 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.OafEntity; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -68,24 +69,26 @@ public class SparkAtomicActionCountJobTest { @Test void testMatch() { String usageScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats") .getPath(); SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc + 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()); + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)); + //.map(aa -> (Result) aa.getPayload()); - Assertions.assertEquals(9, tmp.count()); + Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("50|")).count()); + Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("10|")).count()); + Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("40|")).count()); - tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); + tmp.foreach(r -> Assertions.assertEquals(2, ((OafEntity)r.getPayload()).getMeasures().size())); tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( @@ -95,14 +98,14 @@ public class SparkAtomicActionCountJobTest { .forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( @@ -113,7 +116,7 @@ public class SparkAtomicActionCountJobTest { tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( @@ -127,7 +130,7 @@ public class SparkAtomicActionCountJobTest { u.getDataInfo().getProvenanceaction().getClassid())))); tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( @@ -142,7 +145,7 @@ public class SparkAtomicActionCountJobTest { tmp .foreach( - r -> r + r -> ((OafEntity)r.getPayload()) .getMeasures() .stream() .forEach( @@ -157,12 +160,13 @@ public class SparkAtomicActionCountJobTest { Assertions .assertEquals( - 1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + 1, tmp.filter(r -> ((OafEntity)r.getPayload()).getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); Assertions .assertEquals( "0", tmp + .map(r -> ((OafEntity)r.getPayload())) .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) .collect() .get(0) @@ -178,7 +182,8 @@ public class SparkAtomicActionCountJobTest { .assertEquals( "5", tmp - .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) .collect() .get(0) .getMeasures() @@ -194,7 +199,8 @@ public class SparkAtomicActionCountJobTest { .assertEquals( "0", tmp - .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) .collect() .get(0) .getMeasures() @@ -209,7 +215,8 @@ public class SparkAtomicActionCountJobTest { .assertEquals( "1", tmp - .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) .collect() .get(0) .getMeasures() @@ -225,7 +232,8 @@ public class SparkAtomicActionCountJobTest { .assertEquals( "2", tmp - .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) .collect() .get(0) .getMeasures() @@ -240,7 +248,8 @@ public class SparkAtomicActionCountJobTest { .assertEquals( "6", tmp - .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) .collect() .get(0) .getMeasures() @@ -251,6 +260,206 @@ public class SparkAtomicActionCountJobTest { .getUnit() .get(0) .getValue()); + + + Assertions + .assertEquals( + "0", + tmp + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f1__________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f1__________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f11_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f11_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f12_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("40|f12_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + + Assertions + .assertEquals( + "0", + tmp + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d1__________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d1__________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d11_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d11_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d12_________::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 + .map(r -> ((OafEntity)r.getPayload())) + .filter(r -> r.getId().equals("10|d12_________::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/datasourceDb b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/datasourceDb new file mode 100644 index 000000000..efbb4cfbd --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/datasourceDb @@ -0,0 +1,9 @@ +{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5} +{"id":"d11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"d11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"d11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6} +{"id":"d12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"d12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10} +{"id":"d13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/datasourceDb_old b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/datasourceDb_old new file mode 100644 index 000000000..7337ba3e2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/datasourceDb_old @@ -0,0 +1,12 @@ +{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4} +{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1} +{"id":"d11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"d11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"d11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3} +{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3} +{"id":"d12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"d12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8} +{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2} +{"id":"d13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb new file mode 100644 index 000000000..0b8cd1d70 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb @@ -0,0 +1,9 @@ +{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5} +{"id":"f11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"f11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"f11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6} +{"id":"f12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"f12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10} +{"id":"f13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb_old b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb_old new file mode 100644 index 000000000..0ecab2a82 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/projectDb_old @@ -0,0 +1,12 @@ +{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4} +{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1} +{"id":"f11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"f11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"f11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3} +{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3} +{"id":"f12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"f12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8} +{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2} +{"id":"f13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb new file mode 100644 index 000000000..495ae0fc5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb @@ -0,0 +1,9 @@ +{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5} +{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6} +{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10} +{"id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb_old b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb_old new file mode 100644 index 000000000..eb3290eda --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usageDb_old @@ -0,0 +1,12 @@ +{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4} +{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1} +{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3} +{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3} +{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8} +{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2} +{"id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file 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 deleted file mode 100644 index fee74f697..000000000 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb +++ /dev/null @@ -1,12 +0,0 @@ -{"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/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java index cf3562193..4792a7719 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java @@ -37,12 +37,24 @@ public class SubscriptionUtils { } public static boolean verifyDateRange(final long date, final String min, final String max) { + + long from = 0; + long to = Long.MAX_VALUE; + try { - return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime() - && date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY; + from = min != null ? DateUtils.parseDate(min, "yyyy-MM-dd").getTime() : 0; } catch (final ParseException e) { - return false; + from = 0; } + + try { + to = max != null ? DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY : Long.MAX_VALUE; + } catch (final ParseException e) { + to = Long.MAX_VALUE; + } + + return date >= from && date < to; + } public static boolean verifyExact(final String s1, final String s2) { diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java index d93390e4a..63b49d362 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -41,6 +41,18 @@ public class SubscriptionUtilsTest { assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01")); assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01")); + + assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "NULL")); + assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", null)); + assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "2011-01-01")); + assertTrue(SubscriptionUtils.verifyDateRange(date, null, "2011-01-01")); + assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "NULL")); + assertTrue(SubscriptionUtils.verifyDateRange(date, null, null)); + + assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", null)); + assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "NULL")); + assertFalse(SubscriptionUtils.verifyDateRange(date, null, "2005-01-01")); + assertFalse(SubscriptionUtils.verifyDateRange(date, "NULL", "2005-01-01")); } @Test 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 7fb10863f..75aa4a024 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 @@ -370,10 +370,50 @@ case object Crossref2Oaf { case dataset: Dataset => convertDataset(dataset) } + val doisReference: List[String] = for { + JObject(reference_json) <- json \ "reference" + JField("DOI", JString(doi_json)) <- reference_json + } yield doi_json + + if (doisReference != null && doisReference.nonEmpty) { + val citation_relations: List[Relation] = generateCitationRelations(doisReference, result) + resultList = resultList ::: citation_relations + } resultList = resultList ::: List(result) resultList } + private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = { + + val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true) + + val from = new Relation + from.setSource(source.getId) + from.setTarget(targetId) + from.setRelType(ModelConstants.RESULT_RESULT) + from.setRelClass(ModelConstants.CITES) + from.setSubRelType(ModelConstants.CITATION) + from.setCollectedfrom(source.getCollectedfrom) + from.setDataInfo(source.getDataInfo) + from.setLastupdatetimestamp(source.getLastupdatetimestamp) + + val to = new Relation + to.setTarget(source.getId) + to.setSource(targetId) + to.setRelType(ModelConstants.RESULT_RESULT) + to.setRelClass(ModelConstants.IS_CITED_BY) + to.setSubRelType(ModelConstants.CITATION) + to.setCollectedfrom(source.getCollectedfrom) + to.setDataInfo(source.getDataInfo) + to.setLastupdatetimestamp(source.getLastupdatetimestamp) + + List(from, to) + } + + def generateCitationRelations(dois: List[String], result: Result): List[Relation] = { + dois.flatMap(d => createCiteRelation(result, d, "doi")) + } + def mappingFunderToRelations( funders: List[mappingFunder], sourceId: String, @@ -446,6 +486,7 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + generateSimpleRelationFromAward(funder, "corda_____he", 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) @@ -487,6 +528,34 @@ case object Crossref2Oaf { val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //ASAP + case "10.13039/100018231" => generateSimpleRelationFromAward(funder, "asap________", a => a) + //CHIST-ERA + case "10.13039/501100001942" => + val targetId = getProjectId("chistera____", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //HE + case "10.13039/100018693" | "10.13039/100018694" | "10.13039/100019188" | "10.13039/100019180" | + "10.13039/100018695" | "10.13039/100019185" | "10.13039/100019186" | "10.13039/100019187" => + generateSimpleRelationFromAward(funder, "corda_____he", extractECAward) + //FCT + case "10.13039/501100001871" => + generateSimpleRelationFromAward(funder, "fct_________", extractECAward) + //NHMRC + case "10.13039/501100000925" => + generateSimpleRelationFromAward(funder, "mhmrc_______", extractECAward) + //NIH + case "10.13039/100000002" => + generateSimpleRelationFromAward(funder, "nih_________", extractECAward) + //NWO + case "10.13039/501100003246" => + generateSimpleRelationFromAward(funder, "nwo_________", extractECAward) + //UKRI + case "10.13039/100014013" | "10.13039/501100000267" | "10.13039/501100000268" | "10.13039/501100000269" | + "10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" | + "10.13039/501100013589" | "10.13039/501100000271" => + generateSimpleRelationFromAward(funder, "nwo_________", extractECAward) case _ => logger.debug("no match for " + funder.DOI.get) 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 788946fea..b66147b2d 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 @@ -1,1537 +1,1475 @@ { -"indexed": { -"date-parts": [ -[ -2021, -7, -2 -] -], -"date-time": "2021-07-02T07:30:10Z", -"timestamp": 1625211010708 -}, -"reference-count": 83, -"publisher": "Springer Science and Business Media LLC", -"issue": "5", -"license": [ -{ -"URL": "https://www.springer.com/tdm", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "tdm" -}, -{ -"URL": "https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "vor" -} -], -"content-domain": { -"domain": [ -"link.springer.com" -], -"crossmark-restriction": false -}, -"short-container-title": [ -"Nat Astron" -], -"published-print": { -"date-parts": [ -[ -2021, -5 -] -] -}, -"DOI": "10.1038/s41550-020-01295-8", -"type": "journal-article", -"created": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T17:03:42Z", -"timestamp": 1614013422000 -}, -"page": "510-518", -"update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy", -"source": "Crossref", -"is-referenced-by-count": 6, -"title": [ -"A tidal disruption event coincident with a high-energy neutrino" -], -"prefix": "10.1038", -"volume": "5", -"author": [ -{ -"ORCID": "http://orcid.org/0000-0003-2434-0387", -"authenticated-orcid": false, -"given": "Robert", -"family": "Stein", -"sequence": "first", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3859-8074", -"authenticated-orcid": false, -"given": "Sjoert van", -"family": "Velzen", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8594-8666", -"authenticated-orcid": false, -"given": "Marek", -"family": "Kowalski", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Anna", -"family": "Franckowiak", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3703-5154", 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J." + } + ], + "container-title": [ + "Nature Astronomy" + ], + "original-title": [ + ], + "language": "en", + "link": [ + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", + "content-type": "application/pdf", + "content-version": "vor", + "intended-application": "text-mining" + }, + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8", + "content-type": "text/html", + "content-version": "vor", + "intended-application": "text-mining" + }, + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", + "content-type": "application/pdf", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2021, + 5, + 17 + ] + ], + "date-time": "2021-05-17T15:08:12Z", + "timestamp": 1621264092000 + }, + "score": 1.0, + "subtitle": [ + ], + "short-title": [ + ], + "issued": { + "date-parts": [ + [ + 3021, + 2, + 22 + ] + ] + }, + "references-count": 83, + "journal-issue": { + "published-print": { + "date-parts": [ + [ + 2021, + 5 + ] + ] + }, + "issue": "5" + }, + "alternative-id": [ + "1295" + ], + "URL": "http://dx.doi.org/10.1038/s41550-020-01295-8", + "relation": { + "cites": [ + ] + }, + "ISSN": [ + "2397-3366" + ], + "issn-type": [ + { + "value": "2397-3366", + "type": "electronic" + } + ], + "assertion": [ + { + "value": "21 July 2020", + "order": 1, + "name": "received", + "label": "Received", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "16 December 2020", + "order": 2, + "name": "accepted", + "label": "Accepted", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "22 February 2021", + "order": 3, + "name": "first_online", + "label": "First Online", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "The authors declare no competing interests.", + "order": 1, + "name": "Ethics", + "group": { + "name": "EthicsHeading", + "label": "Competing interests" + } + } + ] } } \ 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 12a61454d..e0ef0e65c 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 @@ -1,9 +1,14 @@ package eu.dnetlib.dhp.doiboost.crossref +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf._ import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.doiboost.crossref.Crossref2Oaf import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.json4s +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.{DefaultFormats, JValue} +import org.json4s.jackson.JsonMethods import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Test import org.slf4j.{Logger, LoggerFactory} @@ -109,6 +114,47 @@ class CrossrefMappingTest { } + private def parseJson(input: String): JValue = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = JsonMethods.parse(input) + + json + } + + @Test + def testCitationRelations(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")) + .mkString + + assertNotNull(json) + assertFalse(json.isEmpty) + + val result: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(result.nonEmpty) + + val j = parseJson(json) + + val doisReference: List[String] = for { + JObject(reference_json) <- j \ "reference" + JField("DOI", JString(doi_json)) <- reference_json + } yield doi_json + + val relationList: List[Relation] = result + .filter(s => s.isInstanceOf[Relation]) + .map(r => r.asInstanceOf[Relation]) + .filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION)) + + assertNotNull(relationList) + assertFalse(relationList.isEmpty) + + assertEquals(doisReference.size * 2, relationList.size) + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + relationList.foreach(p => println(mapper.writeValueAsString(p))) + } + @Test def testEmptyTitle(): Unit = { val json = Source diff --git a/dhp-workflows/dhp-monitor-update/pom.xml b/dhp-workflows/dhp-monitor-update/pom.xml new file mode 100644 index 000000000..ca0bb9837 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/pom.xml @@ -0,0 +1,32 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.4-SNAPSHOT + + 4.0.0 + dhp-monitor-update + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + + + + pl.project13.maven + git-commit-id-plugin + 2.1.11 + + false + + + + + diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml new file mode 100644 index 000000000..63fc84d75 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hive_jdbc_url + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228 + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + stats_tool_api_url + ${stats_tool_api_url} + + \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh new file mode 100644 index 000000000..10c1ed4ca --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh @@ -0,0 +1,18 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +export SOURCE=$1 +export TARGET=$2 +export SCRIPT_PATH=$3 + +echo "Getting file from " $3 +hdfs dfs -copyToLocal $3 + +echo "Updating monitor database" +cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - +echo "Impala shell finished" diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql new file mode 100644 index 000000000..265610e90 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -0,0 +1,146 @@ +DROP TABLE IF EXISTS TARGET.result_new; + +create table TARGET.result_new as + select distinct * from ( + select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( +-- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork +-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University + 'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech + ) )) foo; + +COMPUTE STATS TARGET.result_new; + +INSERT INTO TARGET.result select * from TARGET.result_new; +COMPUTE STATS TARGET.result; + +INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_citations; + +INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_references_oc; + +INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_citations_oc; + +INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_classifications; + +INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_apc; + +INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_concepts; + +INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_datasources; + +INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_fundercount; + +INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_gold; + +INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_greenoa; + +INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_languages; + +INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_licenses; + +INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_oids; + +INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_organization; + +INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_peerreviewed; + +INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_pids; + +INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_projectcount; + +INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_projects; + +INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_refereed; + +INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_sources; + +INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_topics; + +INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.result_fos; + +create view TARGET.foo1 as select * from TARGET.result_result rr where rr.source in (select id from TARGET.result_new); +create view TARGET.foo2 as select * from TARGET.result_result rr where rr.target in (select id from TARGET.result_new); +INSERT INTO TARGET.result_result 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; + +-- indicators +-- Sprint 1 ---- +INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_green_oa; +INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_grey_lit; +INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_doi_from_crossref; +-- Sprint 2 ---- +INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_result_has_cc_licence; +INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_result_has_cc_licence_url; +INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_has_abstract; +INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_result_with_orcid; +---- Sprint 3 ---- +INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_funded_result_with_fundref; +---- Sprint 4 ---- +INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_diamond; +INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_in_transformative; +INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_closed_other_open; +---- Sprint 5 ---- +INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_result_no_of_copies; +---- Sprint 6 ---- +INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc; +INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id); +COMPUTE STATS TARGET.indi_pub_downloads; +INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id); +COMPUTE STATS TARGET.indi_pub_downloads_datasource; +INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id); +COMPUTE STATS TARGET.indi_pub_downloads_year; +INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id); +COMPUTE STATS TARGET.indi_pub_downloads_datasource_year; +---- Sprint 7 ---- +INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_gold_oa; +INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_hybrid; + +INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_has_preprint; +INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_pub_in_subscribed; +INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id); +COMPUTE STATS TARGET.indi_result_with_pid; +--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; +DROP TABLE TARGET.result_new; diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml new file mode 100644 index 000000000..dda645d8f --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml @@ -0,0 +1,77 @@ + + + + stats_db_name + the target stats database name + + + stats_db_shadow_name + the name of the shadow schema + + + monitor_db_name + the target monitor db name + + + monitor_db_shadow_name + the name of the shadow monitor db + + + stats_tool_api_url + The url of the API of the stats tool. Is used to trigger the cache update. + + + hive_metastore_uris + hive server metastore URIs + + + hive_jdbc_url + hive server jdbc url + + + hive_timeout + the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds. + + + context_api_url + the base url of the context api (https://services.openaire.eu/openaire) + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hive_metastore_uris} + + + hive.txn.timeout + ${hive_timeout} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + monitor.sh + ${stats_db_name} + ${monitor_db_name} + ${wf:appPath()}/scripts/createMonitorDB.sql + monitor.sh + + + + + + + \ 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/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 86ead4a2c..753d61ca0 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 @@ -30,11 +30,16 @@ from rcount group by rcount.pid; create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture; +create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure; +create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents; +create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers; +create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft; +create view ${stats_db_name}.hrrst as select * from stats_ext.hrrst; create table ${stats_db_name}.result_instance stored as parquet as select distinct r.* from ( - select substr(r.id, 4) as id, inst.accessright.classname as accessright, substr(inst.collectedfrom.key, 4) as collectedfrom, + select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom, substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r join ${stats_db_name}.result res on res.id=r.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 2bdcbfa3d..237f68fae 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 @@ -10,6 +10,11 @@ create view if not exists TARGET.creation_date as select * from SOURCE.creation_ create view if not exists TARGET.funder as select * from SOURCE.funder; create view if not exists TARGET.fundref as select * from SOURCE.fundref; create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture; +create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure; +create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents; +create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers; +create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft; +create view if not exists TARGET.hrrst as select * from SOURCE.hrrst; create table TARGET.result stored as parquet as select distinct * from ( @@ -50,8 +55,16 @@ create table TARGET.result stored as parquet as 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona - 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University - ) )) foo; + 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University + 'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia + 'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University + 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje + 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan + 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork + 'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University + 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech + 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e' -- University of Cape Town + ))) 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); diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 08d33f4e8..c68ae46ca 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -70,7 +70,40 @@ - + + + + + ${wf:conf('resumeFrom') eq 'Step1'} + ${wf:conf('resumeFrom') eq 'Step2'} + ${wf:conf('resumeFrom') eq 'Step3'} + ${wf:conf('resumeFrom') eq 'Step4'} + ${wf:conf('resumeFrom') eq 'Step5'} + ${wf:conf('resumeFrom') eq 'Step6'} + ${wf:conf('resumeFrom') eq 'Step7'} + ${wf:conf('resumeFrom') eq 'Step8'} + ${wf:conf('resumeFrom') eq 'Step9'} + ${wf:conf('resumeFrom') eq 'Step10'} + ${wf:conf('resumeFrom') eq 'Step11'} + ${wf:conf('resumeFrom') eq 'Step12'} + ${wf:conf('resumeFrom') eq 'Step13'} + ${wf:conf('resumeFrom') eq 'Step14'} + ${wf:conf('resumeFrom') eq 'Step15'} + ${wf:conf('resumeFrom') eq 'Step15_5'} + ${wf:conf('resumeFrom') eq 'Contexts'} + ${wf:conf('resumeFrom') eq 'Step16-createIndicatorsTables'} + ${wf:conf('resumeFrom') eq 'Step16_1-definitions'} + ${wf:conf('resumeFrom') eq 'Step16_5'} + ${wf:conf('resumeFrom') eq 'Step19-finalize'} + ${wf:conf('resumeFrom') eq 'step20-createMonitorDB'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'} + ${wf:conf('resumeFrom') eq 'Step22'} + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] diff --git a/pom.xml b/pom.xml index 9b60b9078..839188a62 100644 --- a/pom.xml +++ b/pom.xml @@ -807,7 +807,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.15.0] + [3.15.1-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6]