From b00771c7cc9025b2c4401d3e5029f2da506e106d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 Dec 2023 15:12:44 +0100 Subject: [PATCH 1/6] [Transformative Agreement] added code to extract relations from the transformative agreement file for the IE products got from OpenAPC --- .../CreateActionSetSparkJob.java | 148 ++++++++++++++++++ .../ReadTransformativeAgreement.java | 90 +++++++++++ .../model/TransformativeAgreementModel.java | 42 +++++ .../as_parameters.json | 26 +++ .../input_read_parameters.json | 30 ++++ .../oozie_app/config-default.xml | 58 +++++++ .../oozie_app/download.sh | 2 + .../oozie_app/workflow.xml | 82 ++++++++++ 8 files changed, 478 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java new file mode 100644 index 000000000..fe77344f5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java @@ -0,0 +1,148 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; +import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.*; +import scala.Tuple2; + +public class CreateActionSetSparkJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63"; + private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement"; + + public static void main(final String[] args) throws IOException, ParseException { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + CreateActionSetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json")))); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> getRelations(spark, inputPath, outputPath)); + + } + + private static void getRelations(SparkSession spark, String inputPath, String outputPath) { + spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, TransformativeAgreementModel.class), + Encoders.bean(TransformativeAgreementModel.class)) + .flatMap( + (FlatMapFunction) value -> createRelation( + value) + .iterator(), + Encoders.bean(Relation.class)) + .filter((FilterFunction) Objects::nonNull) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + } + + private static List createRelation(TransformativeAgreementModel value) { + + List relationList = new ArrayList<>(); + + String paper; + + paper = "50|doi_________::" + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())); + + relationList + .add( + getRelation( + paper, + IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); + + relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES)); + + return relationList; + } + + public static Relation getRelation( + String source, + String target, + String relClass) { + + return OafMapperUtils + .getRelation( + source, + target, + ModelConstants.RESULT_PROJECT, + ModelConstants.OUTCOME, + relClass, + Arrays + .asList( + OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + TRANSFORMATIVE_AGREEMENT, "Transformative Agreement", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java new file mode 100644 index 000000000..ec921c89d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java @@ -0,0 +1,90 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement; + +import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER; +import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Arrays; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; +import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class ReadTransformativeAgreement implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(ReadTransformativeAgreement.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ReadTransformativeAgreement.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String inputFile = parser.get("inputFile"); + log.info("inputFile {}", inputFile); + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + SparkConf sconf = new SparkConf(); + + final String delimiter = Optional + .ofNullable(parser.get("delimiter")) + .orElse(DEFAULT_DELIMITER); + + runWithSparkSession( + sconf, + isSparkSessionManaged, + spark -> { + doRead( + spark, + inputFile, + outputPath, + delimiter); + }); + } + + private static void doRead(SparkSession spark, String inputFile, + String outputPath, + String delimiter) { + + Dataset data = spark + .read() + .format("csv") + .option("sep", delimiter) + .option("inferSchema", "true") + .option("header", "true") + .load(inputFile) + .repartition(100); + + data.map((MapFunction) row -> { + TransformativeAgreementModel trm = new TransformativeAgreementModel(); + + trm.setInstitution(row.getString(2)); + trm.setDoi(row.getString(7)); + + return trm; + }, Encoders.bean(TransformativeAgreementModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + inputFile); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java new file mode 100644 index 000000000..b427a09cc --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement.model; + +import java.io.Serializable; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +/** + * @author miriam.baglioni + * @Date 18/12/23 + */ +@JsonIgnoreProperties(ignoreUnknown = true) + +public class TransformativeAgreementModel implements Serializable { + private String institution; + private String doi; + private String agreement; + + public String getInstitution() { + return institution; + } + + public void setInstitution(String institution) { + this.institution = institution; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getAgreement() { + return agreement; + } + + public void setAgreement(String agreement) { + this.agreement = agreement; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json new file mode 100644 index 000000000..5244a6fe4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, + { + "paramName": "sdr", + "paramLongName": "shouldDuplicateRels", + "paramDescription": "activates/deactivates the construction of bidirectional relations Cites/IsCitedBy", + "paramRequired": false + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json new file mode 100644 index 000000000..5986abd55 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json @@ -0,0 +1,30 @@ +[ + + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, + { + "paramName": "d", + "paramLongName": "delimiter", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the hdfs name node", + "paramRequired": true + }, + { + "paramName": "if", + "paramLongName": "inputFile", + "paramDescription": "the hdfs name node", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml new file mode 100644 index 000000000..a1755f329 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh new file mode 100644 index 000000000..66b1a1bf6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh @@ -0,0 +1,2 @@ +#!/bin/bash +curl -L $1 | hdfs dfs -put - $2 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml new file mode 100644 index 000000000..0c5b1c119 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml @@ -0,0 +1,82 @@ + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + ${wf:conf('resumeFrom') eq 'DownloadDump'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${inputFile} + ${workingDir}/transformativeagreement/transformativeAgreement.json + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + + + yarn + cluster + Produces the AS for the Transformative Agreement + eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${workingDir}/transformativeagreement/ + --outputPath${outputPath} + + + + + + \ No newline at end of file From 354e02e6a9c7cf33fa69740d10c2a7c6a38310e0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 Dec 2023 15:20:27 +0100 Subject: [PATCH 2/6] [Transformative Agreement] removed not needed class. Read directly the json and no need to pass from the csv --- .../ReadTransformativeAgreement.java | 90 ------------------- 1 file changed, 90 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java deleted file mode 100644 index ec921c89d..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/ReadTransformativeAgreement.java +++ /dev/null @@ -1,90 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.transformativeagreement; - -import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER; -import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Arrays; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; -import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -public class ReadTransformativeAgreement implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(ReadTransformativeAgreement.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ReadTransformativeAgreement.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String inputFile = parser.get("inputFile"); - log.info("inputFile {}", inputFile); - Boolean isSparkSessionManaged = isSparkSessionManaged(parser); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - SparkConf sconf = new SparkConf(); - - final String delimiter = Optional - .ofNullable(parser.get("delimiter")) - .orElse(DEFAULT_DELIMITER); - - runWithSparkSession( - sconf, - isSparkSessionManaged, - spark -> { - doRead( - spark, - inputFile, - outputPath, - delimiter); - }); - } - - private static void doRead(SparkSession spark, String inputFile, - String outputPath, - String delimiter) { - - Dataset data = spark - .read() - .format("csv") - .option("sep", delimiter) - .option("inferSchema", "true") - .option("header", "true") - .load(inputFile) - .repartition(100); - - data.map((MapFunction) row -> { - TransformativeAgreementModel trm = new TransformativeAgreementModel(); - - trm.setInstitution(row.getString(2)); - trm.setDoi(row.getString(7)); - - return trm; - }, Encoders.bean(TransformativeAgreementModel.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + inputFile); - } - -} From 624f5f3f2127bc1caf7849514940b2c052ed1c1f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 Dec 2023 15:28:19 +0100 Subject: [PATCH 3/6] [Transformative Agreement] added check to verify the APC were paid byu the IReL funder --- .../CreateActionSetSparkJob.java | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java index fe77344f5..cab3f24e4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java @@ -102,20 +102,21 @@ public class CreateActionSetSparkJob implements Serializable { List relationList = new ArrayList<>(); - String paper; + if(value.getAgreement().startsWith("IReL")) { + String paper; - paper = "50|doi_________::" - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())); + paper = "50|doi_________::" + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())); - relationList - .add( - getRelation( - paper, - IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); - - relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES)); + relationList + .add( + getRelation( + paper, + IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); + relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES)); + } return relationList; } From eca021f4d6791ec875b8ea67671664811d190e17 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Feb 2024 12:21:07 +0100 Subject: [PATCH 4/6] [Transformative Agreement] add results with information abount the agreement and the country of the organization paid for it --- .../CreateActionSetSparkJob.java | 67 +- .../model/TransformativeAgreementModel.java | 9 + .../as_parameters.json | 6 - .../CreateTAActionSetTest.java | 324 + .../transformativeagreement/facts.json | 96499 ++++++++++++++++ .../crossref/CrossrefMappingTest.scala | 11 +- .../main/java/eu/dnetlib/dhp/MoveResult.java | 2 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 1 + .../oa/provision/XmlRecordFactoryTest.java | 8 +- pom.xml | 2 +- 10 files changed, 96903 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java index cab3f24e4..70145d800 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java @@ -13,7 +13,6 @@ import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; @@ -24,12 +23,13 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Country; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.*; import scala.Tuple2; @@ -72,11 +72,11 @@ public class CreateActionSetSparkJob implements Serializable { runWithSparkSession( conf, isSparkSessionManaged, - spark -> getRelations(spark, inputPath, outputPath)); + spark -> createActionSet(spark, inputPath, outputPath)); } - private static void getRelations(SparkSession spark, String inputPath, String outputPath) { + private static void createActionSet(SparkSession spark, String inputPath, String outputPath) { spark .read() .textFile(inputPath) @@ -92,28 +92,73 @@ public class CreateActionSetSparkJob implements Serializable { .filter((FilterFunction) Objects::nonNull) .toJavaRDD() .map(p -> new AtomicAction(p.getClass(), p)) + .union( + spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, TransformativeAgreementModel.class), + Encoders.bean(TransformativeAgreementModel.class)) + .map( + (MapFunction) value -> createResult( + value), + Encoders.bean(Result.class)) + .filter((FilterFunction) r -> r != null) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p))) .mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + .saveAsHadoopFile( + outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + } + + private static Result createResult(TransformativeAgreementModel value) { + Result r = new Result(); + r + .setId( + "50|doi_________::" + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()))); + r.setTransformativeAgreement(value.getAgreement()); + Country country = new Country(); + country.setClassid(value.getCountry()); + country.setClassname(value.getCountry()); + country + .setDataInfo( + OafMapperUtils + .dataInfo( + false, ModelConstants.SYSIMPORT_ACTIONSET, false, false, + OafMapperUtils + .qualifier( + "openapc::transformativeagreement", + "Harvested from Trnasformative Agreement file from OpenAPC", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9")); + country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE); + country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE); + r.setCountry(Arrays.asList(country)); + return r; } private static List createRelation(TransformativeAgreementModel value) { List relationList = new ArrayList<>(); - if(value.getAgreement().startsWith("IReL")) { + if (value.getAgreement().startsWith("IReL")) { String paper; paper = "50|doi_________::" - + IdentifierFactory + + IdentifierFactory .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())); relationList - .add( - getRelation( - paper, - IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); + .add( + getRelation( + paper, + IREL_PROJECT, ModelConstants.IS_PRODUCED_BY)); relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES)); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java index b427a09cc..3a53fec0a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java @@ -15,6 +15,15 @@ public class TransformativeAgreementModel implements Serializable { private String institution; private String doi; private String agreement; + private String country; + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } public String getInstitution() { return institution; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json index 5244a6fe4..5c55bbabe 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json @@ -16,11 +16,5 @@ "paramLongName": "isSparkSessionManaged", "paramDescription": "the hdfs name node", "paramRequired": false - }, - { - "paramName": "sdr", - "paramLongName": "shouldDuplicateRels", - "paramDescription": "activates/deactivates the construction of bidirectional relations Cites/IsCitedBy", - "paramRequired": false } ] diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java new file mode 100644 index 000000000..0ec34311f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java @@ -0,0 +1,324 @@ + +package eu.dnetlib.dhp.actionmanager.transformativeagreement; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob; +import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; + +/** + * @author miriam.baglioni + * @Date 13/02/24 + */ +public class CreateTAActionSetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateOpenCitationsASTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateTAActionSetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateTAActionSetTest.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(CreateTAActionSetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void createActionSet() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json") + .getPath(); + + eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + } + + @Test + void testNumberofRelations2() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet2" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + assertEquals(23, tmp.count()); + + // tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + + } + + @Test + void testRelationsCollectedFrom() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet3" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue()); + assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey()); + }); + + } + + @Test + void testRelationsDataInfo() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet4" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(false, r.getDataInfo().getInferred()); + assertEquals(false, r.getDataInfo().getDeletedbyinference()); + assertEquals("0.91", r.getDataInfo().getTrust()); + assertEquals( + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSID, + r.getDataInfo().getProvenanceaction().getClassid()); + assertEquals( + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, + r.getDataInfo().getProvenanceaction().getClassname()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename()); + }); + + } + + @Test + void testRelationsSemantics() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet5" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("citation", r.getSubRelType()); + assertEquals("resultResult", r.getRelType()); + }); + assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count()); + assertEquals(0, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count()); + + } + + @Test + void testRelationsSourceTargetPrefix() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet6" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("50|doi_________::", r.getSource().substring(0, 17)); + assertEquals("50|doi_________::", r.getTarget().substring(0, 17)); + }); + + } + + @Test + void testRelationsSourceTargetCouple() throws Exception { + final String doi1 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); + final String doi2 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); + final String doi3 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); + final String doi4 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); + final String doi5 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); + final String doi6 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet7" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + JavaRDD check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1)); + + assertEquals(5, check.count()); + +// check.foreach(r -> { +// if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) || +// r.getSource().equals(doi5) || r.getSource().equals(doi6)) { +// assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass()); +// assertEquals(doi1, r.getTarget()); +// } +// }); + + assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count()); + check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass())); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json new file mode 100644 index 000000000..e2801ddf3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json @@ -0,0 +1,96499 @@ +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Soft Computing", "issn": "1432-7643", "doi": "10.1007/s00500-015-1923-y", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Geoheritage", "issn": "1867-2477", "doi": "10.1007/s12371-015-0172-x", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Studies in Philosophy and Education", "issn": "0039-3746", "doi": "10.1007/s11217-016-9515-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Language Policy", "issn": "1568-4555", "doi": "10.1007/s10993-016-9402-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Conservation Genetics Resources", "issn": "1877-7252", "doi": "10.1007/s12686-016-0537-8", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aberystwyth University", "institution": "Aberystwyth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Sports Medicine", "issn": "0112-1642", "doi": "10.1007/s40279-016-0559-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Journal of Autism and Developmental Disorders", "issn": "0162-3257", "doi": "10.1007/s10803-015-2693-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Experimental Brain Research", "issn": "0014-4819", "doi": "10.1007/s00221-016-4567-y", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Morphology", "issn": "1871-5621", "doi": "10.1007/s11525-016-9286-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Anglia Ruskin University", "institution": "Anglia Ruskin University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "The International Sports Law Journal", "issn": "1567-7559", "doi": "10.1007/s40318-016-0091-2", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aston University", "institution": "Aston University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "International Journal of Clinical Pharmacy", "issn": "2210-7703", "doi": "10.1007/s11096-015-0236-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Aston University", "institution": "Aston University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Small Business Economics", "issn": "0921-898X", "doi": "10.1007/s11187-015-9698-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "European Journal of Ageing", "issn": "1613-9372", "doi": "10.1007/s10433-015-0359-7", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2015", "publisher": "Springer Nature", "journal_full_title": "Plant and Soil", "issn": "0032-079X", "doi": "10.1007/s11104-015-2747-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Biology and Fertility of Soils", "issn": "0178-2762", "doi": "10.1007/s00374-016-1092-x", "is_hybrid": "TRUE", "country": "GBR", 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"Biotechnology and Bioengineering", "issn": "0006-3592", "doi": "10.1002/bit.28208", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Conservation Biology", "issn": "0888-8892", "doi": "10.1111/cobi.13940", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "European Journal of Inorganic Chemistry", "issn": "1434-1948", "doi": "10.1002/ejic.202100992", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Biological Reviews", "issn": "1464-7931", "doi": "10.1111/brv.12837", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Area", "issn": "0004-0894", "doi": "10.1111/area.12815", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "History and Theory", "issn": "0018-2656", "doi": "10.1111/hith.12281", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Zeitschrift f\u00fcr anorganische und allgemeine Chemie", "issn": "0044-2313", "doi": "10.1002/zaac.202200370", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Economics & Management Strategy", "issn": "1058-6407", "doi": "10.1111/jems.12502", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Angewandte Chemie International Edition", "issn": "1433-7851", "doi": "10.1002/anie.202116468", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Angewandte Chemie", "issn": "0044-8249", "doi": "10.1002/ange.202116468", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "ELECTROPHORESIS", "issn": "0173-0835", "doi": "10.1002/elps.202200174", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Sleep Research", "issn": "0962-1105", "doi": "10.1111/jsr.13569", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Sleep Research", "issn": "0962-1105", "doi": "10.1111/jsr.13723", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Child Abuse Review", "issn": "0952-9136", "doi": "10.1002/car.2799", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Advanced Materials Interfaces", "issn": "2196-7350", "doi": "10.1002/admi.202201385", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "ChemBioChem", "issn": "1439-4227", "doi": "10.1002/cbic.202200329", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "History and Theory", "issn": "0018-2656", "doi": "10.1111/hith.12285", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Chemistry - A European Journal", "issn": "0947-6539", "doi": "10.1002/chem.202203476", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Angewandte Chemie International Edition", "issn": "1433-7851", "doi": "10.1002/anie.202213056", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Small", "issn": "1613-6810", "doi": "10.1002/smll.202205602", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Advanced Electronic Materials", "issn": "2199-160X", "doi": "10.1002/aelm.202200082", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Sleep Research", "issn": "0962-1105", "doi": "10.1111/jsr.13591", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Applied Polymer Science", "issn": "0021-8995", "doi": "10.1002/app.53313", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Traumatic Stress", "issn": "0894-9867", "doi": "10.1002/jts.22862", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Traumatic Stress", "issn": "0894-9867", "doi": "10.1002/jts.22871", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Bulletin of the London Mathematical Society", "issn": "0024-6093", "doi": "10.1112/blms.12749", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "ChemBioChem", "issn": "1439-4227", "doi": "10.1002/cbic.202200552", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "International Migration", "issn": "0020-7985", "doi": "10.1111/imig.13029", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "History and Theory", "issn": "0018-2656", "doi": "10.1111/hith.12259", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Journal of Morphology", "issn": "0362-2525", "doi": "10.1002/jmor.21462", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "Advanced Optical Materials", "issn": "2195-1071", "doi": "10.1002/adom.202200700", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} +{"__fact_key__": "Bielefeld U", "institution": "Bielefeld U", "period": "2022", "publisher": "Wiley-Blackwell", "journal_full_title": "European Journal of Inorganic Chemistry", "issn": "1434-1948", "doi": "10.1002/ejic.202200650", "is_hybrid": "TRUE", "country": "DEU", "agreement": "DEAL Wiley Germany"} 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 c27cebf65..9bf1e1f53 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 @@ -23,10 +23,15 @@ class CrossrefMappingTest { val mapper = new ObjectMapper() @Test - def testMissingAuthorParser():Unit = { - val json: String = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json")).mkString + def testMissingAuthorParser(): Unit = { + val json: String = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json")) + .mkString val result = Crossref2Oaf.convert(json) - result.filter(o => o.isInstanceOf[Publication]).map(p=> p.asInstanceOf[Publication]).foreach(p =>assertTrue(p.getAuthor.size()>0)) + result + .filter(o => o.isInstanceOf[Publication]) + .map(p => p.asInstanceOf[Publication]) + .foreach(p => assertTrue(p.getAuthor.size() > 0)) } @Test diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java index c71ccb439..6731f2332 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/MoveResult.java @@ -30,7 +30,7 @@ public class MoveResult implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( - MoveResult.class + MoveResult.class .getResourceAsStream( "/eu/dnetlib/dhp/wf/subworkflows/input_moveresult_parameters.json")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index a6bbd30cf..405f91b9f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1293,6 +1293,7 @@ class MappersTest { p.getInstance().get(0).getAlternateIdentifier().forEach(x -> System.out.println(x.getValue())); } + @Test void testNotWellFormed() throws IOException { final String xml = IOUtils diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index ef6370bf3..ba9572b17 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -249,12 +249,12 @@ public class XmlRecordFactoryTest { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, - XmlConverterJob.schemaLocation); + XmlConverterJob.schemaLocation); final Publication p = OBJECT_MAPPER - .readValue( - IOUtils.toString(getClass().getResourceAsStream("iris-odf-4.json")), - Publication.class); + .readValue( + IOUtils.toString(getClass().getResourceAsStream("iris-odf-4.json")), + Publication.class); final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); diff --git a/pom.xml b/pom.xml index 6ef320253..c8514a3cb 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.2] + [5.17.3] [4.0.3] [6.0.5] [3.1.6] From f0dc12634bac955c87d327b7666440a5b41ad635 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Sun, 18 Feb 2024 18:02:09 +0200 Subject: [PATCH 5/6] Add Action Set creation for affiliations inferred from the OpenAPC data --- .../PrepareAffiliationRelations.java | 9 +++++++++ .../bipaffiliations/input_actionset_parameter.json | 6 ++++++ .../actionmanager/bipaffiliations/job.properties | 3 ++- .../bipaffiliations/oozie_app/workflow.xml | 5 +++++ .../PrepareAffiliationRelationsTest.java | 13 +++++-------- 5 files changed, 27 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 1bdb06ecc..f9a5c539f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -64,6 +64,9 @@ public class PrepareAffiliationRelations implements Serializable { final String pubmedInputPath = parser.get("pubmedInputPath"); log.info("pubmedInputPath: {}", pubmedInputPath); + final String openapcInputPath = parser.get("openapcInputPath"); + log.info("openapcInputPath: {}", openapcInputPath); + final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); @@ -85,8 +88,14 @@ public class PrepareAffiliationRelations implements Serializable { JavaPairRDD pubmedRelations = prepareAffiliationRelations( spark, pubmedInputPath, collectedFromPubmed); + List collectedFromOpenAPC = OafMapperUtils + .listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC"); + JavaPairRDD openAPCRelations = prepareAffiliationRelations( + spark, openapcInputPath, collectedFromOpenAPC); + crossrefRelations .union(pubmedRelations) + .union(openAPCRelations) .saveAsHadoopFile( outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json index c6f905199..5a91ace75 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json @@ -17,6 +17,12 @@ "paramDescription": "the path to get the input data from Pubmed", "paramRequired": true }, + { + "paramName": "oip", + "paramLongName": "openapcInputPath", + "paramDescription": "the path to get the input data from OpenAPC", + "paramRequired": true + }, { "paramName": "o", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties index a3d55ff0c..69c667732 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties @@ -31,6 +31,7 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen # The following is needed as a property of a workflow oozie.wf.application.path=${oozieTopWfApplicationPath} -crossrefInputPath=/data/bip-affiliations/data.json +crossrefInputPath=/data/bip-affiliations/crossref-data.json pubmedInputPath=/data/bip-affiliations/pubmed-data.json +openapcInputPath=/data/bip-affiliations/openapc-data.json outputPath=/tmp/crossref-affiliations-output-v5 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml index c5ac6f884..e42437396 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml @@ -9,6 +9,10 @@ pubmedInputPath the path where to find the inferred affiliation relations from Pubmed + + openapcInputPath + the path where to find the inferred affiliation relations from OpenAPC + outputPath the path where to store the actionset @@ -102,6 +106,7 @@ --crossrefInputPath${crossrefInputPath} --pubmedInputPath${pubmedInputPath} + --openapcInputPath${openapcInputPath} --outputPath${outputPath} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java index b87738879..c164aad8b 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java @@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest { .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getPath(); - String pubmedAffiliationRelationsPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") - .getPath(); - String outputPath = workingDir.toString() + "/actionSet"; PrepareAffiliationRelations @@ -89,7 +85,8 @@ public class PrepareAffiliationRelationsTest { new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-crossrefInputPath", crossrefAffiliationRelationPath, - "-pubmedInputPath", pubmedAffiliationRelationsPath, + "-pubmedInputPath", crossrefAffiliationRelationPath, + "-openapcInputPath", crossrefAffiliationRelationPath, "-outputPath", outputPath }); @@ -106,7 +103,7 @@ public class PrepareAffiliationRelationsTest { // ); // } // count the number of relations - assertEquals(40, tmp.count()); + assertEquals(60, tmp.count()); Dataset dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); dataset.createOrReplaceTempView("result"); @@ -117,7 +114,7 @@ public class PrepareAffiliationRelationsTest { // verify that we have equal number of bi-directional relations Assertions .assertEquals( - 20, execVerification + 30, execVerification .filter( "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") .collectAsList() @@ -125,7 +122,7 @@ public class PrepareAffiliationRelationsTest { Assertions .assertEquals( - 20, execVerification + 30, execVerification .filter( "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") .collectAsList() From 72bae7af76631c680289bf0ae7472665a9198b10 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 19 Feb 2024 16:20:12 +0100 Subject: [PATCH 6/6] [Transformative Agreement] removed the relations from the ActionSet waiting to have the gree light from Ioanna --- .../CreateActionSetSparkJob.java | 35 ++++++++++--------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java index 70145d800..e1c3226cd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java @@ -13,6 +13,7 @@ import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; @@ -77,22 +78,22 @@ public class CreateActionSetSparkJob implements Serializable { } private static void createActionSet(SparkSession spark, String inputPath, String outputPath) { - spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER - .readValue(value, TransformativeAgreementModel.class), - Encoders.bean(TransformativeAgreementModel.class)) - .flatMap( - (FlatMapFunction) value -> createRelation( - value) - .iterator(), - Encoders.bean(Relation.class)) - .filter((FilterFunction) Objects::nonNull) - .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p)) - .union( + JavaRDD relations = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, TransformativeAgreementModel.class), + Encoders.bean(TransformativeAgreementModel.class)) + .flatMap( + (FlatMapFunction) value -> createRelation( + value) + .iterator(), + Encoders.bean(Relation.class)) + .filter((FilterFunction) Objects::nonNull) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)); +//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file spark .read() .textFile(inputPath) @@ -106,7 +107,7 @@ public class CreateActionSetSparkJob implements Serializable { Encoders.bean(Result.class)) .filter((FilterFunction) r -> r != null) .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p))) + .map(p -> new AtomicAction(p.getClass(), p)) .mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), new Text(OBJECT_MAPPER.writeValueAsString(aa))))