From b00771c7cc9025b2c4401d3e5029f2da506e106d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 Dec 2023 15:12:44 +0100 Subject: [PATCH 01/34] [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 02/34] [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 03/34] [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 e0ec800d7eac5ee2f821c2f4348848d4a6328a15 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 23 Jan 2024 11:34:53 +0100 Subject: [PATCH 04/34] [BulkTagging] extend the definition of the pathMap to include also actions that should be performed of the value extracted from the result befor applying the constraint --- .../bipfinder/SparkAtomicActionScoreJob.java | 2 +- .../dnetlib/dhp/bulktag/actions/Action.java | 38 + .../bulktag/actions/ExecSubstringAction.java | 54 + .../dnetlib/dhp/bulktag/actions/MapModel.java | 30 + .../dhp/bulktag/actions/Parameters.java | 28 + .../dhp/bulktag/community/ProtoMap.java | 4 +- .../dhp/bulktag/community/ResultTagger.java | 45 +- .../dhp/bulktag/criteria/GreatThanVerb.java | 34 + .../dhp/bulktag/criteria/LessThanVerb.java | 34 + .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 89 +- .../tagging_conf_publicationdate.xml | 1431 +++++++++++++++++ .../sample/dataset/publicationyear/dataset | 10 + .../sample/dataset/publicationyear/datasource | 0 .../publicationyear/otherresearchproduct | 0 .../dataset/publicationyear/publication | 0 .../sample/dataset/publicationyear/software | 0 pom.xml | 2 +- 17 files changed, 1781 insertions(+), 20 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/dataset create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/software diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c89782..76c8ec7fa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + //project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java new file mode 100644 index 000000000..6c9e7694f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java @@ -0,0 +1,38 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Action implements Serializable { + private String clazz; + private String method; + private List params; + + public String getClazz() { + return clazz; + } + + public void setClazz(String clazz) { + this.clazz = clazz; + } + + public String getMethod() { + return method; + } + + public void setMethod(String method) { + this.method = method; + } + + public List getParams() { + return params; + } + + public void setParams(List params) { + this.params = params; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java new file mode 100644 index 000000000..fd3091fd0 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 19/01/24 + */ +public class ExecSubstringAction implements Serializable { + + private String value; + private String from; + private String to; + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getFrom() { + return from; + } + + public void setFrom(String from) { + this.from = from; + } + + public String getTo() { + return to; + } + + public void setTo(String to) { + this.to = to; + } + + public String execSubstring(){ + int to = Integer.valueOf(this.to); + int from = Integer.valueOf(this.from); + + if(to < from || from > this.value.length()) + return ""; + + if(from < 0) + from = 0; + if (to > this.value.length()) + to = this.value.length(); + + return this.value.substring(from, to); + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java new file mode 100644 index 000000000..ef3eb43cc --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java @@ -0,0 +1,30 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class MapModel implements Serializable { + + private String path; + private Action action; + + + public String getPath() { + return path; + } + + public void setPath(String path) { + this.path = path; + } + + public Action getAction() { + return action; + } + + public void setAction(Action action) { + this.action = action; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java new file mode 100644 index 000000000..d23634605 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Parameters implements Serializable { + private String paramName; + private String paramValue; + + public String getParamName() { + return paramName; + } + + public void setParamName(String paramName) { + this.paramName = paramName; + } + + public String getParamValue() { + return paramValue; + } + + public void setParamValue(String paramValue) { + this.paramValue = paramValue; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java index fd7481719..15b4d10b7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java @@ -1,10 +1,12 @@ package eu.dnetlib.dhp.bulktag.community; +import eu.dnetlib.dhp.bulktag.actions.MapModel; + import java.io.Serializable; import java.util.HashMap; -public class ProtoMap extends HashMap implements Serializable { +public class ProtoMap extends HashMap implements Serializable { public ProtoMap() { super(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 98c46cf00..67422c2ad 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -5,9 +5,14 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.lang.reflect.Method; import java.util.*; import java.util.stream.Collectors; +import com.jayway.jsonpath.PathNotFoundException; +import eu.dnetlib.dhp.bulktag.actions.MapModel; +import eu.dnetlib.dhp.bulktag.actions.Parameters; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -35,27 +40,55 @@ public class ResultTagger implements Serializable { return (tmp != clist.size()); } - private Map> getParamMap(final Result result, Map params) { + private Map> getParamMap(final Result result, Map params) throws NoSuchMethodException, InvocationTargetException { Map> param = new HashMap<>(); String json = new Gson().toJson(result, Result.class); DocumentContext jsonContext = JsonPath.parse(json); + if (params == null) { params = new HashMap<>(); } for (String key : params.keySet()) { + MapModel mapModel = params.get(key); + try { - param.put(key, jsonContext.read(params.get(key))); - } catch (com.jayway.jsonpath.PathNotFoundException e) { + String path = mapModel.getPath(); + Object obj = jsonContext.read(path); + List pathValue ; + if(obj instanceof java.lang.String) + pathValue = Arrays.asList((String)obj); + else + pathValue = (List)obj; + if(Optional.ofNullable(mapModel.getAction()).isPresent()){ + Class c = Class.forName(mapModel.getAction().getClazz()); + Object class_instance = c.newInstance(); + Method setField = c.getMethod("setValue", String.class); + setField.invoke(class_instance, pathValue.get(0)); + for(Parameters p : mapModel.getAction().getParams()){ + setField = c.getMethod("set" + p.getParamName(), String.class); + setField.invoke(class_instance, p.getParamValue()); + } + + param.put(key,Arrays.asList((String)c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance))); + + } + + else{ + param.put(key, pathValue); + } + + } catch (PathNotFoundException | ClassNotFoundException | InstantiationException | IllegalAccessException e) { param.put(key, new ArrayList<>()); } } return param; + } public R enrichContextCriteria( - final R result, final CommunityConfiguration conf, final Map criteria) { + final R result, final CommunityConfiguration conf, final Map criteria) throws InvocationTargetException, NoSuchMethodException { + - final Map> param = getParamMap(result, criteria); // Verify if the entity is deletedbyinference. In case verify if to clean the context list // from all the zenodo communities @@ -64,6 +97,8 @@ public class ResultTagger implements Serializable { return result; } + final Map> param = getParamMap(result, criteria); + // Execute the EOSCTag for the services switch (result.getResulttype().getClassid()) { case PUBLICATION_RESULTTYPE_CLASSID: diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java new file mode 100644 index 000000000..f77120800 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("greater_than") +public class GreatThanVerb implements Selection, Serializable { + + private String param; + + public GreatThanVerb() { + } + + public GreatThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) > 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java new file mode 100644 index 000000000..4aa52bfae --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("lesser_than") +public class LessThanVerb implements Selection, Serializable { + + private String param; + + public LessThanVerb() { + } + + public LessThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) < 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 743e62b5f..01be4d0a3 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -13,6 +13,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -31,18 +32,26 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," - + " \"title\" : \"$['title'][*]['value']\"," - + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," - + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\", " - + " \"subject\" :\"$['subject'][*]['value']\" , " + - "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + - "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + - "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + - "\"publisher\":\"$['publisher'].value\"," + - "\"publicationyear\":\"$['dateofacceptance'].value\"} "; + public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," + + " \"title\":{\"path\":\"$['title'][*]['value']\"}, "+ + " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " + + " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"+ + "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"},"+ + " \"description\" : {\"path\":\"$['description'][*]['value']\"},"+ + " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " + + " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , "+ + "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," + + "\"journal\":{\"path\":\"$['journal'].name\"}," + + "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," + + "\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," + + "\"publisher\":{\"path\":\"$['publisher'].value\"}," + + "\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " + + " \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," + + "\"method\":\"execSubstring\","+ + "\"params\":[" + + "{\"paramName\":\"From\", \"paramValue\":0}, " + + "{\"paramName\":\"To\",\"paramValue\":4}]}}}"; + private static SparkSession spark; @@ -1600,4 +1609,60 @@ public class BulkTagJobTest { Assertions.assertEquals(0, spark.sql(query).count()); } + + @Test + void pubdateTest() throws Exception { + + + final String pathMap = BulkTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(), + "-taggingConf", + IOUtils + .toString( + BulkTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")), + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + + String query = "select id, MyT.id community, MyD.provenanceaction.classid " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset queryResult = spark.sql(query); + queryResult.show(false); + Assertions.assertEquals(5, queryResult.count()); + + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")).count()); + + + } + + + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml new file mode 100644 index 000000000..26f1ca822 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml @@ -0,0 +1,1431 @@ + + + + + + + zenodo + + + + + + + + + + + + + + + + + + + + + + 10|re3data_____::a507cdacc5bbcc08761c92185dee5cab + + + + + + + + + + + + rda + + + + + + + + SDG13 - Climate action + SDG8 - Decent work and economic growth + SDG15 - Life on land + SDG2 - Zero hunger + SDG17 - Partnerships for the goals + SDG10 - Reduced inequalities + SDG5 - Gender equality + SDG12 - Responsible consumption and production + SDG14 - Life below water + SDG6 - Clean water and sanitation + SDG11 - Sustainable cities and communities + SDG1 - No poverty + SDG3 - Good health and well being + SDG7 - Affordable and clean energy + SDG4 - Quality education + SDG9 - Industry innovation and infrastructure + SDG16 - Peace justice and strong institutions + + + + + + + + modern art + monuments + europeana data model + sites + field walking + frescoes + LIDO metadata schema + art history + excavation + Arts and Humanities General + cities + coins + temples + numismatics + lithics + roads + environmental archaeology + digital cultural heritage + archaeological reports + history + CRMba + churches + cultural heritage + archaeological stratigraphy + religious art + buidings + digital humanities + survey + archaeological sites + linguistic studies + bioarchaeology + architectural orders + palaeoanthropology + fine arts + europeana + CIDOC CRM + decorations + classic art + stratigraphy + digital archaeology + intangible cultural heritage + walls + humanities + chapels + CRMtex + Language and Literature + paintings + archaeology + fair data + mosaics + burials + architecture + medieval art + castles + CARARE metadata schema + statues + natural language processing + inscriptions + CRMsci + vaults + contemporary art + Arts and Humanities + CRMarchaeo + pottery + site + architectural + vessels + + + + 10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + 10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + 10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + 10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + + 10|doajarticles::0da84e9dfdc8419576169e027baa8028 + + + + 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 + + + + 10|openaire____::c5502a43e76feab55dd00cf50f519125 + + + + 10|re3data_____::a48f09c562b247a9919acfe195549b47 + + + + 10|opendoar____::97275a23ca44226c9964043c8462be96 + + + + + + storm + + + + crosscult + + + + wholodance_eu + + + + digcur2013 + + + + gravitate + + + + dipp2014 + + + + digitalhumanities + + + + dimpo + + + + adho + + + + chc + + + + wahr + + + + ibe + + + + ariadne + + + + parthenos-hub + + + + parthenos-training + + + + gandhara + + + + cmsouthasia + + + + nilgirihills + + + + shamsa_mustecio + + + + bodhgaya + + + + oac_dh-ch + + + + + + + Stock Assessment + pelagic + Acoustic + Fish farming + Fisheries + Fishermen + maximum sustainable yield + trawler + Fishing vessel + Fisherman + Fishing gear + mackerel + RFMO + Fish Aggregating Device + Bycatch + Fishery + common fisheries policy + Fishing fleet + Aquaculture + + + + 10|doajarticles::8cec81178926caaca531afbd8eb5d64c + + + + 10|doajarticles::0f7a7f30b5400615cae1829f3e743982 + + + + 10|doajarticles::9740f7f5af3e506d2ad2c215cdccd51a + + + + 10|doajarticles::9f3fbaae044fa33cb7069b72935a3254 + + + + 10|doajarticles::cb67f33eb9819f5c624ce0313957f6b3 + + + + 10|doajarticles::e21c97cbb7a209afc75703681c462906 + + + + 10|doajarticles::554cde3be9e5c4588b4c4f9f503120cb + + + + 10|tubitakulakb::11e22f49e65b9fd11d5b144b93861a1b + + + + 10|doajarticles::57c5d3837da943e93b28ec4db82ec7a5 + + + + 10|doajarticles::a186f5ddb8e8c7ecc992ef51cf3315b1 + + + + 10|doajarticles::e21c97cbb7a209afc75703681c462906 + + + + 10|doajarticles::dca64612dfe0963fffc119098a319957 + + + + 10|doajarticles::dd70e44479f0ade25aa106aef3e87a0a + + + + + + discardless + + + + farfish2020 + + + + 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opensourcebrain + + + + brainspeak + + + + braincom + + + + nextgenvis + + + + meso-brain + + + + neuroplasticity-workshop + + + + bionics + + + + brainmattrain-676408 + + + + repronim + + + + affectiveneuro + + + + con + + + + lab_neurol_sperim_irfmn_irccs_milano_it + + + + + + + + marine + ocean + fish + aqua + sea + + + + + adriplan + + + + devotes-project + + + + euro-basin + + + + naclim + + + + discardless + + + + assisibf + + + + meece + + + + facts + + + + proeel + + + + aquatrace + + + + myfish + + + + atlas + + + + blue-actionh2020 + + + + sponges + + + + merces_project + + + + bigdataocean + + + + columbus + + + + h2020-aquainvad-ed + + + + aquarius + + + + southern-ocean-observing-system + + + + eawag + + + + mossco + + + + onc + + + + oceanbiogeochemistry + + + + oceanliteracy + + + + openearth + + + + ocean + + + + calcifierraman + + + + bermudabream + + + + brcorp1 + + + + mce + + + + biogeochem + + + + ecc2014 + + + + fisheries + + + + sedinstcjfas + + + + narmada + + + + umr-entropie + + + + farfish2020 + + + + primefish + + + + zf-ilcs + + + + climefish + + + + afrimed_eu + + + + spi-ace + + + + cice-consortium + + + + nemo-ocean + + + + mesopp-h2020 + + + + marxiv + + + + + + + + + + + instruct + + + + west-life + + + + + + + + + + + + + + animal production and health + fisheries and aquaculture + food safety and human nutrition + information management + food technology + agri-food education and extension + natural resources and environment + food system + engineering technology and Research + agriculture + food safety risk assessment + food security + farming practices and systems + plant production and protection + agri-food economics and policy + Agri-food + food distribution + forestry + + + + 10|opendoar____::1a551829d50f1400b0dab21fdd969c04 + + + + 10|opendoar____::49af6c4e558a7569d80eee2e035e2bd7 + + + + 10|opendoar____::0266e33d3f546cb5436a10798e657d97 + + + + 10|opendoar____::fd4c2dc64ccb8496e6f1f94c85f30d06 + + + + 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10|opendoar____::96da2f590cd7246bbde0051047b0d6f7 + {"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]} + + + + + dimpo + + + + + + + + + + + + + + + + + + + + Green Transport + City mobility systems + Vulnerable road users + Traffic engineering + Transport electrification + Mobility + Intermodal freight transport + Clean vehicle fleets + Intelligent mobility + Inflight refueling + District mobility systems + Navigation and control systems for optimised planning and routing + European Space Technology Platform + European Transport networks + Green cars + Inter-modality infrastructures + Advanced Take Off and Landing Ideas + Sustainable urban systems + port-area railway networks + Innovative forms of urban transport + Alliance for Logistics Innovation through Collaboration in Europe + Advisory Council for Aeronautics Research in Europe + Mobility services for people and goods + Guidance and traffic management + Passenger mobility + Smart mobility and services + transport innovation + high-speed railway + Vehicle design + Inland shipping + public transportation + aviation’s climate impact + Road transport + On-demand public transport + Personal Air Transport + Transport + transport vulnerability + Pipeline transport + European Association of Aviation Training and Education Organisations + Defrosting of railway infrastructure + Inclusive and affordable transport + River Information Services + jel:L92 + Increased use of public transport + Seamless mobility + STRIA + trolleybus transport + Intelligent Transport System + Low-emission alternative energy for transport + Shared mobility for people and goods + Business model for urban mobility + Interoperability of transport systems + Cross-border train slot booking + Air transport + Transport pricing + Sustainable transport + European Rail Transport Research Advisory Council + Alternative aircraft configurations + Transport and Mobility + Railways applications + urban transport + Environmental impact of transport + urban freight delivery systems + Automated Road Transport + Alternative fuels in public transport + Active LIDAR-sensor for GHG-measurements + Autonomous logistics operations + Rational use of motorised transport + Network and traffic management systems + electrification of railway wagons + Single European Sky + Electrified road systems + transportation planning + Railway dynamics + Motorway of the Sea + smart railway communications + Maritime transport + Environmental- friendly transport + Combined transport + Connected automated driving technology + Innovative freight logistics services + automated and shared vehicles + Alternative Aircraft Systems + Land-use and transport interaction + Public transport system + Business plan for shared mobility + Shared mobility + Growing of mobility demand + European Road Transport Research Advisory Council + WATERBORNE ETP + Effective transport management system + Short Sea Shipping + air traffic management + Sea hubs and the motorways of the sea + Urban mobility solutions + Smart city planning + Maritime spatial planning + EUropean rail Research Network of Excellence + Transport governance + ENERGY CONSUMPTION BY THE TRANSPORT SECTOR + Integrated urban plan + inland waterway services + European Conference of Transport Research Institutes + air vehicles + E-freight + Automated Driving + Automated ships + pricing for cross-border passenger transport + Vehicle efficiency + Railway transport + Electric vehicles + Road traffic monitoring + Deep sea shipping + Circular economy in transport + Traffic congestion + air transport system + Urban logistics + Rail transport + OpenStreetMap + high speed rail + Transportation engineering + Intermodal travel information + Flight Data Recorders + Advanced driver assistance systems + long distance freight transport + Inland waterway transport + Smart mobility + Mobility integration + Personal Rapid Transit system + Safety measures & requirements for roads + Green rail transport + Electrical + Vehicle manufacturing + Future Airport Layout + Rail technologies + European Intermodal Research Advisory Council + inland navigation + Automated urban vehicles + ECSS-standards + Traveller services + Polluting transport + Air Traffic Control + Cooperative and connected and automated transport + Innovative powertrains + Quality of transport system and services + door-to- door logistics chain + Inter-modal aspects of urban mobility + travel (and mobility) + Innovative freight delivery systems + urban freight delivery infrastructures + + + + 10|doajarticles::1c5bdf8fca58937894ad1441cca99b76 + + + + 10|doajarticles::b37a634324a45c821687e6e80e6f53b4 + + + + 10|doajarticles::4bf64f2a104040e4e055cd9594b2d77c + + + + 10|doajarticles::479ca537c12755d1868bbf02938a900c + + + + 10|doajarticles::55f31df96a60e2309f45b7c265fcf7a2 + + + + 10|doajarticles::c52a09891a5301f9986ebbfe3761810c + + + + 10|doajarticles::379807bc7f6c71a227ef1651462c414c + + + + 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+ + + iecteim + + + + iccpt2019 + + + + + + + + + + + + + + + + + + + + + + + + + + + {"criteria":[{"constraint":[{"verb":"equals_caseinsensitive","field":"subject","value":"ciencias de la comunicación"}, + {"verb":"equals","field":"subject","value":"Miriam"}]}, + {"constraint":[{"verb":"equals","field":"subject","value":"miriam"}]}]} + + Sustainability-oriented science policy + STI policies + science—society relations + Science & Technology Policy + Innovation policy + science policy + Policy and Law + + + + 10|doajarticles::c6f0ed5fa41e98863e7c73501fe4bd6d + + + + 10|doajarticles::ae4c7286c79590f19fdca670156ce816 + + + + 10|doajarticles::0f664bce92ce953e0c7a92068c46bfb3 + + + + 10|doajarticles::00017183dc4c858fb77541985323a4ef + + + + 10|doajarticles::93b306f458cce3d7aaaf58c0a725f4f9 + + + + 10|doajarticles::9dbf8fbf3e9fe0fe1fc01e55fbd90bfc + + + + 10|doajarticles::a2bda8785c863279bba4b8f34827b4c9 + + + + 10|doajarticles::019a1fcb42c3fea1c1b689df76330b58 + + + + 10|doajarticles::0daa8281938831e9c82bfed8b55a2975 + + + + 10|doajarticles::f67ad6d268162079b3abd51a24468744 + + + + 10|doajarticles::c6f0ed5fa41e98863e7c73501fe4bd6d + + + + 10|doajarticles::ad114356e196a4a3d84dda59c720dacd + + + + 10|doajarticles::01e8a54fdecaaf354c67a2dd74ae7d4f + + + + 10|doajarticles::449305f096b10a9464449ff2d0e10e06 + + + + 10|doajarticles::982c0c0ac378256254cce2fa6572bb6c + + + + 10|doajarticles::49d6ed47138884566ce93cf0ccb12c02 + + + + 10|doajarticles::a98e820dbc2e8ee0fc84ab66f263267c + + + + 10|doajarticles::50b1ce37427b36368f8f0f1317e47f83 + + + + 10|doajarticles::f0ec29b7450b2ac5d0ad45327eeb531a + + + + 10|doajarticles::d8d421d3b0349a7aaa93758b27a54e84 + + + + 10|doajarticles::7ffc35ac5133da01d421ccf8af5b70bc + + + + + + risis + + + + + + + + COVID-19 + Severe acute respiratory syndrome coronavirus 2 + SARS-CoV-2 + COVID19 + 2019 novel coronavirus + coronavirus disease 2019 + HCoV-19 + mesh:C000657245 + 2019-nCoV + coronavirus disease-19 + mesh:COVID-19 + COVID2019 + + + + 10|opendoar____::358aee4cc897452c00244351e4d91f69 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}}]} + + + + 10|re3data_____::7b0ad08687b2c960d5aeef06f811d5e6 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|driver______::bee53aa31dc2cbb538c10c2b65fa5824 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|openaire____::437f4b072b1aa198adcbc35910ff3b98 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|share_______::4719356ec8d7d55d3feb384ce879ad6c + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|opendoar____::6f4922f45568161a8cdf4ad2299f6d23 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + 10|re3data_____::7980778c78fb4cf0fab13ce2159030dc + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} + + + 10|re3data_____::978378def740bbf2bfb420de868c460b + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} + + + + + chicago-covid-19 + + + + covid-19-senacyt-panama-sample + + + + covid-19-tx-rct-stats-review + + + + covid_19_senacyt_abc_panama + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/dataset b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/dataset new file mode 100644 index 000000000..b3ac15d4c --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/dataset @@ -0,0 +1,10 @@ +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055868909,"id":"50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529","originalId":["od______3989::02dd5d2c222191b0b9bd4f33c8e96529"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital 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[4.17.2] + [4.17.3] [4.0.3] [6.0.5] [3.1.6] From f7d06dc661f370ac4275188537958cb9e6a0a7c9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 23 Jan 2024 11:43:08 +0100 Subject: [PATCH 05/34] compilation after merging --- .../bipfinder/SparkAtomicActionScoreJob.java | 2 +- .../main/java/eu/dnetlib/dhp/MoveResult.java | 2 +- .../dnetlib/dhp/bulktag/actions/Action.java | 43 +++--- .../bulktag/actions/ExecSubstringAction.java | 65 ++++----- .../dnetlib/dhp/bulktag/actions/MapModel.java | 30 ++-- .../dhp/bulktag/actions/Parameters.java | 29 ++-- .../dhp/bulktag/community/ProtoMap.java | 4 +- .../dhp/bulktag/community/ResultTagger.java | 36 ++--- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 136 +++++++++++------- 9 files changed, 194 insertions(+), 153 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 76c8ec7fa..040c89782 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - //project.setId(bipProjectScores.getProjectId()); + project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) 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-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java index 6c9e7694f..987e7afef 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.actions; import java.io.Serializable; @@ -8,31 +9,31 @@ import java.util.List; * @Date 22/01/24 */ public class Action implements Serializable { - private String clazz; - private String method; - private List params; + private String clazz; + private String method; + private List params; - public String getClazz() { - return clazz; - } + public String getClazz() { + return clazz; + } - public void setClazz(String clazz) { - this.clazz = clazz; - } + public void setClazz(String clazz) { + this.clazz = clazz; + } - public String getMethod() { - return method; - } + public String getMethod() { + return method; + } - public void setMethod(String method) { - this.method = method; - } + public void setMethod(String method) { + this.method = method; + } - public List getParams() { - return params; - } + public List getParams() { + return params; + } - public void setParams(List params) { - this.params = params; - } + public void setParams(List params) { + this.params = params; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java index fd3091fd0..0ada4ebfb 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.actions; import java.io.Serializable; @@ -8,47 +9,47 @@ import java.io.Serializable; */ public class ExecSubstringAction implements Serializable { - private String value; - private String from; - private String to; + private String value; + private String from; + private String to; - public String getValue() { - return value; - } + public String getValue() { + return value; + } - public void setValue(String value) { - this.value = value; - } + public void setValue(String value) { + this.value = value; + } - public String getFrom() { - return from; - } + public String getFrom() { + return from; + } - public void setFrom(String from) { - this.from = from; - } + public void setFrom(String from) { + this.from = from; + } - public String getTo() { - return to; - } + public String getTo() { + return to; + } - public void setTo(String to) { - this.to = to; - } + public void setTo(String to) { + this.to = to; + } - public String execSubstring(){ - int to = Integer.valueOf(this.to); - int from = Integer.valueOf(this.from); + public String execSubstring() { + int to = Integer.valueOf(this.to); + int from = Integer.valueOf(this.from); - if(to < from || from > this.value.length()) - return ""; + if (to < from || from > this.value.length()) + return ""; - if(from < 0) - from = 0; - if (to > this.value.length()) - to = this.value.length(); + if (from < 0) + from = 0; + if (to > this.value.length()) + to = this.value.length(); - return this.value.substring(from, to); + return this.value.substring(from, to); - } + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java index ef3eb43cc..6a0d20b57 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.actions; import java.io.Serializable; @@ -8,23 +9,22 @@ import java.io.Serializable; */ public class MapModel implements Serializable { - private String path; - private Action action; + private String path; + private Action action; + public String getPath() { + return path; + } - public String getPath() { - return path; - } + public void setPath(String path) { + this.path = path; + } - public void setPath(String path) { - this.path = path; - } + public Action getAction() { + return action; + } - public Action getAction() { - return action; - } - - public void setAction(Action action) { - this.action = action; - } + public void setAction(Action action) { + this.action = action; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java index d23634605..973b00b77 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.actions; import java.io.Serializable; @@ -7,22 +8,22 @@ import java.io.Serializable; * @Date 22/01/24 */ public class Parameters implements Serializable { - private String paramName; - private String paramValue; + private String paramName; + private String paramValue; - public String getParamName() { - return paramName; - } + public String getParamName() { + return paramName; + } - public void setParamName(String paramName) { - this.paramName = paramName; - } + public void setParamName(String paramName) { + this.paramName = paramName; + } - public String getParamValue() { - return paramValue; - } + public String getParamValue() { + return paramValue; + } - public void setParamValue(String paramValue) { - this.paramValue = paramValue; - } + public void setParamValue(String paramValue) { + this.paramValue = paramValue; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java index 15b4d10b7..dc75aec37 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java @@ -1,11 +1,11 @@ package eu.dnetlib.dhp.bulktag.community; -import eu.dnetlib.dhp.bulktag.actions.MapModel; - import java.io.Serializable; import java.util.HashMap; +import eu.dnetlib.dhp.bulktag.actions.MapModel; + public class ProtoMap extends HashMap implements Serializable { public ProtoMap() { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 67422c2ad..2ea229e3e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -10,9 +10,6 @@ import java.lang.reflect.Method; import java.util.*; import java.util.stream.Collectors; -import com.jayway.jsonpath.PathNotFoundException; -import eu.dnetlib.dhp.bulktag.actions.MapModel; -import eu.dnetlib.dhp.bulktag.actions.Parameters; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -20,7 +17,10 @@ import org.slf4j.LoggerFactory; import com.google.gson.Gson; import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.JsonPath; +import com.jayway.jsonpath.PathNotFoundException; +import eu.dnetlib.dhp.bulktag.actions.MapModel; +import eu.dnetlib.dhp.bulktag.actions.Parameters; import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @@ -40,7 +40,8 @@ public class ResultTagger implements Serializable { return (tmp != clist.size()); } - private Map> getParamMap(final Result result, Map params) throws NoSuchMethodException, InvocationTargetException { + private Map> getParamMap(final Result result, Map params) + throws NoSuchMethodException, InvocationTargetException { Map> param = new HashMap<>(); String json = new Gson().toJson(result, Result.class); DocumentContext jsonContext = JsonPath.parse(json); @@ -54,30 +55,34 @@ public class ResultTagger implements Serializable { try { String path = mapModel.getPath(); Object obj = jsonContext.read(path); - List pathValue ; - if(obj instanceof java.lang.String) - pathValue = Arrays.asList((String)obj); + List pathValue; + if (obj instanceof java.lang.String) + pathValue = Arrays.asList((String) obj); else - pathValue = (List)obj; - if(Optional.ofNullable(mapModel.getAction()).isPresent()){ + pathValue = (List) obj; + if (Optional.ofNullable(mapModel.getAction()).isPresent()) { Class c = Class.forName(mapModel.getAction().getClazz()); Object class_instance = c.newInstance(); Method setField = c.getMethod("setValue", String.class); setField.invoke(class_instance, pathValue.get(0)); - for(Parameters p : mapModel.getAction().getParams()){ + for (Parameters p : mapModel.getAction().getParams()) { setField = c.getMethod("set" + p.getParamName(), String.class); setField.invoke(class_instance, p.getParamValue()); } - param.put(key,Arrays.asList((String)c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance))); + param + .put( + key, Arrays + .asList((String) c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance))); } - else{ + else { param.put(key, pathValue); } - } catch (PathNotFoundException | ClassNotFoundException | InstantiationException | IllegalAccessException e) { + } catch (PathNotFoundException | ClassNotFoundException | InstantiationException + | IllegalAccessException e) { param.put(key, new ArrayList<>()); } } @@ -86,9 +91,8 @@ public class ResultTagger implements Serializable { } public R enrichContextCriteria( - final R result, final CommunityConfiguration conf, final Map criteria) throws InvocationTargetException, NoSuchMethodException { - - + final R result, final CommunityConfiguration conf, final Map criteria) + throws InvocationTargetException, NoSuchMethodException { // Verify if the entity is deletedbyinference. In case verify if to clean the context list // from all the zenodo communities diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 01be4d0a3..433e046cc 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -33,25 +33,25 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," + - " \"title\":{\"path\":\"$['title'][*]['value']\"}, "+ - " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " + - " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"+ - "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"},"+ - " \"description\" : {\"path\":\"$['description'][*]['value']\"},"+ - " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " + - " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , "+ - "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," + - "\"journal\":{\"path\":\"$['journal'].name\"}," + - "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," + - "\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," + - "\"publisher\":{\"path\":\"$['publisher'].value\"}," + - "\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " + - " \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," + - "\"method\":\"execSubstring\","+ - "\"params\":[" + - "{\"paramName\":\"From\", \"paramValue\":0}, " + - "{\"paramName\":\"To\",\"paramValue\":4}]}}}"; - + " \"title\":{\"path\":\"$['title'][*]['value']\"}, " + + " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " + + " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ," + + + "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," + + " \"description\" : {\"path\":\"$['description'][*]['value']\"}," + + " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " + + " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " + + "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," + + "\"journal\":{\"path\":\"$['journal'].name\"}," + + "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," + + "\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," + + "\"publisher\":{\"path\":\"$['publisher'].value\"}," + + "\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " + + " \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," + + "\"method\":\"execSubstring\"," + + "\"params\":[" + + "{\"paramName\":\"From\", \"paramValue\":0}, " + + "{\"paramName\":\"To\",\"paramValue\":4}]}}}"; private static SparkSession spark; @@ -1609,60 +1609,94 @@ public class BulkTagJobTest { Assertions.assertEquals(0, spark.sql(query).count()); } - @Test void pubdateTest() throws Exception { - final String pathMap = BulkTagJobTest.pathMap; SparkBulkTagJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(), - "-taggingConf", - IOUtils - .toString( - BulkTagJobTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")), - "-outputPath", workingDir.toString() + "/", - "-pathMap", pathMap - }); + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(), + "-taggingConf", + IOUtils + .toString( + BulkTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")), + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); Assertions.assertEquals(10, tmp.count()); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); verificationDataset.createOrReplaceTempView("dataset"); - String query = "select id, MyT.id community, MyD.provenanceaction.classid " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; org.apache.spark.sql.Dataset queryResult = spark.sql(query); queryResult.show(false); Assertions.assertEquals(5, queryResult.count()); - Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")).count()); - Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")).count()); - Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")).count()); - Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")).count()); - Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")).count()); - + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")) + .count()); + Assertions + .assertEquals( + 1, + queryResult + .filter( + (FilterFunction) r -> r + .getAs("id") + .equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")) + .count()); } - - } From 9aebca77a031f8e76e119bc32adf27153f413a87 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 29 Jan 2024 14:41:02 +0100 Subject: [PATCH 06/34] Added exception throwing in Hadoop transformation when TR is not syntactically valid --- .../xslt/XSLTTransformationFunction.java | 19 +- .../transformation/TransformationJobTest.java | 14 ++ .../eu/dnetlib/dhp/transform/invalid.xslt | 185 ++++++++++++++++++ 3 files changed, 212 insertions(+), 6 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/invalid.xslt diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java index 54192a7be..247915d17 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java @@ -48,7 +48,7 @@ public class XSLTTransformationFunction implements MapFunctiontr.call(mr)); + + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final LongAccumulator la = new LongAccumulator(); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/invalid.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/invalid.xslt new file mode 100644 index 000000000..3c84e08e7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/invalid.xslt @@ -0,0 +1,185 @@ + + + + + + + + +asdf;klamsdof'sdn & + + c:format'" /> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From 07a373a0bd88902e486aaa95644bf72721848a81 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 30 Jan 2024 13:51:11 +0100 Subject: [PATCH 07/34] [bulkTagging] removing checks while performing the substring action so that it will fire an Exception if the paramneters are wrongly set --- .../bipfinder/SparkAtomicActionScoreJob.java | 2 +- .../dhp/bulktag/actions/ExecSubstringAction.java | 12 +----------- 2 files changed, 2 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c89782..76c8ec7fa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + //project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java index 0ada4ebfb..444e8b82d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java @@ -38,18 +38,8 @@ public class ExecSubstringAction implements Serializable { } public String execSubstring() { - int to = Integer.valueOf(this.to); - int from = Integer.valueOf(this.from); - if (to < from || from > this.value.length()) - return ""; - - if (from < 0) - from = 0; - if (to > this.value.length()) - to = this.value.length(); - - return this.value.substring(from, to); + return this.value.substring(Integer.valueOf(this.from), Integer.valueOf(this.to)); } } From eca021f4d6791ec875b8ea67671664811d190e17 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 13 Feb 2024 12:21:07 +0100 Subject: [PATCH 08/34] [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", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Facies", "issn": "0172-9179", "doi": "10.1007/s10347-016-0468-6", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Agroforestry Systems", "issn": "0167-4366", "doi": "10.1007/s10457-016-9912-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Polar Biology", "issn": "0722-4060", "doi": "10.1007/s00300-016-1914-1", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Small-scale Forestry", "issn": "1873-7617", "doi": "10.1007/s11842-016-9331-4", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Environmental Management", "issn": "0364-152X", "doi": "10.1007/s00267-016-0696-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Estuaries and Coasts", "issn": "1559-2723", "doi": "10.1007/s12237-016-0103-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Regional Environmental Change", "issn": "1436-3798", "doi": "10.1007/s10113-016-0978-3", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Biodiversity and Conservation", "issn": "0960-3115", "doi": "10.1007/s10531-016-1131-9", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bangor University", "institution": "Bangor University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Organisms Diversity & Evolution", "issn": "1439-6092", "doi": "10.1007/s13127-016-0289-z", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "Psychonomic Bulletin & Review", "issn": "1069-9384", "doi": "10.3758/s13423-015-0995-0", "is_hybrid": "TRUE", "country": "GBR", "agreement": "Springer Compact"} +{"__fact_key__": "Bournemouth University", "institution": "Bournemouth University", "period": "2016", "publisher": "Springer Nature", "journal_full_title": "European Journal of Nutrition", "issn": "1436-6207", "doi": "10.1007/s00394-015-1130-8", 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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 09/34] 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 10/34] [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)))) From 3f07390a58475db233add51dbe55313941a181f2 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 28 Feb 2024 10:10:10 +0100 Subject: [PATCH 11/34] WIP --- .../dhp/oa/provision/model/TupleWrapper.java | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java new file mode 100644 index 000000000..c23a7f550 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java @@ -0,0 +1,40 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.oa.provision.model; + +import java.io.Serializable; + +public class TupleWrapper implements Serializable { + + private String xml; + + private String json; + + public TupleWrapper() { + } + + public TupleWrapper(String xml, String json) { + this.xml = xml; + this.json = json; + } + + public String getXml() { + return xml; + } + + public void setXml(String xml) { + this.xml = xml; + } + + public String getJson() { + return json; + } + + public void setJson(String json) { + this.json = json; + } +} From fd34372c4077e1e93b00b1965c044d5000a91e69 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 6 Mar 2024 13:42:00 +0100 Subject: [PATCH 12/34] [OCNEW] first implementation --- .../CreateActionSetSparkJob.java | 68 +++++----- .../opencitations/GetOpenCitationsRefs.java | 64 +++++---- .../opencitations/MapOCIdsInPids.java | 123 ++++++++++++++++++ .../actionmanager/opencitations/ReadCOCI.java | 53 ++++---- .../opencitations/model/COCI.java | 17 +++ .../opencitations/input_parameters.json | 14 +- .../input_readcoci_parameters.json | 16 +-- .../opencitations/oozie_app/workflow.xml | 84 ++++++++++-- .../opencitations/remap_parameters.json | 20 +++ 9 files changed, 329 insertions(+), 130 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java index b707fdcd3..47949a4bb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java @@ -28,6 +28,7 @@ import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; 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.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.*; import eu.dnetlib.dhp.utils.DHPUtils; @@ -37,12 +38,6 @@ public class CreateActionSetSparkJob implements Serializable { public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations"; public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations"; - // DOI-to-DOI citations - public static final String COCI = "COCI"; - - // PMID-to-PMID citations - public static final String POCI = "POCI"; - private static final String DOI_PREFIX = "50|doi_________::"; private static final String PMID_PREFIX = "50|pmid________::"; @@ -95,22 +90,21 @@ public class CreateActionSetSparkJob implements Serializable { private static void extractContent(SparkSession spark, String inputPath, String outputPath, boolean shouldDuplicateRels) { - getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI) - .union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI)) + getTextTextJavaPairRDD(spark, inputPath) + // .union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI)) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); } - private static JavaPairRDD getTextTextJavaPairRDD(SparkSession spark, String inputPath, - boolean shouldDuplicateRels, String prefix) { + private static JavaPairRDD getTextTextJavaPairRDD(SparkSession spark, String inputPath) { return spark .read() - .textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*") + .textFile(inputPath) .map( (MapFunction) value -> OBJECT_MAPPER.readValue(value, COCI.class), Encoders.bean(COCI.class)) .flatMap( (FlatMapFunction) value -> createRelation( - value, shouldDuplicateRels, prefix) + value) .iterator(), Encoders.bean(Relation.class)) .filter((FilterFunction) Objects::nonNull) @@ -121,34 +115,41 @@ public class CreateActionSetSparkJob implements Serializable { new Text(OBJECT_MAPPER.writeValueAsString(aa)))); } - private static List createRelation(COCI value, boolean duplicate, String p) { + private static List createRelation(COCI value) { List relationList = new ArrayList<>(); - String prefix; + String citing; String cited; - switch (p) { - case COCI: - prefix = DOI_PREFIX; - citing = prefix + switch (value.getCiting_pid()) { + case "doi": + citing = DOI_PREFIX + IdentifierFactory .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); - cited = prefix - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited())); break; - case POCI: - prefix = PMID_PREFIX; - citing = prefix + case "pmid": + citing = PMID_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting())); - cited = prefix - + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited())); + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); break; default: - throw new IllegalStateException("Invalid prefix: " + p); + throw new IllegalStateException("Invalid prefix: " + value.getCiting_pid()); + } + + switch (value.getCited_pid()) { + case "doi": + cited = DOI_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); + break; + case "pmid": + cited = PMID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); + break; + default: + throw new IllegalStateException("Invalid prefix: " + value.getCited_pid()); } if (!citing.equals(cited)) { @@ -157,15 +158,6 @@ public class CreateActionSetSparkJob implements Serializable { getRelation( citing, cited, ModelConstants.CITES)); - - if (duplicate && value.getCiting().endsWith(".refs")) { - citing = prefix + IdentifierFactory - .md5( - CleaningFunctions - .normalizePidValue( - "doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs")))); - relationList.add(getRelation(citing, cited, ModelConstants.CITES)); - } } return relationList; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java index 600cf7df1..be653aed2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java @@ -12,10 +12,7 @@ import java.util.zip.ZipInputStream; import org.apache.commons.cli.ParseException; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataInputStream; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -37,17 +34,17 @@ public class GetOpenCitationsRefs implements Serializable { parser.parseArgument(args); - final String[] inputFile = parser.get("inputFile").split(";"); - log.info("inputFile {}", Arrays.asList(inputFile)); +// final String[] inputFile = parser.get("inputFile").split(";"); +// log.info("inputFile {}", Arrays.asList(inputFile)); - final String workingPath = parser.get("workingPath"); - log.info("workingPath {}", workingPath); + final String inputPath = parser.get("inputPath"); + log.info("inputPath {}", inputPath); final String hdfsNameNode = parser.get("hdfsNameNode"); log.info("hdfsNameNode {}", hdfsNameNode); - final String prefix = parser.get("prefix"); - log.info("prefix {}", prefix); + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); @@ -56,41 +53,42 @@ public class GetOpenCitationsRefs implements Serializable { GetOpenCitationsRefs ocr = new GetOpenCitationsRefs(); - for (String file : inputFile) { - ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix); - } + ocr.doExtract(inputPath, outputPath, fileSystem); } - private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix) + private void doExtract(String inputPath, String outputPath, FileSystem fileSystem) throws IOException { - final Path path = new Path(inputFile); + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(inputPath), true); + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + // do stuff with the file like ... + FSDataInputStream oc_zip = fileSystem.open(fileStatus.getPath()); + try (ZipInputStream zis = new ZipInputStream(oc_zip)) { + ZipEntry entry = null; + while ((entry = zis.getNextEntry()) != null) { - FSDataInputStream oc_zip = fileSystem.open(path); + if (!entry.isDirectory()) { + String fileName = entry.getName(); + // fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count; + fileName = fileName.substring(0, fileName.lastIndexOf(".")); + // count++; + try ( + FSDataOutputStream out = fileSystem + .create(new Path(outputPath + "/" + fileName + ".gz")); + GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { - // int count = 1; - try (ZipInputStream zis = new ZipInputStream(oc_zip)) { - ZipEntry entry = null; - while ((entry = zis.getNextEntry()) != null) { - - if (!entry.isDirectory()) { - String fileName = entry.getName(); - // fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count; - fileName = fileName.substring(0, fileName.lastIndexOf(".")); - // count++; - try ( - FSDataOutputStream out = fileSystem - .create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz")); - GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { - - IOUtils.copy(zis, gzipOs); + IOUtils.copy(zis, gzipOs); + } } + } } - } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java new file mode 100644 index 000000000..c6c5bc0ba --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java @@ -0,0 +1,123 @@ + +package eu.dnetlib.dhp.actionmanager.opencitations; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.io.Serializable; +import java.util.Arrays; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +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.application.ArgumentApplicationParser; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 29/02/24 + */ +public class MapOCIdsInPids implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); + private static final String DELIMITER = ","; + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws IOException, ParseException { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + MapOCIdsInPids.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/opencitations/remap_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 -> mapIdentifiers(spark, inputPath, outputPath)); + + } + + private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) { + Dataset coci = spark + .read() + .textFile(inputPath + "/JSON") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, COCI.class), + Encoders.bean(COCI.class)); + + Dataset> correspondenceData = spark + .read() + .format("csv") + .option("sep", DELIMITER) + .option("inferSchema", "true") + .option("header", "true") + .option("quotes", "\"") + .load(inputPath + "/correspondence/omid.zip") + .repartition(5000) + .flatMap((FlatMapFunction>) r -> { + String ocIdentifier = r.getAs("omid"); + String[] correspondentIdentifiers = ((String) r.getAs("id")).split(" "); + return Arrays + .stream(correspondentIdentifiers) + .map(ci -> new Tuple2(ocIdentifier, ci)) + .collect(Collectors.toList()) + .iterator(); + }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); + + Dataset mappedCitingDataset = coci + .joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left") + .map((MapFunction>, COCI>) t2 -> { + String correspondent = t2._2()._2(); + t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":"))); + t2._1().setCiting(correspondent.substring(correspondent.indexOf(":") + 1)); + return t2._1(); + }, Encoders.bean(COCI.class)); + + mappedCitingDataset + .joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1"))) + .map((MapFunction>, COCI>) t2 -> { + String correspondent = t2._2()._2(); + t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":"))); + t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1)); + return t2._1(); + }, Encoders.bean(COCI.class)) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .json(outputPath); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java index b9c24df3b..afbd43176 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java @@ -12,10 +12,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; +import org.apache.hadoop.fs.*; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; @@ -42,19 +39,21 @@ public class ReadCOCI implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String[] inputFile = parser.get("inputFile").split(";"); - log.info("inputFile {}", Arrays.asList(inputFile)); + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode {}", hdfsNameNode); + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); + final String workingPath = parser.get("inputPath"); log.info("workingPath {}", workingPath); - final String format = parser.get("format"); - log.info("format {}", format); - SparkConf sconf = new SparkConf(); + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); final String delimiter = Optional .ofNullable(parser.get("delimiter")) .orElse(DEFAULT_DELIMITER); @@ -66,19 +65,20 @@ public class ReadCOCI implements Serializable { doRead( spark, workingPath, - inputFile, + fileSystem, outputPath, - delimiter, - format); + delimiter); }); } - private static void doRead(SparkSession spark, String workingPath, String[] inputFiles, + private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem, String outputPath, - String delimiter, String format) { - - for (String inputFile : inputFiles) { - String pString = workingPath + "/" + inputFile + ".gz"; + String delimiter) throws IOException { + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(workingPath), true); + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); Dataset cociData = spark .read() @@ -87,26 +87,23 @@ public class ReadCOCI implements Serializable { .option("inferSchema", "true") .option("header", "true") .option("quotes", "\"") - .load(pString) + .load(fileStatus.getPath().toString()) .repartition(100); cociData.map((MapFunction) row -> { COCI coci = new COCI(); - if (format.equals("COCI")) { - coci.setCiting(row.getString(1)); - coci.setCited(row.getString(2)); - } else { - coci.setCiting(String.valueOf(row.getInt(1))); - coci.setCited(String.valueOf(row.getInt(2))); - } + + coci.setCiting(row.getString(1)); + coci.setCited(row.getString(2)); + coci.setOci(row.getString(0)); return coci; }, Encoders.bean(COCI.class)) .write() - .mode(SaveMode.Overwrite) + .mode(SaveMode.Append) .option("compression", "gzip") - .json(outputPath + inputFile); + .json(outputPath); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java index c1ef1abad..42fca5dd3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java @@ -9,8 +9,10 @@ public class COCI implements Serializable { private String oci; private String citing; + private String citing_pid; private String cited; + private String cited_pid; public String getOci() { return oci; @@ -36,4 +38,19 @@ public class COCI implements Serializable { this.cited = cited; } + public String getCiting_pid() { + return citing_pid; + } + + public void setCiting_pid(String citing_pid) { + this.citing_pid = citing_pid; + } + + public String getCited_pid() { + return cited_pid; + } + + public void setCited_pid(String cited_pid) { + this.cited_pid = cited_pid; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json index 96db7eeb7..f4b6e2d68 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json @@ -1,13 +1,13 @@ [ { - "paramName": "if", - "paramLongName": "inputFile", + "paramName": "ip", + "paramLongName": "inputPath", "paramDescription": "the zipped opencitations file", "paramRequired": true }, { - "paramName": "wp", - "paramLongName": "workingPath", + "paramName": "op", + "paramLongName": "outputPath", "paramDescription": "the working path", "paramRequired": true }, @@ -16,11 +16,5 @@ "paramLongName": "hdfsNameNode", "paramDescription": "the hdfs name node", "paramRequired": true - }, - { - "paramName": "p", - "paramLongName": "prefix", - "paramDescription": "COCI or POCI", - "paramRequired": true } ] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json index fa840089d..a74ceb983 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json @@ -1,7 +1,7 @@ [ { - "paramName": "wp", - "paramLongName": "workingPath", + "paramName": "ip", + "paramLongName": "inputPath", "paramDescription": "the zipped opencitations file", "paramRequired": true }, @@ -24,15 +24,9 @@ "paramLongName": "outputPath", "paramDescription": "the hdfs name node", "paramRequired": true - }, - { - "paramName": "if", - "paramLongName": "inputFile", - "paramDescription": "the hdfs name node", - "paramRequired": true - }, { - "paramName": "f", - "paramLongName": "format", + }, { + "paramName": "nn", + "paramLongName": "hdfsNameNode", "paramDescription": "the hdfs name node", "paramRequired": true } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml index deb32459b..e28b021bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml @@ -27,7 +27,8 @@ ${wf:conf('resumeFrom') eq 'DownloadDump'} ${wf:conf('resumeFrom') eq 'ExtractContent'} ${wf:conf('resumeFrom') eq 'ReadContent'} - + ${wf:conf('resumeFrom') eq 'CreateAS'} + @@ -35,6 +36,15 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + ${jobTracker} @@ -47,7 +57,28 @@ download.sh ${filelist} - ${workingPath}/${prefix}/Original + ${inputPath}/Original + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download_corr.sh + ${filecorrespondence} + ${inputPath}/correspondence HADOOP_USER_NAME=${wf:user()} download.sh @@ -60,9 +91,19 @@ eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs --hdfsNameNode${nameNode} - --inputFile${inputFile} - --workingPath${workingPath}/${prefix} - --prefix${prefix} + --inputPath${inputPath}/Original + --outputPath${inputPath}/Extracted + + + + + + + + eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs + --hdfsNameNode${nameNode} + --inputPath${inputPath}/correspondence + --outputPath${inputPath}/correspondence_extracted @@ -85,11 +126,34 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --workingPath${workingPath}/${prefix}/${prefix} - --outputPath${workingPath}/${prefix}/${prefix}_JSON/ + --inputPath${inputPath}/Extracted + --outputPath${inputPath}/JSON --delimiter${delimiter} - --inputFile${inputFileCoci} - --format${prefix} + --hdfsNameNode${nameNode} + + + + + + + + yarn + cluster + Produces the AS for OC + eu.dnetlib.dhp.actionmanager.opencitations.MapOCIdsInPids + dhp-aggregation-${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=${sparkSqlWarehouseDir} + + --inputPath${inputPath} + --outputPath${outputPathExtraction} @@ -112,7 +176,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --inputPath${workingPath} + --inputPath${outputPathExtraction} --outputPath${outputPath} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json new file mode 100644 index 000000000..95ab5f6d9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManged", + "paramDescription": "the hdfs name node", + "paramRequired": false + } +] From 7827a2d66b30577e75b509c706289275db5e0126 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 7 Mar 2024 10:36:30 +0100 Subject: [PATCH 13/34] [OCNEW] added creation of the actionset for the results classified with FoS based ont he OpenAIRE identifier --- .../GetFOSSparkJob.java | 1 + .../PrepareFOSSparkJob.java | 114 +++++++----- .../fosnodoi/CreateActionSetSparkJob.java | 92 +++++++++ .../prepare_parameters.json | 7 +- .../actionmanager/fosnodoi/as_parameters.json | 20 ++ .../fosnodoi/oozie_app/config-default.xml | 30 +++ .../fosnodoi/oozie_app/workflow.xml | 153 +++++++++++++++ .../fosnodoi/CreateActionSetSparkJobTest.java | 176 ++++++++++++++++++ .../actionmanager/fosnodoi/GetFosTest.java | 104 +++++++++++ .../actionmanager/fosnodoi/PrepareTest.java | 99 ++++++++++ .../dhp/actionmanager/fosnodoi/fosnodoi.csv | 19 ++ .../dhp/actionmanager/fosnodoi/fosnodoi.json | 18 ++ .../dhp/actionmanager/fosnodoi/results.json | 9 + 13 files changed, 799 insertions(+), 43 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/GetFosTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/PrepareTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/results.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java index abea6acd7..c98f4cffc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java @@ -75,6 +75,7 @@ public class GetFOSSparkJob implements Serializable { fosData.map((MapFunction) r -> { FOSDataModel fosDataModel = new FOSDataModel(); fosDataModel.setDoi(r.getString(0).toLowerCase()); + fosDataModel.setOaid(r.getString(1).toLowerCase()); fosDataModel.setLevel1(r.getString(2)); fosDataModel.setLevel2(r.getString(3)); fosDataModel.setLevel3(r.getString(4)); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java index b1ffe7f37..ffcaedda7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java @@ -16,12 +16,14 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.Subject; @@ -52,62 +54,90 @@ public class PrepareFOSSparkJob implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); + final Boolean distributeDOI = Optional + .ofNullable(parser.get("distributeDoi")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { - distributeFOSdois( - spark, - sourcePath, + if (distributeDOI) + distributeFOSdois( + spark, + sourcePath, - outputPath); + outputPath); + else + distributeFOSoaid(spark, sourcePath, outputPath); }); } + private static void distributeFOSoaid(SparkSession spark, String sourcePath, String outputPath) { + Dataset fosDataset = readPath(spark, sourcePath, FOSDataModel.class); + + fosDataset + .groupByKey((MapFunction) v -> v.getOaid().toLowerCase(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it); + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/fos"); + } + + @NotNull + private static Result getResult(String k, Iterator it) { + Result r = new Result(); + FOSDataModel first = it.next(); + r.setId(k); + + HashSet level1 = new HashSet<>(); + HashSet level2 = new HashSet<>(); + HashSet level3 = new HashSet<>(); + HashSet level4 = new HashSet<>(); + addLevels(level1, level2, level3, level4, first); + it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v)); + List sbjs = new ArrayList<>(); + level1 + .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); + level2 + .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); + level3 + .forEach( + l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); + level4 + .forEach( + l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); + r.setSubject(sbjs); + r + .setDataInfo( + OafMapperUtils + .dataInfo( + false, null, true, + false, + OafMapperUtils + .qualifier( + ModelConstants.PROVENANCE_ENRICH, + null, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + null)); + return r; + } + private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) { Dataset fosDataset = readPath(spark, sourcePath, FOSDataModel.class); fosDataset .groupByKey((MapFunction) v -> v.getDoi().toLowerCase(), Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> { - Result r = new Result(); - FOSDataModel first = it.next(); - r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI)); - - HashSet level1 = new HashSet<>(); - HashSet level2 = new HashSet<>(); - HashSet level3 = new HashSet<>(); - HashSet level4 = new HashSet<>(); - addLevels(level1, level2, level3, level4, first); - it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v)); - List sbjs = new ArrayList<>(); - level1 - .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); - level2 - .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); - level3 - .forEach( - l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); - level4 - .forEach( - l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); - r.setSubject(sbjs); - r - .setDataInfo( - OafMapperUtils - .dataInfo( - false, null, true, - false, - OafMapperUtils - .qualifier( - ModelConstants.PROVENANCE_ENRICH, - null, - ModelConstants.DNET_PROVENANCE_ACTIONS, - ModelConstants.DNET_PROVENANCE_ACTIONS), - null)); - return r; - }, Encoders.bean(Result.class)) + .mapGroups( + (MapGroupsFunction) (k, + it) -> getResult(DHPUtils.generateUnresolvedIdentifier(k, DOI), it), + Encoders.bean(Result.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java new file mode 100644 index 000000000..e86fccb84 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java @@ -0,0 +1,92 @@ + +package eu.dnetlib.dhp.actionmanager.fosnodoi; + +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.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.Result; +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(); + + 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/fosnodoi/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("sourcePath"); + log.info("inputPath {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> createActionSet(spark, inputPath, outputPath)); + + } + + private static void createActionSet(SparkSession spark, String inputPath, String outputPath) { + spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Result.class), + Encoders.bean(Result.class)) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile( + outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json index b7bad73e6..b7f0f2aa3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json @@ -16,5 +16,10 @@ "paramLongName": "outputPath", "paramDescription": "the path of the new ActionSet", "paramRequired": true - } + }, { + "paramName": "fd", + "paramLongName": "distributeDoi", + "paramDescription": "the path of the new ActionSet", + "paramRequired": false +} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json new file mode 100644 index 000000000..3f056edf7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "sp", + "paramLongName": "sourcePath", + "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 + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/workflow.xml new file mode 100644 index 000000000..ec3e25ac0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/workflow.xml @@ -0,0 +1,153 @@ + + + + + fosPath + the input path of the resources to be extended + + + outputPath + the path where to store the actionset + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + yarn + cluster + Gets Data from FOS csv file + eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob + 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} + + --sourcePath${fosPath} + --outputPath${workingDir}/input/fos + --delimiter${delimiter} + + + + + + + + + yarn + cluster + Produces the results from FOS + eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob + dhp-aggregation-${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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/input/fos + --outputPath${workingDir}/prepared + --distributeDoifalse + + + + + + + + + + yarn + cluster + Save the action set grouping results with the same id + eu.dnetlib.dhp.actionmanager.fosnodoi.CreateActionSetSparkJob + dhp-aggregation-${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=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/prepared/fos + --outputPath${outputPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java new file mode 100644 index 000000000..fa98e96d2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java @@ -0,0 +1,176 @@ + +package eu.dnetlib.dhp.actionmanager.fosnodoi; + +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.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.OafEntity; + +public class CreateActionSetSparkJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateActionSetSparkJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateActionSetSparkJobTest.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(CreateActionSetSparkJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + private void runJob(String resultsInputPath, String outputPath) throws Exception { + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", resultsInputPath, + + "-outputPath", outputPath, + }); + } + + @Test + void testScores() throws Exception { + + String resultsInputPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/results.json") + .getPath(); + + String outputPath = workingDir.toString() + "/actionSet"; + + // execute the job to generate the action sets for result scores + runJob(resultsInputPath, outputPath); + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + sc + .sequenceFile(outputPath, Text.class, Text.class) + .foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t))); + + } + + void assertResultImpactScores(Dataset testDataset) { + Assertions + .assertEquals( + "6.63451994567e-09", testDataset + .filter( + "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + + "and id = 'influence'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "0.348694533145", testDataset + .filter( + "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + + "and id = 'popularity_alt'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "2.16094680115e-09", testDataset + .filter( + "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + + "and id = 'popularity'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + } + + void assertProjectImpactScores(Dataset testDataset) throws Exception { + + Assertions + .assertEquals( + "0", testDataset + .filter( + "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + + "and id = 'numOfInfluentialResults'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "1", testDataset + .filter( + "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + + "and id = 'numOfPopularResults'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "25", testDataset + .filter( + "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + + "and id = 'totalImpulse'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + Assertions + .assertEquals( + "43", testDataset + .filter( + "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + + "and id = 'totalCitationCount'") + .select("value") + .collectAsList() + .get(0) + .getString(0)); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/GetFosTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/GetFosTest.java new file mode 100644 index 000000000..4e558dbd4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/GetFosTest.java @@ -0,0 +1,104 @@ + +package eu.dnetlib.dhp.actionmanager.fosnodoi; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +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.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareTest; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel; + +/** + * @author miriam.baglioni + * @Date 13/02/23 + */ +public class GetFosTest { + + private static final Logger log = LoggerFactory.getLogger(ProduceTest.class); + + private static Path workingDir; + private static SparkSession spark; + private static LocalFileSystem fs; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName()); + + fs = FileSystem.getLocal(new Configuration()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + @Disabled + void test3() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv") + .getPath(); + + final String outputPath = workingDir.toString() + "/fos.json"; + GetFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + + "-outputPath", outputPath, + "-delimiter", "," + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(outputPath) + .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class)); + + tmp.foreach(t -> Assertions.assertTrue(t.getOaid() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null)); + + tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t))); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/PrepareTest.java new file mode 100644 index 000000000..f0cc471d8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/PrepareTest.java @@ -0,0 +1,99 @@ + +package eu.dnetlib.dhp.actionmanager.fosnodoi; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class PrepareTest { + + private static final Logger log = LoggerFactory.getLogger(ProduceTest.class); + + private static Path workingDir; + private static SparkSession spark; + private static LocalFileSystem fs; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName()); + + fs = FileSystem.getLocal(new Configuration()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void fosPrepareTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json") + .getPath(); + + PrepareFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + + "-outputPath", workingDir.toString() + "/work", + "-distributeDoi", Boolean.FALSE.toString() + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/work/fos") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t))); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv new file mode 100644 index 000000000..00c97cff0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv @@ -0,0 +1,19 @@ +DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4 +N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0 +N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0 +N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050109 social psychology,05010904 Group processes/Collective identity,0.5589094161987305,0.5166763067245483 +N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050105 experimental psychology,05010501 Emotion/Affective science,0.44109055399894714,0.4833236634731293 +N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050203 business & management,05020302 Supply chain management/Business terms,0.5459638833999634,0.5460261106491089 +N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050211 marketing,05021102 Services marketing/Retailing,0.4540362060070038,0.4539738595485687 +N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010504 meteorology & atmospheric sciences,01050407 Geomagnetism/Ionosphere,0.5131047964096069,0.4990350902080536 +N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010502 geochemistry & geophysics,01050203 Seismology/Seismology measurement,0.4868951737880707,0.500964879989624 +N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022002 Medical imaging/Medical physics,0.5068133473396301,0.10231181626910052 +N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,N/A,0.49318668246269226,0.0 +N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5 +N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5 +N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021702 Aging-associated diseases/Cognitive disorders,0.5134317874908447,0.09614889098529535 +N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.48656824231147766,0.0 +N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation,02090105 Control theory/Advanced driver assistance systems,0.5178514122962952,0.5198937654495239 +N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020201 artificial intelligence & image processing,02020108 Fuzzy logic/Artificial neural networks/Computational neuroscience,0.48214852809906006,0.4801062345504761 +N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021708 Neurotrauma/Stroke,0.5014800429344177,0.5109656453132629 +N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,02 engineering and technology,0206 medical engineering,020601 biomedical engineering,02060102 Medical terminology/Patient,0.4985199570655823,0.4890343248844147 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json new file mode 100644 index 000000000..782954d49 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json @@ -0,0 +1,18 @@ +{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"} +{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0303 health sciences","level3":"030304 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"} +{"doi":"n/a","oaid":"od______3978::6704dcced0fe3dd6fbf985dc2507f61c","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030217 neurology & neurosurgery","level4":"03021702 Aging-associated diseases/Cognitive disorders","scoreL3":"0.5134317874908447","scoreL4":"0.09614889098529535"} +{"doi":"n/a","oaid":"od______2806::a1da9d2678b12969a9ab5f50b5e71d0a","level1":"05 social sciences","level2":"0501 psychology and cognitive sciences","level3":"050109 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psychology","qualifier":{"classid":"FOS","classname":"Fields of Science and Technology classification","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.44109055399894714","inferenceprovenance":"update","provenanceaction":{"classid":"subject:fos","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"050109 social psychology","qualifier":{"classid":"FOS","classname":"Fields of Science and Technology classification","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.5589094161987305","inferenceprovenance":"update","provenanceaction":{"classid":"subject:fos","classname":"Inferred by 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classification","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.4833236634731293","inferenceprovenance":"update","provenanceaction":{"classid":"subject:fos","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"context":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"isGreen":null,"isInDiamondJournal":null} \ No newline at end of file From 5180b6ec8a764ac52a92dbcf10cc20742f3d8fd1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 7 Mar 2024 10:47:13 +0100 Subject: [PATCH 14/34] [FOSNEW] removed test class --- .../fosnodoi/CreateActionSetSparkJobTest.java | 176 ------------------ 1 file changed, 176 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java deleted file mode 100644 index fa98e96d2..000000000 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJobTest.java +++ /dev/null @@ -1,176 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.fosnodoi; - -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.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - -public class CreateActionSetSparkJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(CreateActionSetSparkJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(CreateActionSetSparkJobTest.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(CreateActionSetSparkJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - private void runJob(String resultsInputPath, String outputPath) throws Exception { - CreateActionSetSparkJob - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", resultsInputPath, - - "-outputPath", outputPath, - }); - } - - @Test - void testScores() throws Exception { - - String resultsInputPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/results.json") - .getPath(); - - String outputPath = workingDir.toString() + "/actionSet"; - - // execute the job to generate the action sets for result scores - runJob(resultsInputPath, outputPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - sc - .sequenceFile(outputPath, Text.class, Text.class) - .foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t))); - - } - - void assertResultImpactScores(Dataset testDataset) { - Assertions - .assertEquals( - "6.63451994567e-09", testDataset - .filter( - "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + - "and id = 'influence'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - Assertions - .assertEquals( - "0.348694533145", testDataset - .filter( - "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + - "and id = 'popularity_alt'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - Assertions - .assertEquals( - "2.16094680115e-09", testDataset - .filter( - "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " + - "and id = 'popularity'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - } - - void assertProjectImpactScores(Dataset testDataset) throws Exception { - - Assertions - .assertEquals( - "0", testDataset - .filter( - "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + - "and id = 'numOfInfluentialResults'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - Assertions - .assertEquals( - "1", testDataset - .filter( - "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + - "and id = 'numOfPopularResults'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - Assertions - .assertEquals( - "25", testDataset - .filter( - "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + - "and id = 'totalImpulse'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - Assertions - .assertEquals( - "43", testDataset - .filter( - "oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " + - "and id = 'totalCitationCount'") - .select("value") - .collectAsList() - .get(0) - .getString(0)); - } -} From d4871b31e87f5dfc9227a177ccc2780e8f803421 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 8 Mar 2024 11:43:20 +0100 Subject: [PATCH 15/34] WIP: extended provision workflow to create the JSON based payload --- .../oa/provision/SolrAdminApplication.java | 12 +- .../dhp/oa/provision/XmlConverterJob.java | 49 +- .../dhp/oa/provision/XmlIndexingJob.java | 71 +- .../dhp/oa/provision/model/JoinedEntity.java | 16 +- .../model/ProvisionModelSupport.java | 662 +++++++++++++++++- .../dhp/oa/provision/model/RelatedEntity.java | 2 + .../provision/model/RelatedEntityWrapper.java | 2 + .../utils/StreamingInputDocumentFactory.java | 19 +- .../provision/input_params_update_index.json | 6 + .../provision/input_params_xml_converter.json | 6 + .../provision/input_solradmin_parameters.json | 6 + .../dhp/oa/provision/oozie_app/workflow.xml | 29 +- .../dhp/oa/provision/EOSCFuture_Test.java | 2 +- .../provision/IndexRecordTransformerTest.java | 6 +- .../dhp/oa/provision/JoinedEntityTest.java | 51 ++ .../oa/provision/SolrConfigExploreTest.java | 2 +- .../dhp/oa/provision/SolrConfigTest.java | 2 +- .../dhp/oa/provision/XmlIndexingJobTest.java | 101 ++- .../oa/provision/XmlRecordFactoryTest.java | 14 +- .../solr/conf/testConfig/managed-schema | 319 ++++----- .../dnetlib/dhp/oa/provision/xml/part-00000 | Bin 293298 -> 0 bytes .../dhp/oa/provision/xml/part-00000.json.gz | Bin 0 -> 66906 bytes pom.xml | 2 +- 23 files changed, 1097 insertions(+), 282 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/JoinedEntityTest.java delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000.json.gz diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java index 0033978bf..d4d414fed 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java @@ -62,8 +62,16 @@ public class SolrAdminApplication implements Closeable { final String collection = ProvisionConstants.getCollectionName(format); log.info("collection: {}", collection); - try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) { - app.execute(action, collection, query, commit); + final boolean shouldIndex = Optional + .ofNullable(parser.get("shouldIndex")) + .map(Boolean::valueOf) + .orElse(false); + log.info("shouldIndex: {}", shouldIndex); + + if (shouldIndex) { + try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) { + app.execute(action, collection, query, commit); + } } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java index 6f43ca3f7..4353e863f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.provision; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.utils.DHPUtils.toSeq; +import static org.apache.spark.sql.functions.*; import java.util.List; import java.util.Map; @@ -14,22 +15,31 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.SparkContext; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.*; +import org.apache.spark.sql.expressions.UserDefinedFunction; +import org.apache.spark.sql.types.DataTypes; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport; +import eu.dnetlib.dhp.oa.provision.model.TupleWrapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.solr.SolrRecord; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; /** @@ -65,13 +75,20 @@ public class XmlConverterJob { final String contextApiBaseUrl = parser.get("contextApiBaseUrl"); log.info("contextApiBaseUrl: {}", contextApiBaseUrl); + String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + final SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ProvisionModelSupport.getModelClasses()); runWithSparkSession(conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - convertToXml(spark, inputPath, outputPath, ContextMapper.fromAPI(contextApiBaseUrl)); + convertToXml( + spark, inputPath, outputPath, ContextMapper.fromAPI(contextApiBaseUrl), + VocabularyGroup.loadVocsFromIS(isLookup)); }); } @@ -79,7 +96,8 @@ public class XmlConverterJob { final SparkSession spark, final String inputPath, final String outputPath, - final ContextMapper contextMapper) { + final ContextMapper contextMapper, + final VocabularyGroup vocabularies) { final XmlRecordFactory recordFactory = new XmlRecordFactory( prepareAccumulators(spark.sparkContext()), @@ -92,20 +110,25 @@ public class XmlConverterJob { log.info("Found paths: {}", String.join(",", paths)); + final ObjectMapper mapper = new ObjectMapper(); + mapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY); spark .read() .load(toSeq(paths)) .as(Encoders.kryo(JoinedEntity.class)) .map( - (MapFunction>) je -> new Tuple2<>( - je.getEntity().getId(), - recordFactory.build(je)), - Encoders.tuple(Encoders.STRING(), Encoders.STRING())) - .javaRDD() - .mapToPair( - (PairFunction, Text, Text>) t -> new Tuple2<>(new Text(t._1()), - new Text(t._2()))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + (MapFunction>) je -> new Tuple2<>( + recordFactory.build(je), + ProvisionModelSupport.transform(je, contextMapper, vocabularies)), + Encoders.tuple(Encoders.STRING(), Encoders.bean(SolrRecord.class))) + .map( + (MapFunction, TupleWrapper>) t -> new TupleWrapper( + t._1(), mapper.writeValueAsString(t._2())), + Encoders.bean(TupleWrapper.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } private static void removeOutputDir(final SparkSession spark, final String path) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index cd401c6cb..3c107a985 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -21,9 +21,8 @@ import org.apache.solr.common.SolrInputDocument; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -31,11 +30,13 @@ import com.lucidworks.spark.util.SolrSupport; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.model.TupleWrapper; import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import scala.Tuple2; public class XmlIndexingJob { @@ -59,6 +60,8 @@ public class XmlIndexingJob { private final String outputPath; + private boolean shouldIndex; + private final SparkSession spark; public static void main(String[] args) throws Exception { @@ -101,7 +104,14 @@ public class XmlIndexingJob { .orElse(OutputFormat.SOLR); log.info("outputFormat: {}", outputFormat); + final boolean shouldIndex = Optional + .ofNullable(parser.get("shouldIndex")) + .map(Boolean::valueOf) + .orElse(false); + log.info("shouldIndex: {}", shouldIndex); + final SparkConf conf = new SparkConf(); + conf.registerKryoClasses(new Class[] { SerializableSolrInputDocument.class }); @@ -113,18 +123,19 @@ public class XmlIndexingJob { final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl)); - new XmlIndexingJob(spark, inputPath, format, batchSize, outputFormat, outputPath).run(isLookup); + new XmlIndexingJob(spark, inputPath, format, batchSize, outputFormat, shouldIndex, outputPath) + .run(isLookup); }); } public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize, - OutputFormat outputFormat, - String outputPath) { + OutputFormat outputFormat, boolean shouldIndex, String outputPath) { this.spark = spark; this.inputPath = inputPath; this.format = format; this.batchSize = batchSize; this.outputFormat = outputFormat; + this.shouldIndex = shouldIndex; this.outputPath = outputPath; } @@ -140,33 +151,45 @@ public class XmlIndexingJob { final String zkHost = isLookup.getZkHost(); log.info("zkHost: {}", zkHost); - final String version = getRecordDatestamp(); - final String indexRecordXslt = getLayoutTransformer(format, fields, xslt); log.info("indexRecordTransformer {}", indexRecordXslt); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD docs = sc - .sequenceFile(inputPath, Text.class, Text.class) - .map(t -> t._2().toString()) - .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s)) - .map(s -> new StreamingInputDocumentFactory().parseDocument(s)); + final Encoder encoder = Encoders.bean(TupleWrapper.class); + final Dataset records = spark + .read() + .schema(encoder.schema()) + .json(inputPath) + .as(encoder) + .map( + (MapFunction) t -> new TupleWrapper( + toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()), + t.getJson()), + Encoders.bean(TupleWrapper.class)); switch (outputFormat) { case SOLR: - final String collection = ProvisionConstants.getCollectionName(format); + if (shouldIndex) { + final String collection = ProvisionConstants.getCollectionName(format); - // SparkSolr >= 4 - // com.lucidworks.spark.BatchSizeType bt = com.lucidworks.spark.BatchSizeType.NUM_DOCS; - // SolrSupport.indexDocs(zkHost, collection, batchSize, bt, docs.rdd()); - // SparkSolr < 4 - SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd()); + // SparkSolr >= 4 + // com.lucidworks.spark.BatchSizeType bt = com.lucidworks.spark.BatchSizeType.NUM_DOCS; + // SolrSupport.indexDocs(zkHost, collection, batchSize, bt, docs.rdd()); + // SparkSolr < 4 + JavaRDD docs = records + .javaRDD() + .map( + t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson())); + SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd()); + } break; case HDFS: - spark - .createDataset( - docs.map(SerializableSolrInputDocument::new).rdd(), + records + .map( + (MapFunction) t -> { + SolrInputDocument s = new StreamingInputDocumentFactory() + .parseDocument(t.getXml(), t.getJson()); + return new SerializableSolrInputDocument(s); + }, Encoders.kryo(SerializableSolrInputDocument.class)) .write() .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java index 0fb109fbb..da3915aee 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java @@ -5,11 +5,15 @@ import java.io.Serializable; import java.util.LinkedList; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.OafEntity; +import com.fasterxml.jackson.annotation.JsonSubTypes; +import com.fasterxml.jackson.annotation.JsonTypeInfo; -public class JoinedEntity implements Serializable { +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.oaf.*; - private E entity; +public class JoinedEntity implements Serializable { + + private OafEntity entity; private List links; @@ -17,16 +21,16 @@ public class JoinedEntity implements Serializable { links = new LinkedList<>(); } - public JoinedEntity(E entity) { + public JoinedEntity(OafEntity entity) { this(); this.entity = entity; } - public E getEntity() { + public OafEntity getEntity() { return entity; } - public void setEntity(E entity) { + public void setEntity(OafEntity entity) { this.entity = entity; } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java index d4ee24c14..6af692ed9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java @@ -1,13 +1,46 @@ package eu.dnetlib.dhp.oa.provision.model; -import java.util.List; +import static org.apache.commons.lang3.StringUtils.substringBefore; +import java.io.StringReader; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.io.SAXReader; +import org.jetbrains.annotations.Nullable; + +import com.google.common.base.Splitter; import com.google.common.collect.Lists; +import com.google.common.collect.Maps; +import com.google.common.collect.Sets; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm; import eu.dnetlib.dhp.oa.provision.RelationList; import eu.dnetlib.dhp.oa.provision.SortableRelation; +import eu.dnetlib.dhp.oa.provision.utils.ContextDef; +import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.solr.*; +import eu.dnetlib.dhp.schema.solr.AccessRight; +import eu.dnetlib.dhp.schema.solr.Author; +import eu.dnetlib.dhp.schema.solr.Context; +import eu.dnetlib.dhp.schema.solr.Country; +import eu.dnetlib.dhp.schema.solr.Datasource; +import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines; +import eu.dnetlib.dhp.schema.solr.Instance; +import eu.dnetlib.dhp.schema.solr.Journal; +import eu.dnetlib.dhp.schema.solr.OpenAccessColor; +import eu.dnetlib.dhp.schema.solr.OpenAccessRoute; +import eu.dnetlib.dhp.schema.solr.Organization; +import eu.dnetlib.dhp.schema.solr.Project; +import eu.dnetlib.dhp.schema.solr.Result; +import eu.dnetlib.dhp.schema.solr.Subject; public class ProvisionModelSupport { @@ -28,4 +61,631 @@ public class ProvisionModelSupport { RelationList.class)); return modelClasses.toArray(new Class[] {}); } + + public static SolrRecord transform(JoinedEntity je, ContextMapper contextMapper, VocabularyGroup vocs) { + SolrRecord s = new SolrRecord(); + final OafEntity e = je.getEntity(); + s + .setHeader( + SolrRecordHeader + .newInstance( + e.getId(), e.getOriginalId(), RecordType.valueOf(e.getClass().getSimpleName().toLowerCase()))); + s.setCollectedfrom(asProvenance(e.getCollectedfrom())); + s.setContext(asContext(e.getContext(), contextMapper)); + s.setPid(asPid(e.getPid())); + + if (e instanceof eu.dnetlib.dhp.schema.oaf.Result) { + s.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e)); + } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Datasource) { + s.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e)); + } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Organization) { + s.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e)); + } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Project) { + s.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs)); + } + s + .setLinks( + Optional + .ofNullable(je.getLinks()) + .map( + links -> links + .stream() + .map(rew -> mapRelatedRecord(rew, vocs)) + .collect(Collectors.toList())) + .orElse(null)); + + return s; + } + + private static RelatedRecord mapRelatedRecord(RelatedEntityWrapper rew, VocabularyGroup vocs) { + RelatedRecord rr = new RelatedRecord(); + + final RelatedEntity re = rew.getTarget(); + final RecordType relatedRecordType = RecordType.valueOf(re.getType()); + final Relation relation = rew.getRelation(); + rr + .setHeader( + RelatedRecordHeader + .newInstance( + relation.getRelType(), + relation.getRelClass(), + relation.getTarget(), relatedRecordType)); + + rr.setAcronym(re.getAcronym()); + rr.setCode(re.getCode()); + rr.setContracttype(mapCodeLabel(re.getContracttype())); + rr.setCollectedfrom(asProvenance(re.getCollectedfrom())); + rr.setCodeRepositoryUrl(re.getCodeRepositoryUrl()); + rr.setCountry(asCountry(re.getCountry())); + rr.setDatasourcetype(mapCodeLabel(re.getDatasourcetype())); + rr.setDatasourcetypeui(mapCodeLabel(re.getDatasourcetypeui())); + rr.setDateofacceptance(re.getDateofacceptance()); + rr.setFunding(mapFunding(re.getFundingtree(), vocs)); + rr.setInstances(mapInstances(re.getInstances())); + rr.setLegalname(re.getLegalname()); + rr.setLegalshortname(re.getLegalshortname()); + rr.setOfficialname(re.getOfficialname()); + rr.setOpenairecompatibility(mapCodeLabel(re.getOpenairecompatibility())); + rr.setPid(asPid(re.getPid())); + rr.setProjectTitle(rr.getProjectTitle()); + rr.setPublisher(re.getPublisher()); + rr.setResulttype(mapQualifier(re.getResulttype())); + rr.setTitle(Optional.ofNullable(re.getTitle()).map(StructuredProperty::getValue).orElse(null)); + + return rr; + } + + private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p, VocabularyGroup vocs) { + Project ps = new Project(); + ps.setAcronym(mapField(p.getAcronym())); + ps.setCode(mapField(p.getCode())); + ps.setContracttype(mapCodeLabel(p.getContracttype())); + ps.setCurrency(mapField(p.getCurrency())); + ps.setDuration(mapField(p.getDuration())); + ps.setCallidentifier(mapField(p.getCallidentifier())); + ps.setEcarticle29_3(mapField(p.getEcarticle29_3())); + ps.setEnddate(mapField(p.getEnddate())); + ps.setFundedamount(p.getFundedamount()); + ps.setKeywords(mapField(p.getKeywords())); + ps.setStartdate(mapField(p.getStartdate())); + ps.setSubjects(asSubjectSP(p.getSubjects())); + ps.setSummary(mapField(p.getSummary())); + ps.setTitle(mapField(p.getTitle())); + ps.setTotalcost(p.getTotalcost()); + ps.setWebsiteurl(mapField(p.getWebsiteurl())); + ps.setFunding(mapFundingField(p.getFundingtree(), vocs)); + return ps; + } + + private static Funding mapFunding(List fundingtree, VocabularyGroup vocs) { + SAXReader reader = new SAXReader(); + return Optional + .ofNullable(fundingtree) + .flatMap( + ftree -> ftree + .stream() + .map(ft -> { + try { + Document doc = reader.read(new StringReader(ft)); + String countryCode = doc.valueOf("/fundingtree/funder/jurisdiction/text()"); + Country country = vocs + .find("dnet:countries") + .map(voc -> voc.getTerm(countryCode)) + .map(VocabularyTerm::getName) + .map(label -> Country.newInstance(countryCode, label)) + .orElse(null); + + String level0_id = doc.valueOf("//funding_level_0/id/text()"); + String level1_id = doc.valueOf("//funding_level_1/id/text()"); + String level2_id = doc.valueOf("//funding_level_2/id/text()"); + + return Funding + .newInstance( + Funder + .newInstance( + doc.valueOf("/fundingtree/funder/id/text()"), + doc.valueOf("/fundingtree/funder/shortname/text()"), + doc.valueOf("/fundingtree/funder/name/text()"), + country, new ArrayList<>()), + Optional + .ofNullable(level0_id) + .map( + id -> FundingLevel + .newInstance( + id, + doc.valueOf("//funding_level_0/description/text()"), + doc.valueOf("//funding_level_0/name/text()"))) + .orElse(null), + Optional + .ofNullable(level1_id) + .map( + id -> FundingLevel + .newInstance( + id, + doc.valueOf("//funding_level_1/description/text()"), + doc.valueOf("//funding_level_1/name/text()"))) + .orElse(null), + Optional + .ofNullable(level2_id) + .map( + id -> FundingLevel + .newInstance( + id, + doc.valueOf("//funding_level_2/description/text()"), + doc.valueOf("//funding_level_2/name/text()"))) + .orElse(null)); + + } catch (DocumentException e) { + throw new IllegalArgumentException(e); + } + }) + .findFirst()) + .orElse(null); + } + + private static Funding mapFundingField(List> fundingtree, VocabularyGroup vocs) { + return mapFunding( + Optional + .ofNullable(fundingtree) + .map(fts -> fts.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null), + vocs); + } + + private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization o) { + Organization org = new Organization(); + org.setCountry(mapCodeLabel(o.getCountry())); + org.setLegalname(mapField(o.getLegalname())); + org.setLegalshortname(mapField(o.getLegalshortname())); + org.setAlternativeNames(mapFieldList(o.getAlternativeNames())); + org.setWebsiteurl(mapField(o.getWebsiteurl())); + org.setLogourl(mapField(o.getLogourl())); + + org.setEcenterprise(mapField(o.getEcenterprise())); + org.setEchighereducation(mapField(o.getEchighereducation())); + org.setEclegalbody(mapField(o.getEclegalbody())); + org.setEcinternationalorganization(mapField(o.getEcinternationalorganization())); + org.setEcinternationalorganizationeurinterests(mapField(o.getEcinternationalorganizationeurinterests())); + org.setEclegalperson(mapField(o.getEclegalperson())); + org.setEcnonprofit(mapField(o.getEcnonprofit())); + org.setEcnutscode(mapField(o.getEcnutscode())); + org.setEcresearchorganization(mapField(o.getEcresearchorganization())); + org.setEcsmevalidated(mapField(o.getEcsmevalidated())); + + return org; + } + + private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) { + Datasource ds = new Datasource(); + ds.setEnglishname(mapField(d.getEnglishname())); + ds.setOfficialname(mapField(d.getOfficialname())); + ds.setDescription(mapField(d.getDescription())); + ds.setJournal(mapJournal(d.getJournal())); + ds.setLogourl(mapField(d.getLogourl())); + ds.setAccessinfopackage(mapFieldList(d.getAccessinfopackage())); + ds.setCertificates(mapField(d.getCertificates())); + ds.setCitationguidelineurl(mapField(d.getCitationguidelineurl())); + ds.setConsenttermsofuse(d.getConsenttermsofuse()); + ds.setConsenttermsofusedate(d.getConsenttermsofusedate()); + ds.setContactemail(mapField(d.getContactemail())); + ds.setContentpolicies(mapCodeLabel(d.getContentpolicies())); + ds.setDatabaseaccessrestriction(mapField(d.getDatabaseaccessrestriction())); + ds.setDatabaseaccesstype(mapField(d.getDatabaseaccesstype())); + ds.setDataprovider(mapField(d.getDataprovider())); + ds.setDatasourcetype(mapCodeLabel(d.getDatasourcetype())); + ds.setDatasourcetypeui(mapCodeLabel(d.getDatasourcetypeui())); + ds.setDatauploadrestriction(mapField(d.getDatauploadrestriction())); + ds.setDatauploadtype(mapField(d.getDatauploadtype())); + ds.setDateofvalidation(mapField(d.getDateofvalidation())); + ds.setEoscdatasourcetype(mapCodeLabel(d.getEoscdatasourcetype())); + ds.setEosctype(mapCodeLabel(d.getEosctype())); + ds.setFulltextdownload(d.getFulltextdownload()); + ds.setJurisdiction(mapCodeLabel(d.getJurisdiction())); + ds.setLanguages(d.getLanguages()); + ds.setLatitude(mapField(d.getLatitude())); + ds.setLongitude(mapField(d.getLongitude())); + ds.setLastconsenttermsofusedate(d.getLastconsenttermsofusedate()); + ds.setMissionstatementurl(mapField(d.getMissionstatementurl())); + ds.setNamespaceprefix(mapField(d.getNamespaceprefix())); + ds.setOdcontenttypes(mapFieldList(d.getOdcontenttypes())); + ds.setOdlanguages(mapFieldList(d.getOdlanguages())); + ds.setOdnumberofitems(mapField(d.getOdnumberofitems())); + ds.setOdnumberofitemsdate(mapField(d.getOdnumberofitemsdate())); + ds.setOdpolicies(mapField(d.getOdpolicies())); + ds.setOpenairecompatibility(mapCodeLabel(d.getOpenairecompatibility())); + ds.setPidsystems(mapField(d.getPidsystems())); + ds.setPolicies(mapCodeLabelKV(d.getPolicies())); + ds.setPreservationpolicyurl(d.getPreservationpolicyurl()); + ds.setProvidedproducttypes(ds.getProvidedproducttypes()); + ds.setReleaseenddate(mapField(d.getReleasestartdate())); + ds.setReleasestartdate(mapField(d.getReleasestartdate())); + ds.setResearchentitytypes(ds.getResearchentitytypes()); + ds.setResearchproductaccesspolicies(d.getResearchproductaccesspolicies()); + ds.setResearchproductmetadataaccesspolicies(d.getResearchproductmetadataaccesspolicies()); + ds.setServiceprovider(mapField(d.getServiceprovider())); + ds.setSubjects(asSubjectSP(d.getSubjects())); + ds.setSubmissionpolicyurl(d.getSubmissionpolicyurl()); + ds.setThematic(d.getThematic()); + ds.setVersioncontrol(d.getVersioncontrol()); + ds.setVersioning(mapField(d.getVersioning())); + + return ds; + } + + private static Result mapResult(eu.dnetlib.dhp.schema.oaf.Result r) { + Result rs = new Result(); + + rs.setResulttype(mapQualifier(r.getResulttype())); + rs.setAuthor(asAuthor(r.getAuthor())); + rs.setMaintitle(getMaintitle(r.getTitle())); + rs.setOtherTitles(getOtherTitles(r.getTitle())); + rs.setDescription(mapFieldList(r.getDescription())); + rs.setSubject(asSubject(r.getSubject())); + rs.setPublicationdate(mapField(r.getDateofacceptance())); + rs.setPublisher(mapField(r.getPublisher())); + rs.setEmbargoenddate(mapField(r.getEmbargoenddate())); + rs.setSource(mapFieldList(r.getSource())); + rs.setFormat(mapFieldList(r.getFormat())); + rs.setContributor(mapFieldList(r.getContributor())); + rs.setCoverage(mapFieldList(r.getCoverage())); + rs + .setBestaccessright( + BestAccessRight + .newInstance(r.getBestaccessright().getClassid(), r.getBestaccessright().getClassname())); + rs.setFulltext(mapFieldList(r.getFulltext())); + rs.setCountry(asCountry(r.getCountry())); + rs.setEoscifguidelines(asEOSCIF(r.getEoscifguidelines())); + + rs.setGreen(r.getIsGreen()); + rs + .setOpenAccessColor( + Optional + .ofNullable(r.getOpenAccessColor()) + .map(color -> OpenAccessColor.valueOf(color.toString())) + .orElse(null)); + rs.setInDiamondJournal(r.getIsInDiamondJournal()); + rs.setPubliclyFunded(r.getPubliclyFunded()); + rs.setTransformativeAgreement(r.getTransformativeAgreement()); + + rs.setInstance(mapInstances(r.getInstance())); + + if (r instanceof Publication) { + Publication pub = (Publication) r; + rs.setJournal(mapJournal(pub.getJournal())); + } else if (r instanceof Dataset) { + Dataset d = (Dataset) r; + rs.setSize(mapField(d.getSize())); + rs.setVersion(mapField(d.getVersion())); + } else if (r instanceof Software) { + Software sw = (Software) r; + rs.setCodeRepositoryUrl(mapField(sw.getCodeRepositoryUrl())); + rs.setProgrammingLanguage(mapQualifier(sw.getProgrammingLanguage())); + rs.setDocumentationUrl(mapFieldList(sw.getDocumentationUrl())); + } else if (r instanceof OtherResearchProduct) { + OtherResearchProduct orp = (OtherResearchProduct) r; + rs.setContactperson(mapFieldList(orp.getContactperson())); + rs.setContactgroup(mapFieldList(orp.getContactgroup())); + rs.setTool(mapFieldList(orp.getTool())); + } + return rs; + } + + @Nullable + private static List getOtherTitles(List titleList) { + return Optional + .ofNullable(titleList) + .map( + titles -> titles + .stream() + .filter( + t -> !"main title" + .equals( + Optional + .ofNullable(t.getQualifier()) + .map(Qualifier::getClassid) + .orElse(null))) + .map(StructuredProperty::getValue) + .collect(Collectors.toList())) + .orElse(null); + } + + private static String getMaintitle(List titleList) { + return Optional + .ofNullable(titleList) + .flatMap( + titles -> titles + .stream() + .filter( + t -> "main title" + .equals( + Optional + .ofNullable(t.getQualifier()) + .map(Qualifier::getClassid) + .orElse(null))) + .map(StructuredProperty::getValue) + .findFirst()) + .orElse(null); + } + + private static List mapInstances(List instanceList) { + return Optional + .ofNullable(instanceList) + .map( + instances -> instances + .stream() + .map(instance -> { + Instance i = new Instance(); + i.setCollectedfrom(asProvenance(instance.getCollectedfrom())); + i.setHostedby(asProvenance(instance.getHostedby())); + i.setFulltext(i.getFulltext()); + i.setPid(asPid(instance.getPid())); + i.setAlternateIdentifier(asPid(instance.getAlternateIdentifier())); + i.setAccessright(mapAccessRight(instance.getAccessright())); + i.setInstancetype(mapQualifier(instance.getInstancetype())); + i.setLicense(mapField(instance.getLicense())); + i.setUrl(instance.getUrl()); + i.setRefereed(mapQualifier(instance.getRefereed())); + i.setDateofacceptance(mapField(instance.getDateofacceptance())); + i.setDistributionlocation(instance.getDistributionlocation()); + i.setProcessingcharges(getProcessingcharges(instance)); + return i; + }) + .collect(Collectors.toList())) + .orElse(null); + } + + private static APC getProcessingcharges(eu.dnetlib.dhp.schema.oaf.Instance instance) { + return Optional + .of( + APC + .newInstance( + mapField(instance.getProcessingchargecurrency()), + mapField(instance.getProcessingchargeamount()))) + .filter(apc -> Objects.nonNull(apc.getAmount()) && Objects.nonNull(apc.getCurrency())) + .orElse(null); + } + + private static AccessRight mapAccessRight(eu.dnetlib.dhp.schema.oaf.AccessRight accessright) { + return AccessRight + .newInstance( + mapQualifier(accessright), + Optional + .ofNullable(accessright.getOpenAccessRoute()) + .map(route -> OpenAccessRoute.valueOf(route.toString())) + .orElse(null)); + } + + private static T mapField(eu.dnetlib.dhp.schema.oaf.Field f) { + return Optional.ofNullable(f).map(Field::getValue).orElse(null); + } + + private static List mapFieldList(List> fl) { + return Optional + .ofNullable(fl) + .map(v -> v.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null); + } + + private static String mapQualifier(eu.dnetlib.dhp.schema.oaf.Qualifier q) { + return Optional.ofNullable(q).map(Qualifier::getClassid).orElse(null); + } + + private static Journal mapJournal(eu.dnetlib.dhp.schema.oaf.Journal joaf) { + return Optional + .ofNullable(joaf) + .map(jo -> { + Journal j = new Journal(); + j.setConferencedate(jo.getConferencedate()); + j.setConferenceplace(jo.getConferenceplace()); + j.setEdition(jo.getEdition()); + j.setSp(jo.getSp()); + j.setEp(jo.getEp()); + j.setVol(jo.getVol()); + j.setIss(jo.getEdition()); + j.setName(jo.getName()); + j.setIssnPrinted(jo.getIssnPrinted()); + j.setIssnOnline(jo.getIssnOnline()); + j.setIssnLinking(jo.getIssnLinking()); + return j; + }) + .orElse(null); + } + + private static List asProvenance(List keyValueList) { + return Optional + .ofNullable(keyValueList) + .map( + kvs -> kvs + .stream() + .map(ProvisionModelSupport::asProvenance) + .collect(Collectors.toList())) + .orElse(null); + } + + private static Provenance asProvenance(KeyValue keyValue) { + return Optional.ofNullable(keyValue).map(cf -> Provenance.newInstance(cf.getKey(), cf.getValue())).orElse(null); + } + + private static List asContext(List ctxList, + ContextMapper contextMapper) { + + final Set contexts = Optional + .ofNullable(ctxList) + .map( + ctx -> ctx + .stream() + .map(eu.dnetlib.dhp.schema.oaf.Context::getId) + .collect(Collectors.toCollection(HashSet::new))) + .orElse(new HashSet<>()); + + /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */ + if (contexts.contains("dh-ch::subcommunity::2")) { + contexts.add("clarin"); + } + + return Optional + .ofNullable(contexts) + .map( + ctx -> ctx + .stream() + .map(contextPath -> { + Context context = new Context(); + String id = ""; + Map categoryMap = Maps.newHashMap(); + for (final String token : Splitter.on("::").split(contextPath)) { + id += token; + + final ContextDef def = contextMapper.get(id); + + if (def == null) { + continue; + } + if (def.getName().equals("context")) { + context.setId(def.getId()); + context.setLabel(def.getLabel()); + context.setType(def.getType()); + } + if (def.getName().equals("category")) { + Category category = Category.newInstance(def.getId(), def.getLabel()); + if (Objects.isNull(context.getCategory())) { + context.setCategory(Lists.newArrayList()); + } + context.getCategory().add(category); + categoryMap.put(def.getId(), category); + } + if (def.getName().equals("concept")) { + String parentId = StringUtils.substringBeforeLast(def.getId(), "::"); + if (categoryMap.containsKey(parentId)) { + categoryMap + .get(parentId) + .getConcept() + .add(Concept.newInstance(def.getId(), def.getLabel())); + } + } + id += "::"; + } + return context; + }) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List asPid(List pidList) { + return Optional + .ofNullable(pidList) + .map( + pids -> pids + .stream() + .map(p -> Pid.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List asAuthor(List authorList) { + return Optional + .ofNullable(authorList) + .map( + authors -> authors + .stream() + .map( + a -> Author + .newInstance(a.getFullname(), a.getName(), a.getSurname(), a.getRank(), asPid(a.getPid()))) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List asSubject(List subjectList) { + return Optional + .ofNullable(subjectList) + .map( + subjects -> subjects + .stream() + .filter(s -> Objects.nonNull(s.getQualifier())) + .filter(s -> Objects.nonNull(s.getQualifier().getClassid())) + .map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassid())) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List asSubjectSP(List subjectList) { + return Optional + .ofNullable(subjectList) + .map( + subjects -> subjects + .stream() + .filter(s -> Objects.nonNull(s.getQualifier())) + .filter(s -> Objects.nonNull(s.getQualifier().getClassid())) + .map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassid())) + .collect(Collectors.toList())) + .orElse(null); + } + + private static Country asCountry(eu.dnetlib.dhp.schema.oaf.Qualifier country) { + return Optional + .ofNullable(country) + .filter(c -> Objects.nonNull(c.getClassid()) && Objects.nonNull(c.getClassname())) + .map(c -> Country.newInstance(c.getClassid(), c.getClassname())) + .orElse(null); + } + + private static List asCountry(List countryList) { + return Optional + .ofNullable(countryList) + .map( + countries -> countries + .stream() + .map(c -> Country.newInstance(c.getClassid(), c.getClassname())) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List asEOSCIF(List eoscIfGuidelines) { + return Optional + .ofNullable(eoscIfGuidelines) + .map( + eoscif -> eoscif + .stream() + .map( + e -> EoscIfGuidelines + .newInstance(e.getCode(), e.getLabel(), e.getUrl(), e.getSemanticRelation())) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List mapCodeLabelKV(List kvList) { + return Optional + .ofNullable(kvList) + .map( + kvs -> kvs + .stream() + .map(ProvisionModelSupport::mapCodeLabel) + .collect(Collectors.toList())) + .orElse(null); + } + + private static List mapCodeLabel(List qualifiers) { + return Optional + .ofNullable(qualifiers) + .map( + list -> list + .stream() + .map(ProvisionModelSupport::mapCodeLabel) + .collect(Collectors.toList())) + .orElse(null); + } + + private static CodeLabel mapCodeLabel(Qualifier qualifier) { + return Optional + .ofNullable(qualifier) + .map(q -> CodeLabel.newInstance(q.getClassid(), q.getClassname())) + .orElse(null); + } + + private static CodeLabel mapCodeLabel(KeyValue kv) { + return Optional + .ofNullable(kv) + .map(q -> CodeLabel.newInstance(kv.getKey(), kv.getValue())) + .orElse(null); + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java index 5c78d1826..f13c6c90e 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java @@ -13,6 +13,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class RelatedEntity implements Serializable { + private static final long serialVersionUID = -4982643490443810597L; + private String id; private String type; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntityWrapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntityWrapper.java index 4a4a4a5be..4939ec8e9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntityWrapper.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntityWrapper.java @@ -9,6 +9,8 @@ import eu.dnetlib.dhp.schema.oaf.Relation; public class RelatedEntityWrapper implements Serializable { + private static final long serialVersionUID = -2624854064081757234L; + private Relation relation; private RelatedEntity target; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java index b42f9ee83..51f65c7ac 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.oa.provision.utils; +import java.io.Serializable; import java.io.StringReader; import java.io.StringWriter; import java.util.HashMap; @@ -32,7 +33,7 @@ import com.google.common.collect.Lists; * * @author claudio */ -public class StreamingInputDocumentFactory { +public class StreamingInputDocumentFactory implements Serializable { private static final String INDEX_FIELD_PREFIX = "__"; @@ -40,6 +41,8 @@ public class StreamingInputDocumentFactory { private static final String INDEX_RESULT = INDEX_FIELD_PREFIX + RESULT; + private static final String INDEX_JSON_RESULT = INDEX_FIELD_PREFIX + "json"; + private static final String INDEX_RECORD_ID = INDEX_FIELD_PREFIX + "indexrecordidentifier"; private static final String DEFAULTDNETRESULT = "dnetResult"; @@ -71,13 +74,17 @@ public class StreamingInputDocumentFactory { this.resultName = resultName; } - public SolrInputDocument parseDocument(final String inputDocument) { + public SolrInputDocument parseDocument(final String xml) { + return parseDocument(xml, ""); + } + + public SolrInputDocument parseDocument(final String xml, final String json) { final StringWriter results = new StringWriter(); final List nsList = Lists.newLinkedList(); try { - XMLEventReader parser = inputFactory.get().createXMLEventReader(new StringReader(inputDocument)); + XMLEventReader parser = inputFactory.get().createXMLEventReader(new StringReader(xml)); final SolrInputDocument indexDocument = new SolrInputDocument(new HashMap<>()); @@ -95,13 +102,13 @@ public class StreamingInputDocumentFactory { } else if (TARGETFIELDS.equals(localName)) { parseTargetFields(indexDocument, parser); } else if (resultName.equals(localName)) { - copyResult(indexDocument, results, parser, nsList, resultName); + copyResult(indexDocument, json, results, parser, nsList, resultName); } } } if (!indexDocument.containsKey(INDEX_RECORD_ID)) { - throw new IllegalStateException("cannot extract record ID from: " + inputDocument); + throw new IllegalStateException("cannot extract record ID from: " + xml); } return indexDocument; @@ -171,6 +178,7 @@ public class StreamingInputDocumentFactory { */ protected void copyResult( final SolrInputDocument indexDocument, + final String json, final StringWriter results, final XMLEventReader parser, final List nsList, @@ -205,6 +213,7 @@ public class StreamingInputDocumentFactory { } writer.close(); indexDocument.addField(INDEX_RESULT, results.toString()); + indexDocument.addField(INDEX_JSON_RESULT, json); } finally { outputFactory.remove(); eventFactory.remove(); diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json index 46286e06a..2960e5aaa 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json @@ -29,6 +29,12 @@ "paramDescription": "decides the job output format, SOLR | HDFS", "paramRequired": false }, + { + "paramName": "si", + "paramLongName": "shouldIndex", + "paramDescription": "should the action actually index the records?", + "paramRequired": true + }, { "paramName": "op", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json index 653a69ed1..4509eb9de 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json @@ -16,5 +16,11 @@ "paramLongName": "contextApiBaseUrl", "paramDescription": "URL of the context API", "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the context ISLookup Service", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json index 23eca2f7b..53805d3c1 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "commit", "paramDescription": "should the action be followed by a commit?", "paramRequired": false + }, + { + "paramName": "i", + "paramLongName": "shouldIndex", + "paramDescription": "should the action actually index the records?", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 9eab960f0..8908c5c83 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -591,22 +591,18 @@ --conf spark.sql.shuffle.partitions=3840 --conf spark.network.timeout=${sparkNetworkTimeout} - --inputPath${workingDir}/join_entities - --outputPath${workingDir}/xml + + --inputPath/user/claudio.atzori/data/provision/join_entities + + + --outputPath/user/claudio.atzori/data/provision/xml_json_test --contextApiBaseUrl${contextApiBaseUrl} + --isLookupUrl${isLookupUrl} - + - - - ${wf:conf('shouldIndex') eq 'true'} - ${wf:conf('shouldIndex') eq 'false'} - - - - @@ -621,6 +617,7 @@ --actionDELETE_BY_QUERY --query${solrDeletionQuery} --committrue + --shouldIndex${shouldIndex} @@ -646,12 +643,17 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - --inputPath${workingDir}/xml + + --inputPath/user/claudio.atzori/data/provision/xml_json_test --isLookupUrl${isLookupUrl} --format${format} --batchSize${batchSize} --outputFormat${outputFormat} - --outputPath${workingDir}/solr_documents + + + --outputPath/user/claudio.atzori/data/provision/solr_documents + + --shouldIndex${shouldIndex} @@ -669,6 +671,7 @@ --isLookupUrl${isLookupUrl} --format${format} --actionCOMMIT + --shouldIndex${shouldIndex} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java index 8800abf95..1a982ca39 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java @@ -57,7 +57,7 @@ public class EOSCFuture_Test { IOUtils.toString(getClass().getResourceAsStream("eosc-future/photic-zone.json")), OtherResearchProduct.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + final String xml = xmlRecordFactory.build(new JoinedEntity(p)); assertNotNull(xml); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index e72883055..8d5aa3f3a 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -63,7 +63,7 @@ public class IndexRecordTransformerTest { final Project pj = load("project.json", Project.class); final Relation rel = load("relToValidatedProject.json", Relation.class); - final JoinedEntity je = new JoinedEntity<>(p); + final JoinedEntity je = new JoinedEntity(p); je .setLinks( Lists @@ -86,7 +86,7 @@ public class IndexRecordTransformerTest { final Publication p = load("publication.json", Publication.class); - final JoinedEntity je = new JoinedEntity<>(p); + final JoinedEntity je = new JoinedEntity(p); final String record = xmlRecordFactory.build(je); assertNotNull(record); SolrInputDocument solrDoc = testRecordTransformation(record); @@ -102,7 +102,7 @@ public class IndexRecordTransformerTest { final Publication p = load("riunet.json", Publication.class); - final JoinedEntity je = new JoinedEntity<>(p); + final JoinedEntity je = new JoinedEntity(p); final String record = xmlRecordFactory.build(je); assertNotNull(record); testRecordTransformation(record); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/JoinedEntityTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/JoinedEntityTest.java new file mode 100644 index 000000000..d836eddd8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/JoinedEntityTest.java @@ -0,0 +1,51 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; + +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Publication; + +class JoinedEntityTest { + + private static final Logger log = LoggerFactory.getLogger(JoinedEntityTest.class); + + @Test + void test_serialisation() throws IOException { + + Publication p = new Publication(); + p.setId("p1"); + Journal j = new Journal(); + j.setIss("1234-5678"); + p.setJournal(j); + + Organization o = new Organization(); + o.setId("o1"); + Field lName = new Field<>(); + lName.setValue("CNR"); + o.setLegalname(lName); + + ObjectMapper mapper = new ObjectMapper(); + mapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY); + + final String json = mapper.writeValueAsString(new JoinedEntity(p)); + log.info(json); + + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java index 3beca7e7e..c749781ec 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java @@ -86,7 +86,7 @@ public class SolrConfigExploreTest extends SolrExploreTest { String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null) .run(isLookupClient); Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java index a9d885ecf..91dbf8978 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java @@ -95,7 +95,7 @@ public class SolrConfigTest extends SolrTest { String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, false, null) .run(isLookupClient); Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java index a3a140cf6..be481cc37 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java @@ -1,35 +1,35 @@ package eu.dnetlib.dhp.oa.provision; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; import java.io.StringReader; import java.net.URI; -import java.util.Map; +import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; import org.apache.solr.client.solrj.SolrQuery; import org.apache.solr.client.solrj.response.QueryResponse; import org.apache.solr.common.SolrInputField; import org.apache.solr.common.params.CommonParams; -import org.apache.solr.common.params.ModifiableSolrParams; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.dom4j.io.SAXReader; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.model.TupleWrapper; import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -70,6 +70,7 @@ public class XmlIndexingJobTest extends SolrTest { SparkConf conf = new SparkConf(); conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { SerializableSolrInputDocument.class }); @@ -97,12 +98,15 @@ public class XmlIndexingJobTest extends SolrTest { String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - long nRecord = JavaSparkContext - .fromSparkContext(spark.sparkContext()) - .sequenceFile(inputPath, Text.class, Text.class) - .count(); + Dataset records = spark + .read() + .schema(Encoders.bean(TupleWrapper.class).schema()) + .json(inputPath) + .as(Encoders.bean(TupleWrapper.class)); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + long nRecord = records.count(); + + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null) .run(isLookupClient); assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); @@ -137,40 +141,93 @@ public class XmlIndexingJobTest extends SolrTest { assertEquals( 0, rsp.getResults().getNumFound(), "the number of indexed records having peerreviewed = true"); + + rsp = miniCluster + .getSolrClient() + .query( + new SolrQuery() + .add(CommonParams.Q, "objidentifier:\"iddesignpres::ae77e56e84ad058d9e7f19fa2f7325db\"") + .add(CommonParams.FL, "__json")); + assertEquals( + 1, rsp.getResults().getNumFound(), + "the number of indexed records having the given identifier"); + Optional json = rsp + .getResults() + .stream() + .map(d -> d.getFieldValues("__json")) + .flatMap(d -> d.stream()) + .findFirst(); + + assertTrue(json.isPresent()); + + log.info((String) json.get()); + } @Test void testXmlIndexingJob_saveOnHDFS() throws Exception { - final String ID_XPATH = "//header/*[local-name()='objIdentifier']"; + final String ID_XPATH = "//*[local-name()='header']/*[local-name()='objIdentifier']"; String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + // String inputPath = "/Users/claudio/workspace/data/index"; - final JavaPairRDD xmlRecords = JavaSparkContext - .fromSparkContext(spark.sparkContext()) - .sequenceFile(inputPath, Text.class, Text.class); - long nRecord = xmlRecords.count(); - long xmlIdUnique = xmlRecords - .map(t -> t._2().toString()) - .map(s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH)) + Dataset records = spark + .read() + .schema(Encoders.bean(TupleWrapper.class).schema()) + .json(inputPath) + .as(Encoders.bean(TupleWrapper.class)); + + records.printSchema(); + + long nRecord = records.count(); + log.info("found {} records", nRecord); + + final Dataset ids = records + .map((MapFunction) TupleWrapper::getXml, Encoders.STRING()) + .map( + (MapFunction) s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH), + Encoders.STRING()); + + log.info("found {} ids", ids.count()); + + long xmlIdUnique = ids .distinct() .count(); + + log.info("found {} unique ids", xmlIdUnique); + assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records"); final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString(); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.HDFS, outputPath) + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.HDFS, false, outputPath) .run(isLookupClient); final Dataset solrDocs = spark .read() .load(outputPath) .as(Encoders.kryo(SerializableSolrInputDocument.class)); + + solrDocs.foreach(doc -> { + assertNotNull(doc.get("__result")); + assertNotNull(doc.get("__json")); + }); + long docIdUnique = solrDocs.map((MapFunction) doc -> { final SolrInputField id = doc.getField("__indexrecordidentifier"); return id.getFirstValue().toString(); }, Encoders.STRING()) .distinct() .count(); - assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output records"); + assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output XML records"); + + long jsonUnique = solrDocs + .map( + (MapFunction) je -> (String) je.getField("__json").getValue(), + Encoders.STRING()) + .distinct() + .count(); + + assertEquals(jsonUnique, docIdUnique, "IDs should be unique among the output JSON records"); } 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 ba9572b17..f26c384d2 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 @@ -42,7 +42,7 @@ public class XmlRecordFactoryTest { final Publication p = OBJECT_MAPPER .readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + final String xml = xmlRecordFactory.build(new JoinedEntity(p)); assertNotNull(xml); @@ -117,7 +117,7 @@ public class XmlRecordFactoryTest { final List links = Lists.newArrayList(); final RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject); links.add(rew); - final JoinedEntity je = new JoinedEntity<>(p); + final JoinedEntity je = new JoinedEntity(p); je.setLinks(links); final String xml = xmlRecordFactory.build(je); @@ -148,7 +148,7 @@ public class XmlRecordFactoryTest { final List links = Lists.newArrayList(); final RelatedEntityWrapper rew = new RelatedEntityWrapper(rel, relatedProject); links.add(rew); - final JoinedEntity je = new JoinedEntity<>(p); + final JoinedEntity je = new JoinedEntity(p); je.setLinks(links); final String xml = xmlRecordFactory.build(je); @@ -171,7 +171,7 @@ public class XmlRecordFactoryTest { final Datasource d = OBJECT_MAPPER .readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(d)); + final String xml = xmlRecordFactory.build(new JoinedEntity(d)); assertNotNull(xml); @@ -210,7 +210,7 @@ public class XmlRecordFactoryTest { IOUtils.toString(getClass().getResourceAsStream("d4science-1-training.json")), OtherResearchProduct.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + final String xml = xmlRecordFactory.build(new JoinedEntity(p)); assertNotNull(xml); @@ -233,7 +233,7 @@ public class XmlRecordFactoryTest { IOUtils.toString(getClass().getResourceAsStream("d4science-2-dataset.json")), OtherResearchProduct.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + final String xml = xmlRecordFactory.build(new JoinedEntity(p)); assertNotNull(xml); @@ -256,7 +256,7 @@ public class XmlRecordFactoryTest { IOUtils.toString(getClass().getResourceAsStream("iris-odf-4.json")), Publication.class); - final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + final String xml = xmlRecordFactory.build(new JoinedEntity(p)); assertNotNull(xml); diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema index e191c6223..d9381b58e 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema @@ -195,186 +195,147 @@ - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + @@ -382,26 +343,20 @@ - - - - - - - - - + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000 b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000 deleted file mode 100644 index ff4095a11b566129a3de425341f042d29717a094..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 293298 zcmZ^JV{9)@&~9zpc6;ic^3=B7Uv1mAZQHhO+qP}p|NH4pZtk7zB%7Jp51Z`H&OY-f 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zCth8;F9_rcOiddpERIh;(q)(1I-cbDe1U6PW~FP<6oEaPfgndRI*x))g)EK3?o zl7v%^sRk(!6!&Q2Ndycqj{yY*pwE1Y&ZBxRUY!oHv FzW}!ckwpLi literal 0 HcmV?d00001 diff --git a/pom.xml b/pom.xml index 6ef320253..a95bf100d 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.2] + [6.0.0-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 9092075760fc6d1a4ba23637adc2071844f03d5c Mon Sep 17 00:00:00 2001 From: Giambattista Bloisi Date: Sun, 4 Feb 2024 10:07:15 +0100 Subject: [PATCH 16/34] Enrich authors with ORCID info using new matching algorithm --- .../eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 99 -------- .../dhp/enrich/orcid/oozie_app/workflow.xml | 14 +- .../dhp/enrich/orcid/AuthorEnricher.scala | 40 --- .../enrich/orcid/ORCIDAuthorEnricher.scala | 128 ++++++++++ .../enrich/orcid/ORCIDAuthorMatchers.scala | 65 +++++ .../SparkEnrichGraphWithOrcidAuthors.scala | 228 +++++++++++------- .../enrich/orcid/ORCIDAuthorEnricherTest.java | 38 +-- .../enrich/orcid}/authors_orcid_sample.json | 0 .../orcid}/authors_publication_sample.json | 0 .../orcid/ORCIDAuthorMatchersTest.scala | 35 +++ 10 files changed, 388 insertions(+), 259 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala rename dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java => dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java (71%) rename {dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge => dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid}/authors_orcid_sample.json (100%) rename {dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge => dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid}/authors_publication_sample.json (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 0461c9353..b413a0bb9 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -145,105 +145,6 @@ public class AuthorMerger { return null; } - /** - * This method tries to figure out when two author are the same in the contest - * of ORCID enrichment - * - * @param left Author in the OAF entity - * @param right Author ORCID - * @return based on a heuristic on the names of the authors if they are the same. - */ - public static boolean checkORCIDSimilarity(final Author left, final Author right) { - final Person pl = parse(left); - final Person pr = parse(right); - - // If one of them didn't have a surname we verify if they have the fullName not empty - // and verify if the normalized version is equal - if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && - pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) { - - if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null - && !pr.getFullname().isEmpty()) { - return pl - .getFullname() - .stream() - .anyMatch( - fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr)))); - } else { - return false; - } - } - // The Authors have one surname in common - if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { - - // If one of them has only a surname and is the same we can say that they are the same author - if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) || - (pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank))) - return true; - // The authors have the same initials of Name in common - if (pl - .getName() - .stream() - .anyMatch( - nl -> pr - .getName() - .stream() - .anyMatch(nr -> nr.equalsIgnoreCase(nl)))) - return true; - } - - // Sometimes we noticed that publication have author wrote in inverse order Surname, Name - // We verify if we have an exact match between name and surname - if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) && - pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl)))) - return true; - else - return false; - } - // - - /** - * Method to enrich ORCID information in one list of authors based on another list - * - * @param baseAuthor the Author List in the OAF Entity - * @param orcidAuthor The list of ORCID Author intersected - * @return The Author List of the OAF Entity enriched with the orcid Author - */ - public static List enrichOrcid(List baseAuthor, List orcidAuthor) { - - if (baseAuthor == null || baseAuthor.isEmpty()) - return orcidAuthor; - - if (orcidAuthor == null || orcidAuthor.isEmpty()) - return baseAuthor; - - if (baseAuthor.size() == 1 && orcidAuthor.size() > 10) - return baseAuthor; - - final List oAuthor = new ArrayList<>(); - oAuthor.addAll(orcidAuthor); - - baseAuthor.forEach(ba -> { - Optional aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst(); - if (aMatch.isPresent()) { - final Author sameAuthor = aMatch.get(); - addPid(ba, sameAuthor.getPid()); - oAuthor.remove(sameAuthor); - } - }); - return baseAuthor; - } - - private static void addPid(final Author a, final List pids) { - - if (a.getPid() == null) { - a.setPid(new ArrayList<>()); - } - - a.getPid().addAll(pids); - - } - public static String pidToComparableString(StructuredProperty pid) { final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml index 3493ecb2f..72fc9e338 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml @@ -12,6 +12,16 @@ targetPath the output path of the graph enriched + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + @@ -31,8 +41,8 @@ --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.executor.memoryOverhead=2g - --conf spark.sql.shuffle.partitions=3000 + --conf spark.executor.memoryOverhead=${sparkExecutorMemory} + --conf spark.sql.shuffle.partitions=5000 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala deleted file mode 100644 index 15513c8af..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala +++ /dev/null @@ -1,40 +0,0 @@ -package eu.dnetlib.dhp.enrich.orcid - -import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.{Author, Publication} -import eu.dnetlib.dhp.schema.sx.OafUtils -import org.apache.spark.sql.Row - -import scala.collection.JavaConverters._ - -object AuthorEnricher extends Serializable { - - def createAuthor(givenName: String, familyName: String, orcid: String): Author = { - val a = new Author - a.setName(givenName) - a.setSurname(familyName) - a.setFullname(s"$givenName $familyName") - val pid = OafUtils.createSP(orcid, ModelConstants.ORCID, ModelConstants.ORCID) - pid.setDataInfo(OafUtils.generateDataInfo()) - pid.getDataInfo.setProvenanceaction(OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT")) - a.setPid(List(pid).asJava) - a - } - - def toOAFAuthor(r: Row): java.util.List[Author] = { - r.getList[Row](1) - .asScala - .map(s => createAuthor(s.getAs[String]("givenName"), s.getAs[String]("familyName"), s.getAs[String]("orcid"))) - .toList - .asJava - } - -// def enrichAuthor(p:Publication,r:Row): Unit = { -// val k:Map[String, OAuthor] =r.getList[Row](1).asScala.map(s => (s.getAs[String]("orcid"), OAuthor(s.getAs[String]("givenName") ,s.getAs[String]("familyName") ))).groupBy(_._1).mapValues(_.map(_._2).head) -// println(k) -// -// -// -// } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala new file mode 100644 index 000000000..f7ea7e5a4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala @@ -0,0 +1,128 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Author, StructuredProperty} +import eu.dnetlib.dhp.schema.sx.OafUtils + +import java.util +import scala.beans.BeanProperty +import scala.collection.JavaConverters._ +import scala.util.control.Breaks.{break, breakable} + +case class ORCIDAuthorEnricherResult( + @BeanProperty var id: String, + @BeanProperty var enriched_author: java.util.List[Author], + @BeanProperty var author_matched: java.util.List[MatchedAuthors], + @BeanProperty var author_unmatched: java.util.List[Author], + @BeanProperty var orcid_unmatched: java.util.List[OrcidAutor] +) + +object ORCIDAuthorEnricher extends Serializable { + + def enrichOrcid( + id: String, + graph_authors: java.util.List[Author], + orcid_authors: java.util.List[OrcidAutor] + ): ORCIDAuthorEnricherResult = { + // Author enriching strategy: + // 1) create a copy of graph author list in unmatched_authors + // 2) find best match in unmatched_authors, remove it from unmatched_authors and enrich it so + // that the enrichment is reflected in graph_authors (they share author instances) + // 3) repeat (2) till the end of the list and then with different matching algorithms that have decreasing + // trust in their output + // At the end unmatched_authors will contain authors not matched with any of the matching algos + val unmatched_authors = new util.ArrayList[Author](graph_authors) + + val matches = { + // Look after exact fullname match, reconstruct ORCID fullname as givenName + familyName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.givenName + " " + orcid.familyName), + "fullName" + ) ++ + // Look after exact reversed fullname match, reconstruct ORCID fullname as familyName + givenName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.familyName + " " + orcid.givenName), + "reversedFullName" + ) ++ + // split author names in tokens, order the tokens, then check for matches of full tokens or abbreviations + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + ORCIDAuthorMatchers + .matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName), + "orderedTokens" + ) ++ + // look after exact matches of ORCID creditName + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.creditName), + "creditName" + ) ++ + // look after exact matches in ORCID otherNames + extractAndEnrichMatches( + unmatched_authors, + orcid_authors, + (author, orcid) => + orcid.otherNames != null && ORCIDAuthorMatchers.matchOtherNames(author.getFullname, orcid.otherNames.asScala), + "otherNames" + ) + } + + ORCIDAuthorEnricherResult(id, graph_authors, matches.asJava, unmatched_authors, orcid_authors) + } + + private def extractAndEnrichMatches( + graph_authors: java.util.List[Author], + orcid_authors: java.util.List[OrcidAutor], + matchingFunc: (Author, OrcidAutor) => Boolean, + matchName: String + ) = { + val matched = scala.collection.mutable.ArrayBuffer.empty[MatchedAuthors] + + if (graph_authors != null && graph_authors.isEmpty) { + val ait = graph_authors.iterator + + while (ait.hasNext) { + val author = ait.next() + val oit = orcid_authors.iterator + + breakable { + while (oit.hasNext) { + val orcid = oit.next() + + if (matchingFunc(author, orcid)) { + ait.remove() + oit.remove() + matched += MatchedAuthors(author, orcid, matchName) + + if (author.getPid == null) { + author.setPid(new util.ArrayList[StructuredProperty]()) + } + + val orcidPID = OafUtils.createSP(orcid.orcid, ModelConstants.ORCID, ModelConstants.ORCID) + orcidPID.setDataInfo(OafUtils.generateDataInfo()) + orcidPID.getDataInfo.setProvenanceaction( + OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT") + ) + + author.getPid.add(orcidPID) + + break() + } + } + } + } + } + + matched + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala new file mode 100644 index 000000000..49574fe2d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala @@ -0,0 +1,65 @@ +package eu.dnetlib.dhp.enrich.orcid + +import java.util.Locale +import java.util.regex.Pattern + +object ORCIDAuthorMatchers { + val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+") + + val WORD_DIFF = 2 + + def matchEqualsIgnoreCase(a1: String, a2: String): Boolean = { + if (a1 == null || a2 == null) + false + else + a1 == a2 || a1.toLowerCase(Locale.ROOT).equals(a2.toLowerCase(Locale.ROOT)) + } + + def matchOtherNames(fullName: String, otherNames: Seq[String]): Boolean = { + if (otherNames != null) { + otherNames.exists(matchEqualsIgnoreCase(fullName, _)) + } else { + false + } + } + + def matchOrderedTokenAndAbbreviations(a1: String, a2: String): Boolean = { + val p1: Array[String] = SPLIT_REGEX.split(a1.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted + val p2: Array[String] = SPLIT_REGEX.split(a2.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted + + if (p1.length < 2 || p2.length < 2) return false + if (Math.abs(p1.length - p2.length) > WORD_DIFF) return false // use alternative comparison algo + + var p1Idx: Int = 0 + var p2Idx: Int = 0 + var shortMatches: Int = 0 + var longMatches: Int = 0 + while (p1Idx < p1.length && p2Idx < p2.length) { + val e1: String = p1(p1Idx) + val c1: Char = e1.charAt(0) + val e2: String = p2(p2Idx) + val c2: Char = e2.charAt(0) + if (c1 < c2) p1Idx += 1 + else if (c1 > c2) p2Idx += 1 + else { + var res: Boolean = false + if (e1.length != 1 && e2.length != 1) { + res = e1 == e2 + longMatches += 1 + } else { + res = true + shortMatches += 1 + } + if (res) { + p1Idx += 1 + p2Idx += 1 + } else { + val diff: Int = e1.compareTo(e2) + if (diff < 0) p1Idx += 1 + else if (diff > 0) p2Idx += 1 + } + } + } + longMatches > 0 && (shortMatches + longMatches) == Math.min(p1.length, p2.length) + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala index 4822059c6..e2d218247 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -1,14 +1,39 @@ package eu.dnetlib.dhp.enrich.orcid import eu.dnetlib.dhp.application.AbstractScalaApplication -import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.common.ModelSupport -import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software} -import org.apache.spark.sql.functions._ +import eu.dnetlib.dhp.schema.oaf._ import org.apache.spark.sql._ +import org.apache.spark.sql.functions._ import org.slf4j.{Logger, LoggerFactory} + +import scala.beans.BeanProperty import scala.collection.JavaConverters._ +case class OrcidAutor( + @BeanProperty var orcid: String, + @BeanProperty var familyName: String, + @BeanProperty var givenName: String, + @BeanProperty var creditName: String, + @BeanProperty var otherNames: java.util.List[String] +) { + def this() = this("null", "null", "null", "null", null) +} + +case class MatchData( + @BeanProperty var id: String, + @BeanProperty var graph_authors: java.util.List[Author], + @BeanProperty var orcid_authors: java.util.List[OrcidAutor] +) { + def this() = this("null", null, null) +} + +case class MatchedAuthors( + @BeanProperty var author: Author, + @BeanProperty var orcid: OrcidAutor, + @BeanProperty var `type`: String +) + class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) extends AbstractScalaApplication(propertyPath, args, log: Logger) { @@ -22,107 +47,132 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] log.info(s"orcidPath is '$orcidPath'") val targetPath = parser.get("targetPath") log.info(s"targetPath is '$targetPath'") - val orcidPublication: Dataset[Row] = generateOrcidTable(spark, orcidPath) -// ModelSupport.entityTypes.entrySet().asScala.filter(k => k.getKey.getClass isInstance(Result)) - enrichResult( - spark, - s"$graphPath/publication", - orcidPublication, - s"$targetPath/publication", - Encoders.bean(classOf[Publication]) - ) - enrichResult( - spark, - s"$graphPath/dataset", - orcidPublication, - s"$targetPath/dataset", - Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset]) - ) - enrichResult( - spark, - s"$graphPath/software", - orcidPublication, - s"$targetPath/software", - Encoders.bean(classOf[Software]) - ) - enrichResult( - spark, - s"$graphPath/otherresearchproduct", - orcidPublication, - s"$targetPath/otherresearchproduct", - Encoders.bean(classOf[OtherResearchProduct]) - ) + createTemporaryData(graphPath, orcidPath, targetPath) + analisys(targetPath) + generateGraph(graphPath, targetPath) } - private def enrichResult[T <: Result]( - spark: SparkSession, - graphPath: String, - orcidPublication: Dataset[Row], - outputPath: String, - enc: Encoder[T] - ): Unit = { + private def generateGraph(graphPath: String, targetPath: String): Unit = { - val entities = spark.read - .schema(enc.schema) - .json(graphPath) - .select(col("id"), col("datainfo"), col("instance")) - .where("datainfo.deletedbyinference != true") - .drop("datainfo") - .withColumn("instances", explode(col("instance"))) - .withColumn("pids", explode(col("instances.pid"))) - .select( - col("pids.qualifier.classid").alias("pid_schema"), - col("pids.value").alias("pid_value"), - col("id").alias("dnet_id") - ) + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + val enc = Encoders.bean(e._2) - val orcidDnet = orcidPublication - .join( - entities, - lower(col("schema")).equalTo(lower(col("pid_schema"))) && - lower(col("value")).equalTo(lower(col("pid_value"))), - "inner" - ) - .groupBy(col("dnet_id")) - .agg(collect_set(orcidPublication("author")).alias("orcid_authors")) - .select("dnet_id", "orcid_authors") - .cache() - orcidDnet.count() - val result = spark.read.schema(enc.schema).json(graphPath).as[T](enc) + val matched = spark.read + .schema(Encoders.bean(classOf[ORCIDAuthorEnricherResult]).schema) + .parquet(s"${targetPath}/${resultType}_matched") + .selectExpr("id", "enriched_author") + + spark.read + .schema(enc.schema) + .json(s"$graphPath/$resultType") + .join(matched, Seq("id"), "left") + .withColumn( + "author", + when(size(col("enriched_author")).gt(1), col("enriched_author")) + .otherwise(col("author")) + ) + .drop("enriched_author") + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(s"${targetPath}/${resultType}") + + }) - result - .joinWith(orcidDnet, result("id").equalTo(orcidDnet("dnet_id")), "left") - .map { - case (r: T, null) => - r - case (p: T, r: Row) => - p.setAuthor(AuthorMerger.enrichOrcid(p.getAuthor, AuthorEnricher.toOAFAuthor(r))) - p - }(enc) - .write - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath) } - private def generateOrcidTable(spark: SparkSession, inputPath: String): Dataset[Row] = { + private def createTemporaryData(graphPath: String, orcidPath: String, targetPath: String): Unit = { val orcidAuthors = - spark.read.load(s"$inputPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + spark.read.load(s"$orcidPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + val orcidWorks = spark.read - .load(s"$inputPath/Works") + .load(s"$orcidPath/Works") .select(col("orcid"), explode(col("pids")).alias("identifier")) .where( - "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" + "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" // scopus eid ? ) - val orcidPublication = orcidAuthors - .join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) + + val orcidWorksWithAuthors = orcidAuthors + .join(orcidWorks, Seq("orcid")) .select( - col("identifier.schema").alias("schema"), - col("identifier.value").alias("value"), - struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") + lower(col("identifier.schema")).alias("pid_schema"), + lower(col("identifier.value")).alias("pid_value"), + struct( + col("orcid"), + col("givenName"), + col("familyName"), + col("creditName"), + col("otherNames") + ).alias("author") ) - orcidPublication.cache() + .cache() + + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + val enc = Encoders.bean(e._2) + + val oaEntities = spark.read + .schema(enc.schema) + .json(s"$graphPath/$resultType") + .select(col("id"), col("datainfo"), col("instance")) + .where("datainfo.deletedbyinference != true") + .drop("datainfo") + .withColumn("instances", explode(col("instance"))) + .withColumn("pids", explode(col("instances.pid"))) + .select( + lower(col("pids.qualifier.classid")).alias("pid_schema"), + lower(col("pids.value")).alias("pid_value"), + col("id") + ) + + val orcidDnet = orcidWorksWithAuthors + .join( + oaEntities, + Seq("pid_schema", "pid_value"), + "inner" + ) + .groupBy(col("id")) + .agg(collect_set(col("author")).alias("orcid_authors")) + .select("id", "orcid_authors") + + val result = + spark.read.schema(enc.schema).json(s"$graphPath/$resultType").selectExpr("id", "author as graph_authors") + + result + .join(orcidDnet, Seq("id")) + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .parquet(s"$targetPath/${resultType}_unmatched") + }) + + orcidWorksWithAuthors.unpersist() + } + + private def analisys(targetPath: String): Unit = { + ModelSupport.entityTypes.asScala + .filter(e => ModelSupport.isResult(e._1)) + .foreach(e => { + val resultType = e._1.name() + + spark.read + .parquet(s"$targetPath/${resultType}_unmatched") + .where("size(graph_authors) > 0") + .as[MatchData](Encoders.bean(classOf[MatchData])) + .map(md => { + ORCIDAuthorEnricher.enrichOrcid(md.id, md.graph_authors, md.orcid_authors) + })(Encoders.bean(classOf[ORCIDAuthorEnricherResult])) + .write + .option("compression", "gzip") + .mode("overwrite") + .parquet(s"$targetPath/${resultType}_matched") + }) } } diff --git a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java similarity index 71% rename from dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java rename to dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java index c0a8d6927..0b50312a5 100644 --- a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricherTest.java @@ -1,10 +1,9 @@ -package eu.dnetlib.oa.merge; - -import static org.junit.jupiter.api.Assertions.*; +package eu.dnetlib.dhp.enrich.orcid; import java.io.BufferedReader; import java.io.InputStreamReader; +import java.util.Collections; import java.util.List; import java.util.Objects; @@ -14,10 +13,9 @@ import org.junit.platform.commons.util.StringUtils; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.oaf.Author; -public class AuthorMergerTest { +public class ORCIDAuthorEnricherTest { @Test public void testEnrcichAuthor() throws Exception { @@ -26,12 +24,13 @@ public class AuthorMergerTest { BufferedReader pr = new BufferedReader(new InputStreamReader( Objects .requireNonNull( - AuthorMergerTest.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); + ORCIDAuthorEnricherTest.class + .getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json")))); BufferedReader or = new BufferedReader(new InputStreamReader( Objects .requireNonNull( - AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); + ORCIDAuthorEnricherTest.class + .getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json")))); TypeReference> aclass = new TypeReference>() { }; @@ -67,7 +66,8 @@ public class AuthorMergerTest { long start = System.currentTimeMillis(); // final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); - final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + final List enrichedList = Collections.emptyList(); // SparkEnrichGraphWithOrcidAuthors.enrichOrcid(publicationAuthors, + // orcidAuthors); long enrichedAuthorWithPid = enrichedList .stream() @@ -91,24 +91,4 @@ public class AuthorMergerTest { } } - @Test - public void checkSimilarityTest() { - final Author left = new Author(); - left.setName("Anand"); - left.setSurname("Rachna"); - left.setFullname("Anand, Rachna"); - - System.out.println(AuthorMerger.normalizeFullName(left.getFullname())); - - final Author right = new Author(); - right.setName("Rachna"); - right.setSurname("Anand"); - right.setFullname("Rachna, Anand"); -// System.out.println(AuthorMerger.normalize(right.getFullname())); - boolean same = AuthorMerger.checkORCIDSimilarity(left, right); - - assertTrue(same); - - } - } diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json similarity index 100% rename from dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json similarity index 100% rename from dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala new file mode 100644 index 000000000..f109ebe24 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala @@ -0,0 +1,35 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.enrich.orcid.ORCIDAuthorMatchers.matchOrderedTokenAndAbbreviations +import org.junit.jupiter.api.Assertions.{assertFalse, assertTrue} +import org.junit.jupiter.api.Test + +class ORCIDAuthorMatchersTest { + + @Test def testShortNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Lasagni Mariozzi Federico", "Lasagni F. Mariozzi")) + } + + @Test def testInvertedNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Andrea, Paolo Marcello", "Marcello Paolo, Andrea")) + } + + @Test def testHomonymy(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("Jang Myung Lee", "J Lee")) + } + + @Test def testAmbiguousShortNames(): Unit = { + assertFalse(matchOrderedTokenAndAbbreviations("P. Mariozzi", "M. Paolozzi")) + } + + @Test def testNonMatches(): Unit = { + assertFalse(matchOrderedTokenAndAbbreviations("Giovanni Paolozzi", "Francesco Paolozzi")) + assertFalse(matchOrderedTokenAndAbbreviations("G. Paolozzi", "F. Paolozzi")) + } + + @Test def testChineseNames(): Unit = { + assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin")) + // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented + } + +} From db66555ebb0d6cd065a2029187b8a23c8f890c66 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 12 Mar 2024 09:56:09 +0100 Subject: [PATCH 17/34] WIP: updated provision workflow to create a JSON based representation of the payload --- .../AbstractSolrRecordTransformJob.java | 52 ++++++ .../oa/provision/SolrAdminApplication.java | 12 +- .../dhp/oa/provision/SolrRecordDumpJob.java | 144 +++++++++++++++ .../dhp/oa/provision/XmlIndexingJob.java | 140 ++------------- .../model/ProvisionModelSupport.java | 29 +-- .../dhp/oa/provision/model/TupleWrapper.java | 1 + .../input_params_solr_record_dump.json | 26 +++ .../provision/input_params_update_index.json | 18 -- .../provision/input_solradmin_parameters.json | 6 - .../dhp/oa/provision/oozie_app/workflow.xml | 53 ++++-- .../oa/provision/SolrConfigExploreTest.java | 3 +- .../dhp/oa/provision/SolrConfigTest.java | 2 +- .../oa/provision/SolrRecordDumpJobTest.java | 170 ++++++++++++++++++ .../eu/dnetlib/dhp/oa/provision/SolrTest.java | 2 +- .../dhp/oa/provision/XmlIndexingJobTest.java | 77 +------- .../conf/exploreTestConfig/managed-schema | 6 + 16 files changed, 477 insertions(+), 264 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AbstractSolrRecordTransformJob.java create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java create mode 100644 dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJobTest.java diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AbstractSolrRecordTransformJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AbstractSolrRecordTransformJob.java new file mode 100644 index 000000000..fd7bf4d71 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AbstractSolrRecordTransformJob.java @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.StringReader; +import java.io.StringWriter; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.stream.StreamResult; +import javax.xml.transform.stream.StreamSource; + +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; + +public abstract class AbstractSolrRecordTransformJob { + + protected static String toIndexRecord(Transformer tr, final String xmlRecord) { + final StreamResult res = new StreamResult(new StringWriter()); + try { + tr.transform(new StreamSource(new StringReader(xmlRecord)), res); + return res.getWriter().toString(); + } catch (TransformerException e) { + throw new IllegalArgumentException("XPathException on record: \n" + xmlRecord, e); + } + } + + /** + * Creates the XSLT responsible for building the index xml records. + * + * @param format Metadata format name (DMF|TMF) + * @param xslt xslt for building the index record transformer + * @param fields the list of fields + * @return the javax.xml.transform.Transformer + * @throws TransformerException could happen + */ + protected static String getLayoutTransformer(String format, String fields, String xslt) + throws TransformerException { + + final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); + final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter()); + + layoutTransformer.setParameter("format", format); + layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt); + + return layoutToXsltXslt.getWriter().toString(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java index d4d414fed..0033978bf 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java @@ -62,16 +62,8 @@ public class SolrAdminApplication implements Closeable { final String collection = ProvisionConstants.getCollectionName(format); log.info("collection: {}", collection); - final boolean shouldIndex = Optional - .ofNullable(parser.get("shouldIndex")) - .map(Boolean::valueOf) - .orElse(false); - log.info("shouldIndex: {}", shouldIndex); - - if (shouldIndex) { - try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) { - app.execute(action, collection, query, commit); - } + try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) { + app.execute(action, collection, query, commit); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java new file mode 100644 index 000000000..faa18851b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java @@ -0,0 +1,144 @@ + +package eu.dnetlib.dhp.oa.provision; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import javax.xml.transform.TransformerException; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.solr.common.SolrInputDocument; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.model.TupleWrapper; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; + +public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob { + + private static final Logger log = LoggerFactory.getLogger(SolrRecordDumpJob.class); + + private static final Integer DEFAULT_BATCH_SIZE = 1000; + + private final String inputPath; + + private final String format; + + private final String outputPath; + + private final SparkSession spark; + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SolrRecordDumpJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.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 format = parser.get("format"); + log.info("format: {}", format); + + final String outputPath = Optional + .ofNullable(parser.get("outputPath")) + .map(StringUtils::trim) + .orElse(null); + log.info("outputPath: {}", outputPath); + + final Integer batchSize = Optional + .ofNullable(parser.get("batchSize")) + .map(Integer::valueOf) + .orElse(DEFAULT_BATCH_SIZE); + log.info("batchSize: {}", batchSize); + + final boolean shouldIndex = Optional + .ofNullable(parser.get("shouldIndex")) + .map(Boolean::valueOf) + .orElse(false); + log.info("shouldIndex: {}", shouldIndex); + + final SparkConf conf = new SparkConf(); + + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl)); + new SolrRecordDumpJob(spark, inputPath, format, outputPath).run(isLookup); + }); + } + + public SolrRecordDumpJob(SparkSession spark, String inputPath, String format, String outputPath) { + this.spark = spark; + this.inputPath = inputPath; + this.format = format; + this.outputPath = outputPath; + } + + public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException { + final String fields = isLookup.getLayoutSource(format); + log.info("fields: {}", fields); + + final String xslt = isLookup.getLayoutTransformer(); + + final String dsId = isLookup.getDsId(format); + log.info("dsId: {}", dsId); + + final String indexRecordXslt = getLayoutTransformer(format, fields, xslt); + log.info("indexRecordTransformer {}", indexRecordXslt); + + final Encoder encoder = Encoders.bean(TupleWrapper.class); + spark + .read() + .schema(encoder.schema()) + .json(inputPath) + .as(encoder) + .map( + (MapFunction) t -> new TupleWrapper( + toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()), + t.getJson()), + Encoders.bean(TupleWrapper.class)) + .map( + (MapFunction) t -> { + SolrInputDocument s = new StreamingInputDocumentFactory() + .parseDocument(t.getXml(), t.getJson()); + return new SerializableSolrInputDocument(s); + }, + Encoders.kryo(SerializableSolrInputDocument.class)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index 3c107a985..d49a0596b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -3,26 +3,18 @@ package eu.dnetlib.dhp.oa.provision; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.io.StringReader; -import java.io.StringWriter; -import java.text.SimpleDateFormat; -import java.util.Date; import java.util.Optional; -import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; -import javax.xml.transform.stream.StreamResult; -import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.hadoop.io.Text; import org.apache.solr.common.SolrInputDocument; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -36,32 +28,19 @@ import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import scala.Tuple2; -public class XmlIndexingJob { +public class XmlIndexingJob extends AbstractSolrRecordTransformJob { private static final Logger log = LoggerFactory.getLogger(XmlIndexingJob.class); - public enum OutputFormat { - SOLR, HDFS - } - private static final Integer DEFAULT_BATCH_SIZE = 1000; - protected static final String DATE_FORMAT = "yyyy-MM-dd'T'hh:mm:ss'Z'"; - private final String inputPath; private final String format; private final int batchSize; - private final OutputFormat outputFormat; - - private final String outputPath; - - private boolean shouldIndex; - private final SparkSession spark; public static void main(String[] args) throws Exception { @@ -86,30 +65,12 @@ public class XmlIndexingJob { final String format = parser.get("format"); log.info("format: {}", format); - final String outputPath = Optional - .ofNullable(parser.get("outputPath")) - .map(StringUtils::trim) - .orElse(null); - log.info("outputPath: {}", outputPath); - final Integer batchSize = Optional .ofNullable(parser.get("batchSize")) .map(Integer::valueOf) .orElse(DEFAULT_BATCH_SIZE); log.info("batchSize: {}", batchSize); - final OutputFormat outputFormat = Optional - .ofNullable(parser.get("outputFormat")) - .map(OutputFormat::valueOf) - .orElse(OutputFormat.SOLR); - log.info("outputFormat: {}", outputFormat); - - final boolean shouldIndex = Optional - .ofNullable(parser.get("shouldIndex")) - .map(Boolean::valueOf) - .orElse(false); - log.info("shouldIndex: {}", shouldIndex); - final SparkConf conf = new SparkConf(); conf.registerKryoClasses(new Class[] { @@ -123,20 +84,16 @@ public class XmlIndexingJob { final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl)); - new XmlIndexingJob(spark, inputPath, format, batchSize, outputFormat, shouldIndex, outputPath) + new XmlIndexingJob(spark, inputPath, format, batchSize) .run(isLookup); }); } - public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize, - OutputFormat outputFormat, boolean shouldIndex, String outputPath) { + public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize) { this.spark = spark; this.inputPath = inputPath; this.format = format; this.batchSize = batchSize; - this.outputFormat = outputFormat; - this.shouldIndex = shouldIndex; - this.outputPath = outputPath; } public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException { @@ -148,6 +105,9 @@ public class XmlIndexingJob { final String dsId = isLookup.getDsId(format); log.info("dsId: {}", dsId); + final String collection = ProvisionConstants.getCollectionName(format); + log.info("collection: {}", collection); + final String zkHost = isLookup.getZkHost(); log.info("zkHost: {}", zkHost); @@ -155,7 +115,8 @@ public class XmlIndexingJob { log.info("indexRecordTransformer {}", indexRecordXslt); final Encoder encoder = Encoders.bean(TupleWrapper.class); - final Dataset records = spark + + JavaRDD docs = spark .read() .schema(encoder.schema()) .json(inputPath) @@ -164,80 +125,11 @@ public class XmlIndexingJob { (MapFunction) t -> new TupleWrapper( toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()), t.getJson()), - Encoders.bean(TupleWrapper.class)); - - switch (outputFormat) { - case SOLR: - if (shouldIndex) { - final String collection = ProvisionConstants.getCollectionName(format); - - // SparkSolr >= 4 - // com.lucidworks.spark.BatchSizeType bt = com.lucidworks.spark.BatchSizeType.NUM_DOCS; - // SolrSupport.indexDocs(zkHost, collection, batchSize, bt, docs.rdd()); - // SparkSolr < 4 - JavaRDD docs = records - .javaRDD() - .map( - t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson())); - SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd()); - } - break; - case HDFS: - records - .map( - (MapFunction) t -> { - SolrInputDocument s = new StreamingInputDocumentFactory() - .parseDocument(t.getXml(), t.getJson()); - return new SerializableSolrInputDocument(s); - }, - Encoders.kryo(SerializableSolrInputDocument.class)) - .write() - .mode(SaveMode.Overwrite) - .parquet(outputPath); - break; - default: - throw new IllegalArgumentException("invalid outputFormat: " + outputFormat); - } - } - - protected static String toIndexRecord(Transformer tr, final String xmlRecord) { - final StreamResult res = new StreamResult(new StringWriter()); - try { - tr.transform(new StreamSource(new StringReader(xmlRecord)), res); - return res.getWriter().toString(); - } catch (TransformerException e) { - throw new IllegalArgumentException("XPathException on record: \n" + xmlRecord, e); - } - } - - /** - * Creates the XSLT responsible for building the index xml records. - * - * @param format Metadata format name (DMF|TMF) - * @param xslt xslt for building the index record transformer - * @param fields the list of fields - * @return the javax.xml.transform.Transformer - * @throws TransformerException could happen - */ - protected static String getLayoutTransformer(String format, String fields, String xslt) - throws TransformerException { - - final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); - final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter()); - - layoutTransformer.setParameter("format", format); - layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt); - - return layoutToXsltXslt.getWriter().toString(); - } - - /** - * method return a solr-compatible string representation of a date, used to mark all records as indexed today - * - * @return the parsed date - */ - public static String getRecordDatestamp() { - return new SimpleDateFormat(DATE_FORMAT).format(new Date()); + Encoders.bean(TupleWrapper.class)) + .javaRDD() + .map( + t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson())); + SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd()); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java index 6af692ed9..7705c62c0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java @@ -63,27 +63,32 @@ public class ProvisionModelSupport { } public static SolrRecord transform(JoinedEntity je, ContextMapper contextMapper, VocabularyGroup vocs) { - SolrRecord s = new SolrRecord(); + SolrRecord record = new SolrRecord(); final OafEntity e = je.getEntity(); - s + final RecordType type = RecordType.valueOf(e.getClass().getSimpleName().toLowerCase()); + final Boolean deletedbyinference = Optional + .ofNullable(e.getDataInfo()) + .map(DataInfo::getDeletedbyinference) + .orElse(null); + record .setHeader( SolrRecordHeader .newInstance( - e.getId(), e.getOriginalId(), RecordType.valueOf(e.getClass().getSimpleName().toLowerCase()))); - s.setCollectedfrom(asProvenance(e.getCollectedfrom())); - s.setContext(asContext(e.getContext(), contextMapper)); - s.setPid(asPid(e.getPid())); + e.getId(), e.getOriginalId(), type, deletedbyinference)); + record.setCollectedfrom(asProvenance(e.getCollectedfrom())); + record.setContext(asContext(e.getContext(), contextMapper)); + record.setPid(asPid(e.getPid())); if (e instanceof eu.dnetlib.dhp.schema.oaf.Result) { - s.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e)); + record.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Datasource) { - s.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e)); + record.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Organization) { - s.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e)); + record.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Project) { - s.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs)); + record.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs)); } - s + record .setLinks( Optional .ofNullable(je.getLinks()) @@ -94,7 +99,7 @@ public class ProvisionModelSupport { .collect(Collectors.toList())) .orElse(null)); - return s; + return record; } private static RelatedRecord mapRelatedRecord(RelatedEntityWrapper rew, VocabularyGroup vocs) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java index c23a7f550..1556a5eee 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TupleWrapper.java @@ -10,6 +10,7 @@ import java.io.Serializable; public class TupleWrapper implements Serializable { + private static final long serialVersionUID = -1418439827125577822L; private String xml; private String json; diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json new file mode 100644 index 000000000..7e5734222 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "inputPath", + "paramDescription": "the path of the sequence file to read the XML records", + "paramRequired": true + }, + { + "paramName": "f", + "paramLongName": "format", + "paramDescription": "MDFormat name found in the IS profile", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "path on hdfs activating an alternative output for the SolrInputDocuments", + "paramRequired": false + } +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json index 2960e5aaa..3396020e0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json @@ -22,23 +22,5 @@ "paramLongName": "batchSize", "paramDescription": "size of the batch of documents sent to solr", "paramRequired": false - }, - { - "paramName": "of", - "paramLongName": "outputFormat", - "paramDescription": "decides the job output format, SOLR | HDFS", - "paramRequired": false - }, - { - "paramName": "si", - "paramLongName": "shouldIndex", - "paramDescription": "should the action actually index the records?", - "paramRequired": true - }, - { - "paramName": "op", - "paramLongName": "outputPath", - "paramDescription": "path on hdfs activating an alternative output for the SolrInputDocuments", - "paramRequired": false } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json index 53805d3c1..23eca2f7b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json @@ -28,11 +28,5 @@ "paramLongName": "commit", "paramDescription": "should the action be followed by a commit?", "paramRequired": false - }, - { - "paramName": "i", - "paramLongName": "shouldIndex", - "paramDescription": "should the action actually index the records?", - "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 8908c5c83..f60c531e4 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -591,18 +591,23 @@ --conf spark.sql.shuffle.partitions=3840 --conf spark.network.timeout=${sparkNetworkTimeout} - - --inputPath/user/claudio.atzori/data/provision/join_entities - - - --outputPath/user/claudio.atzori/data/provision/xml_json_test + --inputPath${workingDir}/join_entities + --outputPath${workingDir}/xml_json --contextApiBaseUrl${contextApiBaseUrl} --isLookupUrl${isLookupUrl} - + + + + ${wf:conf('shouldIndex') eq 'true'} + ${wf:conf('shouldIndex') eq 'false'} + + + + @@ -617,7 +622,6 @@ --actionDELETE_BY_QUERY --query${solrDeletionQuery} --committrue - --shouldIndex${shouldIndex} @@ -643,17 +647,10 @@ --conf spark.hadoop.mapreduce.map.speculative=false --conf spark.hadoop.mapreduce.reduce.speculative=false - - --inputPath/user/claudio.atzori/data/provision/xml_json_test + --inputPath${workingDir}/xml_json --isLookupUrl${isLookupUrl} --format${format} --batchSize${batchSize} - --outputFormat${outputFormat} - - - --outputPath/user/claudio.atzori/data/provision/solr_documents - - --shouldIndex${shouldIndex} @@ -671,11 +668,35 @@ --isLookupUrl${isLookupUrl} --format${format} --actionCOMMIT - --shouldIndex${shouldIndex} + + + yarn + cluster + dump_solr_records_hdfs + eu.dnetlib.dhp.oa.provision.SolrRecordDumpJob + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputPath${workingDir}/xml_json + --isLookupUrl${isLookupUrl} + --format${format} + --outputPath${workingDir}/solr_documents + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java index c749781ec..424262eef 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java @@ -86,8 +86,7 @@ public class SolrConfigExploreTest extends SolrExploreTest { String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null) - .run(isLookupClient); + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient); Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); String[] queryStrings = { diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java index 91dbf8978..625b6d131 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java @@ -95,7 +95,7 @@ public class SolrConfigTest extends SolrTest { String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, false, null) + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize) .run(isLookupClient); Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJobTest.java new file mode 100644 index 000000000..c2cd3497a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJobTest.java @@ -0,0 +1,170 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.oa.provision; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.io.IOException; +import java.io.StringReader; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.solr.common.SolrInputField; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.junit.jupiter.api.io.TempDir; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.model.TupleWrapper; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +class SolrRecordDumpJobTest { + + protected static final Logger log = LoggerFactory.getLogger(SolrRecordDumpJobTest.class); + + protected static SparkSession spark; + + protected static final String FORMAT = "test"; + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private ISLookupClient isLookupClient; + + @TempDir + public static Path workingDir; + + @BeforeAll + public static void before() { + + SparkConf conf = new SparkConf(); + conf.setAppName(SolrRecordDumpJobTest.class.getSimpleName()); + + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + conf.setMaster("local[1]"); + 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.resolve("spark").toString()); + + spark = SparkSession + .builder() + .appName(SolrRecordDumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void shutDown() throws Exception { + spark.stop(); + FileUtils.deleteDirectory(workingDir.toFile()); + } + + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); + + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } + + @Test + void testXmlIndexingJob_saveOnHDFS() throws Exception { + final String ID_XPATH = "//*[local-name()='header']/*[local-name()='objIdentifier']"; + + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + // String inputPath = "/Users/claudio/workspace/data/index"; + + Dataset records = spark + .read() + .schema(Encoders.bean(TupleWrapper.class).schema()) + .json(inputPath) + .as(Encoders.bean(TupleWrapper.class)); + + records.printSchema(); + + long nRecord = records.count(); + log.info("found {} records", nRecord); + + final Dataset ids = records + .map((MapFunction) TupleWrapper::getXml, Encoders.STRING()) + .map( + (MapFunction) s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH), + Encoders.STRING()); + + log.info("found {} ids", ids.count()); + + long xmlIdUnique = ids + .distinct() + .count(); + + log.info("found {} unique ids", xmlIdUnique); + + assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records"); + + final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString(); + new SolrRecordDumpJob(spark, inputPath, FORMAT, outputPath).run(isLookupClient); + + final Dataset solrDocs = spark + .read() + .load(outputPath) + .as(Encoders.kryo(SerializableSolrInputDocument.class)); + + solrDocs.foreach(doc -> { + assertNotNull(doc.get("__result")); + assertNotNull(doc.get("__json")); + }); + + long docIdUnique = solrDocs.map((MapFunction) doc -> { + final SolrInputField id = doc.getField("__indexrecordidentifier"); + return id.getFirstValue().toString(); + }, Encoders.STRING()) + .distinct() + .count(); + assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output XML records"); + + long jsonUnique = solrDocs + .map( + (MapFunction) je -> (String) je.getField("__json").getValue(), + Encoders.STRING()) + .distinct() + .count(); + + assertEquals(jsonUnique, docIdUnique, "IDs should be unique among the output JSON records"); + + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java index 186cb964a..79527b891 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java @@ -92,7 +92,7 @@ public abstract class SolrTest { FileUtils.deleteDirectory(workingDir.toFile()); } - protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, + public static NamedList createCollection(CloudSolrClient client, String name, int numShards, int replicationFactor, int maxShardsPerNode, String configName) throws Exception { ModifiableSolrParams modParams = new ModifiableSolrParams(); modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java index be481cc37..522c34ef1 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java @@ -1,24 +1,21 @@ package eu.dnetlib.dhp.oa.provision; -import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; import java.io.IOException; -import java.io.StringReader; import java.net.URI; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.solr.client.solrj.SolrQuery; import org.apache.solr.client.solrj.response.QueryResponse; -import org.apache.solr.common.SolrInputField; import org.apache.solr.common.params.CommonParams; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; -import org.dom4j.io.SAXReader; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeEach; @@ -106,8 +103,7 @@ public class XmlIndexingJobTest extends SolrTest { long nRecord = records.count(); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null) - .run(isLookupClient); + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient); assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); @@ -164,71 +160,4 @@ public class XmlIndexingJobTest extends SolrTest { } - @Test - void testXmlIndexingJob_saveOnHDFS() throws Exception { - final String ID_XPATH = "//*[local-name()='header']/*[local-name()='objIdentifier']"; - - String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; - // String inputPath = "/Users/claudio/workspace/data/index"; - - Dataset records = spark - .read() - .schema(Encoders.bean(TupleWrapper.class).schema()) - .json(inputPath) - .as(Encoders.bean(TupleWrapper.class)); - - records.printSchema(); - - long nRecord = records.count(); - log.info("found {} records", nRecord); - - final Dataset ids = records - .map((MapFunction) TupleWrapper::getXml, Encoders.STRING()) - .map( - (MapFunction) s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH), - Encoders.STRING()); - - log.info("found {} ids", ids.count()); - - long xmlIdUnique = ids - .distinct() - .count(); - - log.info("found {} unique ids", xmlIdUnique); - - assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records"); - - final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString(); - new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.HDFS, false, outputPath) - .run(isLookupClient); - - final Dataset solrDocs = spark - .read() - .load(outputPath) - .as(Encoders.kryo(SerializableSolrInputDocument.class)); - - solrDocs.foreach(doc -> { - assertNotNull(doc.get("__result")); - assertNotNull(doc.get("__json")); - }); - - long docIdUnique = solrDocs.map((MapFunction) doc -> { - final SolrInputField id = doc.getField("__indexrecordidentifier"); - return id.getFirstValue().toString(); - }, Encoders.STRING()) - .distinct() - .count(); - assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output XML records"); - - long jsonUnique = solrDocs - .map( - (MapFunction) je -> (String) je.getField("__json").getValue(), - Encoders.STRING()) - .distinct() - .count(); - - assertEquals(jsonUnique, docIdUnique, "IDs should be unique among the output JSON records"); - - } - } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema index 4e85ca3be..9720d3f37 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema @@ -202,6 +202,7 @@ + @@ -223,17 +224,22 @@ + + + + + From 48c052215c06d081131034b5fda24fe57821bb67 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 12 Mar 2024 23:12:32 +0100 Subject: [PATCH 18/34] [OC New] last fix --- .../bipfinder/SparkAtomicActionScoreJob.java | 2 +- .../CreateActionSetSparkJob.java | 55 ++++++++---- .../opencitations/MapOCIdsInPids.java | 61 ++++++++++++- .../actionmanager/opencitations/ReadCOCI.java | 6 +- .../opencitations/model/COCI.java | 4 + .../opencitations/oozie_app/workflow.xml | 2 + .../opencitations/remap_parameters.json | 7 +- .../CreateOpenCitationsASTest.java | 9 +- .../opencitations/RemapTest.java | 90 +++++++++++++++++++ .../COCI/inputremap/JSON/part-00000 | 31 +++++++ .../COCI/inputremap/correspondence/omid.csv | 48 ++++++++++ .../opencitations/COCI/inputremap/jsonforas | 27 ++++++ 12 files changed, 316 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c89782..8adc88920 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + // project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java index 47949a4bb..950b2eb57 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java @@ -22,6 +22,7 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; @@ -41,7 +42,9 @@ public class CreateActionSetSparkJob implements Serializable { private static final String DOI_PREFIX = "50|doi_________::"; private static final String PMID_PREFIX = "50|pmid________::"; + private static final String ARXIV_PREFIX = "50|arXiv_______::"; + private static final String PMCID_PREFIX = "50|pmcid_______::"; private static final String TRUST = "0.91"; private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); @@ -74,25 +77,18 @@ public class CreateActionSetSparkJob implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath {}", outputPath); - final boolean shouldDuplicateRels = Optional - .ofNullable(parser.get("shouldDuplicateRels")) - .map(Boolean::valueOf) - .orElse(Boolean.FALSE); - SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, - spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels)); + spark -> extractContent(spark, inputPath, outputPath)); } - private static void extractContent(SparkSession spark, String inputPath, String outputPath, - boolean shouldDuplicateRels) { + private static void extractContent(SparkSession spark, String inputPath, String outputPath) { getTextTextJavaPairRDD(spark, inputPath) - // .union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI)) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class); } private static JavaPairRDD getTextTextJavaPairRDD(SparkSession spark, String inputPath) { @@ -115,7 +111,7 @@ public class CreateActionSetSparkJob implements Serializable { new Text(OBJECT_MAPPER.writeValueAsString(aa)))); } - private static List createRelation(COCI value) { + private static List createRelation(COCI value) throws JsonProcessingException { List relationList = new ArrayList<>(); @@ -131,25 +127,52 @@ public class CreateActionSetSparkJob implements Serializable { case "pmid": citing = PMID_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); + .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting())); break; + case "arxiv": + citing = ARXIV_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting())); + break; + case "pmcid": + citing = PMCID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting())); + break; + case "isbn": + case "issn": + return relationList; + default: - throw new IllegalStateException("Invalid prefix: " + value.getCiting_pid()); + throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value)); } switch (value.getCited_pid()) { case "doi": cited = DOI_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited())); break; case "pmid": cited = PMID_PREFIX + IdentifierFactory - .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); + .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited())); break; + case "arxiv": + cited = ARXIV_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited())); + break; + case "pmcid": + cited = PMCID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited())); + break; + case "isbn": + case "issn": + return relationList; default: - throw new IllegalStateException("Invalid prefix: " + value.getCited_pid()); + throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value)); } if (!citing.equals(cited)) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java index c6c5bc0ba..d4fc33f01 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java @@ -9,11 +9,19 @@ import java.util.Arrays; import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import java.util.zip.ZipEntry; +import java.util.zip.ZipInputStream; import org.apache.commons.cli.ParseException; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -62,6 +70,10 @@ public class MapOCIdsInPids implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath {}", outputPath); + final String nameNode = parser.get("nameNode"); + log.info("nameNode {}", nameNode); + + unzipCorrespondenceFile(inputPath, nameNode); SparkConf conf = new SparkConf(); runWithSparkSession( conf, @@ -70,6 +82,41 @@ public class MapOCIdsInPids implements Serializable { } + private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException { + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + final Path path = new Path(inputPath + "/correspondence/omid.zip"); + FileSystem fileSystem = FileSystem.get(conf); + + FSDataInputStream project_zip = fileSystem.open(path); + + try (ZipInputStream zis = new ZipInputStream(project_zip)) { + ZipEntry entry = null; + while ((entry = zis.getNextEntry()) != null) { + + if (!entry.isDirectory()) { + String fileName = entry.getName(); + byte buffer[] = new byte[1024]; + int count; + + try ( + FSDataOutputStream out = fileSystem + .create(new Path(inputPath + "/correspondence/omid.csv"))) { + + while ((count = zis.read(buffer, 0, buffer.length)) != -1) + out.write(buffer, 0, count); + + } + + } + + } + + } + + } + private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) { Dataset coci = spark .read() @@ -85,7 +132,7 @@ public class MapOCIdsInPids implements Serializable { .option("inferSchema", "true") .option("header", "true") .option("quotes", "\"") - .load(inputPath + "/correspondence/omid.zip") + .load(inputPath + "/correspondence/omid.csv") .repartition(5000) .flatMap((FlatMapFunction>) r -> { String ocIdentifier = r.getAs("omid"); @@ -98,7 +145,7 @@ public class MapOCIdsInPids implements Serializable { }, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); Dataset mappedCitingDataset = coci - .joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left") + .joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1"))) .map((MapFunction>, COCI>) t2 -> { String correspondent = t2._2()._2(); t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":"))); @@ -118,6 +165,16 @@ public class MapOCIdsInPids implements Serializable { .mode(SaveMode.Append) .option("compression", "gzip") .json(outputPath); + + mappedCitingDataset + .joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1"))) + .map((MapFunction>, COCI>) t2 -> { + String correspondent = t2._2()._2(); + t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":"))); + t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1)); + return t2._1(); + }, Encoders.bean(COCI.class)) + .foreach((ForeachFunction) c -> System.out.println(OBJECT_MAPPER.writeValueAsString(c))); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java index afbd43176..479aea458 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java @@ -14,6 +14,7 @@ import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -79,7 +80,7 @@ public class ReadCOCI implements Serializable { new Path(workingPath), true); while (fileStatusListIterator.hasNext()) { LocatedFileStatus fileStatus = fileStatusListIterator.next(); - + log.info("extracting file {}", fileStatus.getPath().toString()); Dataset cociData = spark .read() .format("csv") @@ -91,6 +92,7 @@ public class ReadCOCI implements Serializable { .repartition(100); cociData.map((MapFunction) row -> { + COCI coci = new COCI(); coci.setCiting(row.getString(1)); @@ -100,10 +102,12 @@ public class ReadCOCI implements Serializable { return coci; }, Encoders.bean(COCI.class)) + .filter((FilterFunction) c -> c != null) .write() .mode(SaveMode.Append) .option("compression", "gzip") .json(outputPath); + fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE")); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java index 42fca5dd3..22a3fb52d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java @@ -27,6 +27,8 @@ public class COCI implements Serializable { } public void setCiting(String citing) { + if (citing != null && citing.startsWith("omid:")) + citing = citing.substring(5); this.citing = citing; } @@ -35,6 +37,8 @@ public class COCI implements Serializable { } public void setCited(String cited) { + if (cited != null && cited.startsWith("omid:")) + cited = cited.substring(5); this.cited = cited; } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml index e28b021bc..566cf7d02 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml @@ -27,6 +27,7 @@ ${wf:conf('resumeFrom') eq 'DownloadDump'} ${wf:conf('resumeFrom') eq 'ExtractContent'} ${wf:conf('resumeFrom') eq 'ReadContent'} + ${wf:conf('resumeFrom') eq 'MapContent'} ${wf:conf('resumeFrom') eq 'CreateAS'} @@ -154,6 +155,7 @@ --inputPath${inputPath} --outputPath${outputPathExtraction} + --nameNode${nameNode} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json index 95ab5f6d9..7ebaddfdf 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json @@ -16,5 +16,10 @@ "paramLongName": "isSparkSessionManged", "paramDescription": "the hdfs name node", "paramRequired": false - } + },{ + "paramName": "nn", + "paramLongName": "nameNode", + "paramDescription": "the hdfs name node", + "paramRequired": true +} ] diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java index 523437950..ed80ed5c5 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java @@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest { String inputPath = getClass() .getResource( - "/eu/dnetlib/dhp/actionmanager/opencitations/COCI") + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas") .getPath(); CreateActionSetSparkJob @@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest { new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-shouldDuplicateRels", - Boolean.TRUE.toString(), "-inputPath", inputPath, "-outputPath", @@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest { .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(aa -> ((Relation) aa.getPayload())); - assertEquals(31, tmp.count()); + Assertions.assertEquals(27, tmp.count()); + tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size())); - // tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java new file mode 100644 index 000000000..5fc732bcf --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/RemapTest.java @@ -0,0 +1,90 @@ + +package eu.dnetlib.dhp.actionmanager.opencitations; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; + +/** + * @author miriam.baglioni + * @Date 07/03/24 + */ +public class RemapTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(RemapTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(RemapTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(RemapTest.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(RemapTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testRemap() throws Exception { + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap") + .getPath(); + + MapOCIdsInPids + .main( + new String[] { + "-isSparkSessionManged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/out/", + "-nameNode", "input1;input2;input3;input4;input5" + }); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000 new file mode 100644 index 000000000..50f731b17 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/JSON/part-00000 @@ -0,0 +1,31 @@ +{"cited":"br/061201599020", "citing":"br/06203041400","oci":"oci:06701327944-06504326071"} +{"cited":"br/061201599020","citing":"br/06502272390","oci":"oci:06502272390-061301355525"} +{"cited":"br/061201599020", "citing":"br/06120941789","oci":"oci:0670804699-067055659"} +{"cited":"br/06210273177","citing":"br/06203041400","oci":"oci:061502003994-062201281456"} +{"cited":"br/06210273177", "citing":"br/06502272390","oci":"oci:06502272390-0660806688"} +{"cited":"br/06210273177", "citing":"br/06120941789","oci":"oci:06502307119-0620223645"} +{"cited":"br/0660613430","citing":"br/06203041400","oci":"oci:061502004011-061902692285"} +{"cited":"br/0660613430", "citing":"br/06502272390","oci":"oci:0660549063-0610398792"} +{"cited":"br/0660613430", "citing":"br/06120941789","oci":"oci:06420189324-06301543046"} +{"cited":"br/062602732073","citing":"br/06203041400","oci":"oci:06380130275-061502004367"} +{"cited":"br/062602732073","citing":"br/06502272390","oci":"oci:062403449086-062501448395"} +{"cited":"br/062602732073","citing":"br/06120941789","oci":"oci:06420189328-061202007182"} +{"cited":"br/061103703697","citing":"br/06203041400","oci":"oci:062603906965-061701362658"} +{"cited":"br/061103703697", "citing":"br/06502272390","oci":"oci:0670294309-06104327031"} +{"cited":"br/061103703697","citing":"br/06120941789","oci":"oci:061702060228-061301712529"} +{"cited":"br/06230199640", "citing":"br/0670517081","oci":"oci:06901104174-06503692526"} +{"cited":"br/061703513967","citing":"br/061702310822","oci":"oci:061702310822-061703513967"} +{"cited":"br/062104002953","citing":"br/061702311472","oci":"oci:061702311472-062104002953"} +{"cited":"br/061101204417","citing":"br/062102701590","oci":"oci:062102701590-061101204417"} +{"cited":"br/062403787088","citing":"br/061401499173","oci":"oci:061401499173-062403787088"} +{"cited":"br/061203576338","citing":"br/06110279619","oci":"oci:06110279619-061203576338"} +{"cited":"br/061601962207","citing":"br/061502004018","oci":"oci:061502004018-061601962207"} +{"cited":"br/06101014588", "citing":"br/061502004027","oci":"oci:061502004027-06101014588"} +{"cited":"br/06704040804", "citing":"br/06220799044","oci":"oci:06220799044-06704040804"} +{"cited":"br/061401105151","citing":"br/061502004037","oci":"oci:061502004037-061401105151"} +{"cited":"br/0640821079", "citing":"br/061702311537","oci":"oci:061702311537-0640821079"} +{"cited":"br/06604165310", "citing":"br/062501970289","oci":"oci:062501970289-06604165310"} +{"cited":"br/061501351689","citing":"br/061203895786","oci":"oci:061203895786-061501351689"} +{"cited":"br/06202223692", "citing":"br/06110298832","oci":"oci:06110298832-06202223692"} +{"cited":"br/06104310727", "citing":"br/0660439086","oci":"oci:0660439086-06104310727"} +{"cited":"br/06150216214", "citing":"br/06340150329","oci":"oci:06340150329-06150216214"} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv new file mode 100644 index 000000000..0e34ba936 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/correspondence/omid.csv @@ -0,0 +1,48 @@ +omid,id +br/061201599020,doi:10.1142/s0219887817501687 +br/06203041400,doi:10.1111/j.1523-5378.2005.00327.x pmid:16104945 +br/06210273177,doi:10.1090/qam/20394 +br/06502272390,pmid:32235596 doi:10.3390/nano10040644 +br/0660613430,doi:10.1007/bf00470411 +br/06120941789,doi:10.1098/rspa.2006.1747 +br/062602732073,doi:10.1007/978-3-642-38844-6_25 +br/06230199640,pmid:25088780 doi:10.1016/j.ymeth.2014.07.008 +br/061103703697,pmid:2682767 +br/0670517081,doi:10.1016/j.foodpol.2021.102189 +br/06502310477,doi:10.1142/s0218127416500450 +br/06520113284,doi:10.1109/cfasta57821.2023.10243367 +br/062303652439,pmid:5962654 doi:10.1016/0020-708x(66)90001-9 +br/06250691436,doi:10.1042/bst20150052 pmid:26009172 +br/061201665577,doi:10.1097/00115550-200205000-00018 +br/06503490336,pmid:34689254 doi:10.1007/s10072-021-05687-0 +br/06220615942,pmid:25626134 doi:10.1016/j.jcis.2015.01.008 +br/061103389243,doi:10.4324/9780203702819-10 +br/062303011271,doi:10.1109/icassp.2011.5946250 +br/061302926083,doi:10.4018/978-1-6684-3937-1.ch002 +br/061402485360,doi:10.1109/iciict.2015.7396079 +br/06410101083,doi:10.1016/j.autcon.2023.104828 +br/062202243386,doi:10.1016/0001-8791(81)90022-1 +br/06170421486,doi:10.1130/0016-7606(2003)115<0166:dsagmf>2.0.co;2 +br/061201983865,doi:10.4324/9781315109008 isbn:9781315109008 +br/061701697230,doi:10.1016/j.trd.2012.07.006 +br/061201137111,doi:10.1109/access.2020.2971656 +br/06120436283,pmid:2254430 doi:10.1128/jcm.28.11.2551-2554.1990 +br/061903968916,doi:10.1111/j.1742-1241.1988.tb08627.x +br/06201583482,doi:10.1016/0016-5085(78)93139-6 +br/06130338317,doi:10.2134/agronj1952.00021962004400080013x +br/062601538320,doi:10.1371/journal.pone.0270593 pmid:35789338 +br/062401098626,pmid:22385804 doi:10.1016/j.talanta.2011.12.034 +br/06190436492,doi:10.1039/c7dt01499f pmid:28644489 +br/06202819247,doi:10.1007/978-3-319-45823-6_57 +br/0648013560,doi:10.1080/14772000.2012.705356 +br/0690214059,doi:10.2752/175630608x329217 +br/06601640415,doi:10.1080/18128600508685647 +br/061503394761,doi:10.1002/0471443395.img018 +br/061702861849,pmid:31203682 doi:10.1080/10428194.2019.1627538 +br/06450133713,doi:10.1093/acprof:oso/9780199670888.003.0008 +br/0628074892,doi:10.1097/hnp.0000000000000597 +br/061601032219,doi:10.1002/bdm.2102 +br/06602079930,doi:10.1101/2020.08.25.267500 +br/0604192147,doi:10.11501/3307395 +br/061101933800,doi:10.1142/s0217732398002242 +br/06504184118,pmid:10091417 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas new file mode 100644 index 000000000..4b8853d6e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas @@ -0,0 +1,27 @@ +{"oci":"oci:06701327944-06504326071","citing":"16104945","citing_pid":"pmid","cited":"10.1142/s0219887817501687","cited_pid":"doi"} +{"oci":"oci:06701327944-06504326071","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"} +{"oci":"oci:06502272390-061301355525","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"} +{"oci":"oci:06502272390-061301355525","citing":"32235596","citing_pid":"pmid","cited":"10.1142/s0219887817501687","cited_pid":"doi"} +{"oci":"oci:0670804699-067055659","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1142/s0219887817501687","cited_pid":"doi"} +{"oci":"oci:061502003994-062201281456","citing":"16104945","citing_pid":"pmid","cited":"10.1090/qam/20394","cited_pid":"doi"} +{"oci":"oci:061502003994-062201281456","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"} +{"oci":"oci:06502272390-0660806688","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"} +{"oci":"oci:06502272390-0660806688","citing":"32235596","citing_pid":"pmid","cited":"10.1090/qam/20394","cited_pid":"doi"} +{"oci":"oci:06502307119-0620223645","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1090/qam/20394","cited_pid":"doi"} +{"oci":"oci:061502004011-061902692285","citing":"16104945","citing_pid":"pmid","cited":"10.1007/bf00470411","cited_pid":"doi"} +{"oci":"oci:061502004011-061902692285","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"} +{"oci":"oci:0660549063-0610398792","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"} +{"oci":"oci:0660549063-0610398792","citing":"32235596","citing_pid":"pmid","cited":"10.1007/bf00470411","cited_pid":"doi"} +{"oci":"oci:06420189324-06301543046","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1007/bf00470411","cited_pid":"doi"} +{"oci":"oci:06380130275-061502004367","citing":"16104945","citing_pid":"pmid","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"} +{"oci":"oci:06380130275-061502004367","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"} +{"oci":"oci:062403449086-062501448395","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"} +{"oci":"oci:062403449086-062501448395","citing":"32235596","citing_pid":"pmid","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"} +{"oci":"oci:06420189328-061202007182","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"10.1007/978-3-642-38844-6_25","cited_pid":"doi"} +{"oci":"oci:062603906965-061701362658","citing":"16104945","citing_pid":"pmid","cited":"2682767","cited_pid":"pmid"} +{"oci":"oci:062603906965-061701362658","citing":"10.1111/j.1523-5378.2005.00327.x","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"} +{"oci":"oci:0670294309-06104327031","citing":"10.3390/nano10040644","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"} +{"oci":"oci:0670294309-06104327031","citing":"32235596","citing_pid":"pmid","cited":"2682767","cited_pid":"pmid"} +{"oci":"oci:061702060228-061301712529","citing":"10.1098/rspa.2006.1747","citing_pid":"doi","cited":"2682767","cited_pid":"pmid"} +{"oci":"oci:06901104174-06503692526","citing":"10.1016/j.foodpol.2021.102189","citing_pid":"doi","cited":"10.1016/j.ymeth.2014.07.008","cited_pid":"doi"} +{"oci":"oci:06901104174-06503692526","citing":"10.1016/j.foodpol.2021.102189","citing_pid":"doi","cited":"25088780","cited_pid":"pmid"} \ No newline at end of file From 5a32bb9578d437e669539d07c66eb84c0ddc58c5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 13 Mar 2024 09:36:18 +0100 Subject: [PATCH 19/34] [OC New] last fix --- .../actionmanager/opencitations/MapOCIdsInPids.java | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java index d4fc33f01..f7de4ac08 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java @@ -166,15 +166,6 @@ public class MapOCIdsInPids implements Serializable { .option("compression", "gzip") .json(outputPath); - mappedCitingDataset - .joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1"))) - .map((MapFunction>, COCI>) t2 -> { - String correspondent = t2._2()._2(); - t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":"))); - t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1)); - return t2._1(); - }, Encoders.bean(COCI.class)) - .foreach((ForeachFunction) c -> System.out.println(OBJECT_MAPPER.writeValueAsString(c))); - } + } } From eb5887cb9a0ad8adc7fcfc62e38e257e7ad98b9c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 Mar 2024 14:46:00 +0100 Subject: [PATCH 20/34] including related organization url in the XML record serialization (ticket #9498) --- .../eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 4d9d9c341..b2a4ad8ff 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -1133,6 +1133,9 @@ public class XmlRecordFactory implements Serializable { if (re.getCountry() != null && !re.getCountry().isBlank()) { metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry())); } + if (StringUtils.isNotBlank(re.getWebsiteurl())) { + metadata.add(XmlSerializationUtils.asXmlElement("websiteurl", re.getWebsiteurl())); + } break; case project: if (isNotBlank(re.getProjectTitle())) { From 7863c92466c34eb9b77b8c4ebebe66c147d7f4a2 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 13 Mar 2024 16:25:31 +0100 Subject: [PATCH 21/34] expanded paper abstract in the result/children XML element (ticket #9497) --- .../oa/provision/CreateRelatedEntitiesJob_phase1.java | 6 ++++++ .../eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java | 9 +++++++++ .../dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 3 +++ 3 files changed, 18 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index 48e5945c0..8cbda0903 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -161,6 +161,12 @@ public class CreateRelatedEntitiesJob_phase1 { title.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH)); re.setTitle(title); } + if (result.getDescription() != null && !result.getDescription().isEmpty()) { + final Field description = result.getDescription().stream().findFirst().get(); + if (StringUtils.isNotBlank(description.getValue())) { + re.setDescription(StringUtils.left(description.getValue(), ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH)); + } + } re.setDateofacceptance(getValue(result.getDateofacceptance())); re.setPublisher(getValue(result.getPublisher())); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java index f13c6c90e..12540aba0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java @@ -23,6 +23,7 @@ public class RelatedEntity implements Serializable { private String websiteurl; // datasource, organizations, projects // results + private String description; private String dateofacceptance; private String publisher; private List pid; @@ -77,6 +78,14 @@ public class RelatedEntity implements Serializable { return websiteurl; } + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + public void setWebsiteurl(String websiteurl) { this.websiteurl = websiteurl; } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index b2a4ad8ff..304171399 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -1071,6 +1071,9 @@ public class XmlRecordFactory implements Serializable { if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { metadata.add(XmlSerializationUtils.mapStructuredProperty("title", re.getTitle())); } + if (StringUtils.isNotBlank(re.getDescription())) { + metadata.add(XmlSerializationUtils.asXmlElement("description", re.getDescription())); + } if (isNotBlank(re.getDateofacceptance())) { metadata .add(XmlSerializationUtils.asXmlElement("dateofacceptance", re.getDateofacceptance())); From af154d44566af258fd00b832f23f9d1c0a6f7503 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 14 Mar 2024 16:21:23 +0100 Subject: [PATCH 22/34] implemented changes from #9497: sort abstracts by string length, included author fullnames in the related results, expanded instance details within each children/result XML element --- .../oaf/utils/GraphCleaningFunctions.java | 2 + .../CreateRelatedEntitiesJob_phase1.java | 45 ++++++++----- .../model/ProvisionModelSupport.java | 22 +++---- .../dhp/oa/provision/model/RelatedEntity.java | 9 +++ .../oa/provision/utils/TemplateFactory.java | 6 +- .../oa/provision/utils/XmlRecordFactory.java | 66 ++++++++++++++++++- 6 files changed, 118 insertions(+), 32 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index f01f90fe4..9386db933 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -506,6 +506,8 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(Objects::nonNull) .filter(sp -> StringUtils.isNotBlank(sp.getValue())) .map(GraphCleaningFunctions::cleanValue) + .sorted((s1, s2) -> s2.getValue().length() - s1.getValue().length()) + .limit(ModelHardLimits.MAX_ABSTRACTS) .collect(Collectors.toList())); } if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index 8cbda0903..9084f3ae3 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.yarn.webapp.hamlet.Hamlet; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -27,14 +28,7 @@ import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; import scala.Tuple2; @@ -156,16 +150,33 @@ public class CreateRelatedEntitiesJob_phase1 { case software: final Result result = (Result) entity; - if (result.getTitle() != null && !result.getTitle().isEmpty()) { - final StructuredProperty title = result.getTitle().stream().findFirst().get(); - title.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH)); - re.setTitle(title); + if (Objects.nonNull(result.getTitle()) && !result.getTitle().isEmpty()) { + result + .getTitle() + .stream() + .findFirst() + .map(StructuredProperty::getValue) + .ifPresent( + title -> re.getTitle().setValue(StringUtils.left(title, ModelHardLimits.MAX_TITLE_LENGTH))); } - if (result.getDescription() != null && !result.getDescription().isEmpty()) { - final Field description = result.getDescription().stream().findFirst().get(); - if (StringUtils.isNotBlank(description.getValue())) { - re.setDescription(StringUtils.left(description.getValue(), ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH)); - } + if (Objects.nonNull(result.getDescription()) && !result.getDescription().isEmpty()) { + result + .getDescription() + .stream() + .findFirst() + .map(Field::getValue) + .ifPresent( + d -> re.setDescription(StringUtils.left(d, ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH))); + } + if (Objects.nonNull(result.getAuthor()) && !result.getAuthor().isEmpty()) { + re + .setAuthor( + result + .getAuthor() + .stream() + .map(Author::getFullname) + .filter(StringUtils::isNotBlank) + .collect(Collectors.toList())); } re.setDateofacceptance(getValue(result.getDateofacceptance())); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java index 7705c62c0..0e6e95de5 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java @@ -63,32 +63,32 @@ public class ProvisionModelSupport { } public static SolrRecord transform(JoinedEntity je, ContextMapper contextMapper, VocabularyGroup vocs) { - SolrRecord record = new SolrRecord(); + SolrRecord r = new SolrRecord(); final OafEntity e = je.getEntity(); final RecordType type = RecordType.valueOf(e.getClass().getSimpleName().toLowerCase()); final Boolean deletedbyinference = Optional .ofNullable(e.getDataInfo()) .map(DataInfo::getDeletedbyinference) .orElse(null); - record + r .setHeader( SolrRecordHeader .newInstance( e.getId(), e.getOriginalId(), type, deletedbyinference)); - record.setCollectedfrom(asProvenance(e.getCollectedfrom())); - record.setContext(asContext(e.getContext(), contextMapper)); - record.setPid(asPid(e.getPid())); + r.setCollectedfrom(asProvenance(e.getCollectedfrom())); + r.setContext(asContext(e.getContext(), contextMapper)); + r.setPid(asPid(e.getPid())); if (e instanceof eu.dnetlib.dhp.schema.oaf.Result) { - record.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e)); + r.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Datasource) { - record.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e)); + r.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Organization) { - record.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e)); + r.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e)); } else if (e instanceof eu.dnetlib.dhp.schema.oaf.Project) { - record.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs)); + r.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs)); } - record + r .setLinks( Optional .ofNullable(je.getLinks()) @@ -99,7 +99,7 @@ public class ProvisionModelSupport { .collect(Collectors.toList())) .orElse(null)); - return record; + return r; } private static RelatedRecord mapRelatedRecord(RelatedEntityWrapper rew, VocabularyGroup vocs) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java index 12540aba0..ee010910c 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java @@ -24,6 +24,7 @@ public class RelatedEntity implements Serializable { // results private String description; + private List author; private String dateofacceptance; private String publisher; private List pid; @@ -86,6 +87,14 @@ public class RelatedEntity implements Serializable { this.description = description; } + public List getAuthor() { + return author; + } + + public void setAuthor(List author) { + this.author = author; + } + public void setWebsiteurl(String websiteurl) { this.websiteurl = websiteurl; } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java index 87c0261ac..befebe0bb 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java @@ -100,13 +100,17 @@ public class TemplateFactory { public String getInstance( final List instancemetadata, final String url) { + return getInstance(instancemetadata, Lists.newArrayList(url)); + } + + public String getInstance( + final List instancemetadata, final List url) { return getTemplate(resources.getInstance()) .add("metadata", instancemetadata) .add( "webresources", Optional .ofNullable(url) - .map(u -> Lists.newArrayList(url)) .orElse(Lists.newArrayList()) .stream() .filter(StringUtils::isNotBlank) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 304171399..e1f5addfd 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -49,6 +49,7 @@ import eu.dnetlib.dhp.schema.common.*; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; import scala.Tuple2; public class XmlRecordFactory implements Serializable { @@ -365,6 +366,7 @@ public class XmlRecordFactory implements Serializable { .getDescription() .stream() .filter(Objects::nonNull) + .limit(ModelHardLimits.MAX_ABSTRACTS) .map(c -> XmlSerializationUtils.asXmlElement("description", c.getValue())) .collect(Collectors.toCollection(HashSet::new))); } @@ -1057,7 +1059,8 @@ public class XmlRecordFactory implements Serializable { return kv != null && StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue()); } - private List mapFields(final RelatedEntityWrapper link, final Set contexts) { + private List mapFields(final TemplateFactory templateFactory, final RelatedEntityWrapper link, + final Set contexts) { final Relation rel = link.getRelation(); final RelatedEntity re = link.getTarget(); final String targetType = link.getTarget().getType(); @@ -1074,6 +1077,15 @@ public class XmlRecordFactory implements Serializable { if (StringUtils.isNotBlank(re.getDescription())) { metadata.add(XmlSerializationUtils.asXmlElement("description", re.getDescription())); } + if (re.getAuthor() != null) { + metadata + .addAll( + re + .getAuthor() + .stream() + .map(author -> XmlSerializationUtils.asXmlElement("creator", author)) + .collect(Collectors.toList())); + } if (isNotBlank(re.getDateofacceptance())) { metadata .add(XmlSerializationUtils.asXmlElement("dateofacceptance", re.getDateofacceptance())); @@ -1107,6 +1119,54 @@ public class XmlRecordFactory implements Serializable { .map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p)) .collect(Collectors.toList())); } + if (re.getInstances() != null) { + re + .getInstances() + .forEach(i -> { + final List instanceFields = Lists.newArrayList(); + if (i.getAccessright() != null && !i.getAccessright().isBlank()) { + instanceFields + .add(XmlSerializationUtils.mapQualifier("accessright", i.getAccessright())); + } + if (i.getHostedby() != null) { + instanceFields.add(XmlSerializationUtils.mapKeyValue("hostedby", i.getHostedby())); + } + if (i.getDateofacceptance() != null && isNotBlank(i.getDateofacceptance().getValue())) { + instanceFields + .add( + XmlSerializationUtils + .asXmlElement("dateofacceptance", i.getDateofacceptance().getValue())); + } + if (i.getInstancetype() != null && !i.getInstancetype().isBlank()) { + instanceFields + .add(XmlSerializationUtils.mapQualifier("instancetype", i.getInstancetype())); + } + + if (i.getRefereed() != null && !i.getRefereed().isBlank()) { + instanceFields.add(XmlSerializationUtils.mapQualifier("refereed", i.getRefereed())); + } + + if (i.getLicense() != null && isNotBlank(i.getLicense().getValue())) { + instanceFields + .add(XmlSerializationUtils.asXmlElement("license", i.getLicense().getValue())); + } + if (isNotBlank(i.getFulltext())) { + instanceFields.add(XmlSerializationUtils.asXmlElement("fulltext", i.getFulltext())); + } + if (i.getUrl() != null && !i.getUrl().isEmpty()) { + instanceFields + .addAll( + i + .getUrl() + .stream() + .filter(StringUtils::isNotBlank) + .map(url -> XmlSerializationUtils.asXmlElement("url", url)) + .collect(Collectors.toList())); + } + metadata.add(templateFactory.getInstance(instanceFields, i.getUrl())); + }); + } + break; case datasource: if (isNotBlank(re.getOfficialname())) { @@ -1188,7 +1248,7 @@ public class XmlRecordFactory implements Serializable { throw new IllegalArgumentException( String.format("missing scheme for: <%s - %s>", type, targetType)); } - final HashSet fields = Sets.newHashSet(mapFields(link, contexts)); + final HashSet fields = Sets.newHashSet(mapFields(templateFactory, link, contexts)); if (rel.getValidated() == null) { rel.setValidated(false); } @@ -1212,7 +1272,7 @@ public class XmlRecordFactory implements Serializable { .map(link -> { final String targetType = link.getTarget().getType(); final String name = ModelSupport.getMainType(EntityType.valueOf(targetType)); - final HashSet fields = Sets.newHashSet(mapFields(link, null)); + final HashSet fields = Sets.newHashSet(mapFields(templateFactory, link, null)); return templateFactory .getChild(name, link.getTarget().getId(), Lists.newArrayList(fields)); }) From 078169b92278ae96802004e0120a0334cd1f158f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 15 Mar 2024 09:56:04 +0100 Subject: [PATCH 23/34] cleanup --- .../dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index 9084f3ae3..da80deee0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -10,7 +10,6 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.hadoop.yarn.webapp.hamlet.Hamlet; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; From 455f2e1e07a2e5382d99e8c9a7b9e0494fab6c61 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 15 Mar 2024 14:56:39 +0100 Subject: [PATCH 24/34] apply commits from master --- .../dhp/collection/plugin/base/BaseCollectorPlugin.java | 9 ++++++++- .../eu/dnetlib/dhp/collection/plugin/base/sql/base.sql | 2 +- .../dhp/collection/plugin/base/sql/opendoar-accepted.sql | 8 +++++--- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java index 0cd68b12a..42341b406 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java @@ -45,15 +45,22 @@ public class BaseCollectorPlugin implements CollectorPlugin { @Override public Stream collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException { - // get path to file + // the path of the dump file on HDFS + // http://oai.base-search.net/initial_load/base_oaipmh_dump-current.tar + // it could be downloaded from iis-cdh5-test-gw.ocean.icm.edu.pl and then copied on HDFS final Path filePath = Optional .ofNullable(api.getBaseUrl()) .map(Path::new) .orElseThrow(() -> new CollectorException("missing baseUrl")); + // get the parameters for the connection to the OpenAIRE database. + // the database is used to obtain the list of the datasources that the plugin will collect final String dbUrl = api.getParams().get("dbUrl"); final String dbUser = api.getParams().get("dbUser"); final String dbPassword = api.getParams().get("dbPassword"); + + // the types(comma separated, empty value for all) that the plugin will collect, + // the types should be expressed in the format of the normalized types of BASE (for example 1,121,...) final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes"); log.info("baseUrl: {}", filePath); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql index b9300f6a8..0303962fd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql @@ -108,7 +108,7 @@ INSERT INTO dsm_apiparams( 'api_________::openaire____::base_search::dump@@acceptedNormTypes', 'api_________::openaire____::base_search::dump', 'acceptedNormTypes', - '' + '1,11,111,121,13,14,15,18,181,182,183,1A,6,7' ); COMMIT; \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql index b7dd835ee..7b3cb9610 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql @@ -2,6 +2,8 @@ select s.id as id from dsm_services s where collectedfrom = 'openaire____::opendoar' and jurisdiction = 'Institutional' -and s.id not in ( - select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%' or last_collection_total > 0 -); \ No newline at end of file +and s.id in ( + select service from dsm_api where coalesce(compatibility_override, compatibility) = 'driver' or coalesce(compatibility_override, compatibility) = 'UNKNOWN' +) and s.id not in ( + select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%' +); From 85b844d57e75af6241047d34a564fa533a28f6c2 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 15 Mar 2024 15:03:27 +0100 Subject: [PATCH 25/34] updated BASE filter param --- .../eu/dnetlib/dhp/collection/plugin/base/sql/base.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql index 0303962fd..9a3012949 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql @@ -108,7 +108,7 @@ INSERT INTO dsm_apiparams( 'api_________::openaire____::base_search::dump@@acceptedNormTypes', 'api_________::openaire____::base_search::dump', 'acceptedNormTypes', - '1,11,111,121,13,14,15,18,181,182,183,1A,6,7' + '1,11,111,121,14,15,18,181,182,183,1A,6,7' ); COMMIT; \ No newline at end of file From cb29b9773c694ac64d00851680479cf8aa574c08 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 18 Mar 2024 15:31:34 +0100 Subject: [PATCH 26/34] xslt rules --- .../base/xml/base2oaf.transformationRule.xml | 158 ++++++++++++++-- .../base/xml/base2odf.transformationRule.xml | 175 +++++++++++++++--- .../plugin/base/BaseTransfomationTest.java | 9 +- 3 files changed, 301 insertions(+), 41 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml index 7a09fec2e..cee649805 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml @@ -66,10 +66,6 @@ dc:language (I used base_dc:lang) base_dc:link (I used dc:identifier) --> - - - - @@ -112,9 +108,13 @@ base_dc:link (I used dc:identifier) - - - + + + + + + + @@ -162,12 +162,144 @@ base_dc:link (I used dc:identifier) - - - - - - + + + + + + 0013 + + + + + 0002 + + + + + 0001 + + + + + + 0043 + + + + + 0017 + + + + + 0015 + + + + + 0010 + + + + + 0008 + + + + + 0007 + + + + + 0006 + + + + + 0044 + + + + + 0019 + + + + + 0001 + + + + + 0029 + + + + + 0021 + + + + + 0025 + + + + + 0024 + + + + + 0033 + + + + + 0030 + + + + + 0020 + + + + + 0020 + + + + + 0038 + + + + + 0038 + + + + + 0038 + + + + + 0004 + + + + + 0000 + + + 0000 + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml index 917a351b3..4565b81f5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml @@ -51,10 +51,6 @@ base_dc:link (I used dc:identifier) --> - - - - @@ -93,7 +89,9 @@ - + + + @@ -185,26 +183,157 @@ - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - + + + + + + 0013 + + + + + 0002 + + + + + 0001 + + + + + + 0043 + + + + + 0017 + + + + + 0015 + + + + + 0010 + + + + + 0008 + + + + + 0007 + + + + + 0006 + + + + + 0044 + + + + + 0019 + + + + + 0001 + + + + + 0029 + + + + + 0021 + + + + + 0025 + + + + + 0024 + + + + + 0033 + + + + 0030 + + + + + 0020 + + + + + 0020 + + + + + 0038 + + + + + 0038 + + + + + 0038 + + + + + 0004 + + + + + 0000 + + + 0000 + + + OPEN diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java index f4539014d..2bbd87117 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java @@ -8,7 +8,6 @@ import org.apache.spark.SparkConf; import org.apache.spark.util.LongAccumulator; import org.dom4j.io.SAXReader; import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.junit.jupiter.MockitoExtension; @@ -20,7 +19,7 @@ import eu.dnetlib.dhp.schema.mdstore.Provenance; import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -@Disabled +// @Disabled @ExtendWith(MockitoExtension.class) public class BaseTransfomationTest extends AbstractVocabularyTest { @@ -66,9 +65,9 @@ public class BaseTransfomationTest extends AbstractVocabularyTest { private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String xslt = new SAXReader() - .read(this.getClass().getResourceAsStream(path)) - .selectSingleNode("//CODE/*") - .asXML(); + .read(this.getClass().getResourceAsStream(path)) + .selectSingleNode("//CODE/*") + .asXML(); final LongAccumulator la = new LongAccumulator(); From 664a381d31415afa9e847e524f45fd8330c7c70d Mon Sep 17 00:00:00 2001 From: Giambattista Bloisi Date: Thu, 14 Dec 2023 11:43:58 +0100 Subject: [PATCH 27/34] Unify merge logic of entities in MergeUtils.class --- .../dhp/oa/merge/GroupEntitiesSparkJob.java | 289 ++++--- .../dhp/schema/oaf/utils/MergeComparator.java | 79 ++ .../dhp/schema/oaf/utils/MergeUtils.java | 707 ++++++++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 60 -- .../dhp/schema/oaf/utils/MergeUtilsTest.java | 111 +++ .../schema/oaf/utils/OafMapperUtilsTest.java | 12 +- .../actionmanager/promote/MergeAndGet.java | 24 +- .../score/deserializers/BipProjectModel.java | 5 + .../project/SparkAtomicActionJob.java | 50 +- .../dhp/oa/dedup/DedupRecordFactory.java | 312 ++++---- .../dhp/oa/dedup/SparkPropagateRelation.java | 7 +- .../doiboost/SparkGenerateDoiBoost.scala | 18 +- .../dnetlib/doiboost/mag/MagDataModel.scala | 7 +- ...kResultToCommunityFromOrganizationJob.java | 2 +- .../SparkResultToCommunityFromProject.java | 5 +- ...parkResultToCommunityThroughSemRelJob.java | 184 ++--- .../graph/merge/MergeGraphTableSparkJob.java | 6 +- .../raw/GenerateEntitiesApplication.java | 43 +- .../resolution/SparkResolveEntities.scala | 8 +- .../dhp/sx/graph/SparkCreateInputGraph.scala | 6 +- .../raw/GenerateEntitiesApplicationTest.java | 28 +- 21 files changed, 1389 insertions(+), 574 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java create mode 100644 dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index 0225a5063..eadca231e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -1,24 +1,6 @@ package eu.dnetlib.dhp.oa.merge; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.spark.sql.functions.col; -import static org.apache.spark.sql.functions.when; - -import java.util.Map; -import java.util.Optional; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ForkJoinPool; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.ReduceFunction; -import org.apache.spark.sql.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -26,169 +8,186 @@ import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.ReduceFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; +import java.util.Map; +import java.util.Optional; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.ForkJoinPool; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.col; +import static org.apache.spark.sql.functions.when; + /** * Groups the graph content by entity identifier to ensure ID uniqueness */ public class GroupEntitiesSparkJob { - private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); - private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); - private ArgumentApplicationParser parser; + private ArgumentApplicationParser parser; - public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { - this.parser = parser; - } + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - GroupEntitiesSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + GroupEntitiesSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); - final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); - new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); - } + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } - public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) - throws ISLookUpException { + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { - String graphInputPath = parser.get("graphInputPath"); - log.info("graphInputPath: {}", graphInputPath); + String graphInputPath = parser.get("graphInputPath"); + log.info("graphInputPath: {}", graphInputPath); - String checkpointPath = parser.get("checkpointPath"); - log.info("checkpointPath: {}", checkpointPath); + String checkpointPath = parser.get("checkpointPath"); + log.info("checkpointPath: {}", checkpointPath); - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); - log.info("filterInvisible: {}", filterInvisible); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); + log.info("filterInvisible: {}", filterInvisible); - SparkConf conf = new SparkConf(); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); + }); + } - private static void groupEntities( - SparkSession spark, - String inputPath, - String checkpointPath, - String outputPath, - boolean filterInvisible, VocabularyGroup vocs) { + private static void groupEntities( + SparkSession spark, + String inputPath, + String checkpointPath, + String outputPath, + boolean filterInvisible, VocabularyGroup vocs) { - Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); + Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); - String entityInputPath = inputPath + "/" + entity; + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); + String entityInputPath = inputPath + "/" + entity; - if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { - continue; - } + if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { + continue; + } - allEntities = allEntities - .union( - ((Dataset) spark - .read() - .schema(Encoders.bean(entityClass).schema()) - .json(entityInputPath) - .filter("length(id) > 0") - .as(Encoders.bean(entityClass))) - .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); - } + allEntities = allEntities + .union( + ((Dataset) spark + .read() + .schema(Encoders.bean(entityClass).schema()) + .json(entityInputPath) + .filter("length(id) > 0") + .as(Encoders.bean(entityClass))) + .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); + } - Dataset groupedEntities = allEntities - .map( - (MapFunction) entity -> GraphCleaningFunctions - .applyCoarVocabularies(entity, vocs), - OAFENTITY_KRYO_ENC) - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) - .map( - (MapFunction, Tuple2>) t -> new Tuple2<>( - t._2().getClass().getName(), t._2()), - Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); + Dataset groupedEntities = allEntities + .map( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) MergeUtils::checkedMerge) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( + t._2().getClass().getName(), t._2()), + Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); - // pivot on "_1" (classname of the entity) - // created columns containing only entities of the same class - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + // pivot on "_1" (classname of the entity) + // created columns containing only entities of the same class + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - groupedEntities = groupedEntities - .withColumn( - entity, - when(col("_1").equalTo(entityClass.getName()), col("_2"))); - } + groupedEntities = groupedEntities + .withColumn( + entity, + when(col("_1").equalTo(entityClass.getName()), col("_2"))); + } - groupedEntities - .drop("_1", "_2") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .save(checkpointPath); + groupedEntities + .drop("_1", "_2") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .save(checkpointPath); - ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); + ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); - ModelSupport.entityTypes - .entrySet() - .stream() - .map(e -> parPool.submit(() -> { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + ModelSupport.entityTypes + .entrySet() + .stream() + .map(e -> parPool.submit(() -> { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - spark - .read() - .load(checkpointPath) - .select(col(entity).as("value")) - .filter("value IS NOT NULL") - .as(OAFENTITY_KRYO_ENC) - .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) - .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + entity); - })) - .collect(Collectors.toList()) - .forEach(t -> { - try { - t.get(); - } catch (InterruptedException | ExecutionException e) { - throw new RuntimeException(e); - } - }); - } + spark + .read() + .load(checkpointPath) + .select(col(entity).as("value")) + .filter("value IS NOT NULL") + .as(OAFENTITY_KRYO_ENC) + .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) + .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + entity); + })) + .collect(Collectors.toList()) + .forEach(t -> { + try { + t.get(); + } catch (InterruptedException | ExecutionException e) { + throw new RuntimeException(e); + } + }); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java new file mode 100644 index 000000000..ffb0e600a --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java @@ -0,0 +1,79 @@ +package eu.dnetlib.dhp.schema.oaf.utils; + +// +// Source code recreated from a .class file by IntelliJ IDEA +// (powered by FernFlower decompiler) +// + + +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; + +import java.util.Comparator; +import java.util.HashSet; +import java.util.Optional; +import java.util.stream.Collectors; + +public class MergeComparator implements Comparator { + public MergeComparator() { + } + + public int compare(Oaf left, Oaf right) { + // nulls at the end + if (left == null && right == null) { + return 0; + } else if (left == null) { + return -1; + } else if (right == null) { + return 1; + } + + // invisible + if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) { + if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) { + return -1; + } + } + + // collectedfrom + HashSet lCf = getCollectedFromIds(left); + HashSet rCf = getCollectedFromIds(right); + if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return -1; + } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return 1; + } + + + + SubEntityType lClass = SubEntityType.fromClass(left.getClass()); + SubEntityType rClass = SubEntityType.fromClass(right.getClass()); + return lClass.ordinal() - rClass.ordinal(); + + } + + protected HashSet getCollectedFromIds(Oaf left) { + return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> { + return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); + }).orElse(new HashSet()); + } + + enum SubEntityType { + publication, dataset, software, otherresearchproduct, datasource, organization, project; + + /** + * Resolves the EntityType, given the relative class name + * + * @param clazz the given class name + * @param actual OafEntity subclass + * @return the EntityType associated to the given class + */ + public static SubEntityType fromClass(Class clazz) { + return valueOf(clazz.getSimpleName().toLowerCase()); + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java new file mode 100644 index 000000000..072a86bf1 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -0,0 +1,707 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import eu.dnetlib.dhp.schema.common.AccessRightComparator; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.tuple.ImmutablePair; +import org.apache.commons.lang3.tuple.Pair; + +import java.text.ParseException; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static com.google.common.base.Objects.firstNonNull; +import static com.google.common.base.Preconditions.checkArgument; + +public class MergeUtils { + + public static T checkedMerge(final T left, final T right) { + return (T) merge(left, right, false); + } + + public static Oaf merge(final Oaf left, final Oaf right) { + return merge(left, right, false); + } + + public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) { + if (sameClass(left, right, OafEntity.class)) { + return mergeEntities(left, right, checkDelegatedAuthority); + } else if (sameClass(left, right, Relation.class)) { + return mergeRelation((Relation) left, (Relation) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } + + private static boolean sameClass(Object left, Object right, Class cls) { + return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass()); + } + + private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) { + + if (sameClass(left, right, Result.class)) { + if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) { + return mergeResultsOfDifferentTypes((Result)left, (Result) right); + } + + if (sameClass(left, right, Publication.class)) { + return mergePublication((Publication) left, (Publication) right); + } + if (sameClass(left, right, Dataset.class)) { + return mergeDataset((Dataset) left, (Dataset) right); + } + if (sameClass(left, right, OtherResearchProduct.class)) { + return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right); + } + if (sameClass(left, right, Software.class)) { + return mergeSoftware((Software) left, (Software) right); + } + + return mergeResult((Result) left, (Result) right); + } else if (sameClass(left, right, Datasource.class)) { + // TODO + final int trust = compareTrust(left, right); + return mergeOafEntityFields((Datasource) left, (Datasource) right, trust); + } else if (sameClass(left, right, Organization.class)) { + return mergeOrganization((Organization) left, (Organization) right); + } else if (sameClass(left, right, Project.class)) { + return mergeProject((Project) left, (Project) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } + + /** + * This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority + * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers + * such version. + *

    + * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator} + * and proceeds with the canonical property merging. + * + * @param left + * @param right + * @return + */ + private static T mergeResultsOfDifferentTypes(T left, T right) { + + final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); + final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); + + if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { + return left; + } + if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { + return right; + } + //TODO: raise trust to have preferred fields from one or the other?? + if (new ResultTypeComparator().compare(left, right) < 0) { + return mergeResult(left, right); + } else { + return mergeResult(right, left); + } + } + + private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) { + return right; + } else { + return left; + } + } else { + return right; + } + } + + private static String chooseString(String left, String right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return StringUtils.isNotBlank(left) ? left : right; + } else { + return right; + } + } + + private static T chooseReference(T left, T right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return left != null ? left : right; + } else { + return right; + } + } + + private static Long max(Long left, Long right) { + if (left == null) + return right; + if (right == null) + return left; + + return Math.max(left, right); + } + + // trust ?? + private static Boolean booleanOR(Boolean a, Boolean b) { + if (a == null) { + return b; + } else if (b == null) { + return a; + } + + return a || b; + } + + + private static List unionDistinctLists(final List left, final List right, int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream.concat(h.stream(), l.stream()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + + private static List unionDistinctListOfString(final List l, final List r) { + if (l == null) { + return r; + } else if (r == null) { + return l; + } + + return Stream.concat(l.stream(), r.stream()) + .filter(StringUtils::isNotBlank) + .distinct() + .collect(Collectors.toList()); + } + + //TODO review + private static List mergeKeyValue(List left, List right, int trust) { + if (trust < 0) { + List s = left; + left = right; + right = s; + } + + HashMap values = new HashMap<>(); + left.forEach(kv -> values.put(kv.getKey(), kv)); + right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv)); + + return new ArrayList<>(values.values()); + } + + private static List unionTitle(List left, List right, int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream.concat(h.stream(), l.stream()) + .filter(Objects::isNull) + .distinct() + .collect(Collectors.toList()); + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param merged + * @param enrich + * @param + * @return + */ + private static T mergeOafFields(T merged, T enrich, int trust) { + + //TODO: union of all values, but what does it mean with KeyValue pairs??? + merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust)); + merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust)); + merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp())); + + return merged; + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param original + * @param enrich + * @param + * @return + */ + private static T mergeOafEntityFields(T original, T enrich, int trust) { + final T merged = mergeOafFields(original, enrich, trust); + + merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId())); + merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust)); + // dateofcollection mettere today quando si fa merge + merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust)); + // setDateoftransformation mettere vuota in dedup, nota per Claudio + merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust)); + // TODO: was missing in OafEntity.merge + merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust)); + //oaiprovenanze da mettere a null quando si genera merge + merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust)); + merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust)); + + return merged; + } + + + public static T mergeRelation(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeOafFields(original, enrich, trust); + + checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal"); + checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal"); + checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal"); + checkArgument( + Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal"); + checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal"); + + //merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance())); + + //TODO: trust ?? + merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated())); + try { + merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate())); + } catch (ParseException e) { + throw new IllegalArgumentException(String + .format( + "invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(), + merge.getTarget(), + merge.getValidationDate())); + } + + // TODO keyvalue merge + merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust)); + + return merge; + } + + public static T mergeResult(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merge = mergeOafEntityFields(original, enrich, trust); + + if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) { + merge.setProcessingchargeamount(enrich.getProcessingchargeamount()); + merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency()); + } + + // author = usare la stessa logica che in dedup + merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust)); + // il primo che mi arriva secondo l'ordinamento per priorita' + merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust)); + // gestito come il resulttype perche' e' un subtype + merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust)); + // spostiamo nell'instance e qui prendo il primo che arriva + merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust)); + // country lasicamo,o cosi' -> parentesi sul datainfo + merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust)); + //ok + merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust)); + // union per priority quindi vanno in append + merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust)); + //ok + merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust)); + // prima trust e poi longest list + merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription())); + // trust piu' alto e poi piu' vecchia + merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust)); + // ok, ma publisher va messo ripetibile + merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust)); + // ok + merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust)); + // ok + merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust)); + // ok + merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust)); + // ok + merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust)); + // ok + merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust)); + + // prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO + // trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario) + // vedi note + merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype())); + + // ok + merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust)); + + // most open ok + if (enrich.getBestaccessright() != null + && new AccessRightComparator<>() + .compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) { + merge.setBestaccessright(enrich.getBestaccessright()); + } + + // TODO merge of datainfo given same id + merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust)); + + //ok + merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust)); + + //instance enrichment or union + // review instance equals => add pid to comparision + if (!isAnEnrichment(merge) && !isAnEnrichment(enrich)) + merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust)); + else { + final List enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance() + : enrich.getInstance(); + final List enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance() + : merge.getInstance(); + if (isAnEnrichment(merge)) + merge.setDataInfo(enrich.getDataInfo()); + merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances)); + } + + merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust)); + merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen())); + // OK but should be list of values + merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust)); + merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal())); + merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded())); + + return merge; + } + + private static T mergeORP(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust)); + merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust)); + merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust)); + + return merge; + } + + private static T mergeSoftware(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust)); + merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust)); + merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust)); + merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust)); + + return merge; + } + + private static T mergeDataset(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeResult(original, enrich); + + merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust)); + merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust)); + merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust)); + merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust)); + merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust)); + merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust)); + merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust)); + + return merge; + } + + public static T mergePublication(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merged = mergeResult(original, enrich); + + merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust)); + + return merged; + } + + private static T mergeOrganization(T left, T enrich) { + int trust = compareTrust(left, enrich); + T merged = mergeOafEntityFields(left, enrich, trust); + + merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust)); + merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust)); + merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust)); + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust)); + merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust)); + merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust)); + merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust)); + merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust)); + merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust)); + merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust)); + merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust)); + merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust)); + merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust)); + merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust)); + merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust)); + + return merged; + } + + public static T mergeProject(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merged = mergeOafEntityFields(original, enrich, trust); + + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust)); + merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust)); + merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust)); + merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust)); + merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust)); + merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust)); + merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust)); + merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust)); + merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust)); + merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust)); + merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust)); + merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust)); + merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust)); + merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust)); + merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust)); + merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust)); + merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust)); + merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust)); + merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust)); + merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust)); + merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust)); + merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust)); + merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust)); + + //missin in Project.merge + merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust)); + merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust)); + + // trust ?? + if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) { + merged.setH2020topiccode(enrich.getH2020topiccode()); + merged.setH2020topicdescription(enrich.getH2020topicdescription()); + } + + merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust)); + + return merged; + } + + + /** + * Longest lists list. + * + * @param a the a + * @param b the b + * @return the list + */ + public static List> longestLists(List> a, List> b) { + if (a == null || b == null) + return a == null ? b : a; + + return a.size() >= b.size() ? a : b; + } + + /** + * This main method apply the enrichment of the instances + * + * @param toEnrichInstances the instances that could be enriched + * @param enrichmentInstances the enrichment instances + * @return list of instances possibly enriched + */ + private static List enrichInstances(final List toEnrichInstances, + final List enrichmentInstances) { + final List enrichmentResult = new ArrayList<>(); + + if (toEnrichInstances == null) { + return enrichmentResult; + } + if (enrichmentInstances == null) { + return enrichmentResult; + } + Map ri = toInstanceMap(enrichmentInstances); + + toEnrichInstances.forEach(i -> { + final List e = findEnrichmentsByPID(i.getPid(), ri); + if (e != null && e.size() > 0) { + e.forEach(enr -> applyEnrichment(i, enr)); + } else { + final List a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri); + if (a != null && a.size() > 0) { + a.forEach(enr -> applyEnrichment(i, enr)); + } + } + enrichmentResult.add(i); + }); + return enrichmentResult; + } + + /** + * This method converts the list of instance enrichments + * into a Map where the key is the normalized identifier + * and the value is the instance itself + * + * @param ri the list of enrichment instances + * @return the result map + */ + private static Map toInstanceMap(final List ri) { + return ri + .stream() + .filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null) + .flatMap(i -> { + final List> result = new ArrayList<>(); + if (i.getPid() != null) + i + .getPid() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + if (i.getAlternateIdentifier() != null) + i + .getAlternateIdentifier() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + return result.stream(); + }) + .collect( + Collectors + .toMap( + Pair::getLeft, + Pair::getRight, + (a, b) -> a)); + } + + private static boolean isFromDelegatedAuthority(Result r) { + return Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .filter(i -> Objects.nonNull(i.getCollectedfrom())) + .map(i -> i.getCollectedfrom().getKey()) + .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) + .orElse(false); + } + + /** + * Valid pid boolean. + * + * @param p the p + * @return the boolean + */ + private static boolean validPid(final StructuredProperty p) { + return p.getValue() != null && p.getQualifier() != null && p.getQualifier().getClassid() != null; + } + + /** + * Normalize pid string. + * + * @param pid the pid + * @return the string + */ + private static String extractKeyFromPid(final StructuredProperty pid) { + if (pid == null) + return null; + final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid); + + return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue()); + } + + /** + * This utility method finds the list of enrichment instances + * that match one or more PIDs in the input list + * + * @param pids the list of PIDs + * @param enrichments the List of enrichment instances having the same pid + * @return the list + */ + private static List findEnrichmentsByPID(final List pids, + final Map enrichments) { + if (pids == null || enrichments == null) + return null; + return pids + .stream() + .map(MergeUtils::extractKeyFromPid) + .map(enrichments::get) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } + + /** + * Is an enrichment boolean. + * + * @param e the e + * @return the boolean + */ + private static boolean isAnEnrichment(OafEntity e) { + return e.getDataInfo() != null && + e.getDataInfo().getProvenanceaction() != null + && ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid()); + } + + /** + * This method apply enrichment on a single instance + * The enrichment consists of replacing values on + * single attribute only if in the current instance is missing + * The only repeatable field enriched is measures + * + * @param merge the current instance + * @param enrichment the enrichment instance + */ + private static void applyEnrichment(final Instance merge, final Instance enrichment) { + if (merge == null || enrichment == null) + return; + + merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense())); + merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright())); + merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype())); + merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping())); + merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby())); + merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0)); + merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation())); + merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom())); + // pid and alternateId are used for matching + merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance())); + merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount())); + merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency())); + merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed())); + merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0)); + merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext())); + } + + private static int compareTrust(Oaf a, Oaf b) { + String left = Optional + .ofNullable(a.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + String right = Optional + .ofNullable(b.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + return left.compareTo(right); + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 4cecd0895..417516b0f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -14,7 +14,6 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; -import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; public class OafMapperUtils { @@ -22,65 +21,6 @@ public class OafMapperUtils { private OafMapperUtils() { } - public static Oaf merge(final Oaf left, final Oaf right) { - if (ModelSupport.isSubClass(left, OafEntity.class)) { - return mergeEntities((OafEntity) left, (OafEntity) right); - } else if (ModelSupport.isSubClass(left, Relation.class)) { - ((Relation) left).mergeFrom((Relation) right); - } else { - throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName()); - } - return left; - } - - public static OafEntity mergeEntities(OafEntity left, OafEntity right) { - if (ModelSupport.isSubClass(left, Result.class)) { - return mergeResults((Result) left, (Result) right); - } else if (ModelSupport.isSubClass(left, Datasource.class)) { - left.mergeFrom(right); - } else if (ModelSupport.isSubClass(left, Organization.class)) { - left.mergeFrom(right); - } else if (ModelSupport.isSubClass(left, Project.class)) { - left.mergeFrom(right); - } else { - throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName()); - } - return left; - } - - public static Result mergeResults(Result left, Result right) { - - final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); - final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); - - if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { - return left; - } - if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { - return right; - } - - if (new ResultTypeComparator().compare(left, right) < 0) { - left.mergeFrom(right); - return left; - } else { - right.mergeFrom(left); - return right; - } - } - - private static boolean isFromDelegatedAuthority(Result r) { - return Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .filter(i -> Objects.nonNull(i.getCollectedfrom())) - .map(i -> i.getCollectedfrom().getKey()) - .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) - .orElse(false); - } - public static KeyValue keyValue(final String k, final String v) { final KeyValue kv = new KeyValue(); kv.setKey(k); diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java new file mode 100644 index 000000000..ef35b50fb --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java @@ -0,0 +1,111 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.util.HashSet; +import java.util.List; +import java.util.stream.Collectors; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class MergeUtilsTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Test + void testMergePubs() throws IOException { + Publication p1 = read("publication_1.json", Publication.class); + Publication p2 = read("publication_2.json", Publication.class); + Dataset d1 = read("dataset_1.json", Dataset.class); + Dataset d2 = read("dataset_2.json", Dataset.class); + + assertEquals(1, p1.getCollectedfrom().size()); + assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey()); + assertEquals(1, d2.getCollectedfrom().size()); + assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + + assertEquals(1, p2.getCollectedfrom().size()); + assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + assertEquals(1, d1.getCollectedfrom().size()); + assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); + + final Result p1d2 = MergeUtils.checkedMerge(p1, d2); + assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid()); + assertTrue(p1d2 instanceof Publication); + assertEquals(p1.getId(), p1d2.getId()); + } + + @Test + void testMergePubs_1() throws IOException { + Publication p2 = read("publication_2.json", Publication.class); + Dataset d1 = read("dataset_1.json", Dataset.class); + + final Result p2d1 = MergeUtils.checkedMerge(p2, d1); + assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid()); + assertTrue(p2d1 instanceof Dataset); + assertEquals(d1.getId(), p2d1.getId()); + assertEquals(2, p2d1.getCollectedfrom().size()); + } + + @Test + void testMergePubs_2() throws IOException { + Publication p1 = read("publication_1.json", Publication.class); + Publication p2 = read("publication_2.json", Publication.class); + + Result p1p2 = MergeUtils.checkedMerge(p1, p2); + assertTrue(p1p2 instanceof Publication); + assertEquals(p1.getId(), p1p2.getId()); + assertEquals(2, p1p2.getCollectedfrom().size()); + } + + @Test + void testDelegatedAuthority_1() throws IOException { + Dataset d1 = read("dataset_2.json", Dataset.class); + Dataset d2 = read("dataset_delegated.json", Dataset.class); + + assertEquals(1, d2.getCollectedfrom().size()); + assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); + + Result res = (Result) MergeUtils.merge(d1, d2, true); + + assertEquals(d2, res); + } + + @Test + void testDelegatedAuthority_2() throws IOException { + Dataset p1 = read("publication_1.json", Dataset.class); + Dataset d2 = read("dataset_delegated.json", Dataset.class); + + assertEquals(1, d2.getCollectedfrom().size()); + assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); + + Result res = (Result) MergeUtils.merge(p1, d2, true); + + assertEquals(d2, res); + } + + protected HashSet cfId(List collectedfrom) { + return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); + } + + protected T read(String filename, Class clazz) throws IOException { + final String json = IOUtils.toString(getClass().getResourceAsStream(filename)); + return OBJECT_MAPPER.readValue(json, clazz); + } + +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index 9111ac2df..2bbc3bc3e 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -149,7 +149,7 @@ class OafMapperUtilsTest { void testDate() { final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998"); assertNotNull(date); - System.out.println(date); + assertEquals("1998-02-23", date); } @Test @@ -166,8 +166,8 @@ class OafMapperUtilsTest { assertEquals( ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, - OafMapperUtils - .mergeResults(p1, d2) + MergeUtils + .mergeResult(p1, d2) .getResulttype() .getClassid()); @@ -178,8 +178,8 @@ class OafMapperUtilsTest { assertEquals( ModelConstants.DATASET_RESULTTYPE_CLASSID, - OafMapperUtils - .mergeResults(p2, d1) + MergeUtils + .mergeResult(p2, d1) .getResulttype() .getClassid()); } @@ -192,7 +192,7 @@ class OafMapperUtilsTest { assertEquals(1, d2.getCollectedfrom().size()); assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); - Result res = OafMapperUtils.mergeResults(d1, d2); + Result res = MergeUtils.mergeResult(d1, d2); assertEquals(d2, res); diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java index eccfa445c..6de631173 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java @@ -1,14 +1,13 @@ package eu.dnetlib.dhp.actionmanager.promote; -import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import java.util.function.BiFunction; -import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Relation; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; /** OAF model merging support. */ public class MergeAndGet { @@ -46,20 +45,7 @@ public class MergeAndGet { } private static G mergeFromAndGet(G x, A y) { - if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { - ((Relation) x).mergeFrom((Relation) y); - return x; - } else if (isSubClass(x, OafEntity.class) - && isSubClass(y, OafEntity.class) - && isSubClass(x, y)) { - ((OafEntity) x).mergeFrom((OafEntity) y); - return x; - } - throw new RuntimeException( - String - .format( - "MERGE_FROM_AND_GET incompatible types: %s, %s", - x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + return (G) MergeUtils.merge(x, y); } @SuppressWarnings("unchecked") diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java index 680e12504..a41540564 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java @@ -34,6 +34,11 @@ public class BipProjectModel { String totalCitationCount; + public String getProjectId() { + return projectId; + } + + // each project bip measure has exactly one value, hence one key-value pair private Measure createMeasure(String measureId, String measureValue) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index a32d04e1f..21f3044a5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -1,12 +1,20 @@ package eu.dnetlib.dhp.actionmanager.project; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Arrays; -import java.util.Objects; -import java.util.Optional; - +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject; +import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic; +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.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.H2020Classification; +import eu.dnetlib.dhp.schema.oaf.H2020Programme; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -18,24 +26,14 @@ 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.project.utils.model.CSVProgramme; -import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject; -import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic; -import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic; -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.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.H2020Classification; -import eu.dnetlib.dhp.schema.oaf.H2020Programme; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; +import java.util.Arrays; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + /** * Class that makes the ActionSet. To prepare the AS two joins are needed * @@ -160,9 +158,11 @@ public class SparkAtomicActionJob { (MapFunction) OafEntity::getId, Encoders.STRING()) .mapGroups((MapGroupsFunction) (s, it) -> { - Project first = it.next(); - it.forEachRemaining(first::mergeFrom); - return first; + Project merge = it.next(); + while (it.hasNext()) { + merge = MergeUtils.mergeProject(merge, it.next()); + } + return merge; }, Encoders.bean(Project.class)) .toJavaRDD() .map(p -> new AtomicAction(Project.class, p)) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d5b106c81..35fa61b94 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.dedup; import java.util.*; import java.util.stream.Stream; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.FlatMapFunction; @@ -14,6 +15,7 @@ import org.apache.spark.sql.*; import eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.OafEntity; @@ -23,190 +25,190 @@ import scala.Tuple3; import scala.collection.JavaConversions; public class DedupRecordFactory { - public static final class DedupRecordReduceState { - public final String dedupId; + public static final class DedupRecordReduceState { + public final String dedupId; - public final ArrayList aliases = new ArrayList<>(); + public final ArrayList aliases = new ArrayList<>(); - public final HashSet acceptanceDate = new HashSet<>(); + public final HashSet acceptanceDate = new HashSet<>(); - public OafEntity entity; + public OafEntity entity; - public DedupRecordReduceState(String dedupId, String id, OafEntity entity) { - this.dedupId = dedupId; - this.entity = entity; - if (entity == null) { - aliases.add(id); - } else { - if (Result.class.isAssignableFrom(entity.getClass())) { - Result result = (Result) entity; - if (result.getDateofacceptance() != null - && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { - acceptanceDate.add(result.getDateofacceptance().getValue()); - } - } - } - } + public DedupRecordReduceState(String dedupId, String id, OafEntity entity) { + this.dedupId = dedupId; + this.entity = entity; + if (entity == null) { + aliases.add(id); + } else { + if (Result.class.isAssignableFrom(entity.getClass())) { + Result result = (Result) entity; + if (result.getDateofacceptance() != null + && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) { + acceptanceDate.add(result.getDateofacceptance().getValue()); + } + } + } + } - public String getDedupId() { - return dedupId; - } - } + public String getDedupId() { + return dedupId; + } + } - private static final int MAX_ACCEPTANCE_DATE = 20; + private static final int MAX_ACCEPTANCE_DATE = 20; - private DedupRecordFactory() { - } + private DedupRecordFactory() { + } - public static Dataset createDedupRecord( - final SparkSession spark, - final DataInfo dataInfo, - final String mergeRelsInputPath, - final String entitiesInputPath, - final Class clazz) { + public static Dataset createDedupRecord( + final SparkSession spark, + final DataInfo dataInfo, + final String mergeRelsInputPath, + final String entitiesInputPath, + final Class clazz) { - final long ts = System.currentTimeMillis(); - final Encoder beanEncoder = Encoders.bean(clazz); - final Encoder kryoEncoder = Encoders.kryo(clazz); + final long ts = System.currentTimeMillis(); + final Encoder beanEncoder = Encoders.bean(clazz); + final Encoder kryoEncoder = Encoders.kryo(clazz); - // - Dataset entities = spark - .read() - .schema(Encoders.bean(clazz).schema()) - .json(entitiesInputPath) - .as(beanEncoder) - .map( - (MapFunction>) entity -> { - return new Tuple2<>(entity.getId(), entity); - }, - Encoders.tuple(Encoders.STRING(), kryoEncoder)) - .selectExpr("_1 AS id", "_2 AS kryoObject"); + // + Dataset entities = spark + .read() + .schema(Encoders.bean(clazz).schema()) + .json(entitiesInputPath) + .as(beanEncoder) + .map( + (MapFunction>) entity -> { + return new Tuple2<>(entity.getId(), entity); + }, + Encoders.tuple(Encoders.STRING(), kryoEncoder)) + .selectExpr("_1 AS id", "_2 AS kryoObject"); - // : source is the dedup_id, target is the id of the mergedIn - Dataset mergeRels = spark - .read() - .load(mergeRelsInputPath) - .where("relClass == 'merges'") - .selectExpr("source as dedupId", "target as id"); + // : source is the dedup_id, target is the id of the mergedIn + Dataset mergeRels = spark + .read() + .load(mergeRelsInputPath) + .where("relClass == 'merges'") + .selectExpr("source as dedupId", "target as id"); - return mergeRels - .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left") - .select("dedupId", "id", "kryoObject") - .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder)) - .map( - (MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState( - t._1(), t._2(), t._3()), - Encoders.kryo(DedupRecordReduceState.class)) - .groupByKey( - (MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) - .reduceGroups( - (ReduceFunction) (t1, t2) -> { - if (t1.entity == null) { - t2.aliases.addAll(t1.aliases); - return t2; - } - if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) { - t1.acceptanceDate.addAll(t2.acceptanceDate); - } - t1.aliases.addAll(t2.aliases); - t1.entity = reduceEntity(t1.entity, t2.entity); + return mergeRels + .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left") + .select("dedupId", "id", "kryoObject") + .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder)) + .map( + (MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState( + t._1(), t._2(), t._3()), + Encoders.kryo(DedupRecordReduceState.class)) + .groupByKey( + (MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) + .reduceGroups( + (ReduceFunction) (t1, t2) -> { + if (t1.entity == null) { + t2.aliases.addAll(t1.aliases); + return t2; + } + if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) { + t1.acceptanceDate.addAll(t2.acceptanceDate); + } + t1.aliases.addAll(t2.aliases); + t1.entity = reduceEntity(t1.entity, t2.entity); - return t1; - }) - .flatMap((FlatMapFunction, OafEntity>) t -> { - String dedupId = t._1(); - DedupRecordReduceState agg = t._2(); + return t1; + }) + .flatMap((FlatMapFunction, OafEntity>) t -> { + String dedupId = t._1(); + DedupRecordReduceState agg = t._2(); - if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { - return Collections.emptyIterator(); - } + if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { + return Collections.emptyIterator(); + } - return Stream - .concat( - Stream - .of(agg.getDedupId()) - .map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)), - agg.aliases - .stream() - .map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts))) - .iterator(); - }, beanEncoder); - } + return Stream + .concat( + Stream + .of(agg.getDedupId()) + .map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)), + agg.aliases + .stream() + .map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts))) + .iterator(); + }, beanEncoder); + } - private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { - try { - OafEntity res = (OafEntity) BeanUtils.cloneBean(base); - res.setId(id); - res.setDataInfo(dataInfo); - res.setLastupdatetimestamp(ts); - return res; - } catch (Exception e) { - throw new RuntimeException(e); - } - } + private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { + try { + OafEntity res = (OafEntity) BeanUtils.cloneBean(base); + res.setId(id); + res.setDataInfo(dataInfo); + res.setLastupdatetimestamp(ts); + return res; + } catch (Exception e) { + throw new RuntimeException(e); + } + } - private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { - try { - OafEntity res = createDedupOafEntity(id, base, dataInfo, ts); - DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo); - ds.setDeletedbyinference(true); - res.setDataInfo(ds); - return res; - } catch (Exception e) { - throw new RuntimeException(e); - } - } + private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) { + try { + OafEntity res = createDedupOafEntity(id, base, dataInfo, ts); + DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo); + ds.setDeletedbyinference(true); + res.setDataInfo(ds); + return res; + } catch (Exception e) { + throw new RuntimeException(e); + } + } - private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) { + private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) { - if (duplicate == null) { - return entity; - } + if (duplicate == null) { + return entity; + } - int compare = new IdentifierComparator<>() - .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); + int compare = new IdentifierComparator<>() + .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); - if (compare > 0) { - OafEntity swap = duplicate; - duplicate = entity; - entity = swap; - } + if (compare > 0) { + OafEntity swap = duplicate; + duplicate = entity; + entity = swap; + } - entity.mergeFrom(duplicate); + entity = MergeUtils.checkedMerge(entity, duplicate); - if (ModelSupport.isSubClass(duplicate, Result.class)) { - Result re = (Result) entity; - Result rd = (Result) duplicate; + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result re = (Result) entity; + Result rd = (Result) duplicate; - List> authors = new ArrayList<>(); - if (re.getAuthor() != null) { - authors.add(re.getAuthor()); - } - if (rd.getAuthor() != null) { - authors.add(rd.getAuthor()); - } + List> authors = new ArrayList<>(); + if (re.getAuthor() != null) { + authors.add(re.getAuthor()); + } + if (rd.getAuthor() != null) { + authors.add(rd.getAuthor()); + } - re.setAuthor(AuthorMerger.merge(authors)); - } + re.setAuthor(AuthorMerger.merge(authors)); + } - return entity; - } + return entity; + } - public static T entityMerger( - String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { - T base = entities.next()._2(); + public static T entityMerger( + String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { + T base = entities.next()._2(); - while (entities.hasNext()) { - T duplicate = entities.next()._2(); - if (duplicate != null) - base = (T) reduceEntity(base, duplicate); - } + while (entities.hasNext()) { + T duplicate = entities.next()._2(); + if (duplicate != null) + base = (T) reduceEntity(base, duplicate); + } - base.setId(id); - base.setDataInfo(dataInfo); - base.setLastupdatetimestamp(ts); + base.setId(id); + base.setDataInfo(dataInfo); + base.setLastupdatetimestamp(ts); - return base; - } + return base; + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index cb1c70059..77e696501 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup; import static org.apache.spark.sql.functions.col; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -127,10 +128,8 @@ public class SparkPropagateRelation extends AbstractSparkAction { (MapFunction) r -> String .join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()), Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> { - b.mergeFrom(a); - return b; - }) + .reduceGroups((ReduceFunction) MergeUtils::mergeRelation + ) .map((MapFunction, Relation>) Tuple2::_2, REL_BEAN_ENC); final String outputRelationPath = graphOutputPath + "/relation"; diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9ffaeeeef..42332b02e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -3,17 +3,18 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.functions.col import org.apache.spark.sql._ import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkGenerateDoiBoost { @@ -78,8 +79,10 @@ object SparkGenerateDoiBoost { if (item._2 != null) { val otherPub = item._2._2 if (otherPub != null) { - crossrefPub.mergeFrom(otherPub) - crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)) + val mergedAuthor = AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor) + val res = MergeUtils.mergePublication(crossrefPub, otherPub) + res.setAuthor(mergedAuthor); + return res } } crossrefPub @@ -130,14 +133,13 @@ object SparkGenerateDoiBoost { // So we have to merge val b1 = left._2 val b2 = right._2 - b1.mergeFrom(b2) - b1.mergeOAFDataInfo(b2) val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) + val merged = MergeUtils.mergePublication(b1, b2); + merged.setAuthor(authors) if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) + merged.setId(b2.getId) //Return publication Merged - (b1.getId, b1) + (merged.getId, merged) } } else { // Left is Null so we return right diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala index 9a0b0d845..185381f8f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -1,8 +1,8 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory -import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject} +import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, MergeUtils} +import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, Subject} import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import org.json4s @@ -142,8 +142,7 @@ case object ConversionUtil { def mergePublication(a: Publication, b: Publication): Publication = { if ((a != null) && (b != null)) { - a.mergeFrom(b) - a + MergeUtils.mergePublication(a, b) } else { if (a == null) b else a } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 4f755266a..f84a10d1c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -149,7 +149,7 @@ public class SparkResultToCommunityFromOrganizationJob { } } // res.setContext(propagatedContexts); - // ret.mergeFrom(res); + // return MergeUtils.mergeResult(ret, res); } return ret; }; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index f9c36d7ca..f791825a7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -13,6 +13,7 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -24,8 +25,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; -import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Context; @@ -162,7 +161,7 @@ public class SparkResultToCommunityFromProject implements Serializable { } } res.setContext(propagatedContexts); - ret.mergeFrom(res); + return MergeUtils.checkedMerge(ret, res); } return ret; }; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java index 3cf2f73c3..d2bfd75c1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java @@ -25,118 +25,118 @@ import scala.Tuple2; public class SparkResultToCommunityThroughSemRelJob { - private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class); + private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkResultToCommunityThroughSemRelJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")); + String jsonConfiguration = IOUtils + .toString( + SparkResultToCommunityThroughSemRelJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + parser.parseArgument(args); - Boolean isSparkSessionManaged = isSparkSessionManaged(parser); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - final String preparedInfoPath = parser.get("preparedInfoPath"); - log.info("preparedInfoPath: {}", preparedInfoPath); + final String preparedInfoPath = parser.get("preparedInfoPath"); + log.info("preparedInfoPath: {}", preparedInfoPath); - SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); + final Boolean saveGraph = Optional + .ofNullable(parser.get("saveGraph")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("saveGraph: {}", saveGraph); - @SuppressWarnings("unchecked") - Class resultClazz = (Class) Class.forName(resultClassName); + @SuppressWarnings("unchecked") + Class resultClazz = (Class) Class.forName(resultClassName); - runWithSparkHiveSession( - conf, - isSparkSessionManaged, - spark -> { - if (isTest(parser)) { - removeOutputDir(spark, outputPath); - } - if (saveGraph) { - execPropagation( - spark, inputPath, outputPath, preparedInfoPath, resultClazz); - } - }); - } + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + if (isTest(parser)) { + removeOutputDir(spark, outputPath); + } + if (saveGraph) { + execPropagation( + spark, inputPath, outputPath, preparedInfoPath, resultClazz); + } + }); + } - private static void execPropagation( - SparkSession spark, - String inputPath, - String outputPath, - String preparedInfoPath, - Class resultClazz) { + private static void execPropagation( + SparkSession spark, + String inputPath, + String outputPath, + String preparedInfoPath, + Class resultClazz) { - Dataset possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class); - Dataset result = readPath(spark, inputPath, resultClazz); + Dataset possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class); + Dataset result = readPath(spark, inputPath, resultClazz); - result - .joinWith( - possibleUpdates, - result.col("id").equalTo(possibleUpdates.col("resultId")), - "left_outer") - .map(contextUpdaterFn(), Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + result + .joinWith( + possibleUpdates, + result.col("id").equalTo(possibleUpdates.col("resultId")), + "left_outer") + .map(contextUpdaterFn(), Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); - } + } - private static MapFunction, R> contextUpdaterFn() { - return value -> { - R ret = value._1(); - Optional rcl = Optional.ofNullable(value._2()); - if (rcl.isPresent()) { - Set contexts = new HashSet<>(); - ret.getContext().forEach(c -> contexts.add(c.getId())); - rcl - .get() - .getCommunityList() - .stream() - .forEach( - c -> { - if (!contexts.contains(c)) { - Context newContext = new Context(); - newContext.setId(c); - newContext - .setDataInfo( - Arrays - .asList( - getDataInfo( - PROPAGATION_DATA_INFO_TYPE, - PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, - PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS))); - ret.getContext().add(newContext); - } + private static MapFunction, R> contextUpdaterFn() { + return value -> { + R ret = value._1(); + Optional rcl = Optional.ofNullable(value._2()); + if (rcl.isPresent()) { + Set contexts = new HashSet<>(); + ret.getContext().forEach(c -> contexts.add(c.getId())); + rcl + .get() + .getCommunityList() + .stream() + .forEach( + c -> { + if (!contexts.contains(c)) { + Context newContext = new Context(); + newContext.setId(c); + newContext + .setDataInfo( + Arrays + .asList( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, + PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS))); + ret.getContext().add(newContext); + } - }); + }); - } + } - return ret; - }; - } + return ret; + }; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java index d4f1d9f55..66a178c70 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java @@ -7,6 +7,7 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -24,7 +25,6 @@ import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import scala.Tuple2; /** @@ -248,11 +248,11 @@ public class MergeGraphTableSparkJob { private T mergeAndGet(T b, T a) { if (Objects.nonNull(a) && Objects.nonNull(b)) { if (ModelSupport.isSubClass(a, OafEntity.class) && ModelSupport.isSubClass(b, OafEntity.class)) { - return (T) OafMapperUtils.mergeEntities((OafEntity) b, (OafEntity) a); + return (T) MergeUtils.merge(b, a); } if (a instanceof Relation && b instanceof Relation) { ((Relation) a).mergeFrom(b); - return a; + return (T) MergeUtils.mergeRelation((Relation)a, (Relation) b); } } return Objects.isNull(a) ? b : a; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 79ee5c5b6..9e1f3c78c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -1,14 +1,16 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.util.Arrays; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; - +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.Text; @@ -16,27 +18,18 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.rdd.RDD; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.dom4j.DocumentException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + public class GenerateEntitiesApplication extends AbstractMigrationApplication { private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); @@ -137,7 +130,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication { save( inputRdd .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf)) - .reduceByKey(OafMapperUtils::merge) + .reduceByKey(MergeUtils::merge) .map(Tuple2::_2), targetPath); break; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala index f5a13e72b..0c9f0d7ba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.IOUtils import org.apache.hadoop.fs.{FileSystem, Path} @@ -118,15 +119,12 @@ object SparkResolveEntities { currentEntityDataset .joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left") .map(k => { - val a = k._1 val b = k._2 if (b == null) a._2 - else { - a._2.mergeFrom(b._2) - a._2 - } + else + MergeUtils.mergeResult(a._2, b._2) }) .map(r => mapper.writeValueAsString(r))(Encoders.STRING) .write diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala index 704c9ab5c..ecf612cc7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.sx.graph import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf @@ -130,10 +131,7 @@ object SparkCreateInputGraph { val ds: Dataset[T] = spark.read.load(sourcePath).as[T] ds.groupByKey(_.getId) - .reduceGroups { (x: T, y: T) => - x.mergeFrom(y) - x - } + .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] } .map(_._2) .write .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 6d6b2ffbd..bf275814c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -1,13 +1,12 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.Mockito.lenient; - -import java.io.IOException; -import java.util.List; - +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.dom4j.DocumentException; import org.junit.jupiter.api.BeforeEach; @@ -16,13 +15,12 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.util.List; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; @ExtendWith(MockitoExtension.class) class GenerateEntitiesApplicationTest { @@ -72,7 +70,7 @@ class GenerateEntitiesApplicationTest { protected void verifyMerge(Result publication, Result dataset, Class clazz, String resultType) { - final Result merge = OafMapperUtils.mergeResults(publication, dataset); + final Result merge = MergeUtils.mergeResult(publication, dataset); assertTrue(clazz.isAssignableFrom(merge.getClass())); assertEquals(resultType, merge.getResulttype().getClassid()); } From f9c74c98fab3b8f7461ca4f8f6c94c19255f8050 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Fri, 22 Mar 2024 11:08:45 +0100 Subject: [PATCH 28/34] fixed an identifier xpath --- .../plugin/base/xml/base2oaf.transformationRule.xml | 2 +- .../plugin/base/xml/base2odf.transformationRule.xml | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml index cee649805..201e5c363 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml @@ -340,7 +340,7 @@ base_dc:link (I used dc:identifier) + select="//oai:header/oai:identifier" /> diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml index 4565b81f5..ff03e9d59 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml @@ -82,8 +82,9 @@ + select="//oai:header/oai:identifier" /> + @@ -374,7 +375,7 @@ + select="//oai:header/oai:identifier" /> From 0ff7faad72a6db5bf6602721c81f91558c327354 Mon Sep 17 00:00:00 2001 From: Giambattista Bloisi Date: Fri, 22 Mar 2024 16:24:49 +0100 Subject: [PATCH 29/34] Fix conditions that prevented ORCID Enrichment --- .../scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala | 2 +- .../dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala index f7ea7e5a4..e2e7fada6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala @@ -87,7 +87,7 @@ object ORCIDAuthorEnricher extends Serializable { ) = { val matched = scala.collection.mutable.ArrayBuffer.empty[MatchedAuthors] - if (graph_authors != null && graph_authors.isEmpty) { + if (graph_authors != null && !graph_authors.isEmpty) { val ait = graph_authors.iterator while (ait.hasNext) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala index e2d218247..0824c2a71 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -72,7 +72,7 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] .join(matched, Seq("id"), "left") .withColumn( "author", - when(size(col("enriched_author")).gt(1), col("enriched_author")) + when(size(col("enriched_author")).gt(0), col("enriched_author")) .otherwise(col("author")) ) .drop("enriched_author") From 6ffb1faf09467616e2c8ab4efe6e67ee8473e961 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 25 Mar 2024 12:15:51 +0100 Subject: [PATCH 30/34] fixed a problem with multiple nodes --- .../base/xml/base2odf.transformationRule.xml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml index ff03e9d59..407c51015 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml @@ -153,14 +153,18 @@ - - - - - - - + + + + + + + + + + + From e1149eb5c482208f2e462ce46e364ac4590e4fe6 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 25 Mar 2024 15:01:42 +0100 Subject: [PATCH 31/34] xslt rules and tests --- .../base/xml/base2oaf.transformationRule.xml | 2 ++ .../base/xml/base2odf.transformationRule.xml | 5 +++ .../plugin/base/BaseTransfomationTest.java | 17 +++++++++ .../collection/plugin/base/record_wrong_1.xml | 36 +++++++++++++++++++ 4 files changed, 60 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record_wrong_1.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml index 201e5c363..a49687e3a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml @@ -303,7 +303,9 @@ base_dc:link (I used dc:identifier) + CLOSED OPEN + UNKNOWN diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml index 407c51015..0e0e41f12 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml @@ -178,6 +178,9 @@ + + restricted access + open access @@ -341,7 +344,9 @@ + CLOSED OPEN + UNKNOWN diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java index 2bbd87117..6c0c23922 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.collection.plugin.base; +import static org.junit.jupiter.api.Assertions.assertThrows; + import java.io.IOException; import org.apache.commons.io.IOUtils; @@ -63,6 +65,21 @@ public class BaseTransfomationTest extends AbstractVocabularyTest { System.out.println(result.getBody()); } + @Test + void testBase2ODF_wrong_date() throws Exception { + + final MetadataRecord mr = new MetadataRecord(); + mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record_wrong_1.xml"))); + + final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml"); + + assertThrows(NullPointerException.class, () -> { + final MetadataRecord result = tr.call(mr); + System.out.println(result.getBody()); + }); + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String xslt = new SAXReader() .read(this.getClass().getResourceAsStream(path)) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record_wrong_1.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record_wrong_1.xml new file mode 100644 index 000000000..f6dccc006 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record_wrong_1.xml @@ -0,0 +1,36 @@ + + +

    + ftunivminnesdc:oai:conservancy.umn.edu:11299/109914 + 2023-07-18T20:05:40Z +
    + + + ftunivminnesdc:oai:conservancy.umn.edu:11299/109914 + cna + us + ftunivminnesdc + University of Minnesota Digital Conservancy + An Experimental Investigation of the influence of an air bubble layer on radiated noise and surface pressure fluctuations in a turbulent boundary layer + Killen, John M. + Boundary layer noise + Kinetic energy dissipation + Air bubble layer + Maximum stable bubble size + bubble noise spectra + between the noise spectra of a layer of air bubbles in a turbulent flow and' a maximum stable bubble size which can exist in the same flow. An air bubbie layer with individual bubble sizes greater than a maximum stable size was introduced into the boundary layer of water flowing along a smooth flat plate. It was found that the maximum stable bubble size was related to the turbulent kinetic energy dissipation as had been previously shown by other investigators ; Office of Naval Research Arlington, Virginia 22217 + 1981-09-31T21:42:52Z + 1981 + Report + 14 + http://purl.umn.edu/109914 + http://purl.umn.edu/109914 + en_US + Project Reports + 202 + http://purl.umn.edu/109914 + 2 + eng + + + \ No newline at end of file From 63067d4b241bc0a921a9b0fb7ed249d2bd388898 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Mar 2024 15:50:05 +0100 Subject: [PATCH 32/34] align dhp-schema.version with the beta branch --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 3b6e3a82b..c8514a3cb 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.3] + [5.17.3] [4.0.3] [6.0.5] [3.1.6] From 6c3b692f60dac106080eea32052d11fc24badfda Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Mar 2024 16:10:23 +0100 Subject: [PATCH 33/34] integrated minor change from beta branch --- .../dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 8adc88920..76c8ec7fa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - // project.setId(bipProjectScores.getProjectId()); + //project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) From 4b978ffa2daeba1973759e4c65836ac7ed825c99 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Mar 2024 16:12:36 +0100 Subject: [PATCH 34/34] align dhp-schema.version with the beta branch --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a95bf100d..c8514a3cb 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [6.0.0-SNAPSHOT] + [5.17.3] [4.0.3] [6.0.5] [3.1.6]