From 7a1c1b6f53b8c7ca51633b440338fffc997e81bb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:36:02 +0200 Subject: [PATCH] [EOSC context TAG] Add test class and resourcesK --- .../dhp/bulktag/eosc/DatasourceMaster.java | 29 +- .../eosc/ReadMasterDatasourceFromDB.java | 62 ++-- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 229 +++++++------ .../bulktag/datasourcemaster_parameters.json | 32 ++ .../input_eosc_bulkTag_parameters.json | 34 ++ .../dhp/bulktag/oozie_app/workflow.xml | 139 +++++++- .../dhp/bulktag/EOSCContextTaggingTest.java | 152 +++++++++ .../dhp/bulktag/eosc/dataset/dataset_10.json | 10 + .../datasourceMaster | 318 ++++++++++++++++++ 9 files changed, 855 insertions(+), 150 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java index 537356586..ee01597e7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.eosc; import java.io.Serializable; @@ -7,22 +8,22 @@ import java.io.Serializable; * @Date 21/07/22 */ public class DatasourceMaster implements Serializable { - private String datasource; - private String master; + private String datasource; + private String master; - public String getDatasource() { - return datasource; - } + public String getDatasource() { + return datasource; + } - public void setDatasource(String datasource) { - this.datasource = datasource; - } + public void setDatasource(String datasource) { + this.datasource = datasource; + } - public String getMaster() { - return master; - } + public String getMaster() { + return master; + } - public void setMaster(String master) { - this.master = master; - } + public void setMaster(String master) { + this.master = master; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 7d6964707..9ad108749 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -1,27 +1,6 @@ package eu.dnetlib.dhp.bulktag.eosc; -/** - * @author miriam.baglioni - * @Date 21/07/22 - */ - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.common.RelationInverse; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - import java.io.BufferedWriter; import java.io.Closeable; import java.io.IOException; @@ -34,6 +13,28 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + public class ReadMasterDatasourceFromDB implements Closeable { private final DbClient dbClient; @@ -43,18 +44,18 @@ public class ReadMasterDatasourceFromDB implements Closeable { private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + - "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + - "FULL JOIN " + - "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + - "ON dso.id = d.duplicate"; + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - ReadMasterDatasourceFromDB.class + ReadMasterDatasourceFromDB.class .getResourceAsStream( - "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + "/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json"))); parser.parseArgument(args); @@ -64,8 +65,9 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; final String hdfsNameNode = parser.get("hdfsNameNode"); - try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, - dbPassword)) { + try ( + final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { log.info("Processing datasources..."); rmd.execute(QUERY, rmd::datasourceMasterMap); @@ -75,7 +77,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { public void execute(final String sql, final Function producer) { - dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); } public DatasourceMaster datasourceMasterMap(ResultSet rs) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index aa709cb29..600a5cec8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -1,18 +1,22 @@ + package eu.dnetlib.dhp.bulktag.eosc; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; -import eu.dnetlib.dhp.bulktag.community.*; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import javax.print.attribute.DocAttributeSet; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -21,16 +25,15 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.print.attribute.DocAttributeSet; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** * @author miriam.baglioni @@ -38,108 +41,124 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION */ public class SparkEoscBulkTag implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscBulkTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String datasourceMapPath = parser.get("datasourceMapPath"); - log.info("datasourceMapPath: {}", datasourceMapPath); + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - Class resultClazz = (Class) Class.forName(resultClassName); + Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - CommunityConfiguration cc; + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, workingPath); + execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); + }); + } - private static void execBulkTag( - SparkSession spark, - String inputPath, - String outputPath, - String datasourceMapPath, - Class resultClazz) { + private static void execBulkTag( + SparkSession spark, + String inputPath, + String workingPath, + String datasourceMapPath, + Class resultClazz) { - final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) - .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collect()); - readPath(spark, inputPath, resultClazz) - .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) - .map( - (MapFunction) value -> enrich(value, hostedByList), - Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } + List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collectAsList(); - private static R enrich(R value, List hostedByList) { - if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ - Context context = new Context(); - context.setId("eosc"); - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); - value.getContext().add(context); - } - return value; - } - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - // TODO remove this hack as soon as the values fixed by this method will be provided as NON null - private static MapFunction patchResult() { - return r -> { - if (r.getDataInfo().getDeletedbyinference() == null) { - r.getDataInfo().setDeletedbyinference(false); - } - if (r.getContext() == null) { - r.setContext(new ArrayList<>()); - } - return r; - }; - } + readPath(spark, workingPath, resultClazz) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + + } + + private static R enrich(R value, List hostedByList) { + if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json new file mode 100644 index 000000000..9a2eadaa7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json new file mode 100644 index 000000000..ebbbd408b --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json @@ -0,0 +1,34 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "dmp", + "paramLongName":"datasourceMapPath", + "paramDescription": "the path where the association datasource master has been stored", + "paramRequired": true + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f34c5110f..6016e0179 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -16,6 +16,21 @@ outputPath the output path + + + + postgresURL + the url of the postgress server to query + + + postgresUser + the username to access the postgres db + + + postgresPassword + the postgres password + + @@ -29,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,10 +241,132 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag + + + + + + + eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB + --hdfsPath${workingDir}/datasourcemaster + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/publication + --workingPath${workingDir}/eoscContextTag/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/dataset + --workingPath${workingDir}/eoscContextTag/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/software + --workingPath${workingDir}/eoscContextTag/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/otherresearchproduct + --workingPath${workingDir}/eoscContextTag/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --datasourceMapPath${workingDir}/datasourcemaster + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java new file mode 100644 index 000000000..d6785acc7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -0,0 +1,152 @@ + +package eu.dnetlib.dhp.bulktag; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc +//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc +//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc +//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag + +public class EOSCContextTaggingTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void EoscContextTagTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + } + + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json new file mode 100644 index 000000000..63aa87e93 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json @@ -0,0 +1,10 @@ +{"author":[{"affiliation":[],"fullname":"Government of Alberta | Gouvernement de l'Alberta","name":"Government Of Alberta Gouvernement L.","pid":[],"rank":1,"surname":"Alberta"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::3795d6478e30e2c9f787d427ff160944","value":"Federated Research Data Repository / Dépôt fédéré de données de 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