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migration of claims

This commit is contained in:
Michele Artini 2020-02-19 15:11:17 +01:00
parent 173f1df1e5
commit 5d3739b5cf
8 changed files with 238 additions and 207 deletions
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14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java
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@ -227,7 +227,21 @@ public class AbstractMigrationExecutor implements Closeable {
final String nsPrefix = StringUtils.substringBefore(originalId, "::");
final String rest = StringUtils.substringAfter(originalId, "::");
return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest));
}
public static String createOpenaireId(final String type, final String originalId) {
switch (type) {
case "datasource":
return createOpenaireId(10, originalId);
case "organization":
return createOpenaireId(20, originalId);
case "person":
return createOpenaireId(30, originalId);
case "project":
return createOpenaireId(40, originalId);
default:
return createOpenaireId(50, originalId);
}
}
public static String asString(final Object o) {

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java
View File

@ -398,6 +398,8 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
protected DataInfo prepareDataInfo(final Document doc) {
final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { return null; }
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");

84
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java
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@ -1,56 +1,68 @@
package eu.dnetlib.dhp.migration;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
import java.util.Arrays;
import java.util.List;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import scala.Tuple2;
public class ExtractEntitiesFromHDFSJob {
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
parser.parseArgument(args);
private static List<String> folderNames = Arrays.asList("db_entities", "oaf_entities", "odf_entities");
final SparkSession spark = SparkSession
.builder()
.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
parser.parseArgument(args);
final List<String> sourcePaths = Arrays.asList(parser.get("sourcePaths").split(","));
final String targetPath = parser.get("graphRawPath");
final SparkSession spark = SparkSession
.builder()
.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
processEntity(sc, Publication.class, sourcePaths, targetPath);
processEntity(sc, Dataset.class, sourcePaths, targetPath);
processEntity(sc, Software.class, sourcePaths, targetPath);
processEntity(sc, OtherResearchProduct.class, sourcePaths, targetPath);
processEntity(sc, Datasource.class, sourcePaths, targetPath);
processEntity(sc, Organization.class, sourcePaths, targetPath);
processEntity(sc, Project.class, sourcePaths, targetPath);
processEntity(sc, Relation.class, sourcePaths, targetPath);
}
}
final String sourcePath = parser.get("sourcePath");
final String targetPath = parser.get("graphRawPath");
final String entity = parser.get("entity");
private static void processEntity(final JavaSparkContext sc, final Class<?> clazz, final List<String> sourcePaths, final String targetPath) {
final String type = clazz.getSimpleName().toLowerCase();
final JavaRDD<String> inputRdd = sc.emptyRDD();
sourcePaths.forEach(sourcePath -> inputRdd.union(sc.sequenceFile(sourcePath, Text.class, Text.class)
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
.filter(k -> isEntityType(k._1(), type))
.map(Tuple2::_2)));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
inputRdd.saveAsTextFile(targetPath + "/" + type);
}
JavaRDD<String> inputRdd = sc.emptyRDD();
folderNames.forEach(p -> inputRdd.union(
sc.sequenceFile(sourcePath+"/"+p, Text.class, Text.class)
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
.filter(k -> isEntityType(k._1(), entity))
.map(Tuple2::_2))
);
inputRdd.saveAsTextFile(targetPath+"/"+entity);
}
private static boolean isEntityType(final String item, final String entity) {
return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity);
}
private static boolean isEntityType(final String item, final String entity) {
return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity);
}
}

113
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java
View File

@ -17,15 +17,21 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor implements Closeable {
@ -53,22 +59,28 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
final String hdfsNameNode = parser.get("namenode");
final String hdfsUser = parser.get("hdfsUser");
final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) {
log.info("Processing datasources...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
if (processClaims) {
log.info("Processing claims...");
smdbe.execute("queryClaims.sql", smdbe::processClaims);
} else {
log.info("Processing datasources...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
log.info("Processing projects...");
smdbe.execute("queryProjects.sql", smdbe::processProject);
log.info("Processing projects...");
smdbe.execute("queryProjects.sql", smdbe::processProject);
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing relations ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
log.info("Processing relations ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
}
log.info("All done.");
}
}
@ -377,7 +389,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
r2.setTarget(dsId);
r2.setCollectedFrom(collectedFrom);
r2.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
emitOaf(r2);
// rs.getString("datasource");
@ -426,7 +438,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
r2.setTarget(projectId);
r2.setCollectedFrom(collectedFrom);
r2.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
emitOaf(r2);
// rs.getString("project");
@ -450,6 +462,81 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor impl
}
}
public void processClaims(final ResultSet rs) {
final DataInfo info =
dataInfo(false, null, false, false, qualifier("user:claim", "user:claim", "dnet:provenanceActions", "dnet:provenanceActions"), "0.9");
try {
if (rs.getString("source_type").equals("context")) {
final Result r;
if (rs.getString("target_type").equals("dataset")) {
r = new Dataset();
} else if (rs.getString("target_type").equals("software")) {
r = new Software();
} else if (rs.getString("target_type").equals("other")) {
r = new OtherResearchProduct();
} else {
r = new Publication();
}
r.setId(createOpenaireId(50, rs.getString("target_id")));
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setContext(prepareContext(rs.getString("source_id"), info));
r.setDataInfo(info);
emitOaf(r);
} else {
final String sourceId = createOpenaireId(rs.getString("source_type"), rs.getString("source_id"));
final String targetId = createOpenaireId(rs.getString("target_type"), rs.getString("target_id"));
final Relation r1 = new Relation();
final Relation r2 = new Relation();
if (rs.getString("source_type").equals("project")) {
r1.setRelType("resultProject");
r1.setSubRelType("outcome");
r1.setRelClass("produces");
r2.setRelType("resultProject");
r2.setSubRelType("outcome");
r2.setRelClass("isProducedBy");
} else {
r1.setRelType("resultResult");
r1.setSubRelType("relationship");
r1.setRelClass("isRelatedTo");
r2.setRelType("resultResult");
r2.setSubRelType("relationship");
r2.setRelClass("isRelatedTo");
}
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
emitOaf(r1);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
emitOaf(r2);
}
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
private List<Context> prepareContext(final String id, final DataInfo dataInfo) {
final Context context = new Context();
context.setId(id);
context.setDataInfo(Arrays.asList(dataInfo));
return Arrays.asList(context);
}
private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
final String inferenceprovenance = rs.getString("inferenceprovenance");

10
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the HDFS source path which contains the sequential file",
"paramLongName": "sourcePaths",
"paramDescription": "the HDFS source paths which contains the sequential file (comma separated)",
"paramRequired": true
},
{
@ -16,11 +16,5 @@
"paramLongName": "graphRawPath",
"paramDescription": "the path of the graph Raw in hdfs",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "The entity to extract",
"paramRequired": true
}
]

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json
View File

@ -34,5 +34,11 @@
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false
},
{
"paramName": "a",
"paramLongName": "action",
"paramDescription": "process claims",
"paramRequired": false
}
]

213
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml
View File

@ -43,8 +43,7 @@
</property>
</parameters>
<start to="ImportODFEntitiesFromMongoDB"/>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@ -71,6 +70,23 @@
<arg>-dbuser</arg><arg>${postgresUser}</arg>
<arg>-dbpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportClaimsFromPostgres"/>
<error to="Kill"/>
</action>
<action name="ImportClaimsFromPostgres">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${workingPath}/db_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-dburl</arg><arg>${postgresURL}</arg>
<arg>-dbuser</arg><arg>${postgresUser}</arg>
<arg>-dbpasswd</arg><arg>${postgresPassword}</arg>
<arg>-a</arg><arg>claims</arg>
</java>
<ok to="ImportODFEntitiesFromMongoDB"/>
<error to="Kill"/>
</action>
@ -113,170 +129,69 @@
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ExtractPublication"/>
<ok to="ImportODFClaimsFromMongoDB"/>
<error to="Kill"/>
</action>
<action name="ImportODFClaimsFromMongoDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingPath}/odf_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongourl}</arg>
<arg>-db</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportOAFClaimsFromMongoDB"/>
<error to="Kill"/>
</action>
<action name="ExtractPublication">
<action name="ImportOAFClaimsFromMongoDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingPath}/oaf_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongourl}</arg>
<arg>-db</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ExtractEntities"/>
<error to="Kill"/>
</action>
<action name="ExtractEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: publication</name>
<name>ExtractEntities</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/publication</arg>
<arg>-e</arg><arg>publication</arg>
</spark>
<ok to="ExtractDataset"/>
<error to="Kill"/>
</action>
<action name="ExtractDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: dataset</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/dataset</arg>
<arg>-e</arg><arg>dataset</arg>
</spark>
<ok to="ExtractSoftware"/>
<error to="Kill"/>
</action>
<action name="ExtractSoftware">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: software</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/software</arg>
<arg>-e</arg><arg>software</arg>
</spark>
<ok to="ExtractORP"/>
<error to="Kill"/>
</action>
<action name="ExtractORP">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: otherresearchproduct</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/otherresearchproduct</arg>
<arg>-e</arg><arg>otherresearchproduct</arg>
</spark>
<ok to="ExtractDatasource"/>
<error to="Kill"/>
</action>
<action name="ExtractDatasource">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: datasource</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/datasource</arg>
<arg>-e</arg><arg>datasource</arg>
</spark>
<ok to="ExtractOrganization"/>
<error to="Kill"/>
</action>
<action name="ExtractOrganization">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: organization</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/organization</arg>
<arg>-e</arg><arg>organization</arg>
</spark>
<ok to="ExtractProject"/>
<error to="Kill"/>
</action>
<action name="ExtractProject">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: project</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/project</arg>
<arg>-e</arg><arg>project</arg>
</spark>
<ok to="ExtractRelation"/>
<error to="Kill"/>
</action>
<action name="ExtractRelation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities: relation</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>-g</arg><arg>${graphRawPath}/relation</arg>
<arg>-e</arg><arg>relation</arg>
<arg>-s</arg><arg>${workingPath}/db_entities,${workingPath}/oaf_entities,${workingPath}/odf_entities</arg>
<arg>-g</arg><arg>${graphRawPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

1
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryClaims.sql Normal file
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SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;