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Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

This commit is contained in:
Claudio Atzori 2020-03-02 17:03:10 +01:00
parent bc7cfd5975 4b29a121b0
commit 9cf5ce2e66
28 changed files with 1115 additions and 447 deletions
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68
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java
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@ -1,68 +0,0 @@
package eu.dnetlib.dhp.migration;
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 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);
final SparkSession spark = SparkSession
.builder()
.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final List<String> sourcePaths = Arrays.asList(parser.get("sourcePaths").split(","));
final String targetPath = parser.get("graphRawPath");
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);
}
}
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)));
inputRdd.saveAsTextFile(targetPath + "/" + type);
}
private static boolean isEntityType(final String item, final String entity) {
return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity);
}
}

45
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateMongoMdstoresApplication.java
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@ -1,45 +0,0 @@
package eu.dnetlib.dhp.migration;
import org.apache.commons.io.IOUtils;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class MigrateMongoMdstoresApplication {
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json")));
parser.parseArgument(args);
final String mongoBaseUrl = parser.get("mongoBaseUrl");
final String mongoDb = parser.get("mongoDb");
final String mdFormat = parser.get("mdFormat");
final String mdLayout = parser.get("mdLayout");
final String mdInterpretation = parser.get("mdInterpretation");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("namenode");
final String hdfsUser = parser.get("hdfsUser");
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
if (mdFormat.equalsIgnoreCase("oaf")) {
try (final OafMigrationExecutor mig =
new OafMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) {
mig.processMdRecords(mdFormat, mdLayout, mdInterpretation);
}
} else if (mdFormat.equalsIgnoreCase("odf")) {
try (final OdfMigrationExecutor mig =
new OdfMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) {
mig.processMdRecords(mdFormat, mdLayout, mdInterpretation);
}
} else {
throw new RuntimeException("Format not supported: " + mdFormat);
}
}
}

16
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplication.java
View File

@ -1,4 +1,14 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.step1;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.asString;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.journal;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty;
import java.io.Closeable;
import java.io.IOException;
@ -17,6 +27,8 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.migration.utils.AbstractMigrationApplication;
import eu.dnetlib.dhp.migration.utils.DbClient;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -34,7 +46,7 @@ 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 {
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions");

70
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateMongoMdstoresApplication.java Normal file
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@ -0,0 +1,70 @@
package eu.dnetlib.dhp.migration.step1;
import java.io.Closeable;
import java.io.IOException;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.migration.utils.AbstractMigrationApplication;
import eu.dnetlib.dhp.migration.utils.MdstoreClient;
public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication implements Closeable {
private static final Log log = LogFactory.getLog(MigrateMongoMdstoresApplication.class);
private final MdstoreClient mdstoreClient;
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json")));
parser.parseArgument(args);
final String mongoBaseUrl = parser.get("mongoBaseUrl");
final String mongoDb = parser.get("mongoDb");
final String mdFormat = parser.get("mdFormat");
final String mdLayout = parser.get("mdLayout");
final String mdInterpretation = parser.get("mdInterpretation");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("namenode");
final String hdfsUser = parser.get("hdfsUser");
try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb)) {
app.execute(mdFormat, mdLayout, mdInterpretation);
}
}
public MigrateMongoMdstoresApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
final String mongoDb) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser);
this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
}
public void execute(final String format, final String layout, final String interpretation) {
final Map<String, String> colls = mdstoreClient.validCollections(format, layout, interpretation);
log.info("Found " + colls.size() + " mdstores");
for (final Entry<String, String> entry : colls.entrySet()) {
log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
final String currentColl = entry.getValue();
for (final String xml : mdstoreClient.listRecords(currentColl)) {
emit(xml, "native_" + format);
}
}
}
@Override
public void close() throws IOException {
super.close();
mdstoreClient.close();
}
}

123
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java
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@ -1,20 +1,24 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.step2;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.journal;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.keyValue;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.oaiIProvenance;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
@ -37,11 +41,9 @@ import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
public abstract class AbstractMdRecordToOafMapper {
protected final Map<String, String> code2name = new HashMap<>();
protected final MdstoreClient mdstoreClient;
protected final Map<String, String> code2name;
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
@ -51,79 +53,36 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
private static final Log log = LogFactory.getLog(AbstractMongoExecutor.class);
public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
final String mongoDb, final String dbUrl, final String dbUser,
final String dbPassword) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser);
this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
loadClassNames(dbUrl, dbUser, dbPassword);
final Map<String, String> nsContext = new HashMap<>();
registerNamespaces(nsContext);
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name;
}
private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
public List<Oaf> processMdRecord(final String xml) {
try {
final Map<String, String> nsContext = new HashMap<>();
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
log.info("Loading vocabulary terms from db...");
final Document doc = DocumentHelper.parseText(xml);
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
code2name.clear();
dbClient.processResults("select code, name from class", rs -> {
try {
code2name.put(rs.getString("code"), rs.getString("name"));
} catch (final SQLException e) {
e.printStackTrace();
}
});
final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom
: keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name"));
final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
} catch (final Exception e) {
throw new RuntimeException(e);
}
log.info("Found " + code2name.size() + " terms.");
}
public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException {
log.info(String.format("Searching mdstores (format: %s, layout: %s, interpretation: %s)", mdFormat, mdLayout, mdInterpretation));
final Map<String, String> colls = mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation);
log.info("Found " + colls.size() + " mdstores");
for (final Entry<String, String> entry : colls.entrySet()) {
log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
final String currentColl = entry.getValue();
for (final String xml : mdstoreClient.listRecords(currentColl)) {
final Document doc = DocumentHelper.parseText(xml);
final String type = doc.valueOf("//dr:CobjCategory/@type");
final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name"));
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom
: keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name"));
final DataInfo info = prepareDataInfo(doc);
final long lastUpdateTimestamp = new Date().getTime();
for (final Oaf oaf : createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp)) {
emitOaf(oaf);
}
}
}
log.info("All Done.");
}
protected void registerNamespaces(final Map<String, String> nsContext) {
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
}
protected List<Oaf> createOafs(final Document doc,
@ -432,10 +391,4 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
return res;
}
@Override
public void close() throws IOException {
super.close();
mdstoreClient.close();
}
}

170
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/GenerateEntitiesApplication.java Normal file
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@ -0,0 +1,170 @@
package eu.dnetlib.dhp.migration.step2;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
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.fs.FileSystem;
import org.apache.hadoop.fs.Path;
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 com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication;
import eu.dnetlib.dhp.migration.utils.DbClient;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf;
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 GenerateEntitiesApplication {
private static final Log log = LogFactory.getLog(GenerateEntitiesApplication.class);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/migration/generate_entities_parameters.json")));
parser.parseArgument(args);
final String sourcePaths = parser.get("sourcePaths");
final String targetPath = parser.get("targetPath");
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final SparkSession spark = SparkSession
.builder()
.appName(GenerateEntitiesApplication.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final Map<String, String> code2name = loadClassNames(dbUrl, dbUser, dbPassword);
try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
final List<String> existingSourcePaths = Arrays.stream(sourcePaths.split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList());
generateEntities(sc, code2name, existingSourcePaths, targetPath);
}
}
private static void generateEntities(final JavaSparkContext sc,
final Map<String, String> code2name,
final List<String> sourcePaths,
final String targetPath) {
log.info("Generate entities from files:");
sourcePaths.forEach(log::info);
JavaRDD<String> inputRdd = sc.emptyRDD();
for (final String sp : sourcePaths) {
inputRdd = inputRdd.union(sc.sequenceFile(sp, Text.class, Text.class)
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
.map(k -> convertToListOaf(k._1(), k._2(), code2name))
.flatMap(list -> list.iterator())
.map(oaf -> oaf.getClass().getSimpleName().toLowerCase() + "|" + convertToJson(oaf)));
}
inputRdd.saveAsTextFile(targetPath);
}
private static List<Oaf> convertToListOaf(final String id, final String s, final Map<String, String> code2name) {
final String type = StringUtils.substringAfter(id, ":");
switch (type.toLowerCase()) {
case "native_oaf":
return new OafToOafMapper(code2name).processMdRecord(s);
case "native_odf":
return new OafToOafMapper(code2name).processMdRecord(s);
case "datasource":
return Arrays.asList(convertFromJson(s, Datasource.class));
case "organization":
return Arrays.asList(convertFromJson(s, Organization.class));
case "project":
return Arrays.asList(convertFromJson(s, Project.class));
case "relation":
return Arrays.asList(convertFromJson(s, Relation.class));
case "publication":
return Arrays.asList(convertFromJson(s, Publication.class));
case "dataset":
return Arrays.asList(convertFromJson(s, Dataset.class));
case "software":
return Arrays.asList(convertFromJson(s, Software.class));
case "otherresearchproducts":
default:
return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
}
}
private static Map<String, String> loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
log.info("Loading vocabulary terms from db...");
final Map<String, String> map = new HashMap<>();
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
dbClient.processResults("select code, name from class", rs -> {
try {
map.put(rs.getString("code"), rs.getString("name"));
} catch (final SQLException e) {
e.printStackTrace();
}
});
}
log.info("Found " + map.size() + " terms.");
return map;
}
private static String convertToJson(final Oaf oaf) {
try {
return new ObjectMapper().writeValueAsString(oaf);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
try {
return new ObjectMapper().readValue(s, clazz);
} catch (final Exception e) {
log.error("Error parsing object of class: " + clazz);
log.error(s);
throw new RuntimeException(e);
}
}
private static boolean exists(final JavaSparkContext context, final String pathToFile) {
try {
final FileSystem hdfs = org.apache.hadoop.fs.FileSystem.get(context.hadoopConfiguration());
final Path path = new Path(pathToFile);
return hdfs.exists(path);
} catch (final IOException e) {
throw new RuntimeException(e);
}
}
}

25
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OafToOafMapper.java
View File

@ -1,16 +1,17 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.step2;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document;
import org.dom4j.Node;
import eu.dnetlib.dhp.migration.pace.PacePerson;
import eu.dnetlib.dhp.migration.utils.PacePerson;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
@ -22,20 +23,10 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OafMigrationExecutor extends AbstractMongoExecutor {
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
private static final Log log = LogFactory.getLog(OafMigrationExecutor.class);
public OafMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb,
final String dbUrl, final String dbUser,
final String dbPassword) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword);
}
@Override
protected void registerNamespaces(final Map<String, String> nsContext) {
super.registerNamespaces(nsContext);
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
public OafToOafMapper(final Map<String, String> code2name) {
super(code2name);
}
@Override

78
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OdfToOafMapper.java
View File

@ -1,4 +1,8 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.step2;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field;
import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty;
import java.util.ArrayList;
import java.util.Arrays;
@ -6,8 +10,6 @@ import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document;
import org.dom4j.Node;
@ -22,38 +24,28 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OdfMigrationExecutor extends AbstractMongoExecutor {
public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
private static final Log log = LogFactory.getLog(OdfMigrationExecutor.class);
public OdfMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb,
final String dbUrl, final String dbUser,
final String dbPassword) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword);
}
@Override
protected void registerNamespaces(final Map<String, String> nsContext) {
super.registerNamespaces(nsContext);
nsContext.put("dc", "http://datacite.org/schema/kernel-3");
public OdfToOafMapper(final Map<String, String> code2name) {
super(code2name);
}
@Override
protected List<StructuredProperty> prepareTitles(final Document doc, final DataInfo info) {
return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info);
return prepareListStructProps(doc, "//datacite:title", MAIN_TITLE_QUALIFIER, info);
}
@Override
protected List<Author> prepareAuthors(final Document doc, final DataInfo info) {
final List<Author> res = new ArrayList<>();
int pos = 1;
for (final Object o : doc.selectNodes("//dc:creator")) {
for (final Object o : doc.selectNodes("//datacite:creator")) {
final Node n = (Node) o;
final Author author = new Author();
author.setFullname(n.valueOf("./dc:creatorName"));
author.setName(n.valueOf("./dc:givenName"));
author.setSurname(n.valueOf("./dc:familyName"));
author.setAffiliation(prepareListFields(doc, "./dc:affiliation", info));
author.setFullname(n.valueOf("./datacite:creatorName"));
author.setName(n.valueOf("./datacite:givenName"));
author.setSurname(n.valueOf("./datacite:familyName"));
author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info));
author.setPid(preparePids(doc, info));
author.setRank(pos++);
res.add(author);
@ -63,7 +55,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
private List<StructuredProperty> preparePids(final Document doc, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : doc.selectNodes("./dc:nameIdentifier")) {
for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) {
res.add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", "dnet:pid_types", "dnet:pid_types"), info));
}
return res;
@ -72,7 +64,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected List<Instance> prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) {
final List<Instance> res = new ArrayList<>();
for (final Object o : doc.selectNodes("//dc:alternateIdentifier[@alternateIdentifierType='URL']")) {
for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
final Instance instance = new Instance();
instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
@ -98,7 +90,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected List<StructuredProperty> prepareRelevantDates(final Document doc, final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : doc.selectNodes("//dc:date")) {
for (final Object o : doc.selectNodes("//datacite:date")) {
final String dateType = ((Node) o).valueOf("@dateType");
if (StringUtils.isBlank(dateType) && !dateType.equalsIgnoreCase("Accepted") && !dateType.equalsIgnoreCase("Issued")
&& !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) {
@ -115,32 +107,32 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected List<Field<String>> prepareContributors(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:contributorName", info);
return prepareListFields(doc, "//datacite:contributorName", info);
}
@Override
protected List<Field<String>> prepareFormats(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:format", info);
return prepareListFields(doc, "//datacite:format", info);
}
@Override
protected Field<String> preparePublisher(final Document doc, final DataInfo info) {
return prepareField(doc, "//dc:publisher", info);
return prepareField(doc, "//datacite:publisher", info);
}
@Override
protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:description[@descriptionType='Abstract']", info);
return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info);
}
@Override
protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
return prepareListStructProps(doc, "//dc:subject", info);
return prepareListStructProps(doc, "//datacite:subject", info);
}
@Override
protected Qualifier prepareLanguages(final Document doc) {
return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages");
return prepareQualifier(doc, "//datacite:language", "dnet:languages", "dnet:languages");
}
@Override
@ -150,17 +142,17 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected List<Field<String>> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:contributor[@contributorType='ContactGroup']/dc:contributorName", info);
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
}
@Override
protected List<Field<String>> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:contributor[@contributorType='ContactPerson']/dc:contributorName", info);
return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
}
@Override
protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
return prepareQualifier(doc, "//dc:format", "dnet:programming_languages", "dnet:programming_languages");
return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages");
}
@Override
@ -175,7 +167,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected List<Field<String>> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) {
return prepareListFields(doc, "//dc:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
}
// DATASETS
@ -184,11 +176,11 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
protected List<GeoLocation> prepareDatasetGeoLocations(final Document doc, final DataInfo info) {
final List<GeoLocation> res = new ArrayList<>();
for (final Object o : doc.selectNodes("//dc:geoLocation")) {
for (final Object o : doc.selectNodes("//datacite:geoLocation")) {
final GeoLocation loc = new GeoLocation();
loc.setBox(((Node) o).valueOf("./dc:geoLocationBox"));
loc.setPlace(((Node) o).valueOf("./dc:geoLocationPlace"));
loc.setPoint(((Node) o).valueOf("./dc:geoLocationPoint"));
loc.setBox(((Node) o).valueOf("./datacite:geoLocationBox"));
loc.setPlace(((Node) o).valueOf("./datacite:geoLocationPlace"));
loc.setPoint(((Node) o).valueOf("./datacite:geoLocationPoint"));
res.add(loc);
}
return res;
@ -201,17 +193,17 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected Field<String> prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) {
return prepareField(doc, "//dc:date[@dateType='Updated']", info);
return prepareField(doc, "//datacite:date[@dateType='Updated']", info);
}
@Override
protected Field<String> prepareDatasetVersion(final Document doc, final DataInfo info) {
return prepareField(doc, "//dc:version", info);
return prepareField(doc, "//datacite:version", info);
}
@Override
protected Field<String> prepareDatasetSize(final Document doc, final DataInfo info) {
return prepareField(doc, "//dc:size", info);
return prepareField(doc, "//datacite:size", info);
}
@Override
@ -221,7 +213,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
@Override
protected Field<String> prepareDatasetStorageDate(final Document doc, final DataInfo info) {
return prepareField(doc, "//dc:date[@dateType='Issued']", info);
return prepareField(doc, "//datacite:date[@dateType='Issued']", info);
}
@Override

68
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step3/DispatchEntitiesApplication.java Normal file
View File

@ -0,0 +1,68 @@
package eu.dnetlib.dhp.migration.step3;
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.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication;
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;
public class DispatchEntitiesApplication {
private static final Log log = LogFactory.getLog(DispatchEntitiesApplication.class);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(MigrateMongoMdstoresApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(DispatchEntitiesApplication.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
try (final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) {
final String sourcePath = parser.get("sourcePath");
final String targetPath = parser.get("graphRawPath");
processEntity(sc, Publication.class, sourcePath, targetPath);
processEntity(sc, Dataset.class, sourcePath, targetPath);
processEntity(sc, Software.class, sourcePath, targetPath);
processEntity(sc, OtherResearchProduct.class, sourcePath, targetPath);
processEntity(sc, Datasource.class, sourcePath, targetPath);
processEntity(sc, Organization.class, sourcePath, targetPath);
processEntity(sc, Project.class, sourcePath, targetPath);
processEntity(sc, Relation.class, sourcePath, targetPath);
}
}
private static void processEntity(final JavaSparkContext sc, final Class<?> clazz, final String sourcePath, final String targetPath) {
final String type = clazz.getSimpleName().toLowerCase();
log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath));
sc.textFile(sourcePath)
.filter(l -> isEntityType(l, type))
.map(l -> StringUtils.substringAfter(l, "|"))
.saveAsTextFile(targetPath + "/" + type); // use repartition(XXX) ???
}
private static boolean isEntityType(final String line, final String type) {
return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type);
}
}

80
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/AbstractMigrationApplication.java Normal file
View File

@ -0,0 +1,80 @@
package eu.dnetlib.dhp.migration.utils;
import java.io.Closeable;
import java.io.IOException;
import java.net.URI;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.codehaus.jackson.map.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
public class AbstractMigrationApplication implements Closeable {
private final AtomicInteger counter = new AtomicInteger(0);
private final Text key = new Text();
private final Text value = new Text();
private final SequenceFile.Writer writer;
private final ObjectMapper objectMapper = new ObjectMapper();
private static final Log log = LogFactory.getLog(AbstractMigrationApplication.class);
public AbstractMigrationApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception {
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser));
this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
.keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class));
}
private Configuration getConf(final String hdfsNameNode, final String hdfsUser) throws IOException {
final Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
System.setProperty("HADOOP_USER_NAME", hdfsUser);
System.setProperty("hadoop.home.dir", "/");
FileSystem.get(URI.create(hdfsNameNode), conf);
return conf;
}
protected void emit(final String s, final String type) {
try {
key.set(counter.getAndIncrement() + ":" + type);
value.set(s);
writer.append(key, value);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
protected void emitOaf(final Oaf oaf) {
try {
emit(objectMapper.writeValueAsString(oaf), oaf.getClass().getSimpleName().toLowerCase());
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
public ObjectMapper getObjectMapper() {
return objectMapper;
}
@Override
public void close() throws IOException {
writer.hflush();
writer.close();
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/DbClient.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/DbClient.java
View File

@ -1,4 +1,4 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.utils;
import java.io.Closeable;
import java.io.IOException;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MdstoreClient.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/MdstoreClient.java
View File

@ -1,4 +1,4 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.utils;
import java.io.Closeable;
import java.io.IOException;

65
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/OafMapperUtils.java
View File

@ -1,24 +1,12 @@
package eu.dnetlib.dhp.migration;
package eu.dnetlib.dhp.migration.utils;
import java.io.Closeable;
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
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.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.codehaus.jackson.map.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
@ -26,60 +14,12 @@ 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.OAIProvenance;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OriginDescription;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.DHPUtils;
public class AbstractMigrationExecutor implements Closeable {
private final AtomicInteger counter = new AtomicInteger(0);
private final Text key = new Text();
private final Text value = new Text();
private final ObjectMapper objectMapper = new ObjectMapper();
private final SequenceFile.Writer writer;
private static final Log log = LogFactory.getLog(AbstractMigrationExecutor.class);
public AbstractMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception {
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser));
this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
.keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class));
}
private Configuration getConf(final String hdfsNameNode, final String hdfsUser) throws IOException {
final Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
System.setProperty("HADOOP_USER_NAME", hdfsUser);
System.setProperty("hadoop.home.dir", "/");
FileSystem.get(URI.create(hdfsNameNode), conf);
return conf;
}
protected void emitOaf(final Oaf oaf) {
try {
key.set(counter.getAndIncrement() + ":" + oaf.getClass().getSimpleName().toLowerCase());
value.set(objectMapper.writeValueAsString(oaf));
writer.append(key, value);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
@Override
public void close() throws IOException {
writer.hflush();
writer.close();
}
public class OafMapperUtils {
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
@ -247,4 +187,5 @@ public class AbstractMigrationExecutor implements Closeable {
public static String asString(final Object o) {
return o == null ? "" : o.toString();
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/pace/PacePerson.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/PacePerson.java
View File

@ -1,4 +1,4 @@
package eu.dnetlib.dhp.migration.pace;
package eu.dnetlib.dhp.migration.utils;
import java.nio.charset.Charset;
import java.text.Normalizer;

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json
View File

@ -1,8 +1,8 @@
[
{
"paramName": "s",
"paramLongName": "sourcePaths",
"paramDescription": "the HDFS source paths which contains the sequential file (comma separated)",
"paramLongName": "sourcePath",
"paramDescription": "the source path",
"paramRequired": true
},
{

39
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/generate_entities_parameters.json Normal file
View File

@ -0,0 +1,39 @@
[
{
"paramName": "s",
"paramLongName": "sourcePaths",
"paramDescription": "the HDFS source paths which contains the sequential file (comma separated)",
"paramRequired": true
},
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the path of the target file",
"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
}
]

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

@ -18,19 +18,19 @@
"paramRequired": true
},
{
"paramName": "dburl",
"paramName": "pgurl",
"paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramRequired": true
},
{
"paramName": "dbuser",
"paramName": "pguser",
"paramLongName": "postgresUser",
"paramDescription": "postgres user",
"paramRequired": false
},
{
"paramName": "dbpasswd",
"paramName": "pgpasswd",
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json
View File

@ -24,7 +24,7 @@
"paramRequired": true
},
{
"paramName": "db",
"paramName": "mongodb",
"paramLongName": "mongoDb",
"paramDescription": "mongo database",
"paramRequired": true
@ -46,23 +46,5 @@
"paramLongName": "mdInterpretation",
"paramDescription": "metadata interpretation",
"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
}
]

0
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/config-default.xml → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/config-default.xml
View File

174
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml → dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/workflow.xml
View File

@ -1,14 +1,17 @@
<workflow-app name="import Entities from aggretor to HDFS" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<name>migrationClaimsPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<name>graphRawPath</name>
<name>migrationClaimsPathStep2</name>
<description>the temporary path to store entities before dispatching</description>
</property>
<property>
<name>migrationClaimsPathStep3</name>
<description>the graph Raw base path</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
@ -22,7 +25,7 @@
<description>the password postgres</description>
</property>
<property>
<name>mongourl</name>
<name>mongoURL</name>
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
</property>
<property>
@ -43,7 +46,7 @@
</property>
</parameters>
<start to="ResetWorkingPath"/>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@ -51,143 +54,118 @@
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}'/>
<mkdir path='${workingPath}'/>
<delete path='${migrationClaimsPathStep1}'/>
<mkdir path='${migrationClaimsPathStep1}'/>
</fs>
<ok to="ImportEntitiesFromPostgres"/>
<ok to="ImportDBClaims"/>
<error to="Kill"/>
</action>
<action name="ImportEntitiesFromPostgres">
<action name="ImportDBClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${workingPath}/db_entities</arg>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
<arg>-n</arg><arg>${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>
</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>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>-a</arg><arg>claims</arg>
</java>
<ok to="ImportODFEntitiesFromMongoDB"/>
<error to="Kill"/>
</action>
<action name="ImportODFEntitiesFromMongoDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingPath}/odf_entities</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>cleaned</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportOAFEntitiesFromMongoDB"/>
<error to="Kill"/>
</action>
<action name="ImportOAFEntitiesFromMongoDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingPath}/oaf_entities</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>cleaned</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportODFClaimsFromMongoDB"/>
<ok to="ImportODFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportODFClaimsFromMongoDB">
<action name="ImportODFClaims">
<java>
<job-tracker>${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>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongourl}</arg>
<arg>-db</arg><arg>${mongoDb}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</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"/>
<ok to="ImportOAFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportOAFClaimsFromMongoDB">
<action name="ImportOAFClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${workingPath}/oaf_claims</arg>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/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>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${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>${postgresPassword}</arg>
</java>
<ok to="ExtractEntities"/>
<ok to="ResetClaimEntities"/>
<error to="Kill"/>
</action>
<action name="ExtractEntities">
<action name="ResetClaimEntities">
<fs>
<delete path='${migrationClaimsPathStep2}'/>
<mkdir path='${migrationClaimsPathStep2}'/>
</fs>
<ok to="GenerateClaimEntities"/>
<error to="Kill"/>
</action>
<action name="GenerateClaimEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractEntities</name>
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
<name>GenerateClaimEntities</name>
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${workingPath}/db_entities,${workingPath}/oaf_entities,${workingPath}/odf_entities</arg>
<arg>-g</arg><arg>${graphRawPath}</arg>
<arg>-s</arg><arg>${migrationClaimsPathStep1}/db_claims,${migrationClaimsPathStep1}/oaf_claims,${migrationClaimsPathStep1}/odf_claims</arg>
<arg>-t</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="ResetClaimGraph"/>
<error to="Kill"/>
</action>
<action name="ResetClaimGraph">
<fs>
<delete path='${migrationClaimsPathStep3}'/>
<mkdir path='${migrationClaimsPathStep3}'/>
</fs>
<ok to="GenerateClaimGraph"/>
<error to="Kill"/>
</action>
<action name="GenerateClaimGraph">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateClaimGraph</name>
<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
<arg>-g</arg><arg>${migrationClaimsPathStep3}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

22
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/config-default.xml Normal file
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@ -0,0 +1,22 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

174
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/workflow.xml Normal file
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@ -0,0 +1,174 @@
<workflow-app name="import regular entities as Graph (all steps)" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<name>migrationPathStep2</name>
<description>the temporary path to store entities before dispatching</description>
</property>
<property>
<name>migrationPathStep3</name>
<description>the graph Raw base path</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>mongoURL</name>
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
</property>
<property>
<name>mongoDb</name>
<description>mongo database</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${migrationPathStep1}'/>
<mkdir path='${migrationPathStep1}'/>
</fs>
<ok to="ImportDB"/>
<error to="Kill"/>
</action>
<action name="ImportDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportODF"/>
<error to="Kill"/>
</action>
<action name="ImportODF">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/odf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
</java>
<ok to="ImportOAF"/>
<error to="Kill"/>
</action>
<action name="ImportOAF">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/oaf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
</java>
<ok to="ResetEntities"/>
<error to="Kill"/>
</action>
<action name="ResetEntities">
<fs>
<delete path='${migrationPathStep2}'/>
<mkdir path='${migrationPathStep2}'/>
</fs>
<ok to="GenerateEntities"/>
<error to="Kill"/>
</action>
<action name="GenerateEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateEntities</name>
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${migrationPathStep1}/db_records,${migrationPathStep1}/oaf_records,${migrationPathStep1}/odf_records</arg>
<arg>-t</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="ResetGraph"/>
<error to="Kill"/>
</action>
<action name="ResetGraph">
<fs>
<delete path='${migrationPathStep3}'/>
<mkdir path='${migrationPathStep3}'/>
</fs>
<ok to="GenerateGraph"/>
<error to="Kill"/>
</action>
<action name="GenerateGraph">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateGraph</name>
<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-g</arg><arg>${migrationPathStep3}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

22
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/config-default.xml Normal file
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@ -0,0 +1,22 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

109
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/workflow.xml Normal file
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@ -0,0 +1,109 @@
<workflow-app name="import regular entities as Graph (step 1)" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>mongoURL</name>
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
</property>
<property>
<name>mongoDb</name>
<description>mongo database</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${migrationPathStep1}'/>
<mkdir path='${migrationPathStep1}'/>
</fs>
<ok to="ImportDB"/>
<error to="Kill"/>
</action>
<action name="ImportDB">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportODF"/>
<error to="Kill"/>
</action>
<action name="ImportODF">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/odf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
</java>
<ok to="ImportOAF"/>
<error to="Kill"/>
</action>
<action name="ImportOAF">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/oaf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

22
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/config-default.xml Normal file
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@ -0,0 +1,22 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

74
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/workflow.xml Normal file
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<workflow-app name="import regular entities as Graph (step 2)" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<name>migrationPathStep2</name>
<description>the temporary path to store entities before dispatching</description>
</property>
<property>
<name>postgresURL</name>
<description>the postgres URL to access to the database</description>
</property>
<property>
<name>postgresUser</name>
<description>the user postgres</description>
</property>
<property>
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetEntities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetEntities">
<fs>
<delete path='${migrationPathStep2}'/>
<mkdir path='${migrationPathStep2}'/>
</fs>
<ok to="GenerateEntities"/>
<error to="Kill"/>
</action>
<action name="GenerateEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateEntities</name>
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${migrationPathStep1}/db_records,${migrationPathStep1}/oaf_records,${migrationPathStep1}/odf_records</arg>
<arg>-t</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

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dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/workflow.xml Normal file
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<workflow-app name="import regular entities as Graph (step 3)" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationPathStep2</name>
<description>the temporary path to store entities before dispatching</description>
</property>
<property>
<name>migrationPathStep3</name>
<description>the graph Raw base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetGraph"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetGraph">
<fs>
<delete path='${migrationPathStep3}'/>
<mkdir path='${migrationPathStep3}'/>
</fs>
<ok to="GenerateGraph"/>
<error to="Kill"/>
</action>
<action name="GenerateGraph">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateGraph</name>
<class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
<jar>dhp-aggregation-${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>-s</arg><arg>${migrationPathStep2}/all_entities</arg>
<arg>-g</arg><arg>${migrationPathStep3}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>