actionsets migration workflow moved in dhp-workflows/dhp-actionmanager
This commit is contained in:
parent
d714bfb4d4
commit
9147af7fed
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@ -47,6 +47,16 @@
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<artifactId>jaxen</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.hadoop</groupId>
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<artifactId>hadoop-distcp</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-openaire-data-protos</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-schemas</artifactId>
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@ -57,6 +67,44 @@
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-api</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-common</artifactId>
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<exclusions>
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<exclusion>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-openaireplus-mapping-utils</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon-dom</artifactId>
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</exclusion>
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<exclusion>
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<groupId>jgrapht</groupId>
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<artifactId>jgrapht</artifactId>
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</exclusion>
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<exclusion>
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<groupId>net.sf.ehcache</groupId>
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<artifactId>ehcache</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.springframework</groupId>
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<artifactId>spring-test</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.*</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>apache</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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</dependencies>
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</project>
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@ -1,4 +1,4 @@
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package eu.dnetlib.dhp.migration.actions;
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package eu.dnetlib.dhp.actionmanager.migration;
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
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import java.util.Comparator;
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@ -1,4 +1,4 @@
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package eu.dnetlib.dhp.migration.actions;
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package eu.dnetlib.dhp.actionmanager.migration;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Lists;
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@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.OutputStream;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.Properties;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.tools.DistCp;
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import org.apache.hadoop.tools.DistCpOptions;
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import org.apache.hadoop.util.ToolRunner;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class MigrateActionSet {
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private static final Log log = LogFactory.getLog(MigrateActionSet.class);
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private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
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private static final String SEPARATOR = "/";
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private static final String TARGET_PATHS = "target_paths";
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private static final String RAWSET_PREFIX = "rawset_";
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private static Boolean DEFAULT_TRANSFORM_ONLY = false;
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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MigrateActionSet.class.getResourceAsStream(
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"/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json")));
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"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
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parser.parseArgument(args);
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new MigrateActionSet().run(parser);
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@ -56,11 +57,11 @@ public class MigrateActionSet {
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final String transform_only_s = parser.get("transform_only");
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log.info("transform only param: " + transform_only_s);
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log.info("transform only param: {}", transform_only_s);
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final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
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log.info("transform only: " + transformOnly);
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log.info("transform only: {}", transformOnly);
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ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
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@ -79,22 +80,19 @@ public class MigrateActionSet {
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final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
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log.info(
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String.format(
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"paths to process:\n%s",
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sourcePaths.stream()
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.map(p -> p.toString())
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.collect(Collectors.joining("\n"))));
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"paths to process:\n{}",
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sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
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for (Path source : sourcePaths) {
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if (!sourceFS.exists(source)) {
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log.warn(String.format("skipping unexisting path: %s", source));
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log.warn("skipping unexisting path: {}", source);
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} else {
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LinkedList<String> pathQ =
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Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
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final String rawSet = pathQ.pollLast();
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log.info(String.format("got RAWSET: %s", rawSet));
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log.info("got RAWSET: {}", rawSet);
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if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
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@ -109,7 +107,7 @@ public class MigrateActionSet {
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+ SEPARATOR
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+ rawSet);
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log.info(String.format("using TARGET PATH: %s", targetPath));
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log.info("using TARGET PATH: {}", targetPath);
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if (!transformOnly) {
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if (targetFS.exists(targetPath)) {
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@ -1,4 +1,9 @@
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package eu.dnetlib.dhp.migration.actions;
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package eu.dnetlib.dhp.actionmanager.migration;
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import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
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import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
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import static eu.dnetlib.data.proto.TypeProtos.*;
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import static eu.dnetlib.data.proto.TypeProtos.Type.*;
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import com.google.common.collect.Lists;
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import com.googlecode.protobuf.format.JsonFormat;
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@ -0,0 +1,174 @@
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package eu.dnetlib.dhp.actionmanager.migration;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Lists;
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import com.google.protobuf.InvalidProtocolBufferException;
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import eu.dnetlib.data.proto.OafProtos;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.LinkedList;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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public class TransformActions implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String SEPARATOR = "/";
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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MigrateActionSet.class.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
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parser.parseArgument(args);
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Boolean isSparkSessionManaged =
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Optional.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final String inputPaths = parser.get("inputPaths");
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if (StringUtils.isBlank(inputPaths)) {
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throw new RuntimeException("empty inputPaths");
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}
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log.info("inputPaths: {}", inputPaths);
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final String targetBaseDir = getTargetBaseDir(isLookupUrl);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> transformActions(inputPaths, targetBaseDir, spark));
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}
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private static void transformActions(
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String inputPaths, String targetBaseDir, SparkSession spark) throws IOException {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
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for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
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LinkedList<String> pathQ =
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Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
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final String rawset = pathQ.pollLast();
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final String actionSetDirectory = pathQ.pollLast();
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final Path targetDirectory =
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new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
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if (fs.exists(targetDirectory)) {
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log.info("found target directory '{}", targetDirectory);
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fs.delete(targetDirectory, true);
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log.info("deleted target directory '{}", targetDirectory);
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}
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log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
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sc.sequenceFile(sourcePath, Text.class, Text.class)
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.map(
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a ->
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eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
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a._2().toString()))
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.map(a -> doTransform(a))
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// .filter(Objects::isNull)
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// .filter(a -> a.getPayload() == null)
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.mapToPair(
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a ->
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new Tuple2<>(
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a.getClazz().toString(),
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OBJECT_MAPPER.writeValueAsString(a)))
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.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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.saveAsNewAPIHadoopFile(
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targetDirectory.toString(),
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Text.class,
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Text.class,
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SequenceFileOutputFormat.class,
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sc.hadoopConfiguration());
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}
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}
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private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
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throws InvalidProtocolBufferException {
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final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
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final Oaf oaf = ProtoConverter.convert(proto_oaf);
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switch (proto_oaf.getKind()) {
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case entity:
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switch (proto_oaf.getEntity().getType()) {
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case datasource:
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return new AtomicAction<>(Datasource.class, (Datasource) oaf);
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case organization:
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return new AtomicAction<>(Organization.class, (Organization) oaf);
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case project:
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return new AtomicAction<>(Project.class, (Project) oaf);
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case result:
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final String resulttypeid =
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proto_oaf
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.getEntity()
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.getResult()
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.getMetadata()
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.getResulttype()
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.getClassid();
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switch (resulttypeid) {
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case "publication":
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return new AtomicAction<>(Publication.class, (Publication) oaf);
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case "software":
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return new AtomicAction<>(Software.class, (Software) oaf);
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case "other":
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return new AtomicAction<>(
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OtherResearchProduct.class, (OtherResearchProduct) oaf);
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case "dataset":
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return new AtomicAction<>(Dataset.class, (Dataset) oaf);
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default:
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// can be an update, where the resulttype is not specified
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return new AtomicAction<>(Result.class, (Result) oaf);
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}
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default:
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throw new IllegalArgumentException(
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"invalid entity type: " + proto_oaf.getEntity().getType());
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}
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case relation:
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return new AtomicAction<>(Relation.class, (Relation) oaf);
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default:
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throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
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}
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}
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private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
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ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
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String XQUERY =
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"collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
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return isLookUp.getResourceProfileByQuery(XQUERY);
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}
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}
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@ -0,0 +1,56 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "is",
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"paramLongName": "isLookupUrl",
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"paramDescription": "URL of the isLookUp Service",
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"paramRequired": true
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},
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{
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"paramName": "sn",
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"paramLongName": "sourceNameNode",
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"paramDescription": "nameNode of the source cluster",
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"paramRequired": true
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},
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{
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"paramName": "tn",
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"paramLongName": "targetNameNode",
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"paramDescription": "namoNode of the target cluster",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "workingDirectory",
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"paramDescription": "working directory",
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"paramRequired": true
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},
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{
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"paramName": "nm",
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"paramLongName": "distcp_num_maps",
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"paramDescription": "maximum number of map tasks used in the distcp process",
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"paramRequired": true
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},
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{
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"paramName": "mm",
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"paramLongName": "distcp_memory_mb",
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"paramDescription": "memory for distcp action copying actionsets from remote cluster",
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"paramRequired": true
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},
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{
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"paramName": "tt",
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"paramLongName": "distcp_task_timeout",
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"paramDescription": "timeout for distcp copying actions from remote cluster",
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"paramRequired": true
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},
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{
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"paramName": "tr",
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"paramLongName": "transform_only",
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"paramDescription": "activate tranform-only mode. Only apply transformation step",
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"paramRequired": true
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}
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]
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@ -0,0 +1,20 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "is",
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"paramLongName": "isLookupUrl",
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"paramDescription": "URL of the isLookUp Service",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "inputPaths",
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"paramDescription": "URL of the isLookUp Service",
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"paramRequired": true
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}
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]
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@ -10,7 +10,6 @@
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</property>
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<property>
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<name>workingDirectory</name>
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<value>/tmp/actionsets</value>
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<description>working directory</description>
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</property>
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<property>
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@ -44,6 +43,20 @@
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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@ -66,23 +79,27 @@
|
|||
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||
<value>${oozieLauncherQueueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to='migrate_actionsets' />
|
||||
<start to="migrate_actionsets"/>
|
||||
|
||||
<action name='migrate_actionsets'>
|
||||
<action name="migrate_actionsets">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.migration.actions.MigrateActionSet</main-class>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.migration.MigrateActionSet</main-class>
|
||||
<java-opt>-Dmapred.task.timeout=${distcp_task_timeout}</java-opt>
|
||||
<arg>-is</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>-sn</arg><arg>${sourceNN}</arg>
|
||||
<arg>-tn</arg><arg>${nameNode}</arg>
|
||||
<arg>-w</arg><arg>${workingDirectory}</arg>
|
||||
<arg>-nm</arg><arg>${distcp_num_maps}</arg>
|
||||
<arg>-mm</arg><arg>${distcp_memory_mb}</arg>
|
||||
<arg>-tt</arg><arg>${distcp_task_timeout}</arg>
|
||||
<arg>-tr</arg><arg>${transform_only}</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--sourceNameNode</arg><arg>${sourceNN}</arg>
|
||||
<arg>--targetNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--workingDirectory</arg><arg>${workingDirectory}</arg>
|
||||
<arg>--distcp_num_maps</arg><arg>${distcp_num_maps}</arg>
|
||||
<arg>--distcp_memory_mb</arg><arg>${distcp_memory_mb}</arg>
|
||||
<arg>--distcp_task_timeout</arg><arg>${distcp_task_timeout}</arg>
|
||||
<arg>--transform_only</arg><arg>${transform_only}</arg>
|
||||
<capture-output/>
|
||||
</java>
|
||||
<ok to="transform_actions" />
|
||||
|
|
@ -94,19 +111,18 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>transform_actions</name>
|
||||
<class>eu.dnetlib.dhp.migration.actions.TransformActions</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<class>eu.dnetlib.dhp.actionmanager.migration.TransformActions</class>
|
||||
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores ${sparkExecutorCores}
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
|
||||
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg><arg>yarn</arg>
|
||||
<arg>-is</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--inputPaths</arg><arg>${wf:actionData('migrate_actionsets')['target_paths']}</arg>
|
||||
</spark>
|
||||
<ok to="end"/>
|
||||
|
|
@ -1,213 +0,0 @@
|
|||
package eu.dnetlib.dhp.migration.actions;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.google.common.base.Splitter;
|
||||
import com.google.common.collect.Lists;
|
||||
import com.google.protobuf.InvalidProtocolBufferException;
|
||||
import eu.dnetlib.data.proto.OafProtos;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.util.LinkedList;
|
||||
import java.util.Objects;
|
||||
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.hadoop.io.compress.GzipCodec;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
||||
public class TransformActions implements Serializable {
|
||||
|
||||
private static final Log log = LogFactory.getLog(TransformActions.class);
|
||||
private static final String SEPARATOR = "/";
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
MigrateActionSet.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
new TransformActions().run(parser);
|
||||
}
|
||||
|
||||
private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException {
|
||||
|
||||
final String isLookupUrl = parser.get("isLookupUrl");
|
||||
log.info("isLookupUrl: " + isLookupUrl);
|
||||
|
||||
final String inputPaths = parser.get("inputPaths");
|
||||
|
||||
if (StringUtils.isBlank(inputPaths)) {
|
||||
throw new RuntimeException("empty inputPaths");
|
||||
}
|
||||
log.info("inputPaths: " + inputPaths);
|
||||
|
||||
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
|
||||
|
||||
try (SparkSession spark = getSparkSession(parser)) {
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
|
||||
|
||||
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
|
||||
|
||||
LinkedList<String> pathQ =
|
||||
Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
|
||||
|
||||
final String rawset = pathQ.pollLast();
|
||||
final String actionSetDirectory = pathQ.pollLast();
|
||||
|
||||
final Path targetDirectory =
|
||||
new Path(
|
||||
targetBaseDir
|
||||
+ SEPARATOR
|
||||
+ actionSetDirectory
|
||||
+ SEPARATOR
|
||||
+ rawset);
|
||||
|
||||
if (fs.exists(targetDirectory)) {
|
||||
log.info(String.format("found target directory '%s", targetDirectory));
|
||||
fs.delete(targetDirectory, true);
|
||||
log.info(String.format("deleted target directory '%s", targetDirectory));
|
||||
}
|
||||
|
||||
log.info(
|
||||
String.format(
|
||||
"transforming actions from '%s' to '%s'",
|
||||
sourcePath, targetDirectory));
|
||||
|
||||
sc.sequenceFile(sourcePath, Text.class, Text.class)
|
||||
.map(
|
||||
a ->
|
||||
eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
|
||||
a._2().toString()))
|
||||
.map(a -> doTransform(a))
|
||||
.filter(Objects::isNull)
|
||||
.filter(a -> a.getPayload() == null)
|
||||
.map(a -> new ObjectMapper().writeValueAsString(a))
|
||||
.saveAsTextFile(targetDirectory.toString(), GzipCodec.class);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private Text transformAction(eu.dnetlib.actionmanager.actions.AtomicAction aa)
|
||||
throws InvalidProtocolBufferException, JsonProcessingException {
|
||||
final Text out = new Text();
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) {
|
||||
out.set(mapper.writeValueAsString(doTransform(aa)));
|
||||
}
|
||||
return out;
|
||||
}
|
||||
|
||||
private AtomicAction<Relation> getRelationAtomicAction(String atomicaActionId) {
|
||||
final String[] splitId = atomicaActionId.split("@");
|
||||
|
||||
String source = splitId[0];
|
||||
String target = splitId[2];
|
||||
|
||||
String[] relSemantic = splitId[1].split("_");
|
||||
|
||||
Relation rel = new Relation();
|
||||
rel.setSource(source);
|
||||
rel.setTarget(target);
|
||||
rel.setRelType(relSemantic[0]);
|
||||
rel.setSubRelType(relSemantic[1]);
|
||||
rel.setRelClass(relSemantic[2]);
|
||||
|
||||
DataInfo d = new DataInfo();
|
||||
d.setDeletedbyinference(false);
|
||||
d.setInferenceprovenance("deduplication");
|
||||
d.setInferred(true);
|
||||
d.setInvisible(false);
|
||||
Qualifier provenanceaction = new Qualifier();
|
||||
|
||||
provenanceaction.setClassid("deduplication");
|
||||
provenanceaction.setClassname("deduplication");
|
||||
provenanceaction.setSchemeid("dnet:provenanceActions");
|
||||
provenanceaction.setSchemename("dnet:provenanceActions");
|
||||
|
||||
d.setProvenanceaction(provenanceaction);
|
||||
|
||||
rel.setDataInfo(d);
|
||||
|
||||
return new AtomicAction<>(Relation.class, rel);
|
||||
}
|
||||
|
||||
private AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
|
||||
throws InvalidProtocolBufferException {
|
||||
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
|
||||
final Oaf oaf = ProtoConverter.convert(proto_oaf);
|
||||
switch (proto_oaf.getKind()) {
|
||||
case entity:
|
||||
switch (proto_oaf.getEntity().getType()) {
|
||||
case datasource:
|
||||
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
|
||||
case organization:
|
||||
return new AtomicAction<>(Organization.class, (Organization) oaf);
|
||||
case project:
|
||||
return new AtomicAction<>(Project.class, (Project) oaf);
|
||||
case result:
|
||||
final String resulttypeid =
|
||||
proto_oaf
|
||||
.getEntity()
|
||||
.getResult()
|
||||
.getMetadata()
|
||||
.getResulttype()
|
||||
.getClassid();
|
||||
switch (resulttypeid) {
|
||||
case "publication":
|
||||
return new AtomicAction<>(Publication.class, (Publication) oaf);
|
||||
case "software":
|
||||
return new AtomicAction<>(Software.class, (Software) oaf);
|
||||
case "other":
|
||||
return new AtomicAction<>(
|
||||
OtherResearchProduct.class, (OtherResearchProduct) oaf);
|
||||
case "dataset":
|
||||
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
|
||||
default:
|
||||
// can be an update, where the resulttype is not specified
|
||||
return new AtomicAction<>(Result.class, (Result) oaf);
|
||||
}
|
||||
default:
|
||||
throw new IllegalArgumentException(
|
||||
"invalid entity type: " + proto_oaf.getEntity().getType());
|
||||
}
|
||||
case relation:
|
||||
return new AtomicAction<>(Relation.class, (Relation) oaf);
|
||||
default:
|
||||
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
|
||||
}
|
||||
}
|
||||
|
||||
private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
|
||||
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||
String XQUERY =
|
||||
"collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
|
||||
return isLookUp.getResourceProfileByQuery(XQUERY);
|
||||
}
|
||||
|
||||
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
return SparkSession.builder()
|
||||
.appName(TransformActions.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
}
|
||||
}
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
[
|
||||
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
|
||||
{"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true},
|
||||
{"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true},
|
||||
{"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true},
|
||||
{"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true},
|
||||
{"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true},
|
||||
{"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"inputPaths", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}
|
||||
]
|
||||
Loading…
Reference in New Issue