forked from D-Net/dnet-hadoop
Merge branch 'master' into deduptesting
This commit is contained in:
commit
ede1af3d85
|
|
@ -47,6 +47,16 @@
|
|||
<artifactId>jaxen</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.hadoop</groupId>
|
||||
<artifactId>hadoop-distcp</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-openaire-data-protos</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<artifactId>dhp-schemas</artifactId>
|
||||
|
|
@ -57,6 +67,44 @@
|
|||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-actionmanager-api</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-actionmanager-common</artifactId>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-openaireplus-mapping-utils</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>saxonica</groupId>
|
||||
<artifactId>saxon</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>saxonica</groupId>
|
||||
<artifactId>saxon-dom</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>jgrapht</groupId>
|
||||
<artifactId>jgrapht</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>net.sf.ehcache</groupId>
|
||||
<artifactId>ehcache</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>org.springframework</groupId>
|
||||
<artifactId>spring-test</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>org.apache.*</groupId>
|
||||
<artifactId>*</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>apache</groupId>
|
||||
<artifactId>*</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
</project>
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
package eu.dnetlib.dhp.migration.actions;
|
||||
package eu.dnetlib.dhp.actionmanager.migration;
|
||||
|
||||
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
|
||||
import java.util.Comparator;
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package eu.dnetlib.dhp.migration.actions;
|
||||
package eu.dnetlib.dhp.actionmanager.migration;
|
||||
|
||||
import com.google.common.base.Splitter;
|
||||
import com.google.common.collect.Lists;
|
||||
|
|
@ -9,35 +9,36 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|||
import java.io.File;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.OutputStream;
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Properties;
|
||||
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.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.tools.DistCp;
|
||||
import org.apache.hadoop.tools.DistCpOptions;
|
||||
import org.apache.hadoop.util.ToolRunner;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class MigrateActionSet {
|
||||
|
||||
private static final Log log = LogFactory.getLog(MigrateActionSet.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
|
||||
|
||||
private static final String SEPARATOR = "/";
|
||||
private static final String TARGET_PATHS = "target_paths";
|
||||
private static final String RAWSET_PREFIX = "rawset_";
|
||||
|
||||
private static Boolean DEFAULT_TRANSFORM_ONLY = false;
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
MigrateActionSet.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json")));
|
||||
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
new MigrateActionSet().run(parser);
|
||||
|
|
@ -56,11 +57,11 @@ public class MigrateActionSet {
|
|||
|
||||
final String transform_only_s = parser.get("transform_only");
|
||||
|
||||
log.info("transform only param: " + transform_only_s);
|
||||
log.info("transform only param: {}", transform_only_s);
|
||||
|
||||
final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
|
||||
|
||||
log.info("transform only: " + transformOnly);
|
||||
log.info("transform only: {}", transformOnly);
|
||||
|
||||
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||
|
||||
|
|
@ -79,22 +80,19 @@ public class MigrateActionSet {
|
|||
|
||||
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
|
||||
log.info(
|
||||
String.format(
|
||||
"paths to process:\n%s",
|
||||
sourcePaths.stream()
|
||||
.map(p -> p.toString())
|
||||
.collect(Collectors.joining("\n"))));
|
||||
"paths to process:\n{}",
|
||||
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
|
||||
for (Path source : sourcePaths) {
|
||||
|
||||
if (!sourceFS.exists(source)) {
|
||||
log.warn(String.format("skipping unexisting path: %s", source));
|
||||
log.warn("skipping unexisting path: {}", source);
|
||||
} else {
|
||||
|
||||
LinkedList<String> pathQ =
|
||||
Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
|
||||
|
||||
final String rawSet = pathQ.pollLast();
|
||||
log.info(String.format("got RAWSET: %s", rawSet));
|
||||
log.info("got RAWSET: {}", rawSet);
|
||||
|
||||
if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
|
||||
|
||||
|
|
@ -109,7 +107,7 @@ public class MigrateActionSet {
|
|||
+ SEPARATOR
|
||||
+ rawSet);
|
||||
|
||||
log.info(String.format("using TARGET PATH: %s", targetPath));
|
||||
log.info("using TARGET PATH: {}", targetPath);
|
||||
|
||||
if (!transformOnly) {
|
||||
if (targetFS.exists(targetPath)) {
|
||||
|
|
@ -1,4 +1,9 @@
|
|||
package eu.dnetlib.dhp.migration.actions;
|
||||
package eu.dnetlib.dhp.actionmanager.migration;
|
||||
|
||||
import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
|
||||
import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
|
||||
import static eu.dnetlib.data.proto.TypeProtos.*;
|
||||
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
|
||||
|
||||
import com.google.common.collect.Lists;
|
||||
import com.googlecode.protobuf.format.JsonFormat;
|
||||
|
|
@ -0,0 +1,179 @@
|
|||
package eu.dnetlib.dhp.actionmanager.migration;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
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 java.util.Optional;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class TransformActions implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
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/actionmanager/migration/transform_actionsets_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged =
|
||||
Optional.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String isLookupUrl = parser.get("isLookupUrl");
|
||||
log.info("isLookupUrl: {}", isLookupUrl);
|
||||
|
||||
final String inputPaths = parser.get("inputPaths");
|
||||
|
||||
if (StringUtils.isBlank(inputPaths)) {
|
||||
throw new RuntimeException("empty inputPaths");
|
||||
}
|
||||
log.info("inputPaths: {}", inputPaths);
|
||||
|
||||
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> transformActions(inputPaths, targetBaseDir, spark));
|
||||
}
|
||||
|
||||
private static void transformActions(
|
||||
String inputPaths, String targetBaseDir, SparkSession spark) throws IOException {
|
||||
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("found target directory '{}", targetDirectory);
|
||||
fs.delete(targetDirectory, true);
|
||||
log.info("deleted target directory '{}", targetDirectory);
|
||||
}
|
||||
|
||||
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
|
||||
|
||||
sc.sequenceFile(sourcePath, Text.class, Text.class)
|
||||
.map(
|
||||
a ->
|
||||
eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(
|
||||
a._2().toString()))
|
||||
.map(TransformActions::doTransform)
|
||||
.filter(Objects::nonNull)
|
||||
.mapToPair(
|
||||
a ->
|
||||
new Tuple2<>(
|
||||
a.getClazz().toString(),
|
||||
OBJECT_MAPPER.writeValueAsString(a)))
|
||||
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
|
||||
.saveAsNewAPIHadoopFile(
|
||||
targetDirectory.toString(),
|
||||
Text.class,
|
||||
Text.class,
|
||||
SequenceFileOutputFormat.class,
|
||||
sc.hadoopConfiguration());
|
||||
}
|
||||
}
|
||||
|
||||
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
|
||||
throws InvalidProtocolBufferException {
|
||||
|
||||
// dedup similarity relations had empty target value, don't migrate them
|
||||
if (aa.getTargetValue().length == 0) {
|
||||
return null;
|
||||
}
|
||||
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 static 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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"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
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "is",
|
||||
"paramLongName": "isLookupUrl",
|
||||
"paramDescription": "URL of the isLookUp Service",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPaths",
|
||||
"paramDescription": "URL of the isLookUp Service",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -10,7 +10,6 @@
|
|||
</property>
|
||||
<property>
|
||||
<name>workingDirectory</name>
|
||||
<value>/tmp/actionsets</value>
|
||||
<description>working directory</description>
|
||||
</property>
|
||||
<property>
|
||||
|
|
@ -44,6 +43,20 @@
|
|||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
|
|
@ -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