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

This commit is contained in:
Sandro La Bruzzo 2020-07-10 14:44:57 +02:00
parent a7d3977481 2d742a84ae
commit c01efed79b
37 changed files with 677 additions and 421 deletions
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4
dhp-workflows/dhp-broker-events/pom.xml
View File

@ -57,9 +57,9 @@
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dnet-openaire-broker-common</artifactId>
<version>[3.0.4,4.0.0)</version>
<version>[3.0.0-SNAPSHOT,)</version>
</dependency>
</dependencies>

112
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java Normal file
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@ -0,0 +1,112 @@
package eu.dnetlib.dhp.broker.oa;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.TypedColumn;
import org.apache.spark.sql.expressions.Aggregator;
import org.apache.spark.util.LongAccumulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.broker.model.Event;
import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
import scala.Tuple2;
public class CheckDuplictedIdsJob {
private static final Logger log = LoggerFactory.getLogger(CheckDuplictedIdsJob.class);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
CheckDuplictedIdsJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
parser.parseArgument(args);
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
log.info("eventsPath: {}", eventsPath);
final String countPath = parser.get("workingPath") + "/counts";
log.info("countPath: {}", countPath);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final LongAccumulator total = spark.sparkContext().longAccumulator("invaild_event_id");
final TypedColumn<Tuple2<String, Long>, Tuple2<String, Long>> agg = new CountAggregator().toColumn();
ClusterUtils
.readPath(spark, eventsPath, Event.class)
.map(e -> new Tuple2<>(e.getEventId(), 1l), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.groupByKey(t -> t._1, Encoders.STRING())
.agg(agg)
.map(t -> t._2, Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.filter(t -> t._2 > 1)
.map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.write()
.mode(SaveMode.Overwrite)
.json(countPath);
;
}
private static String eventAsJsonString(final Event f) throws JsonProcessingException {
return new ObjectMapper().writeValueAsString(f);
}
}
class CountAggregator extends Aggregator<Tuple2<String, Long>, Tuple2<String, Long>, Tuple2<String, Long>> {
/**
*
*/
private static final long serialVersionUID = 1395935985734672538L;
@Override
public Encoder<Tuple2<String, Long>> bufferEncoder() {
return Encoders.tuple(Encoders.STRING(), Encoders.LONG());
}
@Override
public Tuple2<String, Long> finish(final Tuple2<String, Long> arg0) {
return arg0;
}
@Override
public Tuple2<String, Long> merge(final Tuple2<String, Long> arg0, final Tuple2<String, Long> arg1) {
final String s = StringUtils.defaultIfBlank(arg0._1, arg1._1);
return new Tuple2<>(s, arg0._2 + arg1._2);
}
@Override
public Encoder<Tuple2<String, Long>> outputEncoder() {
return Encoders.tuple(Encoders.STRING(), Encoders.LONG());
}
@Override
public Tuple2<String, Long> reduce(final Tuple2<String, Long> arg0, final Tuple2<String, Long> arg1) {
final String s = StringUtils.defaultIfBlank(arg0._1, arg1._1);
return new Tuple2<>(s, arg0._2 + arg1._2);
}
@Override
public Tuple2<String, Long> zero() {
return new Tuple2<>(null, 0l);
}
}

60
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java
View File

@ -3,8 +3,6 @@ package eu.dnetlib.dhp.broker.oa;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
@ -20,8 +18,6 @@ import org.apache.spark.util.LongAccumulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.broker.model.Event;
import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
@ -29,9 +25,6 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
import eu.dnetlib.dhp.broker.oa.util.EventFinder;
import eu.dnetlib.dhp.broker.oa.util.EventGroup;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
public class GenerateEventsJob {
@ -54,30 +47,20 @@ public class GenerateEventsJob {
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String dedupConfigProfileId = parser.get("dedupConfProfile");
log.info("dedupConfigProfileId: {}", dedupConfigProfileId);
final String eventsPath = workingPath + "/events";
log.info("eventsPath: {}", eventsPath);
final Set<String> dsIdWhitelist = parseParamAsList(parser, "datasourceIdWhitelist");
final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
log.info("datasourceIdWhitelist: {}", StringUtils.join(dsIdWhitelist, ","));
final Set<String> dsTypeWhitelist = parseParamAsList(parser, "datasourceTypeWhitelist");
final Set<String> dsTypeWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceTypeWhitelist");
log.info("datasourceTypeWhitelist: {}", StringUtils.join(dsTypeWhitelist, ","));
final Set<String> dsIdBlacklist = parseParamAsList(parser, "datasourceIdBlacklist");
final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ","));
final SparkConf conf = new SparkConf();
// TODO UNCOMMENT
// final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId);
final DedupConfig dedupConfig = null;
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
ClusterUtils.removeDir(spark, eventsPath);
@ -92,7 +75,7 @@ public class GenerateEventsJob {
final Dataset<Event> dataset = groups
.map(
g -> EventFinder
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, dedupConfig, accumulators),
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
Encoders
.bean(EventGroup.class))
.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));
@ -103,22 +86,6 @@ public class GenerateEventsJob {
}
private static Set<String> parseParamAsList(final ArgumentApplicationParser parser, final String key) {
final String s = parser.get(key).trim();
final Set<String> res = new HashSet<>();
if (s.length() > 1) { // A value of a single char (for example: '-') indicates an empty list
Arrays
.stream(s.split(","))
.map(String::trim)
.filter(StringUtils::isNotBlank)
.forEach(res::add);
}
return res;
}
public static Map<String, LongAccumulator> prepareAccumulators(final SparkContext sc) {
return EventFinder
@ -130,23 +97,4 @@ public class GenerateEventsJob {
}
private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception {
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final String conf = isLookUpService
.getResourceProfileByQuery(
String
.format(
"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
profId));
final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class);
dedupConfig.getPace().initModel();
dedupConfig.getPace().initTranslationMap();
// dedupConfig.getWf().setConfigurationId("???");
return dedupConfig;
}
}

2
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java
View File

@ -48,7 +48,7 @@ public class IndexOnESJob {
final JavaRDD<String> inputRdd = ClusterUtils
.readPath(spark, eventsPath, Event.class)
.limit(10000) // TODO REMOVE
// .limit(10000) // TODO REMOVE
.map(IndexOnESJob::eventAsJsonString, Encoders.STRING())
.javaRDD();

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java
View File

@ -17,7 +17,6 @@ import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.pace.config.DedupConfig;
public abstract class UpdateMatcher<T> {
@ -37,7 +36,6 @@ public abstract class UpdateMatcher<T> {
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity res,
final Collection<OaBrokerMainEntity> others,
final DedupConfig dedupConfig,
final Map<String, LongAccumulator> accumulators) {
final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
@ -49,7 +47,7 @@ public abstract class UpdateMatcher<T> {
if (topic != null) {
final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, res,
getCompileHighlightFunction(),
getHighlightToStringFunction(), dedupConfig);
getHighlightToStringFunction());
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {

2
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java
View File

@ -15,7 +15,7 @@ public class EnrichMissingProject extends UpdateMatcher<OaBrokerProject> {
super(20,
prj -> Topic.ENRICH_MISSING_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
prj -> prj.getOpenaireId());
}
@Override

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java
View File

@ -18,11 +18,7 @@ public class EnrichMoreProject extends UpdateMatcher<OaBrokerProject> {
super(20,
prj -> Topic.ENRICH_MORE_PROJECT,
(p, prj) -> p.getProjects().add(prj),
prj -> projectAsString(prj));
}
private static String projectAsString(final OaBrokerProject prj) {
return prj.getFunder() + "::" + prj.getFundingProgram() + "::" + prj.getCode();
prj -> prj.getOpenaireId());
}
@Override
@ -36,13 +32,13 @@ public class EnrichMoreProject extends UpdateMatcher<OaBrokerProject> {
final Set<String> existingProjects = target
.getProjects()
.stream()
.map(EnrichMoreProject::projectAsString)
.map(p -> p.getOpenaireId())
.collect(Collectors.toSet());
return source
.getProjects()
.stream()
.filter(p -> !existingProjects.contains(projectAsString(p)))
.filter(p -> !existingProjects.contains(p.getOpenaireId()))
.collect(Collectors.toList());
}

26
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java
View File

@ -1,6 +1,11 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -10,6 +15,7 @@ import org.apache.spark.util.LongAccumulator;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
public class ClusterUtils {
@ -53,7 +59,9 @@ public class ClusterUtils {
return o;
}
public static <T> void save(final Dataset<T> dataset, final String path, final Class<T> clazz,
public static <T> void save(final Dataset<T> dataset,
final String path,
final Class<T> clazz,
final LongAccumulator acc) {
dataset
.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
@ -62,4 +70,20 @@ public class ClusterUtils {
.json(path);
}
public static Set<String> parseParamAsList(final ArgumentApplicationParser parser, final String key) {
final String s = parser.get(key).trim();
final Set<String> res = new HashSet<>();
if (s.length() > 1) { // A value of a single char (for example: '-') indicates an empty list
Arrays
.stream(s.split(","))
.map(String::trim)
.filter(StringUtils::isNotBlank)
.forEach(res::add);
}
return res;
}
}

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -142,6 +142,7 @@ public class ConversionUtils {
.filter(pid -> pid.getQualifier().getClassid() != null)
.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid"))
.map(pid -> pid.getValue())
.map(pid -> cleanOrcid(pid))
.filter(StringUtils::isNotBlank)
.findFirst()
.orElse(null) : null;
@ -149,6 +150,11 @@ public class ConversionUtils {
return new OaBrokerAuthor(author.getFullname(), pids);
}
private static String cleanOrcid(final String s) {
final String match = "//orcid.org/";
return s.contains(match) ? StringUtils.substringAfter(s, match) : s;
}
private static OaBrokerJournal oafJournalToBrokerJournal(final Journal journal) {
if (journal == null) {
return null;

5
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java
View File

@ -37,7 +37,6 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess;
import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid;
import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.pace.config.DedupConfig;
public class EventFinder {
@ -70,14 +69,12 @@ public class EventFinder {
matchers.add(new EnrichMissingDatasetReferences());
matchers.add(new EnrichMissingDatasetIsSupplementedTo());
matchers.add(new EnrichMissingDatasetIsSupplementedBy());
matchers.add(new EnrichMissingAbstract());
}
public static EventGroup generateEvents(final ResultGroup results,
final Set<String> dsIdWhitelist,
final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist,
final DedupConfig dedupConfig,
final Map<String, LongAccumulator> accumulators) {
final List<UpdateInfo<?>> list = new ArrayList<>();
@ -85,7 +82,7 @@ public class EventFinder {
for (final OaBrokerMainEntity target : results.getData()) {
if (verifyTarget(target, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), dedupConfig, accumulators));
list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), accumulators));
}
}
}

54
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java
View File

@ -1,8 +1,62 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.io.IOException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.tree.support.TreeProcessor;
import eu.dnetlib.pace.util.MapDocumentUtil;
public class TrustUtils {
private static final Logger log = LoggerFactory.getLogger(TrustUtils.class);
private static DedupConfig dedupConfig;
static {
final ObjectMapper mapper = new ObjectMapper();
try {
dedupConfig = mapper
.readValue(
DedupConfig.class.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
DedupConfig.class);
} catch (final IOException e) {
log.error("Error loading dedupConfig, e");
}
}
protected static float calculateTrust(final OaBrokerMainEntity r1, final OaBrokerMainEntity r2) {
if (dedupConfig == null) {
return BrokerConstants.MIN_TRUST;
}
try {
final ObjectMapper objectMapper = new ObjectMapper();
final MapDocument doc1 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1));
final MapDocument doc2 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2));
final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2);
final double threshold = dedupConfig.getWf().getThreshold();
return TrustUtils.rescale(score, threshold);
} catch (final Exception e) {
log.error("Error computing score between results", e);
return BrokerConstants.MIN_TRUST;
}
}
public static float rescale(final double score, final double threshold) {
if (score >= BrokerConstants.MAX_TRUST) {
return BrokerConstants.MAX_TRUST;

41
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java
View File

@ -4,20 +4,11 @@ package eu.dnetlib.dhp.broker.oa.util;
import java.util.function.BiConsumer;
import java.util.function.Function;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.broker.objects.OaBrokerEventPayload;
import eu.dnetlib.broker.objects.OaBrokerInstance;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerProvenance;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.tree.support.TreeProcessor;
import eu.dnetlib.pace.util.MapDocumentUtil;
public final class UpdateInfo<T> {
@ -35,20 +26,17 @@ public final class UpdateInfo<T> {
private final float trust;
private static final Logger log = LoggerFactory.getLogger(UpdateInfo.class);
public UpdateInfo(final Topic topic, final T highlightValue, final OaBrokerMainEntity source,
final OaBrokerMainEntity target,
final BiConsumer<OaBrokerMainEntity, T> compileHighlight,
final Function<T, String> highlightToString,
final DedupConfig dedupConfig) {
final Function<T, String> highlightToString) {
this.topic = topic;
this.highlightValue = highlightValue;
this.source = source;
this.target = target;
this.compileHighlight = compileHighlight;
this.highlightToString = highlightToString;
this.trust = calculateTrust(dedupConfig, source, target);
this.trust = TrustUtils.calculateTrust(source, target);
}
public T getHighlightValue() {
@ -63,31 +51,6 @@ public final class UpdateInfo<T> {
return target;
}
private float calculateTrust(final DedupConfig dedupConfig,
final OaBrokerMainEntity r1,
final OaBrokerMainEntity r2) {
if (dedupConfig == null) {
return BrokerConstants.MIN_TRUST;
}
try {
final ObjectMapper objectMapper = new ObjectMapper();
final MapDocument doc1 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1));
final MapDocument doc2 = MapDocumentUtil
.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2));
final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2);
final double threshold = dedupConfig.getWf().getThreshold();
return TrustUtils.rescale(score, threshold);
} catch (final Exception e) {
log.error("Error computing score between results", e);
return BrokerConstants.MIN_TRUST;
}
}
protected Topic getTopic() {
return topic;
}

122
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json Normal file
View File

@ -0,0 +1,122 @@
{
"wf": {
},
"pace": {
"clustering": [
{
"name": "wordssuffixprefix",
"fields": [
"title"
],
"params": {
"max": "2",
"len": "3"
}
},
{
"name": "lowercase",
"fields": [
"doi"
],
"params": {
}
}
],
"decisionTree": {
"start": {
"fields": [
{
"field": "doi",
"comparator": "exactMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer1",
"undefined": "layer1",
"ignoreUndefined": "true"
},
"layer1": {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 0.9,
"countIfUndefined": "false",
"params": {
}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 0.9,
"countIfUndefined": "false",
"params": {
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {
}
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model": [
{
"name": "doi",
"type": "String",
"path": "$.pids[?(@.type == 'doi')].value"
},
{
"name": "title",
"type": "String",
"path": "$.titles",
"length": 250,
"size": 5
},
{
"name": "authors",
"type": "List",
"path": "$.creators[*].fullname",
"size": 200
}
],
"blacklists": {
},
"synonyms": {
}
}
}

12
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
View File

@ -8,14 +8,6 @@
<property>
<name>workingPath</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>dedupConfProfId</name>
<description>the id of a valid Dedup Configuration Profile</description>
</property>
<property>
<name>datasourceIdWhitelist</name>
@ -427,8 +419,6 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--dedupConfProfile</arg><arg>${dedupConfProfId}</arg>
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
@ -447,7 +437,7 @@
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="2"
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

12
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json
View File

@ -5,18 +5,6 @@
"paramDescription": "the path where the generated events will be stored",
"paramRequired": true
},
{
"paramName": "lu",
"paramLongName": "isLookupUrl",
"paramDescription": "the address of the ISLookUpService",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dedupConfProfile",
"paramDescription": "the id of a valid Dedup Configuration Profile",
"paramRequired": true
},
{
"paramName": "datasourceIdWhitelist",
"paramLongName": "datasourceIdWhitelist",

22
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml
View File

@ -9,15 +9,6 @@
<name>workingPath</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>dedupConfProfId</name>
<description>the id of a valid Dedup Configuration Profile</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -73,33 +64,32 @@
</configuration>
</global>
<start to="index_es"/>
<start to="count"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="index_es">
<action name="count">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexOnESJob</class>
<name>Count</name>
<class>eu.dnetlib.dhp.broker.oa.CheckDuplictedIdsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="2"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--index</arg><arg>${esIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

12
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java
View File

@ -30,7 +30,7 @@ class UpdateMatcherTest {
final OaBrokerMainEntity p4 = new OaBrokerMainEntity();
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -46,7 +46,7 @@ class UpdateMatcherTest {
res.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -62,7 +62,7 @@ class UpdateMatcherTest {
p2.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.size() == 1);
}
@ -79,7 +79,7 @@ class UpdateMatcherTest {
p2.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -98,7 +98,7 @@ class UpdateMatcherTest {
p4.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.isEmpty());
}
@ -117,7 +117,7 @@ class UpdateMatcherTest {
p4.setPublicationdate("2018");
final Collection<UpdateInfo<String>> list = matcher
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
assertTrue(list.size() == 1);
}

21
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java
View File

@ -5,6 +5,10 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.Test;
import eu.dnetlib.broker.objects.OaBrokerAuthor;
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerTypedValue;
public class TrustUtilsTest {
private static final double THRESHOLD = 0.95;
@ -64,6 +68,23 @@ public class TrustUtilsTest {
verifyValue(2.00, BrokerConstants.MAX_TRUST);
}
@Test
public void test() throws Exception {
final OaBrokerMainEntity r1 = new OaBrokerMainEntity();
r1.getTitles().add("D-NET Service Package: Data Import");
r1.getPids().add(new OaBrokerTypedValue("doi", "123"));
r1.getCreators().add(new OaBrokerAuthor("Michele Artini", null));
r1.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
final OaBrokerMainEntity r2 = new OaBrokerMainEntity();
r2.getTitles().add("D-NET Service Package: Data Import");
// r2.getPids().add(new OaBrokerTypedValue("doi", "123"));
r2.getCreators().add(new OaBrokerAuthor("Michele Artini", null));
// r2.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
System.out.println("TRUST: " + TrustUtils.calculateTrust(r1, r2));
}
private void verifyValue(final double originalScore, final float expectedTrust) {
final float trust = TrustUtils.rescale(originalScore, THRESHOLD);
System.out.println(trust);

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java
View File

@ -37,7 +37,7 @@ public class Deduper implements Serializable {
public static JavaPairRDD<String, Block> createSortedBlocks(
JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
final String of = config.getWf().getOrderField();
final int maxQueueSize = config.getWf().getGroupMaxSize();
final int maxQueueSize = config.getWf().getQueueMaxSize();
return mapDocs
// the reduce is just to be sure that we haven't document with same id

10
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -45,6 +45,16 @@ public class EntityMergerTest implements Serializable {
}
@Test
public void softwareMergerTest() throws InstantiationException, IllegalAccessException {
List<Tuple2<String, Software>> softwares = readSample(testEntityBasePath + "/software_merge.json", Software.class);
Software merged = DedupRecordFactory
.entityMerger(dedupId, softwares.iterator(), 0, dataInfo, Software.class);
System.out.println(merged.getBestaccessright().getClassid());
}
@Test
public void publicationMergerTest() throws InstantiationException, IllegalAccessException {

6
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -182,7 +182,7 @@ public class SparkDedupTest implements Serializable {
.count();
assertEquals(3432, orgs_simrel);
assertEquals(7152, pubs_simrel);
assertEquals(7054, pubs_simrel);
assertEquals(344, sw_simrel);
assertEquals(458, ds_simrel);
assertEquals(6750, orp_simrel);
@ -234,7 +234,7 @@ public class SparkDedupTest implements Serializable {
.count();
assertEquals(1276, orgs_mergerel);
assertEquals(1442, pubs_mergerel);
assertEquals(1440, pubs_mergerel);
assertEquals(288, sw_mergerel);
assertEquals(472, ds_mergerel);
assertEquals(718, orp_mergerel);
@ -423,7 +423,7 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(4975, relations);
assertEquals(4971, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels = spark

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json
View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "dataset",
"orderField" : "title",
"queueMaxSize" : "2000",
"queueMaxSize" : "800",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"slidingWindowSize" : "80",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,8 +17,7 @@
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json
View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "otherresearchproduct",
"orderField" : "title",
"queueMaxSize" : "2000",
"queueMaxSize" : "800",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"slidingWindowSize" : "80",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,8 +17,7 @@
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree" : {

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json
View File

@ -6,10 +6,10 @@
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "2000",
"queueMaxSize": "800",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "200",
"slidingWindowSize": "80",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
@ -29,8 +29,7 @@
},
"pace": {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {

7
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json
View File

@ -6,10 +6,10 @@
"subEntityType" : "resulttype",
"subEntityValue" : "software",
"orderField" : "title",
"queueMaxSize" : "2000",
"queueMaxSize" : "800",
"groupMaxSize" : "100",
"maxChildren" : "100",
"slidingWindowSize" : "200",
"slidingWindowSize" : "80",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true",
"idPath" : "$.id",
@ -17,8 +17,7 @@
},
"pace" : {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
{ "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
],
"decisionTree": {

3
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/software_merge.json Normal file
View File

File diff suppressed because one or more lines are too long

17
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java
View File

@ -8,6 +8,7 @@ import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
@ -97,7 +98,7 @@ public class CleanGraphSparkJob {
.json(outputPath);
}
private static <T extends Oaf> T fixDefaults(T value) {
protected static <T extends Oaf> T fixDefaults(T value) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
@ -134,11 +135,6 @@ public class CleanGraphSparkJob {
.setResourcetype(
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
}
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
r
.setBestaccessright(
qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
}
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
@ -152,6 +148,15 @@ public class CleanGraphSparkJob {
}
}
}
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance());
if (Objects.isNull(bestaccessrights)) {
r.setBestaccessright(
qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
} else {
r.setBestaccessright(bestaccessrights);
}
}
if (Objects.nonNull(r.getAuthor())) {
boolean nullRank = r
.getAuthor()

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -378,6 +378,10 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<Qualifier> min = instanceList

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/config-default.xml → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/config-default.xml
View File

157
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,157 @@
<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>reuseContent</name>
<value>false</value>
<description>should import content from the aggregator or reuse a previous version</description>
</property>
<property>
<name>contentPath</name>
<description>path location to store (or reuse) content from the aggregator</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>dbSchema</name>
<value>beta</value>
<description>the database schema according to the D-Net infrastructure (beta or production)</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>isLookupUrl</name>
<description>the address of the lookUp service</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>
<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>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="ImportDB_claims"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportDB_claims">
<java>
<prepare>
<delete path="${contentPath}/db_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>claims</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
</java>
<ok to="ImportODF_claims"/>
<error to="Kill"/>
</action>
<action name="ImportODF_claims">
<java>
<prepare>
<delete path="${contentPath}/odf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/odf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="ImportOAF_claims"/>
<error to="Kill"/>
</action>
<action name="ImportOAF_claims">
<java>
<prepare>
<delete path="${contentPath}/oaf_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
<arg>-mongourl</arg><arg>${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>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

169
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/workflow.xml
View File

@ -1,169 +0,0 @@
<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationClaimsPathStep1</name>
<description>the base path to store hdfs file</description>
</property>
<property>
<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>
</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[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${migrationClaimsPathStep1}'/>
<mkdir path='${migrationClaimsPathStep1}'/>
</fs>
<ok to="ImportDBClaims"/>
<error to="Kill"/>
</action>
<action name="ImportDBClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>-a</arg><arg>claims</arg>
</java>
<ok to="ImportODFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportODFClaims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</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>
</java>
<ok to="ImportOAFClaims"/>
<error to="Kill"/>
</action>
<action name="ImportOAFClaims">
<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>${migrationClaimsPathStep1}/oaf_claims</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>claim</arg>
</java>
<ok to="ResetClaimEntities"/>
<error to="Kill"/>
</action>
<action name="ResetClaimEntities">
<fs>
<delete path='${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>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateClaimEntities</name>
<class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
<jar>dhp-aggregation-${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>${migrationClaimsPathStep1}/db_claims,${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"/>
</action>
<end name="End"/>
</workflow-app>

5
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java
View File

@ -57,6 +57,8 @@ public class CleaningFunctionTest {
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertNull(p_in.getBestaccessright());
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
@ -84,6 +86,9 @@ public class CleaningFunctionTest {
.map(p -> p.getQualifier())
.allMatch(q -> pidTerms.contains(q.getClassid())));
Publication p_defaults = CleanGraphSparkJob.fixDefaults(p_out);
assertEquals("CLOSED", p_defaults.getBestaccessright().getClassid());
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_out));

7
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -185,12 +185,7 @@
"surname": ""
}
],
"bestaccessright": {
"classid": "CLOSED",
"classname": "Closed Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"bestaccessright": null,
"collectedfrom": [
{
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",

1
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java
View File

@ -156,6 +156,7 @@ public class PrepareRelationsJob {
.parquet(outputPath);
}
// experimental
private static void prepareRelationsDataset(
SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
int relPartitions) {

1
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
View File

@ -134,6 +134,7 @@
<arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation</arg>
<arg>--maxRelations</arg><arg>${maxRelations}</arg>
<arg>--relationFilter</arg><arg>${relationFilter}</arg>
<arg>--relPartitions</arg><arg>5000</arg>
</spark>
<ok to="fork_join_related_entities"/>

159
dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_construction.xml
View File

@ -11,6 +11,29 @@
<WORKFLOW_TYPE>Data Provision</WORKFLOW_TYPE>
<WORKFLOW_PRIORITY>30</WORKFLOW_PRIORITY>
<CONFIGURATION start="manual">
<NODE isStart="true" name="setReuseContent" type="SetEnvParameter">
<DESCRIPTION>reuse cached content from the aggregation system</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">reuseContent</PARAM>
<PARAM function="validValues(['true', 'false'])" managedBy="user" name="parameterValue" required="true" type="string">true</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setContentPath" type="SetEnvParameter">
<DESCRIPTION>set the aggregator content path</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">contentPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_aggregator</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setAggregatorGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the path containing the AGGREGATOR graph</DESCRIPTION>
<PARAMETERS>
@ -62,87 +85,94 @@
</ARCS>
</NODE>
<NODE isStart="true" name="setCleanedGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the CLEANED graph</DESCRIPTION>
<NODE isStart="true" name="setOrcidGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the ORCID enriched graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">cleanedGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/05_graph_cleaned</PARAM>
<PARAM managedBy="system" name="parameterName" required="true" type="string">orcidGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/05_graph_orcid</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setOrcidGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the ORCID enriched graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">orcidGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/06_graph_orcid</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setBulkTaggingGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the BULK TAGGED graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">bulkTaggingGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/07_graph_bulktagging</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/06_graph_bulktagging</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setAffiliationGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the AFFILIATION from INSTITUTIONAL REPOS graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">affiliationGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/08_graph_affiliation</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/07_graph_affiliation</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setCommunityOrganizationGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the COMMUNITY from SELECTED SOURCES graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">communityOrganizationGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/09_graph_comunity_organization</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/08_graph_comunity_organization</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setFundingGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the FUNDING from SEMANTIC RELATION graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">fundingGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/10_graph_funding</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/09_graph_funding</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setCommunitySemRelGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the COMMUNITY from SEMANTIC RELATION graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">communitySemRelGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/11_graph_comunity_sem_rel</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/10_graph_comunity_sem_rel</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setCountryGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the COUNTRY enriched graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">countryGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/12_graph_country</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/11_graph_country</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setCleanedGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the CLEANED graph</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="parameterName" required="true" type="string">cleanedGraphPath</PARAM>
<PARAM managedBy="user" name="parameterValue" required="true" type="string">/tmp/beta_provision/graph/12_graph_cleaned</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setBlacklistedGraphPath" type="SetEnvParameter">
<DESCRIPTION>Set the target path to store the blacklisted graph</DESCRIPTION>
<PARAMETERS>
@ -153,6 +183,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setIsLookUpUrl" type="SetEnvParameter">
<DESCRIPTION>Set the lookup address</DESCRIPTION>
<PARAMETERS>
@ -163,6 +194,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setBulkTaggingPathMap" type="SetEnvParameter">
<DESCRIPTION>Set the map of paths for the Bulk Tagging</DESCRIPTION>
<PARAMETERS>
@ -173,6 +205,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setPropagationOrganizationCommunityMap" type="SetEnvParameter">
<DESCRIPTION>Set the map of associations organization, community list for the propagation of community to result through organization</DESCRIPTION>
<PARAMETERS>
@ -185,6 +218,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="setDedupConfig" type="SetEnvParameter">
<DESCRIPTION>Set the dedup orchestrator name</DESCRIPTION>
<PARAMETERS>
@ -195,6 +229,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="actionSetsRaw" type="SetEnvParameter">
<DESCRIPTION>declares the ActionSet ids to promote in the RAW graph</DESCRIPTION>
<PARAMETERS>
@ -205,6 +240,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isStart="true" name="actionSetsIIS" type="SetEnvParameter">
<DESCRIPTION>declares the ActionSet ids to promote in the INFERRED graph</DESCRIPTION>
<PARAMETERS>
@ -215,6 +251,7 @@
<ARC to="waitConfig"/>
</ARCS>
</NODE>
<NODE isJoin="true" name="waitConfig">
<DESCRIPTION>wait configurations</DESCRIPTION>
<PARAMETERS/>
@ -222,6 +259,7 @@
<ARC to="aggregatorGraph"/>
</ARCS>
</NODE>
<NODE name="aggregatorGraph" type="SubmitHadoopJob">
<DESCRIPTION>create the AGGREGATOR graph</DESCRIPTION>
<PARAMETERS>
@ -230,7 +268,9 @@
<PARAM managedBy="system" name="envParams" required="true" type="string">
{
'graphOutputPath' : 'aggregatorGraphPath',
'isLookupUrl' : 'isLookUpUrl'
'isLookupUrl' : 'isLookUpUrl',
'reuseContent' : 'reuseContent',
'contentPath' : 'contentPath'
}
</PARAM>
<PARAM managedBy="system" name="params" required="true" type="string">
@ -241,8 +281,6 @@
'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus',
'postgresUser' : 'dnet',
'postgresPassword' : '',
'reuseContent' : 'false',
'contentPath' : '/tmp/beta_provision/aggregator',
'workingDir' : '/tmp/beta_provision/working_dir/aggregator'
}
</PARAM>
@ -252,6 +290,7 @@
<ARC to="promoteActionsRaw"/>
</ARCS>
</NODE>
<NODE name="promoteActionsRaw" type="SubmitHadoopJob">
<DESCRIPTION>create the RAW graph</DESCRIPTION>
<PARAMETERS>
@ -289,6 +328,7 @@
<ARC to="duplicateScan"/>
</ARCS>
</NODE>
<NODE name="duplicateScan" type="SubmitHadoopJob">
<DESCRIPTION>search for duplicates in the raw graph</DESCRIPTION>
<PARAMETERS>
@ -314,6 +354,7 @@
<ARC to="promoteActionsIIS"/>
</ARCS>
</NODE>
<NODE name="promoteActionsIIS" type="SubmitHadoopJob">
<DESCRIPTION>create the INFERRED graph</DESCRIPTION>
<PARAMETERS>
@ -351,6 +392,7 @@
<ARC to="dedupConsistency"/>
</ARCS>
</NODE>
<NODE name="dedupConsistency" type="SubmitHadoopJob">
<DESCRIPTION>mark duplicates as deleted and redistribute the relationships</DESCRIPTION>
<PARAMETERS>
@ -375,41 +417,6 @@
</ARCS>
</NODE>
<NODE name="graphCleaning" type="SubmitHadoopJob">
<DESCRIPTION>clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="hadoopJob" required="true" type="string">executeOozieJob</PARAM>
<PARAM managedBy="system" name="cluster" required="true" type="string">IIS</PARAM>
<PARAM managedBy="system" name="envParams" required="true" type="string">
{
'graphInputPath' : 'consistentGraphPath',
'graphOutputPath': 'cleanedGraphPath',
'isLookupUrl': 'isLookUpUrl'
}
</PARAM>
<PARAM managedBy="system" name="params" required="true" type="string">
{
'oozie.wf.application.path' : '/lib/dnet/oa/graph/clean/oozie_app',
'workingPath' : '/tmp/beta_provision/working_dir/clean'
}
</PARAM>
<PARAM managedBy="system" name="oozieReportActionsCsv" required="true" type="string">build-report</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="SKIP_ENRICHMENT"/>
</ARCS>
</NODE>
<NODE name="SKIP_ENRICHMENT" type="Selection">
<DESCRIPTION>Do we skip the graph enrichment steps? (Yes to prepare the graph for the IIS)</DESCRIPTION>
<PARAMETERS>
<PARAM function="validValues(['YES', 'NO'])" managedBy="user" name="selection" required="true" type="string">NO</PARAM>
</PARAMETERS>
<ARCS>
<ARC name="YES" to="success"/>
<ARC name="NO" to="orcidPropagation"/>
</ARCS>
</NODE>
<NODE name="orcidPropagation" type="SubmitHadoopJob">
<DESCRIPTION>propagates ORCID among results linked by allowedsemrels semantic relationships</DESCRIPTION>
<PARAMETERS>
@ -417,7 +424,7 @@
<PARAM managedBy="system" name="cluster" required="true" type="string">IIS</PARAM>
<PARAM managedBy="system" name="envParams" required="true" type="string">
{
'sourcePath' : 'cleanedGraphPath',
'sourcePath' : 'consistentGraphPath',
'outputPath': 'orcidGraphPath'
}
</PARAM>
@ -435,6 +442,7 @@
<ARC to="bulkTagging"/>
</ARCS>
</NODE>
<NODE name="bulkTagging" type="SubmitHadoopJob">
<DESCRIPTION>mark results respecting some rules as belonging to communities</DESCRIPTION>
<PARAMETERS>
@ -460,6 +468,7 @@
<ARC to="affiliationPropagation"/>
</ARCS>
</NODE>
<NODE name="affiliationPropagation" type="SubmitHadoopJob">
<DESCRIPTION>creates relashionships between results and organizations when the organizations are associated to institutional repositories</DESCRIPTION>
<PARAMETERS>
@ -484,6 +493,7 @@
<ARC to="communityOrganizationPropagation"/>
</ARCS>
</NODE>
<NODE name="communityOrganizationPropagation" type="SubmitHadoopJob">
<DESCRIPTION>marks as belonging to communities the result collected from datasources related to the organizations specified in the organizationCommunityMap</DESCRIPTION>
<PARAMETERS>
@ -509,6 +519,7 @@
<ARC to="resultProjectPropagation"/>
</ARCS>
</NODE>
<NODE name="resultProjectPropagation" type="SubmitHadoopJob">
<DESCRIPTION>created relation between projects and results linked to other results trough allowedsemrel semantic relations linked to projects</DESCRIPTION>
<PARAMETERS>
@ -534,6 +545,7 @@
<ARC to="communitySemrelPropagation"/>
</ARCS>
</NODE>
<NODE name="communitySemrelPropagation" type="SubmitHadoopJob">
<DESCRIPTION>tag as belonging to communitites result in in allowedsemrels relation with other result already linked to communities </DESCRIPTION>
<PARAMETERS>
@ -560,6 +572,7 @@
<ARC to="countryPropagation"/>
</ARCS>
</NODE>
<NODE name="countryPropagation" type="SubmitHadoopJob">
<DESCRIPTION>associated to results colleced from allowedtypes and those in the whithelist the country of the organization(s) handling the datasource it is collected from </DESCRIPTION>
<PARAMETERS>
@ -584,10 +597,36 @@
</PARAM>
<PARAM managedBy="system" name="oozieReportActionsCsv" required="true" type="string">build-report</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="graphCleaning"/>
</ARCS>
</NODE>
<NODE name="graphCleaning" type="SubmitHadoopJob">
<DESCRIPTION>clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid</DESCRIPTION>
<PARAMETERS>
<PARAM managedBy="system" name="hadoopJob" required="true" type="string">executeOozieJob</PARAM>
<PARAM managedBy="system" name="cluster" required="true" type="string">IIS</PARAM>
<PARAM managedBy="system" name="envParams" required="true" type="string">
{
'graphInputPath' : 'countryGraphPath',
'graphOutputPath': 'cleanedGraphPath',
'isLookupUrl': 'isLookUpUrl'
}
</PARAM>
<PARAM managedBy="system" name="params" required="true" type="string">
{
'oozie.wf.application.path' : '/lib/dnet/oa/graph/clean/oozie_app',
'workingPath' : '/tmp/beta_provision/working_dir/clean'
}
</PARAM>
<PARAM managedBy="system" name="oozieReportActionsCsv" required="true" type="string">build-report</PARAM>
</PARAMETERS>
<ARCS>
<ARC to="blacklistRelations"/>
</ARCS>
</NODE>
<NODE name="blacklistRelations" type="SubmitHadoopJob">
<DESCRIPTION>removes blacklisted relations </DESCRIPTION>
<PARAMETERS>
@ -595,7 +634,7 @@
<PARAM managedBy="system" name="cluster" required="true" type="string">IIS</PARAM>
<PARAM managedBy="system" name="envParams" required="true" type="string">
{
'sourcePath' : 'countryGraphPath',
'sourcePath' : 'cleanedGraphPath',
'outputPath': 'blacklistedGraphPath'
}
</PARAM>

2
pom.xml
View File

@ -315,7 +315,7 @@
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
<version>4.0.1</version>
<version>4.0.2</version>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>