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[raw_all] Aggregator graph creation merges claims (updates) with the corresponding entity

This commit is contained in:
Claudio Atzori 2021-06-23 11:49:42 +02:00
parent 5edcc6832a
commit 50fc5a64a0
4 changed files with 106 additions and 45 deletions

View File

@ -27,6 +27,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
@ -37,6 +38,22 @@ public class GenerateEntitiesApplication {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
/**
* Operation mode
*/
enum Mode {
/**
* Groups all the objects by id to merge them
*/
claim,
/**
* Default mode
*/
graph
}
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
@ -67,13 +84,19 @@ public class GenerateEntitiesApplication {
.orElse(true);
log.info("shouldHashId: {}", shouldHashId);
final Mode mode = Optional
.ofNullable(parser.get("mode"))
.map(Mode::valueOf)
.orElse(Mode.graph);
log.info("mode: {}", mode);
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration());
generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId);
generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode);
});
}
@ -82,7 +105,8 @@ public class GenerateEntitiesApplication {
final VocabularyGroup vocs,
final String sourcePaths,
final String targetPath,
final boolean shouldHashId) {
final boolean shouldHashId,
final Mode mode) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final List<String> existingSourcePaths = Arrays
@ -106,7 +130,23 @@ public class GenerateEntitiesApplication {
.flatMap(list -> list.iterator()));
}
inputRdd
switch (mode) {
case claim:
save(
inputRdd
.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
.reduceByKey((o1, o2) -> OafMapperUtils.merge(o1, o2))
.map(Tuple2::_2),
targetPath);
break;
case graph:
save(inputRdd, targetPath);
break;
}
}
private static void save(final JavaRDD<Oaf> rdd, final String targetPath) {
rdd
.map(
oaf -> oaf.getClass().getSimpleName().toLowerCase()
+ "|"

View File

@ -13,7 +13,6 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.function.Predicate;
@ -36,7 +35,6 @@ import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Organization;
@ -54,6 +52,13 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
private static final Logger log = LoggerFactory.getLogger(MigrateDbEntitiesApplication.class);
private static final DataInfo DATA_INFO_CLAIM = dataInfo(
false, null, false, false,
qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9");
private static final List<KeyValue> COLLECTED_FROM_CLAIM = listKeyValues(
createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
public static final String SOURCE_TYPE = "source_type";
public static final String TARGET_TYPE = "target_type";
@ -443,25 +448,19 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
}
public List<Oaf> processClaims(final ResultSet rs) {
final DataInfo info = dataInfo(
false, null, false, false,
qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9");
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
try {
if (rs.getString(SOURCE_TYPE).equals("context")) {
final String sourceType = rs.getString(SOURCE_TYPE);
final String targetType = rs.getString(TARGET_TYPE);
if (sourceType.equals("context")) {
final Result r;
if (rs.getString(TARGET_TYPE).equals("dataset")) {
if (targetType.equals("dataset")) {
r = new Dataset();
r.setResulttype(DATASET_DEFAULT_RESULTTYPE);
} else if (rs.getString(TARGET_TYPE).equals("software")) {
} else if (targetType.equals("software")) {
r = new Software();
r.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
} else if (rs.getString(TARGET_TYPE).equals("other")) {
} else if (targetType.equals("other")) {
r = new OtherResearchProduct();
r.setResulttype(ORP_DEFAULT_RESULTTYPE);
} else {
@ -470,57 +469,72 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
}
r.setId(createOpenaireId(50, rs.getString("target_id"), false));
r.setLastupdatetimestamp(lastUpdateTimestamp);
r.setContext(prepareContext(rs.getString("source_id"), info));
r.setDataInfo(info);
r.setCollectedfrom(collectedFrom);
r.setContext(prepareContext(rs.getString("source_id"), DATA_INFO_CLAIM));
r.setDataInfo(DATA_INFO_CLAIM);
r.setCollectedfrom(COLLECTED_FROM_CLAIM);
return Arrays.asList(r);
} else {
final String validationDate = rs.getString("curation_date");
final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false);
final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
final String sourceId = createOpenaireId(sourceType, rs.getString("source_id"), false);
final String targetId = createOpenaireId(targetType, rs.getString("target_id"), false);
final Relation r1 = new Relation();
final Relation r2 = new Relation();
r1.setValidated(true);
r1.setValidationDate(validationDate);
r1.setCollectedfrom(collectedFrom);
if (StringUtils.isNotBlank(validationDate)) {
r1.setValidated(true);
r1.setValidationDate(validationDate);
r2.setValidated(true);
r2.setValidationDate(validationDate);
}
r1.setCollectedfrom(COLLECTED_FROM_CLAIM);
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setDataInfo(DATA_INFO_CLAIM);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setValidationDate(validationDate);
r2.setValidated(true);
r2.setCollectedfrom(collectedFrom);
r2.setCollectedfrom(COLLECTED_FROM_CLAIM);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setDataInfo(DATA_INFO_CLAIM);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
if (rs.getString(SOURCE_TYPE).equals("project")) {
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
final String semantics = rs.getString("semantics");
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
} else {
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
switch (semantics) {
case "resultResult_relationship_isRelatedTo":
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
break;
case "resultProject_outcome_produces":
if (!"project".equals(sourceType)) {
throw new IllegalStateException(
String
.format(
"invalid claim, sourceId: %s, targetId: %s, semantics: %s",
sourceId, targetId, semantics));
}
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
break;
default:
throw new IllegalArgumentException("claim semantics not managed: " + semantics);
}
return Arrays.asList(r1, r2);
}
} catch (final Exception e) {
throw new RuntimeException(e);
}

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@ -28,5 +28,11 @@
"paramLongName": "shouldHashId",
"paramDescription": "should ids be hashed?",
"paramRequired": false
},
{
"paramName": "m",
"paramLongName": "mode",
"paramDescription": "operation mode",
"paramRequired": false
}
]

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@ -460,6 +460,7 @@
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--shouldHashId</arg><arg>${shouldHashId}</arg>
<arg>--mode</arg><arg>claim</arg>
</spark>
<ok to="GenerateGraph_claims"/>
<error to="Kill"/>