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Merge remote-tracking branch 'origin/stable_ids' into stable_id_scholexplorer

This commit is contained in:
Sandro La Bruzzo 2021-06-24 17:20:50 +02:00
parent 80e15cc455 67afd06cd1
commit ad50415167
8 changed files with 137 additions and 85 deletions
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20
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -224,24 +224,20 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (Objects.nonNull(i.getPid())) {
i.setPid(processPidCleaning(i.getPid()));
}
if (Objects.nonNull(i.getAlternateIdentifier())) {
i.setAlternateIdentifier(processPidCleaning(i.getAlternateIdentifier()));
}
Optional
.ofNullable(i.getPid())
.ifPresent(pid -> {
final Set<StructuredProperty> pids = pid
.stream()
.filter(Objects::nonNull)
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect(Collectors.toCollection(HashSet::new));
final Set<StructuredProperty> pids = Sets.newHashSet(pid);
Optional
.ofNullable(i.getAlternateIdentifier())
.ifPresent(altId -> {
final Set<StructuredProperty> altIds = altId
.stream()
.filter(Objects::nonNull)
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect(Collectors.toCollection(HashSet::new));
final Set<StructuredProperty> altIds = Sets.newHashSet(altId);
i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids)));
});
});

48
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java
View File

@ -144,22 +144,7 @@ public class PrepareProgramme {
JavaRDD<CSVProgramme> h2020Programmes = programme
.toJavaRDD()
.mapToPair(csvProgramme -> new Tuple2<>(csvProgramme.getCode(), csvProgramme))
.reduceByKey((a, b) -> {
if (!a.getLanguage().equals("en")) {
if (b.getLanguage().equalsIgnoreCase("en")) {
a.setTitle(b.getTitle());
a.setLanguage(b.getLanguage());
}
}
if (StringUtils.isEmpty(a.getShortTitle())) {
if (!StringUtils.isEmpty(b.getShortTitle())) {
a.setShortTitle(b.getShortTitle());
}
}
return a;
})
.reduceByKey(PrepareProgramme::groupProgrammeByCode)
.map(p -> {
CSVProgramme csvProgramme = p._2();
String programmeTitle = csvProgramme.getTitle().trim();
@ -176,20 +161,31 @@ public class PrepareProgramme {
return csvProgramme;
});
// prepareClassification(h2020Programmes);
JavaSparkContext jsc = new JavaSparkContext(spark.sparkContext());
final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CSVProgramme> rdd = jsc.parallelize(prepareClassification(h2020Programmes), 1);
rdd
.map(csvProgramme -> {
String tmp = OBJECT_MAPPER.writeValueAsString(csvProgramme);
return tmp;
})
.map(OBJECT_MAPPER::writeValueAsString)
.saveAsTextFile(outputPath);
}
private static CSVProgramme groupProgrammeByCode(CSVProgramme a, CSVProgramme b) {
if (!a.getLanguage().equals("en")) {
if (b.getLanguage().equalsIgnoreCase("en")) {
a.setTitle(b.getTitle());
a.setLanguage(b.getLanguage());
}
}
if (StringUtils.isEmpty(a.getShortTitle())) {
if (!StringUtils.isEmpty(b.getShortTitle())) {
a.setShortTitle(b.getShortTitle());
}
}
return a;
}
private static List<CSVProgramme> prepareClassification(JavaRDD<CSVProgramme> h2020Programmes) {
Object[] codedescription = h2020Programmes
.map(
@ -240,10 +236,10 @@ public class PrepareProgramme {
if (!ent.contains("Euratom")) {
String parent;
String tmp_key = tmp[0] + ".";
String tmpKey = tmp[0] + ".";
for (int i = 1; i < tmp.length - 1; i++) {
tmp_key += tmp[i] + ".";
parent = map.get(tmp_key)._1().toLowerCase().trim();
tmpKey += tmp[i] + ".";
parent = map.get(tmpKey)._1().toLowerCase().trim();
if (parent.contains("|")) {
parent = parent.substring(parent.lastIndexOf("|") + 1).trim();
}

44
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
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()));
}
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()
+ "|"

82
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
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 {
@ -470,45 +469,42 @@ 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();
if (StringUtils.isNotBlank(validationDate)) {
r1.setValidated(true);
r1.setValidationDate(validationDate);
r1.setCollectedfrom(collectedFrom);
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 {
switch (semantics) {
case "resultResult_relationship_isRelatedTo":
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
@ -516,11 +512,29 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
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);
}

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json
View File

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

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

@ -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"/>

1
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -26,7 +26,6 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.*;

2
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_entry.json
View File

@ -21,7 +21,7 @@
},
{
"field": "semantics",
"type": "not_used",
"type": "string",
"value": "resultProject_outcome_produces"
}
]