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dnet-hadoop
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code formatting

This commit is contained in:
Claudio Atzori 2022-09-27 14:55:10 +02:00
parent b60985cf68
commit 57dbeb08d2
8 changed files with 121 additions and 54 deletions
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3
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java
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@ -5,9 +5,10 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import com.google.gson.Gson;
import org.apache.avro.generic.GenericData;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
public class Community implements Serializable {

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java
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@ -77,7 +77,7 @@ public class CommunityConfiguration implements Serializable {
if (zenodocommunityMap == null) {
zenodocommunityMap = Maps.newHashMap();
}
if(selectionConstraintsMap == null){
if (selectionConstraintsMap == null) {
selectionConstraintsMap = Maps.newHashMap();
}

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java
View File

@ -91,10 +91,11 @@ public class CommunityConfigurationFactory {
private static SelectionConstraints parseConstrains(Node node) {
Node aconstraints = node.selectSingleNode("./advancedConstraints");
if(aconstraints == null){
if (aconstraints == null) {
return null;
}
SelectionConstraints selectionConstraints = new Gson().fromJson(aconstraints.getText(), SelectionConstraints.class);
SelectionConstraints selectionConstraints = new Gson()
.fromJson(aconstraints.getText(), SelectionConstraints.class);
selectionConstraints.setSelection(resolver);
return selectionConstraints;

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java
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@ -70,7 +70,7 @@ public class QueryInformationSystem {
+ " </zenodocommunity>} "
+ " </zenodocommunities> "
+ "<advancedConstraint>"
+"{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} "
+ "{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} "
+ "</advancedConstraint>"
+ " </community>";

106
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
View File

@ -9,16 +9,16 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
/** Created by miriam on 02/08/2018. */
public class ResultTagger implements Serializable {
@ -134,11 +134,17 @@ public class ResultTagger implements Serializable {
/* Tagging for Advanced Constraints */
final Set<String> aconstraints = new HashSet<>();
conf.getSelectionConstraintsMap().keySet()
conf
.getSelectionConstraintsMap()
.keySet()
.forEach(communityId -> {
if(conf.getSelectionConstraintsMap().get(communityId) != null &&
conf.getSelectionConstraintsMap().get(communityId)
.getCriteria().stream().anyMatch(crit -> crit.verifyCriteria(param)))
if (conf.getSelectionConstraintsMap().get(communityId) != null &&
conf
.getSelectionConstraintsMap()
.get(communityId)
.getCriteria()
.stream()
.anyMatch(crit -> crit.verifyCriteria(param)))
aconstraints.add(communityId);
});
@ -163,21 +169,48 @@ public class ResultTagger implements Serializable {
}
if (subjects.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS,
DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (datasources.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS,
DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (czenodo.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS,
DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (aconstraints.contains(c))
dataInfoList
.add(
OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
}
});
@ -198,21 +231,48 @@ public class ResultTagger implements Serializable {
List<DataInfo> dataInfoList = new ArrayList<>();
if (subjects.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS,
DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (datasources.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (czenodo.contains(c))
dataInfoList
.add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
.add(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS,
DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
if (aconstraints.contains(c))
dataInfoList
.add(
OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST));
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST));
context.setDataInfo(dataInfoList);
return context;

13
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
View File

@ -11,11 +11,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.bulktag.community.ProtoMap;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -32,6 +27,12 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.bulktag.community.ProtoMap;
import eu.dnetlib.dhp.schema.oaf.*;
public class BulkTagJobTest {
@ -44,7 +45,7 @@ public class BulkTagJobTest {
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\", "
+" \"subject\" :\"$['subject'][*]['value']\" }";
+ " \"subject\" :\"$['subject'][*]['value']\" }";
private static SparkSession spark;

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java
View File

@ -10,7 +10,6 @@ import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -33,6 +32,7 @@ import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public class CleanCountrySparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
@ -113,7 +113,10 @@ public class CleanCountrySparkJob implements Serializable {
if (r
.getPid()
.stream()
.anyMatch(p -> p.getQualifier().getClassid()
.anyMatch(
p -> p
.getQualifier()
.getClassid()
.equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) {
r
.setCountry(

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -422,7 +422,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final Relation r2 = OafMapperUtils
.getRelation(
orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, lastUpdateTimestamp);
orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info,
lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {