From 3d6be209899806d9c319eb034f26b1248e671091 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Oct 2023 14:26:33 +0200 Subject: [PATCH 01/23] changes to use the API instead of the IS the get the information for the communities to be used during bulktagging and context propagation --- .../bipfinder/SparkAtomicActionScoreJob.java | 2 +- .../dhp/oa/dedup/SparkPropagateRelation.java | 72 +++---- .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 78 +++++++ .../main/java/eu/dnetlib/dhp/api/Utils.java | 136 +++++++++++++ .../api/model/CommunityContentprovider.java | 43 ++++ .../model/CommunityEntityMap.java} | 6 +- .../dnetlib/dhp/api/model/CommunityModel.java | 108 ++++++++++ .../dhp/api/model/CommunitySummary.java | 16 ++ .../dnetlib/dhp/api/model/ContentModel.java | 50 +++++ .../dnetlib/dhp/api/model/DatasourceList.java | 12 ++ .../dhp/api/model/OrganizationList.java | 15 ++ .../dnetlib/dhp/api/model/ProjectModel.java | 23 +++ .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 4 +- .../dhp/bulktag/community/Community.java | 10 +- .../community/CommunityConfiguration.java | 8 +- .../CommunityConfigurationFactory.java | 13 +- .../dhp/bulktag/community/Constraint.java | 20 +- .../community/SelectionConstraints.java | 3 +- .../PrepareResultCommunitySet.java | 17 +- .../oozie_app/workflow.xml | 8 +- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 38 ++++ .../CommunityConfigurationFactoryTest.java | 2 +- .../dhp/bulktag/QueryCommunityAPITest.java | 91 +++++++++ .../group/GroupEntitiesSparkJobTest.java | 190 +++++++++--------- 24 files changed, 787 insertions(+), 178 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java rename dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/{resulttocommunityfromorganization/OrganizationMap.java => api/model/CommunityEntityMap.java} (59%) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c89782..8adc88920 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + // project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java index 739295c91..cb1c70059 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java @@ -67,60 +67,60 @@ public class SparkPropagateRelation extends AbstractSparkAction { log.info("graphOutputPath: '{}'", graphOutputPath); Dataset mergeRels = spark - .read() - .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) - .as(REL_BEAN_ENC); + .read() + .load(DedupUtility.createMergeRelPath(workingPath, "*", "*")) + .as(REL_BEAN_ENC); // Dataset idsToMerge = mergeRels - .where(col("relClass").equalTo(ModelConstants.MERGES)) - .select(col("source").as("dedupID"), col("target").as("mergedObjectID")) - .distinct(); + .where(col("relClass").equalTo(ModelConstants.MERGES)) + .select(col("source").as("dedupID"), col("target").as("mergedObjectID")) + .distinct(); Dataset allRels = spark - .read() - .schema(REL_BEAN_ENC.schema()) - .json(graphBasePath + "/relation"); + .read() + .schema(REL_BEAN_ENC.schema()) + .json(graphBasePath + "/relation"); Dataset dedupedRels = allRels - .joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer") - .joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer") - .select("_1._1", "_1._2.dedupID", "_2.dedupID") - .as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING())) - .map((MapFunction, Relation>) t -> { - Relation rel = t._1(); - String newSource = t._2(); - String newTarget = t._3(); + .joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer") + .joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer") + .select("_1._1", "_1._2.dedupID", "_2.dedupID") + .as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING())) + .map((MapFunction, Relation>) t -> { + Relation rel = t._1(); + String newSource = t._2(); + String newTarget = t._3(); - if (rel.getDataInfo() == null) { - rel.setDataInfo(new DataInfo()); - } + if (rel.getDataInfo() == null) { + rel.setDataInfo(new DataInfo()); + } - if (newSource != null || newTarget != null) { - rel.getDataInfo().setDeletedbyinference(false); + if (newSource != null || newTarget != null) { + rel.getDataInfo().setDeletedbyinference(false); - if (newSource != null) - rel.setSource(newSource); + if (newSource != null) + rel.setSource(newSource); - if (newTarget != null) - rel.setTarget(newTarget); - } + if (newTarget != null) + rel.setTarget(newTarget); + } - return rel; - }, REL_BEAN_ENC); + return rel; + }, REL_BEAN_ENC); // ids of records that are both not deletedbyinference and not invisible Dataset ids = validIds(spark, graphBasePath); // filter relations that point to valid records, can force them to be visible Dataset cleanedRels = dedupedRels - .join(ids, col("source").equalTo(ids.col("id")), "leftsemi") - .join(ids, col("target").equalTo(ids.col("id")), "leftsemi") - .as(REL_BEAN_ENC) - .map((MapFunction) r -> { - r.getDataInfo().setInvisible(false); - return r; - }, REL_KRYO_ENC); + .join(ids, col("source").equalTo(ids.col("id")), "leftsemi") + .join(ids, col("target").equalTo(ids.col("id")), "leftsemi") + .as(REL_BEAN_ENC) + .map((MapFunction) r -> { + r.getDataInfo().setInvisible(false); + return r; + }, REL_KRYO_ENC); Dataset distinctRels = cleanedRels .groupByKey( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java new file mode 100644 index 000000000..635ee2027 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -0,0 +1,78 @@ + +package eu.dnetlib.dhp.api; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.OutputStream; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; + +import org.apache.http.HttpHeaders; +import org.jetbrains.annotations.NotNull; + +import com.google.gson.Gson; + +/** + * @author miriam.baglioni + * @Date 06/10/23 + */ +public class QueryCommunityAPI { + private static final String baseUrl = "https://services.openaire.eu/openaire/"; + + private static String get(String geturl) throws IOException{ + URL url = new URL(geturl); + HttpURLConnection conn = (HttpURLConnection) url.openConnection(); + conn.setDoOutput(true); + conn.setRequestMethod("GET"); + + int responseCode = conn.getResponseCode(); + String body = getBody(conn); + conn.disconnect(); + if (responseCode != HttpURLConnection.HTTP_OK) + throw new IOException("Unexpected code " + responseCode + body); + + return body; + } + + public static String communities() throws IOException { + return get(baseUrl + "community/communities"); + } + + public static String community(String id) throws IOException { + return get(baseUrl + "community/" + id); + } + + public static String communityDatasource(String id)throws IOException{ + return get(baseUrl + "community/" + id + "/contentproviders"); + + } + + public static String communityPropagationOrganization(String id) throws IOException { + return get(baseUrl + "community/" + id + "/propagationOrganizations"); + } + + public static String communityProjects(String id, String page, String size) throws IOException{ + return get(baseUrl + "community/" + id +"/projects/" + page + "/" + size); + } + + @NotNull + private static String getBody(HttpURLConnection conn) throws IOException { + String body = "{}"; + try (BufferedReader br = new BufferedReader( + new InputStreamReader(conn.getInputStream(), "utf-8"))) { + StringBuilder response = new StringBuilder(); + String responseLine = null; + while ((responseLine = br.readLine()) != null) { + response.append(responseLine.trim()); + } + + body = response.toString(); + + } + return body; + } + + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java new file mode 100644 index 000000000..5b3004a5d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -0,0 +1,136 @@ +package eu.dnetlib.dhp.api; + +import com.amazonaws.util.StringUtils; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Maps; +import eu.dnetlib.dhp.api.model.*; +import eu.dnetlib.dhp.bulktag.community.Community; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; +import eu.dnetlib.dhp.bulktag.community.Provider; +import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; +import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory; + +import javax.management.Query; +import java.io.IOException; +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Collectors; + +/** + * @author miriam.baglioni + * @Date 09/10/23 + */ +public class Utils implements Serializable { + private static final ObjectMapper MAPPER = new ObjectMapper(); + private static final VerbResolver resolver = VerbResolverFactory.newInstance(); + + public static CommunityConfiguration getCommunityConfiguration() throws IOException { + final Map communities = Maps.newHashMap(); + List validCommunities = new ArrayList<>(); + getValidCommunities() + .forEach(community -> { + try { + CommunityModel cm = MAPPER.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class); + validCommunities.add(getCommunity(cm)); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + validCommunities.forEach(community ->{ + try { + DatasourceList dl = MAPPER.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class); + community.setProviders(dl.stream().map(d -> { +// if(d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) +// return null; + Provider p = new Provider(); + p.setOpenaireId("10|" + d.getOpenaireId()); + p.setSelectionConstraints(d.getSelectioncriteria()); + if(p.getSelectionConstraints() != null) + p.getSelectionConstraints().setSelection(resolver); + return p; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + + validCommunities.forEach(community ->{ + if(community.isValid()) + communities.put(community.getId(), community); + }); + return new CommunityConfiguration(communities); + } + + private static Community getCommunity(CommunityModel cm){ + Community c = new Community(); + c.setId(cm.getId()); + c.setZenodoCommunities(cm.getOtherZenodoCommunities()); + if(!StringUtils.isNullOrEmpty(cm.getZenodoCommunity())) + c.getZenodoCommunities().add(cm.getZenodoCommunity()); + c.setSubjects(cm.getSubjects()); + c.getSubjects().addAll(cm.getFos()); + c.getSubjects().addAll(cm.getSdg()); + c.setConstraints(cm.getAdvancedConstraints()); + if(c.getConstraints()!=null) + c.getConstraints().setSelection(resolver); + c.setRemoveConstraints(cm.getRemoveConstraints()); + if(c.getRemoveConstraints()!=null) + c.getRemoveConstraints().setSelection(resolver); + return c; + } + + public static List getValidCommunities() throws IOException { + return MAPPER.readValue(QueryCommunityAPI.communities(), CommunitySummary.class) + .stream() + .filter(community -> !community.getStatus().equals("hidden") && + (community.getType().equals("ri") || community.getType().equals("community"))) + .collect(Collectors.toList()); + } + public static CommunityEntityMap getCommunityOrganization() throws IOException { + CommunityEntityMap organizationMap = new CommunityEntityMap(); + getValidCommunities() + .forEach(community -> { + String id = community.getId(); + try { + List associatedOrgs = MAPPER.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class); + if(associatedOrgs.size() >0){ + organizationMap.put(id, associatedOrgs); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + return organizationMap; + } + + public static CommunityEntityMap getCommunityProjects()throws IOException{ + CommunityEntityMap projectMap = new CommunityEntityMap(); + getValidCommunities() + .forEach(community ->{ + int page = -1; + int size = 100; + ContentModel cm = new ContentModel(); + List projectList = new ArrayList<>(); + do{ + page ++; + try { + cm = MAPPER.readValue( QueryCommunityAPI.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), ContentModel.class); + if (cm.getContent().size() > 0){ + + cm.getContent().forEach(p -> + projectList.add ("40|" + p.getOpenaireId())); + projectMap.put(community.getId(), projectList); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + }while (!cm.getLast()); + }); + return projectMap; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java new file mode 100644 index 000000000..5378e556a --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java @@ -0,0 +1,43 @@ +package eu.dnetlib.dhp.api.model; + +import com.fasterxml.jackson.annotation.JsonAutoDetect; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.google.gson.Gson; +import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; + + +@JsonAutoDetect +@JsonIgnoreProperties(ignoreUnknown = true) +public class CommunityContentprovider { + private String openaireId; + private SelectionConstraints selectioncriteria; + + private String enabled; + + public String getEnabled() { + return enabled; + } + + public void setEnabled(String enabled) { + this.enabled = enabled; + } + + public String getOpenaireId() { + return openaireId; + } + + public void setOpenaireId(final String openaireId) { + this.openaireId = openaireId; + } + + + public SelectionConstraints getSelectioncriteria() { + + return this.selectioncriteria; + } + + public void setSelectioncriteria(SelectionConstraints selectioncriteria) { + this.selectioncriteria = selectioncriteria; + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityEntityMap.java similarity index 59% rename from dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java rename to dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityEntityMap.java index 7d786058a..ca3eb2857 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/OrganizationMap.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityEntityMap.java @@ -1,13 +1,13 @@ -package eu.dnetlib.dhp.resulttocommunityfromorganization; +package eu.dnetlib.dhp.api.model; import java.util.ArrayList; import java.util.HashMap; import java.util.List; -public class OrganizationMap extends HashMap> { +public class CommunityEntityMap extends HashMap> { - public OrganizationMap() { + public CommunityEntityMap() { super(); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java new file mode 100644 index 000000000..c5b3fac7c --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java @@ -0,0 +1,108 @@ + +package eu.dnetlib.dhp.api.model; + +import java.io.Serializable; +import java.util.List; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; + + +/** + * @author miriam.baglioni + * @Date 06/10/23 + */ +@JsonIgnoreProperties(ignoreUnknown = true) +public class CommunityModel implements Serializable { + private String id; + private String type; + private String status; + + private String zenodoCommunity; + private List subjects; + private List otherZenodoCommunities; + private List fos; + private List sdg; + private SelectionConstraints advancedConstraints; + private SelectionConstraints removeConstraints; + + public String getZenodoCommunity() { + return zenodoCommunity; + } + + public void setZenodoCommunity(String zenodoCommunity) { + this.zenodoCommunity = zenodoCommunity; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public List getOtherZenodoCommunities() { + return otherZenodoCommunities; + } + + public void setOtherZenodoCommunities(List otherZenodoCommunities) { + this.otherZenodoCommunities = otherZenodoCommunities; + } + + public List getFos() { + return fos; + } + + public void setFos(List fos) { + this.fos = fos; + } + + public List getSdg() { + return sdg; + } + + public void setSdg(List sdg) { + this.sdg = sdg; + } + + public SelectionConstraints getRemoveConstraints() { + return removeConstraints; + } + + public void setRemoveConstraints(SelectionConstraints removeConstraints) { + this.removeConstraints = removeConstraints; + } + + public SelectionConstraints getAdvancedConstraints() { + return advancedConstraints; + } + + public void setAdvancedConstraints(SelectionConstraints advancedConstraints) { + this.advancedConstraints = advancedConstraints; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getStatus() { + return status; + } + + public void setStatus(String status) { + this.status = status; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java new file mode 100644 index 000000000..774b6c874 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java @@ -0,0 +1,16 @@ +package eu.dnetlib.dhp.api.model; + +import java.io.Serializable; +import java.util.ArrayList; + +/** + * @author miriam.baglioni + * @Date 06/10/23 + */ +public class CommunitySummary extends ArrayList implements Serializable { + public CommunitySummary() { + super(); + } + } + + diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java new file mode 100644 index 000000000..a755a9455 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java @@ -0,0 +1,50 @@ +package eu.dnetlib.dhp.api.model; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 09/10/23 + */ +@JsonIgnoreProperties(ignoreUnknown = true) +public class ContentModel implements Serializable { + private List content; + private Integer totalPages; + private Boolean last; + private Integer number; + + public List getContent() { + return content; + } + + public void setContent(List content) { + this.content = content; + } + + public Integer getTotalPages() { + return totalPages; + } + + public void setTotalPages(Integer totalPages) { + this.totalPages = totalPages; + } + + public Boolean getLast() { + return last; + } + + public void setLast(Boolean last) { + this.last = last; + } + + public Integer getNumber() { + return number; + } + + public void setNumber(Integer number) { + this.number = number; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java new file mode 100644 index 000000000..8e31d7612 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java @@ -0,0 +1,12 @@ +package eu.dnetlib.dhp.api.model; + +import eu.dnetlib.dhp.api.model.CommunityContentprovider; + + +import java.io.Serializable; +import java.util.ArrayList; +public class DatasourceList extends ArrayList implements Serializable { + public DatasourceList(){ + super(); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java new file mode 100644 index 000000000..6895967ff --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java @@ -0,0 +1,15 @@ +package eu.dnetlib.dhp.api.model; + +import java.io.Serializable; +import java.util.ArrayList; + +/** + * @author miriam.baglioni + * @Date 09/10/23 + */ +public class OrganizationList extends ArrayList implements Serializable { + + public OrganizationList(){ + super(); + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java new file mode 100644 index 000000000..50bdcf649 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java @@ -0,0 +1,23 @@ +package eu.dnetlib.dhp.api.model; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 09/10/23 + */ +@JsonIgnoreProperties(ignoreUnknown = true) +public class ProjectModel implements Serializable { + + private String openaireId; + + public String getOpenaireId() { + return openaireId; + } + + public void setOpenaireId(String openaireId) { + this.openaireId = openaireId; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 3186ed5c0..b61bc2c9f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -6,10 +6,10 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; +import eu.dnetlib.dhp.api.Utils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -87,7 +87,7 @@ public class SparkBulkTagJob { if (isTest) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { - cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); + cc = Utils.getCommunityConfiguration();//QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); } runWithSparkSession( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index b44376e22..d281f8783 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -4,16 +4,18 @@ package eu.dnetlib.dhp.bulktag.community; import java.io.Serializable; import java.util.ArrayList; import java.util.List; +import java.util.Optional; import com.google.gson.Gson; + /** Created by miriam on 01/08/2018. */ public class Community implements Serializable { private String id; private List subjects = new ArrayList<>(); private List providers = new ArrayList<>(); - private List zenodoCommunities = new ArrayList<>(); + private List zenodoCommunities = new ArrayList<>(); private SelectionConstraints constraints = new SelectionConstraints(); private SelectionConstraints removeConstraints = new SelectionConstraints(); @@ -26,7 +28,7 @@ public class Community implements Serializable { return !getSubjects().isEmpty() || !getProviders().isEmpty() || !getZenodoCommunities().isEmpty() - || getConstraints().getCriteria() != null; + || (Optional.ofNullable(getConstraints()).isPresent() && getConstraints().getCriteria() != null); } public String getId() { @@ -53,11 +55,11 @@ public class Community implements Serializable { this.providers = providers; } - public List getZenodoCommunities() { + public List getZenodoCommunities() { return zenodoCommunities; } - public void setZenodoCommunities(List zenodoCommunities) { + public void setZenodoCommunities(List zenodoCommunities) { this.zenodoCommunities = zenodoCommunities; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index e061ccd5e..a658c7ff5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -81,7 +81,7 @@ public class CommunityConfiguration implements Serializable { this.removeConstraintsMap = removeConstraintsMap; } - CommunityConfiguration(final Map communities) { + public CommunityConfiguration(final Map communities) { this.communities = communities; init(); } @@ -117,10 +117,10 @@ public class CommunityConfiguration implements Serializable { add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap); } // get zenodo communities - for (ZenodoCommunity zc : c.getZenodoCommunities()) { + for (String zc : c.getZenodoCommunities()) { add( - zc.getZenodoCommunityId(), - new Pair<>(id, zc.getSelCriteria()), + zc, + new Pair<>(id, null), zenodocommunityMap); } selectionConstraintsMap.put(id, c.getConstraints()); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 7b9e03ef6..013bf7168 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -5,7 +5,6 @@ import java.io.StringReader; import java.util.ArrayList; import java.util.List; import java.util.Map; - import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -143,16 +142,16 @@ public class CommunityConfigurationFactory { return providerList; } - private static List parseZenodoCommunities(final Node node) { + private static List parseZenodoCommunities(final Node node) { final List list = node.selectNodes("./zenodocommunities/zenodocommunity"); - final List zenodoCommunityList = new ArrayList<>(); + final List zenodoCommunityList = new ArrayList<>(); for (Node n : list) { - ZenodoCommunity zc = new ZenodoCommunity(); - zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText()); - zc.setSelCriteria(n.selectSingleNode("./selcriteria")); +// ZenodoCommunity zc = new ZenodoCommunity(); +// zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText()); +// zc.setSelCriteria(n.selectSingleNode("./selcriteria")); - zenodoCommunityList.add(zc); + zenodoCommunityList.add(n.selectSingleNode("./zenodoid").getText()); } log.info("size of the zenodo community list " + zenodoCommunityList.size()); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java index ed58cc14d..03ae1117b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java @@ -6,12 +6,14 @@ import java.lang.reflect.InvocationTargetException; import eu.dnetlib.dhp.bulktag.criteria.Selection; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; +import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore; public class Constraint implements Serializable { private String verb; private String field; private String value; // private String element; + @JsonIgnore private Selection selection; public String getVerb() { @@ -37,11 +39,11 @@ public class Constraint implements Serializable { public void setValue(String value) { this.value = value; } - - public void setSelection(Selection sel) { - selection = sel; - } - +//@JsonIgnore + //public void setSelection(Selection sel) { +// selection = sel; +// } +@JsonIgnore public void setSelection(VerbResolver resolver) throws InvocationTargetException, NoSuchMethodException, InstantiationException, IllegalAccessException { @@ -52,11 +54,5 @@ public class Constraint implements Serializable { return selection.apply(metadata); } -// public String getElement() { -// return element; -// } -// -// public void setElement(String element) { -// this.element = element; -// } + } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java index c7dcce812..8e6d25e9b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java @@ -7,11 +7,12 @@ import java.util.Collection; import java.util.List; import java.util.Map; +import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.google.gson.Gson; import com.google.gson.reflect.TypeToken; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; - +@JsonAutoDetect public class SelectionConstraints implements Serializable { private List criteria; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 0fc8cb390..ff6b73286 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -6,12 +6,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -48,10 +48,11 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final OrganizationMap organizationMap = new Gson() - .fromJson( - parser.get("organizationtoresultcommunitymap"), - OrganizationMap.class); +// final CommunityEntityMap organizationMap = new Gson() +// .fromJson( +// parser.get("organizationtoresultcommunitymap"), +// CommunityEntityMap.class); + final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(); log.info("organizationMap: {}", new Gson().toJson(organizationMap)); SparkConf conf = new SparkConf(); @@ -70,7 +71,7 @@ public class PrepareResultCommunitySet { SparkSession spark, String inputPath, String outputPath, - OrganizationMap organizationMap) { + CommunityEntityMap organizationMap) { Dataset relation = readPath(spark, inputPath, Relation.class); relation.createOrReplaceTempView("relation"); @@ -115,7 +116,7 @@ public class PrepareResultCommunitySet { } private static MapFunction mapResultCommunityFn( - OrganizationMap organizationMap) { + CommunityEntityMap organizationMap) { return value -> { String rId = value.getResultId(); Optional> orgs = Optional.ofNullable(value.getMerges()); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index 6a329fdc4..d9805ab7b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -4,10 +4,10 @@ sourcePath the source path - - organizationtoresultcommunitymap - organization community map - + + + + outputPath the output path diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 660a55472..745cd7e6f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -1568,4 +1568,42 @@ public class BulkTagJobTest { } + @Test + void newConfTest() throws Exception { + final String pathMap = BulkTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + Assertions.assertEquals(0, spark.sql(query).count()); + } + } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java index c8fd62c8e..7e12bf9c3 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java @@ -47,7 +47,7 @@ class CommunityConfigurationFactoryTest { sc.setVerb("not_contains"); sc.setField("contributor"); sc.setValue("DARIAH"); - sc.setSelection(resolver.getSelectionCriteria(sc.getVerb(), sc.getValue())); + sc.setSelection(resolver);//.getSelectionCriteria(sc.getVerb(), sc.getValue())); String metadata = "This work has been partially supported by DARIAH-EU infrastructure"; Assertions.assertFalse(sc.verifyCriteria(metadata)); } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java new file mode 100644 index 000000000..1b3403535 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java @@ -0,0 +1,91 @@ + +package eu.dnetlib.dhp.bulktag; + +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; +import eu.dnetlib.dhp.bulktag.community.Community; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; + +import eu.dnetlib.dhp.api.model.CommunityModel; +import eu.dnetlib.dhp.api.model.CommunitySummary; +import eu.dnetlib.dhp.api.model.DatasourceList; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.api.QueryCommunityAPI; + +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 06/10/23 + */ +public class QueryCommunityAPITest { + + @Test + void communityList() throws Exception { + String body = QueryCommunityAPI.communities(); + new ObjectMapper() + .readValue(body, CommunitySummary.class) + .forEach(p -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(p)); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + }); + } + + @Test + void community() throws Exception { + String id = "dh-ch"; + String body = QueryCommunityAPI.community(id); + System.out.println(new ObjectMapper().writeValueAsString(new ObjectMapper() + .readValue(body, CommunityModel.class))) + ; + } + + @Test + void communityDatasource() throws Exception { + String id = "dh-ch"; + String body = QueryCommunityAPI.communityDatasource(id); + new ObjectMapper() + .readValue(body, DatasourceList.class) + .forEach(ds-> { + try { + System.out.println(new ObjectMapper().writeValueAsString(ds)); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + }); + ; + } + + @Test + void validCommunities() throws Exception { + CommunityConfiguration cc = Utils.getCommunityConfiguration(); + System.out.println(cc.getCommunities().keySet()); + Community community =cc.getCommunities().get("aurora"); + Assertions.assertEquals(0, community.getSubjects().size()); + Assertions.assertEquals(null, community.getConstraints()); + Assertions.assertEquals(null, community.getRemoveConstraints()); + Assertions.assertEquals(2, community.getZenodoCommunities().size()); + Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network"))); + Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck"))); + Assertions.assertEquals(35, community.getProviders().size()); + Assertions.assertEquals(35, community.getProviders().stream().filter(p->p.getSelectionConstraints()==null).count()); + } + + @Test + void getCommunityProjects() throws Exception { + CommunityEntityMap projectMap = Utils.getCommunityProjects(); + Assertions.assertFalse(projectMap.containsKey("mes")); + Assertions.assertEquals(33, projectMap.size()); + Assertions.assertTrue(projectMap.keySet().stream().allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|")))); + } + +} + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index b878e778e..0887adf45 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -1,14 +1,14 @@ package eu.dnetlib.dhp.oa.graph.group; -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.DHPUtils; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.net.URISyntaxException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -18,108 +18,108 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; -import java.io.IOException; -import java.net.URISyntaxException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; -import static org.junit.jupiter.api.Assertions.assertEquals; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.DHPUtils; @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class GroupEntitiesSparkJobTest { - private static SparkSession spark; + private static SparkSession spark; - private static ObjectMapper mapper = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + private static ObjectMapper mapper = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - private static Path workingDir; - private Path dataInputPath; + private static Path workingDir; + private Path dataInputPath; - private Path checkpointPath; + private Path checkpointPath; - private Path outputPath; + private Path outputPath; - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); - SparkConf conf = new SparkConf(); - conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); - conf.setMaster("local"); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - spark = SparkSession.builder().config(conf).getOrCreate(); - } + SparkConf conf = new SparkConf(); + conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + spark = SparkSession.builder().config(conf).getOrCreate(); + } - @BeforeEach - public void beforeEach() throws IOException, URISyntaxException { - dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); - checkpointPath = workingDir.resolve("grouped_entity"); - outputPath = workingDir.resolve("dispatched_entity"); - } + @BeforeEach + public void beforeEach() throws IOException, URISyntaxException { + dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); + checkpointPath = workingDir.resolve("grouped_entity"); + outputPath = workingDir.resolve("dispatched_entity"); + } - @AfterAll - public static void afterAll() throws IOException { - spark.stop(); - FileUtils.deleteDirectory(workingDir.toFile()); - } + @AfterAll + public static void afterAll() throws IOException { + spark.stop(); + FileUtils.deleteDirectory(workingDir.toFile()); + } - @Test - @Order(1) - void testGroupEntities() throws Exception { - GroupEntitiesSparkJob.main(new String[]{ - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-graphInputPath", - dataInputPath.toString(), - "-checkpointPath", - checkpointPath.toString(), - "-outputPath", - outputPath.toString(), - "-filterInvisible", - Boolean.FALSE.toString() - }); + @Test + @Order(1) + void testGroupEntities() throws Exception { + GroupEntitiesSparkJob.main(new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-graphInputPath", + dataInputPath.toString(), + "-checkpointPath", + checkpointPath.toString(), + "-outputPath", + outputPath.toString(), + "-filterInvisible", + Boolean.FALSE.toString() + }); - Dataset checkpointTable = spark - .read() - .load(checkpointPath.toString()) - .selectExpr("COALESCE(*)") - .as(Encoders.kryo(OafEntity.class)); + Dataset checkpointTable = spark + .read() + .load(checkpointPath.toString()) + .selectExpr("COALESCE(*)") + .as(Encoders.kryo(OafEntity.class)); + assertEquals( + 1, + checkpointTable + .filter( + (FilterFunction) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9" + .equals(r.getId()) && + r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo"))) + .count()); - assertEquals( - 1, - checkpointTable - .filter( - (FilterFunction) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9" - .equals(r.getId()) && - r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo"))) - .count()); + Dataset output = spark + .read() + .textFile( + DHPUtils + .toSeq( + HdfsSupport + .listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration()))) + .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); - - Dataset output = spark - .read() - .textFile( - DHPUtils - .toSeq( - HdfsSupport - .listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration()))) - .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); - - assertEquals(3, output.count()); - assertEquals( - 2, - output - .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) - .filter((FilterFunction) s -> s.equals("publication")) - .count()); - assertEquals( - 1, - output - .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) - .filter((FilterFunction) s -> s.equals("dataset")) - .count()); - } -} \ No newline at end of file + assertEquals(3, output.count()); + assertEquals( + 2, + output + .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) + .filter((FilterFunction) s -> s.equals("publication")) + .count()); + assertEquals( + 1, + output + .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) + .filter((FilterFunction) s -> s.equals("dataset")) + .count()); + } +} From a3d01ccb246e52e7977aef8c57b15d964dcc9834 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Oct 2023 14:52:17 +0200 Subject: [PATCH 02/23] refactoring --- .../CreateActionSetSparkJob.java | 2 +- .../doiboost/crossref/Crossref2Oaf.scala | 16 +- .../crossref/CrossrefMappingTest.scala | 2 +- .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 9 +- .../main/java/eu/dnetlib/dhp/api/Utils.java | 236 +++++++++--------- .../api/model/CommunityContentprovider.java | 6 +- .../dnetlib/dhp/api/model/CommunityModel.java | 2 +- .../dhp/api/model/CommunitySummary.java | 11 +- .../dnetlib/dhp/api/model/ContentModel.java | 61 ++--- .../dnetlib/dhp/api/model/DatasourceList.java | 11 +- .../dhp/api/model/OrganizationList.java | 7 +- .../dnetlib/dhp/api/model/ProjectModel.java | 19 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 4 +- .../dhp/bulktag/community/Community.java | 1 - .../CommunityConfigurationFactory.java | 1 + .../dhp/bulktag/community/Constraint.java | 9 +- .../community/SelectionConstraints.java | 1 + .../PrepareResultCommunitySet.java | 4 +- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 38 +-- .../CommunityConfigurationFactoryTest.java | 2 +- .../dhp/bulktag/QueryCommunityAPITest.java | 65 +++-- 21 files changed, 268 insertions(+), 239 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java index a367ba852..b707fdcd3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java @@ -7,7 +7,6 @@ import java.io.IOException; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.schema.oaf.utils.*; import org.apache.commons.cli.ParseException; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; @@ -30,6 +29,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.*; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index e0fdb9ce4..565d34e62 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -31,9 +31,7 @@ case class mappingAuthor( affiliation: Option[mappingAffiliation] ) {} -case class funderInfo(id:String,uri:String, name:String,synonym:List[String] ) {} - - +case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {} case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {} @@ -41,7 +39,9 @@ case object Crossref2Oaf { val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) val irishFunder: List[funderInfo] = { - val s = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json")).mkString + val s = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json")) + .mkString implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: org.json4s.JValue = parse(s) json.extract[List[funderInfo]] @@ -100,9 +100,11 @@ case object Crossref2Oaf { "report" -> "0017 Report" ) - def getIrishId(doi:String):Option[String] = { - val id =doi.split("/").last - irishFunder.find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id)))).map(f => f.id) + def getIrishId(doi: String): Option[String] = { + val id = doi.split("/").last + irishFunder + .find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id)))) + .map(f => f.id) } def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 7961376c5..fbf6f72c0 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -50,7 +50,7 @@ class CrossrefMappingTest { } } - def checkRelation(generatedOAF: List[Oaf]): Unit = { + def checkRelation(generatedOAF: List[Oaf]): Unit = { val rels: List[Relation] = generatedOAF.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]] diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index 635ee2027..cc615ba46 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -21,7 +21,7 @@ import com.google.gson.Gson; public class QueryCommunityAPI { private static final String baseUrl = "https://services.openaire.eu/openaire/"; - private static String get(String geturl) throws IOException{ + private static String get(String geturl) throws IOException { URL url = new URL(geturl); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setDoOutput(true); @@ -44,7 +44,7 @@ public class QueryCommunityAPI { return get(baseUrl + "community/" + id); } - public static String communityDatasource(String id)throws IOException{ + public static String communityDatasource(String id) throws IOException { return get(baseUrl + "community/" + id + "/contentproviders"); } @@ -53,8 +53,8 @@ public class QueryCommunityAPI { return get(baseUrl + "community/" + id + "/propagationOrganizations"); } - public static String communityProjects(String id, String page, String size) throws IOException{ - return get(baseUrl + "community/" + id +"/projects/" + page + "/" + size); + public static String communityProjects(String id, String page, String size) throws IOException { + return get(baseUrl + "community/" + id + "/projects/" + page + "/" + size); } @NotNull @@ -74,5 +74,4 @@ public class QueryCommunityAPI { return body; } - } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index 5b3004a5d..c1aaa14c4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -1,16 +1,6 @@ + package eu.dnetlib.dhp.api; -import com.amazonaws.util.StringUtils; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.Maps; -import eu.dnetlib.dhp.api.model.*; -import eu.dnetlib.dhp.bulktag.community.Community; -import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; -import eu.dnetlib.dhp.bulktag.community.Provider; -import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; -import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory; - -import javax.management.Query; import java.io.IOException; import java.io.Serializable; import java.util.ArrayList; @@ -19,118 +9,140 @@ import java.util.Map; import java.util.Objects; import java.util.stream.Collectors; +import javax.management.Query; + +import com.amazonaws.util.StringUtils; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Maps; + +import eu.dnetlib.dhp.api.model.*; +import eu.dnetlib.dhp.bulktag.community.Community; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; +import eu.dnetlib.dhp.bulktag.community.Provider; +import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; +import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory; + /** * @author miriam.baglioni * @Date 09/10/23 */ public class Utils implements Serializable { - private static final ObjectMapper MAPPER = new ObjectMapper(); - private static final VerbResolver resolver = VerbResolverFactory.newInstance(); + private static final ObjectMapper MAPPER = new ObjectMapper(); + private static final VerbResolver resolver = VerbResolverFactory.newInstance(); - public static CommunityConfiguration getCommunityConfiguration() throws IOException { - final Map communities = Maps.newHashMap(); - List validCommunities = new ArrayList<>(); - getValidCommunities() - .forEach(community -> { - try { - CommunityModel cm = MAPPER.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class); - validCommunities.add(getCommunity(cm)); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - validCommunities.forEach(community ->{ - try { - DatasourceList dl = MAPPER.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class); - community.setProviders(dl.stream().map(d -> { + public static CommunityConfiguration getCommunityConfiguration() throws IOException { + final Map communities = Maps.newHashMap(); + List validCommunities = new ArrayList<>(); + getValidCommunities() + .forEach(community -> { + try { + CommunityModel cm = MAPPER + .readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class); + validCommunities.add(getCommunity(cm)); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + validCommunities.forEach(community -> { + try { + DatasourceList dl = MAPPER + .readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class); + community.setProviders(dl.stream().map(d -> { // if(d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) // return null; - Provider p = new Provider(); - p.setOpenaireId("10|" + d.getOpenaireId()); - p.setSelectionConstraints(d.getSelectioncriteria()); - if(p.getSelectionConstraints() != null) - p.getSelectionConstraints().setSelection(resolver); - return p; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); + Provider p = new Provider(); + p.setOpenaireId("10|" + d.getOpenaireId()); + p.setSelectionConstraints(d.getSelectioncriteria()); + if (p.getSelectionConstraints() != null) + p.getSelectionConstraints().setSelection(resolver); + return p; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); - validCommunities.forEach(community ->{ - if(community.isValid()) - communities.put(community.getId(), community); - }); - return new CommunityConfiguration(communities); - } + validCommunities.forEach(community -> { + if (community.isValid()) + communities.put(community.getId(), community); + }); + return new CommunityConfiguration(communities); + } - private static Community getCommunity(CommunityModel cm){ - Community c = new Community(); - c.setId(cm.getId()); - c.setZenodoCommunities(cm.getOtherZenodoCommunities()); - if(!StringUtils.isNullOrEmpty(cm.getZenodoCommunity())) - c.getZenodoCommunities().add(cm.getZenodoCommunity()); - c.setSubjects(cm.getSubjects()); - c.getSubjects().addAll(cm.getFos()); - c.getSubjects().addAll(cm.getSdg()); - c.setConstraints(cm.getAdvancedConstraints()); - if(c.getConstraints()!=null) - c.getConstraints().setSelection(resolver); - c.setRemoveConstraints(cm.getRemoveConstraints()); - if(c.getRemoveConstraints()!=null) - c.getRemoveConstraints().setSelection(resolver); - return c; - } + private static Community getCommunity(CommunityModel cm) { + Community c = new Community(); + c.setId(cm.getId()); + c.setZenodoCommunities(cm.getOtherZenodoCommunities()); + if (!StringUtils.isNullOrEmpty(cm.getZenodoCommunity())) + c.getZenodoCommunities().add(cm.getZenodoCommunity()); + c.setSubjects(cm.getSubjects()); + c.getSubjects().addAll(cm.getFos()); + c.getSubjects().addAll(cm.getSdg()); + c.setConstraints(cm.getAdvancedConstraints()); + if (c.getConstraints() != null) + c.getConstraints().setSelection(resolver); + c.setRemoveConstraints(cm.getRemoveConstraints()); + if (c.getRemoveConstraints() != null) + c.getRemoveConstraints().setSelection(resolver); + return c; + } - public static List getValidCommunities() throws IOException { - return MAPPER.readValue(QueryCommunityAPI.communities(), CommunitySummary.class) - .stream() - .filter(community -> !community.getStatus().equals("hidden") && - (community.getType().equals("ri") || community.getType().equals("community"))) - .collect(Collectors.toList()); - } - public static CommunityEntityMap getCommunityOrganization() throws IOException { - CommunityEntityMap organizationMap = new CommunityEntityMap(); - getValidCommunities() - .forEach(community -> { - String id = community.getId(); - try { - List associatedOrgs = MAPPER.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class); - if(associatedOrgs.size() >0){ - organizationMap.put(id, associatedOrgs); - } - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - return organizationMap; - } + public static List getValidCommunities() throws IOException { + return MAPPER + .readValue(QueryCommunityAPI.communities(), CommunitySummary.class) + .stream() + .filter( + community -> !community.getStatus().equals("hidden") && + (community.getType().equals("ri") || community.getType().equals("community"))) + .collect(Collectors.toList()); + } - public static CommunityEntityMap getCommunityProjects()throws IOException{ - CommunityEntityMap projectMap = new CommunityEntityMap(); - getValidCommunities() - .forEach(community ->{ - int page = -1; - int size = 100; - ContentModel cm = new ContentModel(); - List projectList = new ArrayList<>(); - do{ - page ++; - try { - cm = MAPPER.readValue( QueryCommunityAPI.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), ContentModel.class); - if (cm.getContent().size() > 0){ + public static CommunityEntityMap getCommunityOrganization() throws IOException { + CommunityEntityMap organizationMap = new CommunityEntityMap(); + getValidCommunities() + .forEach(community -> { + String id = community.getId(); + try { + List associatedOrgs = MAPPER + .readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class); + if (associatedOrgs.size() > 0) { + organizationMap.put(id, associatedOrgs); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + return organizationMap; + } - cm.getContent().forEach(p -> - projectList.add ("40|" + p.getOpenaireId())); - projectMap.put(community.getId(), projectList); - } - } catch (IOException e) { - throw new RuntimeException(e); - } - }while (!cm.getLast()); - }); - return projectMap; - } + public static CommunityEntityMap getCommunityProjects() throws IOException { + CommunityEntityMap projectMap = new CommunityEntityMap(); + getValidCommunities() + .forEach(community -> { + int page = -1; + int size = 100; + ContentModel cm = new ContentModel(); + List projectList = new ArrayList<>(); + do { + page++; + try { + cm = MAPPER + .readValue( + QueryCommunityAPI + .communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), + ContentModel.class); + if (cm.getContent().size() > 0) { + + cm.getContent().forEach(p -> projectList.add("40|" + p.getOpenaireId())); + projectMap.put(community.getId(), projectList); + } + } catch (IOException e) { + throw new RuntimeException(e); + } + } while (!cm.getLast()); + }); + return projectMap; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java index 5378e556a..9fab5a80c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java @@ -1,10 +1,11 @@ + package eu.dnetlib.dhp.api.model; import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.google.gson.Gson; -import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; +import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; @JsonAutoDetect @JsonIgnoreProperties(ignoreUnknown = true) @@ -30,10 +31,9 @@ public class CommunityContentprovider { this.openaireId = openaireId; } - public SelectionConstraints getSelectioncriteria() { - return this.selectioncriteria; + return this.selectioncriteria; } public void setSelectioncriteria(SelectionConstraints selectioncriteria) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java index c5b3fac7c..745e7efc2 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java @@ -5,8 +5,8 @@ import java.io.Serializable; import java.util.List; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; +import eu.dnetlib.dhp.bulktag.community.SelectionConstraints; /** * @author miriam.baglioni diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java index 774b6c874..a0541f7ee 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.api.model; import java.io.Serializable; @@ -8,9 +9,7 @@ import java.util.ArrayList; * @Date 06/10/23 */ public class CommunitySummary extends ArrayList implements Serializable { - public CommunitySummary() { - super(); - } - } - - + public CommunitySummary() { + super(); + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java index a755a9455..469709f59 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java @@ -1,50 +1,51 @@ -package eu.dnetlib.dhp.api.model; -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +package eu.dnetlib.dhp.api.model; import java.io.Serializable; import java.util.List; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + /** * @author miriam.baglioni * @Date 09/10/23 */ @JsonIgnoreProperties(ignoreUnknown = true) public class ContentModel implements Serializable { - private List content; - private Integer totalPages; - private Boolean last; - private Integer number; + private List content; + private Integer totalPages; + private Boolean last; + private Integer number; - public List getContent() { - return content; - } + public List getContent() { + return content; + } - public void setContent(List content) { - this.content = content; - } + public void setContent(List content) { + this.content = content; + } - public Integer getTotalPages() { - return totalPages; - } + public Integer getTotalPages() { + return totalPages; + } - public void setTotalPages(Integer totalPages) { - this.totalPages = totalPages; - } + public void setTotalPages(Integer totalPages) { + this.totalPages = totalPages; + } - public Boolean getLast() { - return last; - } + public Boolean getLast() { + return last; + } - public void setLast(Boolean last) { - this.last = last; - } + public void setLast(Boolean last) { + this.last = last; + } - public Integer getNumber() { - return number; - } + public Integer getNumber() { + return number; + } - public void setNumber(Integer number) { - this.number = number; - } + public void setNumber(Integer number) { + this.number = number; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java index 8e31d7612..30d0241c3 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java @@ -1,12 +1,13 @@ + package eu.dnetlib.dhp.api.model; -import eu.dnetlib.dhp.api.model.CommunityContentprovider; - - import java.io.Serializable; import java.util.ArrayList; + +import eu.dnetlib.dhp.api.model.CommunityContentprovider; + public class DatasourceList extends ArrayList implements Serializable { - public DatasourceList(){ + public DatasourceList() { super(); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java index 6895967ff..3c81ad179 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.api.model; import java.io.Serializable; @@ -9,7 +10,7 @@ import java.util.ArrayList; */ public class OrganizationList extends ArrayList implements Serializable { - public OrganizationList(){ - super(); - } + public OrganizationList() { + super(); + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java index 50bdcf649..3495d6a63 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java @@ -1,9 +1,10 @@ + package eu.dnetlib.dhp.api.model; -import com.fasterxml.jackson.annotation.JsonIgnoreProperties; - import java.io.Serializable; +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + /** * @author miriam.baglioni * @Date 09/10/23 @@ -11,13 +12,13 @@ import java.io.Serializable; @JsonIgnoreProperties(ignoreUnknown = true) public class ProjectModel implements Serializable { - private String openaireId; + private String openaireId; - public String getOpenaireId() { - return openaireId; - } + public String getOpenaireId() { + return openaireId; + } - public void setOpenaireId(String openaireId) { - this.openaireId = openaireId; - } + public void setOpenaireId(String openaireId) { + this.openaireId = openaireId; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index b61bc2c9f..0d98e4958 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import eu.dnetlib.dhp.api.Utils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; +import eu.dnetlib.dhp.api.Utils; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bulktag.community.*; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -87,7 +87,7 @@ public class SparkBulkTagJob { if (isTest) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { - cc = Utils.getCommunityConfiguration();//QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); + cc = Utils.getCommunityConfiguration();// QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); } runWithSparkSession( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index d281f8783..9cd3a8f82 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -8,7 +8,6 @@ import java.util.Optional; import com.google.gson.Gson; - /** Created by miriam on 01/08/2018. */ public class Community implements Serializable { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 013bf7168..955ca3856 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -5,6 +5,7 @@ import java.io.StringReader; import java.util.ArrayList; import java.util.List; import java.util.Map; + import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java index 03ae1117b..82a6a3b85 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java @@ -4,9 +4,10 @@ package eu.dnetlib.dhp.bulktag.community; import java.io.Serializable; import java.lang.reflect.InvocationTargetException; +import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore; + import eu.dnetlib.dhp.bulktag.criteria.Selection; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; -import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore; public class Constraint implements Serializable { private String verb; @@ -39,11 +40,12 @@ public class Constraint implements Serializable { public void setValue(String value) { this.value = value; } + //@JsonIgnore - //public void setSelection(Selection sel) { + // public void setSelection(Selection sel) { // selection = sel; // } -@JsonIgnore + @JsonIgnore public void setSelection(VerbResolver resolver) throws InvocationTargetException, NoSuchMethodException, InstantiationException, IllegalAccessException { @@ -54,5 +56,4 @@ public class Constraint implements Serializable { return selection.apply(metadata); } - } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java index 8e6d25e9b..57cc658fc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java @@ -12,6 +12,7 @@ import com.google.gson.Gson; import com.google.gson.reflect.TypeToken; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; + @JsonAutoDetect public class SelectionConstraints implements Serializable { private List criteria; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index ff6b73286..e0670b80f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -6,8 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.util.*; -import eu.dnetlib.dhp.api.Utils; -import eu.dnetlib.dhp.api.model.CommunityEntityMap; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; @@ -20,6 +18,8 @@ import org.slf4j.LoggerFactory; import com.google.gson.Gson; +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 745cd7e6f..11dad9055 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -1572,36 +1572,36 @@ public class BulkTagJobTest { void newConfTest() throws Exception { final String pathMap = BulkTagJobTest.pathMap; SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); Assertions.assertEquals(10, tmp.count()); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); verificationDataset.createOrReplaceTempView("dataset"); String query = "select id, MyT.id community " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; Assertions.assertEquals(0, spark.sql(query).count()); } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java index 7e12bf9c3..5f0b1d7f1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java @@ -47,7 +47,7 @@ class CommunityConfigurationFactoryTest { sc.setVerb("not_contains"); sc.setField("contributor"); sc.setValue("DARIAH"); - sc.setSelection(resolver);//.getSelectionCriteria(sc.getVerb(), sc.getValue())); + sc.setSelection(resolver);// .getSelectionCriteria(sc.getVerb(), sc.getValue())); String metadata = "This work has been partially supported by DARIAH-EU infrastructure"; Assertions.assertFalse(sc.verifyCriteria(metadata)); } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java index 1b3403535..b0043d1e8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java @@ -1,14 +1,8 @@ package eu.dnetlib.dhp.bulktag; -import eu.dnetlib.dhp.api.Utils; -import eu.dnetlib.dhp.api.model.CommunityEntityMap; -import eu.dnetlib.dhp.bulktag.community.Community; -import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; +import java.util.List; -import eu.dnetlib.dhp.api.model.CommunityModel; -import eu.dnetlib.dhp.api.model.CommunitySummary; -import eu.dnetlib.dhp.api.model.DatasourceList; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; @@ -16,8 +10,13 @@ import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.api.QueryCommunityAPI; - -import java.util.List; +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; +import eu.dnetlib.dhp.api.model.CommunityModel; +import eu.dnetlib.dhp.api.model.CommunitySummary; +import eu.dnetlib.dhp.api.model.DatasourceList; +import eu.dnetlib.dhp.bulktag.community.Community; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; /** * @author miriam.baglioni @@ -43,9 +42,12 @@ public class QueryCommunityAPITest { void community() throws Exception { String id = "dh-ch"; String body = QueryCommunityAPI.community(id); - System.out.println(new ObjectMapper().writeValueAsString(new ObjectMapper() - .readValue(body, CommunityModel.class))) - ; + System.out + .println( + new ObjectMapper() + .writeValueAsString( + new ObjectMapper() + .readValue(body, CommunityModel.class))); } @Test @@ -53,14 +55,14 @@ public class QueryCommunityAPITest { String id = "dh-ch"; String body = QueryCommunityAPI.communityDatasource(id); new ObjectMapper() - .readValue(body, DatasourceList.class) - .forEach(ds-> { - try { - System.out.println(new ObjectMapper().writeValueAsString(ds)); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } - }); + .readValue(body, DatasourceList.class) + .forEach(ds -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(ds)); + } catch (JsonProcessingException e) { + throw new RuntimeException(e); + } + }); ; } @@ -68,24 +70,33 @@ public class QueryCommunityAPITest { void validCommunities() throws Exception { CommunityConfiguration cc = Utils.getCommunityConfiguration(); System.out.println(cc.getCommunities().keySet()); - Community community =cc.getCommunities().get("aurora"); + Community community = cc.getCommunities().get("aurora"); Assertions.assertEquals(0, community.getSubjects().size()); Assertions.assertEquals(null, community.getConstraints()); Assertions.assertEquals(null, community.getRemoveConstraints()); Assertions.assertEquals(2, community.getZenodoCommunities().size()); - Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network"))); - Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck"))); + Assertions + .assertTrue( + community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network"))); + Assertions + .assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck"))); Assertions.assertEquals(35, community.getProviders().size()); - Assertions.assertEquals(35, community.getProviders().stream().filter(p->p.getSelectionConstraints()==null).count()); + Assertions + .assertEquals( + 35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count()); } @Test void getCommunityProjects() throws Exception { CommunityEntityMap projectMap = Utils.getCommunityProjects(); Assertions.assertFalse(projectMap.containsKey("mes")); - Assertions.assertEquals(33, projectMap.size()); - Assertions.assertTrue(projectMap.keySet().stream().allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|")))); + Assertions.assertEquals(33, projectMap.size()); + Assertions + .assertTrue( + projectMap + .keySet() + .stream() + .allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|")))); } } - From 554551682d0501fa7664fab0a9bee8be6b0309d3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 11 Oct 2023 16:09:19 +0200 Subject: [PATCH 03/23] [raw graph] adopting the new COAR based vocabularies for the resource typing --- .../common/vocabulary/VocabularyGroup.java | 21 ++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 10 +++++- .../raw/AbstractMdRecordToOafMapper.java | 31 ++++++++++++++++++ .../dhp/oa/graph/raw/OafToOafMapper.java | 32 ++++++++++++++++--- .../dhp/oa/graph/raw/OdfToOafMapper.java | 27 ++++++++++++++++ .../oa/graph/raw/OriginalTypeComparator.java | 32 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 21 ++++++++++++ .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 7 +++- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 4 ++- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 4 ++- pom.xml | 2 +- 11 files changed, 182 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index fc7175270..4c1feac45 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -135,6 +135,27 @@ public class VocabularyGroup implements Serializable { return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn); } + public Qualifier lookupTermBySynonym(final String vocId, final String syn) { + if (StringUtils.isBlank(vocId)) { + return OafMapperUtils.unknown("", ""); + } + + final Vocabulary vocabulary = vocs.get(vocId.toLowerCase()); + + return Optional + .ofNullable(vocabulary.getTerm(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse( + Optional + .ofNullable(vocabulary.getTermBySynonym(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse(null)); + } + /** * getSynonymAsQualifierCaseSensitive * diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index c58096d35..1c557c805 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -14,7 +14,6 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -141,6 +140,15 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + final InstanceTypeMapping m = new InstanceTypeMapping(); + m.setVocabularyName(term.getSchemeid()); + m.setOriginalType(originalType); + m.setTypeCode(term.getClassid()); + m.setTypeLabel(term.getClassname()); + return m; + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index b37e6a755..2fed7d627 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -41,6 +41,11 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; + + protected static final String OPENAIRE_COAR_RESOURCE_TYPES_3_1 = "openaire::coar_resource_types_3_1"; + + public static final String OPENAIRE_USER_RESOURCE_TYPES = "openaire::user_resource_types"; + protected static final Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -516,6 +521,32 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + protected abstract String findOriginalType(Document doc); + + protected List prepareInstanceTypeMapping(Document doc) { + return Optional.ofNullable(findOriginalType(doc)) + .map(originalType -> { + final List mappings = Lists.newArrayList(); + + if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { + + // TODO verify what the vocabs return when a synonym is not defined + Qualifier coarTerm = vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + + // TODO verify what the vocabs return when a synonym is not defined + Qualifier userTerm = vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid()); + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, userTerm)); + } + } + + return mappings; + }) + .orElse(new ArrayList<>()); + } + private Journal prepareJournal(final Document doc, final DataInfo info) { final Node n = doc.selectSingleNode("//oaf:journal"); if (n != null) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index a9f9367af..5cdb434f1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -5,12 +5,10 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.net.URLDecoder; -import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -25,6 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; +import static org.apache.commons.lang3.StringUtils.contains; + public class OafToOafMapper extends AbstractMdRecordToOafMapper { public OafToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, @@ -139,6 +139,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -187,6 +189,28 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { return Lists.newArrayList(instance); } + /** + * The Dublin Core element dc:type can be repeated, but we need to base our mapping on a single value + * So this method tries to give precedence to the COAR resource type, when available. Otherwise, it looks for the + * openaire's info:eu-repo type, and as last resort picks the 1st type text available + * + * http://purl.org/coar/resource_type/c_5794 + * info:eu-repo/semantics/article + * Conference article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + return (String) doc.selectNodes("//dc:type") + .stream() + .map(o -> "" + ((Node) o).getText().trim()) + .sorted(new OriginalTypeComparator()) + .findFirst() + .orElse(null); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return prepareListFields(doc, "//dc:source", info); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index bbd1e7ab1..c01775327 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -9,6 +9,7 @@ import java.net.URLDecoder; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Element; @@ -139,6 +140,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); + instance.setInstanceTypeMapping(prepareInstanceTypeMapping(doc)); + final Set pids = new HashSet<>(pid); instance @@ -217,6 +220,30 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } } + @Override + protected List prepareInstanceTypeMapping(Document doc) { + return null; + } + + /** + * The Datacite element + * + * journal article + * + * @param doc the input document + * @return the chosen resource type + */ + @Override + protected String findOriginalType(Document doc) { + final Element resourceType = (Element) doc.selectSingleNode( + "//metadata/*[local-name() = 'resource']/*[local-name() = 'resourceType']"); + + final String resourceTypeURI = resourceType.attributeValue("anyURI"); + final String resourceTypeTxt = resourceType.getText(); + + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + } + @Override protected List> prepareSources(final Document doc, final DataInfo info) { return new ArrayList<>(); // Not present in ODF ??? diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java new file mode 100644 index 000000000..2eeead32e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -0,0 +1,32 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import java.util.Comparator; + +import static org.apache.commons.lang3.StringUtils.contains; +import static org.apache.commons.lang3.StringUtils.startsWith; + +public class OriginalTypeComparator implements Comparator { + + @Override + public int compare(String t1, String t2) { + + if (t1.equals(t2)) { + return 0; + } + if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { + return -1; + } + if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { + return 1; + } + if (startsWith(t1, "info:eu-repo/semantics")) { + return -1; + } + if (startsWith(t2, "info:eu-repo/semantics")) { + return 1; + } + + return t1.compareTo(t2); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b506d3a62..5df2b7a3b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -116,6 +116,27 @@ class MappersTest { assertNotNull(instance.getPid()); assertTrue(instance.getPid().isEmpty()); + assertNotNull(instance.getInstanceTypeMapping()); + assertEquals(2, instance.getInstanceTypeMapping().size()); + + Optional coarType = instance.getInstanceTypeMapping() + .stream() + .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); + assertEquals("conference paper", coarType.get().getTypeLabel()); + + Optional userType = instance.getInstanceTypeMapping() + .stream() + .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); + + assertTrue(userType.isPresent()); + assertEquals("Article", userType.get().getTypeCode()); + assertEquals("Article", userType.get().getTypeLabel()); + assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 409dfd5dc..b3fa94b20 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -1245,4 +1245,9 @@ dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo dnet:relation_subRelType @=@ relationship @=@ publicationDataset dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned FOS @=@ 0101 mathematics @=@ FOS: Mathematics -FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences \ No newline at end of file +FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Proceedings paper +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Conference article +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ http://purl.org/eprint/type/ConferencePaper +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ Conference article +openaire::user_resource_types @=@ Article @=@ http://purl.org/coar/resource_type/c_5794 \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 24ce42fc2..a38c0e987 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1121,4 +1121,6 @@ dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplem dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version FOS @=@ Fields of Science and Technology classification @=@ 0101 mathematics @=@ 0101 mathematics FOS @=@ Fields of Science and Technology classification @=@ 0102 computer and information sciences @=@ 0102 computer and information sciences -FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences \ No newline at end of file +FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences +openaire::coar_resource_types_3_1 @=@ openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_5794 @=@ conference paper +openaire::user_resource_types @=@ openaire::user_resource_types @=@ Article @=@ Article \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 277578185..492fc9a7a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -47,7 +47,9 @@ provisioning services regulating services supporting services - Research Article + conference paper + http://purl.org/coar/resource_type/c_5794 + info:eu-repo/semantics/article 0001 2017-01-01 diff --git a/pom.xml b/pom.xml index 9cd82a343..0f1ec78af 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.17.1] + [4.17.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 89184d5b4f1af674af33fff2a46961804b8da751 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Oct 2023 18:17:35 +0200 Subject: [PATCH 04/23] used the API instead of the IS for bulktagging and propagation for community through organization. Added a new propagation step for communities through projects. Still using the API and not the IS --- .../eu/dnetlib/dhp/PropagationConstant.java | 3 + .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 38 ++-- .../main/java/eu/dnetlib/dhp/api/Utils.java | 64 +++--- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 70 ++++--- .../dhp/bulktag/community/ResultTagger.java | 28 +-- .../PrepareResultCommunitySet.java | 9 +- ...kResultToCommunityFromOrganizationJob.java | 12 +- .../PrepareResultCommunitySet.java | 121 ++++++++++++ .../ResultProjectList.java | 26 +++ .../SparkResultToCommunityFromProject.java | 156 +++++++++++++++ .../dhp/bulktag/input_bulkTag_parameters.json | 28 +-- .../dhp/bulktag/oozie_app/workflow.xml | 108 +--------- .../resources/eu/dnetlib/dhp/bulktag/query.xq | 62 ------ .../input_communitytoresult_parameters.json | 12 -- .../oozie_app/workflow.xml | 7 +- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 187 +++++++++--------- .../dhp/bulktag/QueryCommunityAPITest.java | 19 +- .../ResultToCommunityJobTest.java | 2 +- .../eosc/dataset/{dataset_10.json => dataset} | 0 .../bulktag/eosc/dataset/otherresearchproduct | 0 .../dhp/bulktag/eosc/dataset/publication | 0 .../dnetlib/dhp/bulktag/eosc/dataset/software | 0 .../bulktag/sample/dataset/no_updates/dataset | 10 + .../dataset/no_updates/dataset_10.json.gz | Bin 6736 -> 0 bytes .../sample/dataset/no_updates/datasource | 0 .../dataset/no_updates/otherresearchproduct | 0 .../sample/dataset/no_updates/publication | 0 .../sample/dataset/no_updates/software | 0 .../{dataset_10.json => dataset} | 0 .../datasource | 0 .../otherresearchproduct | 10 + .../publication | 0 .../update_datasourcewithconstraints/software | 0 .../contextnoprovenance/dataset | 10 + .../contextnoprovenance/dataset_10.json.gz | Bin 6888 -> 0 bytes .../contextnoprovenance/datasource | 0 .../contextnoprovenance/otherresearchproduct | 0 .../contextnoprovenance/publication | 0 .../contextnoprovenance/software | 0 .../dataset/update_subject/nocontext/dataset | 10 + .../nocontext/dataset_10.json.gz | Bin 6755 -> 0 bytes .../update_subject/nocontext/datasource | 0 .../nocontext/otherresearchproduct | 0 .../update_subject/nocontext/publication | 0 .../dataset/update_subject/nocontext/software | 0 .../{dataset_10.json => dataset} | 6 +- .../update_subject_datasource/datasource | 0 .../otherresearchproduct | 0 .../update_subject_datasource/publication | 0 .../update_subject_datasource/software | 0 .../update_zenodocommunity/dataset | 0 .../update_zenodocommunity/datasource | 0 .../otherresearchproduct | 10 + .../otherresearchproduct_10.json.gz | Bin 8300 -> 0 bytes .../update_zenodocommunity/publication | 0 .../update_zenodocommunity/software | 0 .../publication/update_datasource/dataset | 0 .../publication/update_datasource/datasource | 0 .../update_datasource/otherresearchproduct | 0 .../publication/update_datasource/publication | 10 + .../update_datasource/publication_10.json.gz | Bin 5257 -> 0 bytes .../publication/update_datasource/software | 0 .../dhp/bulktag/sample/software/dataset | 0 .../sample/software/otherresearchproduct | 0 .../dhp/bulktag/sample/software/publication | 0 .../dhp/bulktag/sample/software/software | 10 + .../sample/software/software_10.json.gz | Bin 6727 -> 0 bytes .../eu/dnetlib/dhp/eosctag/galaxy/publication | 0 .../dnetlib/dhp/eosctag/jupyter/publication | 0 .../dnetlib/dhp/eosctag/twitter/publication | 0 70 files changed, 622 insertions(+), 406 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultProjectList.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java delete mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq rename dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/{dataset_10.json => dataset} (100%) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/dataset delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/dataset_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/software rename dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/{dataset_10.json => dataset} (100%) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/dataset delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/dataset_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/dataset delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/dataset_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/software rename dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/{dataset_10.json => dataset} (93%) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/dataset create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/otherresearchproduct delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/otherresearchproduct_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/dataset create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/datasource create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/publication delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/publication_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/software create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/software/dataset create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/software/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/software/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/software/software delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/software/software_10.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/publication diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 053300696..7c4186663 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -71,6 +71,9 @@ public class PropagationConstant { public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID = "result:community:organization"; public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME = " Propagation of result belonging to community through organization"; + public static final String PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_ID = "result:community:project"; + public static final String PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME = " Propagation of result belonging to community through project"; + public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result"; public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations"; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index cc615ba46..262ca0290 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -4,22 +4,18 @@ package eu.dnetlib.dhp.api; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; -import java.io.OutputStream; import java.net.HttpURLConnection; -import java.net.MalformedURLException; import java.net.URL; -import org.apache.http.HttpHeaders; import org.jetbrains.annotations.NotNull; -import com.google.gson.Gson; - /** * @author miriam.baglioni * @Date 06/10/23 */ public class QueryCommunityAPI { - private static final String baseUrl = "https://services.openaire.eu/openaire/"; + private static final String PRODUCTION_BASE_URL = "https://services.openaire.eu/openaire/"; + private static final String BETA_BASE_URL = "https://beta.services.openaire.eu/openaire/"; private static String get(String geturl) throws IOException { URL url = new URL(geturl); @@ -36,25 +32,35 @@ public class QueryCommunityAPI { return body; } - public static String communities() throws IOException { - return get(baseUrl + "community/communities"); + public static String communities(boolean production) throws IOException { + if (production) + return get(PRODUCTION_BASE_URL + "community/communities"); + return get(BETA_BASE_URL + "community/communities"); } - public static String community(String id) throws IOException { - return get(baseUrl + "community/" + id); + public static String community(String id, boolean production) throws IOException { + if (production) + return get(PRODUCTION_BASE_URL + "community/" + id); + return get(BETA_BASE_URL + "community/" + id); } - public static String communityDatasource(String id) throws IOException { - return get(baseUrl + "community/" + id + "/contentproviders"); + public static String communityDatasource(String id, boolean production) throws IOException { + if (production) + return get(PRODUCTION_BASE_URL + "community/" + id + "/contentproviders"); + return (BETA_BASE_URL + "community/" + id + "/contentproviders"); } - public static String communityPropagationOrganization(String id) throws IOException { - return get(baseUrl + "community/" + id + "/propagationOrganizations"); + public static String communityPropagationOrganization(String id, boolean production) throws IOException { + if (production) + return get(PRODUCTION_BASE_URL + "community/" + id + "/propagationOrganizations"); + return get(BETA_BASE_URL + "community/" + id + "/propagationOrganizations"); } - public static String communityProjects(String id, String page, String size) throws IOException { - return get(baseUrl + "community/" + id + "/projects/" + page + "/" + size); + public static String communityProjects(String id, String page, String size, boolean production) throws IOException { + if (production) + return get(PRODUCTION_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); + return get(BETA_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); } @NotNull diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index c1aaa14c4..a0eacb774 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -30,14 +30,14 @@ public class Utils implements Serializable { private static final ObjectMapper MAPPER = new ObjectMapper(); private static final VerbResolver resolver = VerbResolverFactory.newInstance(); - public static CommunityConfiguration getCommunityConfiguration() throws IOException { + public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException { final Map communities = Maps.newHashMap(); List validCommunities = new ArrayList<>(); - getValidCommunities() + getValidCommunities(production) .forEach(community -> { try { CommunityModel cm = MAPPER - .readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class); + .readValue(QueryCommunityAPI.community(community.getId(), production), CommunityModel.class); validCommunities.add(getCommunity(cm)); } catch (IOException e) { throw new RuntimeException(e); @@ -46,10 +46,11 @@ public class Utils implements Serializable { validCommunities.forEach(community -> { try { DatasourceList dl = MAPPER - .readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class); + .readValue( + QueryCommunityAPI.communityDatasource(community.getId(), production), DatasourceList.class); community.setProviders(dl.stream().map(d -> { -// if(d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) -// return null; + if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) + return null; Provider p = new Provider(); p.setOpenaireId("10|" + d.getOpenaireId()); p.setSelectionConstraints(d.getSelectioncriteria()); @@ -80,18 +81,20 @@ public class Utils implements Serializable { c.setSubjects(cm.getSubjects()); c.getSubjects().addAll(cm.getFos()); c.getSubjects().addAll(cm.getSdg()); - c.setConstraints(cm.getAdvancedConstraints()); - if (c.getConstraints() != null) + if (cm.getAdvancedConstraints() != null) { + c.setConstraints(cm.getAdvancedConstraints()); c.getConstraints().setSelection(resolver); - c.setRemoveConstraints(cm.getRemoveConstraints()); - if (c.getRemoveConstraints() != null) + } + if (cm.getRemoveConstraints() != null) { + c.setRemoveConstraints(cm.getRemoveConstraints()); c.getRemoveConstraints().setSelection(resolver); + } return c; } - public static List getValidCommunities() throws IOException { + public static List getValidCommunities(boolean production) throws IOException { return MAPPER - .readValue(QueryCommunityAPI.communities(), CommunitySummary.class) + .readValue(QueryCommunityAPI.communities(production), CommunitySummary.class) .stream() .filter( community -> !community.getStatus().equals("hidden") && @@ -99,17 +102,26 @@ public class Utils implements Serializable { .collect(Collectors.toList()); } - public static CommunityEntityMap getCommunityOrganization() throws IOException { + /** + * it returns for each organization the list of associated communities + */ + public static CommunityEntityMap getCommunityOrganization(boolean production) throws IOException { CommunityEntityMap organizationMap = new CommunityEntityMap(); - getValidCommunities() + getValidCommunities(production) .forEach(community -> { String id = community.getId(); try { List associatedOrgs = MAPPER - .readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class); - if (associatedOrgs.size() > 0) { - organizationMap.put(id, associatedOrgs); - } + .readValue( + QueryCommunityAPI.communityPropagationOrganization(id, production), OrganizationList.class); + associatedOrgs.forEach(o -> { + if (!organizationMap + .keySet() + .contains( + "20|" + o)) + organizationMap.put("20|" + o, new ArrayList<>()); + organizationMap.get("20|" + o).add(community.getId()); + }); } catch (IOException e) { throw new RuntimeException(e); } @@ -117,26 +129,28 @@ public class Utils implements Serializable { return organizationMap; } - public static CommunityEntityMap getCommunityProjects() throws IOException { + public static CommunityEntityMap getCommunityProjects(boolean production) throws IOException { CommunityEntityMap projectMap = new CommunityEntityMap(); - getValidCommunities() + getValidCommunities(production) .forEach(community -> { int page = -1; int size = 100; ContentModel cm = new ContentModel(); - List projectList = new ArrayList<>(); do { page++; try { cm = MAPPER .readValue( QueryCommunityAPI - .communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), + .communityProjects( + community.getId(), String.valueOf(page), String.valueOf(size), production), ContentModel.class); if (cm.getContent().size() > 0) { - - cm.getContent().forEach(p -> projectList.add("40|" + p.getOpenaireId())); - projectMap.put(community.getId(), projectList); + cm.getContent().forEach(p -> { + if (!projectMap.keySet().contains("40|" + p.getOpenaireId())) + projectMap.put("40|" + p.getOpenaireId(), new ArrayList<>()); + projectMap.get("40|" + p.getOpenaireId()).add(community.getId()); + }); } } catch (IOException e) { throw new RuntimeException(e); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 0d98e4958..b24ee129a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -23,6 +23,8 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.api.Utils; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Result; @@ -53,50 +55,38 @@ public class SparkBulkTagJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - Boolean isTest = Optional - .ofNullable(parser.get("isTest")) - .map(Boolean::valueOf) - .orElse(Boolean.FALSE); - log.info("isTest: {} ", isTest); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); + final boolean production = Boolean.valueOf(parser.get("production")); + log.info("production: {}", production); + ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class); log.info("pathMap: {}", new Gson().toJson(protoMappingParams)); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); - - Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); CommunityConfiguration cc; - String taggingConf = parser.get("taggingConf"); + String taggingConf = Optional + .ofNullable(parser.get("taggingConf")) + .map(String::valueOf) + .orElse(null); - if (isTest) { + if (taggingConf != null) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { - cc = Utils.getCommunityConfiguration();// QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); + cc = Utils.getCommunityConfiguration(production); } runWithSparkSession( conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, outputPath); extendCommunityConfigurationForEOSC(spark, inputPath, cc); - execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc); + execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc); }); } @@ -141,22 +131,30 @@ public class SparkBulkTagJob { String inputPath, String outputPath, ProtoMap protoMappingParams, - Class resultClazz, CommunityConfiguration communityConfiguration) { - ResultTagger resultTagger = new ResultTagger(); - readPath(spark, inputPath, resultClazz) - .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) - .map( - (MapFunction) value -> resultTagger - .enrichContextCriteria( - value, communityConfiguration, protoMappingParams), - Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + ModelSupport.entityTypes + .keySet() + .parallelStream() + .filter(e -> ModelSupport.isResult(e)) + .forEach(e -> { + removeOutputDir(spark, outputPath + e.name()); + ResultTagger resultTagger = new ResultTagger(); + Class resultClazz = ModelSupport.entityTypes.get(e); + readPath(spark, inputPath + e.name(), resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> resultTagger + .enrichContextCriteria( + value, communityConfiguration, protoMappingParams), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + e.name()); + }); + } public static Dataset readPath( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 5f62c10f4..98c46cf00 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -82,19 +82,23 @@ public class ResultTagger implements Serializable { // communities contains all the communities to be not added to the context final Set removeCommunities = new HashSet<>(); + // if (conf.getRemoveConstraintsMap().keySet().size() > 0) conf .getRemoveConstraintsMap() .keySet() - .forEach(communityId -> { - if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && - conf - .getRemoveConstraintsMap() - .get(communityId) - .getCriteria() - .stream() - .anyMatch(crit -> crit.verifyCriteria(param))) - removeCommunities.add(communityId); - }); + .forEach( + communityId -> { + // log.info("Remove constraints for " + communityId); + if (conf.getRemoveConstraintsMap().keySet().contains(communityId) && + conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && + conf + .getRemoveConstraintsMap() + .get(communityId) + .getCriteria() + .stream() + .anyMatch(crit -> crit.verifyCriteria(param))) + removeCommunities.add(communityId); + }); // communities contains all the communities to be added as context for the result final Set communities = new HashSet<>(); @@ -124,10 +128,10 @@ public class ResultTagger implements Serializable { if (Objects.nonNull(result.getInstance())) { for (Instance i : result.getInstance()) { if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) { - collfrom.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|")); + collfrom.add(i.getCollectedfrom().getKey()); } if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) { - hostdby.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|")); + hostdby.add(i.getHostedby().getKey()); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index e0670b80f..e32e94a4b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -48,11 +48,10 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); -// final CommunityEntityMap organizationMap = new Gson() -// .fromJson( -// parser.get("organizationtoresultcommunitymap"), -// CommunityEntityMap.class); - final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(); + final boolean production = Boolean.valueOf(parser.get("production")); + log.info("production: {}", production); + + final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(production); log.info("organizationMap: {}", new Gson().toJson(organizationMap)); SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 50df08f8c..43f425b68 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -56,12 +56,6 @@ public class SparkResultToCommunityFromOrganizationJob { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final Boolean saveGraph = Optional - .ofNullable(parser.get("saveGraph")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("saveGraph: {}", saveGraph); - @SuppressWarnings("unchecked") Class resultClazz = (Class) Class.forName(resultClassName); @@ -73,9 +67,9 @@ public class SparkResultToCommunityFromOrganizationJob { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - if (saveGraph) { - execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath); - } + + execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath); + }); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java new file mode 100644 index 000000000..b0fbf8056 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -0,0 +1,121 @@ + +package eu.dnetlib.dhp.resulttocommunityfromproject; + +import static eu.dnetlib.dhp.PropagationConstant.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.types.DataTypes; +import org.apache.spark.sql.types.StructType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultOrganizations; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +public class PrepareResultCommunitySet { + + private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + PrepareResultCommunitySet.class + .getResourceAsStream( + "/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final boolean production = Boolean.valueOf(parser.get("outputPath")); + log.info("production: {}", production); + + final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); + log.info("projectsMap: {}", new Gson().toJson(projectsMap)); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareInfo(spark, inputPath, outputPath, projectsMap); + }); + } + + private static void prepareInfo( + SparkSession spark, + String inputPath, + String outputPath, + CommunityEntityMap projectMap) { + + final StructType structureSchema = new StructType() + .add( + "dataInfo", new StructType() + .add("deletedbyinference", DataTypes.BooleanType) + .add("invisible", DataTypes.BooleanType)) + .add("source", DataTypes.StringType) + .add("target", DataTypes.StringType) + .add("relClass", DataTypes.StringType); + + spark + .read() + .schema(structureSchema) + .json(inputPath) + .filter( + "dataInfo.deletedbyinference != true " + + "and relClass == '" + ModelConstants.IS_PRODUCED_BY + "'") + .select( + new Column("source").as("resultId"), + new Column("target").as("projectId")) + .groupByKey((MapFunction) r -> (String) r.getAs("source"), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, v) -> { + ResultProjectList rpl = new ResultProjectList(); + rpl.setResultId(k); + ArrayList cl = new ArrayList<>(); + cl.addAll(projectMap.get(v.next().getAs("target"))); + v.forEachRemaining(r -> { + projectMap + .get(r.getAs("target")) + .forEach(c -> { + if (!cl.contains(c)) + cl.add(c); + }); + + }); + rpl.setCommunityList(cl); + return rpl; + }, Encoders.bean(ResultProjectList.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultProjectList.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultProjectList.java new file mode 100644 index 000000000..44798a1f3 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultProjectList.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.resulttocommunityfromproject; + +import java.io.Serializable; +import java.util.ArrayList; + +public class ResultProjectList implements Serializable { + private String resultId; + private ArrayList communityList; + + public String getResultId() { + return resultId; + } + + public void setResultId(String resultId) { + this.resultId = resultId; + } + + public ArrayList getCommunityList() { + return communityList; + } + + public void setCommunityList(ArrayList communityList) { + this.communityList = communityList; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java new file mode 100644 index 000000000..6d4779ea1 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -0,0 +1,156 @@ + +package eu.dnetlib.dhp.resulttocommunityfromproject; + +import static eu.dnetlib.dhp.PropagationConstant.*; +import static eu.dnetlib.dhp.PropagationConstant.PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; +import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 11/10/23 + */ +public class SparkResultToCommunityFromProject implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityFromProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkResultToCommunityFromProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String possibleupdatespath = parser.get("preparedInfoPath"); + log.info("preparedInfoPath: {}", possibleupdatespath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + @SuppressWarnings("unchecked") + Class resultClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { +// removeOutputDir(spark, outputPath); + + execPropagation(spark, inputPath, outputPath, possibleupdatespath); + + }); + } + + private static void execPropagation( + SparkSession spark, + String inputPath, + String outputPath, + + String possibleUpdatesPath) { + + Dataset possibleUpdates = readPath(spark, possibleUpdatesPath, ResultProjectList.class); + + ModelSupport.entityTypes + .keySet() + .parallelStream() + .forEach(e -> { + if (ModelSupport.isResult(e)) { + removeOutputDir(spark, outputPath + e.name()); + Class resultClazz = ModelSupport.entityTypes.get(e); + Dataset result = readPath(spark, inputPath + e.name(), resultClazz); + + result + .joinWith( + possibleUpdates, + result.col("id").equalTo(possibleUpdates.col("resultId")), + "left_outer") + .map(resultCommunityFn(), Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + }); + + } + + private static MapFunction, R> resultCommunityFn() { + return value -> { + R ret = value._1(); + Optional rcl = Optional.ofNullable(value._2()); + if (rcl.isPresent()) { + ArrayList communitySet = rcl.get().getCommunityList(); + List contextList = ret + .getContext() + .stream() + .map(Context::getId) + .collect(Collectors.toList()); + + @SuppressWarnings("unchecked") + R res = (R) ret.getClass().newInstance(); + + res.setId(ret.getId()); + List propagatedContexts = new ArrayList<>(); + for (String cId : communitySet) { + if (!contextList.contains(cId)) { + Context newContext = new Context(); + newContext.setId(cId); + newContext + .setDataInfo( + Arrays + .asList( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_ID, + PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS))); + propagatedContexts.add(newContext); + } + } + res.setContext(propagatedContexts); + ret.mergeFrom(res); + } + return ret; + }; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json index a8be7c32e..dbe2d088f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json @@ -1,10 +1,5 @@ [ - { - "paramName":"is", - "paramLongName":"isLookUpUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, + { "paramName":"s", "paramLongName":"sourcePath", @@ -17,12 +12,7 @@ "paramDescription": "the json path associated to each selection field", "paramRequired": true }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, + { "paramName": "out", "paramLongName": "outputPath", @@ -35,17 +25,19 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { - "paramName": "test", - "paramLongName": "isTest", - "paramDescription": "Parameter intended for testing purposes only. True if the reun is relatesd to a test and so the taggingConf parameter should be loaded", - "paramRequired": false - }, + { "paramName": "tg", "paramLongName": "taggingConf", "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", "paramRequired": false + }, + + { + "paramName": "p", + "paramLongName": "production", + "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index b868e4c72..56eed4703 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -4,10 +4,6 @@ sourcePath the source path - - isLookUpUrl - the isLookup service endpoint - pathMap the json path associated to each selection field @@ -44,7 +40,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -102,16 +98,9 @@ - + - - - - - - - - + yarn-cluster cluster @@ -128,98 +117,15 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${outputPath}/publication + --sourcePath${sourcePath}/ + --outputPath${outputPath}/ --pathMap${pathMap} - --isLookUpUrl${isLookUpUrl} + --production${production} - + - - - yarn-cluster - cluster - bulkTagging-dataset - eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-enrichment-${projectVersion}.jar - - --num-executors=${sparkExecutorNumber} - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${outputPath}/dataset - --pathMap${pathMap} - --isLookUpUrl${isLookUpUrl} - - - - - - - - yarn-cluster - cluster - bulkTagging-orp - eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-enrichment-${projectVersion}.jar - - --num-executors=${sparkExecutorNumber} - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${outputPath}/otherresearchproduct - --pathMap${pathMap} - --isLookUpUrl${isLookUpUrl} - - - - - - - - yarn-cluster - cluster - bulkTagging-software - eu.dnetlib.dhp.bulktag.SparkBulkTagJob - dhp-enrichment-${projectVersion}.jar - - --num-executors=${sparkExecutorNumber} - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${outputPath}/software - --pathMap${pathMap} - --isLookUpUrl${isLookUpUrl} - - - - - - diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq deleted file mode 100644 index 052037efb..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq +++ /dev/null @@ -1,62 +0,0 @@ -for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') -let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() -let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept -let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept -let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept -let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() -let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() -let $zenodo := $x//param[./@name='zenodoCommunity']/text() -where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' -return - -{ $x//CONFIGURATION/context/@id} - -{$x//CONFIGURATION/context/param[./@name='removeConstraints']/text() } - - -{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() } - - - {for $y in tokenize($subj,',') - return - {$y}} - {for $y in tokenize($fos,',') - return - {$y}} - {for $y in tokenize($sdg,',') - return - {$y}} - - - {for $d in $datasources - where $d/param[./@name='enabled']/text()='true' - return - - - {$d//param[./@name='openaireId']/text()} - - - {$d/param[./@name='selcriteria']/text()} - - } - - -{for $zc in $zenodo -return - - -{$zc} - -} -{for $zc in $communities -return - - -{$zc/param[./@name='zenodoid']/text()} - - -{$zc/param[./@name='selcriteria']/text()} - -} - - \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json index eebc1a0ca..b6eb309a5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json @@ -11,18 +11,6 @@ "paramDescription": "the hive metastore uris", "paramRequired": true }, - { - "paramName":"sg", - "paramLongName":"saveGraph", - "paramDescription": "true if the new version of the graph must be saved", - "paramRequired": false - }, - { - "paramName":"test", - "paramLongName":"isTest", - "paramDescription": "true if it is executing a test", - "paramRequired": false - }, { "paramName": "out", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index d9805ab7b..b25822ad0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -4,10 +4,7 @@ sourcePath the source path - - - - + outputPath the output path @@ -106,7 +103,7 @@ --sourcePath${sourcePath}/relation --outputPath${workingDir}/preparedInfo/resultCommunityList --hive_metastore_uris${hive_metastore_uris} - --organizationtoresultcommunitymap${organizationtoresultcommunitymap} + diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 11dad9055..7cbbcaafb 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.HashMap; import java.util.List; import org.apache.commons.io.FileUtils; @@ -98,14 +99,11 @@ public class BulkTagJobTest { SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(), "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-outputPath", workingDir.toString() + "/", "-pathMap", pathMap }); @@ -133,19 +131,16 @@ public class BulkTagJobTest { @Test void bulktagBySubjectNoPreviousContextTest() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/") .getPath(); final String pathMap = BulkTagJobTest.pathMap; SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-outputPath", workingDir.toString() + "/", "-pathMap", pathMap }); @@ -230,19 +225,19 @@ public class BulkTagJobTest { void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/") .getPath(); final String pathMap = BulkTagJobTest.pathMap; SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -311,18 +306,18 @@ public class BulkTagJobTest { @Test void bulktagByDatasourceTest() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") + .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/publication", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -384,25 +379,25 @@ public class BulkTagJobTest { void bulktagByZenodoCommunityTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") + "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/orp", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/orp") + .textFile(workingDir.toString() + "/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); Assertions.assertEquals(10, tmp.count()); @@ -505,18 +500,18 @@ public class BulkTagJobTest { @Test void bulktagBySubjectDatasourceTest() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -636,14 +631,14 @@ public class BulkTagJobTest { SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/software_10.json.gz").getPath(), + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -732,18 +727,18 @@ public class BulkTagJobTest { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -774,19 +769,19 @@ public class BulkTagJobTest { void bulkTagOtherJupyter() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct") + "/eu/dnetlib/dhp/eosctag/jupyter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/otherresearchproduct", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -829,18 +824,18 @@ public class BulkTagJobTest { public void bulkTagDatasetJupyter() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/jupyter/dataset") + "/eu/dnetlib/dhp/eosctag/jupyter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -878,18 +873,18 @@ public class BulkTagJobTest { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/jupyter/software") + "/eu/dnetlib/dhp/eosctag/jupyter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1096,18 +1091,18 @@ public class BulkTagJobTest { void galaxyOtherTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct") + "/eu/dnetlib/dhp/eosctag/galaxy/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/otherresearchproduct", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1214,18 +1209,18 @@ public class BulkTagJobTest { void galaxySoftwareTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/galaxy/software") + "/eu/dnetlib/dhp/eosctag/galaxy/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1333,19 +1328,19 @@ public class BulkTagJobTest { void twitterDatasetTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/twitter/dataset") + "/eu/dnetlib/dhp/eosctag/twitter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1373,19 +1368,19 @@ public class BulkTagJobTest { void twitterOtherTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct") + "/eu/dnetlib/dhp/eosctag/twitter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/otherresearchproduct", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1418,19 +1413,19 @@ public class BulkTagJobTest { void twitterSoftwareTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/eosctag/twitter/software") + "/eu/dnetlib/dhp/eosctag/twitter/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1455,19 +1450,19 @@ public class BulkTagJobTest { void EoscContextTagTest() throws Exception { final String sourcePath = getClass() .getResource( - "/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json") + "/eu/dnetlib/dhp/bulktag/eosc/dataset/") .getPath(); SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", sourcePath, "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); @@ -1533,16 +1528,16 @@ public class BulkTagJobTest { SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/") .getPath(), "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-pathMap", pathMap }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -1574,14 +1569,14 @@ public class BulkTagJobTest { SparkBulkTagJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(), "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + + "-outputPath", workingDir.toString() + "/", + "-production", Boolean.TRUE.toString(), "-pathMap", pathMap }); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java index b0043d1e8..a0083dab8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java @@ -26,7 +26,7 @@ public class QueryCommunityAPITest { @Test void communityList() throws Exception { - String body = QueryCommunityAPI.communities(); + String body = QueryCommunityAPI.communities(true); new ObjectMapper() .readValue(body, CommunitySummary.class) .forEach(p -> { @@ -41,7 +41,7 @@ public class QueryCommunityAPITest { @Test void community() throws Exception { String id = "dh-ch"; - String body = QueryCommunityAPI.community(id); + String body = QueryCommunityAPI.community(id, true); System.out .println( new ObjectMapper() @@ -53,7 +53,7 @@ public class QueryCommunityAPITest { @Test void communityDatasource() throws Exception { String id = "dh-ch"; - String body = QueryCommunityAPI.communityDatasource(id); + String body = QueryCommunityAPI.communityDatasource(id, true); new ObjectMapper() .readValue(body, DatasourceList.class) .forEach(ds -> { @@ -68,7 +68,7 @@ public class QueryCommunityAPITest { @Test void validCommunities() throws Exception { - CommunityConfiguration cc = Utils.getCommunityConfiguration(); + CommunityConfiguration cc = Utils.getCommunityConfiguration(true); System.out.println(cc.getCommunities().keySet()); Community community = cc.getCommunities().get("aurora"); Assertions.assertEquals(0, community.getSubjects().size()); @@ -84,11 +84,20 @@ public class QueryCommunityAPITest { Assertions .assertEquals( 35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count()); + + } + + @Test + void eutopiaCommunityConfiguration() throws Exception { + CommunityConfiguration cc = Utils.getCommunityConfiguration(true); + System.out.println(cc.getCommunities().keySet()); + Community community = cc.getCommunities().get("eutopia"); + community.getProviders().forEach(p -> System.out.println(p.getOpenaireId())); } @Test void getCommunityProjects() throws Exception { - CommunityEntityMap projectMap = Utils.getCommunityProjects(); + CommunityEntityMap projectMap = Utils.getCommunityProjects(true); Assertions.assertFalse(projectMap.containsKey("mes")); Assertions.assertEquals(33, projectMap.size()); Assertions diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java index 4dd8b976c..da3be8b35 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java @@ -78,7 +78,7 @@ public class ResultToCommunityJobTest { .getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample") .getPath(), "-hive_metastore_uris", "", - "-saveGraph", "true", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", "-outputPath", workingDir.toString() + "/dataset", "-preparedInfoPath", preparedInfoPath diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset similarity index 100% rename from dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json rename to dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/otherresearchproduct b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/otherresearchproduct new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/publication b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/publication new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/software b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/software new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/dataset b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/dataset new file 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobretodo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobretodo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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zp*0$J$QG{Kx5@7hULFl?&@gM@?9#WC?NWMS_4|LokD_5d Date: Mon, 16 Oct 2023 08:57:47 +0200 Subject: [PATCH 05/23] [raw graph] WIP: mapping original resource types --- .../raw/AbstractMdRecordToOafMapper.java | 64 +- .../dhp/oa/graph/raw/OafToOafMapper.java | 28 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 22 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 60 +- .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 855 +++++++++++++++++- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 292 +++++- 6 files changed, 1244 insertions(+), 77 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 2fed7d627..5f0acbab7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -42,10 +42,6 @@ public abstract class AbstractMdRecordToOafMapper { protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final String OPENAIRE_COAR_RESOURCE_TYPES_3_1 = "openaire::coar_resource_types_3_1"; - - public static final String OPENAIRE_USER_RESOURCE_TYPES = "openaire::user_resource_types"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, @@ -129,7 +125,9 @@ public abstract class AbstractMdRecordToOafMapper { final String type = getResultType(doc, instances); - return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + final Qualifier metaResourceType = getMetaResourceType(instances); + + return createOafs(doc, type, metaResourceType, instances, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); @@ -155,6 +153,30 @@ public abstract class AbstractMdRecordToOafMapper { return type; } + protected Qualifier getMetaResourceType(final List instances) { + + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional instanceTypeMapping = instances + .stream() + .flatMap(i -> i.getInstanceTypeMapping().stream()) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!instanceTypeMapping.isPresent()) { + throw new IllegalStateException("unable to find an instance from " + OPENAIRE_COAR_RESOURCE_TYPES_3_1); + } else { + final String typeCode = instanceTypeMapping.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow(() -> + new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + } + private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); @@ -169,12 +191,13 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, + final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity(doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -207,6 +230,7 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, + final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, @@ -214,12 +238,12 @@ public abstract class AbstractMdRecordToOafMapper { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -230,7 +254,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -240,7 +264,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -377,11 +401,13 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, + final Qualifier metaResourceType, final Document doc, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { + r.setMetaResourceType(metaResourceType); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); @@ -531,15 +557,17 @@ public abstract class AbstractMdRecordToOafMapper { if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { // TODO verify what the vocabs return when a synonym is not defined - Qualifier coarTerm = vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType); - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + Optional.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) + .ifPresent(coarTerm -> { + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - - // TODO verify what the vocabs return when a synonym is not defined - Qualifier userTerm = vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid()); - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, userTerm)); - } + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) + .ifPresent(type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); + } + }); } return mappings; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 5cdb434f1..6bcc8ec44 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,29 +1,27 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; - -import java.net.URLDecoder; -import java.util.*; -import java.util.stream.Collectors; - -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Element; -import org.dom4j.Node; - import com.google.common.collect.Lists; - import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.Node; -import static org.apache.commons.lang3.StringUtils.contains; +import java.net.URLDecoder; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; public class OafToOafMapper extends AbstractMdRecordToOafMapper { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index c01775327..c383e9300 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -220,11 +220,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } } - @Override - protected List prepareInstanceTypeMapping(Document doc) { - return null; - } - /** * The Datacite element * @@ -235,13 +230,20 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - final Element resourceType = (Element) doc.selectSingleNode( - "//metadata/*[local-name() = 'resource']/*[local-name() = 'resourceType']"); + String resourceType = Optional.ofNullable((Element) doc.selectSingleNode( + "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) + .map(element -> { + final String resourceTypeURI = element.attributeValue("anyURI"); + final String resourceTypeTxt = element.getText(); - final String resourceTypeURI = resourceType.attributeValue("anyURI"); - final String resourceTypeTxt = resourceType.getText(); + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + }) + .orElse(doc.valueOf( + "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'CobjCategory']/text()") + ); + + return resourceType; - return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 5df2b7a3b..4d30a3fa8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -74,7 +74,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -97,14 +97,14 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); + assertFalse(p.getSubject().isEmpty()); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertTrue(p.getPid().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -121,7 +121,7 @@ class MappersTest { Optional coarType = instance.getInstanceTypeMapping() .stream() - .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) .findFirst(); assertTrue(coarType.isPresent()); @@ -130,7 +130,7 @@ class MappersTest { Optional userType = instance.getInstanceTypeMapping() .stream() - .filter(itm -> AbstractMdRecordToOafMapper.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) .findFirst(); assertTrue(userType.isPresent()); @@ -228,7 +228,7 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getDateofcollection())); assertTrue(StringUtils.isNotBlank(p.getDateoftransformation())); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() .stream() @@ -251,13 +251,13 @@ class MappersTest { assertEquals("Votsi", author.get().getSurname()); assertEquals("Nefta", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getPid().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getPid().isEmpty()); assertEquals("PMC1517292", p.getPid().get(0).getValue()); assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -287,7 +287,7 @@ class MappersTest { final List list = new OafToOafMapper(vocs, true, true).processMdRecord(xml); - assertTrue(list.size() > 0); + assertFalse(list.isEmpty()); assertTrue(list.get(0) instanceof Publication); final Publication p = (Publication) list.get(0); @@ -343,7 +343,7 @@ class MappersTest { assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526"))); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); - assertTrue(d.getAuthor().size() > 0); + assertFalse(d.getAuthor().isEmpty()); final Optional author = d .getAuthor() @@ -377,13 +377,13 @@ class MappersTest { final Field affiliation = opAff.get(); assertEquals("ISTI-CNR", affiliation.getValue()); - assertTrue(d.getSubject().size() > 0); - assertTrue(d.getInstance().size() > 0); - assertTrue(d.getContext().size() > 0); - assertTrue(d.getContext().get(0).getId().length() > 0); + assertFalse(d.getSubject().isEmpty()); + assertFalse(d.getInstance().isEmpty()); + assertFalse(d.getContext().isEmpty()); + assertFalse(d.getContext().get(0).getId().isEmpty()); assertNotNull(d.getInstance()); - assertTrue(d.getInstance().size() > 0); + assertFalse(d.getInstance().isEmpty()); d .getInstance() .forEach(i -> { @@ -457,7 +457,7 @@ class MappersTest { // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -469,14 +469,14 @@ class MappersTest { assertEquals("Potwarka", author.get().getSurname()); assertEquals("Luke R.", author.get().getName()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -624,9 +624,9 @@ class MappersTest { assertValidId(s.getId()); assertValidId(s.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); - assertTrue(s.getAuthor().size() > 0); - assertTrue(s.getSubject().size() > 0); - assertTrue(s.getInstance().size() > 0); + assertFalse(s.getAuthor().isEmpty()); + assertFalse(s.getSubject().isEmpty()); + assertFalse(s.getInstance().isEmpty()); final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); @@ -882,7 +882,7 @@ class MappersTest { assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a"))); assertValidId(p.getCollectedfrom().get(0).getKey()); - assertTrue(p.getAuthor().size() > 0); + assertFalse(p.getAuthor().isEmpty()); final Optional author = p .getAuthor() @@ -892,14 +892,14 @@ class MappersTest { assertEquals("Museum Sønderjylland", author.get().getFullname()); - assertTrue(p.getSubject().size() > 0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getSubject().isEmpty()); + assertFalse(p.getInstance().isEmpty()); assertNotNull(p.getTitle()); assertFalse(p.getTitle().isEmpty()); assertNotNull(p.getInstance()); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); p .getInstance() .forEach(i -> { @@ -939,10 +939,10 @@ class MappersTest { System.out.println("***************"); final Dataset p = (Dataset) list.get(0); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); for (String url : p.getInstance().get(0).getUrl()) { System.out.println(url); - assertTrue(!url.contains("&")); + assertFalse(url.contains("&")); } } @@ -959,7 +959,7 @@ class MappersTest { assertTrue(o.isPresent()); Publication p = (Publication) o.get(); - assertTrue(p.getInstance().size() > 0); + assertFalse(p.getInstance().isEmpty()); assertEquals("https://doi.org/10.1155/2015/439379", p.getInstance().get(0).getUrl().get(0)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index b3fa94b20..a17a3949a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -1246,8 +1246,857 @@ dnet:relation_subRelType @=@ relationship @=@ publicationDataset dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned FOS @=@ 0101 mathematics @=@ FOS: Mathematics FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Chemical Structures +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Data Cube +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Dataset/Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Ensemble de données / Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ Research Data +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_ddb1 @=@ http://purl.org/coar/resource_type/c_ddb1 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ collection +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Collection of Datasets +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ RO-crate +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Supplementary Collection of Datasets +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/ACF7-8YT9 @=@ Supplementary Dataset +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cc @=@ http://purl.org/coar/resource_type/c_12cc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cc @=@ Planimetría +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_cb28 @=@ clinicalTrial +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_cb28 @=@ http://purl.org/coar/resource_type/c_cb28 +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ Carte géographique / Map +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ http://purl.org/coar/resource_type/c_12cd +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ map +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_12cd @=@ Mapa +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ Audio +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ http://purl.org/coar/resource_type/c_18cc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_18cc @=@ sound +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Book Prospectus +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Dictionary Entry +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Disclosure +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Literature review +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ Reseña bibliográfica +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ bibliography +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_86bc @=@ http://purl.org/coar/resource_type/c_86bc +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ AUDIOVISUAL_DOCUMENT +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ Audiovisual/Audiovisual +openaire::coar_resource_types_3_1 @=@ http://purl.org/coar/resource_type/c_8a7e @=@ 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http://purl.org/coar/resource_type/H6QP-SC1X +openaire::meta_resource_types @=@ Other Research Products @=@ workflow +openaire::meta_resource_types @=@ Other Research Products @=@ http://purl.org/coar/resource_type/c_393c \ No newline at end of file From 159388f9c220e33810d50c7a4552ac640c78eb92 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 16 Oct 2023 11:26:07 +0200 Subject: [PATCH 06/23] testing and fix some issues --- .../main/java/eu/dnetlib/dhp/api/Utils.java | 7 + .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 11 +- .../community/QueryInformationSystem.java | 34 -- ...kResultToCommunityFromOrganizationJob.java | 50 +-- .../PrepareResultCommunitySet.java | 15 +- .../SparkResultToCommunityFromProject.java | 13 +- .../input_communitytoresult_parameters.json | 13 +- ...t_preparecommunitytoresult_parameters.json | 12 +- .../oozie_app/workflow.xml | 115 +------ .../input_communitytoresult_parameters.json | 28 ++ ...t_preparecommunitytoresult_parameters.json | 33 ++ .../QueryCommunityAPITest.java | 16 +- .../PrepareAssocTest.java | 95 ++++++ .../PrepareAssocTest.java | 88 +++++ .../ResultToCommunityJobTest.java | 323 ++++++++++++++++++ .../preparedInfo/resultCommunityList.json | 36 ++ .../preparedInfo/resultCommunityList.json.gz | Bin 939 -> 0 bytes .../relation/relation | 20 ++ .../preparedInfo/resultcommunitylist | 4 + .../relation/relation | 20 ++ .../sample/dataset | 10 + .../sample/otherresearchproduct | 0 .../sample/publication | 0 .../sample/software | 0 24 files changed, 736 insertions(+), 207 deletions(-) delete mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json rename dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/{bulktag => api}/QueryCommunityAPITest.java (90%) create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json.gz create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/relation/relation create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/preparedInfo/resultcommunitylist create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/relation/relation create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/dataset create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/otherresearchproduct create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/publication create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/software diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index a0eacb774..43d5e7e98 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -11,6 +11,9 @@ import java.util.stream.Collectors; import javax.management.Query; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + import com.amazonaws.util.StringUtils; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; @@ -21,6 +24,7 @@ import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; import eu.dnetlib.dhp.bulktag.community.Provider; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory; +import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; /** * @author miriam.baglioni @@ -30,6 +34,8 @@ public class Utils implements Serializable { private static final ObjectMapper MAPPER = new ObjectMapper(); private static final VerbResolver resolver = VerbResolverFactory.newInstance(); + private static final Logger log = LoggerFactory.getLogger(Utils.class); + public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException { final Map communities = Maps.newHashMap(); List validCommunities = new ArrayList<>(); @@ -126,6 +132,7 @@ public class Utils implements Serializable { throw new RuntimeException(e); } }); + return organizationMap; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index b24ee129a..68c740dd5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -95,10 +95,7 @@ public class SparkBulkTagJob { Dataset datasources = readPath( spark, inputPath - .substring( - 0, - inputPath.lastIndexOf("/")) - + "/datasource", + + "datasource", Datasource.class) .filter((FilterFunction) ds -> isOKDatasource(ds)) .map((MapFunction) ds -> ds.getId(), Encoders.STRING()); @@ -106,10 +103,10 @@ public class SparkBulkTagJob { Map>> dsm = cc.getEoscDatasourceMap(); for (String ds : datasources.collectAsList()) { - final String dsId = ds.substring(3); - if (!dsm.containsKey(dsId)) { + // final String dsId = ds.substring(3); + if (!dsm.containsKey(ds)) { ArrayList> eoscList = new ArrayList<>(); - dsm.put(dsId, eoscList); + dsm.put(ds, eoscList); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java deleted file mode 100644 index 5fe3cf81f..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.bulktag.community; - -import java.io.IOException; -import java.util.List; - -import org.apache.commons.io.IOUtils; -import org.dom4j.DocumentException; -import org.xml.sax.SAXException; - -import com.google.common.base.Joiner; - -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class QueryInformationSystem { - - public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl) - throws ISLookUpException, DocumentException, SAXException, IOException { - ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - final List res = isLookUp - .quickSearchProfile( - IOUtils - .toString( - QueryInformationSystem.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/query.xq"))); - - final String xmlConf = "" + Joiner.on(" ").join(res) + ""; - - return CommunityConfigurationFactory.newInstance(xmlConf); - } -} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index 43f425b68..fe79f1be1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -2,7 +2,7 @@ package eu.dnetlib.dhp.resulttocommunityfromorganization; import static eu.dnetlib.dhp.PropagationConstant.*; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; import java.util.Arrays; @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Result; import scala.Tuple2; @@ -53,22 +54,15 @@ public class SparkResultToCommunityFromOrganizationJob { final String possibleupdatespath = parser.get("preparedInfoPath"); log.info("preparedInfoPath: {}", possibleupdatespath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - @SuppressWarnings("unchecked") - Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + runWithSparkSession( conf, isSparkSessionManaged, spark -> { - removeOutputDir(spark, outputPath); + // removeOutputDir(spark, outputPath); - execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath); + execPropagation(spark, inputPath, outputPath, possibleupdatespath); }); } @@ -77,22 +71,32 @@ public class SparkResultToCommunityFromOrganizationJob { SparkSession spark, String inputPath, String outputPath, - Class resultClazz, String possibleUpdatesPath) { Dataset possibleUpdates = readPath(spark, possibleUpdatesPath, ResultCommunityList.class); - Dataset result = readPath(spark, inputPath, resultClazz); - result - .joinWith( - possibleUpdates, - result.col("id").equalTo(possibleUpdates.col("resultId")), - "left_outer") - .map(resultCommunityFn(), Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + ModelSupport.entityTypes + .keySet() + .parallelStream() + .forEach(e -> { + if (ModelSupport.isResult(e)) { + Class resultClazz = ModelSupport.entityTypes.get(e); + removeOutputDir(spark, outputPath + e.name()); + Dataset result = readPath(spark, inputPath + e.name(), resultClazz); + + result + .joinWith( + possibleUpdates, + result.col("id").equalTo(possibleUpdates.col("resultId")), + "left_outer") + .map(resultCommunityFn(), Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + e.name()); + } + }); + } private static MapFunction, R> resultCommunityFn() { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index b0fbf8056..883f5ca86 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.resulttocommunityfromproject; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; @@ -51,16 +52,15 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("outputPath")); + final boolean production = Boolean.valueOf(parser.get("production")); log.info("production: {}", production); final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); log.info("projectsMap: {}", new Gson().toJson(projectsMap)); SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + runWithSparkSession( conf, isSparkSessionManaged, spark -> { @@ -94,24 +94,27 @@ public class PrepareResultCommunitySet { .select( new Column("source").as("resultId"), new Column("target").as("projectId")) - .groupByKey((MapFunction) r -> (String) r.getAs("source"), Encoders.STRING()) + .groupByKey((MapFunction) r -> (String) r.getAs("resultId"), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, v) -> { ResultProjectList rpl = new ResultProjectList(); rpl.setResultId(k); ArrayList cl = new ArrayList<>(); - cl.addAll(projectMap.get(v.next().getAs("target"))); + cl.addAll(projectMap.get(v.next().getAs("projectId"))); v.forEachRemaining(r -> { projectMap - .get(r.getAs("target")) + .get(r.getAs("projectId")) .forEach(c -> { if (!cl.contains(c)) cl.add(c); }); }); + if(cl.size() == 0) + return null; rpl.setCommunityList(cl); return rpl; }, Encoders.bean(ResultProjectList.class)) + .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index 6d4779ea1..daef6a317 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttocommunityfromproject; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.ArrayList; @@ -61,20 +62,14 @@ public class SparkResultToCommunityFromProject implements Serializable { final String possibleupdatespath = parser.get("preparedInfoPath"); log.info("preparedInfoPath: {}", possibleupdatespath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - @SuppressWarnings("unchecked") - Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + + runWithSparkSession( conf, isSparkSessionManaged, spark -> { -// removeOutputDir(spark, outputPath); execPropagation(spark, inputPath, outputPath, possibleupdatespath); @@ -108,7 +103,7 @@ public class SparkResultToCommunityFromProject implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath); + .json(outputPath + e.name()); } }); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json index b6eb309a5..0db8085d1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json @@ -5,12 +5,7 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", - "paramRequired": true - }, + { "paramName": "out", "paramLongName": "outputPath", @@ -23,12 +18,6 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, { "paramName": "p", "paramLongName": "preparedInfoPath", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json index 8df509abf..8b6291e5d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json @@ -5,12 +5,6 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"ocm", - "paramLongName":"organizationtoresultcommunitymap", - "paramDescription": "the map for the association organization communities", - "paramRequired": true - }, { "paramName":"h", "paramLongName":"hive_metastore_uris", @@ -28,6 +22,12 @@ "paramLongName": "outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true + }, + { + "paramName": "p", + "paramLongName": "production", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index b25822ad0..55490e25c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -22,7 +22,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -90,8 +90,8 @@ eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet dhp-enrichment-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} + --executor-cores=4 + --executor-memory=10G --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} @@ -103,20 +103,13 @@ --sourcePath${sourcePath}/relation --outputPath${workingDir}/preparedInfo/resultCommunityList --hive_metastore_uris${hive_metastore_uris} - + --production${production} - + - - - - - - - - + yarn cluster @@ -135,104 +128,14 @@ --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/publication - --outputPath${outputPath}/publication - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --saveGraph${saveGraph} + --sourcePath${sourcePath}/ + --outputPath${outputPath}/ - + - - - yarn - cluster - community2resultfromorganization-Dataset - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/dataset - --outputPath${outputPath}/dataset - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --saveGraph${saveGraph} - - - - - - - yarn - cluster - community2resultfromorganization-ORP - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/otherresearchproduct - --outputPath${outputPath}/otherresearchproduct - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --saveGraph${saveGraph} - - - - - - - - yarn - cluster - community2resultfromorganization-Software - eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob - dhp-enrichment-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true - --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} - - --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList - --sourcePath${sourcePath}/software - --outputPath${outputPath}/software - --hive_metastore_uris${hive_metastore_uris} - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --saveGraph${saveGraph} - - - - - - diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json new file mode 100644 index 000000000..0db8085d1 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json @@ -0,0 +1,28 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "p", + "paramLongName": "preparedInfoPath", + "paramDescription": "the path where prepared info have been stored", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json new file mode 100644 index 000000000..8b6291e5d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json @@ -0,0 +1,33 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName":"h", + "paramLongName":"hive_metastore_uris", + "paramDescription": "the hive metastore uris", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "p", + "paramLongName": "production", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java similarity index 90% rename from dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java rename to dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java index a0083dab8..6ee01a6f0 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.bulktag; +package eu.dnetlib.dhp.api; import java.util.List; @@ -98,14 +98,22 @@ public class QueryCommunityAPITest { @Test void getCommunityProjects() throws Exception { CommunityEntityMap projectMap = Utils.getCommunityProjects(true); - Assertions.assertFalse(projectMap.containsKey("mes")); - Assertions.assertEquals(33, projectMap.size()); + Assertions .assertTrue( projectMap .keySet() .stream() - .allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|")))); + .allMatch(k -> k.startsWith("40|"))); + + System.out.println(projectMap); + } + + @Test + void getCommunityOrganizations() throws Exception { + CommunityEntityMap organizationMap = Utils.getCommunityOrganization(true); + Assertions.assertTrue(organizationMap.keySet().stream().allMatch(k -> k.startsWith("20|"))); + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java new file mode 100644 index 000000000..6536ecc85 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java @@ -0,0 +1,95 @@ + +package eu.dnetlib.dhp.resulttocommunityfromorganization; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; + +import eu.dnetlib.dhp.api.Utils; +import eu.dnetlib.dhp.api.model.CommunityEntityMap; +import eu.dnetlib.dhp.bulktag.BulkTagJobTest; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.schema.oaf.Dataset; + +/** + * @author miriam.baglioni + * @Date 13/10/23 + */ +public class PrepareAssocTest { + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(PrepareAssocTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(BulkTagJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PrepareAssocTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void test1() throws Exception { + + PrepareResultCommunitySet + .main( + new String[] { + + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/relation/").getPath(), + "-outputPath", workingDir.toString() + "/prepared", + "-production", Boolean.TRUE.toString(), + "-hive_metastore_uris", "" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/prepared") + .map(item -> new ObjectMapper().readValue(item, ResultCommunityList.class)); + + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java new file mode 100644 index 000000000..0e10b3edf --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.resulttocommunityfromproject; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.bulktag.BulkTagJobTest; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; + +/** + * @author miriam.baglioni + * @Date 13/10/23 + */ +public class PrepareAssocTest { + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(PrepareAssocTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(BulkTagJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PrepareAssocTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void test1() throws Exception { + + PrepareResultCommunitySet + .main( + new String[] { + + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromproject/relation/").getPath(), + "-outputPath", workingDir.toString() + "/prepared", + "-production", Boolean.TRUE.toString(), + "-hive_metastore_uris", "" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/prepared") + .map(item -> new ObjectMapper().readValue(item, ResultProjectList.class)); + + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java new file mode 100644 index 000000000..6a5726cbe --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java @@ -0,0 +1,323 @@ + +package eu.dnetlib.dhp.resulttocommunityfromproject; + +import static org.apache.spark.sql.functions.desc; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest; +import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; +import eu.dnetlib.dhp.schema.oaf.Dataset; + +public class ResultToCommunityJobTest { + + private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(ResultToCommunityJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ResultToCommunityJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(OrcidPropagationJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testSparkResultToCommunityFromProjectJob() throws Exception { + final String preparedInfoPath = getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromproject/preparedInfo") + .getPath(); + SparkResultToCommunityFromProject + .main( + new String[] { + + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromproject/sample/") + .getPath(), + + "-outputPath", workingDir.toString() + "/", + "-preparedInfoPath", preparedInfoPath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + tmp.foreach(d -> System.out.println(new ObjectMapper().writeValueAsString(d))); +// Assertions.assertEquals(10, tmp.count()); +// org.apache.spark.sql.Dataset verificationDataset = spark +// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); +// +// verificationDataset.createOrReplaceTempView("dataset"); +// +// String query = "select id, MyT.id community " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD " +// + "where MyD.inferenceprovenance = 'propagation'"; +// +// org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); +// Assertions.assertEquals(5, resultExplodedProvenance.count()); +// Assertions +// .assertEquals( +// 0, +// resultExplodedProvenance +// .filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'") +// .count()); +// Assertions +// .assertEquals( +// 1, +// resultExplodedProvenance +// .filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'") +// .count()); +// Assertions +// .assertEquals( +// "beopen", +// resultExplodedProvenance +// .select("community") +// .where( +// resultExplodedProvenance +// .col("id") +// .equalTo( +// "50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b")) +// .collectAsList() +// .get(0) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 2, +// resultExplodedProvenance +// .filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'") +// .count()); +// Assertions +// .assertEquals( +// "mes", +// resultExplodedProvenance +// .select("community") +// .where( +// resultExplodedProvenance +// .col("id") +// .equalTo( +// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) +// .sort(desc("community")) +// .collectAsList() +// .get(0) +// .getString(0)); +// Assertions +// .assertEquals( +// "euromarine", +// resultExplodedProvenance +// .select("community") +// .where( +// resultExplodedProvenance +// .col("id") +// .equalTo( +// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) +// .sort(desc("community")) +// .collectAsList() +// .get(1) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 1, +// resultExplodedProvenance +// .filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'") +// .count()); +// Assertions +// .assertEquals( +// "mes", +// resultExplodedProvenance +// .select("community") +// .where( +// resultExplodedProvenance +// .col("id") +// .equalTo( +// "50|doajarticles::8d817039a63710fcf97e30f14662c6c8")) +// .sort(desc("community")) +// .collectAsList() +// .get(0) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 1, +// resultExplodedProvenance +// .filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'") +// .count()); +// Assertions +// .assertEquals( +// "mes", +// resultExplodedProvenance +// .select("community") +// .where( +// resultExplodedProvenance +// .col("id") +// .equalTo( +// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) +// .sort(desc("community")) +// .collectAsList() +// .get(0) +// .getString(0)); +// +// query = "select id, MyT.id community " +// + "from dataset " +// + "lateral view explode(context) c as MyT " +// + "lateral view explode(MyT.datainfo) d as MyD "; +// +// org.apache.spark.sql.Dataset resultCommunityId = spark.sql(query); +// +// Assertions.assertEquals(10, resultCommunityId.count()); +// +// Assertions +// .assertEquals( +// 1, +// resultCommunityId +// .filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'") +// .count()); +// Assertions +// .assertEquals( +// "beopen", +// resultCommunityId +// .select("community") +// .where( +// resultCommunityId +// .col("id") +// .equalTo( +// "50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe")) +// .collectAsList() +// .get(0) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 1, +// resultCommunityId +// .filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'") +// .count()); +// +// Assertions +// .assertEquals( +// 3, +// resultCommunityId +// .filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'") +// .count()); +// Assertions +// .assertEquals( +// "beopen", +// resultCommunityId +// .select("community") +// .where( +// resultCommunityId +// .col("id") +// .equalTo( +// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) +// .sort(desc("community")) +// .collectAsList() +// .get(2) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 2, +// resultCommunityId +// .filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'") +// .count()); +// Assertions +// .assertEquals( +// "euromarine", +// resultCommunityId +// .select("community") +// .where( +// resultCommunityId +// .col("id") +// .equalTo( +// "50|doajarticles::8d817039a63710fcf97e30f14662c6c8")) +// .sort(desc("community")) +// .collectAsList() +// .get(1) +// .getString(0)); +// +// Assertions +// .assertEquals( +// 3, +// resultCommunityId +// .filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'") +// .count()); +// Assertions +// .assertEquals( +// "euromarine", +// resultCommunityId +// .select("community") +// .where( +// resultCommunityId +// .col("id") +// .equalTo( +// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) +// .sort(desc("community")) +// .collectAsList() +// .get(2) +// .getString(0)); +// Assertions +// .assertEquals( +// "ni", +// resultCommunityId +// .select("community") +// .where( +// resultCommunityId +// .col("id") +// .equalTo( +// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) +// .sort(desc("community")) +// .collectAsList() +// .get(0) +// .getString(0)); + } +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json new file mode 100644 index 000000000..bd4674c4f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json @@ -0,0 +1,36 @@ +{"communityList":["beopen"],"resultId":"50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe"} +{"communityList":["beopen"],"resultId":"50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b"} +{"communityList":["euromarine","mes"],"resultId":"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::53b70ea6e0769d02ddf93307ec8e3e92"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::ef1ac6efc10f420fa9e190e49644f1f2"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::b738aa93950dddfb0294df2e8fdf0579"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::befccb1f9e6b833fd82e587737ae9e7d"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::bf1cba621615e27db1692865a5f35a0b"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::e105de571b336daae05f0e75cf740c5c"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::1fe4f347c9df657b7ba520987d79436e"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::6d7c00a8c8e59f0215459e2e4ee3fd6c"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::39ec88ef4127db0ea1b88938f1c52889"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::3496709db804d98f76c45d7ed023dd95"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::dc97fffbdb6d35f792fc0ab428ff065c"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::b61d082d96619d9b7a876e6dce44cf65"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::32a96881c3036cf2d2165bb2d276ea82"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::76e9e6a959ba588483c74ec580369864"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::1487a0a92572376d95d6cc3f066504b7"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::413a0a0656f888cce9c15f6be6df60e3"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::25c3e91960cbd7a8f95a2e511cbffddd"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::4d523b52094a689856e479bb99063c7a"} +{"communityList":["euromarine","mes"],"resultId":"50|od______2663::393c7262bb71642b7bb4c67cfeab02c5"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::0b3333d875b91ffa4db0735efec94e7a"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::0699c30043edfae40786d80acd20d300"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::7f29ade677e66ffbf1312fa837bc73ca"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::7ba6627ac7590d367cc01bbac4d518e8"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::8ad9bc047433401947dc0cdb4a989cee"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::cce70f27d85df658479d0ec0046a4eb3"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::74304be834b7013dbaeb73c3a19a654b"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::46fc13a87befb6a83ac9c63580528ab0"} +{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::66f1867488b62d9c9fb734273775e203"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::79236995d5c30e5234a47cee4a728cae"} +{"communityList":["euromarine","mes"],"resultId":"50|od______2386::cb7f6cb01d1a835612731d645842f699"} +{"communityList":["euromarine","mes"],"resultId":"50|dedup_wf_001::d424daa43f97a434eb0a12289410cade"} \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json.gz b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo/resultCommunityList.json.gz deleted file mode 100644 index 8b452d0e17e06baf8f3ac6d62277c2a08d88a13c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 939 zcmV;c162GUiwFqE4x3&819D|^b!>D)Z*6ULZfSIROlfm;E^2dcZUC)UNs44g4Bh(} zx$cD`LZP8@l!t}WKNm@oi~mx3dP9D_`Sa7$m-mmK zfBoU{)92g6kGGT0AM*X}r#H8c`RU8M&)>)G;kMzo$oTT%?JxBfU_3lnS&b<$XG|5I zj$wf?&x`|DdHeR=*L$D6il&!OhKaEW(}bA7QSq3r^Uu%DFCU+u?BnD6yuG~3&%s|TnnNK`39&|9gmQR^^)cy&=s6Bd#i*H5QLtIB+1TkZ{EX71BWqR2%q`4|Ej2kV zLaE`$Xbu`XC&wA2Q)t_+wGHmSqYzhtV#169)z=f?4T2SrFGW$MVAci z#cRb&=If|3Y@6Y=v(gpw{#pKlLaMD5z?D&!2rLu=<}o4q`)eGAYpO*Oa}u@F)L3Jd z$>QU@{Qg;9qjXTxWOLryKfW1p80T2`*F7Zf?_;kvCf4TVfQ)M)3`GtHkAtS7p7*EN zE0oqDLv^;uehEwIGY-fOHYCG57pbymXd_8k?Iti*9Lp|GzHD@<-FQ*EK Date: Mon, 16 Oct 2023 11:46:12 +0200 Subject: [PATCH 07/23] new spark parrameter updated --- .../oozie_app/workflow.xml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index 55490e25c..7a5fd7434 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -90,14 +90,16 @@ eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet dhp-enrichment-${projectVersion}.jar - --executor-cores=4 - --executor-memory=10G + --executor-cores=6 + --executor-memory=5G + --spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --sourcePath${sourcePath}/relation @@ -117,14 +119,15 @@ eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob dhp-enrichment-${projectVersion}.jar - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} + --executor-cores=6 + --executor-memory=5G + --spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList From 6dfcd0c9a2072c589709a97769185a966def58b4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 Oct 2023 12:57:18 +0200 Subject: [PATCH 08/23] [raw graph] mapping original resource types --- .../raw/AbstractMdRecordToOafMapper.java | 63 ++++--- .../dhp/oa/graph/raw/OafToOafMapper.java | 41 +++-- .../dhp/oa/graph/raw/OdfToOafMapper.java | 22 ++- .../oa/graph/raw/OriginalTypeComparator.java | 43 ++--- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 168 ++++++++++++++++-- .../dnetlib/dhp/oa/graph/raw/oaf_crossref.xml | 68 +++++++ 6 files changed, 308 insertions(+), 97 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5f0acbab7..49133cedb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -157,20 +157,20 @@ public abstract class AbstractMdRecordToOafMapper { if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { Optional instanceTypeMapping = instances - .stream() - .flatMap(i -> i.getInstanceTypeMapping().stream()) - .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) - .findFirst(); + .stream() + .flatMap(i -> i.getInstanceTypeMapping().stream()) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); if (!instanceTypeMapping.isPresent()) { - throw new IllegalStateException("unable to find an instance from " + OPENAIRE_COAR_RESOURCE_TYPES_3_1); + return null; } else { final String typeCode = instanceTypeMapping.get().getTypeCode(); return Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) - .orElseThrow(() -> - new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + - OPENAIRE_META_RESOURCE_TYPE)); + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); } } else { throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); @@ -197,7 +197,8 @@ public abstract class AbstractMdRecordToOafMapper { final DataInfo info, final long lastUpdateTimestamp) { - final OafEntity entity = createEntity(doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); + final OafEntity entity = createEntity( + doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -550,29 +551,33 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract String findOriginalType(Document doc); protected List prepareInstanceTypeMapping(Document doc) { - return Optional.ofNullable(findOriginalType(doc)) - .map(originalType -> { - final List mappings = Lists.newArrayList(); + return Optional + .ofNullable(findOriginalType(doc)) + .map(originalType -> { + final List mappings = Lists.newArrayList(); - if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { + if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { - // TODO verify what the vocabs return when a synonym is not defined - Optional.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) - .ifPresent(coarTerm -> { - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) + .ifPresent(coarTerm -> { + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) - .ifPresent(type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); - } - }); - } + // TODO verify what the vocabs return when a synonym is not defined + Optional + .ofNullable( + vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) + .ifPresent( + type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); + } + }); + } - return mappings; - }) - .orElse(new ArrayList<>()); + return mappings; + }) + .orElse(new ArrayList<>()); } private Journal prepareJournal(final Document doc, final DataInfo info) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 6bcc8ec44..a63296d18 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,17 +1,8 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.google.common.collect.Lists; -import eu.dnetlib.dhp.common.PacePerson; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; -import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Element; -import org.dom4j.Node; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.net.URLDecoder; import java.util.ArrayList; @@ -20,8 +11,19 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import static eu.dnetlib.dhp.schema.common.ModelConstants.*; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.Node; + +import com.google.common.collect.Lists; + +import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -201,12 +203,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - return (String) doc.selectNodes("//dc:type") - .stream() - .map(o -> "" + ((Node) o).getText().trim()) - .sorted(new OriginalTypeComparator()) - .findFirst() - .orElse(null); + return (String) doc + .selectNodes("//dc:type") + .stream() + .map(o -> "" + ((Node) o).getText().trim()) + .sorted(new OriginalTypeComparator()) + .findFirst() + .orElse(null); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index c383e9300..e63b01a00 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -230,20 +230,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { */ @Override protected String findOriginalType(Document doc) { - String resourceType = Optional.ofNullable((Element) doc.selectSingleNode( + return Optional + .ofNullable( + (Element) doc + .selectSingleNode( "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'resourceType']")) - .map(element -> { - final String resourceTypeURI = element.attributeValue("anyURI"); - final String resourceTypeTxt = element.getText(); - - return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); - }) - .orElse(doc.valueOf( - "//*[local-name()='metadata']/*[local-name() = 'resource']/*[local-name() = 'CobjCategory']/text()") - ); - - return resourceType; + .map(element -> { + final String resourceTypeURI = element.attributeValue("anyURI"); + final String resourceTypeTxt = element.getText(); + return ObjectUtils.firstNonNull(resourceTypeURI, resourceTypeTxt); + }) + .orElse(null); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java index 2eeead32e..c3d8b4789 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OriginalTypeComparator.java @@ -1,32 +1,33 @@ -package eu.dnetlib.dhp.oa.graph.raw; -import java.util.Comparator; +package eu.dnetlib.dhp.oa.graph.raw; import static org.apache.commons.lang3.StringUtils.contains; import static org.apache.commons.lang3.StringUtils.startsWith; +import java.util.Comparator; + public class OriginalTypeComparator implements Comparator { - @Override - public int compare(String t1, String t2) { + @Override + public int compare(String t1, String t2) { - if (t1.equals(t2)) { - return 0; - } - if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { - return -1; - } - if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { - return 1; - } - if (startsWith(t1, "info:eu-repo/semantics")) { - return -1; - } - if (startsWith(t2, "info:eu-repo/semantics")) { - return 1; - } + if (t1.equals(t2)) { + return 0; + } + if (startsWith(t1, "http") && contains(t1, "coar") && contains(t1, "resource_type")) { + return -1; + } + if (startsWith(t2, "http") && contains(t2, "coar") && contains(t2, "resource_type")) { + return 1; + } + if (startsWith(t1, "info:eu-repo/semantics")) { + return -1; + } + if (startsWith(t2, "info:eu-repo/semantics")) { + return 1; + } - return t1.compareTo(t2); - } + return t1.compareTo(t2); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 4d30a3fa8..e6997ac1d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -14,6 +14,8 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import org.dom4j.DocumentException; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @@ -25,8 +27,11 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.CleaningRuleMap; +import eu.dnetlib.dhp.oa.graph.clean.OafCleaner; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -119,19 +124,21 @@ class MappersTest { assertNotNull(instance.getInstanceTypeMapping()); assertEquals(2, instance.getInstanceTypeMapping().size()); - Optional coarType = instance.getInstanceTypeMapping() - .stream() - .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) - .findFirst(); + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .findFirst(); assertTrue(coarType.isPresent()); assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); assertEquals("conference paper", coarType.get().getTypeLabel()); - Optional userType = instance.getInstanceTypeMapping() - .stream() - .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) - .findFirst(); + Optional userType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) + .findFirst(); assertTrue(userType.isPresent()); assertEquals("Article", userType.get().getTypeCode()); @@ -266,8 +273,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); assertNotNull(p.getInstance().get(0).getPid()); assertEquals(2, p.getInstance().get(0).getPid().size()); @@ -485,8 +492,8 @@ class MappersTest { }); Publication p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -604,8 +611,137 @@ class MappersTest { assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059")); Dataset d_cleaned = cleanup(d, vocs); - assertEquals("0000", d_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", d_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", d_cleaned.getInstance().get(0).getRefereed().getClassname()); + } + + @Test + void test_record_from_Crossref() throws IOException { + + final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); + + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_crossref.xml"))); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Publication); + + final Publication p = OafCleaner.apply(fixVocabularyNames((Publication) list.get(0)), mapping); + + assertNotNull(p.getDateofcollection()); + assertEquals("2020-08-06T07:04:09.62Z", p.getDateofcollection()); + + assertNotNull(p.getDateoftransformation()); + assertEquals("2020-08-06T07:20:57.911Z", p.getDateoftransformation()); + + assertNotNull(p.getDataInfo()); + assertFalse(p.getDataInfo().getInvisible()); + assertFalse(p.getDataInfo().getDeletedbyinference()); + assertEquals("0.9", p.getDataInfo().getTrust()); + + assertValidId(p.getId()); + assertEquals(2, p.getOriginalId().size()); + + assertEquals("50|doi_________::7f0f7807f17db50e5c2b5c452ccaf06d", p.getOriginalId().get(0)); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertEquals(1, p.getTitle().size()); + assertEquals( + "A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine", + p + .getTitle() + .get(0) + .getValue()); + + assertNotNull(p.getDescription()); + assertEquals(0, p.getDescription().size()); + + assertEquals(8, p.getAuthor().size()); + + assertNotNull(p.getInstance()); + assertEquals(1, p.getInstance().size()); + + final Instance i = p.getInstance().get(0); + + assertNotNull(i.getAccessright()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemeid()); + assertEquals(ModelConstants.DNET_ACCESS_MODES, i.getAccessright().getSchemename()); + assertEquals("OPEN", i.getAccessright().getClassid()); + assertEquals("Open Access", i.getAccessright().getClassname()); + + assertNotNull(i.getCollectedfrom()); + assertEquals("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", i.getCollectedfrom().getKey()); + assertEquals("Crossref", i.getCollectedfrom().getValue()); + + assertNotNull(i.getHostedby()); + assertEquals("10|openaire____::55045bd2a65019fd8e6741a755395c8c", i.getHostedby().getKey()); + assertEquals("Unknown Repository", i.getHostedby().getValue()); + + assertNotNull(i.getInstancetype()); + assertEquals("0001", i.getInstancetype().getClassid()); + assertEquals("Article", i.getInstancetype().getClassname()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemeid()); + assertEquals(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getSchemename()); + + assertNull(i.getLicense()); + assertNotNull(i.getDateofacceptance()); + assertEquals("2020-06-04", i.getDateofacceptance().getValue()); + + assertNull(i.getProcessingchargeamount()); + assertNull(i.getProcessingchargecurrency()); + + assertNotNull(i.getPid()); + assertEquals(1, i.getPid().size()); + + assertNotNull(i.getAlternateIdentifier()); + assertEquals(0, i.getAlternateIdentifier().size()); + + assertNotNull(i.getUrl()); + assertEquals(1, i.getUrl().size()); + assertTrue(i.getUrl().contains("http://dx.doi.org/10.1080/23744235.2020.1774644")); + + assertEquals("", p.getInstance().get(0).getRefereed().getClassid()); + assertEquals("", p.getInstance().get(0).getRefereed().getClassname()); + + Publication p_cleaned = cleanup(p, vocs); + + assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + + assertNotNull(p_cleaned.getMetaResourceType()); + assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassid()); + assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassname()); + assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemeid()); + assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemename()); + + assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); + assertEquals(2, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .anyMatch( + t -> "journal-article".equals(t.getOriginalType()) && + ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && + "http://purl.org/coar/resource_type/c_2df8fbb1".equals(t.getTypeCode()) && + "research article".equals(t.getTypeLabel()))); + + assertTrue( + p_cleaned + .getInstance() + .get(0) + .getInstanceTypeMapping() + .stream() + .anyMatch( + t -> "journal-article".equals(t.getOriginalType()) && + ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()) && + "Article".equals(t.getTypeCode()) && + "Article".equals(t.getTypeLabel()))); } @Test @@ -908,8 +1044,8 @@ class MappersTest { }); Dataset p_cleaned = cleanup(p, vocs); - assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); - assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertEquals("0002", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("nonPeerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml new file mode 100644 index 000000000..182820a08 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_crossref.xml @@ -0,0 +1,68 @@ + + +
+ doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + doi_________::7f0f7807f17db50e5c2b5c452ccaf06d + 2020-08-06T07:04:09.62Z + + + + + + 2020-08-06T07:20:57.911Z + openaire____ +
+ + A case report of serious haemolysis in a glucose-6-phosphate dehydrogenase-deficient COVID-19 patient receiving hydroxychloroquine + Maillart, E. + Leemans, S. + Van Noten, H. + Vandergraesen, T. + Mahadeb, B. + Salaouatchi, M. T. + De Bels, D. + Clevenbergh, P. + + http://dx.doi.org/10.1080/23744235.2020.1774644 + + Informa UK Limited + Crossref + Infectious Diseases + Microbiology (medical) + General Immunology and Microbiology + Infectious Diseases + General Medicine + journal-article + 0001 + 2020-06-04 + + OPEN + + + 10.1080/23744235.2020.1774644 + Infectious Diseases + + + + + file%3A%2F%2F%2Fsrv%2Fclaims%2Frecords%2Fpublication%2Fcrossref + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file From d28b7085f6f13a644926302e47da314dcb22de5d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 17 Oct 2023 11:09:31 +0200 Subject: [PATCH 09/23] more NPE checks --- .../common/vocabulary/VocabularyGroup.java | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index 4c1feac45..64b6f91af 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -136,24 +136,21 @@ public class VocabularyGroup implements Serializable { } public Qualifier lookupTermBySynonym(final String vocId, final String syn) { - if (StringUtils.isBlank(vocId)) { - return OafMapperUtils.unknown("", ""); - } - - final Vocabulary vocabulary = vocs.get(vocId.toLowerCase()); - - return Optional - .ofNullable(vocabulary.getTerm(syn)) + return find(vocId) .map( - term -> OafMapperUtils - .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) - .orElse( - Optional - .ofNullable(vocabulary.getTermBySynonym(syn)) + vocabulary -> Optional + .ofNullable(vocabulary.getTerm(syn)) .map( term -> OafMapperUtils .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) - .orElse(null)); + .orElse( + Optional + .ofNullable(vocabulary.getTermBySynonym(syn)) + .map( + term -> OafMapperUtils + .qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName())) + .orElse(null))) + .orElse(null); } /** From a4214ced1e0b71b4af87cf4cdddf05b30f92afb1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 Oct 2023 10:14:20 +0200 Subject: [PATCH 10/23] fixing issue on propagation organization. added --config to workflow definition. added oozie_app to communtiy project --- .../PrepareResultCommunitySet.java | 4 +- .../SparkResultToCommunityFromProject.java | 2 - .../oozie_app/workflow.xml | 4 +- ...t_preparecommunitytoresult_parameters.json | 7 +- .../oozie_app/config-default.xml | 58 +++++++ .../oozie_app/workflow.xml | 144 ++++++++++++++++++ 6 files changed, 207 insertions(+), 12 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index 883f5ca86..c47075272 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -109,12 +109,12 @@ public class PrepareResultCommunitySet { }); }); - if(cl.size() == 0) + if (cl.size() == 0) return null; rpl.setCommunityList(cl); return rpl; }, Encoders.bean(ResultProjectList.class)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index daef6a317..90c30f812 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -62,10 +62,8 @@ public class SparkResultToCommunityFromProject implements Serializable { final String possibleupdatespath = parser.get("preparedInfoPath"); log.info("preparedInfoPath: {}", possibleupdatespath); - SparkConf conf = new SparkConf(); - runWithSparkSession( conf, isSparkSessionManaged, diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml index 7a5fd7434..d5d75fbc1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml @@ -92,7 +92,7 @@ --executor-cores=6 --executor-memory=5G - --spark.executor.memoryOverhead=3g + --conf spark.executor.memoryOverhead=3g --conf spark.sql.shuffle.partitions=3284 --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} @@ -121,7 +121,7 @@ --executor-cores=6 --executor-memory=5G - --spark.executor.memoryOverhead=3g + --conf spark.executor.memoryOverhead=3g --conf spark.sql.shuffle.partitions=3284 --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json index 8b6291e5d..9a50c79fa 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json @@ -5,12 +5,7 @@ "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, - { - "paramName":"h", - "paramLongName":"hive_metastore_uris", - "paramDescription": "the hive metastore uris", - "paramRequired": true - }, + { "paramName": "ssm", "paramLongName": "isSparkSessionManaged", diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/config-default.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/config-default.xml new file mode 100644 index 000000000..2744ea92b --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + sparkExecutorNumber + 4 + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + + spark2MaxExecutors + 50 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml new file mode 100644 index 000000000..21cc2d887 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml @@ -0,0 +1,144 @@ + + + + sourcePath + the source path + + + + outputPath + the output path + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + ${nameNode}/${sourcePath}/relation + ${nameNode}/${outputPath}/relation + + + + + + + + ${nameNode}/${sourcePath}/organization + ${nameNode}/${outputPath}/organization + + + + + + + + ${nameNode}/${sourcePath}/project + ${nameNode}/${outputPath}/project + + + + + + + + ${nameNode}/${sourcePath}/datasource + ${nameNode}/${outputPath}/datasource + + + + + + + + + + yarn + cluster + Prepare-Community-Result-Organization + eu.dnetlib.dhp.resulttocommunityfromproject.PrepareResultCommunitySet + dhp-enrichment-${projectVersion}.jar + + --executor-cores=6 + --executor-memory=5G + --conf spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/preparedInfo/resultCommunityList + --production${production} + + + + + + + + yarn + cluster + community2resultfromproject + eu.dnetlib.dhp.resulttocommunityfromproject.SparkResultToCommunityFromProject + dhp-enrichment-${projectVersion}.jar + + --executor-cores=6 + --executor-memory=5G + --conf spark.executor.memoryOverhead=3g + --conf spark.sql.shuffle.partitions=3284 + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + + --preparedInfoPath${workingDir}/preparedInfo/resultCommunityList + --sourcePath${sourcePath}/ + --outputPath${outputPath}/ + + + + + + + + + + \ No newline at end of file From c80b768af062166e4ae94abcf529af0aac994b7b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 31 Oct 2023 15:49:42 +0100 Subject: [PATCH 11/23] test for project propagation --- .../PrepareResultCommunitySet.java | 2 +- .../PrepareAssocTest.java | 14 +- .../ResultToCommunityJobTest.java | 257 ++---------------- 3 files changed, 36 insertions(+), 237 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index c47075272..9a2f25fa6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -56,7 +56,7 @@ public class PrepareResultCommunitySet { log.info("production: {}", production); final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); - log.info("projectsMap: {}", new Gson().toJson(projectsMap)); + //log.info("projectsMap: {}", new Gson().toJson(projectsMap)); SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java index 0e10b3edf..172873af3 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java @@ -10,9 +10,7 @@ import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -61,6 +59,7 @@ public class PrepareAssocTest { spark.stop(); } + @Disabled @Test void test1() throws Exception { @@ -72,8 +71,8 @@ public class PrepareAssocTest { "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromproject/relation/").getPath(), "-outputPath", workingDir.toString() + "/prepared", - "-production", Boolean.TRUE.toString(), - "-hive_metastore_uris", "" + "-production", Boolean.TRUE.toString() + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); @@ -82,7 +81,10 @@ public class PrepareAssocTest { .textFile(workingDir.toString() + "/prepared") .map(item -> new ObjectMapper().readValue(item, ResultProjectList.class)); - tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + Assertions.assertEquals(4, tmp.count()); + Assertions.assertEquals(2, tmp.filter(rpl -> rpl.getCommunityList().contains("aurora")).count()); + Assertions.assertEquals(1, tmp.filter(rpl -> rpl.getCommunityList().contains("sdsn-gr")).count()); + Assertions.assertEquals(1, tmp.filter(rpl -> rpl.getCommunityList().contains("netherlands")).count()); } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java index 6a5726cbe..b705af8ac 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java @@ -6,7 +6,9 @@ import static org.apache.spark.sql.functions.desc; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.List; +import eu.dnetlib.dhp.schema.oaf.Context; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -89,235 +91,30 @@ public class ResultToCommunityJobTest { .textFile(workingDir.toString() + "/dataset") .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - tmp.foreach(d -> System.out.println(new ObjectMapper().writeValueAsString(d))); -// Assertions.assertEquals(10, tmp.count()); -// org.apache.spark.sql.Dataset verificationDataset = spark -// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); -// -// verificationDataset.createOrReplaceTempView("dataset"); -// -// String query = "select id, MyT.id community " -// + "from dataset " -// + "lateral view explode(context) c as MyT " -// + "lateral view explode(MyT.datainfo) d as MyD " -// + "where MyD.inferenceprovenance = 'propagation'"; -// -// org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); -// Assertions.assertEquals(5, resultExplodedProvenance.count()); -// Assertions -// .assertEquals( -// 0, -// resultExplodedProvenance -// .filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'") -// .count()); -// Assertions -// .assertEquals( -// 1, -// resultExplodedProvenance -// .filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'") -// .count()); -// Assertions -// .assertEquals( -// "beopen", -// resultExplodedProvenance -// .select("community") -// .where( -// resultExplodedProvenance -// .col("id") -// .equalTo( -// "50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b")) -// .collectAsList() -// .get(0) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 2, -// resultExplodedProvenance -// .filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'") -// .count()); -// Assertions -// .assertEquals( -// "mes", -// resultExplodedProvenance -// .select("community") -// .where( -// resultExplodedProvenance -// .col("id") -// .equalTo( -// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) -// .sort(desc("community")) -// .collectAsList() -// .get(0) -// .getString(0)); -// Assertions -// .assertEquals( -// "euromarine", -// resultExplodedProvenance -// .select("community") -// .where( -// resultExplodedProvenance -// .col("id") -// .equalTo( -// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) -// .sort(desc("community")) -// .collectAsList() -// .get(1) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 1, -// resultExplodedProvenance -// .filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'") -// .count()); -// Assertions -// .assertEquals( -// "mes", -// resultExplodedProvenance -// .select("community") -// .where( -// resultExplodedProvenance -// .col("id") -// .equalTo( -// "50|doajarticles::8d817039a63710fcf97e30f14662c6c8")) -// .sort(desc("community")) -// .collectAsList() -// .get(0) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 1, -// resultExplodedProvenance -// .filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'") -// .count()); -// Assertions -// .assertEquals( -// "mes", -// resultExplodedProvenance -// .select("community") -// .where( -// resultExplodedProvenance -// .col("id") -// .equalTo( -// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) -// .sort(desc("community")) -// .collectAsList() -// .get(0) -// .getString(0)); -// -// query = "select id, MyT.id community " -// + "from dataset " -// + "lateral view explode(context) c as MyT " -// + "lateral view explode(MyT.datainfo) d as MyD "; -// -// org.apache.spark.sql.Dataset resultCommunityId = spark.sql(query); -// -// Assertions.assertEquals(10, resultCommunityId.count()); -// -// Assertions -// .assertEquals( -// 1, -// resultCommunityId -// .filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'") -// .count()); -// Assertions -// .assertEquals( -// "beopen", -// resultCommunityId -// .select("community") -// .where( -// resultCommunityId -// .col("id") -// .equalTo( -// "50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe")) -// .collectAsList() -// .get(0) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 1, -// resultCommunityId -// .filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'") -// .count()); -// -// Assertions -// .assertEquals( -// 3, -// resultCommunityId -// .filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'") -// .count()); -// Assertions -// .assertEquals( -// "beopen", -// resultCommunityId -// .select("community") -// .where( -// resultCommunityId -// .col("id") -// .equalTo( -// "50|od________18::8887b1df8b563c4ea851eb9c882c9d7b")) -// .sort(desc("community")) -// .collectAsList() -// .get(2) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 2, -// resultCommunityId -// .filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'") -// .count()); -// Assertions -// .assertEquals( -// "euromarine", -// resultCommunityId -// .select("community") -// .where( -// resultCommunityId -// .col("id") -// .equalTo( -// "50|doajarticles::8d817039a63710fcf97e30f14662c6c8")) -// .sort(desc("community")) -// .collectAsList() -// .get(1) -// .getString(0)); -// -// Assertions -// .assertEquals( -// 3, -// resultCommunityId -// .filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'") -// .count()); -// Assertions -// .assertEquals( -// "euromarine", -// resultCommunityId -// .select("community") -// .where( -// resultCommunityId -// .col("id") -// .equalTo( -// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) -// .sort(desc("community")) -// .collectAsList() -// .get(2) -// .getString(0)); -// Assertions -// .assertEquals( -// "ni", -// resultCommunityId -// .select("community") -// .where( -// resultCommunityId -// .col("id") -// .equalTo( -// "50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6")) -// .sort(desc("community")) -// .collectAsList() -// .get(0) -// .getString(0)); + Assertions.assertEquals(10, tmp.count()); + /** + * {"resultId":"50|57a035e5b1ae::d5be548ca7ae489d762f893be67af52f","communityList":["aurora"]} + * {"resultId":"50|57a035e5b1ae::a77232ffca9115fcad51c3503dbc7e3e","communityList":["aurora"]} + * {"resultId":"50|57a035e5b1ae::803aaad4decab7e27cd4b52a1931b3a1","communityList":["sdsn-gr"]} + * {"resultId":"50|57a035e5b1ae::a02e9e4087bca50687731ae5c765b5e1","communityList":["netherlands"]} + */ + List context = tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::d5be548ca7ae489d762f893be67af52f")) + .first().getContext(); + Assertions.assertTrue(context.stream().anyMatch(c -> containsResultCommunityProject(c))); + + context = tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::a77232ffca9115fcad51c3503dbc7e3e")) + .first().getContext(); + Assertions.assertTrue(context.stream().anyMatch(c -> containsResultCommunityProject(c))); + + Assertions.assertEquals(0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::803aaad4decab7e27cd4b52a1931b3a1")).count()); + + Assertions.assertEquals(0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::a02e9e4087bca50687731ae5c765b5e1")).count()); + + Assertions.assertEquals(2, tmp.filter(r -> r.getContext().stream().anyMatch(c -> c.getId().equals("aurora"))).count()); + + } + + private static boolean containsResultCommunityProject(Context c) { + return c.getDataInfo().stream().anyMatch(di -> di.getProvenanceaction().getClassid().equals("result:community:project")); } } From a737dd47b6268111a18550a3e94241ec8358447c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 31 Oct 2023 15:54:49 +0100 Subject: [PATCH 12/23] removed not needed test class --- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 2 +- .../PrepareAssocTest.java | 90 ------------------- 2 files changed, 1 insertion(+), 91 deletions(-) delete mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 7cbbcaafb..5e106ef45 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -6,7 +6,7 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.HashMap; + import java.util.List; import org.apache.commons.io.FileUtils; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java deleted file mode 100644 index 172873af3..000000000 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareAssocTest.java +++ /dev/null @@ -1,90 +0,0 @@ - -package eu.dnetlib.dhp.resulttocommunityfromproject; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.bulktag.BulkTagJobTest; -import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; - -/** - * @author miriam.baglioni - * @Date 13/10/23 - */ -public class PrepareAssocTest { - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(PrepareAssocTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(BulkTagJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(PrepareAssocTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Disabled - @Test - void test1() throws Exception { - - PrepareResultCommunitySet - .main( - new String[] { - - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromproject/relation/").getPath(), - "-outputPath", workingDir.toString() + "/prepared", - "-production", Boolean.TRUE.toString() - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/prepared") - .map(item -> new ObjectMapper().readValue(item, ResultProjectList.class)); - - Assertions.assertEquals(4, tmp.count()); - Assertions.assertEquals(2, tmp.filter(rpl -> rpl.getCommunityList().contains("aurora")).count()); - Assertions.assertEquals(1, tmp.filter(rpl -> rpl.getCommunityList().contains("sdsn-gr")).count()); - Assertions.assertEquals(1, tmp.filter(rpl -> rpl.getCommunityList().contains("netherlands")).count()); - } - -} From 937ff6a7c77fa6422463471d8f3aff9c22ff775b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 31 Oct 2023 15:56:08 +0100 Subject: [PATCH 13/23] - --- .../dhp/api/QueryCommunityAPITest.java | 119 ------------------ .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 2 - 2 files changed, 121 deletions(-) delete mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java deleted file mode 100644 index 6ee01a6f0..000000000 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/api/QueryCommunityAPITest.java +++ /dev/null @@ -1,119 +0,0 @@ - -package eu.dnetlib.dhp.api; - -import java.util.List; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.api.QueryCommunityAPI; -import eu.dnetlib.dhp.api.Utils; -import eu.dnetlib.dhp.api.model.CommunityEntityMap; -import eu.dnetlib.dhp.api.model.CommunityModel; -import eu.dnetlib.dhp.api.model.CommunitySummary; -import eu.dnetlib.dhp.api.model.DatasourceList; -import eu.dnetlib.dhp.bulktag.community.Community; -import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; - -/** - * @author miriam.baglioni - * @Date 06/10/23 - */ -public class QueryCommunityAPITest { - - @Test - void communityList() throws Exception { - String body = QueryCommunityAPI.communities(true); - new ObjectMapper() - .readValue(body, CommunitySummary.class) - .forEach(p -> { - try { - System.out.println(new ObjectMapper().writeValueAsString(p)); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } - }); - } - - @Test - void community() throws Exception { - String id = "dh-ch"; - String body = QueryCommunityAPI.community(id, true); - System.out - .println( - new ObjectMapper() - .writeValueAsString( - new ObjectMapper() - .readValue(body, CommunityModel.class))); - } - - @Test - void communityDatasource() throws Exception { - String id = "dh-ch"; - String body = QueryCommunityAPI.communityDatasource(id, true); - new ObjectMapper() - .readValue(body, DatasourceList.class) - .forEach(ds -> { - try { - System.out.println(new ObjectMapper().writeValueAsString(ds)); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } - }); - ; - } - - @Test - void validCommunities() throws Exception { - CommunityConfiguration cc = Utils.getCommunityConfiguration(true); - System.out.println(cc.getCommunities().keySet()); - Community community = cc.getCommunities().get("aurora"); - Assertions.assertEquals(0, community.getSubjects().size()); - Assertions.assertEquals(null, community.getConstraints()); - Assertions.assertEquals(null, community.getRemoveConstraints()); - Assertions.assertEquals(2, community.getZenodoCommunities().size()); - Assertions - .assertTrue( - community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network"))); - Assertions - .assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck"))); - Assertions.assertEquals(35, community.getProviders().size()); - Assertions - .assertEquals( - 35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count()); - - } - - @Test - void eutopiaCommunityConfiguration() throws Exception { - CommunityConfiguration cc = Utils.getCommunityConfiguration(true); - System.out.println(cc.getCommunities().keySet()); - Community community = cc.getCommunities().get("eutopia"); - community.getProviders().forEach(p -> System.out.println(p.getOpenaireId())); - } - - @Test - void getCommunityProjects() throws Exception { - CommunityEntityMap projectMap = Utils.getCommunityProjects(true); - - Assertions - .assertTrue( - projectMap - .keySet() - .stream() - .allMatch(k -> k.startsWith("40|"))); - - System.out.println(projectMap); - } - - @Test - void getCommunityOrganizations() throws Exception { - CommunityEntityMap organizationMap = Utils.getCommunityOrganization(true); - Assertions.assertTrue(organizationMap.keySet().stream().allMatch(k -> k.startsWith("20|"))); - - } - -} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 5e106ef45..d02faedec 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -32,8 +32,6 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," + " \"title\" : \"$['title'][*]['value']\"," + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," From edcb17ca9827c39c8662b3083d2246dd91bd26ab Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 3 Nov 2023 13:01:14 +0100 Subject: [PATCH 14/23] refactoring and test --- .../PrepareResultCommunitySet.java | 2 +- .../SparkResultToCommunityFromProject.java | 18 +++++++++-- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 1 - .../ResultToCommunityJobTest.java | 31 +++++++++++++------ 4 files changed, 39 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index 9a2f25fa6..7bee1ea0c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -56,7 +56,7 @@ public class PrepareResultCommunitySet { log.info("production: {}", production); final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); - //log.info("projectsMap: {}", new Gson().toJson(projectsMap)); + // log.info("projectsMap: {}", new Gson().toJson(projectsMap)); SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java index 90c30f812..6e298cf94 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java @@ -112,7 +112,7 @@ public class SparkResultToCommunityFromProject implements Serializable { R ret = value._1(); Optional rcl = Optional.ofNullable(value._2()); if (rcl.isPresent()) { - ArrayList communitySet = rcl.get().getCommunityList(); + // ArrayList communitySet = rcl.get().getCommunityList(); List contextList = ret .getContext() .stream() @@ -124,7 +124,7 @@ public class SparkResultToCommunityFromProject implements Serializable { res.setId(ret.getId()); List propagatedContexts = new ArrayList<>(); - for (String cId : communitySet) { + for (String cId : rcl.get().getCommunityList()) { if (!contextList.contains(cId)) { Context newContext = new Context(); newContext.setId(cId); @@ -138,6 +138,20 @@ public class SparkResultToCommunityFromProject implements Serializable { PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME, ModelConstants.DNET_PROVENANCE_ACTIONS))); propagatedContexts.add(newContext); + } else { + ret + .getContext() + .stream() + .filter(c -> c.getId().equals(cId)) + .findFirst() + .get() + .getDataInfo() + .add( + getDataInfo( + PROPAGATION_DATA_INFO_TYPE, + PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_ID, + PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS)); } } res.setContext(propagatedContexts); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index d02faedec..efabcc6bc 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; - import java.util.List; import org.apache.commons.io.FileUtils; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java index b705af8ac..5642501b3 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromproject/ResultToCommunityJobTest.java @@ -8,7 +8,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import eu.dnetlib.dhp.schema.oaf.Context; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest; import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob; +import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Dataset; public class ResultToCommunityJobTest { @@ -98,23 +98,36 @@ public class ResultToCommunityJobTest { * {"resultId":"50|57a035e5b1ae::803aaad4decab7e27cd4b52a1931b3a1","communityList":["sdsn-gr"]} * {"resultId":"50|57a035e5b1ae::a02e9e4087bca50687731ae5c765b5e1","communityList":["netherlands"]} */ - List context = tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::d5be548ca7ae489d762f893be67af52f")) - .first().getContext(); + List context = tmp + .filter(r -> r.getId().equals("50|57a035e5b1ae::d5be548ca7ae489d762f893be67af52f")) + .first() + .getContext(); Assertions.assertTrue(context.stream().anyMatch(c -> containsResultCommunityProject(c))); - context = tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::a77232ffca9115fcad51c3503dbc7e3e")) - .first().getContext(); + context = tmp + .filter(r -> r.getId().equals("50|57a035e5b1ae::a77232ffca9115fcad51c3503dbc7e3e")) + .first() + .getContext(); Assertions.assertTrue(context.stream().anyMatch(c -> containsResultCommunityProject(c))); - Assertions.assertEquals(0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::803aaad4decab7e27cd4b52a1931b3a1")).count()); + Assertions + .assertEquals( + 0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::803aaad4decab7e27cd4b52a1931b3a1")).count()); - Assertions.assertEquals(0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::a02e9e4087bca50687731ae5c765b5e1")).count()); + Assertions + .assertEquals( + 0, tmp.filter(r -> r.getId().equals("50|57a035e5b1ae::a02e9e4087bca50687731ae5c765b5e1")).count()); - Assertions.assertEquals(2, tmp.filter(r -> r.getContext().stream().anyMatch(c -> c.getId().equals("aurora"))).count()); + Assertions + .assertEquals( + 2, tmp.filter(r -> r.getContext().stream().anyMatch(c -> c.getId().equals("aurora"))).count()); } private static boolean containsResultCommunityProject(Context c) { - return c.getDataInfo().stream().anyMatch(di -> di.getProvenanceaction().getClassid().equals("result:community:project")); + return c + .getDataInfo() + .stream() + .anyMatch(di -> di.getProvenanceaction().getClassid().equals("result:community:project")); } } From 638ad9e74f09a7ea975e49cc7842746096608cbc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 3 Nov 2023 15:06:50 +0100 Subject: [PATCH 15/23] changing test for new implementation --- ...kResultToCommunityFromOrganizationJob.java | 2 - .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 4 +- .../PrepareAssocTest.java | 95 ------------------ .../ResultToCommunityJobTest.java | 8 +- .../sample/dataset | 10 ++ .../sample/dataset_10.json.gz | Bin 7128 -> 0 bytes 6 files changed, 16 insertions(+), 103 deletions(-) delete mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/sample/dataset delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/sample/dataset_10.json.gz diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java index fe79f1be1..df8ca3805 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java @@ -60,8 +60,6 @@ public class SparkResultToCommunityFromOrganizationJob { conf, isSparkSessionManaged, spark -> { - // removeOutputDir(spark, outputPath); - execPropagation(spark, inputPath, outputPath, possibleupdatespath); }); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index efabcc6bc..64eb86338 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -40,7 +40,9 @@ public class BulkTagJobTest { "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} "; + "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + + "\"publisher\":\"$['publisher'].value\"," + + "\"publicationyear\":\"$['dateofacceptance'].value\"} "; private static SparkSession spark; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java deleted file mode 100644 index 6536ecc85..000000000 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareAssocTest.java +++ /dev/null @@ -1,95 +0,0 @@ - -package eu.dnetlib.dhp.resulttocommunityfromorganization; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.api.Utils; -import eu.dnetlib.dhp.api.model.CommunityEntityMap; -import eu.dnetlib.dhp.bulktag.BulkTagJobTest; -import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; -import eu.dnetlib.dhp.schema.oaf.Dataset; - -/** - * @author miriam.baglioni - * @Date 13/10/23 - */ -public class PrepareAssocTest { - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(PrepareAssocTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(BulkTagJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(PrepareAssocTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - PrepareResultCommunitySet - .main( - new String[] { - - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/relation/").getPath(), - "-outputPath", workingDir.toString() + "/prepared", - "-production", Boolean.TRUE.toString(), - "-hive_metastore_uris", "" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/prepared") - .map(item -> new ObjectMapper().readValue(item, ResultCommunityList.class)); - - tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - } - -} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java index da3be8b35..6440ded92 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultToCommunityJobTest.java @@ -72,15 +72,13 @@ public class ResultToCommunityJobTest { SparkResultToCommunityFromOrganizationJob .main( new String[] { - "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", getClass() - .getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample") + .getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample/") .getPath(), - "-hive_metastore_uris", "", - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", + "-outputPath", workingDir.toString() + "/", "-preparedInfoPath", preparedInfoPath }); diff --git 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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ziDusL$PZq5<5@JF1!G4vb40T{63t%ep4GhhlN0@(Y*!`rv2!7Y1I9@m5FG)+u@#Z6q?) zLz)DmVI1+8CleY*aWL`1;cX{-+*-Voag(Wkzy0~+!FV|SfN>Km&!OWcxgyhRgqBKzNq&;md(*HcYJ|y z?1?U#!`;~vCo*rdV0W!1wN}$77$(3?_QLFV#+|aysY+?4>9WR<@Z=P8G7HUCm39%2 z(u^*Yybn<#rsonLQo=hMZYY1<`!xoOXRS1Q?3Z}@5m$P2H~W;$c|54NtIM0h*oN)g zjI3>0v$-EPRpVVNo(gPYs-2=8vFrw2c6q8jAg}QJl+8Ol(Wf~^Cy}N-b*=(S3+a=W zG^^msGq`c{K0o@5s+cS3=py&(4tLqq<@-*jjxN%QdN{g>ql Date: Fri, 3 Nov 2023 15:30:01 +0100 Subject: [PATCH 16/23] refactoring --- .../src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 64eb86338..ba0c6b252 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -41,8 +41,8 @@ public class BulkTagJobTest { "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + - "\"publisher\":\"$['publisher'].value\"," + - "\"publicationyear\":\"$['dateofacceptance'].value\"} "; + "\"publisher\":\"$['publisher'].value\"," + + "\"publicationyear\":\"$['dateofacceptance'].value\"} "; private static SparkSession spark; From 5bc97615d50383c9adc3eab2c69f86bacbe4fb4b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 3 Nov 2023 15:35:10 +0100 Subject: [PATCH 17/23] - --- .../dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 8adc88920..040c89782 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - // project.setId(bipProjectScores.getProjectId()); + project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) From eaf0a702dea01c77a01bfa38acb4c9b1b6c72627 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 14 Nov 2023 14:53:34 +0100 Subject: [PATCH 18/23] - --- .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 50 +++++++++---------- .../main/java/eu/dnetlib/dhp/api/Utils.java | 25 +++++----- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 6 +-- .../PrepareResultCommunitySet.java | 6 +-- .../PrepareResultCommunitySet.java | 7 ++- 5 files changed, 47 insertions(+), 47 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index 262ca0290..dc10fce15 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -14,8 +14,8 @@ import org.jetbrains.annotations.NotNull; * @Date 06/10/23 */ public class QueryCommunityAPI { - private static final String PRODUCTION_BASE_URL = "https://services.openaire.eu/openaire/"; - private static final String BETA_BASE_URL = "https://beta.services.openaire.eu/openaire/"; + + private static String get(String geturl) throws IOException { URL url = new URL(geturl); @@ -32,35 +32,35 @@ public class QueryCommunityAPI { return body; } - public static String communities(boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/communities"); - return get(BETA_BASE_URL + "community/communities"); - } + public static String communities(String baseURL) throws IOException { - public static String community(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id); - return get(BETA_BASE_URL + "community/" + id); - } - - public static String communityDatasource(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/contentproviders"); - return (BETA_BASE_URL + "community/" + id + "/contentproviders"); + return get(baseURL + "community/communities"); } - public static String communityPropagationOrganization(String id, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/propagationOrganizations"); - return get(BETA_BASE_URL + "community/" + id + "/propagationOrganizations"); + public static String community(String id, String baseURL ) throws IOException { + + return get(baseURL + "community/" + id); + } - public static String communityProjects(String id, String page, String size, boolean production) throws IOException { - if (production) - return get(PRODUCTION_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); - return get(BETA_BASE_URL + "community/" + id + "/projects/" + page + "/" + size); + public static String communityDatasource(String id, String baseURL ) throws IOException { + + return get(baseURL + "community/" + id + "/contentproviders"); + + + } + + public static String communityPropagationOrganization(String id, String baseURL ) throws IOException { + + return get(baseURL + "community/" + id + "/propagationOrganizations"); + + } + + public static String communityProjects(String id, String page, String size, String baseURL ) throws IOException { + + return get(baseURL + "community/" + id + "/projects/" + page + "/" + size); + } @NotNull diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index 43d5e7e98..d121b8b7e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -36,14 +36,14 @@ public class Utils implements Serializable { private static final Logger log = LoggerFactory.getLogger(Utils.class); - public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException { + public static CommunityConfiguration getCommunityConfiguration(String baseURL) throws IOException { final Map communities = Maps.newHashMap(); List validCommunities = new ArrayList<>(); - getValidCommunities(production) + getValidCommunities(baseURL) .forEach(community -> { try { CommunityModel cm = MAPPER - .readValue(QueryCommunityAPI.community(community.getId(), production), CommunityModel.class); + .readValue(QueryCommunityAPI.community(community.getId(), baseURL), CommunityModel.class); validCommunities.add(getCommunity(cm)); } catch (IOException e) { throw new RuntimeException(e); @@ -53,7 +53,7 @@ public class Utils implements Serializable { try { DatasourceList dl = MAPPER .readValue( - QueryCommunityAPI.communityDatasource(community.getId(), production), DatasourceList.class); + QueryCommunityAPI.communityDatasource(community.getId(), baseURL), DatasourceList.class); community.setProviders(dl.stream().map(d -> { if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled())) return null; @@ -98,9 +98,9 @@ public class Utils implements Serializable { return c; } - public static List getValidCommunities(boolean production) throws IOException { + public static List getValidCommunities(String baseURL) throws IOException { return MAPPER - .readValue(QueryCommunityAPI.communities(production), CommunitySummary.class) + .readValue(QueryCommunityAPI.communities(baseURL), CommunitySummary.class) .stream() .filter( community -> !community.getStatus().equals("hidden") && @@ -111,15 +111,15 @@ public class Utils implements Serializable { /** * it returns for each organization the list of associated communities */ - public static CommunityEntityMap getCommunityOrganization(boolean production) throws IOException { + public static CommunityEntityMap getCommunityOrganization(String baseURL) throws IOException { CommunityEntityMap organizationMap = new CommunityEntityMap(); - getValidCommunities(production) + getValidCommunities(baseURL) .forEach(community -> { String id = community.getId(); try { List associatedOrgs = MAPPER .readValue( - QueryCommunityAPI.communityPropagationOrganization(id, production), OrganizationList.class); + QueryCommunityAPI.communityPropagationOrganization(id, baseURL), OrganizationList.class); associatedOrgs.forEach(o -> { if (!organizationMap .keySet() @@ -136,9 +136,10 @@ public class Utils implements Serializable { return organizationMap; } - public static CommunityEntityMap getCommunityProjects(boolean production) throws IOException { + public static CommunityEntityMap getCommunityProjects(String baseURL) throws IOException { CommunityEntityMap projectMap = new CommunityEntityMap(); - getValidCommunities(production) + + getValidCommunities(baseURL) .forEach(community -> { int page = -1; int size = 100; @@ -150,7 +151,7 @@ public class Utils implements Serializable { .readValue( QueryCommunityAPI .communityProjects( - community.getId(), String.valueOf(page), String.valueOf(size), production), + community.getId(), String.valueOf(page), String.valueOf(size), baseURL), ContentModel.class); if (cm.getContent().size() > 0) { cm.getContent().forEach(p -> { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 15712ad66..d972cecac 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -62,8 +62,8 @@ public class SparkBulkTagJob { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("production")); - log.info("production: {}", production); + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class); log.info("pathMap: {}", new Gson().toJson(protoMappingParams)); @@ -79,7 +79,7 @@ public class SparkBulkTagJob { if (taggingConf != null) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { - cc = Utils.getCommunityConfiguration(production); + cc = Utils.getCommunityConfiguration(baseURL); } runWithSparkSession( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index e32e94a4b..54fa60168 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -48,10 +48,10 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("production")); - log.info("production: {}", production); + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); - final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(production); + final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(baseURL); log.info("organizationMap: {}", new Gson().toJson(organizationMap)); SparkConf conf = new SparkConf(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index 7bee1ea0c..2c2eb69dd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -52,11 +52,10 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final boolean production = Boolean.valueOf(parser.get("production")); - log.info("production: {}", production); + final String baseURL = parser.get("baseURL"); + log.info("baseUEL: {}", baseURL); - final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production); - // log.info("projectsMap: {}", new Gson().toJson(projectsMap)); + final CommunityEntityMap projectsMap = Utils.getCommunityProjects(baseURL); SparkConf conf = new SparkConf(); From 11a1207f9c8476db4fc926f707915c3209720106 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 22 Nov 2023 12:22:14 +0100 Subject: [PATCH 19/23] [graph cleaning] applying coar based vocabularies in bulk --- .../dhp/oa/merge/GroupEntitiesSparkJob.java | 40 +++++- .../oaf/utils/GraphCleaningFunctions.java | 95 +++++++++++++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 21 ++- .../group_graph_entities_parameters.json | 6 + .../raw/AbstractMdRecordToOafMapper.java | 63 +-------- .../group/GroupEntitiesSparkJobTest.java | 131 ++++++++++++++++-- .../raw/GenerateEntitiesApplicationTest.java | 5 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 28 ++-- .../dhp/oa/graph/group/dataset/dataset.json | 6 +- .../graph/group/publication/publication.json | 6 +- pom.xml | 2 +- 11 files changed, 294 insertions(+), 109 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index f5c8eea19..0225a5063 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -21,10 +21,15 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; /** @@ -35,6 +40,12 @@ public class GroupEntitiesSparkJob { private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private ArgumentApplicationParser parser; + + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -51,6 +62,17 @@ public class GroupEntitiesSparkJob { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } + + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { + String graphInputPath = parser.get("graphInputPath"); log.info("graphInputPath: {}", graphInputPath); @@ -60,19 +82,21 @@ public class GroupEntitiesSparkJob { String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible")); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); log.info("filterInvisible: {}", filterInvisible); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + runWithSparkSession( conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); }); } @@ -81,7 +105,7 @@ public class GroupEntitiesSparkJob { String inputPath, String checkpointPath, String outputPath, - boolean filterInvisible) { + boolean filterInvisible, VocabularyGroup vocs) { Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); @@ -106,10 +130,14 @@ public class GroupEntitiesSparkJob { } Dataset groupedEntities = allEntities - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) (b, a) -> OafMapperUtils.mergeEntities(b, a)) .map( - (MapFunction, Tuple2>) t -> new Tuple2( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) OafMapperUtils::mergeEntities) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( t._2().getClass().getName(), t._2()), Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 324e3dd58..b23dade98 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; import java.time.LocalDate; @@ -784,4 +786,97 @@ public class GraphCleaningFunctions extends CleaningFunctions { return s; } + public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) { + + if (entity instanceof Result) { + final Result result = (Result) entity; + + Optional + .ofNullable(result.getInstance()) + .ifPresent( + instances -> instances + .forEach( + instance -> { + if (Objects.isNull(instance.getInstanceTypeMapping())) { + List mapping = Lists.newArrayList(); + mapping + .add( + OafMapperUtils + .instanceTypeMapping( + instance.getInstancetype().getClassname(), + OPENAIRE_COAR_RESOURCE_TYPES_3_1)); + instance.setInstanceTypeMapping(mapping); + } + Optional optionalItm = instance + .getInstanceTypeMapping() + .stream() + .filter(GraphCleaningFunctions::originalResourceType) + .findFirst(); + if (optionalItm.isPresent()) { + InstanceTypeMapping coarItm = optionalItm.get(); + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType())) + .ifPresent(type -> { + coarItm.setTypeCode(type.getClassid()); + coarItm.setTypeLabel(type.getClassname()); + }); + final List mappings = Lists.newArrayList(); + if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { + Optional + .ofNullable( + vocs + .lookupTermBySynonym( + OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode())) + .ifPresent( + type -> mappings + .add( + OafMapperUtils + .instanceTypeMapping(coarItm.getTypeCode(), type))); + } + if (!mappings.isEmpty()) { + instance.getInstanceTypeMapping().addAll(mappings); + } + } + })); + result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs)); + } + + return entity; + } + + private static boolean originalResourceType(InstanceTypeMapping itm) { + return StringUtils.isNotBlank(itm.getOriginalType()) && + OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) && + StringUtils.isBlank(itm.getTypeCode()) && + StringUtils.isBlank(itm.getTypeLabel()); + } + + private static Qualifier getMetaResourceType(final List instances, final VocabularyGroup vocs) { + + if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { + Optional instanceTypeMapping = instances + .stream() + .flatMap( + i -> Optional.ofNullable(i.getInstanceTypeMapping()).map(Collection::stream).orElse(Stream.empty())) + .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) + .findFirst(); + + if (!instanceTypeMapping.isPresent()) { + return null; + } else { + final String typeCode = instanceTypeMapping.get().getTypeCode(); + return Optional + .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) + .orElseThrow( + () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + + OPENAIRE_META_RESOURCE_TYPE)); + } + } else { + throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); + } + } + } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 1c557c805..4cecd0895 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -140,15 +140,28 @@ public class OafMapperUtils { .collect(Collectors.toList()); } - public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label, + String vocabularyName) { final InstanceTypeMapping m = new InstanceTypeMapping(); - m.setVocabularyName(term.getSchemeid()); + m.setVocabularyName(vocabularyName); m.setOriginalType(originalType); - m.setTypeCode(term.getClassid()); - m.setTypeLabel(term.getClassname()); + m.setTypeCode(code); + m.setTypeLabel(label); return m; } + public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) { + return instanceTypeMapping(originalType, term.getClassid(), term.getClassname(), term.getSchemeid()); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType) { + return instanceTypeMapping(originalType, null, null, null); + } + + public static InstanceTypeMapping instanceTypeMapping(String originalType, String vocabularyName) { + return instanceTypeMapping(originalType, null, null, vocabularyName); + } + public static Qualifier unknown(final String schemeid, final String schemename) { return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json index 58e3ca711..512878457 100644 --- a/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json @@ -28,5 +28,11 @@ "paramLongName": "filterInvisible", "paramDescription": "if true filters out invisible entities", "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 49133cedb..a71908b02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -125,9 +125,7 @@ public abstract class AbstractMdRecordToOafMapper { final String type = getResultType(doc, instances); - final Qualifier metaResourceType = getMetaResourceType(instances); - - return createOafs(doc, type, metaResourceType, instances, collectedFrom, entityInfo, lastUpdateTimestamp); + return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); return Lists.newArrayList(); @@ -153,30 +151,6 @@ public abstract class AbstractMdRecordToOafMapper { return type; } - protected Qualifier getMetaResourceType(final List instances) { - - if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) { - Optional instanceTypeMapping = instances - .stream() - .flatMap(i -> i.getInstanceTypeMapping().stream()) - .filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName())) - .findFirst(); - - if (!instanceTypeMapping.isPresent()) { - return null; - } else { - final String typeCode = instanceTypeMapping.get().getTypeCode(); - return Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode)) - .orElseThrow( - () -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " + - OPENAIRE_META_RESOURCE_TYPE)); - } - } else { - throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available"); - } - } - private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { final String dsId = doc.valueOf(xpathId); final String dsName = doc.valueOf(xpathName); @@ -191,14 +165,13 @@ public abstract class AbstractMdRecordToOafMapper { protected List createOafs( final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { final OafEntity entity = createEntity( - doc, type, metaResourceType, instances, collectedFrom, info, lastUpdateTimestamp); + doc, type, instances, collectedFrom, info, lastUpdateTimestamp); final Set originalId = Sets.newHashSet(entity.getOriginalId()); originalId.add(entity.getId()); @@ -231,7 +204,6 @@ public abstract class AbstractMdRecordToOafMapper { private OafEntity createEntity(final Document doc, final String type, - final Qualifier metaResourceType, final List instances, final KeyValue collectedFrom, final DataInfo info, @@ -239,12 +211,12 @@ public abstract class AbstractMdRecordToOafMapper { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); - populateResultFields(p, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); p.setJournal(prepareJournal(doc, info)); return p; case "dataset": final Dataset d = new Dataset(); - populateResultFields(d, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -255,7 +227,7 @@ public abstract class AbstractMdRecordToOafMapper { return d; case "software": final Software s = new Software(); - populateResultFields(s, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); @@ -265,7 +237,7 @@ public abstract class AbstractMdRecordToOafMapper { case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, metaResourceType, doc, instances, collectedFrom, info, lastUpdateTimestamp); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); @@ -402,13 +374,11 @@ public abstract class AbstractMdRecordToOafMapper { private void populateResultFields( final Result r, - final Qualifier metaResourceType, final Document doc, final List instances, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { - r.setMetaResourceType(metaResourceType); r.setDataInfo(info); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); @@ -555,26 +525,7 @@ public abstract class AbstractMdRecordToOafMapper { .ofNullable(findOriginalType(doc)) .map(originalType -> { final List mappings = Lists.newArrayList(); - - if (vocs.vocabularyExists(OPENAIRE_COAR_RESOURCE_TYPES_3_1)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable(vocs.lookupTermBySynonym(OPENAIRE_COAR_RESOURCE_TYPES_3_1, originalType)) - .ifPresent(coarTerm -> { - mappings.add(OafMapperUtils.instanceTypeMapping(originalType, coarTerm)); - if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) { - - // TODO verify what the vocabs return when a synonym is not defined - Optional - .ofNullable( - vocs.lookupTermBySynonym(OPENAIRE_USER_RESOURCE_TYPES, coarTerm.getClassid())) - .ifPresent( - type -> mappings.add(OafMapperUtils.instanceTypeMapping(originalType, type))); - } - }); - } - + mappings.add(OafMapperUtils.instanceTypeMapping(originalType, OPENAIRE_COAR_RESOURCE_TYPES_3_1)); return mappings; }) .orElse(new ArrayList<>()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java index 0887adf45..242aed88e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -1,15 +1,23 @@ package eu.dnetlib.dhp.oa.graph.group; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; import java.io.IOException; import java.net.URISyntaxException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; @@ -17,20 +25,36 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +@ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class GroupEntitiesSparkJobTest { + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + private static SparkSession spark; private static ObjectMapper mapper = new ObjectMapper() @@ -45,10 +69,10 @@ public class GroupEntitiesSparkJobTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + workingDir = Files.createTempDirectory(GroupEntitiesSparkJobTest.class.getSimpleName()); SparkConf conf = new SparkConf(); - conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setAppName(GroupEntitiesSparkJobTest.class.getSimpleName()); conf.setMaster("local"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); @@ -56,10 +80,17 @@ public class GroupEntitiesSparkJobTest { } @BeforeEach - public void beforeEach() throws IOException, URISyntaxException { + public void beforeEach() throws IOException, URISyntaxException, ISLookUpException { dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); checkpointPath = workingDir.resolve("grouped_entity"); outputPath = workingDir.resolve("dispatched_entity"); + + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); } @AfterAll @@ -71,18 +102,17 @@ public class GroupEntitiesSparkJobTest { @Test @Order(1) void testGroupEntities() throws Exception { - GroupEntitiesSparkJob.main(new String[] { - "-isSparkSessionManaged", - Boolean.FALSE.toString(), - "-graphInputPath", - dataInputPath.toString(), - "-checkpointPath", - checkpointPath.toString(), - "-outputPath", - outputPath.toString(), - "-filterInvisible", - Boolean.FALSE.toString() - }); + new GroupEntitiesSparkJob( + args( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json", + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--graphInputPath", dataInputPath.toString(), + "--checkpointPath", checkpointPath.toString(), + "--outputPath", outputPath.toString(), + "--filterInvisible", Boolean.FALSE.toString(), + "--isLookupUrl", "lookupurl" + })).run(false, isLookUpService); Dataset checkpointTable = spark .read() @@ -109,6 +139,14 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); assertEquals(3, output.count()); + + List resultTypes = output + .map((MapFunction) value -> value.getResulttype().getClassid(), Encoders.STRING()) + .distinct() + .collectAsList(); + + assertEquals(2, resultTypes.size()); + assertEquals( 2, output @@ -121,5 +159,68 @@ public class GroupEntitiesSparkJobTest { .map((MapFunction) r -> r.getResulttype().getClassid(), Encoders.STRING()) .filter((FilterFunction) s -> s.equals("dataset")) .count()); + + Result result = output + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + + result.getInstance().forEach(instance -> { + Optional coarType = instance + .getInstanceTypeMapping() + .stream() + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "journal-article".equals(itm.getOriginalType())) + .findFirst(); + + assertTrue(coarType.isPresent()); + assertEquals("http://purl.org/coar/resource_type/c_2df8fbb1", coarType.get().getTypeCode()); + assertEquals("research article", coarType.get().getTypeLabel()); + }); + + final Dataset filtered = output.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'"); + assertEquals(1, filtered.count()); + result = filtered.first(); + + result + .getInstance() + .stream() + .flatMap(instance -> instance.getInstanceTypeMapping().stream()) + .filter(itm -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName())) + .filter(itm -> "Patent".equals(itm.getOriginalType())) + .forEach(itm -> { + assertEquals("http://purl.org/coar/resource_type/c_15cd", itm.getTypeCode()); + assertEquals("patent", itm.getTypeLabel()); + }); } + + private List vocs() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"))); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"))); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + Objects + .requireNonNull( + GroupEntitiesSparkJobTest.class.getResourceAsStream(path))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 53b3f8432..6d6b2ffbd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -92,13 +92,14 @@ class GenerateEntitiesApplicationTest { private List vocs() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + GenerateEntitiesApplicationTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); } private List synonyms() throws IOException { return IOUtils .readLines( - GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + GenerateEntitiesApplicationTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index e6997ac1d..1f2defa01 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,7 +122,7 @@ class MappersTest { assertTrue(instance.getPid().isEmpty()); assertNotNull(instance.getInstanceTypeMapping()); - assertEquals(2, instance.getInstanceTypeMapping().size()); + assertEquals(1, instance.getInstanceTypeMapping().size()); Optional coarType = instance .getInstanceTypeMapping() @@ -131,8 +131,8 @@ class MappersTest { .findFirst(); assertTrue(coarType.isPresent()); - assertEquals("http://purl.org/coar/resource_type/c_5794", coarType.get().getTypeCode()); - assertEquals("conference paper", coarType.get().getTypeLabel()); + assertNull(coarType.get().getTypeCode()); + assertNull(coarType.get().getTypeLabel()); Optional userType = instance .getInstanceTypeMapping() @@ -140,9 +140,7 @@ class MappersTest { .filter(itm -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(itm.getVocabularyName())) .findFirst(); - assertTrue(userType.isPresent()); - assertEquals("Article", userType.get().getTypeCode()); - assertEquals("Article", userType.get().getTypeLabel()); + assertFalse(userType.isPresent()); assertFalse(instance.getAlternateIdentifier().isEmpty()); assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); @@ -710,14 +708,10 @@ class MappersTest { assertEquals("0001", p_cleaned.getInstance().get(0).getRefereed().getClassid()); assertEquals("peerReviewed", p_cleaned.getInstance().get(0).getRefereed().getClassname()); - assertNotNull(p_cleaned.getMetaResourceType()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassid()); - assertEquals("Research Literature", p_cleaned.getMetaResourceType().getClassname()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemeid()); - assertEquals(ModelConstants.OPENAIRE_META_RESOURCE_TYPE, p_cleaned.getMetaResourceType().getSchemename()); + assertNull(p_cleaned.getMetaResourceType()); assertNotNull(p_cleaned.getInstance().get(0).getInstanceTypeMapping()); - assertEquals(2, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); + assertEquals(1, p_cleaned.getInstance().get(0).getInstanceTypeMapping().size()); assertTrue( p_cleaned @@ -728,8 +722,7 @@ class MappersTest { .anyMatch( t -> "journal-article".equals(t.getOriginalType()) && ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()) && - "http://purl.org/coar/resource_type/c_2df8fbb1".equals(t.getTypeCode()) && - "research article".equals(t.getTypeLabel()))); + Objects.isNull(t.getTypeCode()) && Objects.isNull(t.getTypeLabel()))); assertTrue( p_cleaned @@ -737,11 +730,8 @@ class MappersTest { .get(0) .getInstanceTypeMapping() .stream() - .anyMatch( - t -> "journal-article".equals(t.getOriginalType()) && - ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()) && - "Article".equals(t.getTypeCode()) && - "Article".equals(t.getTypeLabel()))); + .noneMatch( + t -> ModelConstants.OPENAIRE_USER_RESOURCE_TYPES.equals(t.getVocabularyName()))); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json index e30be47e9..efbabb3c8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json @@ -1,3 +1,3 @@ -{"author":[{"affiliation":[],"fullname":"Greenough, B","name":"B","pid":[],"rank":1,"surname":"Greenough"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not 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diff --git a/pom.xml b/pom.xml index 0f1ec78af..3fd351c1d 100644 --- a/pom.xml +++ b/pom.xml @@ -888,7 +888,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [4.17.2-SNAPSHOT] + [4.17.2] [4.0.3] [6.0.5] [3.1.6] From 48e0427a234b1bdee63f21d6c8879f10ceeba3da Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Nov 2023 15:10:27 +0100 Subject: [PATCH 20/23] changed the parameter from production to baseURL. Fixed issue in tagging configuration --- .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 10 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 1 + .../dhp/bulktag/input_bulkTag_parameters.json | 8 +- ...t_preparecommunitytoresult_parameters.json | 8 +- ...t_preparecommunitytoresult_parameters.json | 6 +- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 8 +- .../tagging_conf_remove.xml | 182 +++++++++--------- 7 files changed, 112 insertions(+), 111 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index dc10fce15..b7c0164c1 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -34,32 +34,32 @@ public class QueryCommunityAPI { public static String communities(String baseURL) throws IOException { - return get(baseURL + "community/communities"); + return get(baseURL + "communities"); } public static String community(String id, String baseURL ) throws IOException { - return get(baseURL + "community/" + id); + return get(baseURL + id); } public static String communityDatasource(String id, String baseURL ) throws IOException { - return get(baseURL + "community/" + id + "/contentproviders"); + return get(baseURL + id + "/contentproviders"); } public static String communityPropagationOrganization(String id, String baseURL ) throws IOException { - return get(baseURL + "community/" + id + "/propagationOrganizations"); + return get(baseURL + id + "/propagationOrganizations"); } public static String communityProjects(String id, String page, String size, String baseURL ) throws IOException { - return get(baseURL + "community/" + id + "/projects/" + page + "/" + size); + return get(baseURL + id + "/projects/" + page + "/" + size); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index d972cecac..f01063955 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -80,6 +80,7 @@ public class SparkBulkTagJob { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { cc = Utils.getCommunityConfiguration(baseURL); + log.info(OBJECT_MAPPER.writeValueAsString(cc)); } runWithSparkSession( diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json index dbe2d088f..d88904cd9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json @@ -34,10 +34,10 @@ }, { - "paramName": "p", - "paramLongName": "production", - "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", - "paramRequired": true + "paramName": "bu", + "paramLongName": "baseURL", + "paramDescription": "this parameter is to specify the api to be queried (beta or production)", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json index 8b6291e5d..3601db7ac 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json @@ -24,10 +24,10 @@ "paramRequired": true }, { - "paramName": "p", - "paramLongName": "production", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true + "paramName": "bu", + "paramLongName": "baseURL", + "paramDescription": "the base URL to the community API to use", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json index 9a50c79fa..cbc01c2d5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json @@ -19,10 +19,10 @@ "paramRequired": true }, { - "paramName": "p", - "paramLongName": "production", + "paramName": "bu", + "paramLongName": "baseURL", "paramDescription": "the path used to store temporary output files", - "paramRequired": true + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index ba0c6b252..d193716a8 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -533,6 +533,7 @@ public class BulkTagJobTest { + "where MyD.inferenceprovenance = 'bulktagging'"; org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(7, idExplodeCommunity.count()); Assertions @@ -1572,11 +1573,10 @@ public class BulkTagJobTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(), - "-taggingConf", taggingConf, - "-outputPath", workingDir.toString() + "/", - 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share_______::4719356ec8d7d55d3feb384ce879ad6c + 10|share_______::4719356ec8d7d55d3feb384ce879ad6c {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} - share_______::bbd802baad85d1fd440f32a7a3a2c2b1 + 10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1 {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} - opendoar____::6f4922f45568161a8cdf4ad2299f6d23 + 10|opendoar____::6f4922f45568161a8cdf4ad2299f6d23 {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} - re3data_____::7980778c78fb4cf0fab13ce2159030dc + 10|re3data_____::7980778c78fb4cf0fab13ce2159030dc {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} - re3data_____::978378def740bbf2bfb420de868c460b + 10|re3data_____::978378def740bbf2bfb420de868c460b {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} From 8eb70e6657870e0d661a5c8619076bc013eb23ee Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Nov 2023 15:13:15 +0100 Subject: [PATCH 21/23] refactoring --- .../PrepareAffiliationRelationsTest.java | 4 ++-- .../eu/dnetlib/dhp/api/QueryCommunityAPI.java | 21 ++++++++----------- .../PrepareResultCommunitySet.java | 2 +- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 2 +- 4 files changed, 13 insertions(+), 16 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java index e2639996c..b87738879 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java @@ -79,8 +79,8 @@ public class PrepareAffiliationRelationsTest { .getPath(); String pubmedAffiliationRelationsPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") + .getPath(); String outputPath = workingDir.toString() + "/actionSet"; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java index b7c0164c1..cf33c6509 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java @@ -15,8 +15,6 @@ import org.jetbrains.annotations.NotNull; */ public class QueryCommunityAPI { - - private static String get(String geturl) throws IOException { URL url = new URL(geturl); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); @@ -34,32 +32,31 @@ public class QueryCommunityAPI { public static String communities(String baseURL) throws IOException { - return get(baseURL + "communities"); + return get(baseURL + "communities"); } - public static String community(String id, String baseURL ) throws IOException { + public static String community(String id, String baseURL) throws IOException { - return get(baseURL + id); + return get(baseURL + id); } - public static String communityDatasource(String id, String baseURL ) throws IOException { - - return get(baseURL + id + "/contentproviders"); + public static String communityDatasource(String id, String baseURL) throws IOException { + return get(baseURL + id + "/contentproviders"); } - public static String communityPropagationOrganization(String id, String baseURL ) throws IOException { + public static String communityPropagationOrganization(String id, String baseURL) throws IOException { - return get(baseURL + id + "/propagationOrganizations"); + return get(baseURL + id + "/propagationOrganizations"); } - public static String communityProjects(String id, String page, String size, String baseURL ) throws IOException { + public static String communityProjects(String id, String page, String size, String baseURL) throws IOException { - return get(baseURL + id + "/projects/" + page + "/" + size); + return get(baseURL + id + "/projects/" + page + "/" + size); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java index 2c2eb69dd..7fed2606b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java @@ -52,7 +52,7 @@ public class PrepareResultCommunitySet { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String baseURL = parser.get("baseURL"); + final String baseURL = parser.get("baseURL"); log.info("baseUEL: {}", baseURL); final CommunityEntityMap projectsMap = Utils.getCommunityProjects(baseURL); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index d193716a8..743e62b5f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -1576,7 +1576,7 @@ public class BulkTagJobTest { "-outputPath", workingDir.toString() + "/", // "-baseURL", "https://services.openaire.eu/openaire/community/", "-pathMap", pathMap, - "-taggingConf", taggingConf + "-taggingConf", taggingConf }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); From af1c2634b3fc61c208dfd8e57fff1b11459dba5f Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 29 Nov 2023 12:45:30 +0100 Subject: [PATCH 22/23] added instanceTypeMapping original field in the mapping of - DOIBoost - Datacite - PubMed - Scholexplorer Datasource --- .../DataciteToOAFTransformation.scala | 15 ++++++++----- .../eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala | 21 +++++++++++++++++-- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 18 ++++++++++++---- .../doiboost/crossref/Crossref2Oaf.scala | 8 +++++-- 4 files changed, 49 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 45f5f9729..17f1b90b0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -166,7 +166,7 @@ object DataciteToOAFTransformation { resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup - ): (Qualifier, Qualifier) = { + ): (Qualifier, Qualifier, String) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -176,7 +176,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), resourceType ) } if (schemaOrg != null && schemaOrg.nonEmpty) { @@ -188,7 +188,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), schemaOrg ) } @@ -203,7 +203,7 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ) + ), resourceTypeGeneral ) } @@ -216,12 +216,17 @@ object DataciteToOAFTransformation { schemaOrg: String, vocabularies: VocabularyGroup ): Result = { - val typeQualifiers: (Qualifier, Qualifier) = + val typeQualifiers: (Qualifier, Qualifier, String) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) if (typeQualifiers == null) return null val i = new Instance i.setInstancetype(typeQualifiers._1) + // ADD ORIGINAL TYPE + val itm = new InstanceTypeMapping + itm.setOriginalType(typeQualifiers._3) + i.setInstanceTypeMapping(List(itm).asJava) + typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index c079f7537..3624c5369 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -176,7 +176,7 @@ object BioDBToOAF { i.setUrl(List(s"${resolvedURL(input.pidType)}${input.pid}").asJava) } - if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) + if (input.pidType.equalsIgnoreCase("clinicaltrials.gov")) { i.setInstancetype( OafMapperUtils.qualifier( "0037", @@ -185,7 +185,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) - else + val itm = new InstanceTypeMapping + itm.setOriginalType(input.pidType) + i.setInstanceTypeMapping(List(itm).asJava) + } else { i.setInstancetype( OafMapperUtils.qualifier( "0046", @@ -194,6 +197,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) + } if (input.datasource == null || input.datasource.isEmpty) return null @@ -265,6 +272,9 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("uniprot")) d.setInstance(List(i).asJava) @@ -471,6 +481,9 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("pdb")) d.setInstance(List(i).asJava) @@ -571,6 +584,10 @@ object BioDBToOAF { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + val itm = new InstanceTypeMapping + itm.setOriginalType("Bioentity") + i.setInstanceTypeMapping(List(itm).asJava) + i.setCollectedfrom(collectedFromMap("ebi")) d.setInstance(List(i).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 410686f97..40ac48a7a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -188,12 +188,22 @@ object PubMedToOaf { val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) pubmedInstance.setInstancetype(cojbCategory) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(ja.get.getValue) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala - .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) - .find(q => q != null) - if (i_type.isDefined) - pubmedInstance.setInstancetype(i_type.get) + .map(s => (s.getValue,getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))) + .find(q => q._2 != null) + + if (i_type.isDefined) { + pubmedInstance.setInstancetype(i_type.get._2) + // ADD ORIGINAL TYPE to the publication + val itm = new InstanceTypeMapping + itm.setOriginalType(i_type.get._1) + pubmedInstance.setInstanceTypeMapping(List(itm).asJava) + } else return null } diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 565d34e62..f45c303f0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -107,7 +107,7 @@ case object Crossref2Oaf { .map(f => f.id) } - def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { + def mappingResult(result: Result, json: JValue, cobjCategory: String, originalType:String): Result = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID @@ -283,6 +283,10 @@ case object Crossref2Oaf { ModelConstants.DNET_PUBLICATION_RESOURCE ) ) + //ADD ORIGINAL TYPE to the mapping + val itm = new InstanceTypeMapping + itm.setOriginalType(originalType) + instance.setInstanceTypeMapping(List(itm).asJava) result.setResourcetype( OafMapperUtils.qualifier( cobjCategory.substring(0, 4), @@ -367,7 +371,7 @@ case object Crossref2Oaf { objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type") ) - mappingResult(result, json, cOBJCategory) + mappingResult(result, json, cOBJCategory, originalType) if (result == null || result.getId == null) return List() From 86b5775e0859233ececfbc7425afee5a5b2c2c6f Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 29 Nov 2023 13:15:43 +0100 Subject: [PATCH 23/23] added vocabulary in instanceTypeMapping for - DOIBoost - Datacite - PubMed - Scholexplorer Datasource --- .../dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 ++ .../src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala | 5 +++++ .../scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala | 2 ++ .../scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala | 1 + 4 files changed, 10 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 17f1b90b0..ee3660918 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -225,8 +225,10 @@ object DataciteToOAFTransformation { // ADD ORIGINAL TYPE val itm = new InstanceTypeMapping itm.setOriginalType(typeQualifiers._3) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) + typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index 3624c5369..89bc8d948 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -187,6 +187,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType(input.pidType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) } else { i.setInstancetype( @@ -199,6 +200,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) } @@ -274,6 +276,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("uniprot")) @@ -483,6 +486,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) i.setCollectedfrom(collectedFromMap("pdb")) @@ -586,6 +590,7 @@ object BioDBToOAF { ) val itm = new InstanceTypeMapping itm.setOriginalType("Bioentity") + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 40ac48a7a..f3f8b4f02 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -191,6 +191,7 @@ object PubMedToOaf { // ADD ORIGINAL TYPE to the publication val itm = new InstanceTypeMapping itm.setOriginalType(ja.get.getValue) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala @@ -202,6 +203,7 @@ object PubMedToOaf { // ADD ORIGINAL TYPE to the publication val itm = new InstanceTypeMapping itm.setOriginalType(i_type.get._1) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index f45c303f0..65e395357 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -286,6 +286,7 @@ case object Crossref2Oaf { //ADD ORIGINAL TYPE to the mapping val itm = new InstanceTypeMapping itm.setOriginalType(originalType) + itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) instance.setInstanceTypeMapping(List(itm).asJava) result.setResourcetype( OafMapperUtils.qualifier(