Merge pull request '[ENRICHMENT][BETA] Use of community API in enrichment process AND addition to tagging result for communities through projects' (#359) from propagationapi into beta
Reviewed-on: #359
This commit is contained in:
commit
4cbabc9fbc
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@ -79,8 +79,8 @@ public class PrepareAffiliationRelationsTest {
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.getPath();
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String pubmedAffiliationRelationsPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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@ -71,6 +71,9 @@ public class PropagationConstant {
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public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID = "result:community:organization";
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public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME = " Propagation of result belonging to community through organization";
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public static final String PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_ID = "result:community:project";
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public static final String PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME = " Propagation of result belonging to community through project";
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public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result";
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public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations";
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@ -0,0 +1,80 @@
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package eu.dnetlib.dhp.api;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import org.jetbrains.annotations.NotNull;
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/**
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* @author miriam.baglioni
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* @Date 06/10/23
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*/
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public class QueryCommunityAPI {
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private static String get(String geturl) throws IOException {
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URL url = new URL(geturl);
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HttpURLConnection conn = (HttpURLConnection) url.openConnection();
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conn.setDoOutput(true);
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conn.setRequestMethod("GET");
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int responseCode = conn.getResponseCode();
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String body = getBody(conn);
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conn.disconnect();
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if (responseCode != HttpURLConnection.HTTP_OK)
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throw new IOException("Unexpected code " + responseCode + body);
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return body;
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}
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public static String communities(String baseURL) throws IOException {
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return get(baseURL + "communities");
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}
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public static String community(String id, String baseURL) throws IOException {
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return get(baseURL + id);
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}
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public static String communityDatasource(String id, String baseURL) throws IOException {
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return get(baseURL + id + "/contentproviders");
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}
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public static String communityPropagationOrganization(String id, String baseURL) throws IOException {
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return get(baseURL + id + "/propagationOrganizations");
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}
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public static String communityProjects(String id, String page, String size, String baseURL) throws IOException {
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return get(baseURL + id + "/projects/" + page + "/" + size);
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}
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@NotNull
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private static String getBody(HttpURLConnection conn) throws IOException {
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String body = "{}";
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try (BufferedReader br = new BufferedReader(
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new InputStreamReader(conn.getInputStream(), "utf-8"))) {
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StringBuilder response = new StringBuilder();
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String responseLine = null;
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while ((responseLine = br.readLine()) != null) {
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response.append(responseLine.trim());
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}
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body = response.toString();
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}
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return body;
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}
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}
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@ -0,0 +1,170 @@
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package eu.dnetlib.dhp.api;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.stream.Collectors;
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import javax.management.Query;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.amazonaws.util.StringUtils;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.api.model.*;
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import eu.dnetlib.dhp.bulktag.community.Community;
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import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
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import eu.dnetlib.dhp.bulktag.community.Provider;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
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import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob;
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/**
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* @author miriam.baglioni
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* @Date 09/10/23
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*/
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public class Utils implements Serializable {
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private static final ObjectMapper MAPPER = new ObjectMapper();
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private static final VerbResolver resolver = VerbResolverFactory.newInstance();
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private static final Logger log = LoggerFactory.getLogger(Utils.class);
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public static CommunityConfiguration getCommunityConfiguration(String baseURL) throws IOException {
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final Map<String, Community> communities = Maps.newHashMap();
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List<Community> validCommunities = new ArrayList<>();
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getValidCommunities(baseURL)
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.forEach(community -> {
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try {
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CommunityModel cm = MAPPER
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.readValue(QueryCommunityAPI.community(community.getId(), baseURL), CommunityModel.class);
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validCommunities.add(getCommunity(cm));
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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validCommunities.forEach(community -> {
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try {
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DatasourceList dl = MAPPER
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.readValue(
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QueryCommunityAPI.communityDatasource(community.getId(), baseURL), DatasourceList.class);
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community.setProviders(dl.stream().map(d -> {
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if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
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return null;
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Provider p = new Provider();
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p.setOpenaireId("10|" + d.getOpenaireId());
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p.setSelectionConstraints(d.getSelectioncriteria());
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if (p.getSelectionConstraints() != null)
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p.getSelectionConstraints().setSelection(resolver);
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return p;
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})
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.filter(Objects::nonNull)
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.collect(Collectors.toList()));
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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validCommunities.forEach(community -> {
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if (community.isValid())
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communities.put(community.getId(), community);
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});
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return new CommunityConfiguration(communities);
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}
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private static Community getCommunity(CommunityModel cm) {
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Community c = new Community();
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c.setId(cm.getId());
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c.setZenodoCommunities(cm.getOtherZenodoCommunities());
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if (!StringUtils.isNullOrEmpty(cm.getZenodoCommunity()))
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c.getZenodoCommunities().add(cm.getZenodoCommunity());
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c.setSubjects(cm.getSubjects());
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c.getSubjects().addAll(cm.getFos());
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c.getSubjects().addAll(cm.getSdg());
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if (cm.getAdvancedConstraints() != null) {
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c.setConstraints(cm.getAdvancedConstraints());
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c.getConstraints().setSelection(resolver);
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}
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if (cm.getRemoveConstraints() != null) {
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c.setRemoveConstraints(cm.getRemoveConstraints());
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c.getRemoveConstraints().setSelection(resolver);
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}
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return c;
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}
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public static List<CommunityModel> getValidCommunities(String baseURL) throws IOException {
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return MAPPER
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.readValue(QueryCommunityAPI.communities(baseURL), CommunitySummary.class)
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.stream()
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.filter(
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community -> !community.getStatus().equals("hidden") &&
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(community.getType().equals("ri") || community.getType().equals("community")))
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.collect(Collectors.toList());
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}
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/**
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* it returns for each organization the list of associated communities
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*/
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public static CommunityEntityMap getCommunityOrganization(String baseURL) throws IOException {
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CommunityEntityMap organizationMap = new CommunityEntityMap();
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getValidCommunities(baseURL)
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.forEach(community -> {
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String id = community.getId();
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try {
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List<String> associatedOrgs = MAPPER
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.readValue(
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QueryCommunityAPI.communityPropagationOrganization(id, baseURL), OrganizationList.class);
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associatedOrgs.forEach(o -> {
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if (!organizationMap
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.keySet()
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.contains(
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"20|" + o))
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organizationMap.put("20|" + o, new ArrayList<>());
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organizationMap.get("20|" + o).add(community.getId());
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});
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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return organizationMap;
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}
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public static CommunityEntityMap getCommunityProjects(String baseURL) throws IOException {
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CommunityEntityMap projectMap = new CommunityEntityMap();
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getValidCommunities(baseURL)
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.forEach(community -> {
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int page = -1;
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int size = 100;
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ContentModel cm = new ContentModel();
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do {
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page++;
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try {
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cm = MAPPER
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.readValue(
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QueryCommunityAPI
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.communityProjects(
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community.getId(), String.valueOf(page), String.valueOf(size), baseURL),
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ContentModel.class);
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if (cm.getContent().size() > 0) {
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cm.getContent().forEach(p -> {
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if (!projectMap.keySet().contains("40|" + p.getOpenaireId()))
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projectMap.put("40|" + p.getOpenaireId(), new ArrayList<>());
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projectMap.get("40|" + p.getOpenaireId()).add(community.getId());
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});
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}
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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} while (!cm.getLast());
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});
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return projectMap;
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}
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}
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@ -0,0 +1,43 @@
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package eu.dnetlib.dhp.api.model;
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import com.fasterxml.jackson.annotation.JsonAutoDetect;
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import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
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@JsonAutoDetect
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@JsonIgnoreProperties(ignoreUnknown = true)
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public class CommunityContentprovider {
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private String openaireId;
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private SelectionConstraints selectioncriteria;
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private String enabled;
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public String getEnabled() {
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return enabled;
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}
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public void setEnabled(String enabled) {
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this.enabled = enabled;
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}
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public String getOpenaireId() {
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return openaireId;
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}
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public void setOpenaireId(final String openaireId) {
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this.openaireId = openaireId;
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}
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public SelectionConstraints getSelectioncriteria() {
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return this.selectioncriteria;
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}
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public void setSelectioncriteria(SelectionConstraints selectioncriteria) {
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this.selectioncriteria = selectioncriteria;
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}
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}
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@ -1,13 +1,13 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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package eu.dnetlib.dhp.api.model;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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public class OrganizationMap extends HashMap<String, List<String>> {
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public class CommunityEntityMap extends HashMap<String, List<String>> {
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public OrganizationMap() {
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public CommunityEntityMap() {
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super();
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}
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|
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@ -0,0 +1,108 @@
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package eu.dnetlib.dhp.api.model;
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import java.io.Serializable;
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import java.util.List;
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import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
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import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
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/**
|
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* @author miriam.baglioni
|
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* @Date 06/10/23
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*/
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@JsonIgnoreProperties(ignoreUnknown = true)
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public class CommunityModel implements Serializable {
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private String id;
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private String type;
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private String status;
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private String zenodoCommunity;
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private List<String> subjects;
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private List<String> otherZenodoCommunities;
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private List<String> fos;
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private List<String> sdg;
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private SelectionConstraints advancedConstraints;
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private SelectionConstraints removeConstraints;
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|
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public String getZenodoCommunity() {
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return zenodoCommunity;
|
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}
|
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public void setZenodoCommunity(String zenodoCommunity) {
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this.zenodoCommunity = zenodoCommunity;
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}
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public List<String> getSubjects() {
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return subjects;
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||||
}
|
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|
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public void setSubjects(List<String> subjects) {
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this.subjects = subjects;
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}
|
||||
|
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public List<String> getOtherZenodoCommunities() {
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return otherZenodoCommunities;
|
||||
}
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public void setOtherZenodoCommunities(List<String> otherZenodoCommunities) {
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this.otherZenodoCommunities = otherZenodoCommunities;
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}
|
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|
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public List<String> getFos() {
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return fos;
|
||||
}
|
||||
|
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public void setFos(List<String> fos) {
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this.fos = fos;
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}
|
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|
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public List<String> getSdg() {
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return sdg;
|
||||
}
|
||||
|
||||
public void setSdg(List<String> 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;
|
||||
}
|
||||
}
|
|
@ -0,0 +1,15 @@
|
|||
|
||||
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<CommunityModel> implements Serializable {
|
||||
public CommunitySummary() {
|
||||
super();
|
||||
}
|
||||
}
|
|
@ -0,0 +1,51 @@
|
|||
|
||||
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<ProjectModel> content;
|
||||
private Integer totalPages;
|
||||
private Boolean last;
|
||||
private Integer number;
|
||||
|
||||
public List<ProjectModel> getContent() {
|
||||
return content;
|
||||
}
|
||||
|
||||
public void setContent(List<ProjectModel> 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;
|
||||
}
|
||||
}
|
|
@ -0,0 +1,13 @@
|
|||
|
||||
package eu.dnetlib.dhp.api.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import eu.dnetlib.dhp.api.model.CommunityContentprovider;
|
||||
|
||||
public class DatasourceList extends ArrayList<CommunityContentprovider> implements Serializable {
|
||||
public DatasourceList() {
|
||||
super();
|
||||
}
|
||||
}
|
|
@ -0,0 +1,16 @@
|
|||
|
||||
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<String> implements Serializable {
|
||||
|
||||
public OrganizationList() {
|
||||
super();
|
||||
}
|
||||
}
|
|
@ -0,0 +1,24 @@
|
|||
|
||||
package eu.dnetlib.dhp.api.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||
|
||||
/**
|
||||
* @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;
|
||||
}
|
||||
}
|
|
@ -9,7 +9,6 @@ import java.util.*;
|
|||
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;
|
||||
|
@ -21,8 +20,11 @@ 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.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||
|
@ -54,50 +56,39 @@ 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 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));
|
||||
|
||||
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<? extends Result> resultClazz = (Class<? extends Result>) 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 = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
|
||||
cc = Utils.getCommunityConfiguration(baseURL);
|
||||
log.info(OBJECT_MAPPER.writeValueAsString(cc));
|
||||
}
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
extendCommunityConfigurationForEOSC(spark, inputPath, cc);
|
||||
execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
|
||||
execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
|
||||
});
|
||||
}
|
||||
|
||||
|
@ -106,10 +97,7 @@ public class SparkBulkTagJob {
|
|||
|
||||
Dataset<String> datasources = readPath(
|
||||
spark, inputPath
|
||||
.substring(
|
||||
0,
|
||||
inputPath.lastIndexOf("/"))
|
||||
+ "/datasource",
|
||||
+ "datasource",
|
||||
Datasource.class)
|
||||
.filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds))
|
||||
.map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING());
|
||||
|
@ -117,10 +105,10 @@ public class SparkBulkTagJob {
|
|||
Map<String, List<Pair<String, SelectionConstraints>>> 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<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>();
|
||||
dsm.put(dsId, eoscList);
|
||||
dsm.put(ds, eoscList);
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -142,22 +130,30 @@ public class SparkBulkTagJob {
|
|||
String inputPath,
|
||||
String outputPath,
|
||||
ProtoMap protoMappingParams,
|
||||
Class<R> resultClazz,
|
||||
CommunityConfiguration communityConfiguration) {
|
||||
|
||||
ResultTagger resultTagger = new ResultTagger();
|
||||
readPath(spark, inputPath, resultClazz)
|
||||
.map(patchResult(), Encoders.bean(resultClazz))
|
||||
.filter(Objects::nonNull)
|
||||
.map(
|
||||
(MapFunction<R, R>) 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<R> resultClazz = ModelSupport.entityTypes.get(e);
|
||||
readPath(spark, inputPath + e.name(), resultClazz)
|
||||
.map(patchResult(), Encoders.bean(resultClazz))
|
||||
.filter(Objects::nonNull)
|
||||
.map(
|
||||
(MapFunction<R, R>) value -> resultTagger
|
||||
.enrichContextCriteria(
|
||||
value, communityConfiguration, protoMappingParams),
|
||||
Encoders.bean(resultClazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + e.name());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
public static <R> Dataset<R> readPath(
|
||||
|
|
|
@ -4,6 +4,7 @@ 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;
|
||||
|
||||
|
@ -13,7 +14,7 @@ public class Community implements Serializable {
|
|||
private String id;
|
||||
private List<String> subjects = new ArrayList<>();
|
||||
private List<Provider> providers = new ArrayList<>();
|
||||
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
|
||||
private List<String> zenodoCommunities = new ArrayList<>();
|
||||
private SelectionConstraints constraints = new SelectionConstraints();
|
||||
private SelectionConstraints removeConstraints = new SelectionConstraints();
|
||||
|
||||
|
@ -26,7 +27,7 @@ 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 +54,11 @@ public class Community implements Serializable {
|
|||
this.providers = providers;
|
||||
}
|
||||
|
||||
public List<ZenodoCommunity> getZenodoCommunities() {
|
||||
public List<String> getZenodoCommunities() {
|
||||
return zenodoCommunities;
|
||||
}
|
||||
|
||||
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
|
||||
public void setZenodoCommunities(List<String> zenodoCommunities) {
|
||||
this.zenodoCommunities = zenodoCommunities;
|
||||
}
|
||||
|
||||
|
|
|
@ -81,7 +81,7 @@ public class CommunityConfiguration implements Serializable {
|
|||
this.removeConstraintsMap = removeConstraintsMap;
|
||||
}
|
||||
|
||||
CommunityConfiguration(final Map<String, Community> communities) {
|
||||
public CommunityConfiguration(final Map<String, Community> 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());
|
||||
|
|
|
@ -143,16 +143,16 @@ public class CommunityConfigurationFactory {
|
|||
return providerList;
|
||||
}
|
||||
|
||||
private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {
|
||||
private static List<String> parseZenodoCommunities(final Node node) {
|
||||
|
||||
final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
|
||||
final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>();
|
||||
final List<String> 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());
|
||||
|
|
|
@ -4,6 +4,8 @@ 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;
|
||||
|
||||
|
@ -12,6 +14,7 @@ public class Constraint implements Serializable {
|
|||
private String field;
|
||||
private String value;
|
||||
// private String element;
|
||||
@JsonIgnore
|
||||
private Selection selection;
|
||||
|
||||
public String getVerb() {
|
||||
|
@ -38,10 +41,11 @@ public class Constraint implements Serializable {
|
|||
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 +56,4 @@ public class Constraint implements Serializable {
|
|||
return selection.apply(metadata);
|
||||
}
|
||||
|
||||
// public String getElement() {
|
||||
// return element;
|
||||
// }
|
||||
//
|
||||
// public void setElement(String element) {
|
||||
// this.element = element;
|
||||
// }
|
||||
}
|
||||
|
|
|
@ -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<String> res = isLookUp
|
||||
.quickSearchProfile(
|
||||
IOUtils
|
||||
.toString(
|
||||
QueryInformationSystem.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/bulktag/query.xq")));
|
||||
|
||||
final String xmlConf = "<communities>" + Joiner.on(" ").join(res) + "</communities>";
|
||||
|
||||
return CommunityConfigurationFactory.newInstance(xmlConf);
|
||||
}
|
||||
}
|
|
@ -82,19 +82,23 @@ public class ResultTagger implements Serializable {
|
|||
// communities contains all the communities to be not added to the context
|
||||
final Set<String> 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<String> 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());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -7,11 +7,13 @@ 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<Constraints> criteria;
|
||||
|
||||
|
|
|
@ -9,9 +9,7 @@ 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.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;
|
||||
|
@ -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;
|
||||
|
@ -48,10 +48,10 @@ 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 String baseURL = parser.get("baseURL");
|
||||
log.info("baseURL: {}", baseURL);
|
||||
|
||||
final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(baseURL);
|
||||
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
@ -70,7 +70,7 @@ public class PrepareResultCommunitySet {
|
|||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
OrganizationMap organizationMap) {
|
||||
CommunityEntityMap organizationMap) {
|
||||
|
||||
Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
|
||||
relation.createOrReplaceTempView("relation");
|
||||
|
@ -115,7 +115,7 @@ public class PrepareResultCommunitySet {
|
|||
}
|
||||
|
||||
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
|
||||
OrganizationMap organizationMap) {
|
||||
CommunityEntityMap organizationMap) {
|
||||
return value -> {
|
||||
String rId = value.getResultId();
|
||||
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
|
||||
|
|
|
@ -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;
|
||||
|
@ -53,29 +54,14 @@ public class SparkResultToCommunityFromOrganizationJob {
|
|||
final String possibleupdatespath = parser.get("preparedInfoPath");
|
||||
log.info("preparedInfoPath: {}", possibleupdatespath);
|
||||
|
||||
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<? extends Result> resultClazz = (Class<? extends Result>) 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);
|
||||
if (saveGraph) {
|
||||
execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
|
||||
}
|
||||
execPropagation(spark, inputPath, outputPath, possibleupdatespath);
|
||||
|
||||
});
|
||||
}
|
||||
|
||||
|
@ -83,22 +69,32 @@ public class SparkResultToCommunityFromOrganizationJob {
|
|||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
Class<R> resultClazz,
|
||||
String possibleUpdatesPath) {
|
||||
|
||||
Dataset<ResultCommunityList> possibleUpdates = readPath(spark, possibleUpdatesPath, ResultCommunityList.class);
|
||||
Dataset<R> 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<R> resultClazz = ModelSupport.entityTypes.get(e);
|
||||
removeOutputDir(spark, outputPath + e.name());
|
||||
Dataset<R> 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 <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> resultCommunityFn() {
|
||||
|
|
|
@ -0,0 +1,123 @@
|
|||
|
||||
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.*;
|
||||
|
||||
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 String baseURL = parser.get("baseURL");
|
||||
log.info("baseUEL: {}", baseURL);
|
||||
|
||||
final CommunityEntityMap projectsMap = Utils.getCommunityProjects(baseURL);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
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<Row, String>) r -> (String) r.getAs("resultId"), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Row, ResultProjectList>) (k, v) -> {
|
||||
ResultProjectList rpl = new ResultProjectList();
|
||||
rpl.setResultId(k);
|
||||
ArrayList<String> cl = new ArrayList<>();
|
||||
cl.addAll(projectMap.get(v.next().getAs("projectId")));
|
||||
v.forEachRemaining(r -> {
|
||||
projectMap
|
||||
.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")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
}
|
|
@ -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<String> communityList;
|
||||
|
||||
public String getResultId() {
|
||||
return resultId;
|
||||
}
|
||||
|
||||
public void setResultId(String resultId) {
|
||||
this.resultId = resultId;
|
||||
}
|
||||
|
||||
public ArrayList<String> getCommunityList() {
|
||||
return communityList;
|
||||
}
|
||||
|
||||
public void setCommunityList(ArrayList<String> communityList) {
|
||||
this.communityList = communityList;
|
||||
}
|
||||
}
|
|
@ -0,0 +1,163 @@
|
|||
|
||||
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;
|
||||
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);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
|
||||
execPropagation(spark, inputPath, outputPath, possibleupdatespath);
|
||||
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result> void execPropagation(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath,
|
||||
|
||||
String possibleUpdatesPath) {
|
||||
|
||||
Dataset<ResultProjectList> possibleUpdates = readPath(spark, possibleUpdatesPath, ResultProjectList.class);
|
||||
|
||||
ModelSupport.entityTypes
|
||||
.keySet()
|
||||
.parallelStream()
|
||||
.forEach(e -> {
|
||||
if (ModelSupport.isResult(e)) {
|
||||
removeOutputDir(spark, outputPath + e.name());
|
||||
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
|
||||
Dataset<R> 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 <R extends Result> MapFunction<Tuple2<R, ResultProjectList>, R> resultCommunityFn() {
|
||||
return value -> {
|
||||
R ret = value._1();
|
||||
Optional<ResultProjectList> rcl = Optional.ofNullable(value._2());
|
||||
if (rcl.isPresent()) {
|
||||
// ArrayList<String> communitySet = rcl.get().getCommunityList();
|
||||
List<String> contextList = ret
|
||||
.getContext()
|
||||
.stream()
|
||||
.map(Context::getId)
|
||||
.collect(Collectors.toList());
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
R res = (R) ret.getClass().newInstance();
|
||||
|
||||
res.setId(ret.getId());
|
||||
List<Context> propagatedContexts = new ArrayList<>();
|
||||
for (String cId : rcl.get().getCommunityList()) {
|
||||
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);
|
||||
} 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);
|
||||
ret.mergeFrom(res);
|
||||
}
|
||||
return ret;
|
||||
};
|
||||
}
|
||||
}
|
|
@ -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": "bu",
|
||||
"paramLongName": "baseURL",
|
||||
"paramDescription": "this parameter is to specify the api to be queried (beta or production)",
|
||||
"paramRequired": false
|
||||
}
|
||||
|
||||
]
|
|
@ -4,10 +4,6 @@
|
|||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookUpUrl</name>
|
||||
<description>the isLookup service endpoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>pathMap</name>
|
||||
<description>the json path associated to each selection field</description>
|
||||
|
@ -44,7 +40,7 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
<start to="exec_bulktag"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
@ -102,16 +98,9 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="copy_wait" to="fork_exec_bulktag"/>
|
||||
<join name="copy_wait" to="exec_bulktag"/>
|
||||
|
||||
<fork name="fork_exec_bulktag">
|
||||
<path start="bulktag_publication"/>
|
||||
<path start="bulktag_dataset"/>
|
||||
<path start="bulktag_otherresearchproduct"/>
|
||||
<path start="bulktag_software"/>
|
||||
</fork>
|
||||
|
||||
<action name="bulktag_publication">
|
||||
<action name="exec_bulktag">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
@ -128,98 +117,15 @@
|
|||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/</arg>
|
||||
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--production</arg><arg>${production}</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="bulktag_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-dataset</name>
|
||||
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="bulktag_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-orp</name>
|
||||
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="bulktag_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-software</name>
|
||||
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait" to="End"/>
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
|
|
|
@ -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
|
||||
<community>
|
||||
{ $x//CONFIGURATION/context/@id}
|
||||
<removeConstraints>
|
||||
{$x//CONFIGURATION/context/param[./@name='removeConstraints']/text() }
|
||||
</removeConstraints>
|
||||
<advancedConstraints>
|
||||
{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() }
|
||||
</advancedConstraints>
|
||||
<subjects>
|
||||
{for $y in tokenize($subj,',')
|
||||
return
|
||||
<subject>{$y}</subject>}
|
||||
{for $y in tokenize($fos,',')
|
||||
return
|
||||
<subject>{$y}</subject>}
|
||||
{for $y in tokenize($sdg,',')
|
||||
return
|
||||
<subject>{$y}</subject>}
|
||||
</subjects>
|
||||
<datasources>
|
||||
{for $d in $datasources
|
||||
where $d/param[./@name='enabled']/text()='true'
|
||||
return
|
||||
<datasource>
|
||||
<openaireId>
|
||||
{$d//param[./@name='openaireId']/text()}
|
||||
</openaireId>
|
||||
<selcriteria>
|
||||
{$d/param[./@name='selcriteria']/text()}
|
||||
</selcriteria>
|
||||
</datasource> }
|
||||
</datasources>
|
||||
<zenodocommunities>
|
||||
{for $zc in $zenodo
|
||||
return
|
||||
<zenodocommunity>
|
||||
<zenodoid>
|
||||
{$zc}
|
||||
</zenodoid>
|
||||
</zenodocommunity>}
|
||||
{for $zc in $communities
|
||||
return
|
||||
<zenodocommunity>
|
||||
<zenodoid>
|
||||
{$zc/param[./@name='zenodoid']/text()}
|
||||
</zenodoid>
|
||||
<selcriteria>
|
||||
{$zc/param[./@name='selcriteria']/text()}
|
||||
</selcriteria>
|
||||
</zenodocommunity>}
|
||||
</zenodocommunities>
|
||||
</community>
|
|
@ -5,24 +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":"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",
|
||||
|
@ -35,12 +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",
|
||||
|
|
|
@ -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": "bu",
|
||||
"paramLongName": "baseURL",
|
||||
"paramDescription": "the base URL to the community API to use",
|
||||
"paramRequired": false
|
||||
}
|
||||
|
||||
]
|
|
@ -4,10 +4,7 @@
|
|||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>organizationtoresultcommunitymap</name>
|
||||
<description>organization community map</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the output path</description>
|
||||
|
@ -25,7 +22,7 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
<start to="prepare_result_communitylist"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
@ -93,33 +90,28 @@
|
|||
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=6
|
||||
--executor-memory=5G
|
||||
--conf spark.executor.memoryOverhead=3g
|
||||
--conf spark.sql.shuffle.partitions=3284
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
|
||||
<arg>--production</arg><arg>${production}</arg>
|
||||
</spark>
|
||||
<ok to="fork-join-exec-propagation"/>
|
||||
<ok to="exec-propagation"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork-join-exec-propagation">
|
||||
<path start="join_propagate_publication"/>
|
||||
<path start="join_propagate_dataset"/>
|
||||
<path start="join_propagate_otherresearchproduct"/>
|
||||
<path start="join_propagate_software"/>
|
||||
</fork>
|
||||
|
||||
<action name="join_propagate_publication">
|
||||
<action name="exec-propagation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
|
@ -127,115 +119,26 @@
|
|||
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--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.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>community2resultfromorganization-Dataset</name>
|
||||
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${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}
|
||||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>community2resultfromorganization-ORP</name>
|
||||
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>community2resultfromorganization-Software</name>
|
||||
<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${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}
|
||||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait2" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
|
|
|
@ -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
|
||||
}
|
||||
|
||||
]
|
|
@ -0,0 +1,28 @@
|
|||
[
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the path of the sequencial file to read",
|
||||
"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": "bu",
|
||||
"paramLongName": "baseURL",
|
||||
"paramDescription": "the path used to store temporary output files",
|
||||
"paramRequired": false
|
||||
}
|
||||
|
||||
]
|
|
@ -0,0 +1,58 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorNumber</name>
|
||||
<value>4</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<value>15G</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<value>6G</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<value>1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2MaxExecutors</name>
|
||||
<value>50</value>
|
||||
</property>
|
||||
</configuration>
|
|
@ -0,0 +1,144 @@
|
|||
<workflow-app name="community_to_result_propagation_project" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the output path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="reset_outputpath">
|
||||
<fs>
|
||||
<delete path="${outputPath}"/>
|
||||
<mkdir path="${outputPath}"/>
|
||||
</fs>
|
||||
<ok to="copy_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="copy_entities">
|
||||
<path start="copy_relation"/>
|
||||
<path start="copy_organization"/>
|
||||
<path start="copy_projects"/>
|
||||
<path start="copy_datasources"/>
|
||||
</fork>
|
||||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="copy_wait" to="prepare_result_communitylist"/>
|
||||
|
||||
<action name="prepare_result_communitylist">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Prepare-Community-Result-Organization</name>
|
||||
<class>eu.dnetlib.dhp.resulttocommunityfromproject.PrepareResultCommunitySet</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--production</arg><arg>${production}</arg>
|
||||
</spark>
|
||||
<ok to="exec-propagation"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="exec-propagation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>community2resultfromproject</name>
|
||||
<class>eu.dnetlib.dhp.resulttocommunityfromproject.SparkResultToCommunityFromProject</class>
|
||||
<jar>dhp-enrichment-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=6
|
||||
--executor-memory=5G
|
||||
--conf spark.executor.memoryOverhead=3g
|
||||
--conf spark.sql.shuffle.partitions=3284
|
||||
--driver-memory=${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}
|
||||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
|
@ -31,8 +31,6 @@ public class BulkTagJobTest {
|
|||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp";
|
||||
|
||||
public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\","
|
||||
+ " \"title\" : \"$['title'][*]['value']\","
|
||||
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||
|
@ -42,7 +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;
|
||||
|
||||
|
@ -98,14 +98,11 @@ 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 +130,16 @@ 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 +224,19 @@ 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 +305,18 @@ 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 +378,25 @@ 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<OtherResearchProduct> 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 +499,18 @@ 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
|
||||
});
|
||||
|
||||
|
@ -539,6 +533,7 @@ public class BulkTagJobTest {
|
|||
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||
|
||||
Assertions.assertEquals(7, idExplodeCommunity.count());
|
||||
|
||||
Assertions
|
||||
|
@ -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());
|
||||
|
@ -1568,4 +1563,41 @@ public class BulkTagJobTest {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
void newConfTest() throws Exception {
|
||||
final String pathMap = BulkTagJobTest.pathMap;
|
||||
SparkBulkTagJob
|
||||
.main(
|
||||
new String[] {
|
||||
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-sourcePath",
|
||||
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(),
|
||||
"-outputPath", workingDir.toString() + "/",
|
||||
// "-baseURL", "https://services.openaire.eu/openaire/community/",
|
||||
"-pathMap", pathMap,
|
||||
"-taggingConf", taggingConf
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Dataset> tmp = sc
|
||||
.textFile(workingDir.toString() + "/dataset")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
|
||||
Assertions.assertEquals(10, tmp.count());
|
||||
org.apache.spark.sql.Dataset<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());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -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));
|
||||
}
|
||||
|
|
|
@ -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", "",
|
||||
"-saveGraph", "true",
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||
"-outputPath", workingDir.toString() + "/dataset",
|
||||
|
||||
"-outputPath", workingDir.toString() + "/",
|
||||
"-preparedInfoPath", preparedInfoPath
|
||||
});
|
||||
|
||||
|
|
|
@ -0,0 +1,133 @@
|
|||
|
||||
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 java.util.List;
|
||||
|
||||
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.Context;
|
||||
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<Dataset> tmp = sc
|
||||
.textFile(workingDir.toString() + "/dataset")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||
|
||||
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> 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"));
|
||||
}
|
||||
}
|
|
@ -26,7 +26,7 @@
|
|||
<subjects/>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::a507cdacc5bbcc08761c92185dee5cab</openaireId>
|
||||
<openaireId>10|re3data_____::a507cdacc5bbcc08761c92185dee5cab</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -140,39 +140,39 @@
|
|||
</subjects>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::9ebe127e5f3a0bf401875690f3bb6b81</openaireId>
|
||||
<openaireId>10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::c6cd4b532e12868c1d760a8d7cda6815</openaireId>
|
||||
<openaireId>10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b</openaireId>
|
||||
<openaireId>10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::6eb31d13b12bc06bbac06aef63cf33c9</openaireId>
|
||||
<openaireId>10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::0da84e9dfdc8419576169e027baa8028</openaireId>
|
||||
<openaireId>10|doajarticles::0da84e9dfdc8419576169e027baa8028</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::84e123776089ce3c7a33db98d9cd15a8</openaireId>
|
||||
<openaireId>10|re3data_____::84e123776089ce3c7a33db98d9cd15a8</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>openaire____::c5502a43e76feab55dd00cf50f519125</openaireId>
|
||||
<openaireId>10|openaire____::c5502a43e76feab55dd00cf50f519125</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::a48f09c562b247a9919acfe195549b47</openaireId>
|
||||
<openaireId>10|re3data_____::a48f09c562b247a9919acfe195549b47</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::97275a23ca44226c9964043c8462be96</openaireId>
|
||||
<openaireId>10|opendoar____::97275a23ca44226c9964043c8462be96</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -287,55 +287,55 @@
|
|||
</subjects>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::8cec81178926caaca531afbd8eb5d64c</openaireId>
|
||||
<openaireId>10|doajarticles::8cec81178926caaca531afbd8eb5d64c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::0f7a7f30b5400615cae1829f3e743982</openaireId>
|
||||
<openaireId>10|doajarticles::0f7a7f30b5400615cae1829f3e743982</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::9740f7f5af3e506d2ad2c215cdccd51a</openaireId>
|
||||
<openaireId>10|doajarticles::9740f7f5af3e506d2ad2c215cdccd51a</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::9f3fbaae044fa33cb7069b72935a3254</openaireId>
|
||||
<openaireId>10|doajarticles::9f3fbaae044fa33cb7069b72935a3254</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::cb67f33eb9819f5c624ce0313957f6b3</openaireId>
|
||||
<openaireId>10|doajarticles::cb67f33eb9819f5c624ce0313957f6b3</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::e21c97cbb7a209afc75703681c462906</openaireId>
|
||||
<openaireId>10|doajarticles::e21c97cbb7a209afc75703681c462906</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::554cde3be9e5c4588b4c4f9f503120cb</openaireId>
|
||||
<openaireId>10|doajarticles::554cde3be9e5c4588b4c4f9f503120cb</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>tubitakulakb::11e22f49e65b9fd11d5b144b93861a1b</openaireId>
|
||||
<openaireId>10|tubitakulakb::11e22f49e65b9fd11d5b144b93861a1b</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::57c5d3837da943e93b28ec4db82ec7a5</openaireId>
|
||||
<openaireId>10|doajarticles::57c5d3837da943e93b28ec4db82ec7a5</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::a186f5ddb8e8c7ecc992ef51cf3315b1</openaireId>
|
||||
<openaireId>10|doajarticles::a186f5ddb8e8c7ecc992ef51cf3315b1</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::e21c97cbb7a209afc75703681c462906</openaireId>
|
||||
<openaireId>10|doajarticles::e21c97cbb7a209afc75703681c462906</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::dca64612dfe0963fffc119098a319957</openaireId>
|
||||
<openaireId>10|doajarticles::dca64612dfe0963fffc119098a319957</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::dd70e44479f0ade25aa106aef3e87a0a</openaireId>
|
||||
<openaireId>10|doajarticles::dd70e44479f0ade25aa106aef3e87a0a</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -406,27 +406,27 @@
|
|||
</subjects>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::5b9bf9171d92df854cf3c520692e9122</openaireId>
|
||||
<openaireId>10|re3data_____::5b9bf9171d92df854cf3c520692e9122</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::c7d3de67dc77af72f6747157441252ec</openaireId>
|
||||
<openaireId>10|doajarticles::c7d3de67dc77af72f6747157441252ec</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>re3data_____::8515794670370f49c1d176c399c714f5</openaireId>
|
||||
<openaireId>10|re3data_____::8515794670370f49c1d176c399c714f5</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::d640648c84b10d425f96f11c3de468f3</openaireId>
|
||||
<openaireId>10|doajarticles::d640648c84b10d425f96f11c3de468f3</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a</openaireId>
|
||||
<openaireId>10|doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>rest________::fb1a3d4523c95e63496e3bc7ba36244b</openaireId>
|
||||
<openaireId>10|rest________::fb1a3d4523c95e63496e3bc7ba36244b</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -743,27 +743,27 @@
|
|||
</subjects>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::1a551829d50f1400b0dab21fdd969c04</openaireId>
|
||||
<openaireId>10|opendoar____::1a551829d50f1400b0dab21fdd969c04</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::49af6c4e558a7569d80eee2e035e2bd7</openaireId>
|
||||
<openaireId>10|opendoar____::49af6c4e558a7569d80eee2e035e2bd7</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::0266e33d3f546cb5436a10798e657d97</openaireId>
|
||||
<openaireId>10|opendoar____::0266e33d3f546cb5436a10798e657d97</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::fd4c2dc64ccb8496e6f1f94c85f30d06</openaireId>
|
||||
<openaireId>10|opendoar____::fd4c2dc64ccb8496e6f1f94c85f30d06</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::41bfd20a38bb1b0bec75acf0845530a7</openaireId>
|
||||
<openaireId>10|opendoar____::41bfd20a38bb1b0bec75acf0845530a7</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::87ae6fb631f7c8a627e8e28785d9992d</openaireId>
|
||||
<openaireId>10|opendoar____::87ae6fb631f7c8a627e8e28785d9992d</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -983,11 +983,11 @@
|
|||
<subjects/>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::7e7757b1e12abcb736ab9a754ffb617a</openaireId>
|
||||
<openaireId>10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a</openaireId>
|
||||
<selcriteria>{"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]}</selcriteria>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>opendoar____::96da2f590cd7246bbde0051047b0d6f7</openaireId>
|
||||
<openaireId>10|opendoar____::96da2f590cd7246bbde0051047b0d6f7</openaireId>
|
||||
<selcriteria>{"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]}</selcriteria>
|
||||
</datasource>
|
||||
</datasources>
|
||||
|
@ -1166,87 +1166,87 @@
|
|||
</subjects>
|
||||
<datasources>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::1c5bdf8fca58937894ad1441cca99b76</openaireId>
|
||||
<openaireId>10|doajarticles::1c5bdf8fca58937894ad1441cca99b76</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::b37a634324a45c821687e6e80e6f53b4</openaireId>
|
||||
<openaireId>10|doajarticles::b37a634324a45c821687e6e80e6f53b4</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::4bf64f2a104040e4e055cd9594b2d77c</openaireId>
|
||||
<openaireId>10|doajarticles::4bf64f2a104040e4e055cd9594b2d77c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::479ca537c12755d1868bbf02938a900c</openaireId>
|
||||
<openaireId>10|doajarticles::479ca537c12755d1868bbf02938a900c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::55f31df96a60e2309f45b7c265fcf7a2</openaireId>
|
||||
<openaireId>10|doajarticles::55f31df96a60e2309f45b7c265fcf7a2</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::c52a09891a5301f9986ebbfe3761810c</openaireId>
|
||||
<openaireId>10|doajarticles::c52a09891a5301f9986ebbfe3761810c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::379807bc7f6c71a227ef1651462c414c</openaireId>
|
||||
<openaireId>10|doajarticles::379807bc7f6c71a227ef1651462c414c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::36069db531a00b85a2e8fb301f4bdc19</openaireId>
|
||||
<openaireId>10|doajarticles::36069db531a00b85a2e8fb301f4bdc19</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::b6a898da311ded96fabf49c520b80d5d</openaireId>
|
||||
<openaireId>10|doajarticles::b6a898da311ded96fabf49c520b80d5d</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::d0753d9180b35a271d8b4a31f449749f</openaireId>
|
||||
<openaireId>10|doajarticles::d0753d9180b35a271d8b4a31f449749f</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::172050a92511838393a3fe237ae47e31</openaireId>
|
||||
<openaireId>10|doajarticles::172050a92511838393a3fe237ae47e31</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::301ed96c62abb160a3e29796efe5c95c</openaireId>
|
||||
<openaireId>10|doajarticles::301ed96c62abb160a3e29796efe5c95c</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::0f4f805b3d842f2c7f1b077c3426fa59</openaireId>
|
||||
<openaireId>10|doajarticles::0f4f805b3d842f2c7f1b077c3426fa59</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::ba73728b84437b8d48ae287b867c7215</openaireId>
|
||||
<openaireId>10|doajarticles::ba73728b84437b8d48ae287b867c7215</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
<openaireId>doajarticles::86faef424d804309ccf45f692523aa48</openaireId>
|
||||
<openaireId>10|doajarticles::86faef424d804309ccf45f692523aa48</openaireId>
|
||||
<selcriteria/>
|
||||
</datasource>
|
||||
<datasource>
|
||||
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@ -1345,87 +1345,87 @@
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@ -1454,81 +1454,81 @@
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|
|
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|
@ -0,0 +1,36 @@
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