[stats wf] indicators across stats dbs & updates in the org ids #248
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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_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_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_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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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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@ -4,22 +4,18 @@ package eu.dnetlib.dhp.api;
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import java.io.BufferedReader;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.InputStreamReader;
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import java.io.OutputStream;
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import java.net.HttpURLConnection;
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import java.net.HttpURLConnection;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.net.URL;
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import org.apache.http.HttpHeaders;
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import org.jetbrains.annotations.NotNull;
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import org.jetbrains.annotations.NotNull;
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import com.google.gson.Gson;
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/**
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/**
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* @author miriam.baglioni
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* @author miriam.baglioni
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* @Date 06/10/23
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* @Date 06/10/23
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*/
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*/
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public class QueryCommunityAPI {
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public class QueryCommunityAPI {
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private static final String baseUrl = "https://services.openaire.eu/openaire/";
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private static final String PRODUCTION_BASE_URL = "https://services.openaire.eu/openaire/";
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private static final String BETA_BASE_URL = "https://beta.services.openaire.eu/openaire/";
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private static String get(String geturl) throws IOException {
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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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URL url = new URL(geturl);
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@ -36,25 +32,35 @@ public class QueryCommunityAPI {
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return body;
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return body;
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}
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}
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public static String communities() throws IOException {
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public static String communities(boolean production) throws IOException {
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return get(baseUrl + "community/communities");
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if (production)
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return get(PRODUCTION_BASE_URL + "community/communities");
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return get(BETA_BASE_URL + "community/communities");
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}
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}
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public static String community(String id) throws IOException {
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public static String community(String id, boolean production) throws IOException {
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return get(baseUrl + "community/" + id);
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if (production)
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return get(PRODUCTION_BASE_URL + "community/" + id);
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return get(BETA_BASE_URL + "community/" + id);
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}
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}
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public static String communityDatasource(String id) throws IOException {
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public static String communityDatasource(String id, boolean production) throws IOException {
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return get(baseUrl + "community/" + id + "/contentproviders");
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if (production)
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return get(PRODUCTION_BASE_URL + "community/" + id + "/contentproviders");
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return (BETA_BASE_URL + "community/" + id + "/contentproviders");
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}
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}
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public static String communityPropagationOrganization(String id) throws IOException {
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public static String communityPropagationOrganization(String id, boolean production) throws IOException {
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return get(baseUrl + "community/" + id + "/propagationOrganizations");
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if (production)
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return get(PRODUCTION_BASE_URL + "community/" + id + "/propagationOrganizations");
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return get(BETA_BASE_URL + "community/" + id + "/propagationOrganizations");
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}
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}
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public static String communityProjects(String id, String page, String size) throws IOException {
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public static String communityProjects(String id, String page, String size, boolean production) throws IOException {
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return get(baseUrl + "community/" + id + "/projects/" + page + "/" + size);
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if (production)
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return get(PRODUCTION_BASE_URL + "community/" + id + "/projects/" + page + "/" + size);
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return get(BETA_BASE_URL + "community/" + id + "/projects/" + page + "/" + size);
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}
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}
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@NotNull
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@NotNull
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@ -30,14 +30,14 @@ public class Utils implements Serializable {
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private static final ObjectMapper MAPPER = new ObjectMapper();
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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 VerbResolver resolver = VerbResolverFactory.newInstance();
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public static CommunityConfiguration getCommunityConfiguration() throws IOException {
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public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException {
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final Map<String, Community> communities = Maps.newHashMap();
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final Map<String, Community> communities = Maps.newHashMap();
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List<Community> validCommunities = new ArrayList<>();
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List<Community> validCommunities = new ArrayList<>();
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getValidCommunities()
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getValidCommunities(production)
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.forEach(community -> {
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.forEach(community -> {
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try {
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try {
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CommunityModel cm = MAPPER
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CommunityModel cm = MAPPER
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.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class);
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.readValue(QueryCommunityAPI.community(community.getId(), production), CommunityModel.class);
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validCommunities.add(getCommunity(cm));
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validCommunities.add(getCommunity(cm));
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} catch (IOException e) {
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} catch (IOException e) {
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throw new RuntimeException(e);
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throw new RuntimeException(e);
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@ -46,10 +46,11 @@ public class Utils implements Serializable {
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validCommunities.forEach(community -> {
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validCommunities.forEach(community -> {
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try {
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try {
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DatasourceList dl = MAPPER
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DatasourceList dl = MAPPER
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.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class);
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.readValue(
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QueryCommunityAPI.communityDatasource(community.getId(), production), DatasourceList.class);
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community.setProviders(dl.stream().map(d -> {
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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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if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
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// return null;
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return null;
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Provider p = new Provider();
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Provider p = new Provider();
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p.setOpenaireId("10|" + d.getOpenaireId());
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p.setOpenaireId("10|" + d.getOpenaireId());
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p.setSelectionConstraints(d.getSelectioncriteria());
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p.setSelectionConstraints(d.getSelectioncriteria());
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@ -80,18 +81,20 @@ public class Utils implements Serializable {
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c.setSubjects(cm.getSubjects());
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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.getFos());
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c.getSubjects().addAll(cm.getSdg());
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c.getSubjects().addAll(cm.getSdg());
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c.setConstraints(cm.getAdvancedConstraints());
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if (cm.getAdvancedConstraints() != null) {
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if (c.getConstraints() != null)
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c.setConstraints(cm.getAdvancedConstraints());
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c.getConstraints().setSelection(resolver);
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c.getConstraints().setSelection(resolver);
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c.setRemoveConstraints(cm.getRemoveConstraints());
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}
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if (c.getRemoveConstraints() != null)
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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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c.getRemoveConstraints().setSelection(resolver);
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}
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return c;
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return c;
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}
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}
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public static List<CommunityModel> getValidCommunities() throws IOException {
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public static List<CommunityModel> getValidCommunities(boolean production) throws IOException {
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return MAPPER
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return MAPPER
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.readValue(QueryCommunityAPI.communities(), CommunitySummary.class)
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.readValue(QueryCommunityAPI.communities(production), CommunitySummary.class)
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.stream()
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.stream()
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.filter(
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.filter(
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community -> !community.getStatus().equals("hidden") &&
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community -> !community.getStatus().equals("hidden") &&
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@ -99,17 +102,26 @@ public class Utils implements Serializable {
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.collect(Collectors.toList());
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.collect(Collectors.toList());
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}
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}
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public static CommunityEntityMap getCommunityOrganization() throws IOException {
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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(boolean production) throws IOException {
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CommunityEntityMap organizationMap = new CommunityEntityMap();
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CommunityEntityMap organizationMap = new CommunityEntityMap();
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getValidCommunities()
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getValidCommunities(production)
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.forEach(community -> {
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.forEach(community -> {
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String id = community.getId();
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String id = community.getId();
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try {
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try {
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List<String> associatedOrgs = MAPPER
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List<String> associatedOrgs = MAPPER
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.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class);
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.readValue(
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if (associatedOrgs.size() > 0) {
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QueryCommunityAPI.communityPropagationOrganization(id, production), OrganizationList.class);
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organizationMap.put(id, associatedOrgs);
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associatedOrgs.forEach(o -> {
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}
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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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} catch (IOException e) {
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throw new RuntimeException(e);
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throw new RuntimeException(e);
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}
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}
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@ -117,26 +129,28 @@ public class Utils implements Serializable {
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return organizationMap;
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return organizationMap;
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}
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}
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public static CommunityEntityMap getCommunityProjects() throws IOException {
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public static CommunityEntityMap getCommunityProjects(boolean production) throws IOException {
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CommunityEntityMap projectMap = new CommunityEntityMap();
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CommunityEntityMap projectMap = new CommunityEntityMap();
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getValidCommunities()
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getValidCommunities(production)
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.forEach(community -> {
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.forEach(community -> {
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int page = -1;
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int page = -1;
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int size = 100;
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int size = 100;
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ContentModel cm = new ContentModel();
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ContentModel cm = new ContentModel();
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List<String> projectList = new ArrayList<>();
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do {
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do {
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page++;
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page++;
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try {
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try {
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cm = MAPPER
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cm = MAPPER
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.readValue(
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.readValue(
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QueryCommunityAPI
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QueryCommunityAPI
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.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)),
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.communityProjects(
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community.getId(), String.valueOf(page), String.valueOf(size), production),
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ContentModel.class);
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ContentModel.class);
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if (cm.getContent().size() > 0) {
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if (cm.getContent().size() > 0) {
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cm.getContent().forEach(p -> {
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cm.getContent().forEach(p -> projectList.add("40|" + p.getOpenaireId()));
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if (!projectMap.keySet().contains("40|" + p.getOpenaireId()))
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projectMap.put(community.getId(), projectList);
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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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}
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} catch (IOException e) {
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} catch (IOException e) {
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throw new RuntimeException(e);
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throw new RuntimeException(e);
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@ -23,6 +23,8 @@ import com.google.gson.Gson;
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import eu.dnetlib.dhp.api.Utils;
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import eu.dnetlib.dhp.api.Utils;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bulktag.community.*;
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import eu.dnetlib.dhp.bulktag.community.*;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Result;
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@ -53,50 +55,38 @@ public class SparkBulkTagJob {
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.orElse(Boolean.TRUE);
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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Boolean isTest = Optional
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.ofNullable(parser.get("isTest"))
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.map(Boolean::valueOf)
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.orElse(Boolean.FALSE);
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log.info("isTest: {} ", isTest);
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final String inputPath = parser.get("sourcePath");
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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log.info("outputPath: {}", outputPath);
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final boolean production = Boolean.valueOf(parser.get("production"));
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log.info("production: {}", production);
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ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
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ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
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log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
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log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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SparkConf conf = new SparkConf();
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CommunityConfiguration cc;
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CommunityConfiguration cc;
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|
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String taggingConf = parser.get("taggingConf");
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String taggingConf = Optional
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|
.ofNullable(parser.get("taggingConf"))
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|
.map(String::valueOf)
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.orElse(null);
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|
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if (isTest) {
|
if (taggingConf != null) {
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cc = CommunityConfigurationFactory.newInstance(taggingConf);
|
cc = CommunityConfigurationFactory.newInstance(taggingConf);
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} else {
|
} else {
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cc = Utils.getCommunityConfiguration();// QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
|
cc = Utils.getCommunityConfiguration(production);
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}
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}
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|
|
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runWithSparkSession(
|
runWithSparkSession(
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conf,
|
conf,
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isSparkSessionManaged,
|
isSparkSessionManaged,
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spark -> {
|
spark -> {
|
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removeOutputDir(spark, outputPath);
|
|
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extendCommunityConfigurationForEOSC(spark, inputPath, cc);
|
extendCommunityConfigurationForEOSC(spark, inputPath, cc);
|
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execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
|
execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -141,22 +131,30 @@ public class SparkBulkTagJob {
|
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String inputPath,
|
String inputPath,
|
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String outputPath,
|
String outputPath,
|
||||||
ProtoMap protoMappingParams,
|
ProtoMap protoMappingParams,
|
||||||
Class<R> resultClazz,
|
|
||||||
CommunityConfiguration communityConfiguration) {
|
CommunityConfiguration communityConfiguration) {
|
||||||
|
|
||||||
ResultTagger resultTagger = new ResultTagger();
|
ModelSupport.entityTypes
|
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readPath(spark, inputPath, resultClazz)
|
.keySet()
|
||||||
.map(patchResult(), Encoders.bean(resultClazz))
|
.parallelStream()
|
||||||
.filter(Objects::nonNull)
|
.filter(e -> ModelSupport.isResult(e))
|
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.map(
|
.forEach(e -> {
|
||||||
(MapFunction<R, R>) value -> resultTagger
|
removeOutputDir(spark, outputPath + e.name());
|
||||||
.enrichContextCriteria(
|
ResultTagger resultTagger = new ResultTagger();
|
||||||
value, communityConfiguration, protoMappingParams),
|
Class<R> resultClazz = ModelSupport.entityTypes.get(e);
|
||||||
Encoders.bean(resultClazz))
|
readPath(spark, inputPath + e.name(), resultClazz)
|
||||||
.write()
|
.map(patchResult(), Encoders.bean(resultClazz))
|
||||||
.mode(SaveMode.Overwrite)
|
.filter(Objects::nonNull)
|
||||||
.option("compression", "gzip")
|
.map(
|
||||||
.json(outputPath);
|
(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(
|
public static <R> Dataset<R> readPath(
|
||||||
|
|
|
@ -82,19 +82,23 @@ public class ResultTagger implements Serializable {
|
||||||
// communities contains all the communities to be not added to the context
|
// communities contains all the communities to be not added to the context
|
||||||
final Set<String> removeCommunities = new HashSet<>();
|
final Set<String> removeCommunities = new HashSet<>();
|
||||||
|
|
||||||
|
// if (conf.getRemoveConstraintsMap().keySet().size() > 0)
|
||||||
conf
|
conf
|
||||||
.getRemoveConstraintsMap()
|
.getRemoveConstraintsMap()
|
||||||
.keySet()
|
.keySet()
|
||||||
.forEach(communityId -> {
|
.forEach(
|
||||||
if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
|
communityId -> {
|
||||||
conf
|
// log.info("Remove constraints for " + communityId);
|
||||||
.getRemoveConstraintsMap()
|
if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
|
||||||
.get(communityId)
|
conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
|
||||||
.getCriteria()
|
conf
|
||||||
.stream()
|
.getRemoveConstraintsMap()
|
||||||
.anyMatch(crit -> crit.verifyCriteria(param)))
|
.get(communityId)
|
||||||
removeCommunities.add(communityId);
|
.getCriteria()
|
||||||
});
|
.stream()
|
||||||
|
.anyMatch(crit -> crit.verifyCriteria(param)))
|
||||||
|
removeCommunities.add(communityId);
|
||||||
|
});
|
||||||
|
|
||||||
// communities contains all the communities to be added as context for the result
|
// communities contains all the communities to be added as context for the result
|
||||||
final Set<String> communities = new HashSet<>();
|
final Set<String> communities = new HashSet<>();
|
||||||
|
@ -124,10 +128,10 @@ public class ResultTagger implements Serializable {
|
||||||
if (Objects.nonNull(result.getInstance())) {
|
if (Objects.nonNull(result.getInstance())) {
|
||||||
for (Instance i : result.getInstance()) {
|
for (Instance i : result.getInstance()) {
|
||||||
if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) {
|
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())) {
|
if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) {
|
||||||
hostdby.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|"));
|
hostdby.add(i.getHostedby().getKey());
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -48,11 +48,10 @@ public class PrepareResultCommunitySet {
|
||||||
final String outputPath = parser.get("outputPath");
|
final String outputPath = parser.get("outputPath");
|
||||||
log.info("outputPath: {}", outputPath);
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
// final CommunityEntityMap organizationMap = new Gson()
|
final boolean production = Boolean.valueOf(parser.get("production"));
|
||||||
// .fromJson(
|
log.info("production: {}", production);
|
||||||
// parser.get("organizationtoresultcommunitymap"),
|
|
||||||
// CommunityEntityMap.class);
|
final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(production);
|
||||||
final CommunityEntityMap organizationMap = Utils.getCommunityOrganization();
|
|
||||||
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
|
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
|
||||||
|
|
||||||
SparkConf conf = new SparkConf();
|
SparkConf conf = new SparkConf();
|
||||||
|
|
|
@ -56,12 +56,6 @@ public class SparkResultToCommunityFromOrganizationJob {
|
||||||
final String resultClassName = parser.get("resultTableName");
|
final String resultClassName = parser.get("resultTableName");
|
||||||
log.info("resultTableName: {}", resultClassName);
|
log.info("resultTableName: {}", resultClassName);
|
||||||
|
|
||||||
final Boolean saveGraph = Optional
|
|
||||||
.ofNullable(parser.get("saveGraph"))
|
|
||||||
.map(Boolean::valueOf)
|
|
||||||
.orElse(Boolean.TRUE);
|
|
||||||
log.info("saveGraph: {}", saveGraph);
|
|
||||||
|
|
||||||
@SuppressWarnings("unchecked")
|
@SuppressWarnings("unchecked")
|
||||||
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||||
|
|
||||||
|
@ -73,9 +67,9 @@ public class SparkResultToCommunityFromOrganizationJob {
|
||||||
isSparkSessionManaged,
|
isSparkSessionManaged,
|
||||||
spark -> {
|
spark -> {
|
||||||
removeOutputDir(spark, outputPath);
|
removeOutputDir(spark, outputPath);
|
||||||
if (saveGraph) {
|
|
||||||
execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
|
execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
|
||||||
}
|
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -0,0 +1,121 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.resulttocommunityfromproject;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||||
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||||
|
|
||||||
|
import java.util.*;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.hadoop.io.compress.GzipCodec;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||||
|
import org.apache.spark.sql.*;
|
||||||
|
import org.apache.spark.sql.types.DataTypes;
|
||||||
|
import org.apache.spark.sql.types.StructType;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.google.gson.Gson;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.Utils;
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
|
||||||
|
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultOrganizations;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
public class PrepareResultCommunitySet {
|
||||||
|
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
String jsonConfiguration = IOUtils
|
||||||
|
.toString(
|
||||||
|
PrepareResultCommunitySet.class
|
||||||
|
.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json"));
|
||||||
|
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
||||||
|
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||||
|
|
||||||
|
String inputPath = parser.get("sourcePath");
|
||||||
|
log.info("inputPath: {}", inputPath);
|
||||||
|
|
||||||
|
final String outputPath = parser.get("outputPath");
|
||||||
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
|
final boolean production = Boolean.valueOf(parser.get("outputPath"));
|
||||||
|
log.info("production: {}", production);
|
||||||
|
|
||||||
|
final CommunityEntityMap projectsMap = Utils.getCommunityProjects(production);
|
||||||
|
log.info("projectsMap: {}", new Gson().toJson(projectsMap));
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||||
|
|
||||||
|
runWithSparkHiveSession(
|
||||||
|
conf,
|
||||||
|
isSparkSessionManaged,
|
||||||
|
spark -> {
|
||||||
|
removeOutputDir(spark, outputPath);
|
||||||
|
prepareInfo(spark, inputPath, outputPath, projectsMap);
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void prepareInfo(
|
||||||
|
SparkSession spark,
|
||||||
|
String inputPath,
|
||||||
|
String outputPath,
|
||||||
|
CommunityEntityMap projectMap) {
|
||||||
|
|
||||||
|
final StructType structureSchema = new StructType()
|
||||||
|
.add(
|
||||||
|
"dataInfo", new StructType()
|
||||||
|
.add("deletedbyinference", DataTypes.BooleanType)
|
||||||
|
.add("invisible", DataTypes.BooleanType))
|
||||||
|
.add("source", DataTypes.StringType)
|
||||||
|
.add("target", DataTypes.StringType)
|
||||||
|
.add("relClass", DataTypes.StringType);
|
||||||
|
|
||||||
|
spark
|
||||||
|
.read()
|
||||||
|
.schema(structureSchema)
|
||||||
|
.json(inputPath)
|
||||||
|
.filter(
|
||||||
|
"dataInfo.deletedbyinference != true " +
|
||||||
|
"and relClass == '" + ModelConstants.IS_PRODUCED_BY + "'")
|
||||||
|
.select(
|
||||||
|
new Column("source").as("resultId"),
|
||||||
|
new Column("target").as("projectId"))
|
||||||
|
.groupByKey((MapFunction<Row, String>) r -> (String) r.getAs("source"), 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("target")));
|
||||||
|
v.forEachRemaining(r -> {
|
||||||
|
projectMap
|
||||||
|
.get(r.getAs("target"))
|
||||||
|
.forEach(c -> {
|
||||||
|
if (!cl.contains(c))
|
||||||
|
cl.add(c);
|
||||||
|
});
|
||||||
|
|
||||||
|
});
|
||||||
|
rpl.setCommunityList(cl);
|
||||||
|
return rpl;
|
||||||
|
}, Encoders.bean(ResultProjectList.class))
|
||||||
|
.write()
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.option("compression", "gzip")
|
||||||
|
.json(outputPath);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
|
@ -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 +1,156 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.resulttocommunityfromproject;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||||
|
import static eu.dnetlib.dhp.PropagationConstant.PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME;
|
||||||
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Optional;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
|
||||||
|
import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 11/10/23
|
||||||
|
*/
|
||||||
|
public class SparkResultToCommunityFromProject implements Serializable {
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityFromProject.class);
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
String jsonConfiguration = IOUtils
|
||||||
|
.toString(
|
||||||
|
SparkResultToCommunityFromProject.class
|
||||||
|
.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/resulttocommunityfromproject/input_communitytoresult_parameters.json"));
|
||||||
|
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||||
|
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
||||||
|
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||||
|
|
||||||
|
String inputPath = parser.get("sourcePath");
|
||||||
|
log.info("inputPath: {}", inputPath);
|
||||||
|
|
||||||
|
final String outputPath = parser.get("outputPath");
|
||||||
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
|
final String possibleupdatespath = parser.get("preparedInfoPath");
|
||||||
|
log.info("preparedInfoPath: {}", possibleupdatespath);
|
||||||
|
|
||||||
|
final String resultClassName = parser.get("resultTableName");
|
||||||
|
log.info("resultTableName: {}", resultClassName);
|
||||||
|
|
||||||
|
@SuppressWarnings("unchecked")
|
||||||
|
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||||
|
|
||||||
|
runWithSparkHiveSession(
|
||||||
|
conf,
|
||||||
|
isSparkSessionManaged,
|
||||||
|
spark -> {
|
||||||
|
// removeOutputDir(spark, outputPath);
|
||||||
|
|
||||||
|
execPropagation(spark, inputPath, outputPath, possibleupdatespath);
|
||||||
|
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <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);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
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 : communitySet) {
|
||||||
|
if (!contextList.contains(cId)) {
|
||||||
|
Context newContext = new Context();
|
||||||
|
newContext.setId(cId);
|
||||||
|
newContext
|
||||||
|
.setDataInfo(
|
||||||
|
Arrays
|
||||||
|
.asList(
|
||||||
|
getDataInfo(
|
||||||
|
PROPAGATION_DATA_INFO_TYPE,
|
||||||
|
PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_ID,
|
||||||
|
PROPAGATION_RESULT_COMMUNITY_PROJECT_CLASS_NAME,
|
||||||
|
ModelConstants.DNET_PROVENANCE_ACTIONS)));
|
||||||
|
propagatedContexts.add(newContext);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
res.setContext(propagatedContexts);
|
||||||
|
ret.mergeFrom(res);
|
||||||
|
}
|
||||||
|
return ret;
|
||||||
|
};
|
||||||
|
}
|
||||||
|
}
|
|
@ -1,10 +1,5 @@
|
||||||
[
|
[
|
||||||
{
|
|
||||||
"paramName":"is",
|
|
||||||
"paramLongName":"isLookUpUrl",
|
|
||||||
"paramDescription": "URL of the isLookUp Service",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"paramName":"s",
|
"paramName":"s",
|
||||||
"paramLongName":"sourcePath",
|
"paramLongName":"sourcePath",
|
||||||
|
@ -17,12 +12,7 @@
|
||||||
"paramDescription": "the json path associated to each selection field",
|
"paramDescription": "the json path associated to each selection field",
|
||||||
"paramRequired": true
|
"paramRequired": true
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"paramName":"tn",
|
|
||||||
"paramLongName":"resultTableName",
|
|
||||||
"paramDescription": "the name of the result table we are currently working on",
|
|
||||||
"paramRequired": true
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"paramName": "out",
|
"paramName": "out",
|
||||||
"paramLongName": "outputPath",
|
"paramLongName": "outputPath",
|
||||||
|
@ -35,17 +25,19 @@
|
||||||
"paramDescription": "true if the spark session is managed, false otherwise",
|
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||||
"paramRequired": false
|
"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",
|
"paramName": "tg",
|
||||||
"paramLongName": "taggingConf",
|
"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",
|
"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
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
|
||||||
|
{
|
||||||
|
"paramName": "p",
|
||||||
|
"paramLongName": "production",
|
||||||
|
"paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed",
|
||||||
|
"paramRequired": true
|
||||||
}
|
}
|
||||||
|
|
||||||
]
|
]
|
|
@ -4,10 +4,6 @@
|
||||||
<name>sourcePath</name>
|
<name>sourcePath</name>
|
||||||
<description>the source path</description>
|
<description>the source path</description>
|
||||||
</property>
|
</property>
|
||||||
<property>
|
|
||||||
<name>isLookUpUrl</name>
|
|
||||||
<description>the isLookup service endpoint</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
<property>
|
||||||
<name>pathMap</name>
|
<name>pathMap</name>
|
||||||
<description>the json path associated to each selection field</description>
|
<description>the json path associated to each selection field</description>
|
||||||
|
@ -44,7 +40,7 @@
|
||||||
</configuration>
|
</configuration>
|
||||||
</global>
|
</global>
|
||||||
|
|
||||||
<start to="reset_outputpath"/>
|
<start to="exec_bulktag"/>
|
||||||
|
|
||||||
<kill name="Kill">
|
<kill name="Kill">
|
||||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
@ -102,16 +98,9 @@
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
<join name="copy_wait" to="fork_exec_bulktag"/>
|
<join name="copy_wait" to="exec_bulktag"/>
|
||||||
|
|
||||||
<fork name="fork_exec_bulktag">
|
<action name="exec_bulktag">
|
||||||
<path start="bulktag_publication"/>
|
|
||||||
<path start="bulktag_dataset"/>
|
|
||||||
<path start="bulktag_otherresearchproduct"/>
|
|
||||||
<path start="bulktag_software"/>
|
|
||||||
</fork>
|
|
||||||
|
|
||||||
<action name="bulktag_publication">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
<master>yarn-cluster</master>
|
<master>yarn-cluster</master>
|
||||||
<mode>cluster</mode>
|
<mode>cluster</mode>
|
||||||
|
@ -128,98 +117,15 @@
|
||||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
</spark-opts>
|
</spark-opts>
|
||||||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
|
||||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
<arg>--outputPath</arg><arg>${outputPath}/</arg>
|
||||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
|
||||||
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
<arg>--pathMap</arg><arg>${pathMap}</arg>
|
||||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
<arg>--production</arg><arg>${production}</arg>
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="wait"/>
|
<ok to="End"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</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"/>
|
<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>
|
|
||||||
{$zc/param[./@name='selcriteria']/text()}
|
|
||||||
</selcriteria>
|
|
||||||
</zenodocommunity>}
|
|
||||||
</zenodocommunities>
|
|
||||||
</community>
|
|
|
@ -11,18 +11,6 @@
|
||||||
"paramDescription": "the hive metastore uris",
|
"paramDescription": "the hive metastore uris",
|
||||||
"paramRequired": true
|
"paramRequired": true
|
||||||
},
|
},
|
||||||
{
|
|
||||||
"paramName":"sg",
|
|
||||||
"paramLongName":"saveGraph",
|
|
||||||
"paramDescription": "true if the new version of the graph must be saved",
|
|
||||||
"paramRequired": false
|
|
||||||
},
|
|
||||||
{
|
|
||||||
"paramName":"test",
|
|
||||||
"paramLongName":"isTest",
|
|
||||||
"paramDescription": "true if it is executing a test",
|
|
||||||
"paramRequired": false
|
|
||||||
},
|
|
||||||
{
|
{
|
||||||
"paramName": "out",
|
"paramName": "out",
|
||||||
"paramLongName": "outputPath",
|
"paramLongName": "outputPath",
|
||||||
|
|
|
@ -4,10 +4,7 @@
|
||||||
<name>sourcePath</name>
|
<name>sourcePath</name>
|
||||||
<description>the source path</description>
|
<description>the source path</description>
|
||||||
</property>
|
</property>
|
||||||
<!-- <property>-->
|
|
||||||
<!-- <name>organizationtoresultcommunitymap</name>-->
|
|
||||||
<!-- <description>organization community map</description>-->
|
|
||||||
<!-- </property>-->
|
|
||||||
<property>
|
<property>
|
||||||
<name>outputPath</name>
|
<name>outputPath</name>
|
||||||
<description>the output path</description>
|
<description>the output path</description>
|
||||||
|
@ -106,7 +103,7 @@
|
||||||
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||||
<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
|
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="fork-join-exec-propagation"/>
|
<ok to="fork-join-exec-propagation"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
|
|
|
@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.nio.file.Files;
|
import java.nio.file.Files;
|
||||||
import java.nio.file.Path;
|
import java.nio.file.Path;
|
||||||
|
import java.util.HashMap;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
|
@ -98,14 +99,11 @@ public class BulkTagJobTest {
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath",
|
"-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,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -133,19 +131,16 @@ public class BulkTagJobTest {
|
||||||
@Test
|
@Test
|
||||||
void bulktagBySubjectNoPreviousContextTest() throws Exception {
|
void bulktagBySubjectNoPreviousContextTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
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();
|
.getPath();
|
||||||
final String pathMap = BulkTagJobTest.pathMap;
|
final String pathMap = BulkTagJobTest.pathMap;
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -230,19 +225,19 @@ public class BulkTagJobTest {
|
||||||
void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
|
void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance")
|
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/")
|
||||||
.getPath();
|
.getPath();
|
||||||
final String pathMap = BulkTagJobTest.pathMap;
|
final String pathMap = BulkTagJobTest.pathMap;
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -311,18 +306,18 @@ public class BulkTagJobTest {
|
||||||
@Test
|
@Test
|
||||||
void bulktagByDatasourceTest() throws Exception {
|
void bulktagByDatasourceTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource")
|
.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
|
||||||
"-outputPath", workingDir.toString() + "/publication",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -384,25 +379,25 @@ public class BulkTagJobTest {
|
||||||
void bulktagByZenodoCommunityTest() throws Exception {
|
void bulktagByZenodoCommunityTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity")
|
"/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
|
||||||
"-outputPath", workingDir.toString() + "/orp",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
JavaRDD<OtherResearchProduct> tmp = sc
|
JavaRDD<OtherResearchProduct> tmp = sc
|
||||||
.textFile(workingDir.toString() + "/orp")
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
||||||
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
||||||
|
|
||||||
Assertions.assertEquals(10, tmp.count());
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
@ -505,18 +500,18 @@ public class BulkTagJobTest {
|
||||||
@Test
|
@Test
|
||||||
void bulktagBySubjectDatasourceTest() throws Exception {
|
void bulktagBySubjectDatasourceTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
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();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -636,14 +631,14 @@ public class BulkTagJobTest {
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath",
|
"-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,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
|
|
||||||
"-outputPath", workingDir.toString() + "/software",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -732,18 +727,18 @@ public class BulkTagJobTest {
|
||||||
|
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints")
|
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -774,19 +769,19 @@ public class BulkTagJobTest {
|
||||||
void bulkTagOtherJupyter() throws Exception {
|
void bulkTagOtherJupyter() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct")
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
|
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
|
||||||
"-outputPath", workingDir.toString() + "/otherresearchproduct",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -829,18 +824,18 @@ public class BulkTagJobTest {
|
||||||
public void bulkTagDatasetJupyter() throws Exception {
|
public void bulkTagDatasetJupyter() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/jupyter/dataset")
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -878,18 +873,18 @@ public class BulkTagJobTest {
|
||||||
|
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/jupyter/software")
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
|
|
||||||
"-outputPath", workingDir.toString() + "/software",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1096,18 +1091,18 @@ public class BulkTagJobTest {
|
||||||
void galaxyOtherTest() throws Exception {
|
void galaxyOtherTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct")
|
"/eu/dnetlib/dhp/eosctag/galaxy/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
|
||||||
"-outputPath", workingDir.toString() + "/otherresearchproduct",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1214,18 +1209,18 @@ public class BulkTagJobTest {
|
||||||
void galaxySoftwareTest() throws Exception {
|
void galaxySoftwareTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/galaxy/software")
|
"/eu/dnetlib/dhp/eosctag/galaxy/")
|
||||||
.getPath();
|
.getPath();
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
|
|
||||||
"-outputPath", workingDir.toString() + "/software",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1333,19 +1328,19 @@ public class BulkTagJobTest {
|
||||||
void twitterDatasetTest() throws Exception {
|
void twitterDatasetTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/twitter/dataset")
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
|
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1373,19 +1368,19 @@ public class BulkTagJobTest {
|
||||||
void twitterOtherTest() throws Exception {
|
void twitterOtherTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct")
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
|
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
|
||||||
"-outputPath", workingDir.toString() + "/otherresearchproduct",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1418,19 +1413,19 @@ public class BulkTagJobTest {
|
||||||
void twitterSoftwareTest() throws Exception {
|
void twitterSoftwareTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/eosctag/twitter/software")
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
||||||
.getPath();
|
.getPath();
|
||||||
|
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
|
|
||||||
"-outputPath", workingDir.toString() + "/software",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1455,19 +1450,19 @@ public class BulkTagJobTest {
|
||||||
void EoscContextTagTest() throws Exception {
|
void EoscContextTagTest() throws Exception {
|
||||||
final String sourcePath = getClass()
|
final String sourcePath = getClass()
|
||||||
.getResource(
|
.getResource(
|
||||||
"/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json")
|
"/eu/dnetlib/dhp/bulktag/eosc/dataset/")
|
||||||
.getPath();
|
.getPath();
|
||||||
|
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath", sourcePath,
|
"-sourcePath", sourcePath,
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
@ -1533,16 +1528,16 @@ public class BulkTagJobTest {
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath",
|
"-sourcePath",
|
||||||
getClass()
|
getClass()
|
||||||
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints")
|
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
|
||||||
.getPath(),
|
.getPath(),
|
||||||
"-taggingConf", taggingConf,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
@ -1574,14 +1569,14 @@ public class BulkTagJobTest {
|
||||||
SparkBulkTagJob
|
SparkBulkTagJob
|
||||||
.main(
|
.main(
|
||||||
new String[] {
|
new String[] {
|
||||||
"-isTest", Boolean.TRUE.toString(),
|
|
||||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
"-sourcePath",
|
"-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,
|
"-taggingConf", taggingConf,
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/",
|
||||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
"-production", Boolean.TRUE.toString(),
|
||||||
"-pathMap", pathMap
|
"-pathMap", pathMap
|
||||||
});
|
});
|
||||||
|
|
||||||
|
|
|
@ -26,7 +26,7 @@ public class QueryCommunityAPITest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void communityList() throws Exception {
|
void communityList() throws Exception {
|
||||||
String body = QueryCommunityAPI.communities();
|
String body = QueryCommunityAPI.communities(true);
|
||||||
new ObjectMapper()
|
new ObjectMapper()
|
||||||
.readValue(body, CommunitySummary.class)
|
.readValue(body, CommunitySummary.class)
|
||||||
.forEach(p -> {
|
.forEach(p -> {
|
||||||
|
@ -41,7 +41,7 @@ public class QueryCommunityAPITest {
|
||||||
@Test
|
@Test
|
||||||
void community() throws Exception {
|
void community() throws Exception {
|
||||||
String id = "dh-ch";
|
String id = "dh-ch";
|
||||||
String body = QueryCommunityAPI.community(id);
|
String body = QueryCommunityAPI.community(id, true);
|
||||||
System.out
|
System.out
|
||||||
.println(
|
.println(
|
||||||
new ObjectMapper()
|
new ObjectMapper()
|
||||||
|
@ -53,7 +53,7 @@ public class QueryCommunityAPITest {
|
||||||
@Test
|
@Test
|
||||||
void communityDatasource() throws Exception {
|
void communityDatasource() throws Exception {
|
||||||
String id = "dh-ch";
|
String id = "dh-ch";
|
||||||
String body = QueryCommunityAPI.communityDatasource(id);
|
String body = QueryCommunityAPI.communityDatasource(id, true);
|
||||||
new ObjectMapper()
|
new ObjectMapper()
|
||||||
.readValue(body, DatasourceList.class)
|
.readValue(body, DatasourceList.class)
|
||||||
.forEach(ds -> {
|
.forEach(ds -> {
|
||||||
|
@ -68,7 +68,7 @@ public class QueryCommunityAPITest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void validCommunities() throws Exception {
|
void validCommunities() throws Exception {
|
||||||
CommunityConfiguration cc = Utils.getCommunityConfiguration();
|
CommunityConfiguration cc = Utils.getCommunityConfiguration(true);
|
||||||
System.out.println(cc.getCommunities().keySet());
|
System.out.println(cc.getCommunities().keySet());
|
||||||
Community community = cc.getCommunities().get("aurora");
|
Community community = cc.getCommunities().get("aurora");
|
||||||
Assertions.assertEquals(0, community.getSubjects().size());
|
Assertions.assertEquals(0, community.getSubjects().size());
|
||||||
|
@ -84,11 +84,20 @@ public class QueryCommunityAPITest {
|
||||||
Assertions
|
Assertions
|
||||||
.assertEquals(
|
.assertEquals(
|
||||||
35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count());
|
35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void eutopiaCommunityConfiguration() throws Exception {
|
||||||
|
CommunityConfiguration cc = Utils.getCommunityConfiguration(true);
|
||||||
|
System.out.println(cc.getCommunities().keySet());
|
||||||
|
Community community = cc.getCommunities().get("eutopia");
|
||||||
|
community.getProviders().forEach(p -> System.out.println(p.getOpenaireId()));
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void getCommunityProjects() throws Exception {
|
void getCommunityProjects() throws Exception {
|
||||||
CommunityEntityMap projectMap = Utils.getCommunityProjects();
|
CommunityEntityMap projectMap = Utils.getCommunityProjects(true);
|
||||||
Assertions.assertFalse(projectMap.containsKey("mes"));
|
Assertions.assertFalse(projectMap.containsKey("mes"));
|
||||||
Assertions.assertEquals(33, projectMap.size());
|
Assertions.assertEquals(33, projectMap.size());
|
||||||
Assertions
|
Assertions
|
||||||
|
|
|
@ -78,7 +78,7 @@ public class ResultToCommunityJobTest {
|
||||||
.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample")
|
.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample")
|
||||||
.getPath(),
|
.getPath(),
|
||||||
"-hive_metastore_uris", "",
|
"-hive_metastore_uris", "",
|
||||||
"-saveGraph", "true",
|
|
||||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
"-outputPath", workingDir.toString() + "/dataset",
|
"-outputPath", workingDir.toString() + "/dataset",
|
||||||
"-preparedInfoPath", preparedInfoPath
|
"-preparedInfoPath", preparedInfoPath
|
||||||
|
|
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Loading…
Reference in New Issue