master #59
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@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
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return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
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Project project = new Project();
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Project project = new Project();
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project.setId(bipProjectScores.getProjectId());
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// project.setId(bipProjectScores.getProjectId());
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project.setMeasures(bipProjectScores.toMeasures());
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project.setMeasures(bipProjectScores.toMeasures());
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return project;
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return project;
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}, Encoders.bean(Project.class))
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}, Encoders.bean(Project.class))
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@ -0,0 +1,78 @@
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package eu.dnetlib.dhp.api;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.OutputStream;
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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 org.apache.http.HttpHeaders;
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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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* @author miriam.baglioni
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* @Date 06/10/23
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*/
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public class QueryCommunityAPI {
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private static final String baseUrl = "https://services.openaire.eu/openaire/";
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private static String get(String geturl) throws IOException{
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URL url = new URL(geturl);
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HttpURLConnection conn = (HttpURLConnection) url.openConnection();
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conn.setDoOutput(true);
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conn.setRequestMethod("GET");
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int responseCode = conn.getResponseCode();
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String body = getBody(conn);
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conn.disconnect();
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if (responseCode != HttpURLConnection.HTTP_OK)
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throw new IOException("Unexpected code " + responseCode + body);
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return body;
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}
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public static String communities() throws IOException {
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return get(baseUrl + "community/communities");
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}
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public static String community(String id) throws IOException {
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return get(baseUrl + "community/" + id);
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}
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public static String communityDatasource(String id)throws IOException{
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return get(baseUrl + "community/" + id + "/contentproviders");
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}
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public static String communityPropagationOrganization(String id) throws IOException {
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return get(baseUrl + "community/" + id + "/propagationOrganizations");
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}
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public static String communityProjects(String id, String page, String size) throws IOException{
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return get(baseUrl + "community/" + id +"/projects/" + page + "/" + size);
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}
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@NotNull
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private static String getBody(HttpURLConnection conn) throws IOException {
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String body = "{}";
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try (BufferedReader br = new BufferedReader(
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new InputStreamReader(conn.getInputStream(), "utf-8"))) {
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StringBuilder response = new StringBuilder();
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String responseLine = null;
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while ((responseLine = br.readLine()) != null) {
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response.append(responseLine.trim());
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}
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body = response.toString();
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}
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return body;
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}
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}
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@ -0,0 +1,136 @@
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package eu.dnetlib.dhp.api;
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import com.amazonaws.util.StringUtils;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.api.model.*;
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import eu.dnetlib.dhp.bulktag.community.Community;
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import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
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import eu.dnetlib.dhp.bulktag.community.Provider;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
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import javax.management.Query;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.stream.Collectors;
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/**
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* @author miriam.baglioni
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* @Date 09/10/23
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*/
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public class Utils implements Serializable {
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private static final ObjectMapper MAPPER = new ObjectMapper();
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private static final VerbResolver resolver = VerbResolverFactory.newInstance();
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public static CommunityConfiguration getCommunityConfiguration() throws IOException {
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final Map<String, Community> communities = Maps.newHashMap();
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List<Community> validCommunities = new ArrayList<>();
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getValidCommunities()
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.forEach(community -> {
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try {
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CommunityModel cm = MAPPER.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class);
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validCommunities.add(getCommunity(cm));
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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validCommunities.forEach(community ->{
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try {
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DatasourceList dl = MAPPER.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class);
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community.setProviders(dl.stream().map(d -> {
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// if(d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
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// return null;
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Provider p = new Provider();
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p.setOpenaireId("10|" + d.getOpenaireId());
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p.setSelectionConstraints(d.getSelectioncriteria());
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if(p.getSelectionConstraints() != null)
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p.getSelectionConstraints().setSelection(resolver);
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return p;
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})
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.filter(Objects::nonNull)
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.collect(Collectors.toList()));
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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validCommunities.forEach(community ->{
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if(community.isValid())
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communities.put(community.getId(), community);
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});
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return new CommunityConfiguration(communities);
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}
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private static Community getCommunity(CommunityModel cm){
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Community c = new Community();
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c.setId(cm.getId());
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c.setZenodoCommunities(cm.getOtherZenodoCommunities());
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if(!StringUtils.isNullOrEmpty(cm.getZenodoCommunity()))
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c.getZenodoCommunities().add(cm.getZenodoCommunity());
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c.setSubjects(cm.getSubjects());
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c.getSubjects().addAll(cm.getFos());
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c.getSubjects().addAll(cm.getSdg());
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c.setConstraints(cm.getAdvancedConstraints());
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if(c.getConstraints()!=null)
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c.getConstraints().setSelection(resolver);
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c.setRemoveConstraints(cm.getRemoveConstraints());
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if(c.getRemoveConstraints()!=null)
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c.getRemoveConstraints().setSelection(resolver);
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return c;
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}
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public static List<CommunityModel> getValidCommunities() throws IOException {
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return MAPPER.readValue(QueryCommunityAPI.communities(), CommunitySummary.class)
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.stream()
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.filter(community -> !community.getStatus().equals("hidden") &&
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|
(community.getType().equals("ri") || community.getType().equals("community")))
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.collect(Collectors.toList());
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}
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public static CommunityEntityMap getCommunityOrganization() throws IOException {
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CommunityEntityMap organizationMap = new CommunityEntityMap();
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getValidCommunities()
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.forEach(community -> {
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String id = community.getId();
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try {
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List<String> associatedOrgs = MAPPER.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class);
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|
if(associatedOrgs.size() >0){
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organizationMap.put(id, associatedOrgs);
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|
}
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|
} catch (IOException e) {
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|
throw new RuntimeException(e);
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|
}
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|
});
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|
return organizationMap;
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|
}
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|
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|
public static CommunityEntityMap getCommunityProjects()throws IOException{
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|
CommunityEntityMap projectMap = new CommunityEntityMap();
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|
getValidCommunities()
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|
.forEach(community ->{
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|
int page = -1;
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|
int size = 100;
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ContentModel cm = new ContentModel();
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List<String> projectList = new ArrayList<>();
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|
do{
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|
page ++;
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|
try {
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|
cm = MAPPER.readValue( QueryCommunityAPI.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), ContentModel.class);
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|
if (cm.getContent().size() > 0){
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|
cm.getContent().forEach(p ->
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|
projectList.add ("40|" + p.getOpenaireId()));
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|
projectMap.put(community.getId(), projectList);
|
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|
}
|
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|
} catch (IOException e) {
|
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|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}while (!cm.getLast());
|
||||||
|
});
|
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|
return projectMap;
|
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|
}
|
||||||
|
}
|
|
@ -0,0 +1,43 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonAutoDetect;
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||||
|
import com.google.gson.Gson;
|
||||||
|
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
|
||||||
|
|
||||||
|
|
||||||
|
@JsonAutoDetect
|
||||||
|
@JsonIgnoreProperties(ignoreUnknown = true)
|
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|
public class CommunityContentprovider {
|
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|
private String openaireId;
|
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|
private SelectionConstraints selectioncriteria;
|
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|
|
||||||
|
private String enabled;
|
||||||
|
|
||||||
|
public String getEnabled() {
|
||||||
|
return enabled;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setEnabled(String enabled) {
|
||||||
|
this.enabled = enabled;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getOpenaireId() {
|
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|
return openaireId;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setOpenaireId(final String openaireId) {
|
||||||
|
this.openaireId = openaireId;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public SelectionConstraints getSelectioncriteria() {
|
||||||
|
|
||||||
|
return this.selectioncriteria;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setSelectioncriteria(SelectionConstraints selectioncriteria) {
|
||||||
|
this.selectioncriteria = selectioncriteria;
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
|
@ -1,13 +1,13 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.resulttocommunityfromorganization;
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
public class OrganizationMap extends HashMap<String, List<String>> {
|
public class CommunityEntityMap extends HashMap<String, List<String>> {
|
||||||
|
|
||||||
public OrganizationMap() {
|
public CommunityEntityMap() {
|
||||||
super();
|
super();
|
||||||
}
|
}
|
||||||
|
|
|
@ -0,0 +1,108 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||||
|
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 06/10/23
|
||||||
|
*/
|
||||||
|
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||||
|
public class CommunityModel implements Serializable {
|
||||||
|
private String id;
|
||||||
|
private String type;
|
||||||
|
private String status;
|
||||||
|
|
||||||
|
private String zenodoCommunity;
|
||||||
|
private List<String> subjects;
|
||||||
|
private List<String> otherZenodoCommunities;
|
||||||
|
private List<String> fos;
|
||||||
|
private List<String> sdg;
|
||||||
|
private SelectionConstraints advancedConstraints;
|
||||||
|
private SelectionConstraints removeConstraints;
|
||||||
|
|
||||||
|
public String getZenodoCommunity() {
|
||||||
|
return zenodoCommunity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setZenodoCommunity(String zenodoCommunity) {
|
||||||
|
this.zenodoCommunity = zenodoCommunity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getSubjects() {
|
||||||
|
return subjects;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setSubjects(List<String> subjects) {
|
||||||
|
this.subjects = subjects;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getOtherZenodoCommunities() {
|
||||||
|
return otherZenodoCommunities;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setOtherZenodoCommunities(List<String> otherZenodoCommunities) {
|
||||||
|
this.otherZenodoCommunities = otherZenodoCommunities;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getFos() {
|
||||||
|
return fos;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setFos(List<String> fos) {
|
||||||
|
this.fos = fos;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getSdg() {
|
||||||
|
return sdg;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setSdg(List<String> sdg) {
|
||||||
|
this.sdg = sdg;
|
||||||
|
}
|
||||||
|
|
||||||
|
public SelectionConstraints getRemoveConstraints() {
|
||||||
|
return removeConstraints;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setRemoveConstraints(SelectionConstraints removeConstraints) {
|
||||||
|
this.removeConstraints = removeConstraints;
|
||||||
|
}
|
||||||
|
|
||||||
|
public SelectionConstraints getAdvancedConstraints() {
|
||||||
|
return advancedConstraints;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setAdvancedConstraints(SelectionConstraints advancedConstraints) {
|
||||||
|
this.advancedConstraints = advancedConstraints;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getId() {
|
||||||
|
return id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setId(String id) {
|
||||||
|
this.id = id;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getType() {
|
||||||
|
return type;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setType(String type) {
|
||||||
|
this.type = type;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getStatus() {
|
||||||
|
return status;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setStatus(String status) {
|
||||||
|
this.status = status;
|
||||||
|
}
|
||||||
|
}
|
|
@ -0,0 +1,16 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 06/10/23
|
||||||
|
*/
|
||||||
|
public class CommunitySummary extends ArrayList<CommunityModel> implements Serializable {
|
||||||
|
public CommunitySummary() {
|
||||||
|
super();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
|
@ -0,0 +1,50 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 09/10/23
|
||||||
|
*/
|
||||||
|
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||||
|
public class ContentModel implements Serializable {
|
||||||
|
private List<ProjectModel> content;
|
||||||
|
private Integer totalPages;
|
||||||
|
private Boolean last;
|
||||||
|
private Integer number;
|
||||||
|
|
||||||
|
public List<ProjectModel> getContent() {
|
||||||
|
return content;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setContent(List<ProjectModel> content) {
|
||||||
|
this.content = content;
|
||||||
|
}
|
||||||
|
|
||||||
|
public Integer getTotalPages() {
|
||||||
|
return totalPages;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setTotalPages(Integer totalPages) {
|
||||||
|
this.totalPages = totalPages;
|
||||||
|
}
|
||||||
|
|
||||||
|
public Boolean getLast() {
|
||||||
|
return last;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setLast(Boolean last) {
|
||||||
|
this.last = last;
|
||||||
|
}
|
||||||
|
|
||||||
|
public Integer getNumber() {
|
||||||
|
return number;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setNumber(Integer number) {
|
||||||
|
this.number = number;
|
||||||
|
}
|
||||||
|
}
|
|
@ -0,0 +1,12 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunityContentprovider;
|
||||||
|
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
public class DatasourceList extends ArrayList<CommunityContentprovider> implements Serializable {
|
||||||
|
public DatasourceList(){
|
||||||
|
super();
|
||||||
|
}
|
||||||
|
}
|
|
@ -0,0 +1,15 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 09/10/23
|
||||||
|
*/
|
||||||
|
public class OrganizationList extends ArrayList<String> implements Serializable {
|
||||||
|
|
||||||
|
public OrganizationList(){
|
||||||
|
super();
|
||||||
|
}
|
||||||
|
}
|
|
@ -0,0 +1,23 @@
|
||||||
|
package eu.dnetlib.dhp.api.model;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 09/10/23
|
||||||
|
*/
|
||||||
|
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||||
|
public class ProjectModel implements Serializable {
|
||||||
|
|
||||||
|
private String openaireId;
|
||||||
|
|
||||||
|
public String getOpenaireId() {
|
||||||
|
return openaireId;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setOpenaireId(String openaireId) {
|
||||||
|
this.openaireId = openaireId;
|
||||||
|
}
|
||||||
|
}
|
|
@ -6,10 +6,10 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.Utils;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
import org.apache.spark.api.java.function.ForeachFunction;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
|
@ -87,7 +87,7 @@ public class SparkBulkTagJob {
|
||||||
if (isTest) {
|
if (isTest) {
|
||||||
cc = CommunityConfigurationFactory.newInstance(taggingConf);
|
cc = CommunityConfigurationFactory.newInstance(taggingConf);
|
||||||
} else {
|
} else {
|
||||||
cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
|
cc = Utils.getCommunityConfiguration();//QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
|
||||||
}
|
}
|
||||||
|
|
||||||
runWithSparkSession(
|
runWithSparkSession(
|
||||||
|
|
|
@ -4,16 +4,18 @@ package eu.dnetlib.dhp.bulktag.community;
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
import com.google.gson.Gson;
|
import com.google.gson.Gson;
|
||||||
|
|
||||||
|
|
||||||
/** Created by miriam on 01/08/2018. */
|
/** Created by miriam on 01/08/2018. */
|
||||||
public class Community implements Serializable {
|
public class Community implements Serializable {
|
||||||
|
|
||||||
private String id;
|
private String id;
|
||||||
private List<String> subjects = new ArrayList<>();
|
private List<String> subjects = new ArrayList<>();
|
||||||
private List<Provider> providers = new ArrayList<>();
|
private List<Provider> providers = new ArrayList<>();
|
||||||
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
|
private List<String> zenodoCommunities = new ArrayList<>();
|
||||||
private SelectionConstraints constraints = new SelectionConstraints();
|
private SelectionConstraints constraints = new SelectionConstraints();
|
||||||
private SelectionConstraints removeConstraints = new SelectionConstraints();
|
private SelectionConstraints removeConstraints = new SelectionConstraints();
|
||||||
|
|
||||||
|
@ -26,7 +28,7 @@ public class Community implements Serializable {
|
||||||
return !getSubjects().isEmpty()
|
return !getSubjects().isEmpty()
|
||||||
|| !getProviders().isEmpty()
|
|| !getProviders().isEmpty()
|
||||||
|| !getZenodoCommunities().isEmpty()
|
|| !getZenodoCommunities().isEmpty()
|
||||||
|| getConstraints().getCriteria() != null;
|
|| (Optional.ofNullable(getConstraints()).isPresent() && getConstraints().getCriteria() != null);
|
||||||
}
|
}
|
||||||
|
|
||||||
public String getId() {
|
public String getId() {
|
||||||
|
@ -53,11 +55,11 @@ public class Community implements Serializable {
|
||||||
this.providers = providers;
|
this.providers = providers;
|
||||||
}
|
}
|
||||||
|
|
||||||
public List<ZenodoCommunity> getZenodoCommunities() {
|
public List<String> getZenodoCommunities() {
|
||||||
return zenodoCommunities;
|
return zenodoCommunities;
|
||||||
}
|
}
|
||||||
|
|
||||||
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
|
public void setZenodoCommunities(List<String> zenodoCommunities) {
|
||||||
this.zenodoCommunities = zenodoCommunities;
|
this.zenodoCommunities = zenodoCommunities;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -81,7 +81,7 @@ public class CommunityConfiguration implements Serializable {
|
||||||
this.removeConstraintsMap = removeConstraintsMap;
|
this.removeConstraintsMap = removeConstraintsMap;
|
||||||
}
|
}
|
||||||
|
|
||||||
CommunityConfiguration(final Map<String, Community> communities) {
|
public CommunityConfiguration(final Map<String, Community> communities) {
|
||||||
this.communities = communities;
|
this.communities = communities;
|
||||||
init();
|
init();
|
||||||
}
|
}
|
||||||
|
@ -117,10 +117,10 @@ public class CommunityConfiguration implements Serializable {
|
||||||
add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
|
add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
|
||||||
}
|
}
|
||||||
// get zenodo communities
|
// get zenodo communities
|
||||||
for (ZenodoCommunity zc : c.getZenodoCommunities()) {
|
for (String zc : c.getZenodoCommunities()) {
|
||||||
add(
|
add(
|
||||||
zc.getZenodoCommunityId(),
|
zc,
|
||||||
new Pair<>(id, zc.getSelCriteria()),
|
new Pair<>(id, null),
|
||||||
zenodocommunityMap);
|
zenodocommunityMap);
|
||||||
}
|
}
|
||||||
selectionConstraintsMap.put(id, c.getConstraints());
|
selectionConstraintsMap.put(id, c.getConstraints());
|
||||||
|
|
|
@ -5,7 +5,6 @@ import java.io.StringReader;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
import org.apache.commons.lang3.StringUtils;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
@ -143,16 +142,16 @@ public class CommunityConfigurationFactory {
|
||||||
return providerList;
|
return providerList;
|
||||||
}
|
}
|
||||||
|
|
||||||
private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {
|
private static List<String> parseZenodoCommunities(final Node node) {
|
||||||
|
|
||||||
final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
|
final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
|
||||||
final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>();
|
final List<String> zenodoCommunityList = new ArrayList<>();
|
||||||
for (Node n : list) {
|
for (Node n : list) {
|
||||||
ZenodoCommunity zc = new ZenodoCommunity();
|
// ZenodoCommunity zc = new ZenodoCommunity();
|
||||||
zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
|
// zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
|
||||||
zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
|
// zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
|
||||||
|
|
||||||
zenodoCommunityList.add(zc);
|
zenodoCommunityList.add(n.selectSingleNode("./zenodoid").getText());
|
||||||
}
|
}
|
||||||
|
|
||||||
log.info("size of the zenodo community list " + zenodoCommunityList.size());
|
log.info("size of the zenodo community list " + zenodoCommunityList.size());
|
||||||
|
|
|
@ -6,12 +6,14 @@ import java.lang.reflect.InvocationTargetException;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.bulktag.criteria.Selection;
|
import eu.dnetlib.dhp.bulktag.criteria.Selection;
|
||||||
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
|
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
|
||||||
|
import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
|
||||||
|
|
||||||
public class Constraint implements Serializable {
|
public class Constraint implements Serializable {
|
||||||
private String verb;
|
private String verb;
|
||||||
private String field;
|
private String field;
|
||||||
private String value;
|
private String value;
|
||||||
// private String element;
|
// private String element;
|
||||||
|
@JsonIgnore
|
||||||
private Selection selection;
|
private Selection selection;
|
||||||
|
|
||||||
public String getVerb() {
|
public String getVerb() {
|
||||||
|
@ -37,11 +39,11 @@ public class Constraint implements Serializable {
|
||||||
public void setValue(String value) {
|
public void setValue(String value) {
|
||||||
this.value = value;
|
this.value = value;
|
||||||
}
|
}
|
||||||
|
//@JsonIgnore
|
||||||
public void setSelection(Selection sel) {
|
//public void setSelection(Selection sel) {
|
||||||
selection = sel;
|
// selection = sel;
|
||||||
}
|
// }
|
||||||
|
@JsonIgnore
|
||||||
public void setSelection(VerbResolver resolver)
|
public void setSelection(VerbResolver resolver)
|
||||||
throws InvocationTargetException, NoSuchMethodException, InstantiationException,
|
throws InvocationTargetException, NoSuchMethodException, InstantiationException,
|
||||||
IllegalAccessException {
|
IllegalAccessException {
|
||||||
|
@ -52,11 +54,5 @@ public class Constraint implements Serializable {
|
||||||
return selection.apply(metadata);
|
return selection.apply(metadata);
|
||||||
}
|
}
|
||||||
|
|
||||||
// public String getElement() {
|
|
||||||
// return element;
|
|
||||||
// }
|
|
||||||
//
|
|
||||||
// public void setElement(String element) {
|
|
||||||
// this.element = element;
|
|
||||||
// }
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -7,11 +7,12 @@ import java.util.Collection;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.JsonAutoDetect;
|
||||||
import com.google.gson.Gson;
|
import com.google.gson.Gson;
|
||||||
import com.google.gson.reflect.TypeToken;
|
import com.google.gson.reflect.TypeToken;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
|
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
|
||||||
|
@JsonAutoDetect
|
||||||
public class SelectionConstraints implements Serializable {
|
public class SelectionConstraints implements Serializable {
|
||||||
private List<Constraints> criteria;
|
private List<Constraints> criteria;
|
||||||
|
|
||||||
|
|
|
@ -6,12 +6,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||||
|
|
||||||
import java.util.*;
|
import java.util.*;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.Utils;
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.hadoop.io.compress.GzipCodec;
|
import org.apache.hadoop.io.compress.GzipCodec;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
import org.apache.spark.api.java.function.MapFunction;
|
||||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
|
||||||
import org.apache.spark.sql.Dataset;
|
import org.apache.spark.sql.Dataset;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
@ -48,10 +48,11 @@ public class PrepareResultCommunitySet {
|
||||||
final String outputPath = parser.get("outputPath");
|
final String outputPath = parser.get("outputPath");
|
||||||
log.info("outputPath: {}", outputPath);
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
final OrganizationMap organizationMap = new Gson()
|
// final CommunityEntityMap organizationMap = new Gson()
|
||||||
.fromJson(
|
// .fromJson(
|
||||||
parser.get("organizationtoresultcommunitymap"),
|
// parser.get("organizationtoresultcommunitymap"),
|
||||||
OrganizationMap.class);
|
// CommunityEntityMap.class);
|
||||||
|
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();
|
||||||
|
@ -70,7 +71,7 @@ public class PrepareResultCommunitySet {
|
||||||
SparkSession spark,
|
SparkSession spark,
|
||||||
String inputPath,
|
String inputPath,
|
||||||
String outputPath,
|
String outputPath,
|
||||||
OrganizationMap organizationMap) {
|
CommunityEntityMap organizationMap) {
|
||||||
|
|
||||||
Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
|
Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
|
||||||
relation.createOrReplaceTempView("relation");
|
relation.createOrReplaceTempView("relation");
|
||||||
|
@ -115,7 +116,7 @@ public class PrepareResultCommunitySet {
|
||||||
}
|
}
|
||||||
|
|
||||||
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
|
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
|
||||||
OrganizationMap organizationMap) {
|
CommunityEntityMap organizationMap) {
|
||||||
return value -> {
|
return value -> {
|
||||||
String rId = value.getResultId();
|
String rId = value.getResultId();
|
||||||
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
|
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
|
||||||
|
|
|
@ -4,10 +4,10 @@
|
||||||
<name>sourcePath</name>
|
<name>sourcePath</name>
|
||||||
<description>the source path</description>
|
<description>the source path</description>
|
||||||
</property>
|
</property>
|
||||||
<property>
|
<!-- <property>-->
|
||||||
<name>organizationtoresultcommunitymap</name>
|
<!-- <name>organizationtoresultcommunitymap</name>-->
|
||||||
<description>organization community map</description>
|
<!-- <description>organization community map</description>-->
|
||||||
</property>
|
<!-- </property>-->
|
||||||
<property>
|
<property>
|
||||||
<name>outputPath</name>
|
<name>outputPath</name>
|
||||||
<description>the output path</description>
|
<description>the output path</description>
|
||||||
|
|
|
@ -1568,4 +1568,42 @@ public class BulkTagJobTest {
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void newConfTest() throws Exception {
|
||||||
|
final String pathMap = BulkTagJobTest.pathMap;
|
||||||
|
SparkBulkTagJob
|
||||||
|
.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest", Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(),
|
||||||
|
"-taggingConf", taggingConf,
|
||||||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
"-outputPath", workingDir.toString() + "/dataset",
|
||||||
|
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
"-pathMap", pathMap
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Dataset> tmp = sc
|
||||||
|
.textFile(workingDir.toString() + "/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
|
||||||
|
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
|
||||||
|
String query = "select id, MyT.id community "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
Assertions.assertEquals(0, spark.sql(query).count());
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -47,7 +47,7 @@ class CommunityConfigurationFactoryTest {
|
||||||
sc.setVerb("not_contains");
|
sc.setVerb("not_contains");
|
||||||
sc.setField("contributor");
|
sc.setField("contributor");
|
||||||
sc.setValue("DARIAH");
|
sc.setValue("DARIAH");
|
||||||
sc.setSelection(resolver.getSelectionCriteria(sc.getVerb(), sc.getValue()));
|
sc.setSelection(resolver);//.getSelectionCriteria(sc.getVerb(), sc.getValue()));
|
||||||
String metadata = "This work has been partially supported by DARIAH-EU infrastructure";
|
String metadata = "This work has been partially supported by DARIAH-EU infrastructure";
|
||||||
Assertions.assertFalse(sc.verifyCriteria(metadata));
|
Assertions.assertFalse(sc.verifyCriteria(metadata));
|
||||||
}
|
}
|
||||||
|
|
|
@ -0,0 +1,91 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.bulktag;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.Utils;
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
|
||||||
|
import eu.dnetlib.dhp.bulktag.community.Community;
|
||||||
|
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunityModel;
|
||||||
|
import eu.dnetlib.dhp.api.model.CommunitySummary;
|
||||||
|
import eu.dnetlib.dhp.api.model.DatasourceList;
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.api.QueryCommunityAPI;
|
||||||
|
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author miriam.baglioni
|
||||||
|
* @Date 06/10/23
|
||||||
|
*/
|
||||||
|
public class QueryCommunityAPITest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void communityList() throws Exception {
|
||||||
|
String body = QueryCommunityAPI.communities();
|
||||||
|
new ObjectMapper()
|
||||||
|
.readValue(body, CommunitySummary.class)
|
||||||
|
.forEach(p -> {
|
||||||
|
try {
|
||||||
|
System.out.println(new ObjectMapper().writeValueAsString(p));
|
||||||
|
} catch (JsonProcessingException e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void community() throws Exception {
|
||||||
|
String id = "dh-ch";
|
||||||
|
String body = QueryCommunityAPI.community(id);
|
||||||
|
System.out.println(new ObjectMapper().writeValueAsString(new ObjectMapper()
|
||||||
|
.readValue(body, CommunityModel.class)))
|
||||||
|
;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void communityDatasource() throws Exception {
|
||||||
|
String id = "dh-ch";
|
||||||
|
String body = QueryCommunityAPI.communityDatasource(id);
|
||||||
|
new ObjectMapper()
|
||||||
|
.readValue(body, DatasourceList.class)
|
||||||
|
.forEach(ds-> {
|
||||||
|
try {
|
||||||
|
System.out.println(new ObjectMapper().writeValueAsString(ds));
|
||||||
|
} catch (JsonProcessingException e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void validCommunities() throws Exception {
|
||||||
|
CommunityConfiguration cc = Utils.getCommunityConfiguration();
|
||||||
|
System.out.println(cc.getCommunities().keySet());
|
||||||
|
Community community =cc.getCommunities().get("aurora");
|
||||||
|
Assertions.assertEquals(0, community.getSubjects().size());
|
||||||
|
Assertions.assertEquals(null, community.getConstraints());
|
||||||
|
Assertions.assertEquals(null, community.getRemoveConstraints());
|
||||||
|
Assertions.assertEquals(2, community.getZenodoCommunities().size());
|
||||||
|
Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network")));
|
||||||
|
Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck")));
|
||||||
|
Assertions.assertEquals(35, community.getProviders().size());
|
||||||
|
Assertions.assertEquals(35, community.getProviders().stream().filter(p->p.getSelectionConstraints()==null).count());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void getCommunityProjects() throws Exception {
|
||||||
|
CommunityEntityMap projectMap = Utils.getCommunityProjects();
|
||||||
|
Assertions.assertFalse(projectMap.containsKey("mes"));
|
||||||
|
Assertions.assertEquals(33, projectMap.size());
|
||||||
|
Assertions.assertTrue(projectMap.keySet().stream().allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|"))));
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
|
@ -1,14 +1,14 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.oa.graph.group;
|
package eu.dnetlib.dhp.oa.graph.group;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
import java.io.IOException;
|
||||||
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
import java.net.URISyntaxException;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
import java.nio.file.Files;
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
import java.nio.file.Path;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
import java.nio.file.Paths;
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import org.apache.commons.io.FileUtils;
|
import org.apache.commons.io.FileUtils;
|
||||||
import org.apache.spark.SparkConf;
|
import org.apache.spark.SparkConf;
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
|
@ -18,13 +18,15 @@ import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import org.junit.jupiter.api.*;
|
import org.junit.jupiter.api.*;
|
||||||
|
|
||||||
import java.io.IOException;
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
import java.net.URISyntaxException;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
import java.nio.file.Files;
|
|
||||||
import java.nio.file.Path;
|
|
||||||
import java.nio.file.Paths;
|
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||||
|
import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
|
|
||||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||||
public class GroupEntitiesSparkJobTest {
|
public class GroupEntitiesSparkJobTest {
|
||||||
|
@ -69,7 +71,7 @@ public class GroupEntitiesSparkJobTest {
|
||||||
@Test
|
@Test
|
||||||
@Order(1)
|
@Order(1)
|
||||||
void testGroupEntities() throws Exception {
|
void testGroupEntities() throws Exception {
|
||||||
GroupEntitiesSparkJob.main(new String[]{
|
GroupEntitiesSparkJob.main(new String[] {
|
||||||
"-isSparkSessionManaged",
|
"-isSparkSessionManaged",
|
||||||
Boolean.FALSE.toString(),
|
Boolean.FALSE.toString(),
|
||||||
"-graphInputPath",
|
"-graphInputPath",
|
||||||
|
@ -88,7 +90,6 @@ public class GroupEntitiesSparkJobTest {
|
||||||
.selectExpr("COALESCE(*)")
|
.selectExpr("COALESCE(*)")
|
||||||
.as(Encoders.kryo(OafEntity.class));
|
.as(Encoders.kryo(OafEntity.class));
|
||||||
|
|
||||||
|
|
||||||
assertEquals(
|
assertEquals(
|
||||||
1,
|
1,
|
||||||
checkpointTable
|
checkpointTable
|
||||||
|
@ -98,7 +99,6 @@ public class GroupEntitiesSparkJobTest {
|
||||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||||
.count());
|
.count());
|
||||||
|
|
||||||
|
|
||||||
Dataset<Result> output = spark
|
Dataset<Result> output = spark
|
||||||
.read()
|
.read()
|
||||||
.textFile(
|
.textFile(
|
||||||
|
|
Loading…
Reference in New Issue