Merge pull request #6815 from ORCID/8657-create-a-one-of-csv-file-of-…

…the-mapping-of-ringgold-to-rors

Create a csv file with the Ringgold to RORs ids

orcid-persistence/src/main/java/org/orcid/persistence/dao/OrgDisambiguatedDao.java

@@ -16,6 +16,8 @@ public interface OrgDisambiguatedDao extends GenericDao<OrgDisambiguatedEntity,
     List<OrgDisambiguatedEntity> getOrgs(String searchTerm, int firstResult, int maxResults);
 
     List<OrgDisambiguatedEntity> getChunk(int firstResult, int maxResults);
+
+    List<OrgDisambiguatedEntity> findBySourceType(String sourceType,int firstResult, int maxResults);
 
     OrgDisambiguatedEntity findBySourceIdAndSourceType(String sourceId, String sourceType);
 

orcid-persistence/src/main/java/org/orcid/persistence/dao/impl/OrgDisambiguatedDaoImpl.java

@@ -39,6 +39,16 @@ public OrgDisambiguatedEntity findBySourceIdAndSourceType(String sourceId, Strin
         List<OrgDisambiguatedEntity> results = query.getResultList();
         return results.isEmpty() ? null : results.get(0);
     }
+
+    @Override
+    public List<OrgDisambiguatedEntity> findBySourceType(String sourceType, int firstResult, int maxResults){
+        TypedQuery<OrgDisambiguatedEntity> query = entityManager.createQuery("from OrgDisambiguatedEntity where sourceType = :sourceType",
+                OrgDisambiguatedEntity.class);
+        query.setParameter("sourceType", sourceType);
+        query.setFirstResult(firstResult);
+        query.setMaxResults(maxResults);
+        return query.getResultList();
+    }
 
     @Override
     public List<OrgDisambiguatedEntity> getChunk(int firstResult, int maxResults) {

orcid-scheduler-web/src/main/java/org/orcid/scheduler/loader/source/cli/RingoldToRorCSVMapping.java

@@ -0,0 +1,121 @@
+package org.orcid.scheduler.loader.source.cli;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.HashMap;
+import java.util.List;
+
+import javax.annotation.PostConstruct;
+
+import org.apache.commons.lang.StringUtils;
+
+import org.orcid.core.manager.OrgDisambiguatedManager;
+import org.orcid.core.orgs.OrgDisambiguatedSourceType;
+import org.orcid.core.utils.FunderIdentifierType;
+import org.orcid.persistence.constants.OrganizationStatus;
+import org.orcid.persistence.dao.OrgDisambiguatedDao;
+import org.orcid.persistence.jpa.entities.OrgDisambiguatedEntity;
+import org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity;
+import org.orcid.pojo.OrgDisambiguated;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+public class RingoldToRorCSVMapping {
+    private static final Logger LOGGER = LoggerFactory.getLogger(RingoldToRorCSVMapping.class);
+    private OrgDisambiguatedDao orgDisambiguatedDao;
+    private OrgDisambiguatedManager orgDisambiguatedManager;
+
+    private static final String RINGGOLD_TYPE = "RINGGOLD";
+
+    private static final int INDEXING_CHUNK_SIZE = 10000;
+
+    @Value("${org.orcid.core.orgs.ringgoldtororcsv:/tmp/ringgoldtoror.csv}")
+    private String csvFilePath;
+
+    /**
+     * Setup our spring resources
+     * 
+     */
+    @SuppressWarnings({ "resource" })
+    @PostConstruct
+    private void init() {
+        ApplicationContext context = new ClassPathXmlApplicationContext("orcid-scheduler-context.xml");
+        orgDisambiguatedDao = (OrgDisambiguatedDao) context.getBean("orgDisambiguatedDao");
+        orgDisambiguatedManager = (OrgDisambiguatedManager) context.getBean("orgDisambiguatedManager");
+    }
+
+    public static void main(String[] args) {
+        RingoldToRorCSVMapping mappingData = new RingoldToRorCSVMapping();
+        // TODO Auto-generated method stub
+        try {
+
+            mappingData.init();
+            mappingData.getCSVMapping();
+
+        } catch (Exception e) {
+            LOGGER.error("Exception when generating  csv mapping Ringgolds to Rors", e);
+            System.err.println(e.getMessage());
+        } finally {
+            System.exit(0);
+        }
+
+    }
+
+    public void getCSVMapping() {
+        LOGGER.info("About to start ringgold to ror csv mapping");
+        List<OrgDisambiguatedEntity> entities = null;
+        HashMap<String, String> ringgoldMap = new HashMap<String, String>();
+        ringgoldMap.put("Ringgold", "ROR");
+        int startIndex = 0;
+        do {
+            entities = orgDisambiguatedDao.findBySourceType(RINGGOLD_TYPE, startIndex, INDEXING_CHUNK_SIZE);
+            LOGGER.info("Found chunk of {} disambiguated orgs for indexing", entities.size());
+            for (OrgDisambiguatedEntity entity : entities) {
+                if (StringUtils.equals(entity.getStatus(), OrganizationStatus.PART_OF_GROUP.name())) {
+                    for (OrgDisambiguatedExternalIdentifierEntity externalIdentifier : entity.getExternalIdentifiers()) {
+                        if (StringUtils.equals(externalIdentifier.getIdentifierType(), FunderIdentifierType.ISNI.value())) {
+                            List<OrgDisambiguated> orgsFromExternalIdentifier = orgDisambiguatedManager
+                                    .findOrgDisambiguatedIdsForSameExternalIdentifier(externalIdentifier.getIdentifier(), FunderIdentifierType.ISNI.value());
+                            if (orgsFromExternalIdentifier != null) {
+                                orgsFromExternalIdentifier.stream().forEach((o -> {
+
+                                    if (o.getSourceType().equals(OrgDisambiguatedSourceType.ROR.name())) {
+                                        ringgoldMap.put(entity.getSourceId(), o.getSourceId());
+                                    }
+
+                                }));
+                            }
+                        } else if(StringUtils.equals(externalIdentifier.getIdentifierType(), OrgDisambiguatedSourceType.ROR.name())) {
+                            ringgoldMap.put(entity.getSourceId(),externalIdentifier.getIdentifier());
+                        }
+                    }
+
+                  //TBD check if there is any ROR that has the ringgold as external identifier??
+                }         
+            }
+            startIndex = startIndex + INDEXING_CHUNK_SIZE;
+        } while (!entities.isEmpty());
+
+        generateCsv(ringgoldMap);
+
+    }
+
+    public void generateCsv(HashMap<String, String> ringgoldMap) {
+        String eol = System.getProperty("line.separator");
+        try (Writer writer = new FileWriter("somefile.csv")) {
+          for (HashMap.Entry<String, String> entry : ringgoldMap.entrySet()) {
+            writer.append(entry.getKey())
+                  .append(',')
+                  .append(entry.getValue())
+                  .append(eol);
+          }
+        } catch (IOException ex) {
+          LOGGER.error("Cannot write the ringgold to ror csv", csvFilePath);
+        }
+    }
+
+}