Refactoring license migration

dmp-migration-tool/elastic/src/main/java/eu/old/eudat/elastic/criteria/DatasetCriteria.java

@@ -12,6 +12,7 @@ public class DatasetCriteria extends Criteria {
     private String like;
     private List<UUID> datasetTemplates;
     private Short status;
+    private List<UUID> ids;
     private List<UUID> dmps;
     private List<UUID> groupIds;
     private List<UUID> grants;
@@ -50,6 +51,14 @@ public class DatasetCriteria extends Criteria {
         this.status = status;
     }
 
+    public List<UUID> getIds() {
+        return ids;
+    }
+
+    public void setIds(List<UUID> ids) {
+        this.ids = ids;
+    }
+
     public List<UUID> getDmps() {
         return dmps;
     }

dmp-migration-tool/elastic/src/main/java/eu/old/eudat/elastic/repository/DatasetRepository.java

@@ -1,5 +1,6 @@
 package eu.old.eudat.elastic.repository;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.old.eudat.elastic.criteria.DatasetCriteria;
 import eu.old.eudat.elastic.entities.Dataset;
 import eu.old.eudat.elastic.entities.Dmp;
@@ -13,10 +14,8 @@ import org.elasticsearch.client.RestHighLevelClient;
 import org.elasticsearch.client.indices.GetIndexRequest;
 import org.elasticsearch.common.xcontent.XContentBuilder;
 import org.elasticsearch.common.xcontent.XContentFactory;
-import org.elasticsearch.index.query.BoolQueryBuilder;
+import org.elasticsearch.index.query.*;
-import org.elasticsearch.index.query.InnerHitBuilder;
+import org.elasticsearch.search.SearchHit;
-import org.elasticsearch.index.query.NestedQueryBuilder;
-import org.elasticsearch.index.query.QueryBuilders;
 import org.elasticsearch.search.SearchHits;
 import org.elasticsearch.search.aggregations.AggregationBuilders;
 import org.elasticsearch.search.aggregations.bucket.filter.FiltersAggregationBuilder;
@@ -78,6 +77,24 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
         return null;
     }
 
+    public List<Dataset> findByIds(List<String> ids) throws IOException {
+        if (this.getClient() != null) {
+            SearchRequest searchRequest = new SearchRequest(this.environment.getProperty("elasticsearch.index"));
+            SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
+            BoolQueryBuilder boolQuery = QueryBuilders.boolQuery().should(QueryBuilders.termsQuery("datasets.id.keyword", ids));
+            NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery( "datasets", boolQuery, ScoreMode.Avg).innerHit(new InnerHitBuilder());
+            searchSourceBuilder.query(nestedQueryBuilder);
+            searchSourceBuilder.size(100000);
+            searchRequest.source(searchSourceBuilder);
+            SearchResponse response = this.getClient().search(searchRequest, RequestOptions.DEFAULT);
+            return Arrays.stream(response.getHits().getHits())
+                    .map(hit -> hit.getInnerHits().values()).flatMap(Collection::stream)
+                    .map(SearchHits::getHits).flatMap(Arrays::stream)
+                    .map(x -> new Dataset().fromElasticEntity(this.transformFromString(x.getSourceAsString(), Map.class))).toList();
+        }
+        return null;
+    }
+
     @Override
     public Dataset findDocument(String id) throws IOException {
         if (this.getClient() != null) {
@@ -205,7 +222,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
             }
 
             NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.None).innerHit(new InnerHitBuilder().setFetchSourceContext(new FetchSourceContext(true, new String[]{"datasets.id"}, null)).setSize(this.environment.getProperty("elasticsearch.innerHitsSize", Integer.class)));
-            searchSourceBuilder.query(nestedQueryBuilder)/*.from(criteria.getOffset()).size(criteria.getSize())*/.fetchSource("datasets.id", null);
+            searchSourceBuilder.query(nestedQueryBuilder)/*.from(criteria.getOffset()).size(criteria.getSize())*/;
             sortBuilders.forEach(searchSourceBuilder::sort);
             searchRequest.source(searchSourceBuilder);
             SearchResponse response = this.getClient().search(searchRequest, RequestOptions.DEFAULT);
@@ -267,6 +284,11 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
             boolQuery = boolQuery.should(QueryBuilders.termQuery("datasets.status", criteria.getStatus().toString()));
         }
 
+        if (criteria.getIds() != null && criteria.getIds().size() > 0) {
+            criteria.setIds(criteria.getIds().stream().filter(Objects::nonNull).collect(Collectors.toList()));
+            boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.id.keyword", criteria.getIds().stream().map(UUID::toString).collect(Collectors.toList())));
+        }
+
         if (criteria.getDmps() != null && criteria.getDmps().size() > 0) {
             criteria.setDmps(criteria.getDmps().stream().filter(Objects::nonNull).collect(Collectors.toList()));
             boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.dmp", criteria.getDmps().stream().map(UUID::toString).collect(Collectors.toList())));

dmp-migration-tool/elastic/src/main/java/eu/old/eudat/elastic/repository/ElasticRepository.java

@@ -13,7 +13,7 @@ import java.io.IOException;
 /**
  * Created by ikalyvas on 7/5/2018.
  */
-public abstract class ElasticRepository<T extends ElasticEntity,C extends Criteria> implements Repository<T,C> {
+public abstract class ElasticRepository<T extends ElasticEntity<?>,C extends Criteria> implements Repository<T,C> {
     private static final Logger logger = LoggerFactory.getLogger(ElasticRepository.class);
     private RestHighLevelClient client;
 

dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DmpMigrationService.java

@@ -118,53 +118,6 @@ public class DmpMigrationService {
                             contactEntity.setUserId((String) model.getExtraProperties().get("contact"));
                             dmpProperties.getContacts().add(contactEntity);
                         }
-                        if (model.getExtraProperties().containsKey("license") && model.getExtraProperties().get("license") != null) {
-                            Object license = model.getExtraProperties().get("license");
-                            HashMap<String, String> licenseMap = jsonHandlingService.mapFromJson(jsonHandlingService.toJson(license));
-                            ReferenceEntity referenceEntity = new ReferenceEntity();
-                            if (licenseMap.containsKey("pid")) {
-                                referenceEntity.setReference(licenseMap.get("pid"));
-                            }
-                            ReferenceQuery referenceQuery = queryFactory.query(ReferenceQuery.class)
-                                    .references(referenceEntity.getReference())
-                                    .types(ReferenceType.Licenses)
-                                    .isActive(IsActive.Active);
-                            List<ReferenceEntity> foundReferences = referenceQuery.collect();
-                            boolean licenseExists = foundReferences != null && !foundReferences.isEmpty();
-                            if (!licenseExists) {
-                                if (licenseMap.containsKey("name")) {
-                                    referenceEntity.setLabel(licenseMap.get("name"));
-                                }
-                                if (licenseMap.containsKey("uri")) {
-                                    referenceEntity.setSource(licenseMap.get("uri"));
-                                }
-                                if (licenseMap.containsKey("abbreviation")) {
-                                    referenceEntity.setAbbreviation(licenseMap.get("abbreviation"));
-                                }
-                                referenceEntity.setId(UUID.randomUUID());
-                                referenceEntity.setSourceType(ReferenceSourceType.External);
-                                referenceEntity.setType(ReferenceType.Licenses);
-                                referenceEntity.setCreatedAt(Instant.now());
-                                referenceEntity.setUpdatedAt(Instant.now());
-                                referenceEntity.setIsActive(IsActive.Active);
-                            }
-
-                            DmpReferenceEntity dmpReferenceEntity = new DmpReferenceEntity();
-                            dmpReferenceEntity.setId(UUID.randomUUID());
-                            dmpReferenceEntity.setDmpId(data.getId());
-                            if (licenseExists) {
-                                dmpReferenceEntity.setReferenceId(foundReferences.getFirst().getId());
-                            } else {
-                                dmpReferenceEntity.setReferenceId(referenceEntity.getId());
-                            }
-                            dmpReferenceEntity.setCreatedAt(Instant.now());
-                            dmpReferenceEntity.setUpdatedAt(Instant.now());
-                            dmpReferenceEntity.setIsActive(IsActive.Active);
-
-                            if (!licenseExists)
-                                entityManager.persist(referenceEntity);
-                            entityManager.persist(dmpReferenceEntity);
-                        }
                     }
                     if (model.getProperties() != null) {
                         model.getProperties().forEach((key,val) -> {
@@ -205,4 +158,93 @@ public class DmpMigrationService {
         } while (items != null && !items.isEmpty() && !TestMode);
     }
 
+    public void migrateDmpLicenses() throws JsonProcessingException {
+        DMPDao dmpDao = databaseRepository.getDmpDao();
+        long total = dmpDao.asQueryable().count();
+        logger.debug("Migrate Licenses for Dmp Total : " + total);
+        int page = 0;
+
+        Set<String> collectedLicenses = new HashSet<>();
+        Map<String, UUID> licenseIdByName = new HashMap<>();
+        List<DMP> items;
+        do {
+            items = dmpDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("created"))).orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
+
+            if (items != null && !items.isEmpty()) {
+                logger.debug("Migrate Licenses for Dmp " + page * PageSize + " of " + total);
+
+                for (DMP item : items) {
+                    DataManagementPlan model = new DataManagementPlan();
+                    model.fromDataModel(item);
+                    if (model.getExtraProperties() != null) {
+                        if (model.getExtraProperties().containsKey("license") && model.getExtraProperties().get("license") != null) {
+                            Object license = model.getExtraProperties().get("license");
+                            HashMap<String, String> licenseMap = jsonHandlingService.mapFromJson(jsonHandlingService.toJson(license));
+                            ReferenceEntity referenceEntity = new ReferenceEntity();
+                            String licensePid;
+                            if (licenseMap.containsKey("pid") && licenseMap.get("pid") != null) {
+                                licensePid = licenseMap.get("pid");
+                                referenceEntity.setReference(licensePid);
+                            }
+                            else
+                                continue;
+                            boolean licenseExists = collectedLicenses.contains(licensePid);
+                            if (!licenseExists) {
+                                if (licenseMap.containsKey("name")) {
+                                    referenceEntity.setLabel(licenseMap.get("name"));
+                                }
+                                if (licenseMap.containsKey("uri")) {
+                                    referenceEntity.setSource(licenseMap.get("uri"));
+                                }
+                                if (licenseMap.containsKey("abbreviation")) {
+                                    referenceEntity.setAbbreviation(licenseMap.get("abbreviation"));
+                                }
+                                if (licenseMap.containsKey("source") && licenseMap.get("source") != null) {
+                                    logger.debug("License found with source '{}'", licenseMap.get("source"));
+                                }
+                                if (licenseMap.containsKey("created") && licenseMap.get("created") != null) {
+                                    referenceEntity.setUpdatedAt(Instant.parse(licenseMap.get("created")));
+                                } else {
+                                    referenceEntity.setCreatedAt(Instant.now());
+                                }
+                                if (licenseMap.containsKey("modified") && licenseMap.get("modified") != null) {
+                                    referenceEntity.setUpdatedAt(Instant.parse(licenseMap.get("modified")));
+                                } else {
+                                    referenceEntity.setUpdatedAt(Instant.now());
+                                }
+//                                if (licenseMap.containsKey("tag") && licenseMap.get("tag") != null && !"Open Definition".equals(licenseMap.get("tag"))) {
+//                                    logger.debug("License found with tag '{}'", licenseMap.get("tag"));
+//                                }
+                                referenceEntity.setId(UUID.randomUUID());
+                                referenceEntity.setSourceType(ReferenceSourceType.External);
+                                referenceEntity.setType(ReferenceType.Licenses);
+                                referenceEntity.setIsActive(IsActive.Active);
+
+                                collectedLicenses.add(licensePid);
+                                licenseIdByName.put(licensePid, referenceEntity.getId());
+                                logger.debug("License '{}' migrated", licensePid);
+                            }
+
+                            DmpReferenceEntity dmpReferenceEntity = new DmpReferenceEntity();
+                            dmpReferenceEntity.setId(UUID.randomUUID());
+                            dmpReferenceEntity.setDmpId(item.getId());
+                            dmpReferenceEntity.setReferenceId(licenseIdByName.get(licensePid));
+                            dmpReferenceEntity.setCreatedAt(Instant.now());
+                            dmpReferenceEntity.setUpdatedAt(Instant.now());
+                            dmpReferenceEntity.setIsActive(IsActive.Active);
+
+                            if (!licenseExists)
+                                entityManager.persist(referenceEntity);
+                            entityManager.persist(dmpReferenceEntity);
+                        }
+                    }
+                    this.entityManager.flush();
+                }
+
+                page++;
+            }
+        } while (items != null && !items.isEmpty() && !TestMode);
+        logger.info("Dmp licenses migration finished");
+    }
+
 }

dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/TagMigrationService.java

@@ -7,6 +7,7 @@ import eu.eudat.data.DescriptionTagEntity;
 import eu.eudat.data.TagEntity;
 import eu.old.eudat.data.dao.entities.DatasetDao;
 import eu.old.eudat.data.entities.Dataset;
+import eu.old.eudat.elastic.criteria.DatasetCriteria;
 import eu.old.eudat.elastic.entities.Tag;
 import eu.old.eudat.elastic.repository.DatasetRepository;
 import eu.old.eudat.logic.services.operations.DatabaseRepository;
@@ -50,18 +51,24 @@ public class TagMigrationService {
         Set<String> savedTagNames = new HashSet<>();
         Map<String, UUID> savedTagIdsByName = new HashMap<>();
 
+        DatasetCriteria criteria = new DatasetCriteria();
         List<Dataset> items;
         do {
             items = datasetDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("created"))).orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
             if (items != null && !items.isEmpty()) {
                 logger.debug("Migrate Dataset tags " + page * PageSize + " of " + total);
 
+                criteria.setIds(items.stream().map(Dataset::getId).toList());
+//                List<eu.old.eudat.elastic.entities.Dataset> elasticDatasets = this.datasetRepository.queryIds(criteria);
+                List<eu.old.eudat.elastic.entities.Dataset> elasticDatasets = this.datasetRepository.findByIds(items.stream().map(x -> x.getId().toString()).toList());
+
                  for (Dataset item : items) {
-                    eu.old.eudat.elastic.entities.Dataset elasticDataset = this.datasetRepository.findDocument(item.getId().toString());
+                    List<eu.old.eudat.elastic.entities.Dataset> found = elasticDatasets.stream().filter(x -> item.getId().toString().equals(x.getId())).toList();
-                    if (elasticDataset == null) {
+                    if (found.isEmpty()) {
                         logger.error("No dataset with id {} found on elastic search. Skipping tag migration for this dataset", item.getId());
                         continue;
                     }
+                    eu.old.eudat.elastic.entities.Dataset elasticDataset = found.getFirst();
                     boolean tagAlreadyExists;
                     if (elasticDataset.getTags() != null && !elasticDataset.getTags().isEmpty()) {
                         for(Tag tag : elasticDataset.getTags()) {

dmp-migration-tool/web/src/main/java/eu/old/eudat/publicapi/migration/MigrationController.java

@@ -87,6 +87,7 @@ public class MigrationController {
         this.serviceMigrationService.migrate();
 
         this.dmpMigrationService.migrate();
+        this.dmpMigrationService.migrateDmpLicenses();
         this.dmpDatasetProfileMigrationService.migrate();
         this.datasetMigrationService.migrate();
         this.tagMigrationService.migrate();
@@ -125,6 +126,13 @@ public class MigrationController {
         return true;
     }
 
+    @GetMapping("dmps/licenses")
+    @Transactional
+    public boolean migrateDmpLicenses() throws JsonProcessingException, NoSuchFieldException, IllegalAccessException {
+        this.dmpMigrationService.migrateDmpLicenses();
+        return true;
+    }
+
     @GetMapping("datasets")
     @Transactional
     public boolean migrateDatasets() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {