SCRUM-4190

src/main/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java

@@ -6,8 +6,8 @@
 import org.alliancegenome.curation_api.exceptions.ObjectUpdateException;
 import org.alliancegenome.curation_api.model.entities.GeneOntologyAnnotation;
 import org.alliancegenome.curation_api.model.entities.Organization;
+import org.alliancegenome.curation_api.model.entities.bulkloads.BulkFMSLoad;
 import org.alliancegenome.curation_api.model.entities.bulkloads.BulkLoadFileHistory;
-import org.alliancegenome.curation_api.model.entities.bulkloads.BulkURLLoad;
 import org.alliancegenome.curation_api.model.ingest.dto.GeneOntologyAnnotationDTO;
 import org.alliancegenome.curation_api.services.GeneOntologyAnnotationService;
 import org.alliancegenome.curation_api.services.OrganizationService;
@@ -33,16 +33,11 @@ public class GeneOntologyAnnotationExecutor extends LoadFileExecutor {
 
 	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException {
 
-		String url = ((BulkURLLoad) bulkLoadFileHistory.getBulkLoad()).getBulkloadUrl();
-
-		String[] tok = url.split("/");
-		String orgAbbrev = tok[tok.length - 1].toUpperCase();
-		String abbr = orgAbbrev.split("\\.")[0];
+		String abbr = ((BulkFMSLoad) bulkLoadFileHistory.getBulkLoad()).getFmsDataSubType();
 		Organization organization = organizationService.getByAbbr(abbr).getEntity();
 
 		// curie, List<GO curie>
 		Map<String, List<String>> uiMap = new HashMap<>();
-		Set<String> orgIDs = new HashSet<>();
 		GZIPInputStream stream = new GZIPInputStream(new FileInputStream(bulkLoadFileHistory.getBulkLoadFile().getLocalFilePath()));
 		try (BufferedReader br = new BufferedReader(new InputStreamReader(stream))) {
 			Stream<String> lines = br.lines();
@@ -51,10 +46,9 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException
 			lines.filter(s -> !s.startsWith("!") && StringUtils.isNotEmpty(s)).forEach(s -> {
 				String[] token = s.split("\t");
 				String orgID = token[0];
-				orgIDs.add(orgID);
 				String modID = token[1];
 				String goID = token[4];
-				if (abbr.equals(orgID)) {
+				if (abbr.equalsIgnoreCase(orgID) || orgID.equalsIgnoreCase("Xenbase") || abbr.equals("HUMAN") && orgID.equals("RGD")) {
 					List<String> goIDs = uiMap.computeIfAbsent(modID, list -> new ArrayList<>());
 					goIDs.add(goID);
 				}
@@ -77,7 +71,15 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException
 			.stream()
 			.map(entry -> entry.getValue().stream().map(goID -> {
 				GeneOntologyAnnotationDTO dto = new GeneOntologyAnnotationDTO();
-				dto.setGeneIdentifier(abbr + ":" + entry.getKey());
+				String prefix = abbr;
+				if (abbr.equalsIgnoreCase("XB")) {
+					prefix = "Xenbase";
+				}
+				if (abbr.equalsIgnoreCase("HUMAN")) {
+					prefix = null;
+				}
+				String geneIdentifier = prefix != null ? prefix + ":" + entry.getKey() : entry.getKey();
+				dto.setGeneIdentifier(geneIdentifier);
 				dto.setGoTermCurie(goID);
 				return dto;
 			}).toList()).flatMap(Collection::stream).toList();

src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java

@@ -15,14 +15,17 @@
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 import org.alliancegenome.curation_api.services.validation.DataProviderValidator;
+import org.apache.commons.collections.CollectionUtils;
 
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 @RequestScoped
 public class GeneOntologyAnnotationService extends BaseEntityCrudService<GeneOntologyAnnotation, GeneOntologyAnnotationDAO> {
 
-	private Species species;
+	private List<Species> species;
 	public static final String RESOURCE_DESCRIPTOR_PREFIX = "ENSEMBL";
 	public static final String RESOURCE_DESCRIPTOR_PAGE_NAME = "default";
 	// <crossReference.referencedCurie, DataProvider>
@@ -32,7 +35,6 @@ public class GeneOntologyAnnotationService extends BaseEntityCrudService<GeneOnt
 	private Map<Long, GeneOntologyAnnotationDTO> gafMap = new HashMap<>();
 
 
-
 	@Inject
 	@AuthenticatedUser
 	protected Person authenticatedPerson;
@@ -92,7 +94,8 @@ private void addNewRecordToMap(GeneOntologyAnnotation gafNew, GeneOntologyAnnota
 
 	public Long getGeneID(GeneOntologyAnnotationDTO uiEntity, String orgAbbreviation) {
 		if (accessionGeneMap.isEmpty()) {
-			accessionGeneMap = geneDAO.getAllGeneIdsPerSpecies(getSpecies(orgAbbreviation));
+			List<Species> speciesList = getSpecies(orgAbbreviation);
+			speciesList.forEach(species -> accessionGeneMap.putAll(geneDAO.getAllGeneIdsPerSpecies(species)));
 		}
 		Long geneID = accessionGeneMap.get(uiEntity.getGeneIdentifier());
 		return geneID;
@@ -106,16 +109,24 @@ private Long getGOID(GeneOntologyAnnotationDTO uiEntity) {
 		return goID;
 	}
 
-	private Species getSpecies(String orgAbbreviation) {
-		if (species != null) {
+	private List<Species> getSpecies(String orgAbbreviation) {
+		if (CollectionUtils.isNotEmpty(species)) {
 			return species;
 		}
-		Map<String, Object> map = new HashMap<>();
-		map.put("displayName", orgAbbreviation);
-		species = speciesDAO.findByParams(map).getSingleResult();
+		if (orgAbbreviation.equalsIgnoreCase("XB")) {
+			species = new ArrayList<>();
+			species.add(getSingleSpecies("XBXL"));
+			species.add(getSingleSpecies("XBXT"));
+		} else {
+			species = List.of(getSingleSpecies(orgAbbreviation));
+		}
 		return species;
 	}
 
+	private Species getSingleSpecies(String orgAbbreviation) {
+		return speciesDAO.findByField("displayName", orgAbbreviation).getSingleResult();
+	}
+
 	public ObjectResponse<DataProvider> validate(DataProvider uiEntity) {
 		return dataProviderValidator.validateDataProvider(uiEntity, null, true);
 	}

src/main/java/org/alliancegenome/curation_api/services/OrganizationService.java

@@ -1,23 +1,23 @@
 package org.alliancegenome.curation_api.services;
 
-import java.util.Date;
-import java.util.HashMap;
-
+import io.quarkus.logging.Log;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
 import org.alliancegenome.curation_api.dao.OrganizationDAO;
 import org.alliancegenome.curation_api.model.entities.Organization;
 import org.alliancegenome.curation_api.response.ObjectResponse;
 import org.alliancegenome.curation_api.response.SearchResponse;
 import org.alliancegenome.curation_api.services.base.BaseEntityCrudService;
 
-import io.quarkus.logging.Log;
-import jakarta.annotation.PostConstruct;
-import jakarta.enterprise.context.RequestScoped;
-import jakarta.inject.Inject;
+import java.util.Date;
+import java.util.HashMap;
 
 @RequestScoped
 public class OrganizationService extends BaseEntityCrudService<Organization, OrganizationDAO> {
 
-	@Inject OrganizationDAO organizationDAO;
+	@Inject
+	OrganizationDAO organizationDAO;
 
 	Date orgRequest;
 	HashMap<Long, Organization> orgIdCacheMap = new HashMap<>();
@@ -54,7 +54,7 @@ public ObjectResponse<Organization> getById(Long id) {
 	public ObjectResponse<Organization> getByAbbr(String abbr) {
 
 		Organization org = null;
-		SearchResponse<Organization> orgResponse = null;
+		SearchResponse<Organization> orgResponse;
 
 		if (orgRequest != null) {
 			if (orgAbbrCacheMap.containsKey(abbr)) {

src/main/resources/db/migration/v0.38.0.10__gaf-load.sql

@@ -0,0 +1,90 @@
+-- delete old bulk URL load
+delete
+from bulkurlload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkfmsload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete
+from bulkscheduledload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkloadfilehistory
+where bulkload_id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkload
+where id in (select id FROM bulkload WHERE backendbulkloadtype = 'GAF');
+
+delete from bulkloadgroup where name = 'File Management System (FMS) GAF Loads';
+-- Create bulk loads got the GAF load
+INSERT INTO bulkloadgroup (id, name)
+VALUES (nextval('bulkloadgroup_seq'), 'File Management System (FMS) GAF Loads');
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'FB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'HUMAN GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'MGI GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'RGD GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'SGD GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'WB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'XB GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'GAF', 'ZFIN GAF Load', 'STOPPED', id
+FROM bulkloadgroup
+WHERE name = 'File Management System (FMS) GAF Loads';
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', false
+FROM bulkload
+WHERE backendbulkloadtype = 'GAF';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'FB'
+FROM bulkload
+WHERE name = 'FB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'HUMAN'
+FROM bulkload
+WHERE name = 'HUMAN GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'MGI'
+FROM bulkload
+WHERE name = 'MGI GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'RGD'
+FROM bulkload
+WHERE name = 'RGD GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'SGD'
+FROM bulkload
+WHERE name = 'SGD GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'WB'
+FROM bulkload
+WHERE name = 'WB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'XB'
+FROM bulkload
+WHERE name = 'XB GAF Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'GAF', 'ZFIN'
+FROM bulkload
+WHERE name = 'ZFIN GAF Load';