Merge pull request #1805 from alliance-genome/SCRUM-4754

SCRUM-4754 Fix GAF loads
alliance-genome · Jan 15, 2025 · 0870f18 · 0870f18
2 parents e0f101f + e3dd6c1
commit 0870f18
Show file tree

Hide file tree

Showing 3 changed files with 31 additions and 25 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/dao/GeneOntologyAnnotationDAO.java b/src/main/java/org/alliancegenome/curation_api/dao/GeneOntologyAnnotationDAO.java
@@ -1,15 +1,17 @@
 package org.alliancegenome.curation_api.dao;
 
-import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.persistence.Query;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
 import org.alliancegenome.curation_api.model.entities.GeneOntologyAnnotation;
-import org.alliancegenome.curation_api.model.entities.Organization;
 import org.alliancegenome.curation_api.model.ingest.dto.GeneOntologyAnnotationDTO;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import com.google.common.base.Objects;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.persistence.Query;
 
 @ApplicationScoped
 public class GeneOntologyAnnotationDAO extends BaseSQLDAO<GeneOntologyAnnotation> {
@@ -34,17 +36,24 @@ insert into GeneOntologyAnnotation (id, singlegene_id,goterm_id)
 		return gaf;
 	}
 
-	public Map<Long, GeneOntologyAnnotationDTO> getAllGafIdsPerProvider(Organization sourceOrganization) {
+	public Map<Long, GeneOntologyAnnotationDTO> getAllGafIdsPerProvider(String speciesAbbreviation) {
+		String speciesNameClause = " and spec.displayname = :speciesName";
+		if (Objects.equal(speciesAbbreviation, "XB")) {
+			speciesNameClause = " and spec.displayname in ('XBXL', 'XBXT')";
+		}
+
 		Query query = entityManager.createNativeQuery("""
-			select gga.id, be.primaryexternalid, ot.curie
-			from GeneOntologyAnnotation as gga , BiologicalEntity as be, ontologyterm as ot,
-			species as spec
-			where gga.singlegene_id = be.id
-			and be.taxon_id = spec.taxon_id
-			and spec.displayname = :speciesName
-			and gga.goterm_id = ot.id
-			""");
-		query.setParameter("speciesName", sourceOrganization.getAbbreviation());
+				select gga.id, be.primaryexternalid, ot.curie
+				from GeneOntologyAnnotation as gga , BiologicalEntity as be, ontologyterm as ot,
+				species as spec
+				where gga.singlegene_id = be.id
+				and be.taxon_id = spec.taxon_id
+				and gga.goterm_id = ot.id
+				""" + speciesNameClause);
+		if (!Objects.equal(speciesAbbreviation, "XB")) {
+			query.setParameter("speciesName", speciesAbbreviation);
+		}
+
 		List<Object[]> result = query.getResultList();
 		Map<Long, GeneOntologyAnnotationDTO> map = new HashMap<>();
 		result.forEach(object -> {
@@ -53,6 +62,7 @@ public Map<Long, GeneOntologyAnnotationDTO> getAllGafIdsPerProvider(Organization
 			dto.setGoTermCurie((String) object[2]);
 			map.put((Long) object[0], dto);
 		});
+
 		return map;
 	}
 

diff --git a/...n/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java b/...n/java/org/alliancegenome/curation_api/jobs/executors/GeneOntologyAnnotationExecutor.java
@@ -17,20 +17,17 @@
 
 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.ingest.dto.GeneOntologyAnnotationDTO;
 import org.alliancegenome.curation_api.services.GeneOntologyAnnotationService;
 import org.alliancegenome.curation_api.services.OrganizationService;
 import org.alliancegenome.curation_api.util.ProcessDisplayHelper;
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang.StringUtils;
 
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
-import lombok.extern.jbosslog.JBossLog;
 
-@JBossLog
 @ApplicationScoped
 public class GeneOntologyAnnotationExecutor extends LoadFileExecutor {
 
@@ -42,7 +39,6 @@ public class GeneOntologyAnnotationExecutor extends LoadFileExecutor {
 	public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException {
 
 		String abbr = ((BulkFMSLoad) bulkLoadFileHistory.getBulkLoad()).getFmsDataSubType();
-		Organization organization = organizationService.getByAbbr(abbr).getEntity();
 
 		// curie, List<GO curie>
 		Map<String, List<String>> uiMap = new HashMap<>();
@@ -56,7 +52,7 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException
 				String orgID = token[0];
 				String modID = token[1];
 				String goID = token[4];
-				if (abbr.equalsIgnoreCase(orgID) || orgID.equalsIgnoreCase("Xenbase") || abbr.equals("HUMAN") && orgID.equals("RGD")) {
+				if (abbr.equalsIgnoreCase(orgID) || abbr.equals("XB") && orgID.equalsIgnoreCase("Xenbase") || abbr.equals("HUMAN") && orgID.equals("RGD")) {
 					List<String> goIDs = uiMap.computeIfAbsent(modID, list -> new ArrayList<>());
 					goIDs.add(goID);
 				}
@@ -68,7 +64,7 @@ public void execLoad(BulkLoadFileHistory bulkLoadFileHistory) throws IOException
 
 		String name = bulkLoadFileHistory.getBulkLoad().getName();
 
-		Map<Long, GeneOntologyAnnotationDTO> gafMap = service.getGafMap(organization);
+		Map<Long, GeneOntologyAnnotationDTO> gafMap = service.getGafMap(abbr);
 		List<Long> gafIdsBefore = new ArrayList<>(gafMap.keySet().stream().toList());
 		gafIdsBefore.removeIf(Objects::isNull);
 

diff --git a/src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java b/src/main/java/org/alliancegenome/curation_api/services/GeneOntologyAnnotationService.java
@@ -123,11 +123,11 @@ private Species getSingleSpecies(String orgAbbreviation) {
 	}
 
 
-	public Map<Long, GeneOntologyAnnotationDTO> getGafMap(Organization organization) {
+	public Map<Long, GeneOntologyAnnotationDTO> getGafMap(String dataSubtype) {
 		if (gafMap.size() > 0) {
 			return gafMap;
 		}
-		gafMap = gafDAO.getAllGafIdsPerProvider(organization);
+		gafMap = gafDAO.getAllGafIdsPerProvider(dataSubtype);
 		return gafMap;
 	}