Merge branch 'alpha' into SCRUM-4509

alliance-genome · Nov 8, 2024 · f8d6832 · f8d6832
2 parents 531d8b6 + e640b3c
commit f8d6832
Show file tree

Hide file tree

Showing 11 changed files with 11 additions and 11 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java b/src/main/java/org/alliancegenome/curation_api/services/CodingSequenceService.java
@@ -34,7 +34,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = codingSequenceDAO.findIdsByParams(params);

diff --git a/src/main/java/org/alliancegenome/curation_api/services/ExonService.java b/src/main/java/org/alliancegenome/curation_api/services/ExonService.java
@@ -32,7 +32,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = exonDAO.findIdsByParams(params);

diff --git a/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java b/src/main/java/org/alliancegenome/curation_api/services/TranscriptService.java
@@ -34,7 +34,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> ids = transcriptDAO.findIdsByParams(params);

diff --git a/...ociations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java b/...ociations/codingSequenceAssociations/CodingSequenceGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.CODING_SEQUENCE_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.CODING_SEQUENCE_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = codingSequenceGenomicLocationAssociationDAO.findIdsByParams(params);

diff --git a/...ion_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java b/...ion_api/services/associations/exonAssociations/ExonGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.EXON_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.EXON_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = exonGenomicLocationAssociationDAO.findIdsByParams(params);

diff --git a/...ion_api/services/associations/geneAssociations/GeneGenomicLocationAssociationService.java b/...ion_api/services/associations/geneAssociations/GeneGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.GENE_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = geneGenomicLocationAssociationDAO.findIdsByParams(params);

diff --git a/...vices/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java b/...vices/associations/transcriptAssociations/TranscriptCodingSequenceAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptCodingSequenceAssociationDAO.findIdsByParams(params);

diff --git a/...on_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java b/...on_api/services/associations/transcriptAssociations/TranscriptExonAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptExonAssociationDAO.findIdsByParams(params);

diff --git a/...on_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java b/...on_api/services/associations/transcriptAssociations/TranscriptGeneAssociationService.java
@@ -46,7 +46,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptGeneAssociationDAO.findIdsByParams(params);

diff --git a/...ices/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java b/...ices/associations/transcriptAssociations/TranscriptGenomicLocationAssociationService.java
@@ -45,7 +45,7 @@ protected void init() {
 	public List<Long> getIdsByDataProvider(BackendBulkDataProvider dataProvider) {
 		Map<String, Object> params = new HashMap<>();
 		params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER, dataProvider.sourceOrganization);
-		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD")) {
+		if (StringUtils.equals(dataProvider.sourceOrganization, "RGD") || StringUtils.equals(dataProvider.sourceOrganization, "XB")) {
 			params.put(EntityFieldConstants.TRANSCRIPT_ASSOCIATION_SUBJECT_TAXON, dataProvider.canonicalTaxonCurie);
 		}
 		List<Long> associationIds = transcriptGenomicLocationAssociationDAO.findIdsByParams(params);

diff --git a/...main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java b/...main/java/org/alliancegenome/curation_api/services/helpers/gff3/Gff3AttributesHelper.java
@@ -27,7 +27,7 @@ public static Map<String, String> getAttributes(Gff3DTO dto, BackendBulkDataProv
 		}
 
 		// Ensure identifiers have MOD prefix
-		for (String key : List.of("ID", "Parent")) {
+		for (String key : List.of("ID", "Parent", "gene_id")) {
 			if (attributes.containsKey(key)) {
 				String idsString = attributes.get(key);
 				if (StringUtils.equals(dataProvider.sourceOrganization, "WB")) {