Fix cleanup bug for XB GFF loads

alliance-genome · Nov 7, 2024 · 4234159 · 4234159
1 parent 9172255
commit 4234159
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Showing 10 changed files with 10 additions and 10 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);