hotfix-4.5.x: Clinical legacy Web Services were incorrectly querying the new clinical collection
@@ -105,7 +105,7 @@ public class ClinicalLegacyWSServer extends GenericRestWSServer {
try {
logger.info("VERSION: {}", this.version);
parseQueryParams();
- ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
+ ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalLegacyDBAdaptor(this.species, this.assembly);
if (!queryOptions.containsKey("limit") || ((int) queryOptions.get("limit")) > 1000) {
queryOptions.put("limit", 1000);
}
@@ -166,7 +166,7 @@ public class ClinicalLegacyWSServer extends GenericRestWSServer {
+ "clinvarSet.referenceClinVarAssertion.clinicalSignificance.reviewStatus", required = true) String fields) {
try {
parseQueryParams();
- ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
+ ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalLegacyDBAdaptor(this.species, this.assembly);
return createOkResponse(clinicalDBAdaptor.groupBy(query, Arrays.asList(fields.split(",")), queryOptions));
} catch (Exception e) {
return createErrorResponse(e);
@@ -179,7 +179,7 @@ public class ClinicalLegacyWSServer extends GenericRestWSServer {
public Response getPhenotypeGeneRelations() {
try {
parseQueryParams();
- ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
+ ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalLegacyDBAdaptor(this.species, this.assembly);
return createOkResponse(clinicalDBAdaptor.getPhenotypeGeneRelations(query, queryOptions));
} catch (Exception e) {
return createErrorResponse(e);
@@ -192,7 +192,7 @@ public class ClinicalLegacyWSServer extends GenericRestWSServer {
public Response getAllClinicalSignificances() {
try {
parseQueryParams();
- ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
+ ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalLegacyDBAdaptor(this.species, this.assembly);
query.put("source", "clinvar");
return createOkResponse(clinicalDBAdaptor.distinct(query,
"clinvarSet.referenceClinVarAssertion.clinicalSignificance.description"));
