parse extra params, e.g. excludes, sort if needed. replace more text …

…with constants. #522
opencb · Feb 3, 2020 · 4a2a1b5 · 4a2a1b5
1 parent 8ce23ae
commit 4a2a1b5
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Showing 10 changed files with 85 additions and 372 deletions.
diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java
@@ -63,8 +63,7 @@ public ClinicalWSServer(@PathParam("version")
                     value = "Comma separated list of database sources of the documents to be returned. Possible values "
                             + " are clinvar,cosmic or iarctp53. E.g.: clinvar,cosmic",
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "region",
-                    value = "Comma separated list of genomic regions to be queried, e.g.: 1:6635137-6635325",
+            @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "so",
                     value = "Comma separated list of sequence ontology term names, e.g.: missense_variant. Exact text "
@@ -116,15 +115,15 @@ public ClinicalWSServer(@PathParam("version")
                     required = false, dataType = "java.util.List", paramType = "query")
     })
     public Response getAll(@QueryParam("exclude")
-                           @ApiParam(value = "Set which fields are excluded in the response, e.g.: transcripts.exons.") String exclude,
+                               @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
                            @QueryParam("include")
-                           @ApiParam(value = "Set which fields are include in the response, e.g.: transcripts.exons.") String include,
+                               @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
                            @QueryParam("sort")
-                           @ApiParam(value = "Sort returned results by a certain data model attribute.") String sort,
+                               @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
                            @QueryParam("limit") @DefaultValue("10")
-                           @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                               @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
                            @QueryParam("skip") @DefaultValue("0")
-                           @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
+                               @ApiParam(value = ParamConstants.SKIP_DESCRIPTION)  Integer skip) {
         try {
             parseIncludesAndExcludes(exclude, include, sort);
             parseLimitAndSkip(limit, skip);

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
@@ -432,6 +432,8 @@ public Response getTranscriptsByGeneId(@PathParam("geneId") @ApiParam(name = "ge
             @QueryParam("limit") @DefaultValue("10") @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
             @QueryParam("skip") @DefaultValue("0") @ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
         try {
+            parseIncludesAndExcludes(exclude, include, sort);
+            parseLimitAndSkip(limit, skip);
             parseQueryParams();
             TranscriptDBAdaptor transcriptDBAdaptor = dbAdaptorFactory.getTranscriptDBAdaptor(this.species, this.assembly);
             List<Query> queries = createQueries(geneId, TranscriptDBAdaptor.QueryParams.XREFS.key());
@@ -523,6 +525,8 @@ public Response getSNPByGeneId(@PathParam("geneId")
             @QueryParam("limit") @DefaultValue("10") @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
             @QueryParam("skip") @DefaultValue("0") @ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
         try {
+            parseIncludesAndExcludes(exclude, include, sort);
+            parseLimitAndSkip(limit, skip);
             parseQueryParams();
             VariantDBAdaptor variationDBAdaptor = dbAdaptorFactory.getVariationDBAdaptor(this.species, this.assembly);
             if (merge) {
@@ -615,6 +619,8 @@ public Response getAllTfbs(@PathParam("geneId") @ApiParam(name = "geneId", value
             @QueryParam("limit") @DefaultValue("10") @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
             @QueryParam("skip") @DefaultValue("0") @ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
         try {
+            parseIncludesAndExcludes(exclude, include, sort);
+            parseLimitAndSkip(limit, skip);
             parseQueryParams();
             GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly);
             if (merge) {
@@ -656,6 +662,8 @@ public Response getProteinById(@PathParam("geneId") @ApiParam(name = "geneId", v
             @QueryParam("limit") @DefaultValue("10") @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
             @QueryParam("skip") @DefaultValue("0") @ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
         try {
+            parseIncludesAndExcludes(exclude, include, sort);
+            parseLimitAndSkip(limit, skip);
             parseQueryParams();
             ProteinDBAdaptor proteinDBAdaptor = dbAdaptorFactory.getProteinDBAdaptor(this.species, this.assembly);
             List<Query> queries = createQueries(geneId, ProteinDBAdaptor.QueryParams.XREFS.key());

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java