fix count. #522

opencb · Feb 5, 2020 · e7a3e37 · e7a3e37
1 parent d3f26d2
commit e7a3e37
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Showing 10 changed files with 28 additions and 27 deletions.
diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
@@ -211,8 +211,16 @@ public void parseQueryParams() throws CellbaseException {
 
         // Add all the others QueryParams from the URL
         for (Map.Entry<String, List<String>> entry : multivaluedMap.entrySet()) {
-            if (!queryOptions.containsKey(entry.getKey())) {
-                query.put(entry.getKey(), entry.getValue().get(0));
+
+            String key = entry.getKey();
+            String value = entry.getValue().get(0);
+
+            if (!queryOptions.containsKey(key)) {
+                if ("count".equalsIgnoreCase(key)) {
+                    queryOptions.put("count", Boolean.parseBoolean(value));
+                } else {
+                    query.put(key, value);
+                }
             }
         }
     }

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java
@@ -60,12 +60,9 @@ public SpeciesWSServer(@PathParam("version")
     @ApiOperation(httpMethod = "GET",
             value = "Retrieves info about current species chromosomes.", response = Chromosome.class,
             responseContainer = "QueryResponse")
-    public Response getSpeciesInfo(@QueryParam("exclude")
-                                       @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
-                                   @QueryParam("include")
-                                       @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
-                                   @QueryParam("sort")
-                                       @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort) {
+    public Response getSpeciesInfo(@QueryParam("exclude") @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
+                                   @QueryParam("include") @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
+                                   @QueryParam("sort") @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort) {
         try {
             parseIncludesAndExcludes(exclude, include, sort);
             parseQueryParams();

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
@@ -57,7 +57,7 @@ public ClinicalWSServer(@PathParam("version")
             value = "Retrieves all clinical variants", response = Variant.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "source", value = ParamConstants.SOURCE,
                     required = false, dataType = "java.util.List", paramType = "query"),
@@ -84,16 +84,11 @@ public ClinicalWSServer(@PathParam("version")
             @ApiImplicitParam(name = "alleleOrigin", value = ParamConstants.ALLELE_ORIGIN,
                     required = false, dataType = "java.util.List", paramType = "query")
     })
-    public Response getAll(@QueryParam("exclude")
-                               @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
-                           @QueryParam("include")
-                               @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
-                           @QueryParam("sort")
-                               @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
-                           @QueryParam("limit") @DefaultValue("10")
-                               @ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
-                           @QueryParam("skip") @DefaultValue("0")
-                               @ApiParam(value = ParamConstants.SKIP_DESCRIPTION)  Integer skip) {
+    public Response getAll(@QueryParam("exclude") @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
+                           @QueryParam("include") @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
+                           @QueryParam("sort") @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
+                           @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);

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
@@ -241,7 +241,7 @@ public Response getAggregationStats(@DefaultValue("") @QueryParam("fields")
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query"),
@@ -286,6 +286,7 @@ public Response getAll(@QueryParam("exclude") @ApiParam(value = ParamConstants.E
                            @QueryParam("skip") @DefaultValue("0")
                                @ApiParam(value = ParamConstants.SKIP_DESCRIPTION)  Integer skip) {
         try {
+
             parseIncludesAndExcludes(exclude, include, sort);
             parseLimitAndSkip(limit, skip);
             parseQueryParams();

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java
@@ -102,7 +102,7 @@ public Response getInfoByEnsemblId(@PathParam("proteins")
             value = "Get all proteins", response = Entry.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "accession", value = ParamConstants.PROTEIN_ACCESSIONS,
                     required = false, dataType = "java.util.List", paramType = "query"),

diff --git a/...base-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java b/...base-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java
@@ -136,7 +136,7 @@ public Response getByEnsemblId(@PathParam("transcriptId") String id) {
             response = Gene.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "biotype",  value = ParamConstants.GENE_BIOTYPES,
                     required = false, dataType = "java.util.List", paramType = "query"),
@@ -187,7 +187,7 @@ public Response getGeneById(@PathParam("transcripts") @ApiParam(name = "transcri
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query"),

diff --git a/...base-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java b/...base-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java
@@ -71,7 +71,7 @@ public Response getModel() {
         responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true")
     })
     public Response getAll(@QueryParam("exclude")

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java
@@ -402,7 +402,7 @@ public Response getByEnsemblId(@PathParam("variants")
             value = "Retrieves all variation objects", response = Variant.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query"),

diff --git a/...e-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java b/...e-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java
@@ -103,7 +103,7 @@ public Response getFeatureClasses() {
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query"),

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java
@@ -59,7 +59,7 @@ public TfWSServer(@PathParam("version")
             response = RegulatoryFeature.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
-                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
             @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
                     required = false, dataType = "java.util.List", paramType = "query")