more replacements, fix data type #522

opencb · Feb 3, 2020 · 23a707b · 23a707b
1 parent 44de29b
commit 23a707b
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Showing 4 changed files with 47 additions and 96 deletions.
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
@@ -270,7 +270,7 @@ public Response getAggregationStats(@DefaultValue("") @QueryParam("fields")
             @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
-                    required = false, dataType = "string", paramType = "query"),
+                    required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.expression.value", value = ParamConstants.ANNOTATION_EXPRESSION_VALUE,
                     required = false, dataType = "string", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
@@ -366,7 +366,7 @@ public Response getAllIDs() {
             @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
-                    required = false, dataType = "string", paramType = "query"),
+                    required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.gene", value = ParamConstants.ANNOTATION_DRUGS_GENE,
@@ -603,7 +603,7 @@ public Response getAllRegulatoryElements(@PathParam("geneId")
             @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
-                    required = false, dataType = "string", paramType = "query"),
+                    required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.gene", value = ParamConstants.ANNOTATION_DRUGS_GENE,

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
@@ -89,13 +89,12 @@ public Response first() throws Exception {
     public Response count(@DefaultValue("")
                           @QueryParam("region")
                           @ApiParam(name = "region",
-                                  value = "Comma separated list of genomic regions to be queried, e.g.: 1:6635137-6635325",
+                                  value = ParamConstants.REGION_DESCRIPTION,
                                   required = false) String region,
                           @DefaultValue("")
                           @QueryParam("biotype")
                           @ApiParam(name = "biotype",
-                                  value = "Comma separated list of gene gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                                          + " Exact text matches will be returned",
+                                  value = ParamConstants.GENE_BIOTYPES,
                                   required = false) String biotype,
                           @DefaultValue("")
                           @QueryParam("xrefs")
@@ -137,44 +136,26 @@ public Response getByEnsemblId(@PathParam("transcriptId") String id) {
     @ApiOperation(httpMethod = "GET", value = "Retrieves all gene objects for given ENSEMBL transcript ids.",
             response = Gene.class, responseContainer = "QueryResponse")
     @ApiImplicitParams({
-            @ApiImplicitParam(name = "biotype",
-                    value = "Comma separated list of gene gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
+                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
+                    allowableValues = "false,true"),
+            @ApiImplicitParam(name = "biotype",  value = ParamConstants.GENE_BIOTYPES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "transcripts.biotype",
-                    value = "Comma separated list of transcript gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "transcripts.biotype", value = ParamConstants.TRANSCRIPT_BIOTYPES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "transcripts.tfbs.name",
-                    value = "Comma separated list of TFBS names, e.g.: CTCF,Gabp."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "transcripts.tfbs.name", value = ParamConstants.TRANSCRIPT_TFBS_NAMES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.diseases.id",
-                    value = "Comma separated list of phenotype ids (OMIM, UMLS), e.g.: umls:C0030297,OMIM:613390,"
-                            + "OMIM:613390. Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.diseases.id", value = ParamConstants.ANNOTATION_DISEASES_IDS,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.diseases.name",
-                    value = "Comma separated list of phenotypes, e.g.: Cryptorchidism,Absent thumb,Stage 5 chronic "
-                            + "kidney disease. Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.diseases.name", value = ParamConstants.ANNOTATION_DISEASES_NAMES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.expression.gene",
-                    value = "Comma separated list of ENSEMBL gene ids for which expression values are available, "
-                            + "e.g.: ENSG00000139618,ENSG00000155657. Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.expression.tissue",
-                    value = "Comma separated list of tissues for which expression values are available, "
-                            + "e.g.: adipose tissue,heart atrium,tongue."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.drugs.name",
-                    value = "Comma separated list of drug names, "
-                            + "e.g.: BMN673,OLAPARIB,VELIPARIB."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.drugs.gene",
-                    value = "Comma separated list of gene names for which drug data is available, "
-                            + "e.g.: BRCA2,TTN."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.drugs.gene", value = ParamConstants.ANNOTATION_DRUGS_GENE,
                     required = false, dataType = "java.util.List", paramType = "query")
     })
     public Response getGeneById(@PathParam("transcriptId")
@@ -202,44 +183,36 @@ public Response getGeneById(@PathParam("transcriptId")
             value = "Retrieves all transcript objects", response = Transcript.class,
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
-            @ApiImplicitParam(name = "count",
-                    value = "Get a count of the number of results obtained.",
-                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
+            @ApiImplicitParam(name = "count", value = ParamConstants.COUNT_DESCRIPTION,
+                    required = false, dataType = "java.lang.Boolean", paramType = "query", defaultValue = "false",
                     allowableValues = "false,true"),
-            @ApiImplicitParam(name = "region",
-                    value = "Comma separated list of genomic regions to be queried, e.g.: 1:6635137-6635325",
-                    dataType = "java.util.List", paramType = "query"),
+            @ApiImplicitParam(name = "region", value = ParamConstants.REGION_DESCRIPTION,
+                    required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "id",
                     value = "Comma separated list of ENSEMBL transcript ids, e.g.: ENST00000342992"
                             + " Exact text matches will be returned", dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "name",
-                    value = "Comma separated list of transcript names, e.g.: BRCA2-201,TTN-003."
-                            + " Exact text matches will be returned", dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "biotype",
-                    value = "Comma separated list of transcript gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                            + " Exact text matches will be returned", dataType = "java.util.List", paramType = "query"),
-
+            @ApiImplicitParam(name = "name", value = ParamConstants.TRANSCRIPT_NAMES,
+                    dataType = "java.util.List", paramType = "query"),
+            @ApiImplicitParam(name = "biotype", value = ParamConstants.TRANSCRIPT_BIOTYPES,
+                    dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "xrefs",
                     value = "Comma separated list transcript xrefs ids, e.g.: ENSG00000145113,35912_at,GO:0002020."
                             + " Exact text matches will be returned", dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "tfbs.name",
-                    value = "Comma separated list of TFBS names, e.g.: CTCF,Gabp."
-                            + " Exact text matches will be returned", dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotationFlags",
-                    value = "Comma separated list of annotation flags that must be present in the transcripts returned "
-                            + "within the gene model, e.g.: basic,CCDS. Exact text matches will be returned",
+            @ApiImplicitParam(name = "tfbs.name", value = ParamConstants.TRANSCRIPT_TFBS_NAMES,
+                    dataType = "java.util.List", paramType = "query"),
+            @ApiImplicitParam(name = "annotationFlags", value = ParamConstants.TRANSCRIPT_ANNOTATION_FLAGS,
                     dataType = "string", 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);
@@ -303,10 +276,8 @@ public Response getSequencesByIdList(@PathParam("transcriptId")
     @ApiOperation(httpMethod = "GET", value = "Get the protein info for the given transcript(s)", response = Entry.class,
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
-            @ApiImplicitParam(name = "keyword",
-                    value = "Comma separated list of keywords that may be associated with the protein(s), e.g.: "
-                            + "Transcription,Zinc. Exact text matches will be returned",
-                    required = false, dataType = "java.util.List", paramType = "query")
+            @ApiImplicitParam(name = "keyword", value = ParamConstants.PROTEIN_KEYWORD, required = false,
+                    dataType = "java.util.List", paramType = "query")
     })
     public Response getProtein(@PathParam("transcriptId")
                                    @ApiParam(name = "transcriptId",

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java
@@ -103,44 +103,24 @@ private boolean hasHistogramQueryParam() {
             @ApiImplicitParam(name = "interval",
                     value = "Use only if histogram=true. Boolean indicating the size of the histogram interval",
                     defaultValue = "200000", required = false, dataType = "Integer", paramType = "query"),
-            @ApiImplicitParam(name = "biotype",
-                    value = "Comma separated list of gene gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                            + " Exact text matches will be returned",
-                    required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "transcripts.biotype",
-                    value = "Comma separated list of transcript gencode biotypes, e.g.: protein_coding,miRNA,lincRNA."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "biotype",  value = ParamConstants.GENE_BIOTYPES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "transcripts.xrefs",
-                    value = "Comma separated list transcript xrefs ids, e.g.: ENSG00000145113,35912_at,GO:0002020."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "transcripts.biotype", value = ParamConstants.TRANSCRIPT_BIOTYPES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "transcripts.tfbs.name",
-                    value = "Comma separated list of TFBS names, e.g.: CTCF,Gabp."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "transcripts.xrefs", value = ParamConstants.TRANSCRIPT_XREFS,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.diseases.id",
-                    value = "Comma separated list of phenotype ids (OMIM, UMLS), e.g.: umls:C0030297,OMIM:613390,"
-                            + "OMIM:613390. Exact text matches will be returned",
+            @ApiImplicitParam(name = "transcripts.tfbs.name", value = ParamConstants.TRANSCRIPT_TFBS_NAMES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.diseases.name",
-                    value = "Comma separated list of phenotypes, e.g.: Cryptorchidism,Absent thumb,Stage 5 chronic "
-                            + "kidney disease. Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.diseases.id", value = ParamConstants.ANNOTATION_DISEASES_IDS,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.expression.gene",
-                    value = "Comma separated list of ENSEMBL gene ids for which expression values are available, "
-                            + "e.g.: ENSG00000139618,ENSG00000155657. Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.diseases.name", value = ParamConstants.ANNOTATION_DISEASES_NAMES,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.expression.tissue",
-                    value = "Comma separated list of tissues for which expression values are available, "
-                            + "e.g.: adipose tissue,heart atrium,tongue."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
-            @ApiImplicitParam(name = "annotation.drugs.name",
-                    value = "Comma separated list of drug names, "
-                            + "e.g.: BMN673,OLAPARIB,VELIPARIB."
-                            + " Exact text matches will be returned",
+            @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
                     required = false, dataType = "java.util.List", paramType = "query"),
+            @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
+                    required = false, dataType = "java.util.List", paramType = "query")
     })
     public Response getGenesByRegionPost(@FormParam("region")
                                          @ApiParam(name = "region",
@@ -179,7 +159,7 @@ public Response getGenesByRegionPost(@FormParam("region")
             @ApiImplicitParam(name = "annotation.expression.gene", value = ParamConstants.ANNOTATION_EXPRESSION_GENE,
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.expression.tissue", value = ParamConstants.ANNOTATION_EXPRESSION_TISSUE,
-                    required = false, dataType = "string", paramType = "query"),
+                    required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "annotation.drugs.name", value = ParamConstants.ANNOTATION_DRUGS_NAME,
                     required = false, dataType = "java.util.List", paramType = "query")
     })