Hide redundant end points. Merge Variant and Variation. Default limit…

… is 10 and default skip is 0. CamelCase instead of snake_case. #522

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java

@@ -78,15 +78,15 @@ public class GenericRestWSServer implements IWSServer {
             + " Please note that this parameter may not be enabled for all web services.")
     protected String include;
 
-    @DefaultValue("-1")
+    @DefaultValue("10")
     @QueryParam("limit")
-    @ApiParam(name = "limit", value = "Max number of results to be returned. No limit applied when -1."
+    @ApiParam(name = "limit", value = "Max number of results to be returned. Cannot exceed 5,000."
             + " Please note that this option may not be available for all web services.")
     protected int limit;
 
-    @DefaultValue("-1")
+    @DefaultValue("0")
     @QueryParam("skip")
-    @ApiParam(name = "skip", value = "Number of results to be skipped. No skip applied when -1. "
+    @ApiParam(name = "skip", value = "Number of results to be skipped. No skip applied when 0. "
             + " Please note that this option may not be available for all web services.")
     protected int skip;
 
@@ -252,7 +252,7 @@ private void checkPathParams(boolean checkSpecies) throws VersionException, Spec
     }
 
     @Override
-    public void parseQueryParams() {
+    public void parseQueryParams() throws CellbaseException {
         MultivaluedMap<String, String> multivaluedMap = uriInfo.getQueryParameters();
 
         queryOptions.put("metadata", multivaluedMap.get("metadata") == null || multivaluedMap.get("metadata").get(0).equals("true"));
@@ -276,9 +276,18 @@ public void parseQueryParams() {
             queryOptions.put(QueryOptions.SORT, sort);
         }
 
-        queryOptions.put(QueryOptions.LIMIT, (limit > 0) ? Math.min(limit, LIMIT_MAX) : LIMIT_DEFAULT);
-        queryOptions.put(QueryOptions.SKIP, (skip >= 0) ? skip : -1);
-//        queryOptions.put(QueryOptions.SKIP_COUNT, StringUtils.isNotBlank(skipCount) && Boolean.parseBoolean(skipCount));
+        if (limit < 0) {
+            throw new CellbaseException("Limit is not valid. Expected a number greater than zero but was " + limit);
+        } else if (limit > LIMIT_MAX) {
+            throw new CellbaseException("Limit is not valid. Expected a number less than " + LIMIT_MAX + " but was " + limit);
+        }
+
+        if (skip < 0) {
+            throw new CellbaseException("Skip is not valid. Expected a number greater than zero but was " + skip);
+        }
+
+        queryOptions.put(QueryOptions.LIMIT, limit);
+        queryOptions.put(QueryOptions.SKIP, skip);
         queryOptions.put(QueryOptions.COUNT, StringUtils.isNotBlank(count) && Boolean.parseBoolean(count));
 
         // Add all the others QueryParams from the URL

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/IWSServer.java

@@ -16,14 +16,16 @@
 
 package org.opencb.cellbase.server.rest;
 
+import org.opencb.cellbase.core.exception.CellbaseException;
+
 import javax.ws.rs.core.Response;
 
 public interface IWSServer {
 
 
-    void parseQueryParams();
+    void parseQueryParams() throws CellbaseException;
 
-    default Response first() {
+    default Response first() throws Exception {
         return Response.ok("No implemented yet").build();
     }
 

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java

@@ -128,7 +128,7 @@ public Response getAll() {
     }
 
     @GET
-    @Path("/variant/allele_origin_labels")
+    @Path("/variant/alleleOriginLabels")
     @ApiOperation(httpMethod = "GET", notes = "",
             value = "Retrieves all available allele origin labels", response = Variant.class,
             responseContainer = "QueryResponse")
@@ -143,7 +143,7 @@ public Response getAlleleOriginLabels() {
     }
 
     @GET
-    @Path("/variant/mode_inheritance_labels")
+    @Path("/variant/modeInheritanceLabels")
     @ApiOperation(httpMethod = "GET", notes = "",
             value = "Retrieves all available mode of inheritance labels", response = Variant.class,
             responseContainer = "QueryResponse")
@@ -158,7 +158,7 @@ public Response getModeInheritanceLabels() {
     }
 
     @GET
-    @Path("/variant/clinsig_labels")
+    @Path("/variant/clinsigLabels")
     @ApiOperation(httpMethod = "GET", notes = "",
             value = "Retrieves all available clinical significance labels", response = Variant.class,
             responseContainer = "QueryResponse")
@@ -173,7 +173,7 @@ public Response getClinicalSignificanceLabels() {
     }
 
     @GET
-    @Path("/variant/consistency_labels")
+    @Path("/variant/consistencyLabels")
     @ApiOperation(httpMethod = "GET", notes = "",
             value = "Retrieves all available consistency labels", response = Variant.class,
             responseContainer = "QueryResponse")

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java

@@ -76,7 +76,7 @@ public Response getModel() {
     @Override
     @Deprecated
     @ApiOperation(httpMethod = "GET", value = "Get the first object in the database", response = Gene.class,
-            responseContainer = "QueryResponse")
+            responseContainer = "QueryResponse", hidden = true)
     public Response first() {
         GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly);
         return createOkResponse(geneDBAdaptor.first(queryOptions));
@@ -86,7 +86,7 @@ public Response first() {
     @Path("/count")
     @Deprecated
     @ApiOperation(httpMethod = "GET", value = "Get the number of genes in the database", response = Integer.class,
-            responseContainer = "QueryResponse")
+            responseContainer = "QueryResponse", hidden = true)
     @ApiImplicitParams({
             @ApiImplicitParam(name = "region",
                     value = "Comma separated list of genomic regions to be queried, e.g.: 1:6635137-6635325",

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java

@@ -137,7 +137,7 @@ public Response getAllXrefsByFeatureId(@PathParam("id")
     }
 
     @GET
-    @Path("/{id}/starts_with")
+    @Path("/{id}/startsWith")
     @ApiOperation(httpMethod = "GET", value = "Get the gene HGNC symbols of genes for which there is an Xref id that "
             + "matches the beginning of the given string", response = Map.class, responseContainer = "QueryResponse")
     public Response getByLikeQuery(@PathParam("id")

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java

@@ -135,7 +135,7 @@ public Response getAll() {
     }
 
     @GET
-    @Path("/{proteinId}/substitution_scores")
+    @Path("/{proteinId}/substitutionScores")
     @ApiOperation(httpMethod = "GET", value = "Get the gene corresponding substitution scores for the input protein",
         notes = "Schema of returned objects will vary depending on provided query parameters. If the amino acid "
                 + " position is provided, all scores will be returned for every possible amino acid"
@@ -161,7 +161,6 @@ public Response getSubstitutionScores(@PathParam("proteinId")
                                                   required = true) String id) {
         try {
             parseQueryParams();
-//            query.put(ProteinDBAdaptor.QueryParams.XREFS.key(), id);
 
             // Fetch Ensembl transcriptId to query substiturion scores
             TranscriptDBAdaptor transcriptDBAdaptor = dbAdaptorFactory.getTranscriptDBAdaptor(this.species, this.assembly);

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java

@@ -77,8 +77,8 @@ public Response getModel() {
     @Override
     @Deprecated
     @ApiOperation(httpMethod = "GET", value = "Get the first transcript in the database", response = Transcript.class,
-        responseContainer = "QueryResponse")
-    public Response first() {
+        responseContainer = "QueryResponse", hidden = true)
+    public Response first() throws Exception {
         parseQueryParams();
         TranscriptDBAdaptor transcriptDBAdaptor = dbAdaptorFactory.getTranscriptDBAdaptor(this.species, this.assembly);
         return createOkResponse(transcriptDBAdaptor.first(queryOptions));
@@ -88,7 +88,7 @@ public Response first() {
     @Path("/count")
     @Deprecated
     @ApiOperation(httpMethod = "GET", value = "Get the number of transcripts in the database", response = Integer.class,
-        responseContainer = "QueryResponse")
+        responseContainer = "QueryResponse", hidden = true)
     public Response count(@DefaultValue("")
                           @QueryParam("region")
                           @ApiParam(name = "region",
@@ -315,7 +315,7 @@ public Response getProtein(@PathParam("transcriptId")
     }
 
     @GET
-    @Path("/{transcriptId}/function_prediction")
+    @Path("/{transcriptId}/functionPrediction")
     @ApiOperation(httpMethod = "GET", value = "Get the gene corresponding substitution scores for the protein of a"
             + " certain transcript",
             notes = "Schema of returned objects will vary depending on provided query parameters. If the amino acid "