include count, skip and limit only in /search endpoints. #522

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

@@ -76,26 +76,9 @@ public class GenericRestWSServer implements IWSServer {
     @ApiParam(name = "include", value = "Set which fields are included in the response, e.g.: transcripts.id. ")
     protected String include;
 
-    @DefaultValue("10")
-    @QueryParam("limit")
-    @ApiParam(name = "limit", value = "Max number of results to be returned. Cannot exceed 5,000.")
-    protected int limit;
-
-    @DefaultValue("0")
-    @QueryParam("skip")
-    @ApiParam(name = "skip", value = "Number of results to be skipped. No skip applied when 0.")
-    protected int skip;
-
-    @DefaultValue("false")
-    @QueryParam("count")
-    @ApiParam(name = "count", value = "Get a count of the number of results obtained. Deactivated by default.",
-            defaultValue = "false", allowableValues = "false,true")
-    protected String count;
-
     @DefaultValue("")
     @QueryParam("sort")
-    @ApiParam(name = "sort", value = "Sort returned results by a certain data model attribute.", defaultValue = "ASC",
-            allowableValues = "ASC,DESC")
+    @ApiParam(name = "sort", value = "Sort returned results by a certain data model attribute.")
     protected String sort;
 
     @DefaultValue("json")
@@ -131,8 +114,9 @@ public class GenericRestWSServer implements IWSServer {
     protected DBAdaptorFactory dbAdaptorFactory;
     protected Monitor monitor;
 
+    private static final int SKIP_DEFAULT = 0;
     private static final int LIMIT_DEFAULT = 10;
-    private static final int LIMIT_MAX = 5000;
+    private static final int MAX_RECORDS = 5000;
     private static final String ERROR = "error";
     private static final String OK = "ok";
     // this webservice has no species, do not validate
@@ -264,20 +248,6 @@ public void parseQueryParams() throws CellbaseException {
             queryOptions.put(QueryOptions.SORT, sort);
         }
 
-        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
         for (Map.Entry<String, List<String>> entry : multivaluedMap.entrySet()) {
             if (!queryOptions.containsKey(entry.getKey())) {
@@ -286,6 +256,31 @@ public void parseQueryParams() throws CellbaseException {
         }
     }
 
+    public void parseExtraQueryParams(Integer limit, Integer skip) throws CellbaseException {
+        if (limit != null) {
+            if (limit > MAX_RECORDS) {
+                throw new CellbaseException("Limit cannot exceed " + MAX_RECORDS + " but was " + limit);
+            }
+            if (limit < 0) {
+                throw new CellbaseException("Limit must be >= 0, but was " + limit);
+            }
+            queryOptions.put(QueryOptions.LIMIT, limit);
+        } else {
+            queryOptions.put(QueryOptions.LIMIT, LIMIT_DEFAULT);
+        }
+        if (skip != null) {
+            if (skip > MAX_RECORDS) {
+                throw new CellbaseException("Skip cannot exceed " + MAX_RECORDS + " but was " + skip);
+            }
+            if (skip < 0) {
+                throw new CellbaseException("Skip must be >= 0, but was " + skip);
+            }
+            queryOptions.put(QueryOptions.SKIP, skip);
+        } else {
+            queryOptions.put(QueryOptions.SKIP, SKIP_DEFAULT);
+        }
+    }
+
     protected void logQuery(String status) {
         try {
             logger.info("{}\t{}\t{}\t{}\t{}",

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

@@ -54,7 +54,8 @@ public SpeciesWSServer(@PathParam("version")
                                    + "of potentially available species ids, please refer to: "
                                    + "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/meta/species") String species,
                            @Context UriInfo uriInfo,
-                           @Context HttpServletRequest hsr) throws VersionException, SpeciesException, IOException, CellbaseException {
+                           @Context HttpServletRequest hsr) throws VersionException, SpeciesException, IOException,
+            CellbaseException {
         super(version, species, uriInfo, hsr);
     }
 

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

@@ -27,6 +27,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
 import javax.ws.rs.core.Context;
+import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 import javax.ws.rs.core.UriInfo;
 import java.io.IOException;
@@ -35,12 +36,10 @@
  * Created by fjlopez on 06/12/16.
  */
 @Path("/{version}/{species}/clinical")
-@Produces("application/json")
+@Produces(MediaType.APPLICATION_JSON)
 @Api(value = "Clinical", description = "Clinical RESTful Web Services API")
 public class ClinicalWSServer extends GenericRestWSServer {
 
-
-
     public ClinicalWSServer(@PathParam("version")
                                   @ApiParam(name = "version", value = "Possible values: v4, v5",
                                           defaultValue = "v5") String version,
@@ -58,6 +57,10 @@ public ClinicalWSServer(@PathParam("version")
     @ApiOperation(httpMethod = "GET", notes = "No more than 1000 objects are allowed to be returned at a time. ",
             value = "Retrieves all clinical variants", response = Variant.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",
+                    allowableValues = "false,true"),
             @ApiImplicitParam(name = "source",
                     value = "Comma separated list of database sources of the documents to be returned. Possible values "
                             + " are clinvar,cosmic or iarctp53. E.g.: clinvar,cosmic",
@@ -114,8 +117,12 @@ public ClinicalWSServer(@PathParam("version")
                             + "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/allele_origin_labels",
                     required = false, dataType = "java.util.List", paramType = "query")
     })
-    public Response getAll() {
+    public Response getAll(@QueryParam("limit") @DefaultValue("10")
+                           @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                           @QueryParam("skip") @DefaultValue("0")
+                           @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
 

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

@@ -32,7 +32,6 @@
 import org.opencb.cellbase.server.rest.GenericRestWSServer;
 import org.opencb.commons.datastore.core.Query;
 
-
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
 import javax.ws.rs.core.Context;
@@ -259,6 +258,10 @@ public Response groupBy(@DefaultValue("")
             value = "Retrieves all gene objects", response = Gene.class,
             responseContainer = "QueryResponse")
     @ApiImplicitParams({
+            @ApiImplicitParam(name = "count",
+                    value = "Get a count of the number of results obtained.",
+                    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",
                     required = false, dataType = "java.util.List", paramType = "query"),
@@ -329,8 +332,12 @@ public Response groupBy(@DefaultValue("")
                             + " Exact text matches will be returned",
                     required = false, dataType = "java.util.List", paramType = "query")
     })
-    public Response getAll() {
+    public Response getAll(@QueryParam("limit") @DefaultValue("10")
+                           @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                           @QueryParam("skip") @DefaultValue("0")
+                           @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly);
             return createOkResponse(geneDBAdaptor.nativeGet(query, queryOptions));
@@ -553,7 +560,8 @@ public Response getTranscriptsByGeneId(@PathParam("geneId")
 
     @GET
     @Path("/distinct/{fieldName}")
-    @ApiOperation(httpMethod = "GET", value = "Get a unique list of values for a given field, e.g. biotype")
+    @ApiOperation(httpMethod = "GET", notes = "Gets a unique list of values for specified gene, e.g. biotype or chromosome",
+            value = "Get a unique list of values for a given field.")
     @ApiImplicitParams({
             @ApiImplicitParam(name = "region",
                     value = "Comma separated list of genomic regions to be queried, e.g.: 1:6635137-6635325",
@@ -563,11 +571,11 @@ public Response getTranscriptsByGeneId(@PathParam("geneId")
                             + "Exact text matches will be returned",
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "name",
-                    value = "Comma separated list of gene HGNC names, e.g.: BRCA2,TTN,MUC4"
+                    value = "Comma separated list of gene HGNC names, e.g.: BRCA2,TTN,MUC4. "
                             + "Exact text matches will be returned",
                     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."
+                    value = "Comma separated list transcript xrefs ids, e.g.: ENSG00000145113,35912_at,GO:0002020. "
                             + "Exact text matches will be returned",
                     required = false, dataType = "java.util.List", paramType = "query"),
             @ApiImplicitParam(name = "transcripts.id",
@@ -829,7 +837,8 @@ public Response getProteinById(@PathParam("geneId")
 
     @GET
     @Path("/{geneId}/ppi")
-    @ApiOperation(httpMethod = "GET", value = "Get the protein-protein interactions in which this gene is involved")
+    @ApiOperation(httpMethod = "GET", value = "Get the protein-protein interactions in which this gene is involved",
+            hidden = true)
     public Response getPPIByEnsemblId(@PathParam("geneId") String gene) {
         try {
             parseQueryParams();
@@ -852,7 +861,7 @@ public Response getPPIByEnsemblId(@PathParam("geneId") String gene) {
             + "a look at "
             + "https://github.com/opencb/cellbase/wiki/MongoDB-implementation#clinical for further details.",
             value = "[DEPRECATED] Use {version}/{species}/clinical/variant/search instead.", response = Document.class,
-            responseContainer = "QueryResponse")
+            responseContainer = "QueryResponse", hidden = true)
     @ApiImplicitParams({
             @ApiImplicitParam(name = "source",
                     value = "Comma separated list of database sources of the documents to be returned. Possible values "

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

@@ -29,12 +29,8 @@
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 
-
 import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
+import javax.ws.rs.*;
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
@@ -103,6 +99,10 @@ public Response getInfoByEnsemblId(@PathParam("proteinId")
     @ApiOperation(httpMethod = "GET", notes = "No more than 1000 objects are allowed to be returned at a time.",
             value = "Get all proteins", response = Entry.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",
+                    allowableValues = "false,true"),
             @ApiImplicitParam(name = "accession",
                     value = "Comma separated list of UniProt accession ids, e.g.: Q9UL59,B2R8Q1,Q9UKT9."
                             + "Exact text matches will be returned",
@@ -124,8 +124,12 @@ public Response getInfoByEnsemblId(@PathParam("proteinId")
                             + "Transcription,Zinc. Exact text matches will be returned",
                     required = false, dataType = "java.util.List", paramType = "query")
     })
-    public Response getAll() {
+    public Response getAll(@QueryParam("limit") @DefaultValue("10")
+                           @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                           @QueryParam("skip") @DefaultValue("0")
+                           @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             ProteinDBAdaptor proteinDBAdaptor = dbAdaptorFactory.getProteinDBAdaptor(this.species, this.assembly);
             return createOkResponse(proteinDBAdaptor.nativeGet(query, queryOptions));

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

@@ -205,6 +205,10 @@ 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",
+                    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"),
@@ -229,14 +233,19 @@ public Response getGeneById(@PathParam("transcriptId")
                             + "within the gene model, e.g.: basic,CCDS. Exact text matches will be returned",
                     dataType = "string", paramType = "query"),
     })
-    public Response getAll() {
+    public Response getAll(@QueryParam("limit") @DefaultValue("10")
+                           @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                           @QueryParam("skip") @DefaultValue("0")
+                           @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             TranscriptDBAdaptor transcriptDBAdaptor = dbAdaptorFactory.getTranscriptDBAdaptor(this.species, this.assembly);
             CellBaseDataResult queryResult = transcriptDBAdaptor.nativeGet(query, queryOptions);
             // Total number of results is always same as the number of results. As this is misleading, we set it as -1 until
             // properly fixed
             queryResult.setNumTotalResults(-1);
+            queryResult.setNumResults(-1);
             return createOkResponse(queryResult);
         } catch (Exception e) {
             return createErrorResponse(e);

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java

@@ -17,9 +17,7 @@
 package org.opencb.cellbase.server.rest.genomic;
 
 import com.google.common.base.Splitter;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import io.swagger.annotations.ApiParam;
+import io.swagger.annotations.*;
 import org.opencb.biodata.models.core.Chromosome;
 import org.opencb.cellbase.core.api.GenomeDBAdaptor;
 import org.opencb.cellbase.core.exception.CellbaseException;
@@ -30,10 +28,7 @@
 import org.opencb.commons.datastore.core.QueryOptions;
 
 import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
+import javax.ws.rs.*;
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
@@ -75,8 +70,18 @@ public Response getModel() {
     @Path("/search")
     @ApiOperation(httpMethod = "GET", value = "Retrieves all the chromosome objects", response = Chromosome.class,
         responseContainer = "QueryResponse")
-    public Response getChromosomesAll() {
+    @ApiImplicitParams({
+            @ApiImplicitParam(name = "count",
+                    value = "Get a count of the number of results obtained. Deactivated by default.",
+                    required = false, dataType = "boolean", paramType = "query", defaultValue = "false",
+                    allowableValues = "false,true")
+    })
+    public Response getChromosomesAll(@QueryParam("limit") @DefaultValue("10")
+                                          @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                                      @QueryParam("skip") @DefaultValue("0")
+                                          @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             GenomeDBAdaptor dbAdaptor = dbAdaptorFactory.getGenomeDBAdaptor(this.species, this.assembly);
             return createOkResponse(dbAdaptor.getGenomeInfo(queryOptions));

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java

@@ -411,6 +411,10 @@ public Response getByEnsemblId(@PathParam("id")
     @ApiOperation(httpMethod = "GET", notes = "No more than 1000 objects are allowed to be returned at a time.",
             value = "Retrieves all variation objects", response = Variant.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",
+                    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"),
@@ -433,8 +437,12 @@ public Response getByEnsemblId(@PathParam("id")
                     value = "Comma separated list of possible alternate to be queried, e.g.: A,T",
                     dataType = "java.util.List", paramType = "query")
     })
-    public Response search() {
+    public Response search(@QueryParam("limit") @DefaultValue("10")
+                               @ApiParam(value = "Max number of results to be returned. Cannot exceed 5,000.") Integer limit,
+                           @QueryParam("skip") @DefaultValue("0")
+                               @ApiParam(value = "Number of results to be skipped.")  Integer skip) {
         try {
+            parseExtraQueryParams(limit, skip);
             parseQueryParams();
             VariantDBAdaptor variationDBAdaptor = dbAdaptorFactory.getVariationDBAdaptor(this.species, this.assembly);
             return createOkResponse(variationDBAdaptor.nativeGet(query, queryOptions));