server: set hsapiens as default species, #TASK-5447

Author: jtarraga

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

@@ -97,16 +97,13 @@ public class GenericRestWSServer implements IWSServer {
     protected static org.opencb.cellbase.lib.monitor.Monitor monitor;
     private static final String ERROR = "error";
     private static final String OK = "ok";
-    // this webservice has no species or assembly, do not validate
-    private static final String DONT_CHECK_SPECIES = "do not validate species";
-    private static final String DONT_CHECK_ASSEMBLY = "do not validate assembly";
 
     protected static String defaultApiKey;
     protected static ApiKeyManager apiKeyManager;
 
     public GenericRestWSServer(@PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest hsr)
             throws CellBaseServerException {
-        this(version, DONT_CHECK_SPECIES, DONT_CHECK_ASSEMBLY, uriInfo, hsr);
+        this(version, "hsapiens", null, uriInfo, hsr);
     }
 
     public GenericRestWSServer(@PathParam("version") String version, @PathParam("species") String species,
@@ -121,11 +118,13 @@ public GenericRestWSServer(@PathParam("version") String version, @PathParam("spe
         this.assembly = assembly;
 
         try {
-            if (this.assembly == null && !DONT_CHECK_SPECIES.equals(species)) {
-                this.assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
+            init();
+
+            if (this.assembly == null) {
+                // Default assembly depends on the CellBaseConfiguration (so it has to be already initialized)
+                this.assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, this.species).getName();
             }
 
-            init();
             initQuery();
         } catch (Exception e) {
             throw new CellBaseServerException(e.getMessage());
@@ -205,15 +204,10 @@ private void initQuery() throws CellBaseException {
         checkVersion();
 
         // Set default data release if necessary
-        if (!DONT_CHECK_SPECIES.equals(species) && defaultDataRelease == null) {
-            // As the assembly may not be presented in the query, we have to be sure to get it from the CellBase configuration
-            assembly = SpeciesUtils.getSpecies(cellBaseConfiguration, this.species, assembly).getAssembly();
-
-            if (!DONT_CHECK_ASSEMBLY.equals(assembly) && StringUtils.isNotEmpty(assembly)) {
-                DataReleaseManager releaseManager = cellBaseManagerFactory.getDataReleaseManager(species, assembly);
-                // getDefault launches an exception if no data release is found for that CellBase version
-                defaultDataRelease = releaseManager.getDefault(version);
-            }
+        if (defaultDataRelease == null) {
+            DataReleaseManager releaseManager = cellBaseManagerFactory.getDataReleaseManager(species, assembly);
+            // getDefault launches an exception if no data release is found for that CellBase version
+            defaultDataRelease = releaseManager.getDefault(version);
         }
 
         // Check API key (expiration date, quota,...)
@@ -237,10 +231,6 @@ protected int getDataRelease() throws CellBaseException {
             }
         }
         // If no data release is present in the query, then use the default data release
-        if (!DONT_CHECK_SPECIES.equals(species)) {
-            logger.info("No data release present in query: using the default data release '" + defaultDataRelease + "' for CellBase version"
-                    + " '" + version + "'");
-        }
         return defaultDataRelease.getRelease();
     }
 
@@ -284,11 +274,6 @@ private void checkVersion() throws CellBaseException {
             throw new CellBaseException("Version not valid: '" + version + "'");
         }
 
-//        System.out.println("*************************************");
-//        System.out.println("cellBaseConfiguration = " + cellBaseConfiguration);
-//        System.out.println("cellBaseConfiguration.getVersion() = " + cellBaseConfiguration.getVersion());
-//        System.out.println("version = " + version);
-//        System.out.println("*************************************");
         if (!uriInfo.getPath().contains("health") && !version.startsWith(cellBaseConfiguration.getVersion())) {
             logger.error("URL version '{}' does not match configuration '{}'", this.version, cellBaseConfiguration.getVersion());
             throw new CellBaseException("URL version not valid: '" + version + "'");
@@ -450,23 +435,8 @@ protected Response createOkResponse(Object obj) {
         return  jsonResponse;
     }
 
-//    protected Response createOkResponse(Object obj, MediaType mediaType) {
-//        return buildResponse(Response.ok(obj, mediaType));
-//    }
-//
-//    protected Response createOkResponse(Object obj, MediaType mediaType, String fileName) {
-//        return buildResponse(Response.ok(obj, mediaType).header("content-disposition", "attachment; filename =" + fileName));
-//    }
-//
-//    protected Response createStringResponse(String str) {
-//        return buildResponse(Response.ok(str));
-//    }
-
     protected Response createJsonResponse(CellBaseDataResponse queryResponse) {
         try {
-//            if (CollectionUtils.isNotEmpty(queryResponse.getResponses()) && queryResponse.getResponses().get(0) != null) {
-//                System.out.println("queryResponse.getResponses().get(0).toString() = " + queryResponse.getResponses().get(0).toString());
-//            }
             String value = jsonObjectWriter.writeValueAsString(queryResponse);
             ResponseBuilder ok = Response.ok(value, MediaType.APPLICATION_JSON_TYPE.withCharset("utf-8"));
             Response response = buildResponse(ok);