TASK-5610 - Create the CVDB endpoint analysis/clinical/cvdb/variant/summary and overwrite analysis/clinical/variant

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java

@@ -63,7 +63,7 @@
  */
 public class OpenCGATestExternalResource extends ExternalResource {
 
-    private final CatalogManagerExternalResource catalogManagerExternalResource = new CatalogManagerExternalResource();
+    private final CatalogManagerExternalResource catalogManagerExternalResource;
     private Path opencgaHome;
     private String storageEngine;
     private boolean initiated = false;
@@ -72,21 +72,27 @@ public class OpenCGATestExternalResource extends ExternalResource {
     private StorageConfiguration storageConfiguration;
     private StorageEngineFactory storageEngineFactory;
     private ToolRunner toolRunner;
-
+    protected Path sourceAnalysisPath;
 
     public static HadoopVariantStorageTest.HadoopExternalResource hadoopExternalResource
             = new HadoopVariantStorageTest.HadoopExternalResource();
 
     public OpenCGATestExternalResource() {
-        this(false);
+        this(false, Paths.get("../opencga-app/app/analysis/"));
     }
 
     public OpenCGATestExternalResource(boolean storageHadoop) {
+        this(storageHadoop, Paths.get("../opencga-app/app/analysis/"));
+    }
+
+    public OpenCGATestExternalResource(boolean storageHadoop, Path sourceAnalysisPath) {
         if (storageHadoop) {
             this.storageEngine = HadoopVariantStorageEngine.STORAGE_ENGINE_ID;
         } else {
             this.storageEngine = DummyVariantStorageEngine.STORAGE_ENGINE_ID;
         }
+        this.sourceAnalysisPath = sourceAnalysisPath;
+        catalogManagerExternalResource = new CatalogManagerExternalResource(sourceAnalysisPath);
     }
 
     @Override

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java

@@ -77,7 +77,7 @@ public RestResponse<AuthenticationResponse> login(CustomUsersCommandOptions.Logi
                 String token = session.getSession().getToken();
                 String errorMsg = "Missing password. ";
                 if (StringUtils.isNotEmpty(token)) {
-                    errorMsg += "Active token detected ";
+                    errorMsg += "Active token detected. Please logout first.";
                 }
                 CommandLineUtils.error(errorMsg);
             }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java

@@ -136,9 +136,13 @@ private boolean checkAutoRefresh(OpencgaCommandExecutor commandExecutor) {
 
     public void loadSessionStudies(OpencgaCommandExecutor commandExecutor) {
         Session session = commandExecutor.getSessionManager().getSession();
-        logger.debug("Loading session studies using token: "
-                + session.getToken());
         OpenCGAClient openCGAClient = commandExecutor.getOpenCGAClient();
+        logger.debug("openCGAClient Token: " + openCGAClient.getToken());
+        if(StringUtils.isEmpty(openCGAClient.getToken())) {
+            openCGAClient.setToken(session.getToken());
+        }
+        logger.debug("Loading session studies using token: "
+                + openCGAClient.getToken());
         try {
             // Query the server to retrieve the studies of user projects
             RestResponse<Project> res = openCGAClient.getProjectClient().search(new ObjectMap());

opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerExternalResource.java

@@ -47,17 +47,25 @@
  */
 public class CatalogManagerExternalResource extends ExternalResource {
 
-    private CatalogManager catalogManager;
-    private Configuration configuration;
-    private Path opencgaHome;
-    private String adminToken;
+    protected CatalogManager catalogManager;
+    protected Configuration configuration;
+    protected Path opencgaHome;
+    protected String adminToken;
     public boolean initialized = false;
 
+    protected Path sourceAnalysisPath;
+
     public CatalogManagerExternalResource() {
+        this(Paths.get("../opencga-app/app/analysis/"));
+    }
+
+    public CatalogManagerExternalResource(Path sourceAnalysisPath) {
+        this.sourceAnalysisPath = sourceAnalysisPath;
         Configurator.setLevel("org.mongodb.driver.cluster", Level.WARN);
         Configurator.setLevel("org.mongodb.driver.connection", Level.WARN);
     }
 
+
     @Override
     public void before() throws Exception {
         initialized = true;
@@ -93,8 +101,9 @@ public Path clearOpenCGAHome(String testName) throws IOException {
 
         // Pedigree graph analysis
         Path analysisPath = Files.createDirectories(opencgaHome.resolve("analysis/pedigree-graph")).toAbsolutePath();
-        FileInputStream inputStream = new FileInputStream("../opencga-app/app/analysis/pedigree-graph/ped.R");
-        Files.copy(inputStream, analysisPath.resolve("ped.R"), StandardCopyOption.REPLACE_EXISTING);
+        Files.copy(sourceAnalysisPath.resolve("pedigree-graph/ped.R"),
+                analysisPath.resolve("ped.R"), StandardCopyOption.REPLACE_EXISTING);
+
         return opencgaHome;
     }
 

opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java

@@ -1405,7 +1405,7 @@ protected Query getVariantQuery() {
     }
 
     // FIXME This method must be deleted once deprecated params are not supported any more
-    static Query getVariantQuery(QueryOptions queryOptions) {
+    public static Query getVariantQuery(QueryOptions queryOptions) {
         Query query = VariantStorageManager.getVariantQuery(queryOptions);
         queryOptions.forEach((key, value) -> {
             org.opencb.commons.datastore.core.QueryParam newKey = DEPRECATED_VARIANT_QUERY_PARAM.get(key);