Merge branch 'TASK-6442' of https://github.com/opencb/opencga into TA…

…SK-6442

opencga-analysis/src/main/java/org/opencb/opencga/analysis/resource/DownloadResourcesTool.java

@@ -11,8 +11,6 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.NoSuchAlgorithmException;
-import java.util.Arrays;
-import java.util.List;
 
 import static org.opencb.opencga.core.tools.ResourceManager.RESOURCES_FOLDER_NAME;
 
@@ -24,21 +22,14 @@
         priority = Enums.Priority.HIGH)
 public class DownloadResourcesTool extends OpenCgaTool {
 
-    public static final String ID = "resource-download-all";
-    public static final String DESCRIPTION = "Download all resources";
-
-    public static final String DOWNLOAD_RESOURCES_STEP = "download-resources";
-    public static final String MOVE_RESOURCES_STEP = "move-resources";
+    public static final String ID = "resource-downloader";
+    public static final String DESCRIPTION = "Download all resources from the server";
 
     private Path resourcePath;
 
     @ToolParams
     protected final DownloadResourcesToolParams analysisParams = new DownloadResourcesToolParams();
 
-    protected List<String> getSteps() {
-        return Arrays.asList(DOWNLOAD_RESOURCES_STEP, MOVE_RESOURCES_STEP);
-    }
-
     @Override
     protected void check() throws Exception {
         super.check();
@@ -53,21 +44,12 @@ protected void check() throws Exception {
     @Override
     protected void run() throws Exception {
         // Download all resources
-        step(DOWNLOAD_RESOURCES_STEP, this::downloadResources);
-
-        // Move resources to the installation folder
-        step(MOVE_RESOURCES_STEP, this::moveResources);
+        step(ID, this::downloadResources);
     }
 
     private void downloadResources() throws IOException, NoSuchAlgorithmException {
-        ResourceManager resourceManager = new ResourceManager(getOpencgaHome(), analysisParams.getBaseurl());
+        ResourceManager resourceManager = new ResourceManager(getOpencgaHome(), analysisParams.getBaseUrl());
         resourceManager.downloadAllResources(getOutDir().resolve(RESOURCES_FOLDER_NAME),
                 Boolean.TRUE.equals(analysisParams.getOverwrite()));
     }
-
-    private void moveResources() {
-
-    }
-
-
 }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java

@@ -201,9 +201,8 @@ private RestResponse<Job> downloadAllResource() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), DownloadResourcesToolParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "baseurl", commandOptions.baseurl, true);
+            putNestedIfNotEmpty(beanParams, "baseUrl", commandOptions.baseUrl, true);
             putNestedIfNotNull(beanParams, "overwrite", commandOptions.overwrite, true);
-            putNestedIfNotEmpty(beanParams, "outdir", commandOptions.outdir, true);
 
             downloadResourcesToolParams = JacksonUtils.getDefaultObjectMapper().copy()
                     .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java

@@ -137,7 +137,7 @@ public class JwtCatalogCommandOptions {
 
     }
 
-    @Parameters(commandNames = {"resource-download-all"}, commandDescription ="Download all resources")
+    @Parameters(commandNames = {"resource-download-all"}, commandDescription ="Download all resources from the server")
     public class DownloadAllResourceCommandOptions {
 
         @ParametersDelegate
@@ -170,15 +170,12 @@ public class DownloadAllResourceCommandOptions {
         @Parameter(names = {"--job-dry-run"}, description = "Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.", required = false, arity = 1)
         public Boolean jobDryRun; 
 
-        @Parameter(names = {"--baseurl"}, description = "Base URL where the resources are located", required = false, arity = 1)
-        public String baseurl;
+        @Parameter(names = {"--base-url"}, description = "Base URL where the resources are located, this is an optional parameter, by default the resources will be downloaded from the OpenCB repository.", required = false, arity = 1)
+        public String baseUrl;
 
-        @Parameter(names = {"--overwrite"}, description = "Download and overwrite previously downloaded resources", required = false, arity = 1)
+        @Parameter(names = {"--overwrite"}, description = "Download and overwrite previously downloaded resources if they already exist.", required = false, arity = 1)
         public Boolean overwrite;
 
-        @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1)
-        public String outdir;
-
     }
 
     @Parameters(commandNames = {"users-create"}, commandDescription ="Create a new user")

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java

@@ -679,7 +679,7 @@ public class RunInterpreterExomiserCommandOptions {
         @Parameter(names = {"--job-dry-run"}, description = "Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.", required = false, arity = 1)
         public Boolean jobDryRun; 
 
-        @Parameter(names = {"--clinical-analysis"}, description = "Clinical analysis ID.", required = false, arity = 1)
+        @Parameter(names = {"--clinical-analysis"}, description = "Clinical analysis ID to be analysed.", required = false, arity = 1)
         public String clinicalAnalysis;
 
         @Parameter(names = {"--exomiser-version"}, description = "Exomiser version in the format X.Y where X is the major version and Y the minor version, e.g.: 14.0. If the version is not specified, the default version will be used. Refer to the configuration file to view all installed Exomiser versions and identify the default version.", required = false, arity = 1)

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java

@@ -428,7 +428,7 @@ public class RunExomiserCommandOptions {
         @Parameter(names = {"--job-dry-run"}, description = "Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.", required = false, arity = 1)
         public Boolean jobDryRun; 
 
-        @Parameter(names = {"--sample"}, description = "Sample ID.", required = false, arity = 1)
+        @Parameter(names = {"--sample"}, description = "Sample ID to be analysed.", required = false, arity = 1)
         public String sample;
 
         @Parameter(names = {"--exomiser-version"}, description = "Exomiser version in the format X.Y where X is the major version and Y the minor version, e.g.: 14.0. If the version is not specified, the default version will be used. Refer to the configuration file to view all installed Exomiser versions and identify the default version.", required = false, arity = 1)

opencga-client/src/main/R/R/Admin-methods.R

@@ -67,7 +67,7 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, para
                 subcategoryId=NULL, action="jwt", params=params, httpMethod="POST", as.queryParam=NULL, ...),
 
         #' @section Endpoint /{apiVersion}/admin/resource/downloadAll:
-        #' Download all resources.
+        #' Download all resources from the server.
         #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
         #' @param jobDescription Job description.
         #' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java

@@ -103,7 +103,7 @@ public RestResponse<ObjectMap> jwtCatalog(JWTParams data, ObjectMap params) thro
     }
 
     /**
-     * Download all resources.
+     * Download all resources from the server.
      * @param data Download-resources tool parameters.
      * @param params Map containing any of the following optional parameters.
      *       jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.

opencga-client/src/main/javascript/Admin.js

@@ -69,7 +69,7 @@ export default class Admin extends OpenCGAParentClass {
         return this._post("admin", null, "catalog", null, "jwt", data, params);
     }
 
-    /** Download all resources
+    /** Download all resources from the server
     * @param {Object} data - Download-resources tool parameters.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not

opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py

@@ -67,7 +67,7 @@ def jwt_catalog(self, data=None, **options):
 
     def download_all_resource(self, data=None, **options):
         """
-        Download all resources.
+        Download all resources from the server.
         PATH: /{apiVersion}/admin/resource/downloadAll
 
         :param dict data: Download-resources tool parameters. (REQUIRED)

opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java

@@ -549,14 +549,16 @@ public class FieldConstants {
     public static final String ALIGNMENT_QC_OVERWRITE_DESCRIPTION = "To overwrite the QC metrics already computed.";
 
     // Exomiser
-    public static final String EXOMISER_CLINICAL_ANALYSIS_DESCRIPTION = "Clinical analysis ID.";
-    public static final String EXOMISER_SAMPLE_DESCRIPTION = "Sample ID.";
+    public static final String EXOMISER_CLINICAL_ANALYSIS_DESCRIPTION = "Clinical analysis ID to be analysed.";
+    public static final String EXOMISER_SAMPLE_DESCRIPTION = "Sample ID to be analysed.";
     public static final String EXOMISER_CLINICAL_ANALYSIS_TYPE_DESCRIPTION = "Clinical analysis type: SINGLE or FAMILY.";
     public static final String EXOMISER_VERSION_DESCRIPTION = "Exomiser version in the format X.Y where X is the major version and Y the"
             + " minor version, e.g.: 14.0. If the version is not specified, the default version will be used. Refer to the configuration"
             + " file to view all installed Exomiser versions and identify the default version.";
 
     // Download all resources
-    public static final String DOWNLOAD_ALL_RESOURCES_BASEURL_DESCRIPTION = "Base URL where the resources are located";
-    public static final String DOWNLOAD_ALL_RESOURCES_OVERWRITE_DESCRIPTION = "Download and overwrite previously downloaded resources";
+    public static final String DOWNLOAD_ALL_RESOURCES_BASEURL_DESCRIPTION = "Base URL where the resources are located, this is an optional"
+            + " parameter, by default the resources will be downloaded from the OpenCB repository.";
+    public static final String DOWNLOAD_ALL_RESOURCES_OVERWRITE_DESCRIPTION = "Download and overwrite previously downloaded resources if"
+            + " they already exist.";
 }

opencga-core/src/main/java/org/opencb/opencga/core/models/resource/DownloadResourcesToolParams.java

@@ -20,46 +20,39 @@
 import org.opencb.opencga.core.api.FieldConstants;
 import org.opencb.opencga.core.tools.ToolParams;
 
-import java.util.List;
-
 public class DownloadResourcesToolParams extends ToolParams {
 
     public static final String DESCRIPTION = "Download-resources tool parameters";
 
-    @DataField(id = "baseurl", description = FieldConstants.DOWNLOAD_ALL_RESOURCES_BASEURL_DESCRIPTION)
-    private String baseurl;
+    @DataField(id = "baseUrl", description = FieldConstants.DOWNLOAD_ALL_RESOURCES_BASEURL_DESCRIPTION)
+    private String baseUrl;
 
     @DataField(id = "overwrite", description = FieldConstants.DOWNLOAD_ALL_RESOURCES_OVERWRITE_DESCRIPTION)
     private Boolean overwrite;
 
-    @DataField(id = "outdir", description = FieldConstants.JOB_OUT_DIR_DESCRIPTION)
-    private String outdir;
-
     public DownloadResourcesToolParams() {
     }
 
-    public DownloadResourcesToolParams(String baseurl, Boolean overwrite, String outdir) {
-        this.baseurl = baseurl;
+    public DownloadResourcesToolParams(String baseUrl, Boolean overwrite) {
+        this.baseUrl = baseUrl;
         this.overwrite = overwrite;
-        this.outdir = outdir;
     }
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("DownloadResourcesToolParams{");
-        sb.append("baseurl='").append(baseurl).append('\'');
+        final StringBuilder sb = new StringBuilder("DownloadResourcesParams{");
+        sb.append("baseUrl='").append(baseUrl).append('\'');
         sb.append(", overwrite=").append(overwrite);
-        sb.append(", outdir='").append(outdir).append('\'');
         sb.append('}');
         return sb.toString();
     }
 
-    public String getBaseurl() {
-        return baseurl;
+    public String getBaseUrl() {
+        return baseUrl;
     }
 
-    public DownloadResourcesToolParams setBaseurl(String baseurl) {
-        this.baseurl = baseurl;
+    public DownloadResourcesToolParams setBaseUrl(String baseUrl) {
+        this.baseUrl = baseUrl;
         return this;
     }
 
@@ -71,13 +64,4 @@ public DownloadResourcesToolParams setOverwrite(Boolean overwrite) {
         this.overwrite = overwrite;
         return this;
     }
-
-    public String getOutdir() {
-        return outdir;
-    }
-
-    public DownloadResourcesToolParams setOutdir(String outdir) {
-        this.outdir = outdir;
-        return this;
-    }
 }