catalog: add resource checks, #TASK-6442

opencb · Oct 17, 2024 · 90e7280 · 90e7280
1 parent 6629f3f
commit 90e7280
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Showing 21 changed files with 194 additions and 67 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java
@@ -90,9 +90,17 @@ protected void check() throws Exception {
             }
 
             String userId = jwtPayload.getUserId(catalogFqn.getOrganizationId());
-            // Check write permissions over the path
-            catalogManager.getAuthorizationManager().checkFilePermission(catalogFqn.getOrganizationId(), study.getUid(),
-                    parents.first().getUid(), userId, FilePermissions.WRITE);
+
+            boolean isResource = toolParams.getResource() != null && toolParams.getResource();
+            if (isResource) {
+                // Check it is a study admin
+                catalogManager.getAuthorizationManager().checkIsAtLeastStudyAdministrator(catalogFqn.getOrganizationId(), study.getUid(),
+                        userId);
+            } else {
+                // Check write permissions over the path
+                catalogManager.getAuthorizationManager().checkFilePermission(catalogFqn.getOrganizationId(), study.getUid(),
+                        parents.first().getUid(), userId, FilePermissions.WRITE);
+            }
         } catch (CatalogException e) {
             throw new ToolException(e);
         }
@@ -122,7 +130,8 @@ protected void run() throws Exception {
         step("register", () -> {
             // Move downloaded file and register
             try {
-                moveFile(studyFqn, getOutDir().resolve(fileName), null, toolParams.getPath(), token);
+                boolean isResource = toolParams.getResource() != null && toolParams.getResource();
+                moveFile(studyFqn, getOutDir().resolve(fileName), null, toolParams.getPath(), isResource, token);
             } catch (Exception e) {
                 deleteTemporaryFile();
                 throw new CatalogException(e.getMessage(), e);

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java
@@ -510,10 +510,11 @@ protected final void addAttribute(String key, Object value) throws ToolException
         erm.addAttribute(key, value);
     }
 
-    protected final void moveFile(String study, Path source, Path destiny, String catalogDirectoryPath, String token) throws ToolException {
+    protected final void moveFile(String study, Path source, Path destiny, String catalogDirectoryPath, boolean isResource, String token)
+            throws ToolException {
         File file;
         try {
-            file = catalogManager.getFileManager().moveAndRegister(study, source, destiny, catalogDirectoryPath, token).first();
+            file = catalogManager.getFileManager().moveAndRegister(study, source, destiny, catalogDirectoryPath, isResource, token).first();
         } catch (Exception e) {
             throw new ToolException("Error moving file from " + source + " to " + destiny, e);
         }

diff --git a/...-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/FileCommandExecutor.java b/...-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/FileCommandExecutor.java
@@ -99,7 +99,8 @@ private void fetch() throws ToolException {
 
         Path outDir = Paths.get(options.outDir);
 
-        toolRunner.execute(FetchAndRegisterTask.class, new FileFetch(options.url, options.path), outDir, null, false, options.commonOptions.token);
+        toolRunner.execute(FetchAndRegisterTask.class, new FileFetch(options.url, options.path, options.resource), outDir, null, false,
+                options.commonOptions.token);
     }
 
     private void tsvLoad() throws ToolException {

diff --git a/...cga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/FileCommandOptions.java b/...cga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/FileCommandOptions.java
@@ -121,6 +121,9 @@ public class FetchCommandOptions {
                 description = "Folder path where the downloaded file will be registered", required = true, arity = 1)
         public String path;
 
+        @Parameter(names = {"--resource"}, description = "File resource", arity = 1)
+        public Boolean resource;
+
         @Parameter(names = {"--url"}, description = "External url where the file to be registered can be downloaded from", required = true,
                 arity = 1)
         public String url;

diff --git a/...a-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomFilesCommandOptions.java b/...a-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomFilesCommandOptions.java
@@ -72,6 +72,8 @@ public class UploadCommandOptions {
                 + "removed", arity = 0)
         public boolean replace;
 
+        @Parameter(names = {"--resource"}, description = "File resource", arity = 1)
+        public Boolean resource;
 //        @Parameter(names = {"-ch", "--checksum"}, description = "[PENDING] Calculate checksum", arity = 0)
 //        public boolean checksum;
 

diff --git a/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java
@@ -287,6 +287,7 @@ private RestResponse<File> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "software.website", commandOptions.softwareWebsite, true);
             putNestedMapIfNotEmpty(beanParams, "software.params", commandOptions.softwareParams, true);
             putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
+            putNestedIfNotNull(beanParams, "resource", commandOptions.resource, true);
             putNestedIfNotEmpty(beanParams, "jobId", commandOptions.jobId, true);
             putNestedIfNotEmpty(beanParams, "creationDate", commandOptions.creationDate, true);
             putNestedIfNotEmpty(beanParams, "modificationDate", commandOptions.modificationDate, true);
@@ -372,6 +373,7 @@ private RestResponse<Job> fetch() throws Exception {
         } else {
             ObjectMap beanParams = new ObjectMap();
             putNestedIfNotEmpty(beanParams, "url", commandOptions.url, true);
+            putNestedIfNotNull(beanParams, "resource", commandOptions.resource, true);
             putNestedIfNotEmpty(beanParams, "path", commandOptions.path, true);
 
             fileFetch = JacksonUtils.getDefaultObjectMapper().copy()
@@ -569,6 +571,7 @@ private RestResponse<File> upload() throws Exception {
         queryParams.putIfNotNull("fileFormat", commandOptions.fileFormat);
         queryParams.putIfNotNull("bioformat", commandOptions.bioformat);
         queryParams.putIfNotEmpty("checksum", commandOptions.checksum);
+        queryParams.putIfNotNull("resource", commandOptions.resource);
         queryParams.putIfNotEmpty("study", commandOptions.study);
         queryParams.putIfNotEmpty("relativeFilePath", commandOptions.relativeFilePath);
         queryParams.putIfNotEmpty("description", commandOptions.description);

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java
@@ -227,6 +227,9 @@ public class CreateCommandOptions {
         @Parameter(names = {"--tags"}, description = "The body web service tags parameter", required = false, arity = 1)
         public String tags;
 
+        @Parameter(names = {"--resource"}, description = "Indicates the file is treated as a resource.", required = false, arity = 1)
+        public Boolean resource;
+
         @Parameter(names = {"--job-id"}, description = "The body web service jobId parameter", required = false, arity = 1)
         public String jobId;
 
@@ -378,6 +381,9 @@ public class FetchCommandOptions {
         @Parameter(names = {"--url"}, description = "The body web service url parameter", required = true, arity = 1)
         public String url;
 
+        @Parameter(names = {"--resource"}, description = "Indicates the file is treated as a resource.", required = false, arity = 1)
+        public Boolean resource;
+
         @Parameter(names = {"--path"}, description = "The body web service path parameter", required = false, arity = 1)
         public String path;
 

diff --git a/...src/main/java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/ResourcesMigration.java b/...src/main/java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/ResourcesMigration.java
@@ -54,9 +54,9 @@ protected void run() throws Exception {
                             int release = fileDoc.get("release", Number.class).intValue();
 
                             // Create the RESOURCES folder
-                            File file = new File("RESOURCES", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.UNKNOWN, "RESOURCES/",
-                                    Paths.get(studyUri).resolve("RESOURCES").toUri(), "Default resources folder", FileInternal.init(), 0,
-                                    release).setResource(true);
+                            File file = new File("RESOURCES", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.UNKNOWN,
+                                    "RESOURCES/", Paths.get(studyUri).resolve("RESOURCES").toUri(), "Default resources folder",
+                                    FileInternal.init(), true, 0, release);
                             try {
                                 dbAdaptorFactory.getCatalogFileDBAdaptor(organizationId).insert(studyUid, file, Collections.emptyList(),
                                         Collections.emptyList(), Collections.emptyList(), QueryOptions.empty());

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/FileDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/FileDBAdaptor.java
@@ -58,6 +58,7 @@ enum QueryParams implements QueryParam {
         MODIFICATION_DATE("modificationDate", TEXT_ARRAY, ""),
         DESCRIPTION("description", TEXT_ARRAY, ""),
         EXTERNAL("external", BOOLEAN, ""),
+        RESOURCE("resource", BOOLEAN, ""),
         RELEASE("release", INTEGER, ""),
         STATUS("status", TEXT_ARRAY, ""),
         STATUS_ID("status.id", TEXT, ""),

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java
@@ -283,12 +283,12 @@ Study insert(ClientSession clientSession, Project project, Study study)
         // Create default folders for study
         List<File> files = Arrays.asList(
                 new File(".", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.UNKNOWN, "", study.getUri(),
-                        "study root folder", FileInternal.init(), 0, project.getCurrentRelease()),
+                        "study root folder", FileInternal.init(), false, 0, project.getCurrentRelease()),
                 new File("JOBS", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.UNKNOWN, "JOBS/",
-                        ioManager.getJobsUri(), "Default jobs folder", FileInternal.init(), 0, project.getCurrentRelease()),
+                        ioManager.getJobsUri(), "Default jobs folder", FileInternal.init(), false, 0, project.getCurrentRelease()),
                 new File("RESOURCES", File.Type.DIRECTORY, File.Format.UNKNOWN, File.Bioformat.UNKNOWN, "RESOURCES/",
-                        Paths.get(study.getUri()).resolve("RESOURCES").toUri(), "Default resources folder", FileInternal.init(), 0,
-                        project.getCurrentRelease()).setResource(true)
+                        Paths.get(study.getUri()).resolve("RESOURCES").toUri(), "Default resources folder", FileInternal.init(), true, 0,
+                        project.getCurrentRelease())
         );
 
         // Create default folders