Merge branch 'develop' of github.com:opencb/opencga into develop

opencb · May 9, 2024 · 4138612 · 4138612
2 parents 15ae9a6 + bb2d686
commit 4138612
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Showing 4 changed files with 74 additions and 14 deletions.
diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml
@@ -11,10 +11,15 @@ on:
         type: string
         required: true
       hadoop:
-        type: string
+        type: choice
         description: 'Hadoop flavour. Any of: [hdp3.1, hdi5.1, emr6.1, emr6.13]'
         required: false
-        default: "hdp3.1"
+        default: hdp3.1
+        options:
+          - hdp3.1
+          - hdi5.1
+          - emr6.1
+          - emr6.13
 
 jobs:
   build:

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java
@@ -353,21 +353,16 @@ private void extractSharedProjects(DataResult<User> userDataResult, QueryOptions
                     studyMap.put(study.getFqn(), study);
                     studyProjectMap.put(study.getFqn(), project.getFqn());
 
-                    String owner = study.getFqn().split("@")[0];
-
                     if (study.getGroups() != null) {
                         for (Group group : study.getGroups()) {
                             if (StudyManager.MEMBERS.equals(group.getId())) {
                                 // Add all the users that should be able to see the study to the map
                                 for (String userId : group.getUserIds()) {
-                                    // Exclude owner of the project
-                                    if (!owner.equals(userId)) {
-                                        if (users.contains(userId)) {
-                                            if (!userStudyMap.containsKey(userId)) {
-                                                userStudyMap.put(userId, new ArrayList<>());
-                                            }
-                                            userStudyMap.get(userId).add(study.getFqn());
+                                    if (users.contains(userId)) {
+                                        if (!userStudyMap.containsKey(userId)) {
+                                            userStudyMap.put(userId, new ArrayList<>());
                                         }
+                                        userStudyMap.get(userId).add(study.getFqn());
                                     }
                                 }
                                 break;
@@ -378,7 +373,7 @@ private void extractSharedProjects(DataResult<User> userDataResult, QueryOptions
             }
         }
 
-        // Add sharedProject information
+        // Add project information
         for (User user : userDataResult.getResults()) {
             if (userStudyMap.containsKey(user.getId())) {
                 Map<String, List<Study>> projectStudyMap = new HashMap<>();

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java
@@ -519,7 +519,7 @@ public OpenCGAResult<User> get(String organizationId, String userId, QueryOption
      * @return The requested users
      * @throws CatalogException CatalogException
      */
-    public OpenCGAResult<User> get(String organizationId, List<String> userIdList, QueryOptions options, String token)
+    public OpenCGAResult<User> get(@Nullable String organizationId, List<String> userIdList, QueryOptions options, String token)
             throws CatalogException {
         ParamUtils.checkNotEmptyArray(userIdList, "userId");
         ParamUtils.checkParameter(token, "token");
@@ -532,7 +532,7 @@ public OpenCGAResult<User> get(String organizationId, List<String> userIdList, Q
                 .append("token", token);
         JwtPayload jwtPayload = validateToken(token);
 
-        if (userIdList.size() == 1 && jwtPayload.getUserId().equals(userIdList.get(0)) && StringUtils.isEmpty(organizationId)) {
+        if (StringUtils.isEmpty(organizationId)) {
             organizationId = jwtPayload.getOrganization();
         }
         String userId = jwtPayload.getUserId(organizationId);

diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java
@@ -17,6 +17,7 @@
 package org.opencb.opencga.catalog.managers;
 
 import com.mongodb.BasicDBObject;
+import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.junit.Ignore;
@@ -256,6 +257,65 @@ public void testGetUserInfo() throws CatalogException {
                 studyAdminToken1);
     }
 
+    @Test
+    public void testGetProjectsFromUserInfo() throws CatalogException {
+        String userId = organizationId;
+        catalogManager.getUserManager().create(userId, "test", "[email protected]", TestParamConstants.PASSWORD, organizationId, null,
+                opencgaToken);
+        catalogManager.getStudyManager().updateGroup(studyFqn, ParamConstants.MEMBERS_GROUP, ParamUtils.BasicUpdateAction.ADD,
+                new GroupUpdateParams(Collections.singletonList("test")), ownerToken);
+        String token = catalogManager.getUserManager().login(organizationId, userId, TestParamConstants.PASSWORD).getToken();
+
+        DataResult<User> user = catalogManager.getUserManager().get(organizationId, userId, new QueryOptions(), token);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(organizationId, normalUserId3, new QueryOptions(), normalToken3);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(organizationId, orgOwnerUserId, new QueryOptions(), ownerToken);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(organizationId, orgAdminUserId1, new QueryOptions(), orgAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(organizationId, studyAdminUserId1, new QueryOptions(), studyAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(organizationId, normalUserId1, new QueryOptions(), orgAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+
+        user = catalogManager.getUserManager().get(null, normalUserId1, new QueryOptions(), normalToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(null, normalUserId3, new QueryOptions(), normalToken3);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(null, orgOwnerUserId, new QueryOptions(), ownerToken);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(null, orgAdminUserId1, new QueryOptions(), orgAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(null, studyAdminUserId1, new QueryOptions(), studyAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+
+        user = catalogManager.getUserManager().get(null, normalUserId1, new QueryOptions(), orgAdminToken1);
+        assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects()));
+        System.out.println(user.first().getProjects().size());
+    }
+
     @Test
     public void testModifyUser() throws CatalogException, InterruptedException, IOException {
         ObjectMap params = new ObjectMap();