TASK-3908 - Unable to search for shared projects

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java

@@ -40,6 +40,7 @@
 import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException;
 import org.opencb.opencga.catalog.exceptions.CatalogDBException;
 import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
+import org.opencb.opencga.catalog.utils.FqnUtils;
 import org.opencb.opencga.catalog.utils.UuidUtils;
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.config.Configuration;
@@ -705,13 +706,14 @@ private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Qu
                 studyQuery.putIfNotEmpty(StudyDBAdaptor.QueryParams.UID.key(), query.getString(QueryParams.STUDY_UID.key()));
                 studyQuery.putIfNotEmpty(StudyDBAdaptor.QueryParams.ID.key(), query.getString(QueryParams.STUDY_ID.key()));
                 studyQuery.putIfNotEmpty(StudyDBAdaptor.QueryParams.OWNER.key(), query.getString(QueryParams.USER_ID.key()));
-                OpenCGAResult<Document> queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(clientSession, studyQuery,
+                OpenCGAResult<Document> studiesResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(clientSession, studyQuery,
                         new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.FQN.key()), user);
 
-                if (queryResult.getNumResults() > 0) {
+                if (studiesResult.getNumResults() > 0) {
                     Set<String> projectFqn = new HashSet<>();
-                    for (Document result : queryResult.getResults()) {
-                        projectFqn.add(result.getString(StudyDBAdaptor.QueryParams.FQN.key()).split(":")[0]);
+                    for (Document study : studiesResult.getResults()) {
+                        String studyFqn = study.getString(StudyDBAdaptor.QueryParams.FQN.key());
+                        projectFqn.add(FqnUtils.toProjectFqn(studyFqn));
                     }
                     query.put(QueryParams.FQN.key(), new ArrayList<>(projectFqn));
                     return getMongoCursor(clientSession, query, options);
@@ -730,7 +732,7 @@ private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Qu
             List<Long> externalUids = new ArrayList<>(); // Project uids from projects owned by a user other than "user"
             while (iterator.hasNext()) {
                 Project project = iterator.next();
-                if (project.getFqn().startsWith(user + "@")) {
+                if (FqnUtils.getUser(project.getFqn()).equals(user)) {
                     ownerFqns.add(project.getFqn());
                 } else {
                     externalUids.add(project.getUid());
@@ -741,12 +743,13 @@ private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Qu
             List<String> externalFqns = new ArrayList<>();
             if (!externalUids.isEmpty()) {
                 Query studyQuery = new Query(StudyDBAdaptor.QueryParams.PROJECT_UID.key(), externalUids);
-                OpenCGAResult<Document> queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(clientSession, studyQuery,
+                OpenCGAResult<Document> studiesResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(clientSession, studyQuery,
                         new QueryOptions(QueryOptions.INCLUDE, StudyDBAdaptor.QueryParams.FQN.key()), user);
-                if (queryResult.getNumResults() > 0) {
+                if (studiesResult.getNumResults() > 0) {
                     Set<String> projectFqn = new HashSet<>();
-                    for (Document result : queryResult.getResults()) {
-                        projectFqn.add(result.getString(StudyDBAdaptor.QueryParams.FQN.key().split(":")[0]));
+                    for (Document study : studiesResult.getResults()) {
+                        String studyFqn = study.getString(StudyDBAdaptor.QueryParams.FQN.key());
+                        projectFqn.add(FqnUtils.toProjectFqn(studyFqn));
                     }
                     externalFqns.addAll(projectFqn);
                 }

opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/FqnUtils.java

@@ -0,0 +1,104 @@
+package org.opencb.opencga.catalog.utils;
+
+import org.opencb.opencga.core.api.ParamConstants;
+
+import java.util.Objects;
+
+public class FqnUtils {
+
+    public static class FQN {
+        private final String user;
+        private final String project;
+        private final String study;
+        private final String projectFqn;
+
+        public FQN(String fqn) {
+            if (fqn == null || fqn.isEmpty()) {
+                throw new IllegalArgumentException("Empty FQN");
+            }
+            int idx1 = fqn.indexOf(ParamConstants.USER_PROJECT_SEPARATOR);
+            int idx2 = fqn.indexOf(ParamConstants.PROJECT_STUDY_SEPARATOR, idx1 + 1);
+            if (idx1 < 0) {
+                throw new IllegalArgumentException("Invalid FQN. Expected <user>@<project>[:<study>]. Got '" + fqn + "'");
+            }
+            user = fqn.substring(0, idx1);
+            if (idx2 < 0) {
+                project = fqn.substring(idx1 + 1);
+                projectFqn = fqn;
+                study = null;
+            } else {
+                project = fqn.substring(idx1 + 1, idx2);
+                projectFqn = fqn.substring(0, idx2);
+                study = fqn.substring(idx2 + 1);
+            }
+        }
+
+        public FQN(String user, String project) {
+            this(user, project, null);
+        }
+
+        public FQN(String user, String project, String study) {
+            this.user = Objects.requireNonNull(user);
+            this.project = Objects.requireNonNull(project);
+            projectFqn = user + ParamConstants.USER_PROJECT_SEPARATOR + project;
+            this.study = study;
+        }
+
+        public String getUser() {
+            return user;
+        }
+
+        public String getProject() {
+            return project;
+        }
+
+        public String getProjectFqn() {
+            return projectFqn;
+        }
+
+        public String getStudy() {
+            return study;
+        }
+
+        @Override
+        public String toString() {
+            final StringBuilder sb = new StringBuilder(user)
+                    .append(ParamConstants.USER_PROJECT_SEPARATOR)
+                    .append(project);
+            if (study != null) {
+                sb.append(ParamConstants.PROJECT_STUDY_SEPARATOR)
+                        .append(study);
+            }
+            return sb.toString();
+        }
+    }
+
+    public static FQN parse(String fqn) {
+        return new FQN(fqn);
+    }
+
+    public static String getUser(String fqn) {
+        return new FQN(fqn).getUser();
+    }
+
+    public static String getProject(String fqn) {
+        return new FQN(fqn).getProject();
+    }
+
+    public static String getStudy(String fqn) {
+        return new FQN(fqn).getStudy();
+    }
+
+    public static String toProjectFqn(String fqn) {
+        return new FQN(fqn).getProjectFqn();
+    }
+
+    public static String buildFqn(String user, String project) {
+        return new FQN(user, project).toString();
+    }
+
+    public static String buildFqn(String user, String project, String study) {
+        return new FQN(user, project, study).toString();
+    }
+
+}

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

@@ -125,11 +125,24 @@ public void searchSampleNoPermissions() throws CatalogException {
 
     @Test
     public void searchProjects() throws CatalogException {
-        catalogManager.getUserManager().create("userid", "User Name", "mail@ebi.ac.uk", TestParamConstants.PASSWORD, "", null, Account.AccountType.FULL, null);
-        String token = catalogManager.getUserManager().login("userid", TestParamConstants.PASSWORD).getToken();
-        OpenCGAResult<Project> projectOpenCGAResult = catalogManager.getProjectManager().search(new Query(), QueryOptions.empty(), token);
-        assertTrue(projectOpenCGAResult.getResults().isEmpty());
-        assertEquals(0, projectOpenCGAResult.getEvents().size());
+        String otherUser = "user_tmp";
+        catalogManager.getUserManager().create(otherUser, "User Name", "mail@ebi.ac.uk", TestParamConstants.PASSWORD, "", null, Account.AccountType.FULL, null);
+        String otherUsertoken = catalogManager.getUserManager().login(otherUser, TestParamConstants.PASSWORD).getToken();
+        OpenCGAResult<Project> result = catalogManager.getProjectManager()
+                .search(new Query(), QueryOptions.empty(), otherUsertoken);
+        assertTrue(result.getResults().isEmpty());
+        assertEquals(0, result.getEvents().size());
+
+        // Create a new study in project2 with some dummy permissions for user
+        String s2 = catalogManager.getStudyManager().create(project2, "s2", null, "Study 2", "", null, null, null, null, INCLUDE_RESULT, sessionIdUser2).first().getId();
+        catalogManager.getStudyManager().updateGroup(s2, "@members", ParamUtils.BasicUpdateAction.ADD,
+                new GroupUpdateParams(Collections.singletonList(otherUser)), sessionIdUser2);
+
+        result = catalogManager.getProjectManager()
+                .search(new Query(), QueryOptions.empty(), otherUsertoken);
+        assertEquals(1, result.getNumResults());
+        assertEquals(project2, result.first().getId());
+        assertEquals("user2@pmp", result.first().getFqn());
     }
 
     @Test

opencga-catalog/src/test/java/org/opencb/opencga/catalog/utils/FqnUtilsTest.java

@@ -0,0 +1,28 @@
+package org.opencb.opencga.catalog.utils;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class FqnUtilsTest {
+
+    @Test
+    public void testFqnFull() {
+        FqnUtils.FQN fqn = new FqnUtils.FQN("user@project:study");
+        assertEquals("user", fqn.getUser());
+        assertEquals("project", fqn.getProject());
+        assertEquals("user@project", fqn.getProjectFqn());
+        assertEquals("study", fqn.getStudy());
+        assertEquals("user@project:study", fqn.toString());
+    }
+
+    @Test
+    public void testFqnPartial() {
+        FqnUtils.FQN fqn = new FqnUtils.FQN("user@project");
+        assertEquals("user", fqn.getUser());
+        assertEquals("project", fqn.getProject());
+        assertEquals("user@project", fqn.getProjectFqn());
+        assertEquals(null, fqn.getStudy());
+        assertEquals("user@project", fqn.toString());
+    }
+}