Merge pull request #87 from GReD-Clermont/5_18_0

5.18.0

.github/workflows/maven.yml

@@ -11,41 +11,42 @@ jobs:
 
     env:
       HAVE_SONAR_TOKEN: ${{ secrets.SONAR_TOKEN != '' }}
+      HAVE_SONAR_DETAILS: ${{ vars.SONAR_PROJECTKEY != '' && vars.SONAR_ORGANIZATION != '' }}
       HAVE_DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN != '' }}
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Checkout omero-test-infra
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: openmicroscopy/omero-test-infra
           submodules: true
           path: .omero
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'adopt'
           server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
           settings-path: ${{ github.workspace }} # location for the settings.xml file
       - name: Cache SonarCloud packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.sonar/cache
           key: ${{ runner.os }}-sonar
           restore-keys: ${{ runner.os }}-sonar
       - name: Cache Maven packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ secrets.CACHE_VERSION }}-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2-${{ secrets.CACHE_VERSION }}
       - name: Login to Docker Hub
         if: ${{ env.HAVE_DOCKERHUB_TOKEN == 'true' }}
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -63,20 +64,20 @@ jobs:
       - name: Set folders ownership back to current user
         run: sudo chown -R $(id -u):$(id -g) $GITHUB_WORKSPACE && sudo chown -R $(id -u):$(id -g) $HOME
       - name: Sonar analysis
-        if: ${{ env.HAVE_SONAR_TOKEN == 'true' }}
+        if: ${{ env.HAVE_SONAR_TOKEN == 'true' && env.HAVE_SONAR_DETAILS == 'true' }}
         run: mvn sonar:sonar -Dsonar.host.url=$SONAR_URL -Dsonar.projectKey=$SONAR_PROJECTKEY -Dsonar.organization=$SONAR_ORGANIZATION
         env:
-          SONAR_PROJECTKEY: GReD-Clermont_simple-omero-client
-          SONAR_ORGANIZATION: gred-clermont
-          SONAR_URL: https://sonarcloud.io
+          SONAR_PROJECTKEY: ${{ vars.SONAR_PROJECTKEY }}
+          SONAR_ORGANIZATION: ${{ vars.SONAR_ORGANIZATION }}
+          SONAR_URL: ${{ vars.SONAR_URL }}
           GITHUB_TOKEN: ${{ github.token }}  # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       - name: Upload to codecov after successful tests
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{secrets.CODECOV_TOKEN}}
       - name: Upload Artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: jars
           path: |
@@ -89,19 +90,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'adopt'
           server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
           gpg-private-key: ${{ secrets.GPG_KEY }} # Value of the GPG private key to import
           gpg-passphrase: GPG_PASSPHRASE # env variable for GPG private key passphrase
       - name: Cache Maven packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ secrets.CACHE_VERSION }}-${{ hashFiles('**/pom.xml') }}

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>fr.igred</groupId>
     <artifactId>simple-omero-client</artifactId>
-    <version>5.17.0</version>
+    <version>5.18.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <name>Simple OMERO Client</name>

src/main/java/fr/igred/omero/Client.java

@@ -47,6 +47,7 @@
 import java.util.stream.Collectors;
 
 import static fr.igred.omero.GenericObjectWrapper.flatten;
+import static fr.igred.omero.exception.ExceptionHandler.call;
 
 
 /**
@@ -196,7 +197,9 @@ public void delete(Collection<? extends GenericObjectWrapper<?>> objects)
             }
         }
         if (!objects.isEmpty()) {
-            delete(objects.stream().map(GenericObjectWrapper::asIObject).collect(Collectors.toList()));
+            delete(objects.stream()
+                          .map(GenericObjectWrapper::asIObject)
+                          .collect(Collectors.toList()));
         }
     }
 
@@ -272,7 +275,9 @@ public void deleteTable(TableWrapper table)
      */
     public void deleteTables(Collection<? extends TableWrapper> tables)
     throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
-        deleteFiles(tables.stream().map(TableWrapper::getId).toArray(Long[]::new));
+        deleteFiles(tables.stream()
+                          .map(TableWrapper::getId)
+                          .toArray(Long[]::new));
     }
 
 
@@ -290,14 +295,15 @@ public void deleteTables(Collection<? extends TableWrapper> tables)
      */
     public ExperimenterWrapper getUser(String username)
     throws ExecutionException, ServiceException, AccessException {
-        ExperimenterData experimenter = ExceptionHandler.of(getAdminFacility(),
-                                                            a -> a.lookupExperimenter(getCtx(), username))
-                                                        .handleOMEROException("Cannot retrieve user: " + username)
-                                                        .get();
-        if (experimenter != null) {
-            return new ExperimenterWrapper(experimenter);
+        ExperimenterData user = call(getAdminFacility(),
+                                     a -> a.lookupExperimenter(getCtx(),
+                                                               username),
+                                     "Cannot retrieve user: " + username);
+        if (user != null) {
+            return new ExperimenterWrapper(user);
         } else {
-            throw new NoSuchElementException(String.format("User not found: %s", username));
+            String msg = String.format("User not found: %s", username);
+            throw new NoSuchElementException(msg);
         }
     }
 
@@ -315,7 +321,9 @@ public ExperimenterWrapper getUser(String username)
      */
     public ExperimenterWrapper getUser(long userId)
     throws ServiceException, OMEROServerError {
-        Experimenter user = ExceptionHandler.of(getGateway(), g -> g.getAdminService(getCtx()).getExperimenter(userId))
+        Experimenter user = ExceptionHandler.of(getGateway(),
+                                                g -> g.getAdminService(getCtx())
+                                                      .getExperimenter(userId))
                                             .rethrow(ApiUsageException.class,
                                                      (m, e) -> new NoSuchElementException(m),
                                                      "User not found: " + userId)
@@ -339,13 +347,14 @@ public ExperimenterWrapper getUser(long userId)
      */
     public GroupWrapper getGroup(String groupName)
     throws ExecutionException, ServiceException, AccessException {
-        GroupData group = ExceptionHandler.of(getAdminFacility(), a -> a.lookupGroup(getCtx(), groupName))
-                                          .handleOMEROException("Cannot retrieve group: " + groupName)
-                                          .get();
+        GroupData group = call(getAdminFacility(),
+                               a -> a.lookupGroup(getCtx(), groupName),
+                               "Cannot retrieve group: " + groupName);
         if (group != null) {
             return new GroupWrapper(group);
         } else {
-            throw new NoSuchElementException(String.format("Group not found: %s", groupName));
+            String msg = String.format("Group not found: %s", groupName);
+            throw new NoSuchElementException(msg);
         }
     }
 
@@ -363,7 +372,9 @@ public GroupWrapper getGroup(String groupName)
      */
     public GroupWrapper getGroup(long groupId)
     throws ServiceException, OMEROServerError {
-        ExperimenterGroup group = ExceptionHandler.of(getGateway(), g -> g.getAdminService(getCtx()).getGroup(groupId))
+        ExperimenterGroup group = ExceptionHandler.of(getGateway(),
+                                                      g -> g.getAdminService(getCtx())
+                                                            .getGroup(groupId))
                                                   .rethrow(ApiUsageException.class,
                                                            (m, e) -> new NoSuchElementException(m),
                                                            "Group not found: " + groupId)
@@ -378,21 +389,21 @@ public GroupWrapper getGroup(long groupId)
      *
      * @return See above.
      *
-     * @throws ServiceException       Cannot connect to OMERO.
-     * @throws AccessException        Cannot access data.
+     * @throws ServiceException Cannot connect to OMERO.
+     * @throws AccessException  Cannot access data.
      */
     public List<GroupWrapper> getGroups()
     throws ServiceException, AccessException {
         String error = "Cannot retrieve the groups on OMERO";
-        return ExceptionHandler.of(getGateway(),
-                                   g -> g.getAdminService(getCtx()).lookupGroups())
-                               .handleOMEROException(error)
-                               .get()
-                               .stream()
-                               .filter(Objects::nonNull)
-                               .map(GroupData::new)
-                               .map(GroupWrapper::new)
-                               .collect(Collectors.toList());
+        List<ExperimenterGroup> groups = call(getGateway(),
+                                              g -> g.getAdminService(getCtx())
+                                                    .lookupGroups(),
+                                              error);
+        return groups.stream()
+                     .filter(Objects::nonNull)
+                     .map(GroupData::new)
+                     .map(GroupWrapper::new)
+                     .collect(Collectors.toList());
     }
 
 
@@ -412,8 +423,9 @@ public List<GroupWrapper> getGroups()
     public Client sudoGetUser(String username)
     throws ServiceException, AccessException, ExecutionException {
         ExperimenterWrapper sudoUser = getUser(username);
+        long                groupId  = sudoUser.getDefaultGroup().getId();
 
-        SecurityContext context = new SecurityContext(sudoUser.getDefaultGroup().getId());
+        SecurityContext context = new SecurityContext(groupId);
         context.setExperimenter(sudoUser.asDataObject());
         context.sudo();
 

src/main/java/fr/igred/omero/GatewayWrapper.java

@@ -48,6 +48,8 @@
 import java.util.concurrent.locks.ReentrantLock;
 import java.util.stream.Collectors;
 
+import static fr.igred.omero.exception.ExceptionHandler.call;
+
 
 /**
  * Basic class, contains the gateway, the security context, and multiple facilities.
@@ -175,8 +177,10 @@ public long getCurrentGroupId() {
      * @throws ServiceException If the connection is broken, or not logged in
      */
     public String getSessionId() throws ServiceException {
-        return ExceptionHandler.of(gateway, g -> g.getSessionId(user.asDataObject()))
-                               .rethrow(DSOutOfServiceException.class, ServiceException::new,
+        return ExceptionHandler.of(gateway,
+                                   g -> g.getSessionId(user.asDataObject()))
+                               .rethrow(DSOutOfServiceException.class,
+                                        ServiceException::new,
                                         "Could not retrieve session ID")
                                .get();
     }
@@ -222,7 +226,10 @@ public void connect(String hostname, int port, String sessionId)
      */
     public void connect(String hostname, int port, String username, char[] password, Long groupID)
     throws ServiceException {
-        LoginCredentials cred = new LoginCredentials(username, String.valueOf(password), hostname, port);
+        LoginCredentials cred = new LoginCredentials(username,
+                                                     String.valueOf(password),
+                                                     hostname,
+                                                     port);
         cred.setGroupID(groupID);
         connect(cred);
     }
@@ -242,7 +249,10 @@ public void connect(String hostname, int port, String username, char[] password,
      */
     public void connect(String hostname, int port, String username, char[] password)
     throws ServiceException {
-        connect(new LoginCredentials(username, String.valueOf(password), hostname, port));
+        connect(new LoginCredentials(username,
+                                     String.valueOf(password),
+                                     hostname,
+                                     port));
     }
 
 
@@ -323,7 +333,8 @@ public BrowseFacility getBrowseFacility() throws ExecutionException {
      */
     public IQueryPrx getQueryService() throws ServiceException {
         return ExceptionHandler.of(gateway, g -> g.getQueryService(ctx))
-                               .rethrow(DSOutOfServiceException.class, ServiceException::new,
+                               .rethrow(DSOutOfServiceException.class,
+                                        ServiceException::new,
                                         "Could not retrieve Query Service")
                                .get();
     }
@@ -399,7 +410,8 @@ public AdminFacility getAdminFacility() throws ExecutionException {
     public OMEROMetadataStoreClient getImportStore() throws ServiceException {
         storeUses.incrementAndGet();
         return ExceptionHandler.of(this, GatewayWrapper::getImportStoreLocked)
-                               .rethrow(DSOutOfServiceException.class, ServiceException::new,
+                               .rethrow(DSOutOfServiceException.class,
+                                        ServiceException::new,
                                         "Could not retrieve import store")
                                .get();
     }
@@ -428,7 +440,9 @@ public void closeImport() {
      */
     public List<IObject> findByQuery(String query)
     throws ServiceException, OMEROServerError {
-        return ExceptionHandler.of(gateway, g -> g.getQueryService(ctx).findAllByQuery(query, null))
+        return ExceptionHandler.of(gateway,
+                                   g -> g.getQueryService(ctx)
+                                         .findAllByQuery(query, null))
                                .handleServiceOrServer("Query failed: " + query)
                                .get();
     }
@@ -447,9 +461,9 @@ public List<IObject> findByQuery(String query)
      */
     public IObject save(IObject object)
     throws ServiceException, AccessException, ExecutionException {
-        return ExceptionHandler.of(getDm(), d -> d.saveAndReturnObject(ctx, object))
-                               .handleOMEROException("Cannot save object")
-                               .get();
+        return call(getDm(),
+                    d -> d.saveAndReturnObject(ctx, object),
+                    "Cannot save object");
     }
 
 
@@ -467,7 +481,8 @@ public IObject save(IObject object)
     void delete(IObject object)
     throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
         final long wait = 500L;
-        ExceptionHandler.ofConsumer(getDm(), d -> d.delete(ctx, object).loop(10, wait))
+        ExceptionHandler.ofConsumer(getDm(),
+                                    d -> d.delete(ctx, object).loop(10, wait))
                         .rethrow(InterruptedException.class)
                         .handleException("Cannot delete object")
                         .rethrow();
@@ -488,7 +503,8 @@ void delete(IObject object)
     void delete(List<IObject> objects)
     throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
         final long wait = 500L;
-        ExceptionHandler.ofConsumer(getDm(), d -> d.delete(ctx, objects).loop(10, wait))
+        ExceptionHandler.ofConsumer(getDm(),
+                                    d -> d.delete(ctx, objects).loop(10, wait))
                         .rethrow(InterruptedException.class)
                         .handleException("Cannot delete objects")
                         .rethrow();