feat: extend datasets commands visibility, labels, filter support (#632)

* feat: extend datasets commands visibility, labels, filter support

* chore: update datasets commands to use V2 dataset api

* fix: resolve dataset by name when dataset hidden

* chore: minor doc update

* fix: update reflect-config with new objects

* fix: minor fixes

Author: georgi-seqera

conf/reflect-config.json

@@ -1206,6 +1206,18 @@
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.datasets.DatasetMultiRefOptions",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.datasets.DatasetMultiRefOptions$DatasetMultiRef",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.datasets.DatasetRefOptions",
   "allDeclaredFields":true,
@@ -1230,12 +1242,30 @@
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.datasets.HideCmd",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.datasets.LabelsCmd",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.datasets.ListCmd",
   "allDeclaredFields":true,
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.datasets.ShowCmd",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.datasets.UpdateCmd",
   "allDeclaredFields":true,
@@ -2159,6 +2189,12 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.cli.responses.datasets.DatasetsVisibility",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
 {
   "name":"io.seqera.tower.cli.responses.labels.DeleteLabelsResponse",
   "allDeclaredFields":true,

src/main/java/io/seqera/tower/cli/commands/DatasetsCmd.java

@@ -20,7 +20,10 @@
 import io.seqera.tower.cli.commands.datasets.AddCmd;
 import io.seqera.tower.cli.commands.datasets.DeleteCmd;
 import io.seqera.tower.cli.commands.datasets.DownloadCmd;
+import io.seqera.tower.cli.commands.datasets.HideCmd;
+import io.seqera.tower.cli.commands.datasets.LabelsCmd;
 import io.seqera.tower.cli.commands.datasets.ListCmd;
+import io.seqera.tower.cli.commands.datasets.ShowCmd;
 import io.seqera.tower.cli.commands.datasets.UpdateCmd;
 import io.seqera.tower.cli.commands.datasets.UrlCmd;
 import io.seqera.tower.cli.commands.datasets.ViewCmd;
@@ -33,7 +36,10 @@
                 AddCmd.class,
                 DeleteCmd.class,
                 DownloadCmd.class,
+                HideCmd.class,
+                LabelsCmd.class,
                 ListCmd.class,
+                ShowCmd.class,
                 ViewCmd.class,
                 UpdateCmd.class,
                 UrlCmd.class,

src/main/java/io/seqera/tower/cli/commands/datasets/AbstractDatasetsCmd.java

@@ -26,6 +26,7 @@
 import io.seqera.tower.model.ListDatasetsResponse;
 import picocli.CommandLine;
 
+import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Objects;
@@ -35,7 +36,7 @@
 public abstract class AbstractDatasetsCmd extends AbstractApiCmd {
 
     protected DatasetDto datasetByName(Long workspaceId, String datasetName) throws ApiException {
-        ListDatasetsResponse listDatasetsResponse = datasetsApi().listDatasets(workspaceId);
+        ListDatasetsResponse listDatasetsResponse = datasetsApi().listDatasetsV2(workspaceId, null, null, datasetName, null, null, "all", List.of());
 
         if (listDatasetsResponse == null || listDatasetsResponse.getDatasets() == null) {
             throw new DatasetNotFoundException(workspaceRef(workspaceId));
@@ -49,36 +50,14 @@ protected DatasetDto datasetByName(Long workspaceId, String datasetName) throws
             throw new DatasetNotFoundException(datasetName, workspaceRef(workspaceId));
         }
 
-        return datasetList.stream().findFirst().orElse(null);
-    }
-
-    protected List<DatasetDto> searchByName(Long workspaceId, String datasetName) throws ApiException {
-        ListDatasetsResponse listDatasetsResponse = datasetsApi().listDatasets(workspaceId);
-
-        if (datasetName == null) {
-            return listDatasetsResponse.getDatasets();
-        }
-
-        if (listDatasetsResponse == null || listDatasetsResponse.getDatasets() == null) {
-            throw new DatasetNotFoundException(workspaceRef(workspaceId));
-        }
-
-        List<DatasetDto> datasetList = listDatasetsResponse.getDatasets().stream()
-                .filter(it -> it.getName().startsWith(datasetName))
-                .collect(Collectors.toList());
-
-        if (datasetList.isEmpty()) {
-            throw new DatasetNotFoundException(datasetName, workspaceRef(workspaceId));
-        }
-
-        return datasetList;
+        return datasetList.get(0);
     }
 
     protected DatasetDto fetchDescribeDatasetResponse(DatasetRefOptions datasetRefOptions, Long wspId) throws ApiException {
         DatasetDto response;
 
         if (datasetRefOptions.dataset.datasetId != null) {
-            response = datasetsApi().describeDataset(wspId, datasetRefOptions.dataset.datasetId, List.of()).getDataset();
+            response = datasetsApi().describeDatasetV2(datasetRefOptions.dataset.datasetId, wspId, List.of()).getDataset();
         } else {
             response = datasetByName(wspId, datasetRefOptions.dataset.datasetName);
         }
@@ -89,7 +68,7 @@ protected DatasetDto fetchDescribeDatasetResponse(DatasetRefOptions datasetRefOp
     protected DatasetVersionDto fetchDatasetVersion(Long wspId, String datasetId, String datasetMediaType, Long version) throws ApiException {
         DatasetVersionDto datasetVersion;
 
-        ListDatasetVersionsResponse listDatasetVersionsResponse = datasetsApi().listDatasetVersions(wspId, datasetId, datasetMediaType);
+        ListDatasetVersionsResponse listDatasetVersionsResponse = datasetsApi().listDatasetVersionsV2(datasetId, wspId, datasetMediaType);
 
         if (listDatasetVersionsResponse == null || listDatasetVersionsResponse.getVersions() == null) {
             throw new TowerException(String.format("No versions were found for dataset %s", datasetId));
@@ -129,13 +108,26 @@ protected String getDatasetRef(DatasetRefOptions datasetRefOptions) {
         return datasetRefOptions.dataset.datasetName != null ? datasetRefOptions.dataset.datasetName : datasetRefOptions.dataset.datasetId;
     }
 
+    protected List<String> resolveDatasetIds(DatasetMultiRefOptions options, Long wspId) throws ApiException {
+        List<String> ids = new ArrayList<>();
+        if (options.dataset.datasetIds != null) {
+            ids.addAll(options.dataset.datasetIds);
+        }
+        if (options.dataset.datasetNames != null) {
+            for (String name : options.dataset.datasetNames) {
+                ids.add(datasetByName(wspId, name).getId());
+            }
+        }
+        return ids;
+    }
+
     protected void deleteDatasetByName(String datasetName, Long wspId) throws DatasetNotFoundException, ApiException {
         DatasetDto response = datasetByName(wspId, datasetName);
         deleteDatasetById(response.getId(), wspId);
     }
 
     protected void deleteDatasetById(String datasetId, Long wspId) throws DatasetNotFoundException, ApiException {
-        datasetsApi().deleteDataset(wspId, datasetId);
+        datasetsApi().deleteDatasetV2(datasetId, wspId);
     }
 
 

src/main/java/io/seqera/tower/cli/commands/datasets/AddCmd.java

@@ -72,9 +72,9 @@ protected Response exec() throws ApiException, IOException {
 
         if (overwrite) tryDeleteDataset(name, wspId);
 
-        CreateDatasetResponse response = datasetsApi().createDataset(wspId, request);
+        CreateDatasetResponse response = datasetsApi().createDatasetV2(request, wspId);
 
-        datasetsApi().uploadDataset(wspId, response.getDataset().getId(), header, fileName.toFile());
+        datasetsApi().uploadDatasetV2(response.getDataset().getId(), wspId, header, fileName.toFile());
 
         return new DatasetCreate(response.getDataset().getName(), workspace.workspace, response.getDataset().getId());
     }

src/main/java/io/seqera/tower/cli/commands/datasets/DatasetMultiRefOptions.java

@@ -0,0 +1,36 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package io.seqera.tower.cli.commands.datasets;
+
+import picocli.CommandLine;
+
+import java.util.List;
+
+public class DatasetMultiRefOptions {
+
+    @CommandLine.ArgGroup(multiplicity = "1")
+    public DatasetMultiRef dataset;
+
+    public static class DatasetMultiRef {
+
+        @CommandLine.Option(names = {"-i", "--id"}, arity = "1..*", description = "Dataset unique identifier(s). May be combined with --name.")
+        public List<String> datasetIds;
+
+        @CommandLine.Option(names = {"-n", "--name"}, arity = "1..*", description = "Dataset name(s). May be combined with --id.")
+        public List<String> datasetNames;
+    }
+}

src/main/java/io/seqera/tower/cli/commands/datasets/DatasetsLabelsManager.java

@@ -0,0 +1,51 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package io.seqera.tower.cli.commands.datasets;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.api.LabelsApi;
+import io.seqera.tower.cli.commands.labels.BaseLabelsManager;
+import io.seqera.tower.model.AssociateDatasetsLabelsRequest;
+
+import java.util.List;
+
+public class DatasetsLabelsManager extends BaseLabelsManager<AssociateDatasetsLabelsRequest, String> {
+
+    public DatasetsLabelsManager(LabelsApi api) {
+        super(api, "dataset");
+    }
+
+    @Override
+    protected AssociateDatasetsLabelsRequest getRequest(List<Long> labelsIds, String entityId) {
+        return new AssociateDatasetsLabelsRequest().labelIds(labelsIds).datasetIds(List.of(entityId));
+    }
+
+    @Override
+    protected void apply(AssociateDatasetsLabelsRequest request, Long wspId) throws ApiException {
+        api.applyLabelsToDatasets(request, wspId);
+    }
+
+    @Override
+    protected void remove(AssociateDatasetsLabelsRequest request, Long wspId) throws ApiException {
+        api.removeLabelsFromDatasets(request, wspId);
+    }
+
+    @Override
+    protected void append(AssociateDatasetsLabelsRequest request, Long wspId) throws ApiException {
+        api.addLabelsToDatasets(request, wspId);
+    }
+}

src/main/java/io/seqera/tower/cli/commands/datasets/HideCmd.java

@@ -0,0 +1,51 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package io.seqera.tower.cli.commands.datasets;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.cli.commands.global.WorkspaceRequiredOptions;
+import io.seqera.tower.cli.responses.Response;
+import io.seqera.tower.cli.responses.datasets.DatasetsVisibility;
+import io.seqera.tower.model.ChangeDatasetVisibilityRequest;
+import picocli.CommandLine;
+
+import java.io.IOException;
+import java.util.List;
+
+@CommandLine.Command(
+        name = "hide",
+        description = "Hide one or more datasets"
+)
+public class HideCmd extends AbstractDatasetsCmd {
+
+    @CommandLine.Mixin
+    public DatasetMultiRefOptions datasetMultiRefOptions;
+
+    @CommandLine.Mixin
+    public WorkspaceRequiredOptions workspace;
+
+    @Override
+    protected Response exec() throws ApiException, IOException {
+        Long wspId = workspaceId(workspace.workspace);
+        List<String> ids = resolveDatasetIds(datasetMultiRefOptions, wspId);
+
+        ChangeDatasetVisibilityRequest request = new ChangeDatasetVisibilityRequest().datasetIds(ids);
+        datasetsApi().hideDatasets(request, wspId);
+
+        return new DatasetsVisibility(ids, workspace.workspace, true);
+    }
+}

src/main/java/io/seqera/tower/cli/commands/datasets/LabelsCmd.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package io.seqera.tower.cli.commands.datasets;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.cli.commands.labels.LabelsSubcmdOptions;
+import io.seqera.tower.cli.responses.Response;
+import picocli.CommandLine;
+
+import java.io.IOException;
+
+@CommandLine.Command(name = "labels", description = "Manage dataset labels")
+public class LabelsCmd extends AbstractDatasetsCmd {
+
+    @CommandLine.Mixin
+    public DatasetRefOptions datasetRefOptions;
+
+    @CommandLine.Mixin
+    public LabelsSubcmdOptions labelsSubcmdOptions;
+
+    @Override
+    protected Response exec() throws ApiException, IOException {
+        Long wspId = workspaceId(labelsSubcmdOptions.workspace.workspace);
+        String datasetId = fetchDescribeDatasetResponse(datasetRefOptions, wspId).getId();
+
+        DatasetsLabelsManager manager = new DatasetsLabelsManager(labelsApi());
+        return manager.execute(wspId, datasetId, labelsSubcmdOptions);
+    }
+}