impr: small usability improvements

conf/reflect-config.json

@@ -1172,6 +1172,18 @@
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.datastudios.ParentDataStudioRefOptions",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.datastudios.ParentDataStudioRefOptions$ParentDataStudioRef",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.datastudios.StartAsNewCmd",
   "allDeclaredFields":true,
@@ -1889,6 +1901,12 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.cli.responses.datastudios.DataStudioDeleted",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
 {
   "name":"io.seqera.tower.cli.responses.datastudios.DataStudioStartSubmitted",
   "allDeclaredFields":true,
@@ -1925,12 +1943,6 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
-{
-  "name":"io.seqera.tower.cli.responses.datastudios.DataStudioDeleted",
-  "allDeclaredFields":true,
-  "queryAllDeclaredMethods":true,
-  "queryAllDeclaredConstructors":true
-},
 {
   "name":"io.seqera.tower.cli.responses.labels.DeleteLabelsResponse",
   "allDeclaredFields":true,
@@ -3315,7 +3327,7 @@
   "allDeclaredFields":true,
   "allDeclaredMethods":true,
   "allDeclaredConstructors":true,
-  "methods":[{"name":"<init>","parameterTypes":[] }, {"name":"getAllowInstanceCredentials","parameterTypes":[] }, {"name":"getAllowLocalRepos","parameterTypes":[] }, {"name":"getAnalytics","parameterTypes":[] }, {"name":"getApiVersion","parameterTypes":[] }, {"name":"getArm64Enabled","parameterTypes":[] }, {"name":"getAuthTypes","parameterTypes":[] }, {"name":"getCommitId","parameterTypes":[] }, {"name":"getContentMaxFileSize","parameterTypes":[] }, {"name":"getContentUrl","parameterTypes":[] }, {"name":"getDataExplorerAllowedWorkspaces","parameterTypes":[] }, {"name":"getEvalWorkspaceIds","parameterTypes":[] }, {"name":"getForgePrefix","parameterTypes":[] }, {"name":"getGroundswellAllowedWorkspaces","parameterTypes":[] }, {"name":"getGroundswellEnabled","parameterTypes":[] }, {"name":"getHeartbeatInterval","parameterTypes":[] }, {"name":"getLandingUrl","parameterTypes":[] }, {"name":"getLoginPath","parameterTypes":[] }, {"name":"getNavbar","parameterTypes":[] }, {"name":"getSeqeraCloud","parameterTypes":[] }, {"name":"getTermsOfUseUrl","parameterTypes":[] }, {"name":"getUserWorkspaceEnabled","parameterTypes":[] }, {"name":"getVersion","parameterTypes":[] }, {"name":"getWaveAllowedWorkspaces","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"setAllowInstanceCredentials","parameterTypes":["java.lang.Boolean"] }, {"name":"setAllowLocalRepos","parameterTypes":["java.lang.Boolean"] }, {"name":"setAllowNextflowCliLogs","parameterTypes":["java.lang.Boolean"] }, {"name":"setAnalytics","parameterTypes":["io.seqera.tower.model.Analytics"] }, {"name":"setApiVersion","parameterTypes":["java.lang.String"] }, {"name":"setArm64Enabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setAuthTypes","parameterTypes":["java.util.List"] }, {"name":"setCommitId","parameterTypes":["java.lang.String"] }, {"name":"setContactEmail","parameterTypes":["java.lang.String"] }, {"name":"setContentMaxFileSize","parameterTypes":["java.lang.Long"] }, {"name":"setContentUrl","parameterTypes":["java.lang.String"] }, {"name":"setDataExplorerAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setEvalWorkspaceIds","parameterTypes":["java.util.List"] }, {"name":"setForgePrefix","parameterTypes":["java.lang.String"] }, {"name":"setGroundswellAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setGroundswellEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setHeartbeatInterval","parameterTypes":["java.lang.Integer"] }, {"name":"setLandingUrl","parameterTypes":["java.lang.String"] }, {"name":"setLoginPath","parameterTypes":["java.lang.String"] }, {"name":"setNavbar","parameterTypes":["io.seqera.tower.model.NavbarConfig"] }, {"name":"setSeqeraCloud","parameterTypes":["java.lang.Boolean"] }, {"name":"setTermsOfUseUrl","parameterTypes":["java.lang.String"] }, {"name":"setUserWorkspaceEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setVersion","parameterTypes":["java.lang.String"] }, {"name":"setWaveAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setWaveEnabled","parameterTypes":["java.lang.Boolean"] }]
+  "methods":[{"name":"<init>","parameterTypes":[] }, {"name":"getAllowInstanceCredentials","parameterTypes":[] }, {"name":"getAllowLocalRepos","parameterTypes":[] }, {"name":"getAnalytics","parameterTypes":[] }, {"name":"getApiVersion","parameterTypes":[] }, {"name":"getArm64Enabled","parameterTypes":[] }, {"name":"getAuthTypes","parameterTypes":[] }, {"name":"getCommitId","parameterTypes":[] }, {"name":"getContentMaxFileSize","parameterTypes":[] }, {"name":"getContentUrl","parameterTypes":[] }, {"name":"getDataExplorerAllowedWorkspaces","parameterTypes":[] }, {"name":"getEvalWorkspaceIds","parameterTypes":[] }, {"name":"getForgePrefix","parameterTypes":[] }, {"name":"getGroundswellAllowedWorkspaces","parameterTypes":[] }, {"name":"getGroundswellEnabled","parameterTypes":[] }, {"name":"getHeartbeatInterval","parameterTypes":[] }, {"name":"getLandingUrl","parameterTypes":[] }, {"name":"getLoginPath","parameterTypes":[] }, {"name":"getNavbar","parameterTypes":[] }, {"name":"getSeqeraCloud","parameterTypes":[] }, {"name":"getTermsOfUseUrl","parameterTypes":[] }, {"name":"getUserWorkspaceEnabled","parameterTypes":[] }, {"name":"getVersion","parameterTypes":[] }, {"name":"getWaveAllowedWorkspaces","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"setAllowInstanceCredentials","parameterTypes":["java.lang.Boolean"] }, {"name":"setAllowLocalRepos","parameterTypes":["java.lang.Boolean"] }, {"name":"setAllowNextflowCliLogs","parameterTypes":["java.lang.Boolean"] }, {"name":"setAnalytics","parameterTypes":["io.seqera.tower.model.Analytics"] }, {"name":"setApiVersion","parameterTypes":["java.lang.String"] }, {"name":"setArm64Enabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setAuthTypes","parameterTypes":["java.util.List"] }, {"name":"setCommitId","parameterTypes":["java.lang.String"] }, {"name":"setContactEmail","parameterTypes":["java.lang.String"] }, {"name":"setContentMaxFileSize","parameterTypes":["java.lang.Long"] }, {"name":"setContentUrl","parameterTypes":["java.lang.String"] }, {"name":"setDataExplorerAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setEvalWorkspaceIds","parameterTypes":["java.util.List"] }, {"name":"setForgePrefix","parameterTypes":["java.lang.String"] }, {"name":"setGroundswellAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setGroundswellEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setHeartbeatInterval","parameterTypes":["java.lang.Integer"] }, {"name":"setLandingUrl","parameterTypes":["java.lang.String"] }, {"name":"setLoginPath","parameterTypes":["java.lang.String"] }, {"name":"setLogoutUrl_JsonNullable","parameterTypes":["org.openapitools.jackson.nullable.JsonNullable"] }, {"name":"setNavbar","parameterTypes":["io.seqera.tower.model.NavbarConfig"] }, {"name":"setSeqeraCloud","parameterTypes":["java.lang.Boolean"] }, {"name":"setTermsOfUseUrl","parameterTypes":["java.lang.String"] }, {"name":"setUserWorkspaceEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setVersion","parameterTypes":["java.lang.String"] }, {"name":"setWaveAllowedWorkspaces","parameterTypes":["java.util.List"] }, {"name":"setWaveEnabled","parameterTypes":["java.lang.Boolean"] }]
 },
 {
   "name":"io.seqera.tower.model.ServiceInfoResponse",

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

@@ -243,6 +243,7 @@ protected Integer onBeforeExit(int exitCode, Response response) {
                     WorkflowStatus.CANCELLED, WorkflowStatus.FAILED, WorkflowStatus.SUCCEEDED
             );
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             return exitCode;
         }
     }

src/main/java/io/seqera/tower/cli/commands/computeenvs/add/AbstractAddCmd.java

@@ -89,6 +89,7 @@ protected Integer onBeforeExit(int exitCode, Response response) {
                     ComputeEnvStatus.AVAILABLE, ComputeEnvStatus.ERRORED, ComputeEnvStatus.INVALID
             );
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             return exitCode;
         }
     }

src/main/java/io/seqera/tower/cli/commands/data/links/DataLinkService.java

@@ -63,6 +63,7 @@ void waitForDoneStatus(Long wspId, String credId) {
                     DataLinksFetchStatus.DONE, DataLinksFetchStatus.ERROR
             );
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             throw new RuntimeException(e);
         }
     }

src/main/java/io/seqera/tower/cli/commands/datastudios/AbstractStudiosCmd.java

@@ -31,13 +31,16 @@
 import io.seqera.tower.model.DataStudioProgressStep;
 import io.seqera.tower.model.DataStudioStatus;
 import io.seqera.tower.model.DataStudioStatusInfo;
+import io.seqera.tower.model.DataStudioTemplate;
+import io.seqera.tower.model.DataStudioTemplatesListResponse;
 
 import static io.seqera.tower.cli.utils.ResponseHelper.waitStatus;
 import static io.seqera.tower.model.DataStudioProgressStepStatus.ERRORED;
 import static io.seqera.tower.model.DataStudioProgressStepStatus.IN_PROGRESS;
 
 public class AbstractStudiosCmd extends AbstractApiCmd {
 
+    private static final Integer DEFAULT_MAX_TEMPLATES_TO_QUERY = 20;
     protected String getSessionId(DataStudioRefOptions dataStudioRefOptions, Long wspId) throws ApiException {
         return dataStudioRefOptions.dataStudio.sessionId != null
                 ? dataStudioRefOptions.dataStudio.sessionId
@@ -56,6 +59,24 @@ protected DataStudioDto fetchDataStudio(DataStudioRefOptions dataStudioRefOption
         return dataStudio;
     }
 
+    protected String getParentDataStudioSessionId(ParentDataStudioRefOptions parentDataStudioRefOptions, Long wspId) throws ApiException {
+        if (parentDataStudioRefOptions.studio.sessionId != null) {
+            return parentDataStudioRefOptions.studio.sessionId;
+        } else {
+            DataStudioDto dataStudio = getDataStudioByName(wspId, parentDataStudioRefOptions.studio.name);
+            return dataStudio.getSessionId();
+        }
+    }
+
+    protected List<DataStudioTemplate> fetchDataStudioTemplates(Long workspaceId) throws ApiException {
+        return fetchDataStudioTemplates(workspaceId,DEFAULT_MAX_TEMPLATES_TO_QUERY);
+    }
+
+    protected List<DataStudioTemplate> fetchDataStudioTemplates(Long workspaceId, Integer max) throws ApiException {
+        DataStudioTemplatesListResponse response = api().listDataStudioTemplates(workspaceId,max,0);
+        return response.getTemplates();
+    }
+
     private DataStudioDto getDataStudioByName(Long wspId, String dataStudioName) throws ApiException {
         List<DataStudioDto> studios = api().listDataStudios(wspId, null, null, null).getStudios();
 
@@ -83,6 +104,7 @@ protected Integer onBeforeExit(int exitCode, String sessionId, Long workspaceId,
                     DataStudioStatus.STOPPED, DataStudioStatus.ERRORED, DataStudioStatus.RUNNING
             );
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             return exitCode;
         }
     }

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

@@ -19,6 +19,7 @@
 
 import io.seqera.tower.ApiException;
 import io.seqera.tower.cli.commands.global.WorkspaceOptionalOptions;
+import io.seqera.tower.cli.exceptions.DataStudiosTemplateNotFoundException;
 import io.seqera.tower.cli.exceptions.TowerException;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.datastudios.DataStudiosCreated;
@@ -28,10 +29,13 @@
 import io.seqera.tower.model.DataStudioCreateResponse;
 import io.seqera.tower.model.DataStudioDto;
 import io.seqera.tower.model.DataStudioStatus;
+import io.seqera.tower.model.DataStudioTemplate;
 import picocli.CommandLine;
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.util.List;
+import java.util.stream.Collectors;
 
 @CommandLine.Command(
         name = "add",
@@ -71,6 +75,7 @@ protected Response exec() throws ApiException {
         Long wspId = workspaceId(workspace.workspace);
 
         try {
+            checkIfTemplateIsAvailable(template, wspId);
             DataStudioCreateRequest request = prepareRequest();
             DataStudioCreateResponse response = api().createDataStudio(request, wspId, autoStart);
             DataStudioDto dataStudioDto = response.getStudio();
@@ -84,6 +89,16 @@ protected Response exec() throws ApiException {
         }
     }
 
+    void checkIfTemplateIsAvailable(String template, Long workspaceId) throws ApiException {
+        List<DataStudioTemplate> availableTemplates = fetchDataStudioTemplates(workspaceId);
+        boolean validTemplate = availableTemplates.stream()
+                .anyMatch(t -> t.getRepository() != null && t.getRepository().equals(template));
+
+        if (!validTemplate) {
+            throw new DataStudiosTemplateNotFoundException(template, availableTemplates.stream().map(DataStudioTemplate::getRepository).collect(Collectors.toList()));
+        }
+    }
+
     DataStudioCreateRequest prepareRequest() throws ApiException {
         DataStudioCreateRequest request = new DataStudioCreateRequest();
         request.setName(name);

src/main/java/io/seqera/tower/cli/commands/datastudios/ParentDataStudioRefOptions.java

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2021-2023, 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.datastudios;
+
+import picocli.CommandLine;
+
+public class ParentDataStudioRefOptions {
+
+    @CommandLine.ArgGroup(multiplicity = "1")
+    public ParentDataStudioRefOptions.ParentDataStudioRef studio;
+
+    public static class ParentDataStudioRef {
+        @CommandLine.Option(names = {"-pid", "--parentId"}, description = "Parent DataStudio session ID.")
+        public String sessionId;
+
+        @CommandLine.Option(names = {"-pn", "--parentName"}, description = "Parent DataStudio name.")
+        public String name;
+    }
+}

src/main/java/io/seqera/tower/cli/commands/datastudios/StartAsNewCmd.java

@@ -40,8 +40,8 @@
 )
 public class StartAsNewCmd extends AbstractStudiosCmd{
 
-    @CommandLine.Option(names = {"-pid", "--parentId"}, description = "Parent DataStudio session ID.", required = true)
-    public String parentStudioSessionId;
+    @CommandLine.Mixin
+    public ParentDataStudioRefOptions parentDataStudioRefOptions;
 
     @CommandLine.Option(names = {"-n", "--name"}, description = "Data Studio name.", required = true)
     public String name;
@@ -66,6 +66,7 @@ protected Response exec() throws ApiException {
         Long wspId = workspaceId(workspace.workspace);
 
         try {
+            String parentStudioSessionId = getParentDataStudioSessionId(parentDataStudioRefOptions, wspId);
             DataStudioDto parentDataStudio = api().describeDataStudio(parentStudioSessionId, wspId);
             if (parentDataStudio == null) {
                 throw new TowerException(String.format("Parent DataStudio %s not found at %s workspace", parentStudioSessionId, wspId));

src/main/java/io/seqera/tower/cli/commands/datastudios/TemplatesCmd.java

@@ -44,9 +44,7 @@ protected Response exec() throws ApiException {
         Long wspId = workspaceId(workspace.workspace);
 
         try {
-            DataStudioTemplatesListResponse response = api().listDataStudioTemplates(wspId,max,0);
-
-            return new DataStudiosTemplatesList(response.getTemplates());
+            return new DataStudiosTemplatesList(fetchDataStudioTemplates(wspId, max));
         } catch (ApiException e) {
             if (e.getCode() == 403) {
                 throw new TowerException("User not entitled to list studio templates");

src/main/java/io/seqera/tower/cli/exceptions/DataStudiosTemplateNotFoundException.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright 2021-2023, 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.exceptions;
+
+import java.util.List;
+
+public class DataStudiosTemplateNotFoundException extends TowerException {
+
+    public DataStudiosTemplateNotFoundException(String template, List<String> templatesAvailable) {
+        super(String.format("DataStudio template '%s' is not one of available templates '%s'", template, templatesAvailable));
+    }
+}

src/main/java/io/seqera/tower/cli/utils/TarFileHelper.java

@@ -173,6 +173,7 @@ public void close() throws IOException, TowerException {
                     throw new TowerException("Timeout compressing logs");
                 }
             } catch (InterruptedException e) {
+                Thread.currentThread().interrupt();
                 throw new RuntimeException(e);
             }