Upgrade SDK version

README.md

@@ -154,10 +154,15 @@ tw CLI is a platform binary executable created by a native compilation from Java
     ./gradlew runReflectionConfigGenerator
     ```
 
-    The GraalVM reflection metadata generation relies on code paths being executed with [a tracing agent](https://www.graalvm.org/jdk21/reference-manual/native-image/metadata/AutomaticMetadataCollection/#tracing-agent) to dynamically capture various execution paths and update the reflect-config.json.
+   The GraalVM reflection metadata generation relies on code paths being executed with the [Tracing Agent](https://www.graalvm.org/jdk21/reference-manual/native-image/metadata/AutomaticMetadataCollection/#tracing-agent) to dynamically
+   capture various execution paths and update the `reflect-config.json` and `resource-config.json` files. This is a utility task that uses reflection to make calls to all classes in the Tower SDK package in order to capture and generate
+   methods reflection metadata of any new fields/classes in Tower SDK.
 
-    This is a utility task that uses reflection to make calls to all classes in the Tower SDK package,
-    in order to capture and generate methods reflection metadata of any new fields/classes in Tower SDK and update resource-config.json
+   Additionally, for more complete coverage, run the test suite with the Tracing Agent enabled:
+
+    ```bash
+       ./gradlew test -Dtracing-agent=true
+    ```
 
 1. Create the native client:
 

build.gradle

@@ -23,12 +23,13 @@ repositories {
 }
 
 dependencies {
-    implementation 'javax.activation:activation:1.1.1'
+    implementation 'javax.annotation:javax.annotation-api:1.3.2'
+    implementation 'jakarta.annotation:jakarta.annotation-api:3.0.0'
     implementation 'org.slf4j:slf4j-api:1.7.36'
     implementation 'ch.qos.logback:logback-core:1.5.19'
     implementation 'ch.qos.logback:logback-classic:1.5.19'
 
-    implementation 'io.seqera.tower:tower-java-sdk:1.43.2'
+    implementation 'io.seqera.tower:tower-java-sdk:1.97.0'
     // Upgrade transitive Jersey client dependencies to non-vulnerable 2.x version
     implementation "org.glassfish.jersey.core:jersey-client:2.47"
     implementation "org.glassfish.jersey.media:jersey-media-multipart:2.47"
@@ -119,6 +120,10 @@ test {
     // Use junit platform for unit tests
     useJUnitPlatform()
     dependsOn checkLicenses
+    // Run tests with GraalVM Tracing Agent enabled
+    if (System.getProperty('tracing-agent')?.toBoolean()) {
+        jvmArgs = ["-agentlib:native-image-agent=access-filter-file=conf/access-filter-file.json,config-merge-dir=conf/"]
+    }
 }
 
 graalvmNative {

src/main/java/io/seqera/tower/cli/Tower.java

@@ -107,6 +107,7 @@ protected static CommandLine buildCommandLine() {
         Tower app = new Tower();
         CommandLine cmd = new CommandLine(app);
         cmd.setUsageHelpLongOptionsMaxWidth(40);
+        cmd.setCaseInsensitiveEnumValuesAllowed(true);
         return cmd;
     }
 

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

@@ -63,8 +63,9 @@
 import io.seqera.tower.model.OrgAndWorkspaceDto;
 import io.seqera.tower.model.PipelineDbDto;
 import io.seqera.tower.model.PipelineQueryAttribute;
-import io.seqera.tower.model.UserDbDto;
+import io.seqera.tower.model.UserResponseDto;
 import io.seqera.tower.model.WorkflowQueryAttribute;
+import org.glassfish.jersey.CommonProperties;
 import org.glassfish.jersey.client.ClientConfig;
 import org.glassfish.jersey.logging.LoggingFeature;
 import org.glassfish.jersey.media.multipart.BodyPart;
@@ -272,17 +273,27 @@ protected Properties getCliProperties() throws ApiException {
 
     private ApiClient buildApiClient() {
         return new ApiClient() {
+
+            @Override
+            public ClientConfig getDefaultClientConfig() {
+                ClientConfig config = super.getDefaultClientConfig();
+                // Disable conditionally enabled providers, as warnings get printed when their corresponding classes are not available in the classpath
+                config.property(CommonProperties.PROVIDER_DEFAULT_DISABLE, "ALL");
+
+                return config;
+            }
+
             @Override
-            protected void performAdditionalClientConfiguration(ClientConfig clientConfig) {
+            protected void applyDebugSetting(ClientConfig clientConfig) {
                 if (app().verbose) {
                     clientConfig.register(new LoggingFeature(Logger.getLogger(LoggingFeature.DEFAULT_LOGGER_NAME), java.util.logging.Level.INFO, LoggingFeature.Verbosity.PAYLOAD_ANY, 1024 * 50 /* Log payloads up to 50K */));
                     clientConfig.property(LoggingFeature.LOGGING_FEATURE_VERBOSITY, LoggingFeature.Verbosity.PAYLOAD_ANY);
                 }
             }
 
             @Override
-            public Entity<?> serialize(Object obj, Map<String, Object> formParams, String contentType) throws ApiException {
-                Entity<?> entity = super.serialize(obj, formParams, contentType);
+            public Entity<?> serialize(Object obj, Map<String, Object> formParams, String contentType, boolean isBodyNullable) throws ApiException {
+                Entity<?> entity = super.serialize(obj, formParams, contentType, isBodyNullable);
 
                 // Current SDK sends all multipart files as 'application/octet-stream'
                 // this is a workaround to try to automatically detect the correct
@@ -500,7 +511,7 @@ protected List<Long> findOrCreateLabels(Long wspId, List<Label> labels) throws A
     }
 
     private void loadUser() throws ApiException {
-        UserDbDto user = usersApi().userInfo().getUser();
+        UserResponseDto user = usersApi().userInfo().getUser();
         userName = user.getUserName();
         userId = user.getId();
     }
@@ -538,7 +549,7 @@ private void loadAvailableComputeEnvs(Long workspaceId) throws ApiException {
         if (availableComputeEnvsNameToId == null) {
             availableComputeEnvsNameToId = new HashMap<>();
             availableComputeEnvsIdToName = new HashMap<>();
-            for (ListComputeEnvsResponseEntry ce : computeEnvsApi().listComputeEnvs("AVAILABLE", workspaceId).getComputeEnvs()) {
+            for (ListComputeEnvsResponseEntry ce : computeEnvsApi().listComputeEnvs("AVAILABLE", workspaceId, List.of()).getComputeEnvs()) {
 
                 if (ce.getPrimary() != null && ce.getPrimary()) {
                     primaryComputeEnvId = ce.getId();

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

@@ -32,13 +32,13 @@
 import io.seqera.tower.model.SubmitWorkflowLaunchResponse;
 import io.seqera.tower.model.WorkflowLaunchRequest;
 import io.seqera.tower.model.WorkflowStatus;
+import jakarta.annotation.Nullable;
 import picocli.CommandLine;
 import picocli.CommandLine.ArgGroup;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
 
-import javax.annotation.Nullable;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.Collections;
@@ -156,7 +156,7 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th
 
     protected Response runTowerPipeline(Long wspId) throws ApiException, IOException {
 
-        ListPipelinesResponse pipelines = pipelinesApi().listPipelines(Collections.emptyList(), wspId, 50, 0, pipeline, "all");
+        ListPipelinesResponse pipelines = pipelinesApi().listPipelines(Collections.emptyList(), wspId, 50, 0, null, null, pipeline, "all");
         if (pipelines.getTotalSize() == 0) {
             throw new InvalidResponseException(String.format("Pipeline '%s' not found on this workspace.", pipeline));
         }

src/main/java/io/seqera/tower/cli/commands/actions/ListCmd.java

@@ -24,11 +24,9 @@
 import io.seqera.tower.cli.responses.actions.ActionsList;
 import io.seqera.tower.model.ActionQueryAttribute;
 import io.seqera.tower.model.ListActionsResponse;
-import io.seqera.tower.model.ListLabelsResponse;
 import picocli.CommandLine;
 
 import java.io.IOException;
-import java.util.Collections;
 import java.util.List;
 
 @CommandLine.Command(
@@ -47,7 +45,7 @@ public class ListCmd extends AbstractActionsCmd {
     protected Response exec() throws ApiException, IOException {
         Long wspId = workspaceId(workspace.workspace);
 
-        List<ActionQueryAttribute> actionQueryAttributes = showLabelsOption.showLabels ? List.of(ActionQueryAttribute.LABELS) : NO_ACTION_ATTRIBUTES;
+        List<ActionQueryAttribute> actionQueryAttributes = showLabelsOption.showLabels ? List.of(ActionQueryAttribute.labels) : NO_ACTION_ATTRIBUTES;
 
         ListActionsResponse response = actionsApi().listActions(wspId, actionQueryAttributes);
 

src/main/java/io/seqera/tower/cli/commands/actions/ViewCmd.java

@@ -50,7 +50,7 @@ protected Response exec() throws ApiException, IOException {
         DescribeActionResponse response = fetchDescribeActionResponse(
                 actionRefOptions,
                 wspId,
-                ActionQueryAttribute.LABELS
+                ActionQueryAttribute.labels
         );
 
         return new ActionsView(response.getAction(), baseWorkspaceUrl(wspId));

src/main/java/io/seqera/tower/cli/commands/actions/add/AddGitHubCmd.java

@@ -27,6 +27,6 @@
 public class AddGitHubCmd extends AbstractAddCmd {
     @Override
     protected ActionSource getSource() {
-        return ActionSource.GITHUB;
+        return ActionSource.github;
     }
 }

src/main/java/io/seqera/tower/cli/commands/actions/add/AddTowerCmd.java

@@ -27,6 +27,6 @@
 public class AddTowerCmd extends AbstractAddCmd {
     @Override
     protected ActionSource getSource() {
-        return ActionSource.TOWER;
+        return ActionSource.tower;
     }
 }

src/main/java/io/seqera/tower/cli/commands/computeenvs/AbstractComputeEnvCmd.java

@@ -47,18 +47,18 @@ protected ComputeEnvResponseDto fetchComputeEnv(ComputeEnvRefOptions computeEnvR
 
     protected ComputeEnvResponseDto computeEnvByName(Long workspaceId, String name) throws ApiException {
 
-        List<ListComputeEnvsResponseEntry> computeEnvs = computeEnvsApi().listComputeEnvs(null, workspaceId).getComputeEnvs();
+        List<ListComputeEnvsResponseEntry> computeEnvs = computeEnvsApi().listComputeEnvs(null, workspaceId, List.of()).getComputeEnvs();
         ListComputeEnvsResponseEntry entry = computeEnvs
                 .stream()
                 .filter(ce -> name.equals(ce.getName()))
                 .findFirst()
                 .orElseThrow(() -> new ComputeEnvNotFoundException(name, workspaceId));
 
-        return computeEnvsApi().describeComputeEnv(entry.getId(), workspaceId, List.of(ComputeEnvQueryAttribute.LABELS)).getComputeEnv();
+        return computeEnvsApi().describeComputeEnv(entry.getId(), workspaceId, List.of(ComputeEnvQueryAttribute.labels)).getComputeEnv();
     }
 
     private ComputeEnvResponseDto computeEnvById(Long workspaceId, String id) throws ApiException {
-        return computeEnvsApi().describeComputeEnv(id, workspaceId, List.of(ComputeEnvQueryAttribute.LABELS)).getComputeEnv();
+        return computeEnvsApi().describeComputeEnv(id, workspaceId, List.of(ComputeEnvQueryAttribute.labels)).getComputeEnv();
     }
 }
 

src/main/java/io/seqera/tower/cli/commands/computeenvs/ListCmd.java

@@ -26,6 +26,7 @@
 import picocli.CommandLine.Command;
 
 import java.io.IOException;
+import java.util.List;
 
 @Command(
         name = "list",
@@ -40,7 +41,7 @@ public class ListCmd extends AbstractComputeEnvCmd {
     protected Response exec() throws ApiException, IOException {
         Long wspId = workspaceId(workspace.workspace);
 
-        ListComputeEnvsResponse response = computeEnvsApi().listComputeEnvs(null, wspId);
+        ListComputeEnvsResponse response = computeEnvsApi().listComputeEnvs(null, wspId, List.of());
         return new ComputeEnvList(workspaceRef(wspId), response.getComputeEnvs(), baseWorkspaceUrl(wspId));
     }
 }

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AltairPlatform.java

@@ -60,13 +60,6 @@ public AltairPbsComputeConfig computeConfig() throws ApiException, IOException {
         AltairPbsComputeConfig config = new AltairPbsComputeConfig();
 
         config
-                // Common
-                .environment(environmentVariables())
-                .workDir(workDir)
-                .preRunScript(preRunScriptString())
-                .postRunScript(postRunScriptString())
-                .nextflowConfig(nextflowConfigString())
-
                 // Main
                 .launchDir(launchDir)
                 .userName(userName)
@@ -79,6 +72,13 @@ public AltairPbsComputeConfig computeConfig() throws ApiException, IOException {
                 .maxQueueSize(adv().maxQueueSize)
                 .headJobOptions(adv().headJobOptions);
 
+        // Common
+        config.workDir(workDir)
+                .preRunScript(preRunScriptString())
+                .postRunScript(postRunScriptString())
+                .nextflowConfig(nextflowConfigString())
+                .environment(environmentVariables());
+
         return config;
     }
 

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AwsBatchForgePlatform.java

@@ -105,28 +105,30 @@ public static void clean(AwsBatchConfig config) {
 
     @Override
     public AwsBatchConfig computeConfig() throws ApiException, IOException {
-        return new AwsBatchConfig()
-                .workDir(workDir)
-                .preRunScript(preRunScriptString())
-                .postRunScript(postRunScriptString())
-                .nextflowConfig(nextflowConfigString())
-                .environment(environmentVariables())
+        AwsBatchConfig config = new AwsBatchConfig()
                 .region(region)
                 .fusion2Enabled(isFusionV2Enabled())
                 .waveEnabled(wave)
                 .nvnmeStorageEnabled(fastStorage)
                 .fusionSnapshots(snapshots)
-
                 // Forge
                 .forge(buildForge())
-
                 // Advanced
                 .cliPath(adv().cliPath)
                 .executionRole(adv().batchExecutionRole)
                 .computeJobRole(adv().computeJobRole)
                 .headJobCpus(adv().headJobCpus)
                 .headJobMemoryMb(adv().headJobMemoryMb)
                 .headJobRole(adv().headJobRole);
+
+                // Common
+                config.workDir(workDir)
+                .preRunScript(preRunScriptString())
+                .postRunScript(postRunScriptString())
+                .nextflowConfig(nextflowConfigString())
+                .environment(environmentVariables());
+
+                return config;
     }
 
     private Boolean isFusionV2Enabled() throws TowerException {

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AwsBatchManualPlatform.java

@@ -67,18 +67,12 @@ public static void clean(AwsBatchConfig config) {
 
     @Override
     public AwsBatchConfig computeConfig() throws IOException, ApiException {
-        return new AwsBatchConfig()
-                .workDir(workDir)
-                .preRunScript(preRunScriptString())
-                .postRunScript(postRunScriptString())
-                .nextflowConfig(nextflowConfigString())
-                .environment(environmentVariables())
+        AwsBatchConfig config = new AwsBatchConfig()
+                .region(region)
                 .fusion2Enabled(isFusionV2Enabled())
                 .waveEnabled(wave)
                 .nvnmeStorageEnabled(fastStorage)
 
-                .region(region)
-
                 // Queues
                 .headQueue(headQueue)
                 .computeQueue(computeQueue)
@@ -90,6 +84,15 @@ public AwsBatchConfig computeConfig() throws IOException, ApiException {
                 .headJobCpus(adv().headJobCpus)
                 .headJobMemoryMb(adv().headJobMemoryMb)
                 .headJobRole(adv().headJobRole);
+
+                // Common
+                config.workDir(workDir)
+                .preRunScript(preRunScriptString())
+                .postRunScript(postRunScriptString())
+                .nextflowConfig(nextflowConfigString())
+                .environment(environmentVariables());
+
+                return config;
     }
 
     private Boolean isFusionV2Enabled() throws TowerException {

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AzBatchForgePlatform.java

@@ -73,16 +73,17 @@ public AzBatchForgePlatform() {
     public AzBatchConfig computeConfig(Long workspaceId, CredentialsApi credentialsApi) throws ApiException, IOException {
         AzBatchConfig config = new AzBatchConfig();
 
-        config
-                // Common
-                .workDir(workDir)
+        config.fusion2Enabled(fusionV2)
+                .waveEnabled(wave)
+                .region(location);
+        // Common
+        config.workDir(workDir)
                 .preRunScript(preRunScriptString())
                 .postRunScript(postRunScriptString())
                 .nextflowConfig(nextflowConfigString())
-                .environment(environmentVariables())
-                .fusion2Enabled(fusionV2)
-                .waveEnabled(wave)
-                .region(location);
+                .environment(environmentVariables());
+
+
 
         if (adv != null) {
             config

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/AzBatchManualPlatform.java

@@ -55,12 +55,6 @@ public AzBatchConfig computeConfig() throws ApiException, IOException {
         AzBatchConfig config = new AzBatchConfig();
 
         config
-                // Common
-                .workDir(workDir)
-                .preRunScript(preRunScriptString())
-                .postRunScript(postRunScriptString())
-                .nextflowConfig(nextflowConfigString())
-                .environment(environmentVariables())
                 .fusion2Enabled(fusionV2)
                 .waveEnabled(wave)
                 .region(location)
@@ -72,6 +66,13 @@ public AzBatchConfig computeConfig() throws ApiException, IOException {
                     .tokenDuration(adv.tokenDuration);
         }
 
+        // Common
+        config.workDir(workDir)
+                .preRunScript(preRunScriptString())
+                .postRunScript(postRunScriptString())
+                .nextflowConfig(nextflowConfigString())
+                .environment(environmentVariables());
+
         return config;
     }
 

src/main/java/io/seqera/tower/cli/commands/computeenvs/platforms/EksPlatform.java

@@ -68,12 +68,10 @@ public EksComputeConfig computeConfig() throws ApiException, IOException {
                 .computeServiceAccount(adv().computeAccount)
                 .podCleanup(adv().podCleanup)
                 .headPodSpec(FilesHelper.readString(adv().headPodSpec))
-                .servicePodSpec(FilesHelper.readString(adv().servicePodSpec))
+                .servicePodSpec(FilesHelper.readString(adv().servicePodSpec));
 
-                // Common
-                .workDir(workDir)
-
-                // Staging
+        // Common
+        config.workDir(workDir)
                 .preRunScript(preRunScriptString())
                 .postRunScript(postRunScriptString())
                 .nextflowConfig(nextflowConfigString())