Description

Bump tower-java-sdk from 1.101.0 to 1.107.0 and update the codebase to match the new SDK types.

Affected commands

• pipelines view — type change: Launch → LaunchDbDto
• pipelines export — type change: Launch → LaunchDbDto
• pipelines update — type change: Launch → LaunchDbDto
• launch — type change: Launch → LaunchDbDto
• runs view — type change: Workflow → WorkflowMaxDbDto
• runs dump — type changes: Launch → LaunchDbDto, Workflow → WorkflowMaxDbDto
• runs relaunch — type change: Workflow → WorkflowMaxDbDto
• ModelHelper.createLaunchRequest() — parameter type Launch → LaunchDbDto
• PipelinesView response — field type Launch → LaunchDbDto

Workaround for Task.exit deserialization (PLAT-4625)

The Platform API returns the task exit code as a string ("exit": "0") while the SDK model declares it as Integer. The SDK configures Jackson with ALLOW_COERCION_OF_SCALARS=false, which rejects string-to-integer coercion. This was masked in previous CLI builds that bundled older Jackson versions with different coercion defaults.

This PR adds a targeted Jackson mixin (TaskExitMixin + LenientIntegerDeserializer) that applies lenient deserialization only to the Task.exit field, without changing global behavior. The workaround is marked with FIXME comments linking to PLAT-4625 and should be removed once the Platform-side fix is deployed.

Guidelines for testing

The main focus should be ensuring that passing null as versionId to the describePipelineLaunch endpoint returns the default pipeline version, maintaining backward-compatible behavior. The backend treats null versionId by fetching the default version, so no functional change should be observed.

1. Pipeline view

./tw pipelines view -n <pipeline_name> -w <org>/<workspace>

Verify the pipeline details (ID, name, description, repository, compute env, labels) and configuration are displayed correctly — same output as before the change.

  Pipeline at [seqeratest_JaimeInc / Wsp] workspace:

    --------------+--------------------------------------
     ID           | 30153220095308
     Name         | HelloOptimization
     Description  |
     Repository   | https://github.com/nextflow-io/hello
     Compute env. | AWSCE
     Labels       | can_be_deleted=true,owner=jaime

  Configuration:

     {
       "id" : "7ZHVhQD94mVhiiUj8lRnBa",
       "computeEnvId" : "1M7Np6pDIWIyJzEcKBHXVq",
       "pipeline" : "https://github.com/nextflow-io/hello",
       "workDir" : "s3://jaime-testing",
       "revision" : "master",
       "userSecrets" : [ ],
       "workspaceSecrets" : [ ],
       "resume" : false,
       "pullLatest" : false,
       "stubRun" : false,
       "optimizationId" : "fAdrnFUTzkQEdCWS",
       "optimizationTargets" : "cpus, memory",
       "dateCreated" : "2024-06-18T15:04:39Z"
     }

2. Pipeline export

./tw pipelines export -n <pipeline_name> -w <org>/<workspace>

Verify the exported JSON contains the correct launch configuration. Compare the output against an export produced with the previous CLI version to confirm no differences.

{
  "icon" : "https://cloud.seqera.io/api/avatars/42CjYsReft3lQDqlbtSk0j",
  "launch" : {
    "id" : "7ZHVhQD94mVhiiUj8lRnBa",
    "computeEnvId" : "1M7Np6pDIWIyJzEcKBHXVq",
    "pipeline" : "https://github.com/nextflow-io/hello",
    "workDir" : "s3://jaime-testing",
    "revision" : "master",
    "userSecrets" : [ ],
    "workspaceSecrets" : [ ],
    "resume" : false,
    "pullLatest" : false,
    "stubRun" : false,
    "optimizationId" : "fAdrnFUTzkQEdCWS",
    "optimizationTargets" : "cpus, memory",
    "dateCreated" : "2024-06-18T15:04:39Z"
  }
}

3. Pipeline update

./tw pipelines update -n <pipeline_name> -w <org>/<workspace> --description "Updated description"

Verify the pipeline is updated successfully and the description change is reflected when viewing the pipeline.

Pipeline 'HelloOptimization' updated at [seqeratest_JaimeInc / Wsp] workspace

4. Launch pipeline

./tw launch <pipeline_name> -w <org>/<workspace>

Verify the pipeline launches successfully and the run appears in the workspace with the correct configuration.

Workflow <run_id> submitted at [seqeratest_JaimeInc / Wsp] workspace.

5. Runs view

./tw runs view -i <run_id> -w <org>/<workspace>

Verify the run details (status, workflow info, progress, general info) are displayed correctly — same output as before the change.

  Run at [seqeratest_JaimeInc / Wsp] workspace:

    General
    ---------------------+------------------------------------------
     ID                  | w500oTt9rzi1s
     Operation ID        | 5a4002d4-1bee-4b66-8865-14232c47cad9
     Run name            | cranky_joliot
     Status              | SUCCEEDED
     Starting date       | Mon, 8 Sep 2025 12:54:22 GMT
     Commit ID           | 2ce0b0e2943449188092a0e25102f0dadc70cb0a
     Session ID          | 6775dd0a-3a4e-4a48-a7f2-1dcf2c37b2c5
     Username            | jaime-munoz
     Workdir             | s3://jaime-testing/scratch/w500oTt9rzi1s
     Container           | quay.io/nextflow/bash
     Executors           | awsbatch
     Compute Environment | AWSCE
     Nextflow Version    | 25.04.6
     Labels              | can_be_deleted=true,owner=jaime

6. Runs dump

./tw runs dump -i <run_id> -w <org>/<workspace> -o dump.tar.gz --silent

Extract the tar.gz and verify all expected files are present:

service-info.json
workflow.json
workflow-metadata.json
workflow-load.json
workflow-launch.json
workflow-metrics.json
workflow-tasks.json
nextflow.log

Note: This test exercises the TaskExitMixin workaround (PLAT-4625). Without it, the workflow-tasks.json step fails with Error reading entity from input stream.

7. Runs relaunch

./tw runs relaunch -i <run_id> -w <org>/<workspace>

Verify the relaunch creates a new run with the same configuration as the original.

Workflow <run_id> submitted at [seqeratest_JaimeInc / Wsp] workspace.

8. Unit tests

./gradlew test

Verify all existing tests pass, specifically PipelinesCmdTest and RunsCmdTest which have been updated to use the new types.