Confusing Statuses for Pipelines that Uses NF Tower

[RasmusBurge-CG]

As a TB user, I want accurate job status updates for NF Tower pipelines, So that I can clearly understand the progress of each job

Clarification: Pipelines using NF Tower (e.g., RNAFUSION, TOMTE, TAXPROFILER) do not operate with SLURM in the same way as other pipelines. Specifically, not all jobs are submitted simultaneously. This causes issues in the ‘Status’ field, as the analysis often appears to be 100% complete, even though NF Tower shows that the analysis is still in progress.

Acceptance Criteria

• [ ] Remove progress-bar for these pipelines and set status Running.
• [ ] OR find a fancy way of getting the true status from NF Tower.

Alt Criteria

• Statuses for tower analyses are clear

Notes

• Additional information.
• Dependencies.
• Related user stories.

Implementation plan

• [ ] Work item 1
• [ ] Work item 2

[Vince-janv]

Technical refinement:

• Add logic to FE so that if the analysis runs with workflow_manager=nf_tower render RUNNING instead of progress

• Look at why analyses with the status SUBMITTED in Tower show up as Error in TB

[RasmusBurge-CG]

To Work With the Swagger and Stage Tower

To create a bearer (token to be used for testing), go to Your tokens and create a new token. Paste that into the swagger website.
Tower uses something called "workspace", and you are going to need it if you want to see the response. Go to cg-tower-stage.scilifelab.se, open dev tools -> network -> (refresh the page), and find an item in the list called workspaces. The item below that entry is the workspace ID.

Newly Started Runs - What is the response?

Using: GET - /workflow/{workflowId}/progress

On a fresh started run, cheeky_engelbart. With no submitted jobs, no running or pending.

Gives:

{
  "progress": {
    "workflowProgress": {
      "cpus": 0,
      "cpuTime": 0,
      "cpuLoad": 0,
      "memoryRss": 0,
      "memoryReq": 0,
      "readBytes": 0,
      "writeBytes": 0,
      "volCtxSwitch": 0,
      "invCtxSwitch": 0,
      "cost": null,
      "loadTasks": 0,
      "loadCpus": 0,
      "loadMemory": 0,
      "peakCpus": 0,
      "peakTasks": 0,
      "peakMemory": 0,
      "executors": null,
      "dateCreated": "2024-11-14T12:16:54.54937892Z",
      "lastUpdated": "2024-11-14T12:16:54.549379412Z",
      "submitted": 0,
      "succeeded": 0,
      "running": 0,
      "failed": 0,
      "cached": 0,
      "pending": 0,
      "memoryEfficiency": 0,
      "cpuEfficiency": 0
    },
    "processesProgress": []
  }
}

Let's find out what request is sent to tower from TB.