Moving Jobs to New Workspace / Cannot see them in Tree View

Application
1

Hi folks,

We recently hit an issue where deleted jobs show up on the tree view, but I cannot see them on the card view. I want them to not show up on the tree view. Additionally, and more importantly, new jobs are not showing up on the tree view anymore (after hitting this bug).

We tried moving a pipeline to a new workspace, but unfotunately, we cannot see them in the tree view (in the new workspace). Is there a way for us to choose a pipeline of interest, and move it to a new tree view?

Please let me know.

Thank you so much!
Walid

2

@walidabualafia What version of CryoSPARC do you use? Please can you describe what you mean with pipeline, and you you selected jobs that you wanted to include in the pipeline?

3

Hi @wtempel,

Thanks for your quick response. I am using CryoSPARC 4.4.1.

When I say pipeline, I mean a final job and all its ancestors. In a tree view, my “pipeline” would look like a chain of jobs that depend on each other. I tried two things:

  1. Select the final job, and then select all ancestors, and then move to a new workspace. I still cannot see it in the new workspace’s tree view. The jobs appear in the card view.
  2. Select only the final job (without ancestors) and moving it to a new workspace. I still could not see it in the new workspace’s tree view. The job appears in the card view.

I hope this makes sense. Please let me know if you have any questions.

Thank you for the help.

Walid

4

Hi @walidabualafia .
Has the CryoSPARC project where this problem occurs ever been subject to the detach or archive CryoSPARC project actions?
Please can you also

  • post here the project ID and IDs of the jobs that are missing in tree view
  • email us a compressed copy of the the cryosparc_master/run/command_core.log. (I will send you a private message with the email address to use).
5

We have had the same issue sporadically but it somehow disappear lately. Maybe due to the latest update??

6

@ehanssen we did update, but it did not resolve the issue. We can try to downgrade and see. I will communicate with Wolfram to discuss further. Thanks for the help! :slight_smile:

7

Hi @wtempel,

I apologize for the long delay. Things have been a little hectic.

To answer your question, this specific project has not been a subject to the detach or archive actions. Additionally, we recently started seeing the same behavior in other projects on this instance. No other instances have reported this issue, we are running ~9 managed instances and a couple ad hoc.

  • Project ID: CryoSPARC Project-Workspace: P3-W23
  • Jobs missing in the tree view: J2401, J2404, J2406 and all subsequent jobs
  • Will email you now.

Thank you for the help! I really appreciate this platform, and the community behind CryoSPARC. Y’all are awesome, and I hope to contribute soon. :slight_smile:

8

Thanks for these details.
In CryoSPARC v4.5, it is expected that deleted jobs are visible in tree view if these jobs are internal nodes of the job tree.

  1. Were jobs J2401, J2404, J2406 created inside W23 or were they moved/linked to that workspace?
  2. Are these jobs visible in the card view of W23?
  3. Are these jobs descendants or ancestors of and directly connected to jobs that are visible in the tree view of W23?
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@wtempel @walidabualafia To keep processing the dataset, some jobs were later deleted in the card view. With that in mind, here are the answers to your questions are following:

  1. No jobs were moved or linked to W23.
  2. They were previously visible in the card view, but they were deleted to reduce clutter in W23.
  3. These jobs were descendants of previous jobs. Additionally, any newly deleted job is not visible in any view, as expected.

In the current state of W23:

  • J2502 (J2502-J2503-J2504) is using J2394 as input, but neither J2502 nor the link connecting J2502 to J2394 is showing up in tree view. However, J2394 is visible in tree view.
  • Another example is J2520, which is using J2390 (visible in tree view). J2520 and the subsequent jobs (J2520 to J2524) are not visible in the tree view.

Would you like a copy of the latest “cryosparc_master/run/command_core.log” through email?

10

Welcome to the forum @sachiem .

Do I understand correctly that the absence of jobs J2401, J2404, J2406 is not a concern?

Are jobs J2502 and J2520…J2524 visible in card view?

11

Thank you @wtempel

  1. Absence of jobs 2401, 2404, and 2406 is no longer a concern.
  2. Yes, J2502 and J2520…J2524 are visible in card view.
12

@sachiem @walidabualafia A possible cause of a job’s absence in the tree view is its inclusion in a circle of output connections. Such circles may be created by accident if one mistakes the identity of the job with which one interacts in the job builder. For J2520, you may want to investigate if outputs of J2520 have been connected (as inputs) to J2390, an ancestor of J2390, or another ancestor of J2520.