Jobs with a Results Group Import job as an input attempt to run when the Results Group Import job is still running

Import and Export
1

I’m working on a pipeline that involves exporting jobs, changing some ctf parameters and reimporting them. When I import the .csg file as a Import Results Group job and connect it’s output as input to a new job, the new job attempts to run before the Import Results Group job has finished and gives the following error:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 85, in cryosparc_master.cryosparc_compute.run.main
  File "/home/svc-pncc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1223, in check_default_inputs
    assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ' + missing_inputs + '. Please connect all required inputs.'
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: particles.blob, particles.ctf, particles.alignments3D. Please connect all required inputs.

If I wait for the Results Group Import job to finish before queuing up the next job, that works as expected but this seems like a bug in queuing/scheduling.

2

@rabdella Please can you describe the implementation of your pipeline: Are you using scripts or are you using CryoSPARC Workflows?

3

I’m using scripts. Workflow is something like this:

  • Export job
  • Use cryosparcm icli or a python script to copy, edit, and save a new .cs file
  • Copy the .csg file associate with the original .cs file and edit to point to the new .cs file
  • Place the new .cs and .csg files in the same location as the exported files
  • Use Import Results Group job to import the .csg file
4

Are the jobs exported from the same project as the project to which they will, after modification, be imported?

5

Yes, that is correct.

6

@rabdella Please can you post your script (or a snippet that is sufficient to reproduce the Non-optional inputs from the following input groups and their slots are not connected error).
You may also want to review an example of cryosparc-tools code that awaits the completion of a relevant job.