Project import error in 3.2 name 'audit' is not defined

Dear all,

I tried to import a project in cryoSPARC 3.2 but got this error:
‘Unable to import project from /x/x/x: name ‘audit’ is not defined’
I would appreciate any help!

Best regards,
Gabor

1 Like

Hi @gabor,

Thank you for reporting. This is a bug- I’ll keep you updated on when a fix will be released (hopefully soon).

Hi @gabor,

We’ve fixed this bug in Patch 210401 (for v3.2.0).

To apply this patch, please follow the instructions available here: Apply Patches

3 Likes

Hi Stephan,

Thank you for the patch, it works now.

Best wishes,
Gabor

Hi @stephan

Just to add to this, I followed the above for patching and could now import the project but my workspaces are empty. I followed this.

I can see thumbnails from the Projects window but when I open the workspace window there is nothing there. The details for my project show its size of 1.7 TB and all the data seems fine but I just can’t access it.

Any help would be greatly appreciated?

Best
Mike


1 Like

Hi,

I had the same before. In fact when you first tried to import your project without success, the workspaces.json (in your project directory) is emptied. Luckily I had a backup and I could restore it from there.

Best,
Gabor

1 Like

hi @gabor

that worked wonderfully thank you.

@stephan, would it be possible to have a constant workspaces.json.bak or something similar for these cases?

Best
Mike

Hi @mplockhartuom, @gabor,

Sorry for the inconvenience. This looks like some sort of bug- can you explain in detail what you did? Do you also think you can provide any logs from the failed import (by running cryosparcm log command_core, pressing ctrl+c then scrolling up to any error so you can copy+paste it here)?

Dear @stephan,

I don’t have error in the log, it maybe cleared after the patch install.
What I did was the following:

  1. tried to import a project (P2) to the new cryoSPARC instance - failed with ‘audit’ is not defined
  2. installed the patch
  3. tried again to import P2, but I couldn’t access the workspaces like @mplockhartuom .
  4. I copied from a backup the workspaces.json to P2/ replacing the empty file in the directory.
  5. I re-imported the P2 project and it was successful.

Best,
Gabor

1 Like

We have exactly the same as described by @mplockhartuom

1 Like

Hey Everyone,

We’ve released another patch that addresses the “empty workspaces” issue- please install the patch, restart your instance, and let us know if it helps.

Hi @stephan
I have exactly the same as described by @mplockhartuom
I have installed the newest patch and re-import the project but the workspaces remain empty.
I have no backup for the old workspace.json. What should I do now?
Thanks,
Fang K

Hi @phoeningo - we had the same situation. Not a great solution, but if you just create empty workspaces in the newly imported project, they will populate with your jobs - e.g this is what we did, just creating new workspaces until all jobs are populated:

1 Like

Hi @olibclarke Interesting !
Thank you very much!

I updated to latest version. Trying to import project, I still get the audit error. Trying add’l workspaces doesnt do anything.

Any help appreciated.

Hi @rshek,

Can you paste the logs from cryosparcm log command_core?

I think it was because I didnt restart cryosparcm after the patch.It worked after I reinstalled cryosparc and applied patch again (suprised the latest install files don’t have the patch, but is the base 3.2 ver?) Also, maybe this is a naive question, but I can’t seem to apply the patch cryosparc_worker on a single workstation. I moved the cryosparc patch tar.gz file to the cryosparc_worker folder. Then run tar xvzf on it. But there isn’t a bin/cryosparcw patch? Currently stuck since version mismatch. Thanks in advance

nvm, i was being dump haha. ./cryosparcw patch worked…working fine now

okay, its still happening. No audit error. but blank import.


COMMAND CORE STARTED === 2021-04-04 20:24:32.887411 ==========================
*** BG WORKER START

  • Serving Flask app “command_core” (lazy loading)
  • Environment: production
    WARNING: This is a development server. Do not use it in a production deployment.
    Use a production WSGI server instead.
  • Debug mode: off
    ****** UPDATING WORKER GPU INFO
    ****** UPDATING ALL JOB SIZES IN 10s
    ****** EXPORTING ALL PROJECTS IN 60s
    ======== Creating User: rshek@uw.edu Password123
    ****** UPDATING WORKER GPU INFO
    COMMAND CORE STARTED === 2021-05-26 23:18:48.090824 ==========================
    *** BG WORKER START
  • Serving Flask app “command_core” (lazy loading)
  • Environment: production
    WARNING: This is a development server. Do not use it in a production deployment.
    Use a production WSGI server instead.
  • Debug mode: off
    ****** UPDATING WORKER GPU INFO
    ****** UPDATING ALL JOB SIZES IN 10s
    ****** EXPORTING ALL PROJECTS IN 60s
    [GPU_INFO]: Failed calling the python function to get GPU info on ip-172-31-12-64.us-west-2.compute.internal: Command ‘[‘ssh’, ‘ubuntu@ip-172-31-12-64.us-west-2.compute.internal’, ‘bash -c “eval $(/home/ubuntu/cryosparc_worker/bin/cryosparcw env); timeout 30 python /home/ubuntu/cryosparc_worker/cryosparc_compute/get_gpu_info.py”’]’ returned non-zero exit status 255.
    ****** UPDATING WORKER GPU INFO
    [GPU_INFO]: Failed calling the python function to get GPU info on ip-172-31-12-64.us-west-2.compute.internal: Command ‘[‘ssh’, ‘ubuntu@ip-172-31-12-64.us-west-2.compute.internal’, ‘bash -c “eval $(/home/ubuntu/cryosparc_worker/bin/cryosparcw env); timeout 30 python /home/ubuntu/cryosparc_worker/cryosparc_compute/get_gpu_info.py”’]’ returned non-zero exit status 255.
    COMMAND CORE EXITED ==== 2021-05-26 23:22:28.168126 ==========================
    COMMAND CORE STARTED === 2021-05-26 23:22:28.948310 ==========================
    *** BG WORKER START
  • Serving Flask app “command_core” (lazy loading)
  • Environment: production
    WARNING: This is a development server. Do not use it in a production deployment.
    Use a production WSGI server instead.
  • Debug mode: off
    COMMAND CORE STARTED === 2021-05-26 23:22:48.808913 ==========================
    *** BG WORKER START
  • Serving Flask app “command_core” (lazy loading)
  • Environment: production
    WARNING: This is a development server. Do not use it in a production deployment.
    Use a production WSGI server instead.
  • Debug mode: off
    ****** UPDATING WORKER GPU INFO
    ****** UPDATING ALL JOB SIZES IN 10s
    ****** EXPORTING ALL PROJECTS IN 60s
    COMMAND CORE STARTED === 2021-05-26 23:24:54.300398 ==========================
    *** BG WORKER START
  • Serving Flask app “command_core” (lazy loading)
  • Environment: production
    WARNING: This is a development server. Do not use it in a production deployment.
    Use a production WSGI server instead.
  • Debug mode: off
    ****** UPDATING WORKER GPU INFO
    ****** UPDATING ALL JOB SIZES IN 10s
    ****** EXPORTING ALL PROJECTS IN 60s
    Indexing /home/ubuntu ----
    Base path: /home/ubuntu
    Indexing /home ----
    Base path: /home
    Indexing / ----
    Base path: /
    Indexing /data ----
    Base path: /data
    Indexing /data/P1 ----
    Base path: /data/P1
    [IMPORT_PROJECT] : Importing project from /data/P1
    [IMPORT_PROJECT] : Created project P1
    [IMPORT_PROJECT] : Created workspace W1 in P1
    [IMPORT_PROJECT] : Inserting jobs into project…
    [IMPORT_PROJECT] : Uploading project image data…
    [IMPORT_PROJECT] : Done. Uploaded 7 files in 0.21s
    [IMPORT_PROJECT] : Inserted job document in 0.21s…
    [IMPORT_PROJECT] : Inserting streamlogs into jobs…
    [IMPORT_PROJECT] : Done. Inserted 0 streamlogs in 0.00s…
    [IMPORT_PROJECT] : Imported J1 into P1 in 0.21s…
    [IMPORT_PROJECT] : Imported project from /data/P1 as P1 in 0.24s
    [EXPORT_PROJECT] : Exporting project P1…
    [EXPORT_PROJECT] : Exported project P1 to /data/P1/project.json in 0.00s
    [EXPORT_PROJECT] : Exporting project P1…
    [EXPORT_PROJECT] : Exported project P1 to /data/P1/project.json in 0.00s
    [EXPORT_PROJECT] : Exporting project P1…
    [EXPORT_PROJECT] : Exported project P1 to /data/P1/project.json in 0.00s
    [EXPORT_PROJECT] : Exporting project P1…
    [EXPORT_PROJECT] : Exported project P1 to /data/P1/project.json in 0.00s

This seems to have fixed my issue after installing the patches. Thanks Oli.