Database did not migrate all projects

Troubleshooting
1

Hi,

I updated to 2.11 once it was released and it was working fine. However, some of the projects dont seem to be properly migrated to the new system and are thus not useable anymore.

I checked the project folder and realized that for the projects were the migration failed, dont have the json files in the folder. Is there a possibility to try to migrate these projects again or to create the respective json files?

Best,

David

2

Hi @david.haselbach,

However, some of the projects dont seem to be properly migrated to the new system and are thus not useable anymore.

Can you provide details on how they’re not useable? Logs & screenshots would help

Is there a possibility to try to migrate these projects again or to create the respective json files?

Restarting cryoSPARC will trigger the migration- i.e. cryosparcm restart

The migration does not affect the usability of your cryoSPARC instance- please read the database migration faq for more information

3

I get with any job in this project even copied jobs that ran already fine:
errors like

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/refine/run.py”, line 49, in cryosparc2_compute.jobs.refine.run.run_homo_refine
AttributeError: ‘NoneType’ object has no attribute ‘get_items’

4

Hi @david.haselbach,

Can you try reinstalling cryoSPARC? First, stop cryoSPARC:
cryosparcm stop
Then, ensure there are no running cryoSPARC processes:

ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc2_command” (kill all the matching processes related to your cryosparc2 instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681

Then, run the forced update command (details found in the link below):
https://cryosparc.com/docs/reference/install/#forced-update

5

I tried a round but it seems that it lost these projects somehow. Has these are large it would be sad to need to run them again. Any further idea?

6

Hi David,

Sorry for the delay - were you able to resolve this?

- Suhail