DNAnexus Notebook File Load Error
In the past month or so I've encountered a recurring error when I try to load a recently written DNAnexus Notebook on a dxjupyterlab instance. When I try to open the notebook as a DNAnexus Notebook I get:
File Load Error for my_notebook.ipynb
Expected property name or '}' in JSON at position 1 (line 1 column 2)When I open it as a text file I can see that it appears to be locked:
{'class': 'file',
'created': 1725366189000,
'folder': '/my/notebooks',
'hidden': False,
'id': 'file-GqFPzF8Jg8JY51Pfx7vFpXKB',
'media': 'application/json',
'name': 'my_notebook.ipynb',
'project': 'project-GBvkP10Jg8Jpy18FPjPByv29',
'properties': {'notebook_locked_by': 'job-GqFV9FQJg8JbbG18yZfB75zp',
'notebook_locked_by_project': 'project-GBvkP10Jg8Jpy18FPjPByv29',
'notebook_parent_version': 'file-GqFPkQjJg8JXp79F27f21JZ7'},
'size': 21587412}but I'm not sure why it'd be locked, it's not being used by a job.
I'm able to read the notebook by downloading it ‘locally’ to my cloud instance. But when I upload the notebook back to my cloud folder and try to load it directly as a DNAnexus Notebook it gives the same File Load Error and appears to be locked by my current job.
Comments
3 comments
Hi Nik,
Sorry to hear you are having issues.
Please check the job referenced in ‘notebook_locked_by’ is not running - you can do this by looking in your Monitor tab, or by dx find job --id <job_id> in the CLI.
If the job is not running, since this seems to be an error in your UKB-RAP project, I would suggest contacting ukbiobank-support@dnanexus.com, who should be able to investigate further.
Thank you for getting in touch, and I hope the support team at DNAnexus can help more.
Daisy
The job is not running. I'll contact the support team. Thanks!
For future reference, thanks to the UKB support team I learned that this error was caused by my notebook being more than 20 MB.
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