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BiocPy / scrnaseq

Collection of public single-cell RNA-seq datasets
https://biocpy.github.io/scrnaseq/
MIT License
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list_datasets() throws malformed JSON #17

Closed vjcitn closed 3 weeks ago

vjcitn commented 3 weeks ago

Python 3.10.12 (main, Sep 11 2024, 15:47:36) [GCC 11.4.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import scrnaseq datasets = scrnaseq.list_datasets() Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python3.10/dist-packages/scrnaseq/list_datasets.py", line 61, in list_datasets _qresults = conn.execute(stmt).fetchall() sqlite3.OperationalError: malformed JSON

jkanche commented 3 weeks ago

This is an issue with the sqlite3 library shipped by default, it needs an update. I do this on gothub actions as well, for ref: https://github.com/BiocPy/scrnaseq/blob/master/.github/workflows/pypi-publish.yml#L28

vjcitn commented 3 weeks ago

In all likelihood this issue can be closed, but I can tell you that working within a container using python 3.10 I have gotten nowhere, with the new sqlite installation noted in the action, same error. I see that the action uses python 3.9 -- is this essential?

vjcitn commented 3 weeks ago

works fine on mac with python 3.12 ... debian/ubuntu snafu. sorry for the noise.

jkanche commented 3 weeks ago

The test action runs on multiple python versions from 3.9-3.12 - https://github.com/BiocPy/scrnaseq/actions/runs/10998486432.

I ran into this only on linux, not on macos, and updating sqlite3 has resolved this.

jkanche commented 3 weeks ago

oops, i guess we posted at the same time. all good.