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dieterich-lab / scimodom

Sci- ModoM: A quantitative database of transcriptome-wide high-throughput RNA modification sites
https://dieterich-lab.github.io/scimodom/
GNU Affero General Public License v3.0
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Cannot download BAM files #107

Closed eboileau closed 4 months ago

eboileau commented 4 months ago

A clear and concise description of what the bug is.

Minimal steps to reproduce the bug:

  1. Go to Browse e.g. hSLg7AzyWeZ7 Mouse test dataset, click on the + button, and download any BAM file
  2. We get Internal Server Error.

Output or error messages.

5087c2e04ead 2024-05-28 09:37:56 [ERROR] scimodom | Exception on /api/v0/bam_file/hSLg7AzyWeZ7/test.bam [GET]
5087c2e04ead Traceback (most recent call last):
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask/app.py", line 1473, in wsgi_app
5087c2e04ead     response = self.full_dispatch_request()
5087c2e04ead                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask/app.py", line 882, in full_dispatch_request
5087c2e04ead     rv = self.handle_user_exception(e)
5087c2e04ead          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask_cors/extension.py", line 178, in wrapped_function
5087c2e04ead     return cors_after_request(app.make_response(f(*args, **kwargs)))
5087c2e04ead                                                 ^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask/app.py", line 880, in full_dispatch_request
5087c2e04ead     rv = self.dispatch_request()
5087c2e04ead          ^^^^^^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask/app.py", line 865, in dispatch_request
5087c2e04ead     return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
5087c2e04ead            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/flask_cors/decorator.py", line 130, in wrapped_function
5087c2e04ead     resp = make_response(f(*args, **kwargs))
5087c2e04ead                          ^^^^^^^^^^^^^^^^^^
5087c2e04ead   File "/app/venv/lib/python3.11/site-packages/scimodom/api/bam_file.py", line 57, in get_bam_file
5087c2e04ead     dataset, error, status = get_validate_dataset(dataset_id)
5087c2e04ead     ^^^^^^^^^^^^^^^^^^^^^^
5087c2e04ead TypeError: cannot unpack non-iterable Dataset object

Additional context

I believe this was partly fixed by 880d7f42bf79a2e775b60aaf99b30e190e0e1d8a but not everywhere...

What browser were you using?

Firefox, Chrome

What version of Sci-ModoM were you using?

dev