higlass-server
higlass-server copied to clipboard
AWS-related tests appear to fail
I'm curious if the slashes in an AWS URL are setting up non-existent paths in the media
directory.
From the develop
branch:
(higlass-server) $ ./test.sh
...
(higlass-server) $ python manage.py test tilesets
.[E::hts_open_format] Failed to open file /home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/SRR1770413.sorted.short.bam..
E.....................F................................
======================================================================
ERROR: test_register_bam_url (tilesets.tests.BamTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/ubuntu/higlass-server/tilesets/tests.py", line 425, in test_register_bam_url
response = c.get(f'/api/v1/tileset_info/?d={uid}')
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 527, in get
response = super().get(path, data=data, secure=secure, **extra)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 339, in get
**extra,
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 414, in generic
return self.request(**r)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/test/client.py", line 495, in request
raise exc_value
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/exception.py", line 34, in inner
response = get_response(request)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/base.py", line 126, in _get_response
response = self.process_exception_by_middleware(e, request)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/core/handlers/base.py", line 124, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/views/decorators/csrf.py", line 54, in wrapped_view
return view_func(*args, **kwargs)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/django/views/generic/base.py", line 68, in view
return self.dispatch(request, *args, **kwargs)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 495, in dispatch
response = self.handle_exception(exc)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 455, in handle_exception
self.raise_uncaught_exception(exc)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/views.py", line 492, in dispatch
response = handler(request, *args, **kwargs)
File "/home/ubuntu/anaconda3/envs/higlass-server/lib/python3.6/site-packages/rest_framework/decorators.py", line 54, in handler
return func(*args, **kwargs)
File "/home/ubuntu/higlass-server/tilesets/views.py", line 628, in tileset_info
tileset_object.datafile.path
File "/home/ubuntu/clodius/clodius/tiles/bam.py", line 124, in tileset_info
samfile = pysam.AlignmentFile(filename)
File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 935, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/SRR1770413.sorted.short.bam..`: No such file or directory
======================================================================
FAIL: test_register_url (tilesets.tests.FileUploadTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/ubuntu/higlass-server/tilesets/tests.py", line 1322, in test_register_url
self.assertEqual(200, response.status_code, response.content)
AssertionError: 200 != 500 : b'{"error": "File not found: /home/ubuntu/higlass-server/media/https/s3.amazonaws.com/pkerp/public/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig.."}'
----------------------------------------------------------------------
Ran 56 tests in 29.742s
FAILED (failures=1, errors=1)
Creating test database for alias 'default'...
System check identified no issues (0 silenced).
No coordinate system specified, but we found matching chromsizes. Using coordinate system hg19_1.
Using coordinates for coordinate system: hg19_r
No coordinate system specified, but we found matching chromsizes. Using coordinate system hg19_1.
Destroying test database for alias 'default'...