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lirmm / waves-core

WAVES is a reusable web application dedicated to bioinformatic tool integration
https://waves-core.readthedocs.io
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output file: extension #4

Open vincent-lefort opened 5 years ago

vincent-lefort commented 5 years ago

When configuring a service with an output file, the 'extension' field behaviour is weird. If defined with 'name' and 'extension' fields, a remote output file is correctly retreived by WAVES, but is nammed on the local file system without the extension. Thus, we recommend not to use the 'extension' field.

marcoooo commented 5 years ago

I'll have a look, this is probabely related to this part of the code: https://github.com/lirmm/waves-core/blob/d79e779696215ec90c02e9d310c8d9b979c830c6/waves/wcore/models/jobs.py#L955

https://github.com/lirmm/waves-core/blob/d79e779696215ec90c02e9d310c8d9b979c830c6/waves/wcore/models/jobs.py#L997

more specifically there https://github.com/lirmm/waves-core/blob/d79e779696215ec90c02e9d310c8d9b979c830c6/waves/wcore/models/jobs.py#L1058

Expected output are created here: https://github.com/lirmm/waves-core/blob/d79e779696215ec90c02e9d310c8d9b979c830c6/waves/wcore/models/jobs.py#L538

https://github.com/lirmm/waves-core/blob/d79e779696215ec90c02e9d310c8d9b979c830c6/waves/wcore/api/v2/serializers/services.py#L36

Sylmila commented 5 years ago

in the same way, if output "File name" is inserted without extension : "output" instead of "output.txt". The jobs details page (/waves/jobs/xxxxx) always give an output file 'Not available for now' because WAVES search for a file "output." instead of just "output"

marcoooo commented 5 years ago

I finally figured it out. Extension is not used to compute expected output file full name. Only output value is used. In fact this was made on purpose because extension is only supposed to help adding correct headers when downloading submission output.

marcoooo commented 5 years ago

in the same way, if output "File name" is inserted without extension : "output" instead of "output.txt". The jobs details page (/waves/jobs/xxxxx) always give an output file 'Not available for now' because WAVES search for a file "output." instead of just "output"

Should be fixed: https://github.com/lirmm/waves-core/tree/bugfix/files_inputs. Before submitting PR, I'll correct other tickets: #11 and #1

marcoooo commented 4 years ago

@vincent-lefort can you confirm this has been fixed in v1.6.7?