lirmm / waves-core

WAVES is a reusable web application dedicated to bioinformatic tool integration

Home Page:https://waves-core.readthedocs.io

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output file: extension

vincent-lefort opened this issue · comments

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.

I'll have a look, this is probabely related to this part of the code:

class JobOutputManager(models.Manager):

class JobOutput(Ordered, Slugged, UrlMixin, ApiModel):

more specifically there

def file_name(self):

Expected output are created here:

def create_default_outputs(self):

('file_name', output.file_pattern),

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"

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.

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

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