[Debian-med-packaging] Creation of cwl descriptions in seqan2 does not work

[Andreas Tille]

Hi Michael,

I intended to fix #892223 since a patch was submitted.  I realised that
your last change where you attempt to create CWL descriptions is not
working.  Besides a simple PATH issue which I fixed the whole generation
just throws errors like these:


:/build/seqan2-2.4.0+dfsg# for app in $(ls /build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/lib/seqan/bin);         do /build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/lib/seqan/bin/${app}         --write-ctd ${app}.ctd && CTDConverter cwl -i ${app}.ctd         -o /build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/share/commonwl/.cwl;         done;
INFO: Using cwl converter
WARNING: Validation against a schema has not been enabled.
INFO: Parsing alf.ctd
INFO: Converting Alf (source alf.ctd)
    INFO: Writing to .cwl
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/convert.py", line 220, in main
    converter.convert_models(args, parsed_ctds)
  File "/usr/lib/python3/dist-packages/cwl/converter.py", line 75, in convert_models
    stream = open(output_file, 'w')
FileNotFoundError: [Errno 2] No such file or directory: '/build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/share/commonwl/.cwl'
ERROR: CTDConverter could not complete the requested operation.
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/convert.py", line 220, in main
    converter.convert_models(args, parsed_ctds)
  File "/usr/lib/python3/dist-packages/cwl/converter.py", line 75, in convert_models
    stream = open(output_file, 'w')
FileNotFoundError: [Errno 2] No such file or directory: '/build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/share/commonwl/.cwl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/CTDConverter", line 11, in <module>
    load_entry_point('ctdconverter==2.0', 'console_scripts', 'CTDConverter')()
  File "/usr/lib/python3/dist-packages/convert.py", line 242, in main
    utils.error("Reason: " + e.msg, 0)
AttributeError: 'FileNotFoundError' object has no attribute 'msg'
INFO: Using cwl converter
WARNING: Validation against a schema has not been enabled.
INFO: Parsing bam2roi.ctd
INFO: Converting Bam2roi (source bam2roi.ctd)
    INFO: Writing to .cwl
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/convert.py", line 220, in main
    converter.convert_models(args, parsed_ctds)
  File "/usr/lib/python3/dist-packages/cwl/converter.py", line 75, in convert_models
    stream = open(output_file, 'w')
FileNotFoundError: [Errno 2] No such file or directory: '/build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/share/commonwl/.cwl'
ERROR: CTDConverter could not complete the requested operation.
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/convert.py", line 220, in main
    converter.convert_models(args, parsed_ctds)
  File "/usr/lib/python3/dist-packages/cwl/converter.py", line 75, in convert_models
    stream = open(output_file, 'w')
FileNotFoundError: [Errno 2] No such file or directory: '/build/seqan2-2.4.0+dfsg/debian/seqan-apps/usr/share/commonwl/.cwl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/CTDConverter", line 11, in <module>
    load_entry_point('ctdconverter==2.0', 'console_scripts', 'CTDConverter')()
  File "/usr/lib/python3/dist-packages/convert.py", line 242, in main
    utils.error("Reason: " + e.msg, 0)
AttributeError: 'FileNotFoundError' object has no attribute 'msg'
...


Are you able to fix this easily (and if you are feel free to upload) or
should I rather deactivate this for the moment?

Kind regards

        Andreas.


-- 
http://fam-tille.de