Feature: enhance zipped submissions support

[syphax-bouazzouni]

Changes

• Add gzipped submissions support
• Fix diff process not working for zipped submissions (Diff use the zipped version of the resource (GEMET case) ontoportal-lirmm/ontologies_linked_data#12)
• Fix a bug when generating the output folder path for the diff file (erroneous generated diff output folder  ontoportal-lirmm/ontologies_linked_data#13)
• add the zipped? and parsable? functions to the submissions to know respectively if the submission is zipped and can be parsed.
• Some code refactoring

[alexskr]

Is it worth adding a unit test for zipped file submission?

[syphax-bouazzouni]

Is it worth adding a unit test for zipped file submission?

Yeah indeed, I will do it. (you don't have a lot of gzipped resources in Bioportal, but some zip (22))
In the future, resources will be bigger and bigger, and a lot will be zipped, so yeah being solid on that would be necessary.

Anyway, in my following PRs, I will do specific tests for each of them (now that I master more our system of tests)

[codecov]

Codecov Report

Merging #144 (29153b6) into master (4f9139d) will decrease coverage by 0.08%.
The diff coverage is 80.59%.

@@            Coverage Diff             @@
##           master     #144      +/-   ##
==========================================
- Coverage   80.72%   80.63%   -0.09%     
==========================================
  Files          63       63              
  Lines        4851     4876      +25     
==========================================
+ Hits         3916     3932      +16     
- Misses        935      944       +9     

Flag	Coverage Δ
unittests	80.63% <80.59%> (-0.09%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...tologies_linked_data/models/ontology_submission.rb	78.06% <76.31%> (-0.52%)	⬇️
lib/ontologies_linked_data/utils/file.rb	72.89% <85.18%> (+1.61%)	⬆️
lib/ontologies_linked_data/diff/bubastis_diff.rb	76.19% <100.00%> (ø)

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[syphax-bouazzouni]

- Misses        935      944       +9    

I love this system of Code coverage Report, great work @alexskr (any plans for other GitHub actions on your side?)

[alexskr]

I love this system of Code coverage Report, great work @alexskr (any plans for other GitHub actions on your side?)

yes, the plan is to enable code coverage reports on most projects

[mdorf]

I have not had the chance to investigate the issue, but one of our colleagues from RADx tried submitting an ontology in GZIP (.GZ) format, and the parsing failed. When he re-submitted it as a ZIP file, the parsing succeeded. At this point, I don't have the bandwidth to investigate further; just wanted to record a note of this behavior.

[alexskr]

gzipped ontology submission gets processes correctly when run with ncbo_process_ontology script in ncbo_cron project but fails when it is run as a ncbo_cron job. I think ncbo/ncbo_cron#55 is supposed to fix this.