Merge Develop to Master, release v5.29.0

[alexskr]

Release v5.29.0 includes:

• PR Feature: extract ontology URI automatically in submissions process #153
• Password reset email content doesn't indicate 1 hour time limit #193
• Search for short IDs fails in certain cases ontologies_api#134
• Search index is missing short IDs for many ontologies ontologies_api#135

[codecov]

Codecov Report

Attention: Patch coverage is 97.10145% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 80.09%. Comparing base (0003905) to head (a973d62).

Files	Patch %	Lines
lib/ontologies_linked_data/models/class.rb	92.30%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #194      +/-   ##
==========================================
+ Coverage   79.99%   80.09%   +0.10%     
==========================================
  Files          64       65       +1     
  Lines        4958     5003      +45     
==========================================
+ Hits         3966     4007      +41     
- Misses        992      996       +4     

Flag	Coverage Δ
unittests	80.09% <97.10%> (+0.10%)	⬆️

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[syphax-bouazzouni]

maybe there is a downgrade in the code here, why remove the usage of the helper owlapi_parser(logger: nil) and replaced with LinkedData::Parser::OWLAPICommand.new ?

[jvendetti]

@mdorf and @alexskr - I have the same question as Syphax here. Was this change intended?

[mdorf]

@syphax-bouazzouni, I just merged the code from your earlier pull request. From my understanding, the owlapi_parser(logger: nil) method includes a call to unzip_submission(logger), which is already being run inside the process_submission method on line 1005. That call had to be done earlier because your updated generate_rdf method now requires the file_path to be passed as an argument. So calling owlapi_parser(logger: nil) inside generate_rdf would duplicate the unzipping process. Again, I simply merged your earlier pull request and fixed any code that it had missed.

[mdorf]

@syphax-bouazzouni, I think we can simply remove the file_path from the list of required arguments for generate_rdf and then make a call to the owlapi_parser(logger: nil) method inside generate_rdf instead of the direct call to LinkedData::Parser::OWLAPICommand.new. From what I can see this is the only place in the generate_rdf that needs the file_path.

[syphax-bouazzouni]

Yes removing that argument, would be the right solution here, even in our local branch generate_rdf does not have the file_path argument, I don't know why it ended up in my PR.

[mdorf]

I'll make that change on our end and re-test

[syphax-bouazzouni]

Great, thanks, and sorry for the bother.

[alexskr]

the refactor that @mdorf suggested in #194 (comment) be implemented after this release is complete