Codecov Report

Merging #153 (c1e485b) into master (8196bf3) will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #153      +/-   ##
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+ Coverage   80.84%   80.90%   +0.05%     
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  Files          63       64       +1     
  Lines        4835     4850      +15     
==========================================
+ Hits         3909     3924      +15     
  Misses        926      926              

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This pull request has been merged into the https://github.com/ncbo/ontologies_linked_data/tree/develop branch

@syphax-bouazzouni this PR is missing code. The method generate_rdf has changed from accepting two arguments to accepting three arguments:
FROM:
def generate_rdf(logger, reasoning: true)
TO
def generate_rdf(logger, file_path, reasoning=true)

But the source of the new generate_rdf and calls to it with three arguments are not included in the PR.

  1) Error:
TestSearchController#test_search_obo_id:
ArgumentError: wrong number of arguments (given 3, expected 1)
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/models/ontology_submission.rb:452:in `generate_rdf'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/models/ontology_submission.rb:1005:in `process_submission'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:117:in `block (2 levels) in create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:109:in `each'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:109:in `block in create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:107:in `each'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:107:in `create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_api/test/controllers/test_search_controller.rb:207:in `test_search_obo_id'

merged manually to develop

@syphax-bouazzouni this PR is missing code. The method generate_rdf has changed from accepting two arguments to accepting three arguments: FROM: def generate_rdf(logger, reasoning: true) TO def generate_rdf(logger, file_path, reasoning=true)

But the source of the new generate_rdf and calls to it with three arguments are not included in the PR.

  1) Error:
TestSearchController#test_search_obo_id:
ArgumentError: wrong number of arguments (given 3, expected 1)
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/models/ontology_submission.rb:452:in `generate_rdf'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/models/ontology_submission.rb:1005:in `process_submission'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:117:in `block (2 levels) in create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:109:in `each'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:109:in `block in create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:107:in `each'
    /Users/mdorf/dev/ncbo/ontologies_linked_data/lib/ontologies_linked_data/sample_data/ontology.rb:107:in `create_ontologies_and_submissions'
    /Users/mdorf/dev/ncbo/ontologies_api/test/controllers/test_search_controller.rb:207:in `test_search_obo_id'

Have you been able to figure out this? this PR had not changed generate_rdf, maybe the upstream code changed since the creation of this PR.

Yes, I was able to track down the missing code. The method generate_rdf had changed at some point to accept an extra argument to store the file_path, which is required by this PR to be passed to the OWL API Wrapper for extracting the ontology IRI.