Refactor: ontology_submission.rb file to isolate the processing steps

[syphax-bouazzouni]

Why

The current model ontologies_submission.rb (which represents the submission concept) contains more than 1500 lines, including in the same time the model information (its attributes e.g submissionId) and the model operations ( e.g parsing, diff, ...).

This PL isolates the different operations into separate modules. Making the ontologies_submission.rb file smaller (600 lines), easier to read and maintain

[codecov]

Codecov Report

Attention: Patch coverage is 67.50572% with 284 lines in your changes are missing coverage. Please review.

Project coverage is 78.21%. Comparing base (4dc3b11) to head (b09fd4e).

❗ Current head b09fd4e differs from pull request most recent head c879069. Consider uploading reports for the commit c879069 to get more accurate results

Files	Patch %	Lines
...ion_process/operations/submission_rdf_generator.rb	54.50%	187 Missing ⚠️
...ubmission_process/operations/submission_indexer.rb	59.83%	49 Missing ⚠️
...ocess/operations/submission_mertrics_calculator.rb	82.60%	12 Missing ⚠️
...on_process/operations/submission_diff_generator.rb	79.54%	9 Missing ⚠️
...rocess/operations/submission_properties_indexer.rb	82.60%	8 Missing ⚠️
lib/ontologies_linked_data/metrics/metrics.rb	57.14%	6 Missing ⚠️
...ervices/submission_process/submission_processor.rb	91.93%	5 Missing ⚠️
lib/ontologies_linked_data/diff/bubastis_diff.rb	80.00%	3 Missing ⚠️
lib/ontologies_linked_data/diff/diff.rb	57.14%	3 Missing ⚠️
...tologies_linked_data/models/ontology_submission.rb	50.00%	1 Missing ⚠️
... and 1 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #143      +/-   ##
==========================================
- Coverage   80.07%   78.21%   -1.87%     
==========================================
  Files          65       72       +7     
  Lines        5003     5131     +128     
==========================================
+ Hits         4006     4013       +7     
- Misses        997     1118     +121     

Flag	Coverage Δ
unittests	78.21% <67.50%> (-1.87%)	⬇️

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[mdorf]

manually merged this PR to https://github.com/ncbo/ontologies_linked_data/tree/develop

[alexskr]

this PR overwrite metrics calculation changes introduced in #182. Those changes need to be re-applied.

[syphax-bouazzouni]

Yes, this PR is too old, it needs to be updated.

[alexskr]

this PR overwrite metrics calculation changes introduced in #182. Those changes need to be re-applied.

addressed in da1642e

[alexskr]

manually merged

[syphax-bouazzouni]

manually merged

OK great, keep me informed, If support is needed on this.