Merge branch 'feature/add-diff-parsing-endpoint' into test

Gemfile

@@ -51,7 +51,7 @@ gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branc
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'feature/add-portal-config-model'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'feature/parse-diff-files'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

Gemfile.lock

@@ -57,8 +57,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: d893c08a2c2f11c743fad520873b7f98b0805240
-  branch: feature/add-portal-config-model
+  revision: 99b934317f303f9ea839413de4ff8a5638ac074f
+  branch: feature/parse-diff-files
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -204,7 +204,7 @@ GEM
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.15.0)
+    googleapis-common-protos-types (1.16.0)
       google-protobuf (>= 3.18, < 5.a)
     googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
@@ -236,7 +236,7 @@ GEM
       rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    jwt (2.8.2)
+    jwt (2.9.0)
       base64
     kgio (2.11.4)
     libxml-ruby (5.0.3)
@@ -261,9 +261,9 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.4.1)
     mutex_m (0.2.0)
-    net-http-persistent (4.0.2)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
-    net-imap (0.4.15)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -283,6 +283,7 @@ GEM
     omni_logger (0.1.4)
       logger
     os (1.1.4)
+    ostruct (0.6.0)
     parallel (1.26.3)
     parseconfig (1.1.2)
     pony (1.13.1)
@@ -367,7 +368,7 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
     sinatra (1.4.8)
       rack (~> 1.5)
@@ -382,11 +383,12 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.23.0)
+    sshkit (1.23.1)
       base64
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
+      ostruct
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.4.0)

controllers/ontology_submissions_controller.rb

@@ -140,6 +140,25 @@ class OntologySubmissionsController < ApplicationController
       end
     end
 
+    get '/:ontology_submission_id/diff' do
+      acronym = params["acronym"]
+      submission_attributes = [:submissionId, :submissionStatus, :diffFilePath]
+      ont = Ontology.find(acronym).include(:submissions => submission_attributes).first
+      error 422, "You must provide an existing `acronym` to download" if ont.nil?
+      ont.bring(:viewingRestriction)
+      check_access(ont)
+      ont_restrict_downloads = LinkedData::OntologiesAPI.settings.restrict_download
+      error 403, "License restrictions on download for #{acronym}" if ont_restrict_downloads.include? acronym
+      submission = ont.submission(params['ontology_submission_id'].to_i)
+      error 404, "There is no such submission for download" if submission.nil?
+      file_path = submission.diffFilePath
+      if File.readable? file_path
+        reply submission.parse_diff_report
+      else
+        error 500, "Cannot read submission diff file: #{file_path}"
+      end
+    end
+
     ##
     # Download a submission diff file
     get '/:ontology_submission_id/download_diff' do

test/controllers/test_ontology_submissions_controller.rb

@@ -474,6 +474,16 @@ def test_submissions_param_include
     test_submissions_custom_includes
   end
 
+  def test_submission_diff
+    num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 2,
+                                                                                     process_submission: true,
+                                                                                     process_options: { process_rdf: true, extract_metadata: false, diff: true} )
+
+    ont = onts.first
+    sub = ont.latest_submission(status: :any)
+
+    get "/ontologies/#{ont.acronym}/submissions/#{sub.submissionId}/diff"
+  end
   private
   def submission_keys(sub)
     sub.to_hash.keys - %w[@id @type id]