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

.github/workflows/deploy.yml

@@ -69,7 +69,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: 2.7.6 # Not needed with a .ruby-version file
+          ruby-version: 2.7.8 # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
       - name: get-deployment-config
         uses: actions/checkout@v3

Gemfile

@@ -19,7 +19,6 @@ gem 'json-ld'
 gem 'google-apis-core', '0.15.0'
 gem 'google-protobuf', '3.25.3'
 
-
 # Rack middleware
 gem 'ffi'
 gem 'rack-accept', '~> 0.4'
@@ -53,7 +52,7 @@ 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: 'development'
+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: 9605eb44c4271c60bedda0520e85d8c3fa2513ac
-  branch: development
+  revision: d69ede0a0b3e3c5dee64fa75cb09cc6e16e0f4b5
+  branch: feature/parse-diff-files
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -108,7 +108,7 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    airbrussh (1.5.2)
+    airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.25.0)
     base64 (0.2.0)
@@ -178,7 +178,7 @@ GEM
     google-analytics-data (0.6.1)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.13.0)
+    google-analytics-data-v1beta (0.13.1)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
@@ -202,7 +202,7 @@ 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)
@@ -231,12 +231,12 @@ 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)
     link_header (0.0.8)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -247,17 +247,18 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0820)
+    mime-types-data (3.2024.0903)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    net-http-persistent (4.0.2)
+    mutex_m (0.2.0)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
-    net-imap (0.4.14)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -277,6 +278,7 @@ 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)
@@ -340,8 +342,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.6)
-      strscan
+    rexml (3.3.7)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -362,7 +363,7 @@ 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)
@@ -377,12 +378,12 @@ 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)
-    strscan (3.1.0)
+      ostruct
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.4.0)
@@ -420,7 +421,6 @@ DEPENDENCIES
   faraday (~> 1.9)
   ffi
   goo!
-  google-apis-core (= 0.15.0)
   google-protobuf (= 3.25.3)
   haml (~> 5.2.2)
   json-ld

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]