Fix remote pull ontology process for zipped submissions

Gemfile

@@ -19,10 +19,10 @@ gem 'sys-proctable'
 gem 'cube-ruby', require: 'cube'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'develop'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'master'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
 
 group :test do
   gem 'email_spec'

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 83425ba6c05d051d86c6f5775540727ce4238443
-  branch: develop
+  revision: daea7822af9e5ca1961d6873a758735133a1b2db
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 067104ae94c0e9d058cfbf419364fbf03f34de43
-  branch: develop
+  revision: 04226ac5840a328e6f906f15c769ee6ee5723102
+  branch: master
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 711ebf27722355a25a0e53a8204b4ae472902bd0
-  branch: develop
+  revision: a7ad210e846a390f203457be2459719214d142fe
+  branch: master
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -46,8 +46,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
-  branch: develop
+  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
+  branch: master
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -119,16 +119,16 @@ GEM
     google-cloud-env (1.6.0)
       faraday (>= 0.17.3, < 3.0)
     google-cloud-errors (1.3.1)
-    google-protobuf (3.24.3)
-    google-protobuf (3.24.3-x86_64-darwin)
-    google-protobuf (3.24.3-x86_64-linux)
+    google-protobuf (3.23.4)
+    google-protobuf (3.23.4-x86_64-darwin)
+    google-protobuf (3.23.4-x86_64-linux)
     googleapis-common-protos (1.4.0)
       google-protobuf (~> 3.14)
       googleapis-common-protos-types (~> 1.2)
       grpc (~> 1.27)
-    googleapis-common-protos-types (1.8.0)
+    googleapis-common-protos-types (1.9.0)
       google-protobuf (~> 3.18)
-    googleauth (1.8.0)
+    googleauth (1.8.1)
       faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
@@ -170,7 +170,7 @@ GEM
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
     netrc (0.11.0)
-    oj (3.16.1)
+    oj (3.14.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)

lib/ncbo_cron/ontology_pull.rb

@@ -129,29 +129,14 @@ def create_submission(ont, sub, file, filename, logger = nil,
         new_sub.submissionStatus = nil
         new_sub.creationDate = nil
         new_sub.missingImports = nil
+        new_sub.masterFileName = nil
         new_sub.metrics = nil
         full_file_path = File.expand_path(file_location)
 
         # check if OWLAPI is able to parse the file before creating a new submission
-        owlapi = LinkedData::Parser::OWLAPICommand.new(
-          full_file_path,
-          File.expand_path(new_sub.data_folder.to_s),
-          logger: logger)
-        owlapi.disable_reasoner
-        parsable = true
-
-        begin
-          owlapi.parse
-        rescue Exception => e
-          logger.error("The new file for ontology #{ont.acronym}, submission id: #{submission_id} did not clear OWLAPI: #{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}")
-          logger.error("A new submission has NOT been created.")
-          logger.flush
-          parsable = false
-        end
-
-        if parsable
+        if new_sub.parsable?(logger: logger)
           if new_sub.valid?
-            new_sub.save()
+            new_sub.save
 
             if add_to_pull
               submission_queue = NcboCron::Models::OntologySubmissionParser.new
@@ -163,9 +148,14 @@ def create_submission(ont, sub, file, filename, logger = nil,
             logger.flush
           end
         else
+          logger.error("The new file for ontology #{ont.acronym}, submission id: #{submission_id} did not clear OWLAPI: #{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}")
+          logger.error("A new submission has NOT been created.")
+          logger.flush
+
           # delete the bad file
           File.delete full_file_path if File.exist? full_file_path
         end
+
         new_sub
       end