implemented the first pass at bmir-radx/radx-project#37

ncbo · Dec 17, 2023 · 1f38e8a · 1f38e8a
1 parent 1a62241
commit 1f38e8a
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 067104ae94c0e9d058cfbf419364fbf03f34de43
+  revision: d7ee80860a0eab9293af81083a0700d099c50263
   branch: develop
   specs:
     ncbo_annotator (0.0.1)
@@ -42,7 +42,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: e6d4449d8b854f17bb54af6de142bc64bff22ab3
+  revision: 003b65c5e5ce8b0736085d6825ee1b8e9548826e
   branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -159,11 +159,11 @@ GEM
     google-analytics-data-v1beta (0.9.0)
       gapic-common (>= 0.20.0, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-core (1.6.0)
-      google-cloud-env (~> 1.0)
+    google-cloud-core (1.6.1)
+      google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (1.6.0)
-      faraday (>= 0.17.3, < 3.0)
+    google-cloud-env (2.0.1)
+      faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.3.1)
     google-protobuf (3.25.1-aarch64-linux)
     google-protobuf (3.25.1-arm64-darwin)
@@ -173,22 +173,26 @@ GEM
       google-protobuf (~> 3.14)
       googleapis-common-protos-types (~> 1.2)
       grpc (~> 1.27)
-    googleapis-common-protos-types (1.10.0)
+    googleapis-common-protos-types (1.11.0)
       google-protobuf (~> 3.18)
-    googleauth (1.8.1)
-      faraday (>= 0.17.3, < 3.a)
+    googleauth (1.9.0)
+      faraday (>= 1.0, < 3.a)
+      google-cloud-env (~> 2.0, >= 2.0.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.59.2)
-      google-protobuf (~> 3.24)
+    grpc (1.60.0-aarch64-linux)
+      google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.59.2-x86_64-darwin)
-      google-protobuf (~> 3.24)
+    grpc (1.60.0-arm64-darwin)
+      google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.59.2-x86_64-linux)
-      google-protobuf (~> 3.24)
+    grpc (1.60.0-x86_64-darwin)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.60.0-x86_64-linux)
+      google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
@@ -198,10 +202,10 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
+    json (2.7.1)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.6.3)
+    json_pure (2.7.1)
     jwt (2.7.1)
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
@@ -217,15 +221,15 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2023.1205)
     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)
     net-http-persistent (2.9.4)
-    net-imap (0.4.6)
+    net-imap (0.3.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -265,7 +269,7 @@ GEM
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (3.1.1)
+    rack-mini-profiler (3.3.0)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
@@ -280,14 +284,14 @@ GEM
     redcarpet (3.6.0)
     redis (5.0.8)
       redis-client (>= 0.17.0)
-    redis-client (0.18.0)
+    redis-client (0.19.0)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
     redis-store (1.10.0)
       redis (>= 4, < 6)
-    regexp_parser (2.8.2)
+    regexp_parser (2.8.3)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -297,15 +301,15 @@ GEM
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.57.2)
+    rubocop (1.58.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.30.0)
@@ -420,4 +424,4 @@ DEPENDENCIES
   unicorn-worker-killer
 
 BUNDLED WITH
-   2.4.21
+   2.3.15
diff --git a/controllers/admin_controller.rb b/controllers/admin_controller.rb
@@ -127,6 +127,23 @@ class AdminController < ApplicationController
       halt 204
     end
 
+    # on demand ontology pull
+    post "/ontologies/:acronym/pull" do
+      LOGGER.info "Forcing the pull and processing of ontology #{params['acronym']}"
+      actions = NcboCron::Models::OntologySubmissionParser::ACTIONS.dup
+      actions[:remote_pull] = true
+      ont = Ontology.find(params["acronym"]).first
+      error 404, "You must provide a valid `acronym` to retrieve an ontology" if ont.nil?
+      ont.bring(:acronym, :submissions)
+      latest = ont.latest_submission(status: :any)
+      error 404, "Ontology #{params["acronym"]} contains no submissions" if latest.nil?
+      check_last_modified(latest)
+      latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param))
+      NcboCron::Models::OntologySubmissionParser.new.queue_submission(latest, actions)
+      LOGGER.info "Ontology #{params['acronym']} has been queued for pull and processing"
+      halt 204
+    end
+
     private
 
     def process_long_operation(timeout, args)