From 926fe1e7f928c300aa32d2cd61a4655fb073fdb9 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Fri, 11 Feb 2022 09:34:42 +0100
Subject: [PATCH 1/2] Auto stash before merge of "upstream" and
 "upstream/master"

---
 .gitignore   | 2 ++
 Gemfile.lock | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 68d9c3f8e..4045ab4b2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -68,3 +68,5 @@ test/test_run.log
 test/data/ontology_files/catalog-v001.xml
 
 create_permissions.log
+
+ontologies_api.iml
diff --git a/Gemfile.lock b/Gemfile.lock
index cb883e4f4..991897524 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: d26b364dc5e8a22753cf9f8495a77c398112683f
+  revision: 89a8f665f70644989adf70cd132bf0f38ef3414d
   branch: master
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 94a77bb64f3a5af72d909c597869e9923bac3831
+  revision: e224f46dafc254b7d4a1685eb6c5c26d97ab33b7
   branch: master
   specs:
     ncbo_annotator (0.0.1)
@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 2861124483e60071266f48b2ed6d72e4394de975
+  revision: 3d585ec682d84054668f939b613388186020faa0
   branch: master
   specs:
     ncbo_cron (0.0.1)

From 8770b020b3584fa43a9712854121269915dd94f6 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 6 Oct 2022 17:17:24 +0200
Subject: [PATCH 2/2] add mapping process update

---
 controllers/mappings_controller.rb | 27 +++++++++++++++++----------
 helpers/mappings_helper.rb         | 12 ++++++++++++
 2 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/controllers/mappings_controller.rb b/controllers/mappings_controller.rb
index 29e26483a..ed071e2b7 100644
--- a/controllers/mappings_controller.rb
+++ b/controllers/mappings_controller.rb
@@ -35,6 +35,8 @@ class MappingsController < ApplicationController
     reply mappings
   end
 
+
+
   namespace "/mappings" do
     # Display all mappings
     get do
@@ -76,16 +78,7 @@ class MappingsController < ApplicationController
 
     # Display a single mapping - only rest
     get '/:mapping' do
-      mapping_id = nil
-      if params[:mapping] and params[:mapping].start_with?("http")
-        mapping_id = params[:mapping]
-        mapping_id = mapping_id.gsub("/mappings/","/rest_backup_mappings/")
-        mapping_id = RDF::URI.new(params[:mapping])
-      else
-        mapping_id =
-          "http://data.bioontology.org/rest_backup_mappings/#{mapping_id}"
-        mapping_id = RDF::URI.new(mapping_id)
-      end
+      mapping_id = request_mapping_id
       mapping = LinkedData::Mappings.get_rest_mapping(mapping_id)
       if mapping
         reply populate_mapping_classes([mapping].first)
@@ -147,6 +140,20 @@ class MappingsController < ApplicationController
       reply(201, mapping)
     end
 
+
+    patch '/:mapping' do
+      mapping = LinkedData::Mappings.get_rest_mapping(request_mapping_id)
+      process = mapping.process
+      populate_from_params(process, params)
+      if process.valid?
+        process.save
+      else
+        error 422, process.errors
+      end
+      halt 204
+    end
+
+
     # Delete a mapping
     delete '/:mapping' do
       mapping_id = RDF::URI.new(replace_url_prefix(params[:mapping]))
diff --git a/helpers/mappings_helper.rb b/helpers/mappings_helper.rb
index e65a98d38..246fbcdba 100644
--- a/helpers/mappings_helper.rb
+++ b/helpers/mappings_helper.rb
@@ -33,6 +33,18 @@ def populate_mapping_classes(mappings)
 
         mappings
       end
+
+      def request_mapping_id
+        mapping_id = nil
+        if params[:mapping] and params[:mapping].start_with?("http")
+          mapping_id = RDF::URI.new(params[:mapping])
+        else
+          mapping_id =
+            "http://data.bioontology.org/rest_backup_mappings/#{params[:mapping]}"
+          mapping_id = RDF::URI.new(mapping_id)
+        end
+        mapping_id
+      end
     end
   end
 end