LabiIMotion Integration

* Generic Element * Generic Segment * Generic Dataset --------- Co-authored-by: Chia-Lin (Claire) Lin <[email protected]> Co-authored-by: Pei-Chi (Paggy) Huang <[email protected]>
ComPlat · Aug 31, 2023 · e5f105c · e5f105c
1 parent e29301f
commit e5f105c
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Showing 220 changed files with 5,560 additions and 11,740 deletions.
diff --git a/.gitignore b/.gitignore
@@ -145,6 +145,7 @@
 aliasifyConfig.js
 /app/assets/javascripts/components/extra/*
 /app/packs/src/components/extra/*
+/app/packs/klasses.json
 
 # Backups folder
 backup/deploy_backup

diff --git a/.nvmrc b/.nvmrc
@@ -1 +1 @@
-v14.21.3
+v18.17.1
diff --git a/Gemfile b/Gemfile
@@ -60,6 +60,8 @@ gem 'kaminari'
 gem 'kaminari-grape'
 gem 'ketcherails', git: 'https://github.com/complat/ketcher-rails.git', branch: 'upgrade-to-rails-6'
 
+gem 'labimotion', '1.0.5'
+
 gem 'mimemagic', '0.3.10'
 
 # locked to enforce latest version of net-scp. without lock net-ssh would be updated first which locks

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -456,6 +456,8 @@ GEM
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
+    labimotion (1.0.5)
+      rails (~> 6.1.7)
     latex-decode (0.4.0)
     launchy (2.5.0)
       addressable (~> 2.7)
@@ -917,6 +919,7 @@ DEPENDENCIES
   kaminari
   kaminari-grape
   ketcherails!
+  labimotion (= 1.0.5)
   launchy
   listen
   memory_profiler
@@ -990,4 +993,4 @@ DEPENDENCIES
   yaml_db
 
 BUNDLED WITH
-   2.1.4
+   2.2.29
diff --git a/app/api/api.rb b/app/api/api.rb
@@ -4,12 +4,13 @@
 require 'grape-entity'
 require 'grape-swagger'
 
+# rubocop:disable Metrics/BlockLength
 class API < Grape::API
   format :json
   prefix :api
   version 'v1'
 
-  # TODO needs to be tested,
+  # TODO: needs to be tested,
   # source: http://funonrails.com/2014/03/api-authentication-using-devise-token/
   helpers do
     def present(*args)
@@ -64,25 +65,23 @@ def is_public_request?
         '/api/v1/chemspectra/',
         '/api/v1/ketcher/layout',
         '/api/v1/gate/receiving',
-        '/api/v1/gate/ping'
+        '/api/v1/gate/ping',
       )
     end
 
-    def cache_key search_method, arg, molfile, collection_id, molecule_sort, opt
-      molecule_sort = molecule_sort == 1 ? true : false
+    def cache_key(search_method, arg, molfile, collection_id, molecule_sort, opt) # rubocop:disable Metrics/ParameterLists
+      molecule_sort = molecule_sort == 1
       inchikey = Chemotion::OpenBabelService.inchikey_from_molfile molfile
 
-      cache_key = [
+      [
         latest_updated,
         search_method,
         arg,
         inchikey,
         collection_id,
         molecule_sort,
-        opt
+        opt,
       ]
-
-      return cache_key
     end
 
     def to_snake_case_key(k)
@@ -94,7 +93,7 @@ def to_rails_snake_case(val)
       when Array
         val.map { |v| to_rails_snake_case(v) }
       when Hash
-        Hash[val.map { |k, v| [to_snake_case_key(k), to_rails_snake_case(v)] }]
+        Hash[val.map { |k, v| [to_snake_case_key(k), to_rails_snake_case(v)] }] # rubocop:disable Style/HashConversion
       else
         val
       end
@@ -109,7 +108,7 @@ def to_json_camel_case(val)
       when Array
         val.map { |v| to_json_camel_case(v) }
       when Hash
-        Hash[val.map { |k, v| [to_camelcase_key(k), to_json_camel_case(v)] }]
+        Hash[val.map { |k, v| [to_camelcase_key(k), to_json_camel_case(v)] }] # rubocop:disable Style/HashConversion
       else
         val
       end
@@ -122,13 +121,14 @@ def to_json_camel_case(val)
 
   # desc: whitelisted tables and columns for advanced_search
   WL_TABLES = {
-    'samples' => %w(name short_label external_label xref)
+    'samples' => %w(name short_label external_label xref),
   }
   TARGET = Rails.env.production? ? 'https://www.chemotion-repository.net/' : 'http://localhost:3000/'
 
   ELEMENTS = %w[research_plan screen wellplate reaction sample]
 
-  TEXT_TEMPLATE = %w[SampleTextTemplate ReactionTextTemplate WellplateTextTemplate ScreenTextTemplate ResearchPlanTextTemplate ReactionDescriptionTextTemplate ElementTextTemplate ]
+  TEXT_TEMPLATE = %w[SampleTextTemplate ReactionTextTemplate WellplateTextTemplate ScreenTextTemplate
+                     ResearchPlanTextTemplate ReactionDescriptionTextTemplate ElementTextTemplate]
 
   mount Chemotion::LiteratureAPI
   mount Chemotion::ContainerAPI
@@ -163,29 +163,32 @@ def to_json_camel_case(val)
   mount Chemotion::MessageAPI
   mount Chemotion::AdminAPI
   mount Chemotion::AdminUserAPI
-  mount Chemotion::AdminGenericAPI
   mount Chemotion::EditorAPI
   mount Chemotion::UiAPI
   mount Chemotion::OlsTermsAPI
   mount Chemotion::PredictionAPI
   mount Chemotion::ComputeTaskAPI
   mount Chemotion::TextTemplateAPI
-  mount Chemotion::GenericElementAPI
-  mount Chemotion::SegmentAPI
-  mount Chemotion::GenericDatasetAPI
   mount Chemotion::ReportTemplateAPI
   mount Chemotion::PrivateNoteAPI
   mount Chemotion::NmrdbAPI
   mount Chemotion::MeasurementsAPI
-  mount Chemotion::ConverterAPI
   mount Chemotion::AttachableAPI
   mount Chemotion::SampleTaskAPI
   mount Chemotion::ChemicalAPI
   mount Chemotion::CalendarEntryAPI
   mount Chemotion::CommentAPI
-
-  add_swagger_documentation(info: {
-    "title": "Chemotion ELN",
-    "version": "1.0"
-  }) if Rails.env.development?
+  mount Labimotion::ConverterAPI
+  mount Labimotion::GenericElementAPI
+  mount Labimotion::GenericDatasetAPI
+  mount Labimotion::SegmentAPI
+  mount Labimotion::LabimotionHubAPI
+
+  if Rails.env.development?
+    add_swagger_documentation(info: {
+                                title: 'Chemotion ELN',
+                                version: '1.0',
+                              })
+  end
 end
+# rubocop: enable Metrics/BlockLength