Merge pull request #345 from ComPlat/development

Development prepare v0.3.0
ComPlat · Nov 17, 2017 · 64deda9 · 64deda9
2 parents 6acac1f + dfc4b29
commit 64deda9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,41 @@
 
 # Chemotion_ELN Changelog
 
+## [v0.3.0]
+> 2017-11-15
+* Features
+  * Export reaction smiles
+  * reporting: revamp of UI
+  * reporting: analysis metadata formating
+  * user affiliations management
+  * revamp of sample/reaction detail UI
+  * select the sample molecule_name to display
+  * fetch CAS from pubchem
+  * uuid (qr code) for each element (sample, reaction, analyse)
+  * export samples as sdf
+  * adv search
+  * Docker install
+  * ....
+* Fixes
+  * search result element ordering
+  * dependent destroy of collections-elements
+  * sample density default set to 0
+  * react production build
+  * ....
+
+## [v0.2.1]
+> 2016-11-02
+* Features
+  * Temperature Chart with unit converter (°C, °F , K) for reaction
+  * Import molecules and create samples from a sd file
+    (R group and polymer support are not supported)
+  * Images in report doc are from eps files
+  * rearrange the reaction list for a report by Drag-and-drop -ing
+  * Text editing and formating tool bar for the reaction description
+* Fixes
+  * upgrade to Ruby 2.3.1
+  * The Upload of analyses files does not fail if the thumbnail creation does
+
 ## [v0.2.0]
 
 > 2016-10-17

diff --git a/Gemfile b/Gemfile
@@ -77,8 +77,8 @@ gem 'roo', '>2.5.0'
 
 gem 'faraday', '~> 0.11.0'
 gem 'httparty'
-gem 'ketcherails',  git: 'https://github.com/ComPlat/ketcher-rails',
-                    ref: 'aae1ba59e96ac5604449cf260a347a65e4bdb637'
+gem 'ketcherails', git: 'https://github.com/ComPlat/ketcher-rails',
+                   ref: 'bbc54084cd6365bcc9229dfe43f8e7dc8c16a845'
 # Ketcher editor
 
 # Free font icons

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ComPlat/ketcher-rails
-  revision: aae1ba59e96ac5604449cf260a347a65e4bdb637
-  ref: aae1ba59e96ac5604449cf260a347a65e4bdb637
+  revision: bbc54084cd6365bcc9229dfe43f8e7dc8c16a845
+  ref: bbc54084cd6365bcc9229dfe43f8e7dc8c16a845
   specs:
     ketcherails (0.1.3)
       bootstrap-kaminari-views (= 0.0.5)
@@ -174,7 +174,7 @@ GEM
       nokogiri (~> 1.6)
     chronic (0.10.2)
     chunky_png (1.3.8)
-    climate_control (0.1.0)
+    climate_control (0.2.0)
     closure_tree (6.2.0)
       activerecord (>= 4.1.0)
       with_advisory_lock (>= 3.0.0)
@@ -184,7 +184,7 @@ GEM
     coercible (1.0.0)
       descendants_tracker (~> 0.0.1)
     colored (1.2)
-    concurrent-ruby (1.0.2)
+    concurrent-ruby (1.0.5)
     countries (2.0.8)
       i18n_data (~> 0.7.0)
       money (~> 6.7)
@@ -198,6 +198,7 @@ GEM
       tins (>= 1.6.0, < 2)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
+    crass (1.0.3)
     css_parser (1.4.7)
       addressable
     daemons (1.2.3)
@@ -247,8 +248,8 @@ GEM
       json (~> 1.4)
       listen (>= 1.0, < 4.0)
       thor (~> 0.14)
-    globalid (0.3.7)
-      activesupport (>= 4.1.0)
+    globalid (0.4.1)
+      activesupport (>= 4.2.0)
     gman (7.0.2)
       colored (~> 1.2)
       iso_country_codes (~> 0.6)
@@ -316,10 +317,11 @@ GEM
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
       ruby_dep (~> 1.2)
-    loofah (2.0.3)
+    loofah (2.1.1)
+      crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
-    mail (2.6.4)
-      mime-types (>= 1.16, < 4)
+    mail (2.7.0)
+      mini_mime (>= 0.1.1)
     mailcatcher (0.6.4)
       activesupport (~> 4.0)
       eventmachine (= 1.0.9.1)
@@ -338,8 +340,9 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2016.0521)
     mimemagic (0.3.2)
+    mini_mime (1.0.0)
     mini_portile2 (2.0.0)
-    minitest (5.10.1)
+    minitest (5.10.3)
     money (6.9.0)
       i18n (>= 0.6.4, < 0.9)
     multi_json (1.12.0)
@@ -388,7 +391,7 @@ GEM
       activesupport (>= 3.0.0)
     quiet_assets (1.1.0)
       railties (>= 3.1, < 5.0)
-    rack (1.6.5)
+    rack (1.6.8)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-contrib (1.5.0)
@@ -423,7 +426,7 @@ GEM
       thor (>= 0.18.1, < 2.0)
     rainbow (2.2.2)
       rake
-    rake (12.1.0)
+    rake (12.3.0)
     rb-fsevent (0.10.2)
     rb-inotify (0.9.10)
       ffi (>= 0.5.0, < 2)
@@ -506,7 +509,7 @@ GEM
     sprockets (3.7.1)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
-    sprockets-rails (3.2.0)
+    sprockets-rails (3.2.1)
       actionpack (>= 4.0)
       activesupport (>= 4.0)
       sprockets (>= 3.0.0)
@@ -529,7 +532,7 @@ GEM
     tilt (2.0.7)
     tins (1.11.0)
     ttfunk (1.4.0)
-    tzinfo (1.2.2)
+    tzinfo (1.2.4)
       thread_safe (~> 0.1)
     uglifier (3.0.0)
       execjs (>= 0.3.0, < 3)

diff --git a/INSTALL.md b/INSTALL.md
@@ -80,10 +80,18 @@ This is a setup for a 'pseudo' production stage using passenger and aimed for us
 (For the development environment, change 'RAILS_ENV' to 'development' in docker-compose.yml)
 
 1. Build the image from Dockerfile `docker-compose build` or pull the image: `docker-compose pull`
-2. Initialize database FIRST: `docker-compose run app bundle exec rake db:create db:migrate`
+2. Initialize database FIRST:
+  * `docker-compose run app bundle exec rake db:create`
+  * `docker-compose run app bundle exec rake db:migrate`
+  * `docker-compose run app bundle exec rake db:seed` (optional). A "seed"
+    user will be inserted into the db with the information as below: [email protected] - password: "@eln.edu"
+  * `docker-compose run app rake ketcherails:import:common_templates` (optional)
 3. Precompile assets: `docker-compose run app bundle exec rake assets:precompile`
 4. To start the server: `docker-compose up` or start server and detach: `docker-compose up -d`
 
 * Start interactive shell with docker: `docker-compose run app /bin/bash`
 * NOTE: In this Docker image, we disabled the email verification progress
 
+* To enable email confirmation, uncomment ":confirmable" at line 5 of `app/models/user.rb`, stop the `docker-compose` by `docker-compose stop` and start `docker-compose`.
+
+
diff --git a/app/api/chemotion/report_api.rb b/app/api/chemotion/report_api.rb
@@ -1,5 +1,7 @@
 module Chemotion
   class ReportAPI < Grape::API
+    helpers ReportHelpers
+    helpers SyncHelpers
     helpers do
       def hashize(inputs)
         output = {}
@@ -64,28 +66,7 @@ def time_now
       end
 
       params do
-        requires :columns, type: Array[String]
-        requires :exportType, type: Integer
-        requires :uiState, type: Hash do
-          requires :sample, type: Hash do
-            requires :checkedIds, type: Array
-            requires :uncheckedIds, type: Array
-            requires :checkedAll, type: Boolean
-          end
-          requires :reaction, type: Hash do
-            requires :checkedIds, type: Array
-            requires :uncheckedIds, type: Array
-            requires :checkedAll, type: Boolean
-          end
-          requires :wellplate, type: Hash do
-            requires :checkedIds, type: Array
-            requires :uncheckedIds, type: Array
-            requires :checkedAll, type: Boolean
-          end
-          requires :currentCollection, type: Integer
-          requires :isSync, type: Boolean
-        end
-        requires :columns, type: Array
+        use :export_params
       end
       post :export_samples_from_selections do
         env['api.format'] = :binary
@@ -129,6 +110,29 @@ def time_now
         export.generate_file(excluded_field, included_field, removed_field)
       end
 
+      params do
+        use :export_params
+      end
+      post :export_reactions_from_selections do
+        env['api.format'] = :binary
+        params[:exportType]
+        content_type('text/csv')
+        fileName = 'reaction_smiles_' + time_now + '.csv'
+        fileURI = URI.escape(fileName)
+        header 'Content-Disposition', "attachment; filename=\"#{fileURI}\""
+        real_coll_id = fetch_collection_id_w_current_user(
+          params[:uiState][:currentCollection], params[:uiState][:isSync]
+        )
+        return unless (p_t = params[:uiState][:reaction])
+        results = reaction_smiles_hash(
+          real_coll_id,
+          p_t[:checkedAll] && p_t[:uncheckedIds] || p_t[:checkedIds],
+          p_t[:checkedAll]
+        ) || {}
+        smiles_construct = "r_smiles_#{params[:exportType]}"
+        results.map { |_, v| send(smiles_construct, v) }.join("\r\n")
+      end
+
       params do
         requires :id, type: String
       end