Merge pull request #344 from ComPlat/development

Development

- reporting tools upg
- molecule_name upd on sample change
- disable data collector job
- fix bug on collection destroy and better test coverage
- BE json import-export upg

.fontcustom-manifest.json

@@ -1,13 +1,14 @@
 {
   "checksum": {
-    "previous": "ebea6970ab34b700768ce8bafe0ee0ca02daf2bf9277ec0e6b7ac5d7bbcb09c0",
-    "current": "ebea6970ab34b700768ce8bafe0ee0ca02daf2bf9277ec0e6b7ac5d7bbcb09c0"
+    "previous": "dd832ad0716db3e5d9d4471567047066742da49b6953efd5ce967167d6c61529",
+    "current": "dd832ad0716db3e5d9d4471567047066742da49b6953efd5ce967167d6c61529"
   },
   "fonts": [
     "app/assets/fonts/icons.ttf",
     "app/assets/fonts/icons.svg",
     "app/assets/fonts/icons.woff",
-    "app/assets/fonts/icons.eot"
+    "app/assets/fonts/icons.eot",
+    "app/assets/fonts/icons.woff2"
   ],
   "glyphs": {
     "acidified-hcl": {
@@ -50,6 +51,14 @@
       "codepoint": 61722,
       "source": "app/assets/images/svg_icons/hr.svg"
     },
+    "hr1": {
+      "codepoint": 61726,
+      "source": "app/assets/images/svg_icons/hr1.svg"
+    },
+    "hr2": {
+      "codepoint": 61727,
+      "source": "app/assets/images/svg_icons/hr2.svg"
+    },
     "ir": {
       "codepoint": 61723,
       "source": "app/assets/images/svg_icons/ir.svg"
@@ -124,10 +133,12 @@
     }
   },
   "options": {
-    "autowidth": false,
+    "autowidth": true,
     "config": "fontcustom.yml",
+    "copyright": "",
+    "css3": false,
     "css_selector": ".icon-{{glyph}}",
-    "debug": true,
+    "debug": false,
     "font_ascent": 448,
     "font_descent": 64,
     "font_design_size": 16,

.gitignore

@@ -14,6 +14,7 @@
 /log/*
 !/log/.keep
 /tmp
+/tmp/*
 
 .ruby-gemset
 .ruby-version
@@ -22,6 +23,7 @@
 .env
 /config/mailcollector.yml
 /config/datamailcollector.yml
+/config/datacollectors.yml
 /config/database.yml
 /config/storage.yml
 /node_modules

Gemfile

@@ -35,7 +35,7 @@ group :development do
   gem 'web-console', '~> 2.0'
 end
 
-gem 'pg'
+gem 'pg', '~> 0.20.0'
 gem 'pg_search'
 
 gem 'devise'

Gemfile.lock

@@ -22,7 +22,7 @@ GIT
 
 GIT
   remote: https://github.com/ComPlat/sablon
-  revision: b2d1ff682c4b4d984b91cf410043e42bdc5c25fc
+  revision: 7b688bfd5f7459ca49e786ea9908996d44c2f825
   specs:
     sablon (0.0.19)
       nokogiri (>= 1.6.0)
@@ -167,8 +167,6 @@ GEM
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
-    celluloid (0.16.0)
-      timers (~> 4.0.0)
     childprocess (0.5.9)
       ffi (~> 1.0, >= 1.0.11)
     chromedriver-helper (1.0.0)
@@ -241,13 +239,13 @@ GEM
     faraday (0.11.0)
       multipart-post (>= 1.2, < 3)
     fast_stack (0.2.0)
-    ffi (1.9.10)
+    ffi (1.9.18)
     flamegraph (0.9.5)
     font-awesome-rails (4.6.2.0)
       railties (>= 3.2, < 5.1)
-    fontcustom (1.3.8)
+    fontcustom (2.0.0)
       json (~> 1.4)
-      listen (>= 1.0, < 3.0)
+      listen (>= 1.0, < 4.0)
       thor (~> 0.14)
     globalid (0.3.7)
       activesupport (>= 4.1.0)
@@ -285,7 +283,6 @@ GEM
     hashie-forbidden_attributes (0.1.1)
       hashie (>= 3.0)
     headless (2.0.0)
-    hitimes (1.2.4)
     html2haml (2.1.0)
       erubis (~> 2.7.0)
       haml (~> 4.0)
@@ -315,10 +312,10 @@ GEM
       activesupport (>= 3.0.0)
     launchy (2.4.3)
       addressable (~> 2.3)
-    listen (2.10.1)
-      celluloid (~> 0.16.0)
-      rb-fsevent (>= 0.9.3)
-      rb-inotify (>= 0.9)
+    listen (3.1.5)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+      ruby_dep (~> 1.2)
     loofah (2.0.3)
       nokogiri (>= 1.5.9)
     mail (2.6.4)
@@ -374,7 +371,7 @@ GEM
     parser (2.4.0.0)
       ast (~> 2.2)
     pdf-core (0.6.1)
-    pg (0.18.4)
+    pg (0.20.0)
     pg_search (1.0.5)
       activerecord (>= 3.1)
       activesupport (>= 3.1)
@@ -427,9 +424,9 @@ GEM
     rainbow (2.2.2)
       rake
     rake (12.1.0)
-    rb-fsevent (0.9.7)
-    rb-inotify (0.9.7)
-      ffi (>= 0.5.0)
+    rb-fsevent (0.10.2)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
     rdoc (4.2.2)
       json (~> 1.4)
     redcarpet (3.4.0)
@@ -469,6 +466,7 @@ GEM
     ruby-mailchecker (3.0.27)
     ruby-ole (1.2.12)
     ruby-progressbar (1.8.1)
+    ruby_dep (1.5.0)
     ruby_parser (3.8.4)
       sexp_processor (~> 4.1)
     rubyzip (1.1.7)
@@ -529,8 +527,6 @@ GEM
     thor (0.19.1)
     thread_safe (0.3.6)
     tilt (2.0.7)
-    timers (4.0.4)
-      hitimes
     tins (1.11.0)
     ttfunk (1.4.0)
     tzinfo (1.2.2)
@@ -629,7 +625,7 @@ DEPENDENCIES
   nokogiri
   openbabel (= 2.4.0.1)!
   paranoia (~> 2.0)
-  pg
+  pg (~> 0.20.0)
   pg_search
   prawn
   prawn-svg

INSTALL.md

@@ -9,8 +9,13 @@ if there are errors with nokogiri compilation with new xcode7:
 `gem install nokogiri -- --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 --use-system-libraries`
 
 ## openbabel
-* `brew install cmake` for OSX
-* install openbabel as described in its [documentation](https://github.com/cubuslab/openbabel/blob/master/INSTALL)
+* Require
+  1. CMake (the `cmake` package in Ubuntu)
+  2. Eigen (the `libeigen2-dev` or `libeigen3-dev` package in Ubuntu)
+  3. Swig (the `swig`package in Ubuntu)
+  4. libxml2 (the `libxml2-dev` package in Ubuntu)
+
+* openbabel will be automatically installed through `bundle install`
 
 ## rmagick
 * `brew install imagemagick gs` for OSX
@@ -73,12 +78,12 @@ Icons are now available as css classes: '.icon-<ICON_NAME'
 # Docker setup
 This is a setup for a 'pseudo' production stage using passenger and aimed for user testing.
 (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 directly: `docker pull complat/chemotion_eln`
-* 2 - Initialize database FIRST: `docker-compose run app bundle exec rake db:create db:migrate`
-* 3 - Precompile assets: `docker-compose run app bundle exec rake assets:precompile`
-* 4 - First run: `docker-compose up`
-*     Or initial setup and detach: `docker-compose up -d`
+
+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`
+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
 

app/api/chemotion/molecule_api.rb

@@ -59,7 +59,10 @@ class MoleculeAPI < Grape::API
         mol.create_molecule_name_by_user(new_name, user_id) if new_name.present?
 
         mol.molecule_names.map do |mn|
-          { id: mn.id, name: mn.name }
+          {
+            value: mn.id, label: mn.name,
+            desc: mn.description, mid: mn.molecule_id
+          }
         end
       end
     end

app/api/chemotion/public_api.rb

@@ -2,23 +2,14 @@ module Chemotion
   class PublicAPI < Grape::API
 
     namespace :public do
-      before do
-        error!('Unauthorized' , 401) unless TokenAuthentication.new(request).is_successful?
-      end
-
-      resources :samples do
-        desc "Return samples of all chemotion.net collections"
-
-        get do
-          Collection.for_publication.flat_map(&:samples).uniq
-        end
+      get 'ping' do
+        status 200
       end
     end
-      # TODO further resources?
 
     namespace :upload do
       before do
-        error!('Unauthorized' , 401) unless TokenIPAuthentication.new(request).is_successful?
+        error!('Unauthorized' , 401) unless TokenAuthentication.new(request, with_remote_addr: true).is_successful?
       end
       resource :attachments do
         desc "Upload files"
@@ -33,10 +24,10 @@ class PublicAPI < Grape::API
           params.delete(:recipient_email)
 
           token = request.headers['Auth-Token'] || request.params['auth_token']
-          key = API::AuthenticationKey.find_by(token: token)
+          key = AuthenticationKey.find_by(token: token)
 
 
-          helper = CollectorHelper.new(key.device.email , recipient_email)
+          helper = CollectorHelper.new(key.user.email , recipient_email)
 
           if helper.sender_recipient_known?
             dataset = helper.prepare_dataset(subject)

app/api/token_authentication.rb

@@ -1,12 +1,29 @@
 class TokenAuthentication
-  attr_reader :request
+  attr_reader :request, :args, :key, :token
 
-  def initialize(request)
+  def initialize(request, **args)
     @request = request
+    @args = args
+    @token = request.headers['Authorization']&.match(
+      /^Bearer\s*([\w\-\.\~\+\/]+)=*/) && $1
+    @key = AuthenticationKey.find_by(token: token)
   end
 
   def is_successful?
-    token = request.headers['Auth-Token'] || request.params['auth_token']
-    API::AuthenticationKey.find_by(token: token).present?
+    key && all_checks
+  end
+
+  def all_checks
+    check_keys.map{|check| send(check) }.all?
+  end
+
+  private
+
+  def check_keys
+    args.keys & [:with_remote_addr]
+  end
+
+  def with_remote_addr
+    key && key.ip.include?(request.env['REMOTE_ADDR'])
   end
 end