Merge branch 'ZmagoD-zd_add_image_to_project_preview' into experiment-level

Dockerfile

@@ -2,7 +2,7 @@ FROM rails:4.2.5
 MAINTAINER BioSistemika <info@biosistemika.com>
 
 # additional dependecies
-RUN apt-get update -qq && apt-get install -y default-jre-headless unison sudo --no-install-recommends && rm -rf /var/lib/apt/lists/*
+RUN apt-get update -qq && apt-get install -y default-jre-headless unison sudo graphviz --no-install-recommends && rm -rf /var/lib/apt/lists/*
 
 # heroku tools
 RUN wget -O- https://toolbelt.heroku.com/install-ubuntu.sh | sh

Gemfile

@@ -52,6 +52,7 @@ gem 'aws-sdk', '~> 2.2.8'
 gem 'aws-sdk-v1'
 gem 'delayed_job_active_record'
 gem 'devise-async'
+gem 'ruby-graphviz', '~> 1.2' # Graphviz for rails 
 
 group :development, :test do
   gem 'byebug'

Gemfile.lock

@@ -38,21 +38,19 @@ GEM
       tzinfo (~> 1.1)
     ajax-datatables-rails (0.3.1)
       railties (>= 3.1)
-    algorithms (0.6.1)
     ansi (1.5.0)
     arel (6.0.3)
     aspector (0.14.0)
     ast (2.3.0)
-    autoprefixer-rails (6.1.2)
+    autoprefixer-rails (6.4.0.1)
       execjs
-      json
     awesome_print (1.7.0)
-    aws-sdk (2.2.8)
+    aws-sdk (2.2.37)
-      aws-sdk-resources (= 2.2.8)
+      aws-sdk-resources (= 2.2.37)
-    aws-sdk-core (2.2.8)
+    aws-sdk-core (2.2.37)
       jmespath (~> 1.0)
-    aws-sdk-resources (2.2.8)
+    aws-sdk-resources (2.2.37)
-      aws-sdk-core (= 2.2.8)
+      aws-sdk-core (= 2.2.37)
     aws-sdk-v1 (1.66.0)
       json (~> 1.4)
       nokogiri (>= 1.4.4)
@@ -63,34 +61,34 @@ GEM
       rack (>= 0.9.0)
     binding_of_caller (0.7.2)
       debug_inspector (>= 0.0.1)
-    bootstrap-sass (3.3.6)
+    bootstrap-sass (3.3.7)
       autoprefixer-rails (>= 5.2.1)
       sass (>= 3.3.4)
     bootstrap-select-rails (1.6.3)
     bootstrap3-datetimepicker-rails (4.15.35)
       momentjs-rails (>= 2.8.1)
-    bootstrap_form (2.3.0)
+    bootstrap_form (2.4.0)
     builder (3.2.2)
-    byebug (8.2.1)
+    byebug (9.0.5)
     climate_control (0.0.3)
       activesupport (>= 3.0)
     cocaine (0.5.8)
       climate_control (>= 0.0.3, < 1.0)
     coderay (1.1.1)
-    coffee-rails (4.1.0)
+    coffee-rails (4.2.1)
       coffee-script (>= 2.2.0)
-      railties (>= 4.0.0, < 5.0)
+      railties (>= 4.0.0, < 5.2.x)
     coffee-script (2.4.1)
       coffee-script-source
       execjs
     coffee-script-source (1.10.0)
     commit_param_routing (0.0.1)
-    concurrent-ruby (1.0.0)
+    concurrent-ruby (1.0.2)
     debug_inspector (0.0.2)
-    delayed_job (4.1.1)
+    delayed_job (4.1.2)
-      activesupport (>= 3.0, < 5.0)
+      activesupport (>= 3.0, < 5.1)
-    delayed_job_active_record (4.1.0)
+    delayed_job_active_record (4.1.1)
-      activerecord (>= 3.0, < 5)
+      activerecord (>= 3.0, < 5.1)
       delayed_job (>= 3.0, < 5)
     devise (3.5.6)
       bcrypt (~> 3.0)
@@ -99,29 +97,29 @@ GEM
       responders
       thread_safe (~> 0.1)
       warden (~> 1.2.3)
-    devise-async (0.10.1)
+    devise-async (0.10.2)
-      devise (~> 3.2)
+      devise (>= 3.2, < 4.0)
-    devise_invitable (1.5.5)
+    devise_invitable (1.6.1)
-      actionmailer (>= 3.2.6, < 5)
+      actionmailer (>= 3.2.6)
       devise (>= 3.2.0)
     erubis (2.7.0)
-    execjs (2.6.0)
+    execjs (2.7.0)
-    faker (1.6.1)
+    faker (1.6.6)
       i18n (~> 0.5)
     figaro (1.1.1)
       thor (~> 0.14)
-    globalid (0.3.6)
+    globalid (0.3.7)
       activesupport (>= 4.1.0)
     hammerjs-rails (2.0.4)
     i18n (0.7.0)
-    i18n-js (3.0.0.rc11)
+    i18n-js (3.0.0.rc13)
-      i18n (~> 0.6)
+      i18n (~> 0.6, >= 0.6.6)
     introjs-rails (1.0.0)
       sass-rails (>= 3.2)
       thor (~> 0.14)
-    jmespath (1.1.3)
+    jmespath (1.3.1)
-    jquery-rails (4.0.5)
+    jquery-rails (4.1.1)
-      rails-dom-testing (~> 1.0)
+      rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
     jquery-scrollto-rails (1.4.3)
@@ -131,33 +129,35 @@ GEM
       turbolinks
     jquery-ui-rails (5.0.5)
       railties (>= 3.2.16)
-    js_cookie_rails (1.0.1)
+    js_cookie_rails (2.1.2)
       railties (>= 3.1)
     json (1.8.3)
-    kaminari (0.16.3)
+    kaminari (0.17.0)
       actionpack (>= 3.0.0)
       activesupport (>= 3.0.0)
+    lazy_priority_queue (0.1.1)
     little-plugger (1.1.4)
     logging (2.0.0)
       little-plugger (~> 1.1)
       multi_json (~> 1.10)
     loofah (2.0.3)
       nokogiri (>= 1.5.9)
-    mail (2.6.3)
+    mail (2.6.4)
-      mime-types (>= 1.16, < 3)
+      mime-types (>= 1.16, < 4)
     mime-types (1.25.1)
+    mime-types-data (3.2016.0521)
     mimemagic (0.3.0)
     mini_portile2 (2.1.0)
     minitest (5.9.0)
-    minitest-reporters (1.1.10)
+    minitest-reporters (1.1.11)
       ansi
       builder
       minitest (>= 5.0)
       ruby-progressbar
-    momentjs-rails (2.10.6)
+    momentjs-rails (2.11.1)
       railties (>= 3.1)
-    multi_json (1.11.2)
+    multi_json (1.12.1)
-    nested_form_fields (0.7.4)
+    nested_form_fields (0.7.8)
       coffee-rails (>= 3.2.1)
       jquery-rails
       rails (>= 3.2.0)
@@ -165,7 +165,7 @@ GEM
       mini_portile2 (~> 2.1.0)
       pkg-config (~> 1.1.7)
     orm_adapter (0.5.0)
-    paperclip (4.3.2)
+    paperclip (4.3.7)
       activemodel (>= 3.2.0)
       activesupport (>= 3.2.0)
       cocaine (~> 0.5.5)
@@ -176,7 +176,7 @@ GEM
     pg (0.18.4)
     pkg-config (1.1.7)
     powerpack (0.1.1)
-    puma (2.15.3)
+    puma (3.6.0)
     rack (1.6.4)
     rack-test (0.6.3)
       rack (>= 1.0)
@@ -202,8 +202,8 @@ GEM
     rails_12factor (0.0.3)
       rails_serve_static_assets
       rails_stdout_logging
-    rails_serve_static_assets (0.0.4)
+    rails_serve_static_assets (0.0.5)
-    rails_stdout_logging (0.0.4)
+    rails_stdout_logging (0.0.5)
     railties (4.2.5)
       actionpack (= 4.2.5)
       activesupport (= 4.2.5)
@@ -211,13 +211,14 @@ GEM
       thor (>= 0.18.1, < 2.0)
     rainbow (2.1.0)
     rake (11.2.2)
-    rdoc (4.2.0)
+    rdoc (4.2.2)
-    redcarpet (3.3.3)
+      json (~> 1.4)
+    redcarpet (3.3.4)
     remotipart (1.2.1)
     responders (2.2.0)
       railties (>= 4.2.0, < 5.1)
-    rgl (0.5.1)
+    rgl (0.5.2)
-      algorithms (~> 0.6.1)
+      lazy_priority_queue (~> 0.1.0)
       stream (~> 0.5.0)
     roo (2.1.1)
       nokogiri (~> 1)
@@ -227,12 +228,13 @@ GEM
       powerpack (~> 0.1)
       rainbow (>= 1.99.1, < 3.0)
       ruby-progressbar (~> 1.7)
-			ruby-progressbar (1.8.1)
       unicode-display_width (~> 1.0, >= 1.0.1)
-    rubyzip (1.1.7)
+    ruby-graphviz (1.2.2)
-    sass (3.4.20)
+    ruby-progressbar (1.8.1)
-    sass-rails (5.0.4)
+    rubyzip (1.2.0)
-      railties (>= 4.0.0, < 5.0)
+    sass (3.4.22)
+    sass-rails (5.0.6)
+      railties (>= 4.0.0, < 6)
       sass (~> 3.1)
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
@@ -243,38 +245,38 @@ GEM
     shoulda-context (1.2.1)
     shoulda-matchers (3.1.1)
       activesupport (>= 4.0.0)
-    skylight (0.10.0)
+    skylight (0.10.5)
       activesupport (>= 3.0.0)
     spinjs-rails (1.4)
       rails (>= 3.1)
-    sprockets (3.5.2)
+    sprockets (3.7.0)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
-    sprockets-rails (2.3.3)
+    sprockets-rails (3.1.1)
-      actionpack (>= 3.0)
+      actionpack (>= 4.0)
-      activesupport (>= 3.0)
+      activesupport (>= 4.0)
-      sprockets (>= 2.8, < 4.0)
+      sprockets (>= 3.0.0)
     stream (0.5)
     thor (0.19.1)
     thread_safe (0.3.5)
-    tilt (2.0.1)
+    tilt (2.0.5)
-    turbolinks (2.5.3)
+    turbolinks (5.0.1)
-      coffee-rails
+      turbolinks-source (~> 5)
+    turbolinks-source (5.0.0)
     tzinfo (1.2.2)
       thread_safe (~> 0.1)
-    uglifier (2.7.2)
+    uglifier (3.0.1)
-      execjs (>= 0.3.0)
+      execjs (>= 0.3.0, < 3)
-      json (>= 1.8.0)
     underscore-rails (1.8.3)
     unicode-display_width (1.1.0)
     warden (1.2.6)
       rack (>= 1.0)
-    web-console (2.2.1)
+    web-console (2.3.0)
       activemodel (>= 4.0)
       binding_of_caller (>= 0.7.2)
       railties (>= 4.0)
       sprockets-rails (>= 2.0, < 4.0)
-    wicked_pdf (1.0.3)
+    wicked_pdf (1.0.6)
     wkhtmltopdf-heroku (2.12.3.0)
     yomu (0.2.4)
       json (~> 1.8)
@@ -327,6 +329,7 @@ DEPENDENCIES
   rgl
   roo (~> 2.1.0)
   rubocop
+  ruby-graphviz (~> 1.2)
   sass-rails (~> 5.0)
   sdoc (~> 0.4.0)
   shoulda-context

README.md

@@ -154,6 +154,12 @@ Or create new heroku application by executing following command.
 heroku create
 ```
 
+Add graphviz buildpack:
+
+```
+heroku buildpacks:add --index 2 https://github.com/weibeld/heroku-buildpack-graphviz.git
+```
+
 Before pushing to heroku master branch, some environmental variables should be set.
 
 ### Heroku environmental variables

app/assets/stylesheets/projects.scss

@@ -409,14 +409,16 @@ li.module-hover {
 
 // EXPERIMENT PANEL
 
-.experiment-panel{
+.experiment-panel {
   max-width: 650px;
   margin: 0 auto;
   margin-top: 25px;
+  margin-bottom: 15px;
   @include box-shadow(0px 4px 8px 0px $color-dove-gray);
-
 }
-
+.workflowimg-container {
+  margin: 15px 0;
+}
 // SHOW
 .center-btn{
   margin: 0 auto;

app/controllers/canvas_controller.rb

@@ -231,6 +231,9 @@ class CanvasController < ApplicationController
       end
     end
 
+    # Create workflow image
+    @experiment.delay.generate_workflow_img
+
     flash[:success] = t(
       "experiments.canvas.update.success_flash")
     redirect_to canvas_experiment_path(@experiment)

app/controllers/experiments_controller.rb

@@ -63,7 +63,8 @@ class ExperimentsController < ApplicationController
     if @experiment.save
       flash[:success] = t('experiments.update.success_flash',
                           experiment: @experiment.name)
-      redirect_to canvas_experiment_path(@experiment)
+
+      redirect_to project_path(@experiment.project)
     else
       flash[:alert] = t('experiments.update.error_flash')
       redirect_to :back

app/models/experiment.rb

@@ -1,3 +1,5 @@
+require 'graphviz'
+
 class Experiment < ActiveRecord::Base
   include ArchivableModel, SearchableModel
 
@@ -11,6 +13,10 @@ class Experiment < ActiveRecord::Base
   has_many :my_module_groups, inverse_of: :experiment, dependent: :destroy
   has_many :report_elements, inverse_of: :experiment, dependent: :destroy
 
+  has_attached_file :workflowimg
+  validates_attachment :workflowimg,
+                       content_type: { content_type: ["image/png"] }
+
   validates :name,
             presence: true,
             length: { minimum: 4, maximum: 50 },
@@ -195,6 +201,111 @@ class Experiment < ActiveRecord::Base
     return true
   end
 
+  # This method generate the workflow image and saves it as
+  # experiment attachment
+  def generate_workflow_img
+    graph = GraphViz.new(:G,
+                         type: :digraph,
+                         use: :neato)
+
+    graph[:size] = '5,3'
+    graph.node[color: '#d2d2d2',
+               style: :filled,
+               fontcolor: '#555555',
+               shape: 'circle',
+               fontname: 'Arial',
+               fontsize: '16.0']
+
+    graph.edge[color: '#d2d2d2']
+
+    label = 'T'
+    subg = {}
+    if my_module_groups.many?
+      my_module_groups.each_with_index do |group, gindex|
+        subgraph_name = "cluster-#{gindex}"
+        subg[subgraph_name] = graph.subgraph(rank: 'same')
+        group.ordered_modules.each_with_index do |my_module, index|
+          if my_module.outputs.any?
+            parent = subg[subgraph_name]
+                     .add_nodes("#{subgraph_name}-#{index}",
+                                label: label,
+                                pos: "#{my_module.x},-#{my_module.y}!")
+
+            my_module.outputs.each_with_index do |output, i|
+              child_mod = MyModule.find_by_id(output.input_id)
+              child_node = subg[subgraph_name]
+                           .add_nodes("#{subgraph_name}-O#{child_mod.id}-#{i}",
+                                      label: label,
+                                      pos: "#{child_mod.x},-#{child_mod.y}!")
+
+              subg[subgraph_name].add_edges(parent, child_node)
+            end
+          elsif my_module.inputs.any?
+            parent = subg[subgraph_name]
+                     .add_nodes("#{subgraph_name}-#{index}",
+                                label: label,
+                                pos: "#{my_module.x},-#{my_module.y}!")
+
+            my_module.inputs.each_with_index do |input, i|
+              child_mod = MyModule.find_by_id(input.output_id)
+              child_node = subg[subgraph_name]
+                           .add_nodes("#{subgraph_name}-I#{child_mod.id}-#{i}",
+                                      label: label,
+                                      pos: "#{child_mod.x},-#{child_mod.y}!")
+
+              subg[subgraph_name].add_edges(child_node, parent)
+            end
+          end
+        end
+      end
+    else
+      my_module_groups.each do |group|
+        group.ordered_modules.each_with_index do |my_module, index|
+          if my_module.outputs.any?
+            parent = graph.add_nodes("N-#{index}",
+                                     label: label,
+                                     pos: "#{my_module.x},-#{my_module.y}!")
+
+            my_module.outputs.each_with_index do |output, i|
+              child_mod = MyModule.find_by_id(output.input_id)
+              child_node = graph
+                           .add_nodes("N-O#{child_mod.id}-#{i}",
+                                      label: label,
+                                      pos: "#{child_mod.x},-#{child_mod.y}!")
+              graph.add_edges(parent, child_node)
+            end
+          elsif my_module.inputs.any?
+            parent = graph.add_nodes("N-#{index}",
+                                     label: label,
+                                     pos: "#{my_module.x},-#{my_module.y}!")
+            my_module.inputs.each_with_index do |input, i|
+              child_mod = MyModule.find_by_id(input.output_id)
+              child_node = graph
+                           .add_nodes("N-I#{child_mod.id}-#{i}",
+                                      label: label,
+                                      pos: "#{child_mod.x},-#{child_mod.y}!")
+              graph.add_edges(child_node, parent)
+            end
+          end
+        end
+      end
+    end
+
+    file_location = Tempfile.open(['wimg', '.png'],
+                                  Rails.root.join('tmp'))
+
+    graph.output(png: file_location.path)
+
+    begin
+      file = File.open(file_location)
+      self.workflowimg = file
+      file.close
+      save!
+    rescue => ex
+      logger.error ex.message
+    end
+  end
+
   private
 
   # Archive all modules. Receives an array of module integer IDs.

app/models/organization.rb

@@ -268,6 +268,7 @@ class Organization < ActiveRecord::Base
         end
       end
     end
+    # project.experiments.each |experiment|
     self.space_taken = [st, MINIMAL_ORGANIZATION_SPACE_TAKEN].max
     Rails::logger.info "Organization #{self.id}: " +
       "space (re)calculated to: " +

app/models/project.rb

@@ -105,7 +105,7 @@ class Project < ActiveRecord::Base
   end
 
   def active_experiments
-    experiments.is_archived(false)
+    experiments.is_archived(false).order('created_at DESC')
   end
 
   def archived_experiments

app/views/projects/show.html.erb

@@ -16,10 +16,12 @@
     <% end %>
   </div>
 </div>
-<% @project.active_experiments.each do |experiment| %>
+<div class="row">
-  <%= render partial: 'projects/show/experiment',
+  <% @project.active_experiments.each_with_index do |experiment, index| %>
-             locals: { experiment: experiment } %>
+    <%= render partial: 'projects/show/experiment',
-
+               locals: { experiment: experiment } %>
-<% end %>
 
+    <%= content_tag(:div, '', class: 'clearfix visible-lg-block') if (index + 1) % 2 == 0 %>
+  <% end %>
+</div>
 <%= javascript_include_tag("projects/show") %>

app/views/projects/show/_experiment.html.erb

@@ -2,10 +2,9 @@
   <div class="panel panel-default experiment-panel"
        data-id="<%= experiment.id %>">
     <div class="panel-heading">
-      <h3 class="panel-title"><%= link_to experiment.name, canvas_experiment_path(experiment) %></h3>
 
-      <span class="dropdown pull-right">
+      <div class="dropdown pull-right">
-        <button class="btn btn-default dropdown-toggle"
+        <button class="btn btn-link dropdown-toggle"
                 type="button"
                 id="exActionsMenu-<%= experiment.id %>"
                 data-toggle="dropdown"
@@ -29,12 +28,22 @@
                         data: { confirm: t('experiments.canvas.archive_confirm') } %></li>
           <% end %>
         </ul>
-      </span>
+      </div>
+
+      <h3 class="panel-title"><%= link_to experiment.name, canvas_experiment_path(experiment) %></h3>
+
     </div>
     <div class="panel-body">
+      <% if experiment.workflowimg? %>
+        <div class="workflowimg-container">
+          <%= link_to image_tag(experiment.workflowimg.expiring_url(30),
+                                class: 'img-responsive center-block'),
+                      canvas_experiment_path(experiment) %>
+        </div>
+      <% end %>
       <span>
         <span class="glyphicon glyphicon-calendar" aria-hidden="true"></span>
-        <%= localize(experiment.created_at, format: t('time.formats.full_date')) %>
+        <%= localize(experiment.created_at, format: t('time.formats.full_date')) %> - <%= localize(experiment.updated_at, format: t('time.formats.full_date')) %>
       </span>
       <p><%= experiment.description %></p>
     </div>

db/migrate/20160808083040_add_attachment_workflowimg_to_experiments.rb

@@ -0,0 +1,9 @@
+class AddAttachmentWorkflowimgToExperiments < ActiveRecord::Migration
+  def self.up
+    add_attachment :experiments, :workflowimg
+  end
+
+  def self.down
+    remove_attachment :experiments, :workflowimg
+  end
+end

db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20160803082801) do
+ActiveRecord::Schema.define(version: 20160808083040) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -138,18 +138,22 @@ ActiveRecord::Schema.define(version: 20160803082801) do
   add_index "delayed_jobs", ["queue"], name: "delayed_jobs_queue", using: :btree
 
   create_table "experiments", force: :cascade do |t|
-    t.string   "name",                                null: false
+    t.string   "name",                                     null: false
     t.text     "description"
-    t.integer  "project_id",                          null: false
+    t.integer  "project_id",                               null: false
-    t.integer  "created_by_id",                       null: false
+    t.integer  "created_by_id",                            null: false
-    t.integer  "last_modified_by_id",                 null: false
+    t.integer  "last_modified_by_id",                      null: false
-    t.boolean  "archived",            default: false, null: false
+    t.boolean  "archived",                 default: false, null: false
     t.integer  "archived_by_id"
     t.datetime "archived_on"
     t.integer  "restored_by_id"
     t.datetime "restored_on"
-    t.datetime "created_at",                          null: false
+    t.datetime "created_at",                               null: false
-    t.datetime "updated_at",                          null: false
+    t.datetime "updated_at",                               null: false
+    t.string   "workflowimg_file_name"
+    t.string   "workflowimg_content_type"
+    t.integer  "workflowimg_file_size"
+    t.datetime "workflowimg_updated_at"
   end
 
   add_index "experiments", ["archived_by_id"], name: "index_experiments_on_archived_by_id", using: :btree