From f7c865974da5a04ab2da7de5aaca6c0d8efe8f1d Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Thu, 25 Mar 2021 17:42:57 +0100
Subject: [PATCH] Switch to graphviz gem [SCI-5596]

---
 Gemfile                                       |  2 +-
 Gemfile.lock                                  | 12 +++--
 app/models/user.rb                            |  1 -
 .../generate_workflow_image_service.rb        | 47 ++++++++++---------
 4 files changed, 36 insertions(+), 26 deletions(-)

diff --git a/Gemfile b/Gemfile
index 94e51f529..0c6fe59d3 100644
--- a/Gemfile
+++ b/Gemfile
@@ -97,7 +97,7 @@ gem 'rufus-scheduler', '~> 3.5'
 
 gem 'discard', '~> 1.0'
 
-gem 'ruby-graphviz', '~> 1.2' # Graphviz for rails
+gem 'graphviz'
 gem 'tinymce-rails', '~> 4.9.10' # Rich text editor - SEE BELOW
 # Any time you update tinymce-rails Gem, also update the cache_suffix parameter
 # in sitewide/tiny_mce.js - to prevent browsers from loading old, cached .js
diff --git a/Gemfile.lock b/Gemfile.lock
index 4f665e982..43a3f6eaa 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -295,6 +295,8 @@ GEM
     gherkin (5.1.0)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
+    graphviz (1.2.1)
+      process-pipeline
     hammerjs-rails (2.0.8)
     hashdiff (1.0.1)
     hashie (4.1.0)
@@ -416,6 +418,12 @@ GEM
       activerecord (>= 5.2)
       activesupport (>= 5.2)
     polyglot (0.3.5)
+    process-group (1.2.3)
+      process-terminal (~> 0.2.0)
+    process-pipeline (1.0.2)
+      process-group
+    process-terminal (0.2.0)
+      ffi
     pry (0.13.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
@@ -529,8 +537,6 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 0.82.0)
-    ruby-graphviz (1.2.5)
-      rexml
     ruby-progressbar (1.11.0)
     ruby-vips (2.0.17)
       ffi (~> 1.9)
@@ -656,6 +662,7 @@ DEPENDENCIES
   faker
   fastimage
   figaro
+  graphviz
   hammerjs-rails
   httparty (~> 0.17.3)
   i18n-js (~> 3.6)
@@ -702,7 +709,6 @@ DEPENDENCIES
   rubocop (= 0.83.0)
   rubocop-performance
   rubocop-rails
-  ruby-graphviz (~> 1.2)
   rubyzip
   rufus-scheduler (~> 3.5)
   sanitize (~> 5.2)
diff --git a/app/models/user.rb b/app/models/user.rb
index b0d149ff9..44fea297f 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -10,7 +10,6 @@ class User < ApplicationRecord
   include InputSanitizeHelper
   include ActiveStorageConcerns
 
-  acts_as_token_authenticatable
   devise :invitable, :confirmable, :database_authenticatable, :registerable,
          :async, :recoverable, :rememberable, :trackable, :validatable,
          :timeoutable, :omniauthable, :lockable,
diff --git a/app/services/experiments/generate_workflow_image_service.rb b/app/services/experiments/generate_workflow_image_service.rb
index b8c5ddb1f..47f83019e 100644
--- a/app/services/experiments/generate_workflow_image_service.rb
+++ b/app/services/experiments/generate_workflow_image_service.rb
@@ -9,9 +9,7 @@ module Experiments
 
     def initialize(experiment:)
       @exp = experiment
-      graph_params = {
-        type: :digraph,
-        use: :neato,
+      @graph_params = {
         inputscale: 3,
         size: '2,2',
         pad: '0.4',
@@ -22,15 +20,20 @@ module Experiments
         bgcolor: Constants::COLOR_CONCRETE,
         mode: 'ipsep'
       }
-      @graph = GraphViz.new(:G, graph_params)
-      @graph.node[color: Constants::COLOR_VOLCANO,
-                  style: :filled,
-                  fontcolor: Constants::COLOR_VOLCANO,
-                  shape: 'circle',
-                  fontname: 'Arial',
-                  fontsize: '16.0']
+      @node_params = {
+        color: Constants::COLOR_VOLCANO,
+        style: :filled,
+        fontcolor: Constants::COLOR_VOLCANO,
+        shape: 'circle',
+        fontname: 'Arial',
+        fontsize: '16.0'
+      }
+      @edge_params = {
+        color: Constants::COLOR_VOLCANO,
+        penwidth: '3.0'
+      }
 
-      @graph.edge[color: Constants::COLOR_VOLCANO, penwidth: '3.0']
+      @graph = Graphviz::Graph.new('G', @graph_params)
       @errors = []
     end
 
@@ -48,18 +51,18 @@ module Experiments
 
     def draw_diagram
       # Draw grouped modules
-      subg = {}
       @exp.my_module_groups.each_with_index do |group, gindex|
         subgraph_id = "cluster-#{gindex}"
-        subg[subgraph_id] = @graph.subgraph
         nodes = {}
 
         group.my_modules.workflow_ordered.each_with_index do |my_module, index|
           # draw nodes
-          node = subg[subgraph_id].add_nodes(
+          node = @graph.add_node(
             "#{subgraph_id}-#{index}",
-            label: '',
-            pos: "#{my_module.x / 10},-#{my_module.y / 10}!"
+            @node_params.merge(
+              label: '',
+              pos: "#{my_module.x / 10},-#{my_module.y / 10}!"
+            )
           )
           nodes[my_module.id] = node
         end
@@ -69,17 +72,19 @@ module Experiments
           m.outputs.each do |output|
             parent_node = nodes[m.id]
             child_node = nodes[output.input_id]
-            subg[subgraph_id].add_edges(parent_node, child_node)
+            parent_node.connect(child_node, @edge_params)
           end
         end
       end
 
       # Draw orphan nodes
       @exp.my_modules.without_group.each do |my_module|
-        @graph.subgraph.add_nodes(
+        @graph.add_node(
           "Orphan-#{my_module.id}",
-          label: '',
-          pos: "#{my_module.x / 10},-#{my_module.y / 10}!"
+          @node_params.merge(
+            label: '',
+            pos: "#{my_module.x / 10},-#{my_module.y / 10}!"
+          )
         )
       end
     end
@@ -87,7 +92,7 @@ module Experiments
     def save_file
       file = Tempfile.open(%w(wimg .png), Rails.root.join('tmp'))
       begin
-        @graph.output(png: file.path)
+        Graphviz.output(@graph, path: file.path, format: 'png', dot: 'neato')
         file.rewind
         @exp.workflowimg.attach(io: file, filename: File.basename(file.path))
       ensure