From e1b3dcc2bade24c4f2339f0f96ad08341fbd10a4 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Mon, 27 Feb 2017 13:53:46 +0100
Subject: [PATCH 01/19] adds enum extends to report element part of SCI-1003

---
 app/models/report_element.rb   | 19 +------------------
 config/initializers/extends.rb | 17 +++++++++++++++++
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index 131d3d528..9c5e2345b 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -1,22 +1,5 @@
 class ReportElement < ActiveRecord::Base
-  enum type_of: {
-    project_header: 0,
-    my_module: 1,
-    step: 2,
-    result_asset: 3,
-    result_table: 4,
-    result_text: 5,
-    my_module_activity: 6,
-    my_module_samples: 7,
-    step_checklist: 8,
-    step_asset: 9,
-    step_table: 10,
-    step_comments: 11,
-    result_comments: 12,
-    project_activity: 13, # TODO
-    project_samples: 14, # TODO
-    experiment: 15
-  }
+  enum type_of: Extends::REPORT_ELEMENT_TYPES
 
   # This is only used by certain elements
   enum sort_order: {
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index 7883381d9..9b9728b46 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -17,4 +17,21 @@ class Extends
 
   TASKS_STATES = { uncompleted: 0,
                    completed: 1 }
+
+  REPORT_ELEMENT_TYPES = { project_header: 0,
+                           my_module: 1,
+                           step: 2,
+                           result_asset: 3,
+                           result_table: 4,
+                           result_text: 5,
+                           my_module_activity: 6,
+                           my_module_samples: 7,
+                           step_checklist: 8,
+                           step_asset: 9,
+                           step_table: 10,
+                           step_comments: 11,
+                           result_comments: 12,
+                           project_activity: 13, # TODO
+                           project_samples: 14, # TODO
+                           experiment: 15 }
 end

From 5c2e9a4b0483b0013b7cab27cf828e01d17aea04 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 8 Mar 2017 14:14:03 +0100
Subject: [PATCH 02/19] adds extends and fixes report methods

---
 app/controllers/concerns/report_actions.rb    | 166 ++++++++
 app/controllers/reports_controller.rb         | 357 ++++--------------
 app/helpers/reports_helper.rb                 | 143 +++----
 app/models/report_element.rb                  |  49 +--
 ... _my_module_result_asset_element.html.erb} |   0
 ... _my_module_result_table_element.html.erb} |   0
 ...> _my_module_result_text_element.html.erb} |   0
 ...l.erb => _my_module_step_element.html.erb} |   0
 .../elements/_project_header_element.html.erb |   2 +-
 config/initializers/extends.rb                |   3 +-
 config/initializers/extends/report_extends.rb | 193 ++++++++++
 11 files changed, 505 insertions(+), 408 deletions(-)
 create mode 100644 app/controllers/concerns/report_actions.rb
 rename app/views/reports/elements/{_result_asset_element.html.erb => _my_module_result_asset_element.html.erb} (100%)
 rename app/views/reports/elements/{_result_table_element.html.erb => _my_module_result_table_element.html.erb} (100%)
 rename app/views/reports/elements/{_result_text_element.html.erb => _my_module_result_text_element.html.erb} (100%)
 rename app/views/reports/elements/{_step_element.html.erb => _my_module_step_element.html.erb} (100%)
 create mode 100644 config/initializers/extends/report_extends.rb

diff --git a/app/controllers/concerns/report_actions.rb b/app/controllers/concerns/report_actions.rb
new file mode 100644
index 000000000..936b6cd73
--- /dev/null
+++ b/app/controllers/concerns/report_actions.rb
@@ -0,0 +1,166 @@
+module ReportActions
+  extend ActiveSupport::Concern
+
+  def in_params?(val)
+    params.include? val and params[val] == '1'
+  end
+
+  def generate_new_el(hide)
+    el = {}
+    el[:html] = render_to_string(
+      partial: 'reports/elements/new_element.html.erb',
+      locals: { hide: hide }
+    )
+    el[:children] = []
+    el[:new_element] = true
+    el
+  end
+
+  def generate_el(partial, locals)
+    el = {}
+    el[:html] = render_to_string(
+      partial: partial,
+      locals: locals
+    )
+    el[:children] = []
+    el[:new_element] = false
+    el
+  end
+
+  def generate_project_contents_json
+    res = []
+    if params.include? :modules
+      modules = (params[:modules].select { |_, p| p == '1' })
+                .keys
+                .collect(&:to_i)
+
+      # Get unique experiments from given modules
+      experiments = MyModule.where(id: modules).map(&:experiment).uniq
+      experiments.each do |experiment|
+        res << generate_new_el(false)
+        el = generate_el(
+          'reports/elements/experiment_element.html.erb',
+          experiment: experiment
+        )
+        el[:children] = generate_experiment_contents_json(experiment, modules)
+        res << el
+      end
+    end
+    res << generate_new_el(false)
+    res
+  end
+
+  def generate_experiment_contents_json(experiment, selected_modules)
+    res = []
+    experiment.my_modules.each do |my_module|
+      next unless selected_modules.include?(my_module.id)
+
+      res << generate_new_el(false)
+      el = generate_el(
+        'reports/elements/my_module_element.html.erb',
+        my_module: my_module
+      )
+      el[:children] = generate_module_contents_json(my_module)
+      res << el
+    end
+    res << generate_new_el(false)
+    res
+  end
+
+  def generate_module_contents_json(my_module)
+    res = []
+    ReportExtends::MODULE_CONTENTS.each do |contents|
+      protocol = contents.element == :step ? my_module.protocol.present? : true
+      next unless in_params?("module_#{contents.element}".to_sym) && protocol
+      res << generate_new_el(false)
+      if contents.children
+        contents.collection(my_module).each do |report_el|
+          el = generate_el(
+            "reports/elements/my_module_#{contents
+                                          .element
+                                          .to_s
+                                          .singularize}_element.html.erb",
+            contents.parse_locals([report_el])
+          )
+          el[:children] = generate_step_contents_json(report_el) if contents.element == :step
+          el[:children] = generate_result_contents_json(report_el)
+          res << el
+        end
+      else
+        file_name = contents.element.to_s.singularize
+        file_name = contents.element if contents.element == :samples
+        res << generate_el(
+          "reports/elements/my_module_#{file_name}_element.html.erb",
+          contents.parse_locals([my_module, :asc])
+        )
+      end
+    end
+    res << generate_new_el(false)
+    res
+  end
+
+  def generate_step_contents_json(step)
+    res = []
+    if in_params? :step_checklists then
+      step.checklists.each do |checklist|
+        res << generate_new_el(false)
+        res << generate_el(
+          'reports/elements/step_checklist_element.html.erb',
+          { checklist: checklist }
+        )
+      end
+    end
+    if in_params? :step_assets then
+      step.assets.each do |asset|
+        res << generate_new_el(false)
+        res << generate_el(
+          'reports/elements/step_asset_element.html.erb',
+          { asset: asset }
+        )
+      end
+    end
+    if in_params? :step_tables then
+      step.tables.each do |table|
+        res << generate_new_el(false)
+        res << generate_el(
+          'reports/elements/step_table_element.html.erb',
+          { table: table }
+        )
+      end
+    end
+    if in_params? :step_comments then
+      res << generate_new_el(false)
+      res << generate_el(
+        'reports/elements/step_comments_element.html.erb',
+        { step: step, order: :asc }
+      )
+    end
+    res << generate_new_el(false)
+    res
+  end
+
+  def generate_result_contents_json(result)
+    res = []
+    if in_params? :result_comments
+      res << generate_new_el(true)
+      res << generate_el(
+        'reports/elements/result_comments_element.html.erb',
+        { result: result, order: :asc }
+      )
+    else
+      res << generate_new_el(false)
+    end
+    res
+  end
+
+  def elements_empty?(elements)
+    return true if elements.blank? || elements.count == 0
+
+    if elements.count == 1
+      el = elements[0]
+      return true if el.include?(:new_element) && el[:new_element]
+      return false
+    end
+    false
+  end
+end
diff --git a/app/controllers/reports_controller.rb b/app/controllers/reports_controller.rb
index 1f5cb5ef8..9c33a4512 100644
--- a/app/controllers/reports_controller.rb
+++ b/app/controllers/reports_controller.rb
@@ -1,8 +1,9 @@
 class ReportsController < ApplicationController
   include TeamsHelper
+  include ReportActions
   # Ignore CSRF protection just for PDF generation (because it's
   # used via target='_blank')
-  protect_from_forgery with: :exception, :except => :generate
+  protect_from_forgery with: :exception, except: :generate
 
   before_action :load_vars, only: [
     :edit,
@@ -28,7 +29,7 @@ class ReportsController < ApplicationController
     :result_contents
   ]
 
-  before_action :check_view_permissions, only: [:index]
+  before_action :check_view_permissions, only: :index
   before_action :check_create_permissions, only: [
     :new,
     :create,
@@ -46,9 +47,9 @@ class ReportsController < ApplicationController
     :step_contents,
     :result_contents
   ]
-  before_action :check_destroy_permissions, only: [:destroy]
+  before_action :check_destroy_permissions, only: :destroy
 
-  layout "fluid"
+  layout 'fluid'
 
   # Index showing all reports of a single project
   def index
@@ -73,7 +74,7 @@ class ReportsController < ApplicationController
     @report.user = current_user
     @report.last_modified_by = current_user
 
-    if continue and @report.save_with_contents(report_contents)
+    if continue && @report.save_with_contents(report_contents)
       # record an activity
       Activity.create(
         type_of: :create_report,
@@ -86,15 +87,15 @@ class ReportsController < ApplicationController
         )
       )
       respond_to do |format|
-        format.json {
+        format.json do
           render json: { url: project_reports_path(@project) }, status: :ok
-        }
+        end
       end
     else
       respond_to do |format|
-        format.json {
+        format.json do
           render json: @report.errors, status: :unprocessable_entity
-        }
+        end
       end
     end
   end
@@ -118,7 +119,7 @@ class ReportsController < ApplicationController
     @report.last_modified_by = current_user
     @report.assign_attributes(report_params)
 
-    if continue and @report.save_with_contents(report_contents)
+    if continue && @report.save_with_contents(report_contents)
       # record an activity
       Activity.create(
         type_of: :edit_report,
@@ -131,25 +132,21 @@ class ReportsController < ApplicationController
         )
       )
       respond_to do |format|
-        format.json {
+        format.json do
           render json: { url: project_reports_path(@project) }, status: :ok
-        }
+        end
       end
     else
       respond_to do |format|
-        format.json {
+        format.json do
           render json: @report.errors, status: :unprocessable_entity
-        }
+        end
       end
     end
   end
 
   # Destroy multiple entries action
   def destroy
-    unless params.include? :report_ids
-      render_404
-    end
-
     begin
       report_ids = JSON.parse(params[:report_ids])
     rescue
@@ -158,21 +155,19 @@ class ReportsController < ApplicationController
 
     report_ids.each do |report_id|
       report = Report.find_by_id(report_id)
-
-      if report.present?
-        # record an activity
-        Activity.create(
-          type_of: :delete_report,
-          project: report.project,
-          user: current_user,
-          message: I18n.t(
-            'activities.delete_report',
-            user: current_user.full_name,
-            report: report.name
-          )
+      next unless report.present?
+      # record an activity
+      Activity.create(
+        type_of: :delete_report,
+        project: report.project,
+        user: current_user,
+        message: I18n.t(
+          'activities.delete_report',
+          user: current_user.full_name,
+          report: report.name
         )
-        report.destroy
-      end
+      )
+      report.destroy
     end
 
     redirect_to project_reports_path(@project)
@@ -182,15 +177,13 @@ class ReportsController < ApplicationController
   # Currently, only .PDF is supported
   def generate
     respond_to do |format|
-      format.pdf {
+      format.pdf do
         @html = params[:html]
-        if @html.blank? then
-          @html = "<h1>No content</h1>"
-        end
-        render pdf: "report",
+        @html = '<h1>No content</h1>' if @html.blank?
+        render pdf: 'report',
           header: { right: '[page] of [topage]' },
-          template: "reports/report.pdf.erb"
-      }
+          template: 'reports/report.pdf.erb'
+      end
     end
   end
 
@@ -209,33 +202,32 @@ class ReportsController < ApplicationController
       @url = project_report_path(@project, @report, format: :json)
     end
 
-    if !params.include? :contents
-      render_403 and return
-    end
+    render_403 and return unless params.include? :contents
+
     @report_contents = params[:contents]
 
     respond_to do |format|
-      format.json {
+      format.json do
         render json: {
-          html: render_to_string({
-            partial: "reports/new/modal/save.html.erb"
-          })
+          html: render_to_string(
+            partial: 'reports/new/modal/save.html.erb'
+          )
         }
-      }
+      end
     end
   end
 
   # Modal for adding contents into project element
   def project_contents_modal
     respond_to do |format|
-      format.json {
+      format.json do
         render json: {
-          html: render_to_string({
-            partial: "reports/new/modal/project_contents.html.erb",
+          html: render_to_string(
+            partial: 'reports/new/modal/project_contents.html.erb',
             locals: { project: @project }
-            })
+          )
         }
-      }
+      end
     end
   end
 
@@ -274,7 +266,7 @@ class ReportsController < ApplicationController
         format.json do
           render json: {
             html: render_to_string(
-              partial: "reports/new/modal/module_contents.html.erb",
+              partial: 'reports/new/modal/module_contents.html.erb',
               locals: { project: @project, my_module: my_module }
             )
           }
@@ -289,18 +281,18 @@ class ReportsController < ApplicationController
 
     respond_to do |format|
       if step.blank?
-        format.json {
+        format.json do
           render json: {}, status: :not_found
-        }
+        end
       else
-        format.json {
+        format.json do
           render json: {
-            html: render_to_string({
-              partial: "reports/new/modal/step_contents.html.erb",
+            html: render_to_string(
+              partial: 'reports/new/modal/step_contents.html.erb',
               locals: { project: @project, step: step }
-            })
+            )
           }
-        }
+        end
       end
     end
   end
@@ -311,18 +303,18 @@ class ReportsController < ApplicationController
 
     respond_to do |format|
       if result.blank?
-        format.json {
+        format.json do
           render json: {}, status: :not_found
-        }
+        end
       else
-        format.json {
+        format.json do
           render json: {
-            html: render_to_string({
-              partial: "reports/new/modal/result_contents.html.erb",
+            html: render_to_string(
+              partial: 'reports/new/modal/result_contents.html.erb',
               locals: { project: @project, result: result }
-            })
+            )
           }
-        }
+        end
       end
     end
   end
@@ -384,12 +376,12 @@ class ReportsController < ApplicationController
         if elements_empty? elements
           format.json { render json: {}, status: :no_content }
         else
-          format.json {
+          format.json do
             render json: {
               status: :ok,
               elements: elements
             }
-          }
+          end
         end
       end
     end
@@ -442,242 +434,31 @@ class ReportsController < ApplicationController
 
   private
 
-  def in_params?(val)
-    params.include? val and params[val] == "1"
-  end
-
-  def generate_new_el(hide)
-    el = {}
-    el[:html] = render_to_string({
-        partial: "reports/elements/new_element.html.erb",
-        locals: { hide: hide }
-      })
-    el[:children] = []
-    el[:new_element] = true
-    el
-  end
-
-  def generate_el(partial, locals)
-    el = {}
-    el[:html] = render_to_string({
-      partial: partial,
-      locals: locals
-    })
-    el[:children] = []
-    el[:new_element] = false
-    el
-  end
-
-  def generate_project_contents_json
-    res = []
-    if params.include? :modules
-      modules = (params[:modules].select { |_, p| p == '1' })
-                .keys
-                .collect(&:to_i)
-
-      # Get unique experiments from given modules
-      experiments = MyModule.where(id: modules).map(&:experiment).uniq
-      experiments.each do |experiment|
-        res << generate_new_el(false)
-        el = generate_el(
-          'reports/elements/experiment_element.html.erb',
-          experiment: experiment
-        )
-        el[:children] = generate_experiment_contents_json(experiment, modules)
-        res << el
-      end
-    end
-    res << generate_new_el(false)
-    res
-  end
-
-  def generate_experiment_contents_json(experiment, selected_modules)
-    res = []
-    experiment.my_modules.each do |my_module|
-      next unless selected_modules.include?(my_module.id)
-
-      res << generate_new_el(false)
-      el = generate_el(
-        'reports/elements/my_module_element.html.erb',
-        my_module: my_module
-      )
-      el[:children] = generate_module_contents_json(my_module)
-      res << el
-    end
-    res << generate_new_el(false)
-    res
-  end
-
-  def generate_module_contents_json(my_module)
-    res = []
-    if (in_params? :module_steps) && my_module.protocol.present? then
-      my_module.protocol.completed_steps.each do |step|
-        res << generate_new_el(false)
-        el = generate_el(
-          "reports/elements/step_element.html.erb",
-          { step: step }
-        )
-        el[:children] = generate_step_contents_json(step)
-        res << el
-      end
-    end
-    if in_params? :module_result_assets then
-      (my_module.results.select { |r| r.is_asset && r.active? }).each do |result_asset|
-        res << generate_new_el(false)
-        el = generate_el(
-          "reports/elements/result_asset_element.html.erb",
-          { result: result_asset }
-        )
-        el[:children] = generate_result_contents_json(result_asset)
-        res << el
-      end
-    end
-    if in_params? :module_result_tables then
-      (my_module.results.select { |r| r.is_table && r.active? }).each do |result_table|
-        res << generate_new_el(false)
-        el = generate_el(
-          "reports/elements/result_table_element.html.erb",
-          { result: result_table }
-        )
-        el[:children] = generate_result_contents_json(result_table)
-        res << el
-      end
-    end
-    if in_params? :module_result_texts then
-      (my_module.results.select { |r| r.is_text && r.active? }).each do |result_text|
-        res << generate_new_el(false)
-        el = generate_el(
-          "reports/elements/result_text_element.html.erb",
-          result: result_text
-        )
-        el[:children] = generate_result_contents_json(result_text)
-        res << el
-      end
-    end
-    if in_params? :module_activity then
-      res << generate_new_el(false)
-      res << generate_el(
-        "reports/elements/my_module_activity_element.html.erb",
-        { my_module: my_module, order: :asc }
-      )
-    end
-    if in_params? :module_samples then
-      res << generate_new_el(false)
-      res << generate_el(
-        "reports/elements/my_module_samples_element.html.erb",
-        { my_module: my_module, order: :asc }
-      )
-    end
-    res << generate_new_el(false)
-    res
-  end
-
-  def generate_step_contents_json(step)
-    res = []
-    if in_params? :step_checklists then
-      step.checklists.each do |checklist|
-        res << generate_new_el(false)
-        res << generate_el(
-          "reports/elements/step_checklist_element.html.erb",
-          { checklist: checklist }
-        )
-      end
-    end
-    if in_params? :step_assets then
-      step.assets.each do |asset|
-        res << generate_new_el(false)
-        res << generate_el(
-          "reports/elements/step_asset_element.html.erb",
-          { asset: asset }
-        )
-      end
-    end
-    if in_params? :step_tables then
-      step.tables.each do |table|
-        res << generate_new_el(false)
-        res << generate_el(
-          "reports/elements/step_table_element.html.erb",
-          { table: table }
-        )
-      end
-    end
-    if in_params? :step_comments then
-      res << generate_new_el(false)
-      res << generate_el(
-        "reports/elements/step_comments_element.html.erb",
-        { step: step, order: :asc }
-      )
-    end
-    res << generate_new_el(false)
-    res
-  end
-
-  def generate_result_contents_json(result)
-    res = []
-    if in_params? :result_comments then
-      res << generate_new_el(true)
-      res << generate_el(
-        "reports/elements/result_comments_element.html.erb",
-        { result: result, order: :asc }
-      )
-    else
-      res << generate_new_el(false)
-    end
-    res
-  end
-
-  def elements_empty?(elements)
-    if elements.blank?
-      return true
-    elsif elements.count == 0 then
-      return true
-    elsif elements.count == 1
-      el = elements[0]
-      if el.include? :new_element and el[:new_element]
-        return true
-      else
-        return false
-      end
-    end
-    return false
-  end
-
   def load_vars
     @report = Report.find_by_id(params[:id])
-
-    unless @report
-      render_404
-    end
+    render_404 unless @report
   end
 
   def load_vars_nested
     @project = Project.find_by_id(params[:project_id])
-
-    unless @project
-      render_404
-    end
+    render_404 unless @project
   end
 
   def check_view_permissions
-    unless can_view_reports(@project)
-      render_403
-    end
+    render_403 unless can_view_reports(@project)
   end
 
   def check_create_permissions
-    unless can_create_new_report(@project)
-      render_403
-    end
+    render_403 unless can_create_new_report(@project)
   end
 
   def check_destroy_permissions
-    unless can_delete_reports(@project)
-      render_403
-    end
+    render_403 unless can_delete_reports(@project)
+    render_404 unless params.include? :report_ids
   end
 
   def report_params
-    params.require(:report).permit(:name, :description, :grouped_by, :report_contents)
+    params.require(:report)
+          .permit(:name, :description, :grouped_by, :report_contents)
   end
-
 end
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 091fe00d8..437340319 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -1,99 +1,72 @@
 module ReportsHelper
+  def render_new_element(hide)
+    render partial: 'reports/elements/new_element.html.erb',
+          locals: { hide: hide }
+  end
 
-def render_new_element(hide)
-  render partial: "reports/elements/new_element.html.erb",
-        locals: { hide: hide }
-end
+  def render_report_element(element, provided_locals = nil)
+    children_html = ''.html_safe
 
-def render_report_element(element, provided_locals = nil)
-  children_html = ''.html_safe
-
-  # First, recursively render element's children
-  if element.comments? || element.project_header?
-    # Render no children
-  elsif element.result?
-    # Special handling for result comments
-    if element.has_children?
-      children_html.safe_concat render_new_element(true)
-      element.children.each do |child|
-        children_html.safe_concat render_report_element(child, provided_locals)
+    # First, recursively render element's children
+    if element.comments? || element.project_header?
+      # Render no children
+    elsif element.result?
+      # Special handling for result comments
+      if element.has_children?
+        children_html.safe_concat render_new_element(true)
+        element.children.each do |child|
+          children_html.safe_concat render_report_element(child, provided_locals)
+        end
+      else
+        children_html.safe_concat render_new_element(false)
       end
     else
+      if element.has_children?
+        element.children.each do |child|
+          children_html.safe_concat render_new_element(false)
+          children_html.safe_concat render_report_element(child, provided_locals)
+        end
+      end
       children_html.safe_concat render_new_element(false)
     end
-  else
-    if element.has_children?
-      element.children.each do |child|
-        children_html.safe_concat render_new_element(false)
-        children_html.safe_concat render_report_element(child, provided_locals)
-      end
+
+    file_name = element.type_of
+    file_name = "my_module_#{element.type_of}" if element.type_of.in? %w(step result_asset result_table result_text)
+    view = "reports/elements/#{file_name}_element.html.erb"
+
+    locals = provided_locals.nil? ? {} : provided_locals.clone
+    locals[:children] = children_html
+
+    # ReportExtends is located in config/initializers/extends/report_extends.rb
+    ReportElement.type_ofs.keys.each do |type|
+      next unless element.send("#{type}?")
+      local_sym = type.split('_').last.to_sym
+      local_sym = type.split('_').first.to_sym if type.in? ReportExtends::RESULT_ELEMENTS
+      local_sym = :my_module if type.in? ReportExtends::MY_MODULE_ELEMENTS
+      locals[local_sym] = element.element_reference
+      locals[:order] = element.sort_order if type.in? ReportExtends::SORTED_ELEMENTS
     end
-    children_html.safe_concat render_new_element(false)
+
+    (render partial: view, locals: locals).html_safe
   end
 
-  view = "reports/elements/#{element.type_of}_element.html.erb"
-
-  locals = provided_locals.nil? ? {} : provided_locals.clone
-  locals[:children] = children_html
-
-  if element.project_header?
-    locals[:project] = element.element_reference
-  elsif element.experiment?
-    locals[:experiment] = element.element_reference
-  elsif element.my_module?
-    locals[:my_module] = element.element_reference
-  elsif element.step?
-    locals[:step] = element.element_reference
-  elsif element.result_asset?
-    locals[:result] = element.element_reference
-  elsif element.result_table?
-    locals[:result] = element.element_reference
-  elsif element.result_text?
-    locals[:result] = element.element_reference
-  elsif element.my_module_activity?
-    locals[:my_module] = element.element_reference
-    locals[:order] = element.sort_order
-  elsif element.my_module_samples?
-    locals[:my_module] = element.element_reference
-    locals[:order] = element.sort_order
-  elsif element.step_checklist?
-    locals[:checklist] = element.element_reference
-  elsif element.step_asset?
-    locals[:asset] = element.element_reference
-  elsif element.step_table?
-    locals[:table] = element.element_reference
-  elsif element.step_comments?
-    locals[:step] = element.element_reference
-    locals[:order] = element.sort_order
-  elsif element.result_comments?
-    locals[:result] = element.element_reference
-    locals[:order] = element.sort_order
-  elsif element.project_activity?
-    # TODO
-  elsif element.project_samples?
-    # TODO
+  # "Hack" to omit file preview URL because of WKHTML issues
+  def report_image_asset_url(asset)
+    prefix = (ENV["PAPERCLIP_STORAGE"].present? && ENV["MAIL_SERVER_URL"].present? && ENV["PAPERCLIP_STORAGE"] == "filesystem") ? ENV["MAIL_SERVER_URL"] : ""
+    prefix = (!prefix.empty? && !prefix.include?("http://") && !prefix.include?("https://")) ? "http://#{prefix}" : prefix
+    url = prefix + asset.url(:medium, timeout: Constants::URL_LONG_EXPIRE_TIME)
+    image_tag(url)
   end
 
-  return (render partial: view, locals: locals).html_safe
-end
+  # "Hack" to load Glyphicons css directly from the CDN site so they work in report
+  def bootstrap_cdn_link_tag
+    specs = Gem.loaded_specs["bootstrap-sass"]
+    specs.present? ? stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/#{specs.version.version}/css/bootstrap.min.css", media: "all") : ""
+  end
 
-# "Hack" to omit file preview URL because of WKHTML issues
-def report_image_asset_url(asset)
-  prefix = (ENV["PAPERCLIP_STORAGE"].present? && ENV["MAIL_SERVER_URL"].present? && ENV["PAPERCLIP_STORAGE"] == "filesystem") ? ENV["MAIL_SERVER_URL"] : ""
-  prefix = (!prefix.empty? && !prefix.include?("http://") && !prefix.include?("https://")) ? "http://#{prefix}" : prefix
-  url = prefix + asset.url(:medium, timeout: Constants::URL_LONG_EXPIRE_TIME)
-  image_tag(url)
-end
-
-# "Hack" to load Glyphicons css directly from the CDN site so they work in report
-def bootstrap_cdn_link_tag
-  specs = Gem.loaded_specs["bootstrap-sass"]
-  specs.present? ? stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/#{specs.version.version}/css/bootstrap.min.css", media: "all") : ""
-end
-
-def font_awesome_cdn_link_tag
-  stylesheet_link_tag(
-    'https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css'
-  )
-end
+  def font_awesome_cdn_link_tag
+    stylesheet_link_tag(
+      'https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css'
+    )
+  end
 end
diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index 9c5e2345b..424070b06 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -42,44 +42,27 @@ class ReportElement < ActiveRecord::Base
 
   # Get the referenced element (previously, element's type_of must be set)
   def element_reference
-    if project_header? or project_activity? or project_samples?
-      return project
-    elsif experiment?
-      return experiment
-    elsif my_module? or my_module_activity? or my_module_samples?
-      return my_module
-    elsif step? or step_comments?
-      return step
-    elsif result_asset? or result_table? or result_text? or result_comments?
-      return result
-    elsif step_checklist?
-      return checklist
-    elsif step_asset?
-      return asset
-    elsif step_table?
-      return table
+    ReportExtends::ELEMENT_REFERENCES.each do |el_ref|
+      return eval(el_ref.element.gsub('_id', '')) if el_ref.check(self)
     end
   end
 
-
   # Set the element reference (previously, element's type_of must be set)
   def set_element_reference(ref_id)
-    if project_header? or project_activity? or project_samples?
-      self.project_id = ref_id
-    elsif experiment?
-      self.experiment_id = ref_id
-    elsif my_module? or my_module_activity? or my_module_samples?
-      self.my_module_id = ref_id
-    elsif step? or step_comments?
-      self.step_id = ref_id
-    elsif result_asset? or result_table? or result_text? or result_comments?
-      self.result_id = ref_id
-    elsif step_checklist?
-      self.checklist_id = ref_id
-    elsif step_asset?
-      self.asset_id = ref_id
-    elsif step_table?
-      self.table_id = ref_id
+    # check = true
+    # ReportExtends::REFERENCE_ELEMENTS_IDS.each do |element|
+    #   next unless check
+    #   ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
+    #     check = el_ref.check(self)
+    #     next unless check
+    #     check = false
+    #     self.send("#{element}=", ref_id)
+    #   end
+    # end
+    ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
+      check = el_ref.check(self)
+      next unless check
+      self.send("#{el_ref.element}=", ref_id)
     end
   end
 
diff --git a/app/views/reports/elements/_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_asset_element.html.erb
rename to app/views/reports/elements/_my_module_result_asset_element.html.erb
diff --git a/app/views/reports/elements/_result_table_element.html.erb b/app/views/reports/elements/_my_module_result_table_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_table_element.html.erb
rename to app/views/reports/elements/_my_module_result_table_element.html.erb
diff --git a/app/views/reports/elements/_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_result_text_element.html.erb
rename to app/views/reports/elements/_my_module_result_text_element.html.erb
diff --git a/app/views/reports/elements/_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
similarity index 100%
rename from app/views/reports/elements/_step_element.html.erb
rename to app/views/reports/elements/_my_module_step_element.html.erb
diff --git a/app/views/reports/elements/_project_header_element.html.erb b/app/views/reports/elements/_project_header_element.html.erb
index c39d2a483..beb727530 100644
--- a/app/views/reports/elements/_project_header_element.html.erb
+++ b/app/views/reports/elements/_project_header_element.html.erb
@@ -18,4 +18,4 @@
   <div class="report-element-children">
     <%= children if (defined? children and children.present?) %>
   </div>
-</div>
\ No newline at end of file
+</div>
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index 9b9728b46..544aa2748 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -10,7 +10,7 @@ class Extends
   # > end
   # >
 
-  # Notification types. Should not be freezed, as modules might append to this.
+  # Extends enum types. Should not be freezed, as modules might append to this.
   NOTIFICATIONS_TYPES = { assignment: 0,
                           recent_changes: 1,
                           system_message: 2 }
@@ -34,4 +34,5 @@ class Extends
                            project_activity: 13, # TODO
                            project_samples: 14, # TODO
                            experiment: 15 }
+
 end
diff --git a/config/initializers/extends/report_extends.rb b/config/initializers/extends/report_extends.rb
new file mode 100644
index 000000000..7bfcde7a4
--- /dev/null
+++ b/config/initializers/extends/report_extends.rb
@@ -0,0 +1,193 @@
+#########################################################
+# EXTENDS METHODS. Here you can extend the arrays,      #
+# hashes,.. which is used in methods. Please specify    #
+# the method name and location!                         #
+#########################################################
+
+module ReportExtends
+  # path: app/controllers/concerns/ReportActions
+  # method: generate_module_contents_json
+
+  # ModuleElement struct creates an argument objects which is needed in
+  # generate_module_contents_json method. It takes 3 parameters a Proc and
+  # additional options wich can be extended.
+  # :element => name of module element in plural
+  # :children => bolean if element has children elements in report
+  # :locals => an array of names of local variables which are passed in the view
+  # :coll => a prock which the my_module is passed and have to return a
+  #          collection of element
+  # :options => a hash of options for now only :add_values which
+  #             will add a value to locals
+
+  ModuleElement = Struct.new(:element,
+                             :children,
+                             :locals,
+                             :coll,
+                             :options) do
+    def initialize(element, children, locals, coll = {}, options = {})
+      super(element, children, locals, coll, options)
+    end
+
+    def collection(my_module)
+      coll.call(my_module)
+    end
+
+    def parse_locals(values)
+      container = {}
+      values.concat(add_local_values) unless add_local_values == :no_value
+      locals.each_with_index do |local, index|
+        container[local] = values[index]
+      end
+      container
+    end
+
+    def add_local_values
+      options.fetch(:add_values) { :no_value }
+    end
+  end
+
+  # Module contents element
+  MODULE_CONTENTS = [
+    ModuleElement.new(:steps,
+                      true,
+                      [:step],
+                      proc do |my_module|
+                        my_module.protocol.completed_steps
+                      end),
+    ModuleElement.new(:result_assets,
+                      true,
+                      [:result],
+                      proc do |my_module|
+                        my_module.results.select { |r| r.is_asset && r.active? }
+                      end),
+    ModuleElement.new(:result_tables,
+                      true,
+                      [:result],
+                      proc do |my_module|
+                        my_module.results.select { |r| r.is_table && r.active? }
+                      end),
+    ModuleElement.new(:result_texts,
+                      true,
+                      [:result],
+                      proc do |my_module|
+                        my_module.results.select { |r| r.is_text && r.active? }
+                      end),
+    ModuleElement.new(:activity,
+                      false,
+                      [:my_module, :order]),
+    ModuleElement.new(:samples,
+                      false,
+                      [:my_module, :order])
+  ]
+
+  # path: app/helpers/reports_helpers.rb
+  # method: render_report_element
+
+  # adds :order local to listed elements views
+  SORTED_ELEMENTS = %w(my_module_activity
+                       my_module_samples
+                       step_comments
+                       result_comments)
+  # sets local :my_module to the listed my_module child elements
+  MY_MODULE_ELEMENTS = %w(my_module my_module_activity my_module_samples)
+
+  # sets local name to first element of the listed elements
+  RESULT_ELEMENTS = %w(result_comments
+                       result_text
+                       result_asset
+                       result_table
+                       project_header)
+
+  # path: app/models/report_element.rb
+  # method: set_element_reference
+
+  ElementReference = Struct.new(:checker, :element) do
+    def initialize(checker, element = :element_reference_needed!)
+      super(checker, element)
+    end
+
+    def check(report_element)
+      checker.call(report_element)
+    end
+  end
+
+  SET_ELEMENT_REFERENCES_LIST = [
+    ElementReference.new(
+      proc do |report_element|
+        report_element.project_header? ||
+          report_element.project_activity? ||
+          report_element.project_samples?
+      end,
+      'project_id'
+    ),
+    ElementReference.new(proc(&:experiment?), 'experiment_id'),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.my_module? ||
+          report_element.my_module_activity? ||
+          report_element.my_module_samples?
+      end,
+      'my_module_id'
+    ),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.step? || report_element.step_comments?
+      end,
+      'step_id'
+    ),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.result_asset? ||
+          report_element.result_table? ||
+          report_element.result_text? ||
+          report_element.result_comments?
+      end,
+      'result_id'
+    ),
+    ElementReference.new(proc(&:step_checklist?), 'checklist_id'),
+    ElementReference.new(proc(&:step_asset?), 'asset_id'),
+    ElementReference.new(proc(&:step_table?), 'table_id')
+  ]
+
+  # path: app/models/report_element.rb
+  # method: element_reference
+
+  ELEMENT_REFERENCES = [
+    ElementReference.new(
+      proc do |report_element|
+        report_element.project_header? ||
+          report_element.project_activity? ||
+          report_element.project_samples?
+      end,
+      'project_id'
+    ),
+    ElementReference.new(proc(&:experiment?), 'experiment_id'),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.my_module? ||
+          report_element.my_module_activity? ||
+          report_element.my_module_samples?
+      end,
+      'my_module_id'
+    ),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.step? ||
+          report_element.step_comments?
+      end,
+      'step_id'
+    ),
+    ElementReference.new(
+      proc do |report_element|
+        report_element.result_asset? ||
+          report_element.result_table? ||
+          report_element.result_text? ||
+          report_element.result_comments?
+      end,
+      'result_id'
+    ),
+    ElementReference.new(proc(&:step_checklist?), 'checklist_id'),
+    ElementReference.new(proc(&:step_asset?), 'asset_id'),
+    ElementReference.new(proc(&:step_table?), 'table_id')
+  ]
+end

From f78ef8c82a845d1ecaf76999a68d0c85f9d008e4 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 8 Mar 2017 14:41:42 +0100
Subject: [PATCH 03/19] fixes hound

---
 app/helpers/reports_helper.rb | 40 ++++++++++++++++++++++++++---------
 1 file changed, 30 insertions(+), 10 deletions(-)

diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 437340319..31834567c 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -15,7 +15,8 @@ module ReportsHelper
       if element.has_children?
         children_html.safe_concat render_new_element(true)
         element.children.each do |child|
-          children_html.safe_concat render_report_element(child, provided_locals)
+          children_html
+            .safe_concat render_report_element(child, provided_locals)
         end
       else
         children_html.safe_concat render_new_element(false)
@@ -24,7 +25,8 @@ module ReportsHelper
       if element.has_children?
         element.children.each do |child|
           children_html.safe_concat render_new_element(false)
-          children_html.safe_concat render_report_element(child, provided_locals)
+          children_html
+            .safe_concat render_report_element(child, provided_locals)
         end
       end
       children_html.safe_concat render_new_element(false)
@@ -41,10 +43,14 @@ module ReportsHelper
     ReportElement.type_ofs.keys.each do |type|
       next unless element.send("#{type}?")
       local_sym = type.split('_').last.to_sym
-      local_sym = type.split('_').first.to_sym if type.in? ReportExtends::RESULT_ELEMENTS
+      local_sym = type
+                  .split('_')
+                  .first
+                  .to_sym if type.in? ReportExtends::RESULT_ELEMENTS
       local_sym = :my_module if type.in? ReportExtends::MY_MODULE_ELEMENTS
       locals[local_sym] = element.element_reference
-      locals[:order] = element.sort_order if type.in? ReportExtends::SORTED_ELEMENTS
+      locals[:order] = element
+                       .sort_order if type.in? ReportExtends::SORTED_ELEMENTS
     end
 
     (render partial: view, locals: locals).html_safe
@@ -52,21 +58,35 @@ module ReportsHelper
 
   # "Hack" to omit file preview URL because of WKHTML issues
   def report_image_asset_url(asset)
-    prefix = (ENV["PAPERCLIP_STORAGE"].present? && ENV["MAIL_SERVER_URL"].present? && ENV["PAPERCLIP_STORAGE"] == "filesystem") ? ENV["MAIL_SERVER_URL"] : ""
-    prefix = (!prefix.empty? && !prefix.include?("http://") && !prefix.include?("https://")) ? "http://#{prefix}" : prefix
+    prefix = ''
+    if ENV['PAPERCLIP_STORAGE'].present? &&
+       ENV['MAIL_SERVER_URL'].present? &&
+       ENV['PAPERCLIP_STORAGE'] == 'filesystem'
+      prefix = ENV['MAIL_SERVER_URL']
+    end
+    if !prefix.empty? &&
+       !prefix.include?('http://') &&
+       !prefix.include?('https://')
+      prefix = "http://#{prefix}"
+    end
     url = prefix + asset.url(:medium, timeout: Constants::URL_LONG_EXPIRE_TIME)
     image_tag(url)
   end
 
-  # "Hack" to load Glyphicons css directly from the CDN site so they work in report
+  # "Hack" to load Glyphicons css directly from the CDN
+  # site so they work in report
   def bootstrap_cdn_link_tag
-    specs = Gem.loaded_specs["bootstrap-sass"]
-    specs.present? ? stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/#{specs.version.version}/css/bootstrap.min.css", media: "all") : ""
+    specs = Gem.loaded_specs['bootstrap-sass']
+    return '' unless specs.present?
+    stylesheet_link_tag("http://netdna.bootstrapcdn.com/bootstrap/" \
+                        "#{specs.version.version}/css/bootstrap.min.css",
+                        media: 'all')
   end
 
   def font_awesome_cdn_link_tag
     stylesheet_link_tag(
-      'https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css'
+      'https://maxcdn.bootstrapcdn.com/font-awesome' \
+      '/4.6.3/css/font-awesome.min.css'
     )
   end
 end

From 49f91184da5a7fa711d7cace510e7c0d4293bcbc Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 9 Mar 2017 09:55:15 +0100
Subject: [PATCH 04/19] fixes locals

---
 app/controllers/concerns/report_actions.rb    |  1 +
 config/initializers/extends/report_extends.rb | 14 ++++----------
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/app/controllers/concerns/report_actions.rb b/app/controllers/concerns/report_actions.rb
index 936b6cd73..3c27ae302 100644
--- a/app/controllers/concerns/report_actions.rb
+++ b/app/controllers/concerns/report_actions.rb
@@ -1,6 +1,7 @@
 module ReportActions
   extend ActiveSupport::Concern
 
+
   def in_params?(val)
     params.include? val and params[val] == '1'
   end
diff --git a/config/initializers/extends/report_extends.rb b/config/initializers/extends/report_extends.rb
index 7bfcde7a4..94e25523e 100644
--- a/config/initializers/extends/report_extends.rb
+++ b/config/initializers/extends/report_extends.rb
@@ -22,28 +22,22 @@ module ReportExtends
   ModuleElement = Struct.new(:element,
                              :children,
                              :locals,
-                             :coll,
-                             :options) do
-    def initialize(element, children, locals, coll = {}, options = {})
-      super(element, children, locals, coll, options)
+                             :coll) do
+    def initialize(element, children, locals, coll = nil)
+      super(element, children, locals, coll)
     end
 
     def collection(my_module)
-      coll.call(my_module)
+      coll.call(my_module) if coll
     end
 
     def parse_locals(values)
       container = {}
-      values.concat(add_local_values) unless add_local_values == :no_value
       locals.each_with_index do |local, index|
         container[local] = values[index]
       end
       container
     end
-
-    def add_local_values
-      options.fetch(:add_values) { :no_value }
-    end
   end
 
   # Module contents element

From 9939d8df06d14b28a30509d6cb69d8e69719faca Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 9 Mar 2017 10:51:54 +0100
Subject: [PATCH 05/19] refactor

---
 app/controllers/concerns/report_actions.rb    |  5 +++--
 app/helpers/reports_helper.rb                 |  5 ++++-
 app/models/report_element.rb                  | 21 +++++++------------
 config/initializers/extends/report_extends.rb |  1 +
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/app/controllers/concerns/report_actions.rb b/app/controllers/concerns/report_actions.rb
index 3c27ae302..6ba54c76d 100644
--- a/app/controllers/concerns/report_actions.rb
+++ b/app/controllers/concerns/report_actions.rb
@@ -1,7 +1,6 @@
 module ReportActions
   extend ActiveSupport::Concern
 
-
   def in_params?(val)
     params.include? val and params[val] == '1'
   end
@@ -83,7 +82,9 @@ module ReportActions
                                           .singularize}_element.html.erb",
             contents.parse_locals([report_el])
           )
-          el[:children] = generate_step_contents_json(report_el) if contents.element == :step
+          if contents.element == :step
+            el[:children] = generate_step_contents_json(report_el)
+          end
           el[:children] = generate_result_contents_json(report_el)
           res << el
         end
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 31834567c..9ae544c05 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -33,13 +33,16 @@ module ReportsHelper
     end
 
     file_name = element.type_of
-    file_name = "my_module_#{element.type_of}" if element.type_of.in? %w(step result_asset result_table result_text)
+    if element.type_of.in? %w(step result_asset result_table result_text)
+      file_name = "my_module_#{element.type_of.singularize}"
+    end
     view = "reports/elements/#{file_name}_element.html.erb"
 
     locals = provided_locals.nil? ? {} : provided_locals.clone
     locals[:children] = children_html
 
     # ReportExtends is located in config/initializers/extends/report_extends.rb
+
     ReportElement.type_ofs.keys.each do |type|
       next unless element.send("#{type}?")
       local_sym = type.split('_').last.to_sym
diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index 424070b06..cf75037cf 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -15,8 +15,12 @@ class ReportElement < ActiveRecord::Base
   belongs_to :report, inverse_of: :report_elements
 
   # Hierarchical structure representation
-  has_many :children, -> { order(:position) }, class_name: "ReportElement", foreign_key: "parent_id", dependent: :destroy
-  belongs_to :parent, class_name: "ReportElement"
+  has_many :children,
+           -> { order(:position) },
+           class_name: 'ReportElement',
+           foreign_key: 'parent_id',
+           dependent: :destroy
+  belongs_to :parent, class_name: 'ReportElement'
 
   # References to various report entities
   belongs_to :project, inverse_of: :report_elements
@@ -49,16 +53,6 @@ class ReportElement < ActiveRecord::Base
 
   # Set the element reference (previously, element's type_of must be set)
   def set_element_reference(ref_id)
-    # check = true
-    # ReportExtends::REFERENCE_ELEMENTS_IDS.each do |element|
-    #   next unless check
-    #   ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
-    #     check = el_ref.check(self)
-    #     next unless check
-    #     check = false
-    #     self.send("#{element}=", ref_id)
-    #   end
-    # end
     ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
       check = el_ref.check(self)
       next unless check
@@ -97,7 +91,8 @@ class ReportElement < ActiveRecord::Base
       table
     ].count { |r| r.present? }
     if num_of_refs != 1
-      errors.add(:base, "Report element must have exactly one element reference.")
+      errors.add(:base,
+                 'Report element must have exactly one element reference.')
     end
   end
 end
diff --git a/config/initializers/extends/report_extends.rb b/config/initializers/extends/report_extends.rb
index 94e25523e..2194f4c3c 100644
--- a/config/initializers/extends/report_extends.rb
+++ b/config/initializers/extends/report_extends.rb
@@ -78,6 +78,7 @@ module ReportExtends
   # method: render_report_element
 
   # adds :order local to listed elements views
+  # ADD REPORT ELEMENT TYPE WHICH YOU WANT TO PASS 'ORDER' LOCAL IN THE PARTIAL
   SORTED_ELEMENTS = %w(my_module_activity
                        my_module_samples
                        step_comments

From 30579659409ea621e94046c23eee33dd01c47e51 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 9 Mar 2017 11:48:50 +0100
Subject: [PATCH 06/19] fix bug with filenames

---
 app/controllers/concerns/report_actions.rb    |  2 +-
 config/initializers/extends/report_extends.rb | 16 +++++++++++-----
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/app/controllers/concerns/report_actions.rb b/app/controllers/concerns/report_actions.rb
index 6ba54c76d..8e8a675d3 100644
--- a/app/controllers/concerns/report_actions.rb
+++ b/app/controllers/concerns/report_actions.rb
@@ -89,7 +89,7 @@ module ReportActions
           res << el
         end
       else
-        file_name = contents.element.to_s.singularize
+        file_name = contents.file_name
         file_name = contents.element if contents.element == :samples
         res << generate_el(
           "reports/elements/my_module_#{file_name}_element.html.erb",
diff --git a/config/initializers/extends/report_extends.rb b/config/initializers/extends/report_extends.rb
index 2194f4c3c..5437454a3 100644
--- a/config/initializers/extends/report_extends.rb
+++ b/config/initializers/extends/report_extends.rb
@@ -16,15 +16,16 @@ module ReportExtends
   # :locals => an array of names of local variables which are passed in the view
   # :coll => a prock which the my_module is passed and have to return a
   #          collection of element
-  # :options => a hash of options for now only :add_values which
-  #             will add a value to locals
+  # :singular => true by defaut change the enum type to singular
+  #              needed when querying partials by name
 
   ModuleElement = Struct.new(:element,
                              :children,
                              :locals,
-                             :coll) do
-    def initialize(element, children, locals, coll = nil)
-      super(element, children, locals, coll)
+                             :coll,
+                             :singular) do
+    def initialize(element, children, locals, coll = nil, singular = true)
+      super(element, children, locals, coll, singular)
     end
 
     def collection(my_module)
@@ -38,6 +39,11 @@ module ReportExtends
       end
       container
     end
+
+    def file_name
+      return element.to_s unless singular
+      element.to_s.singularize
+    end
   end
 
   # Module contents element

From 1d42d46c024d01804984aed4a9736db5f43fb0a0 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 9 Mar 2017 16:02:52 +0100
Subject: [PATCH 07/19] fixes bug with step comments

---
 app/controllers/concerns/report_actions.rb    | 11 ++++++-----
 app/helpers/reports_helper.rb                 |  2 +-
 app/models/report.rb                          | 11 ++++++-----
 app/models/report_element.rb                  | 19 +++++++++----------
 config/initializers/extends/report_extends.rb | 11 ++++++-----
 5 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/app/controllers/concerns/report_actions.rb b/app/controllers/concerns/report_actions.rb
index 8e8a675d3..50deeeedc 100644
--- a/app/controllers/concerns/report_actions.rb
+++ b/app/controllers/concerns/report_actions.rb
@@ -84,8 +84,9 @@ module ReportActions
           )
           if contents.element == :step
             el[:children] = generate_step_contents_json(report_el)
+          elsif contents.element == :result
+            el[:children] = generate_result_contents_json(report_el)
           end
-          el[:children] = generate_result_contents_json(report_el)
           res << el
         end
       else
@@ -103,7 +104,7 @@ module ReportActions
 
   def generate_step_contents_json(step)
     res = []
-    if in_params? :step_checklists then
+    if in_params? :step_checklists
       step.checklists.each do |checklist|
         res << generate_new_el(false)
         res << generate_el(
@@ -112,7 +113,7 @@ module ReportActions
         )
       end
     end
-    if in_params? :step_assets then
+    if in_params? :step_assets
       step.assets.each do |asset|
         res << generate_new_el(false)
         res << generate_el(
@@ -121,7 +122,7 @@ module ReportActions
         )
       end
     end
-    if in_params? :step_tables then
+    if in_params? :step_tables
       step.tables.each do |table|
         res << generate_new_el(false)
         res << generate_el(
@@ -130,7 +131,7 @@ module ReportActions
         )
       end
     end
-    if in_params? :step_comments then
+    if in_params? :step_comments
       res << generate_new_el(false)
       res << generate_el(
         'reports/elements/step_comments_element.html.erb',
diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index 9ae544c05..d66f6eeda 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -49,7 +49,7 @@ module ReportsHelper
       local_sym = type
                   .split('_')
                   .first
-                  .to_sym if type.in? ReportExtends::RESULT_ELEMENTS
+                  .to_sym if type.in? ReportExtends::FIRST_PART_ELEMENTS
       local_sym = :my_module if type.in? ReportExtends::MY_MODULE_ELEMENTS
       locals[local_sym] = element.element_reference
       locals[:order] = element
diff --git a/app/models/report.rb b/app/models/report.rb
index 3cd7aa376..5d1b5e599 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -105,12 +105,13 @@ class Report < ActiveRecord::Base
     el.position = index
     el.report = self
     el.parent = parent
-    el.type_of = json_element["type_of"]
-    el.sort_order = json_element["sort_order"]
-    el.set_element_reference(json_element["id"])
+    el.type_of = json_element['type_of']
+    el.sort_order = json_element['sort_order']
+    el.set_element_reference(json_element['id'])
     el.save!
-    if json_element["children"].present?
-      json_element["children"].each_with_index do |child, i|
+
+    if json_element['children'].present?
+      json_element['children'].each_with_index do |child, i|
         save_json_element(child, i, el)
       end
     end
diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index cf75037cf..14cba7cf1 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -57,6 +57,7 @@ class ReportElement < ActiveRecord::Base
       check = el_ref.check(self)
       next unless check
       self.send("#{el_ref.element}=", ref_id)
+      break
     end
   end
 
@@ -80,16 +81,14 @@ class ReportElement < ActiveRecord::Base
   private
 
   def has_one_of_referenced_elements
-    num_of_refs = [
-      project,
-      experiment,
-      my_module,
-      step,
-      result,
-      checklist,
-      asset,
-      table
-    ].count { |r| r.present? }
+    num_of_refs = [project,
+                   experiment,
+                   my_module,
+                   step,
+                   result,
+                   checklist,
+                   asset,
+                   table].count { |r| r.present? }
     if num_of_refs != 1
       errors.add(:base,
                  'Report element must have exactly one element reference.')
diff --git a/config/initializers/extends/report_extends.rb b/config/initializers/extends/report_extends.rb
index 5437454a3..d243c6bb0 100644
--- a/config/initializers/extends/report_extends.rb
+++ b/config/initializers/extends/report_extends.rb
@@ -93,11 +93,12 @@ module ReportExtends
   MY_MODULE_ELEMENTS = %w(my_module my_module_activity my_module_samples)
 
   # sets local name to first element of the listed elements
-  RESULT_ELEMENTS = %w(result_comments
-                       result_text
-                       result_asset
-                       result_table
-                       project_header)
+  FIRST_PART_ELEMENTS = %w(result_comments
+                           result_text
+                           result_asset
+                           result_table
+                           project_header
+                           step_comments)
 
   # path: app/models/report_element.rb
   # method: set_element_reference

From 5d372851d3679bbeb1adc4cc319c9518fed81c2e Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 14 Mar 2017 16:24:02 +0100
Subject: [PATCH 08/19] fixes reports comment bug [fixes SCI-1100]

---
 .../reports/elements/_my_module_result_asset_element.html.erb   | 2 +-
 .../reports/elements/_my_module_result_table_element.html.erb   | 2 +-
 .../reports/elements/_my_module_result_text_element.html.erb    | 2 +-
 app/views/reports/elements/_my_module_step_element.html.erb     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/views/reports/elements/_my_module_result_asset_element.html.erb b/app/views/reports/elements/_my_module_result_asset_element.html.erb
index 7a93830f7..c863c0597 100644
--- a/app/views/reports/elements/_my_module_result_asset_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_asset_element.html.erb
@@ -1,7 +1,7 @@
 <% if result.blank? and @result.present? then result = @result end %>
 <% asset = result.asset %>
 <% is_image = result.asset.is_image? %>
-<% comments = result.comments %>
+<% comments = result.result_comments %>
 <% timestamp = asset.created_at %>
 <% name = result.name %>
 <% icon_class = is_image ? "glyphicon-picture" : "glyphicon-file" %>
diff --git a/app/views/reports/elements/_my_module_result_table_element.html.erb b/app/views/reports/elements/_my_module_result_table_element.html.erb
index 65f564e78..7129f5eed 100644
--- a/app/views/reports/elements/_my_module_result_table_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_table_element.html.erb
@@ -1,6 +1,6 @@
 <% if result.blank? and @result.present? then result = @result end %>
 <% table = result.table %>
-<% comments = result.comments %>
+<% comments = result.result_comments %>
 <% timestamp = table.created_at %>
 <% name = result.name %>
 <div class="report-element report-result-element report-result-table-element" data-ts="<%= timestamp.to_i %>" data-type="result_table" data-id="<%= result.id %>" data-modal-title="<%=t "projects.reports.elements.modals.result_contents.head_title", result: result.name %>" data-name="<%= name %>" data-icon-class="glyphicon-th">
diff --git a/app/views/reports/elements/_my_module_result_text_element.html.erb b/app/views/reports/elements/_my_module_result_text_element.html.erb
index 69a4fd40f..1530aaacb 100644
--- a/app/views/reports/elements/_my_module_result_text_element.html.erb
+++ b/app/views/reports/elements/_my_module_result_text_element.html.erb
@@ -1,6 +1,6 @@
 <% if result.blank? and @result.present? then result = @result end %>
 <% result_text = result.result_text %>
-<% comments = result.comments %>
+<% comments = result.result_comments %>
 <% timestamp = result.created_at %>
 <% name = result.name %>
 <div class="report-element report-result-element report-result-text-element" data-ts="<%= timestamp.to_i %>" data-type="result_text" data-id="<%= result.id %>" data-modal-title="<%=t "projects.reports.elements.modals.result_contents.head_title", result: result.name %>" data-name="<%= name %>" data-icon-class="glyphicon-asterisk">
diff --git a/app/views/reports/elements/_my_module_step_element.html.erb b/app/views/reports/elements/_my_module_step_element.html.erb
index ced4d19f4..7a73b519e 100644
--- a/app/views/reports/elements/_my_module_step_element.html.erb
+++ b/app/views/reports/elements/_my_module_step_element.html.erb
@@ -3,7 +3,7 @@
 <% tables = step.tables %>
 <% assets = step.assets %>
 <% checklists = step.checklists %>
-<% comments = step.comments %>
+<% comments = step.step_comments %>
 <div class="report-element report-step-element" data-ts="<%= timestamp.to_i %>" data-type="step" data-id="<%= step.id %>" data-modal-title="<%=t "projects.reports.elements.modals.step_contents.head_title", step: step.name %>" data-name="<%=t "projects.reports.elements.step.sidebar_name", pos: (step.position + 1), name: step.name %>" data-icon-class="glyphicon-circle-arrow-right">
   <div class="report-element-header">
     <div class="row">

From 7a4e3201e703f86a5570dc9b05463d45f40e58a1 Mon Sep 17 00:00:00 2001
From: Mojca Lorber <mojca.lorber@biosistemika.com>
Date: Tue, 14 Mar 2017 17:32:25 +0100
Subject: [PATCH 09/19] add error messages to sample group/type edit/delete
 actions

---
 .../samples/sample_types_groups.js            | 57 +++++++++++++++++++
 .../sample_groups/_sample_group.html.erb      | 21 ++++---
 app/views/sample_types/_sample_type.html.erb  |  9 ++-
 3 files changed, 75 insertions(+), 12 deletions(-)

diff --git a/app/assets/javascripts/samples/sample_types_groups.js b/app/assets/javascripts/samples/sample_types_groups.js
index bf708d596..0a42fcce9 100644
--- a/app/assets/javascripts/samples/sample_types_groups.js
+++ b/app/assets/javascripts/samples/sample_types_groups.js
@@ -70,6 +70,17 @@
           });
 
           clearModal('#modal-delete');
+        },
+        error: function (e) {
+          $(li).clearFormErrors();
+          var msg = $.parseJSON(e.responseText);
+
+          renderFormError(undefined,
+                          $(li).find('.text-edit'),
+                          Object.keys(msg)[0] + ' ' + msg.name.toString());
+          setTimeout(function() {
+            $(li).clearFormErrors();
+          }, 5000);
         }
       });
     });
@@ -161,6 +172,17 @@
                             $(this).find('#sample_type_name'),
                             Object.keys(msg)[0] + ' '+ msg.name.toString());
           });
+        },
+        error: function (e) {
+          $(li).clearFormErrors();
+          var msg = $.parseJSON(e.responseText);
+
+          renderFormError(undefined,
+                          $(li).find('.text-edit'),
+                          Object.keys(msg)[0] + ' ' + msg.name.toString());
+          setTimeout(function() {
+            $(li).clearFormErrors();
+          }, 5000);
         }
       });
     });
@@ -202,6 +224,40 @@
                             $(this).find('#sample_group_name'),
                             Object.keys(msg)[0] + ' '+ msg.name.toString());
           });
+        },
+        error: function (e) {
+          $(li).clearFormErrors();
+          var msg = $.parseJSON(e.responseText);
+
+          renderFormError(undefined,
+                          $(li).find('.text-edit'),
+                          Object.keys(msg)[0] + ' ' + msg.name.toString());
+          setTimeout(function() {
+            $(li).clearFormErrors();
+          }, 5000);
+        }
+      });
+    });
+  }
+
+  function editSampleGroupColor() {
+    $('.color-picker').on('click', function() {
+      var li = $(this).closest('li');
+      $.ajax({
+        url: li.attr('data-edit'),
+        success: function(data) {
+        },
+        error: function (e) {
+          $('.dropdown-colorselector.open').removeClass('open');
+          $(li).clearFormErrors();
+          var msg = $.parseJSON(e.responseText);
+
+          renderFormError(undefined,
+                          $(li).find('.text-edit'),
+                          Object.keys(msg)[0] + ' ' + msg.name.toString());
+          setTimeout(function() {
+            $(li).clearFormErrors();
+          }, 5000);
         }
       });
     });
@@ -269,6 +325,7 @@
     bindNewSampleGroupAction();
     appendCarretToColorPickerDropdown();
     sampleTypeGroupEditMode();
+    editSampleGroupColor();
   }
 
   // initialize sample types/groups actions
diff --git a/app/views/sample_groups/_sample_group.html.erb b/app/views/sample_groups/_sample_group.html.erb
index 18d702891..2e2a60a99 100644
--- a/app/views/sample_groups/_sample_group.html.erb
+++ b/app/views/sample_groups/_sample_group.html.erb
@@ -5,15 +5,18 @@
       team_sample_group_destroy_confirmation_path(team, sample_group) %>"
     data-color="<%= sample_group.color %>">
   <span class="sample-type-group-name"><%= sample_group.name %></span>
-  <span class="pull-right sample-group-controls">
-    <span class="color-picker">
-      <%= bootstrap_form_for [team, sample_group], remote: true do |f| %>
-        <%= f.color_picker_select :color,
-                                  Constants::TAG_COLORS,
-                                  class: 'edit-sample-group-color' %>
-      <% end %>
+  <span class="form-group">
+    <input class="text-edit" style="display: none;" />
+    <span class="pull-right sample-group-controls">
+      <span class="color-picker">
+        <%= bootstrap_form_for [team, sample_group], remote: true do |f| %>
+          <%= f.color_picker_select :color,
+                                    Constants::TAG_COLORS,
+                                    class: 'edit-sample-group-color' %>
+        <% end %>
+      </span>
+      <span class="edit-sample-group glyphicon glyphicon-pencil"></span>
+      <span class="delete glyphicon glyphicon-trash"></span>
     </span>
-    <span class="edit-sample-group glyphicon glyphicon-pencil"></span>
-    <span class="delete glyphicon glyphicon-trash"></span>
   </span>
 </li>
diff --git a/app/views/sample_types/_sample_type.html.erb b/app/views/sample_types/_sample_type.html.erb
index 36c409bc8..8c6b90388 100644
--- a/app/views/sample_types/_sample_type.html.erb
+++ b/app/views/sample_types/_sample_type.html.erb
@@ -4,8 +4,11 @@
       team_sample_type_destroy_confirmation_path(team, sample_type)
       %>">
   <span class="sample-type-group-name"><%= sample_type.name %></span>
-  <span class="pull-right">
-    <span class="edit-sample-type glyphicon glyphicon-pencil"></span>
-    <span class="delete glyphicon glyphicon-trash"></span>
+  <span class="form-group">
+    <input class="text-edit" style="display: none;" />
+    <span class="pull-right">
+      <span class="edit-sample-type glyphicon glyphicon-pencil"></span>
+      <span class="delete glyphicon glyphicon-trash"></span>
+    </span>
   </span>
 </li>

From 4792bd87b997513801d4398e1352411710176678 Mon Sep 17 00:00:00 2001
From: Mojca Lorber <mojca.lorber@biosistemika.com>
Date: Wed, 15 Mar 2017 14:09:44 +0100
Subject: [PATCH 10/19] fix error message when editing custom column on locked
 task

---
 .../samples/sample_datatable.js.erb           | 76 ++++++++++++-------
 app/controllers/custom_fields_controller.rb   |  2 +-
 2 files changed, 50 insertions(+), 28 deletions(-)

diff --git a/app/assets/javascripts/samples/sample_datatable.js.erb b/app/assets/javascripts/samples/sample_datatable.js.erb
index ae6d86fa1..7fb9cbc25 100644
--- a/app/assets/javascripts/samples/sample_datatable.js.erb
+++ b/app/assets/javascripts/samples/sample_datatable.js.erb
@@ -1193,34 +1193,56 @@ function changeToEditMode() {
 
       cancelEditMode();
 
-      var self = $(this);
-      var li = self.closest('li');
-      var text = li.find('.text');
-      if ($(text).find('.modal-tooltiptext').length > 0) {
-        text = $(text).find('.modal-tooltiptext');
+      var li = $(this).closest('li');
+      var url = li.attr('data-edit-url') + "/electronic_sign_edit";
+      ajaxCallEvent();
+
+      function ajaxCallEvent(){
+        $.ajax({
+          url: url,
+          success: function() {
+            var text = li.find('.text');
+            if ($(text).find('.modal-tooltiptext').length > 0) {
+              text = $(text).find('.modal-tooltiptext');
+            }
+            var textEdit = li.find('.text-edit');
+            var controls = li.find('.controls .vis,.edit,.del');
+            var controlsEdit = li.find('.controls .ok,.cancel');
+
+            // Toggle edit mode
+            columnEditMode = true;
+            li.addClass('editing');
+
+            // Set the text-edit's value
+            textEdit.val(text.text().trim());
+
+            // Toggle elements
+            text.hide();
+            controls.hide();
+            textEdit.css('display', ''); // show() doesn't work
+            controlsEdit.css('display', ''); // show() doesn't work
+            dropdownList.sortable('disable');
+            dropdownList.on('click', function(ev) {
+              ev.stopPropagation();
+            });
+            // Focus input
+            textEdit.focus();
+          },
+          error: function(e) {
+            $(li).clearFormErrors();
+            var msg = $.parseJSON(e.responseText);
+
+            renderFormError(undefined,
+                            $(li).find('.text-edit'),
+                            Object.keys(msg)[0] + ' ' + msg.name.toString());
+            var verticalHeight = $(li).offset().top;
+            dropdownList.scrollTo(verticalHeight,0);
+            setTimeout(function() {
+              $(li).clearFormErrors();
+            }, 5000);
+          }
+        });
       }
-      var textEdit = li.find('.text-edit');
-      var controls = li.find('.controls .vis,.edit,.del');
-      var controlsEdit = li.find('.controls .ok,.cancel');
-
-      // Toggle edit mode
-      columnEditMode = true;
-      li.addClass('editing');
-
-      // Set the text-edit's value
-      textEdit.val(text.text().trim());
-
-      // Toggle elements
-      text.hide();
-      controls.hide();
-      textEdit.css('display', ''); // show() doesn't work
-      controlsEdit.css('display', ''); // show() doesn't work
-      dropdownList.sortable('disable');
-      dropdownList.on('click', function(ev) {
-        ev.stopPropagation();
-      });
-      // Focus input
-      textEdit.focus();
     });
 
     // On hiding dropdown, cancel edit mode throughout dropdown
diff --git a/app/controllers/custom_fields_controller.rb b/app/controllers/custom_fields_controller.rb
index 64fc2519a..059512e75 100644
--- a/app/controllers/custom_fields_controller.rb
+++ b/app/controllers/custom_fields_controller.rb
@@ -1,7 +1,7 @@
 class CustomFieldsController < ApplicationController
   include InputSanitizeHelper
 
-  before_action :load_vars, only: [:update, :destroy, :destroy_html]
+  before_action :load_vars, except: :create
   before_action :load_vars_nested, only: [:create, :destroy_html]
   before_action :check_create_permissions, only: :create
   before_action :check_update_permissions, only: :update

From 70f17a924e67a3b3edd7279970598efc3b982692 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Fri, 17 Mar 2017 16:10:22 +0100
Subject: [PATCH 11/19] adds hooks in team switch [fixes SCI-1092]

---
 app/views/shared/_navigation.html.erb | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/app/views/shared/_navigation.html.erb b/app/views/shared/_navigation.html.erb
index 3b4e97f2d..8870ad0a3 100644
--- a/app/views/shared/_navigation.html.erb
+++ b/app/views/shared/_navigation.html.erb
@@ -86,7 +86,8 @@
             </span>
           </a>
 
-          <ul class="dropdown-menu ">
+          <ul class="dropdown-menu"
+              data-hook="teams-dropdown">
             <%= form_for(current_user,
                          url: user_current_team_path,
                          method: :post) do |f| %>
@@ -103,9 +104,11 @@
               <% end %>
             <% end %>
             <% if current_user.teams.length > 1 %>
-            <li role="separator" class="divider"></li>
+            <li data-hook="new-team-btn"
+                role="separator"
+                class="divider"></li>
             <% end %>
-            <li>
+            <li data-hook="new-team-btn">
               <%= link_to new_team_path do %>
                 <span class="glyphicon glyphicon-plus"></span>
                 <%= t('users.settings.teams.index.new_team') %>

From 83fa8570d7ae10edfd6ea31a75f5c9ef6e9a3796 Mon Sep 17 00:00:00 2001
From: Mojca Lorber <mojca.lorber@biosistemika.com>
Date: Fri, 17 Mar 2017 17:52:15 +0100
Subject: [PATCH 12/19] refactoring

---
 .../javascripts/samples/sample_datatable.js.erb   | 15 +++++++++------
 app/controllers/custom_fields_controller.rb       | 10 ++++++++++
 app/views/shared/_samples.html.erb                |  3 ++-
 config/routes.rb                                  |  2 +-
 4 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/app/assets/javascripts/samples/sample_datatable.js.erb b/app/assets/javascripts/samples/sample_datatable.js.erb
index 7fb9cbc25..9ad53f960 100644
--- a/app/assets/javascripts/samples/sample_datatable.js.erb
+++ b/app/assets/javascripts/samples/sample_datatable.js.erb
@@ -967,6 +967,7 @@ function changeToEditMode() {
             '<th class="custom-field" id="' + data.id + '" ' +
             'data-editable data-deletable ' +
             'data-edit-url="' + data.edit_url + '" ' +
+            'data-update-url="' + data.update_url + '" ' +
             'data-destroy-html-url="' + data.destroy_html_url + '"' +
             '>' + generateColumnNameTooltip(data.name) + '</th>');
 
@@ -1050,6 +1051,7 @@ function changeToEditMode() {
           'data-position="' + colIndex + '" ' +
           'data-id="' + $(el).attr('id') + '" ' +
           'data-edit-url=' + $(el).attr('data-edit-url') + ' ' +
+          'data-update-url=' + $(el).attr('data-update-url') + ' ' +
           'data-destroy-html-url=' + $(el).attr('data-destroy-html-url') + ' ' +
           'class="' + visLi + '"' +
           '>' +
@@ -1151,7 +1153,7 @@ function changeToEditMode() {
       var text = li.find('.text');
       var textEdit = li.find('.text-edit');
       var newName = textEdit.val().trim();
-      var url = li.attr('data-edit-url');
+      var url = li.attr('data-update-url');
 
       $.ajax({
         url: url,
@@ -1194,20 +1196,21 @@ function changeToEditMode() {
       cancelEditMode();
 
       var li = $(this).closest('li');
-      var url = li.attr('data-edit-url') + "/electronic_sign_edit";
+      var url = li.attr('data-edit-url');
       ajaxCallEvent();
 
       function ajaxCallEvent(){
         $.ajax({
           url: url,
           success: function() {
-            var text = li.find('.text');
+            var text, textEdit, controls, controlsEdit;
+            text = li.find('.text');
             if ($(text).find('.modal-tooltiptext').length > 0) {
               text = $(text).find('.modal-tooltiptext');
             }
-            var textEdit = li.find('.text-edit');
-            var controls = li.find('.controls .vis,.edit,.del');
-            var controlsEdit = li.find('.controls .ok,.cancel');
+            textEdit = li.find('.text-edit');
+            controls = li.find('.controls .vis,.edit,.del');
+            controlsEdit = li.find('.controls .ok,.cancel');
 
             // Toggle edit mode
             columnEditMode = true;
diff --git a/app/controllers/custom_fields_controller.rb b/app/controllers/custom_fields_controller.rb
index 059512e75..388d8dc96 100644
--- a/app/controllers/custom_fields_controller.rb
+++ b/app/controllers/custom_fields_controller.rb
@@ -19,6 +19,8 @@ class CustomFieldsController < ApplicationController
             id: @custom_field.id,
             name: escape_input(@custom_field.name),
             edit_url:
+              edit_team_custom_field_path(@team, @custom_field),
+            update_url:
               team_custom_field_path(@team, @custom_field),
             destroy_html_url:
               team_custom_field_destroy_html_path(
@@ -36,6 +38,14 @@ class CustomFieldsController < ApplicationController
     end
   end
 
+  def edit
+    respond_to do |format|
+      format.json do
+        render json: { status: :ok }
+      end
+    end
+  end
+
   def update
     respond_to do |format|
       format.json do
diff --git a/app/views/shared/_samples.html.erb b/app/views/shared/_samples.html.erb
index 79c52a545..2652d0366 100644
--- a/app/views/shared/_samples.html.erb
+++ b/app/views/shared/_samples.html.erb
@@ -145,7 +145,8 @@
             id="<%= cf.id %>"
             <%= 'data-editable' if can_edit_custom_field(cf) %>
             <%= 'data-deletable' if can_delete_custom_field(cf) %>
-            <%= "data-edit-url='#{team_custom_field_path(@team, cf)}'" %>
+            <%= "data-edit-url='#{edit_team_custom_field_path(@team, cf)}'" %>
+            <%= "data-update-url='#{team_custom_field_path(@team, cf)}'" %>
             <%= "data-destroy-html-url='#{team_custom_field_destroy_html_path(@team, cf)}'" %>
         >
           <%= display_tooltip(cf.name) %>
diff --git a/config/routes.rb b/config/routes.rb
index 83da5977b..a8a8a663e 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -123,7 +123,7 @@ Rails.application.routes.draw do
         get 'sample_group_element', to: 'sample_groups#sample_group_element'
         get 'destroy_confirmation', to: 'sample_groups#destroy_confirmation'
       end
-      resources :custom_fields, only: [:create, :update, :destroy] do
+      resources :custom_fields, only: [:create, :edit, :update, :destroy] do
         get 'destroy_html'
       end
       member do

From c7159020589e236df53faacda30ab46bd85de3e1 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Fri, 17 Mar 2017 17:56:58 +0100
Subject: [PATCH 13/19] Move flash message creation JS code to helper method
 [SCI-1087]

---
 app/assets/javascripts/application.js.erb     | 26 +++++++++++++++++++
 .../samples/sample_datatable.js.erb           | 18 +++++++++----
 app/assets/javascripts/samples/samples.js     | 26 -------------------
 3 files changed, 39 insertions(+), 31 deletions(-)

diff --git a/app/assets/javascripts/application.js.erb b/app/assets/javascripts/application.js.erb
index 2ceb50997..56bf2fb5f 100644
--- a/app/assets/javascripts/application.js.erb
+++ b/app/assets/javascripts/application.js.erb
@@ -224,6 +224,32 @@ var HelperModule = (function(){
     }
   }
 
+  helpers.flashAlertMsg = function(message, type) {
+    var alertType;
+    var glyphSign;
+    $('#notifications').html('');
+    if (type === 'success') {
+      alertType = ' alert-success ';
+      glyphSign = ' glyphicon-ok-sign ';
+    } else if (type === 'danger') {
+      alertType = ' alert-danger ';
+      glyphSign = ' glyphicon-exclamation-sign ';
+    }
+    var htmlSnippet = '<div class="alert alert' + alertType +
+                      'alert-dismissable alert-floating">' +
+                        '<div class="container">' +
+                          '<button type="button" class="close" ' +
+                          'data-dismiss="alert" aria-label="Close">' +
+                          '<span aria-hidden="true">×</span></button>' +
+                            '<span class="glyphicon' + glyphSign + '"></span>' +
+                            '<span>' + message + '</span>' +
+                          '</div>' +
+                        '</div>';
+    $('#notifications').html(htmlSnippet);
+    $('#content-wrapper').addClass('alert-shown');
+    helpers.hideFlashMsg();
+  }
+
   $( document ).ready(function() {
     helpers.treeLinkTruncation();
     helpers.hideFlashMsg();
diff --git a/app/assets/javascripts/samples/sample_datatable.js.erb b/app/assets/javascripts/samples/sample_datatable.js.erb
index ae6d86fa1..f2f08f423 100644
--- a/app/assets/javascripts/samples/sample_datatable.js.erb
+++ b/app/assets/javascripts/samples/sample_datatable.js.erb
@@ -503,7 +503,9 @@ function onClickEdit() {
         },
         error: function (e, data, status, xhr) {
             if (e.status == 403) {
-                sampleAlertMsg(I18n.t("samples.js.permission_error"), "danger");
+                HelperModule.flashAlertMsg(
+                  I18n.t('samples.js.permission_error'), 'danger'
+                );
                 changeToViewMode();
                 updateButtons();
             }
@@ -565,7 +567,7 @@ function onClickSave() {
         dataType: "json",
         data: data,
         success: function (data) {
-            sampleAlertMsg(data.flash, "success");
+            HelperModule.flashAlertMsg(data.flash, 'success');
             onClickCancel();
         },
         error: function (e, eData, status, xhr) {
@@ -573,12 +575,16 @@ function onClickSave() {
             clearAllErrors();
 
             if (e.status == 404) {
-                sampleAlertMsg(I18n.t("samples.js.not_found_error"), "danger");
+                HelperModule.flashAlertMsg(
+                  I18n.t('samples.js.not_found_error'), 'danger'
+                );
                 changeToViewMode();
                 updateButtons();
             }
             else if (e.status == 403) {
-                sampleAlertMsg(I18n.t("samples.js.permission_error"), "danger");
+                HelperModule.flashAlertMsg(
+                  I18n.t('samples.js.permission_error'), 'danger'
+                );
                 changeToViewMode();
                 updateButtons();
             }
@@ -794,7 +800,9 @@ function onClickAddSample() {
         },
         error: function (e, eData, status, xhr) {
             if (e.status == 403)
-                sampleAlertMsg(I18n.t("samples.js.permission_error"), "danger");
+                HelperModule.flashAlertMsg(
+                  I18n.t('samples.js.permission_error'), 'danger'
+                );
             changeToViewMode();
             updateButtons();
         }
diff --git a/app/assets/javascripts/samples/samples.js b/app/assets/javascripts/samples/samples.js
index 1e5a3c7bc..5021f95eb 100644
--- a/app/assets/javascripts/samples/samples.js
+++ b/app/assets/javascripts/samples/samples.js
@@ -53,32 +53,6 @@ function updateSamplesTypesandGroups() {
     });
 }
 
-function sampleAlertMsg(message, type) {
-  var alertType;
-  var glyphSign;
-  $('#notifications').html('');
-  if (type === 'success') {
-    alertType = ' alert-success ';
-    glyphSign = ' glyphicon-ok-sign ';
-  } else if (type === 'danger') {
-    alertType = ' alert-danger ';
-    glyphSign = ' glyphicon-exclamation-sign ';
-  }
-  var htmlSnippet = '<div class="alert alert' + alertType +
-                    'alert-dismissable alert-floating">' +
-                      '<div class="container">' +
-                        '<button type="button" class="close" ' +
-                        'data-dismiss="alert" aria-label="Close">' +
-                        '<span aria-hidden="true">×</span></button>' +
-                          '<span class="glyphicon' + glyphSign + '"></span>' +
-                          '<span>' + message + '</span>' +
-                        '</div>' +
-                      '</div>';
-  $('#notifications').html(htmlSnippet);
-  $('#content-wrapper').addClass('alert-shown');
-  HelperModule.hideFlashMsg();
-}
-
 /**
  * Initializes tutorial
  */

From 8a8720fcfe38b5177249f9a9bc70acc09033b6d4 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Tue, 21 Mar 2017 15:03:04 +0100
Subject: [PATCH 14/19] Add missing translation for protocol load [SCI-1125]

---
 config/locales/en.yml | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 65b75d20b..684c25a39 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1040,6 +1040,12 @@ en:
     start_edit_wopi_file_result: "<i>%{user}</i> started editing File %{file} on Result <strong>%{result}</strong>."
     unlock_wopi_file_step: "<i>%{user}</i>  closed File %{file} for editing on Step %{step} <strong>%{step_name}</strong>."
     unlock_wopi_file_result: "<i>%{user}</i> started editing File %{file} on Result <strong>%{result}</strong>."
+    load_protocol_from_file: "<i>%{user}</i> loaded protocol <strong>%{protocol}</strong> from file."
+    load_protocol_from_repository: "<i>%{user}</i> loaded protocol <strong>%{protocol}</strong> from repository."
+    revert_protocol: "<i>%{user}</i> reverted protocol <strong>%{protocol}</strong> from repository."
+    create_report: "<i>%{user}</i> created report <strong>%{report}</strong>."
+    delete_report: "<i>%{user}</i> deleted report <strong>%{report}</strong>."
+    edit_report: "<i>%{user}</i> edited report <strong>%{report}</strong>."
 
   user_my_modules:
     new:
@@ -1071,14 +1077,6 @@ en:
       create: "Add comment"
     create:
       success_flash: "Successfully added comment to result."
-    load_protocol_from_file: "<i>%{user}</i> loaded protocol <strong>%{protocol}</strong> from file."
-    load_protocol_from_repository: "<i>%{user}</i> loaded protocol <strong>%{protocol}</strong> from repository."
-    revert_protocol: "<i>%{user}</i> reverted protocol <strong>%{protocol}</strong> from repository."
-    create_report: "<i>%{user}</i> created report <strong>%{report}</strong>."
-    delete_report: "<i>%{user}</i> deleted report <strong>%{report}</strong>."
-    edit_report: "<i>%{user}</i> edited report <strong>%{report}</strong>."
-    assign_sample: "<i>%{user}</i> assigned sample(s) <strong>%{samples}</strong> to task(s) <strong>%{tasks}</strong>."
-    unassign_sample: "<i>%{user}</i> unassigned sample(s) <strong>%{samples}</strong> from task(s) <strong>%{tasks}</strong>."
 
   users:
     enums:

From ee65e46fc712c49e7c35a6a97f014b432b3e3550 Mon Sep 17 00:00:00 2001
From: Luka Murn <murn.luka@gmail.com>
Date: Wed, 22 Mar 2017 10:37:11 +0100
Subject: [PATCH 15/19] Remove 'nokogiri' Gem being included twice

---
 Gemfile | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Gemfile b/Gemfile
index f8a685000..fa1a3f747 100644
--- a/Gemfile
+++ b/Gemfile
@@ -68,8 +68,6 @@ gem 'tinymce-rails' # Rich text editor
 
 gem 'base62' # Used for smart annotations
 
-gem 'nokogiri' # XML parser
-
 group :development, :test do
   gem 'byebug'
   gem 'better_errors'

From 2edebb282a2e91812cd471180962b572287084d1 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Wed, 22 Mar 2017 16:24:48 +0100
Subject: [PATCH 16/19] Add team_id field to assets and tables [SCI-1046]

---
 app/controllers/protocols_controller.rb       |  4 ++-
 app/controllers/result_assets_controller.rb   |  2 ++
 app/controllers/result_tables_controller.rb   |  4 +--
 app/controllers/steps_controller.rb           | 20 +++++++++++++
 app/models/asset.rb                           |  1 +
 app/models/protocol.rb                        |  4 +--
 app/models/table.rb                           |  1 +
 app/utilities/protocols_importer.rb           | 14 +++++----
 ...2095856_add_team_id_to_asset_and_tables.rb | 29 +++++++++++++++++++
 9 files changed, 68 insertions(+), 11 deletions(-)
 create mode 100644 db/migrate/20170322095856_add_team_id_to_asset_and_tables.rb

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index 302ddcc6c..8b7c5dd93 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -521,7 +521,9 @@ class ProtocolsController < ApplicationController
         transaction_error = false
         Protocol.transaction do
           begin
-            import_into_existing(@protocol, @protocol_json, current_user)
+            import_into_existing(
+              @protocol, @protocol_json, current_user, current_team
+            )
           rescue Exception
             transaction_error = true
             raise ActiveRecord:: Rollback
diff --git a/app/controllers/result_assets_controller.rb b/app/controllers/result_assets_controller.rb
index 6cdea4b86..3ce0b8745 100644
--- a/app/controllers/result_assets_controller.rb
+++ b/app/controllers/result_assets_controller.rb
@@ -29,6 +29,7 @@ class ResultAssetsController < ApplicationController
     @asset = Asset.new(result_params[:asset_attributes])
     @asset.created_by = current_user
     @asset.last_modified_by = current_user
+    @asset.team = current_team
     @result = Result.new(
       user: current_user,
       my_module: @my_module,
@@ -98,6 +99,7 @@ class ResultAssetsController < ApplicationController
       asset = Asset.find_by_id(update_params[:asset_attributes][:id])
       asset.created_by = current_user
       asset.last_modified_by = current_user
+      asset.team = current_team
       @result.asset = asset
     end
 
diff --git a/app/controllers/result_tables_controller.rb b/app/controllers/result_tables_controller.rb
index c2e640474..7c3820625 100644
--- a/app/controllers/result_tables_controller.rb
+++ b/app/controllers/result_tables_controller.rb
@@ -31,6 +31,7 @@ class ResultTablesController < ApplicationController
   def create
     @table = Table.new(result_params[:table_attributes])
     @table.created_by = current_user
+    @table.team = current_team
     @table.last_modified_by = current_user
     @result = Result.new(
       user: current_user,
@@ -92,6 +93,7 @@ class ResultTablesController < ApplicationController
     update_params = result_params
     @result.last_modified_by = current_user
     @result.table.last_modified_by = current_user
+    @result.table.team = current_team
     @result.assign_attributes(update_params)
     flash_success = t("result_tables.update.success_flash",
       module: @my_module.name)
@@ -218,6 +220,4 @@ class ResultTablesController < ApplicationController
       ]
     )
   end
-
 end
-
diff --git a/app/controllers/steps_controller.rb b/app/controllers/steps_controller.rb
index e057c2270..c781102c6 100644
--- a/app/controllers/steps_controller.rb
+++ b/app/controllers/steps_controller.rb
@@ -33,6 +33,14 @@ class StepsController < ApplicationController
     @step.protocol = @protocol
     @step.user = current_user
     @step.last_modified_by = current_user
+    @step.assets.each do |asset|
+      asset.created_by = current_user
+      asset.team = current_team
+    end
+    @step.tables.each do |table|
+      table.created_by = current_user
+      table.team = current_team
+    end
 
     # Update default checked state
     @step.checklists.each do |checklist|
@@ -133,6 +141,18 @@ class StepsController < ApplicationController
       @step.assign_attributes(step_params_all)
       @step.last_modified_by = current_user
 
+      @step.assets.each do |asset|
+        asset.created_by = current_user if asset.new_record?
+        asset.last_modified_by = current_user unless asset.new_record?
+        asset.team = current_team
+      end
+
+      @step.tables.each do |table|
+        table.created_by = current_user if table.new_record?
+        table.last_modified_by = current_user unless table.new_record?
+        table.team = current_team
+      end
+
       if @step.save
         @step.reload
 
diff --git a/app/models/asset.rb b/app/models/asset.rb
index dcce691a1..f31358cef 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -48,6 +48,7 @@ class Asset < ActiveRecord::Base
   belongs_to :last_modified_by,
              foreign_key: 'last_modified_by_id',
              class_name: 'User'
+  belongs_to :team
   has_one :step_asset,
           inverse_of: :asset,
           dependent: :destroy
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 17d658fb4..79efff5ad 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -291,8 +291,6 @@ class Protocol < ActiveRecord::Base
           )
           item2.created_by = current_user
           item2.last_modified_by = current_user
-          p item
-          p item2
           item2.save
         end
 
@@ -306,6 +304,7 @@ class Protocol < ActiveRecord::Base
           asset.file_file_size
         )
         asset2.created_by = current_user
+        asset2.team = dest.team
         asset2.last_modified_by = current_user
         asset2.file_processing = true if asset.is_image?
         asset2.save
@@ -323,6 +322,7 @@ class Protocol < ActiveRecord::Base
         table2 = Table.new(name: table.name, contents: table.contents)
         table2.created_by = current_user
         table2.last_modified_by = current_user
+        table2.team = dest.team
         step2.tables << table2
       end
     end
diff --git a/app/models/table.rb b/app/models/table.rb
index cf9874389..45ed3252e 100644
--- a/app/models/table.rb
+++ b/app/models/table.rb
@@ -10,6 +10,7 @@ class Table < ActiveRecord::Base
 
   belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User'
   belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User'
+  belongs_to :team
   has_one :step_table, inverse_of: :table
   has_one :step, through: :step_table
 
diff --git a/app/utilities/protocols_importer.rb b/app/utilities/protocols_importer.rb
index a44e8c897..0e0edddf1 100644
--- a/app/utilities/protocols_importer.rb
+++ b/app/utilities/protocols_importer.rb
@@ -22,18 +22,18 @@ module ProtocolsImporter
     protocol.save!
 
     # Protocol is saved, populate it
-    populate_protocol(protocol, protocol_json, user)
+    populate_protocol(protocol, protocol_json, user, team)
 
     return protocol
   end
 
-  def import_into_existing(protocol, protocol_json, user)
+  def import_into_existing(protocol, protocol_json, user, team)
     # Firstly, destroy existing protocol's contents
     protocol.destroy_contents(user)
     protocol.reload
 
     # Alright, now populate the protocol
-    populate_protocol(protocol, protocol_json, user)
+    populate_protocol(protocol, protocol_json, user, team)
     protocol.reload
 
     # Unlink the protocol
@@ -43,7 +43,7 @@ module ProtocolsImporter
 
   private
 
-  def populate_protocol(protocol, protocol_json, user)
+  def populate_protocol(protocol, protocol_json, user, team)
     protocol.reload
 
     asset_ids = []
@@ -93,7 +93,8 @@ module ProtocolsImporter
             name: table_json['name'],
             contents: Base64.decode64(table_json['contents']),
             created_by: user,
-            last_modified_by: user
+            last_modified_by: user,
+            team: team
           )
           StepTable.create!(
             step: step,
@@ -106,7 +107,8 @@ module ProtocolsImporter
         step_json["assets"].values.each do |asset_json|
           asset = Asset.new(
             created_by: user,
-            last_modified_by: user
+            last_modified_by: user,
+            team: team
           )
 
           # Decode the file bytes
diff --git a/db/migrate/20170322095856_add_team_id_to_asset_and_tables.rb b/db/migrate/20170322095856_add_team_id_to_asset_and_tables.rb
new file mode 100644
index 000000000..fa6a8b2ae
--- /dev/null
+++ b/db/migrate/20170322095856_add_team_id_to_asset_and_tables.rb
@@ -0,0 +1,29 @@
+class AddTeamIdToAssetAndTables < ActiveRecord::Migration
+  def change
+    add_column :assets, :team_id, :integer
+    add_index :assets, :team_id
+
+    add_column :tables, :team_id, :integer
+    add_index :tables, :team_id
+
+    Asset.find_each do |asset|
+      if asset.result
+        asset.update_columns(
+          team_id: asset.result.my_module.experiment.project.team_id
+        )
+      elsif asset.step
+        asset.update_columns(team_id: asset.step.protocol.team_id)
+      end
+    end
+
+    Table.find_each do |table|
+      if table.result
+        table.update_columns(
+          team_id: table.result.my_module.experiment.project.team_id
+        )
+      elsif table.step
+        table.update_columns(team_id: table.step.protocol.team_id)
+      end
+    end
+  end
+end

From 541998bde623a7a8f6b6d1acf630139927ec64a4 Mon Sep 17 00:00:00 2001
From: Luka Murn <murn.luka@gmail.com>
Date: Thu, 23 Mar 2017 14:37:47 +0100
Subject: [PATCH 17/19] Bump version to 1.9.0

---
 config/initializers/constants.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/initializers/constants.rb b/config/initializers/constants.rb
index 166980bb5..9c4109278 100644
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@@ -190,7 +190,7 @@ class Constants
   #=============================================================================
 
   # Application version
-  APP_VERSION = '1.8.1'.freeze
+  APP_VERSION = '1.9.0'.freeze
 
   TEXT_EXTRACT_FILE_TYPES = [
     'application/pdf',

From d2c8e9a39578b8163285676060a247f731b069fe Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Fri, 24 Mar 2017 14:46:20 +0100
Subject: [PATCH 18/19] Set team for assets and tables in generators [SCI-1046]

---
 app/utilities/delayed_uploader_tutorial.rb | 11 +++++++----
 app/utilities/first_time_data_generator.rb | 23 ++++++++++++++++++++++
 2 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/app/utilities/delayed_uploader_tutorial.rb b/app/utilities/delayed_uploader_tutorial.rb
index d7a7a58db..993e519cb 100644
--- a/app/utilities/delayed_uploader_tutorial.rb
+++ b/app/utilities/delayed_uploader_tutorial.rb
@@ -1,11 +1,12 @@
 module DelayedUploaderTutorial
   # Get asset from tutorial_files folder
-  def self.get_asset(user, file_name)
+  def self.get_asset(user, team, file_name)
     Asset.new(
       file: File.open(
         "#{Rails.root}/app/assets/tutorial_files/#{file_name}", 'r'
       ),
       created_by: user,
+      team: team,
       last_modified_by: user
     )
   end
@@ -15,11 +16,12 @@ module DelayedUploaderTutorial
   def self.generate_result_asset(
     my_module:,
     current_user:,
+    current_team:,
     result_name:,
     created_at: Time.now,
     file_name:
   )
-    temp_asset = get_asset(current_user, file_name)
+    temp_asset = get_asset(current_user, current_team, file_name)
     temp_result = Result.new(
       created_at: created_at,
       user: current_user,
@@ -48,8 +50,9 @@ module DelayedUploaderTutorial
   end
 
   # Adds asset to existing step
-  def self.add_step_asset(step:, current_user:, file_name:)
-    temp_asset = DelayedUploaderTutorial.get_asset(current_user, file_name)
+  def self.add_step_asset(step:, current_user:, current_team:, file_name:)
+    temp_asset =
+      DelayedUploaderTutorial.get_asset(current_user, current_team, file_name)
     step.assets << temp_asset
     temp_asset.post_process_file(step.my_module.experiment.project.team)
   end
diff --git a/app/utilities/first_time_data_generator.rb b/app/utilities/first_time_data_generator.rb
index 82a480e7f..5a30fed09 100644
--- a/app/utilities/first_time_data_generator.rb
+++ b/app/utilities/first_time_data_generator.rb
@@ -422,6 +422,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[0],
       current_user: user,
+      current_team: team,
       result_name: 'sF',
       created_at: generate_random_time(my_modules[0].created_at, 2.days),
       file_name: 'samples.txt'
@@ -440,6 +441,7 @@ module FirstTimeDataGenerator
     )
     temp_result.table = Table.new(
       created_by: user,
+      team: team,
       contents: tab_content['module1']['experimental_design']
     )
     temp_result.save
@@ -467,6 +469,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[1].protocol.steps.where('position = 0').take,
       current_user: user,
+      current_team: team,
       file_name: 'sample-potatoe.txt'
     )
 
@@ -474,6 +477,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[1],
       current_user: user,
+      current_team: team,
       result_name: 'PVY-inoculated plant, symptoms',
       created_at: generate_random_time(my_modules[1].created_at, 1.days),
       file_name: 'DSCN0660.JPG'
@@ -482,6 +486,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[1],
       current_user: user,
+      current_team: team,
       result_name: 'mock-inoculated plant',
       created_at: generate_random_time(my_modules[1].created_at, 2.days),
       file_name: 'DSCN0354.JPG'
@@ -490,6 +495,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[1],
       current_user: user,
+      current_team: team,
       result_name: 'Height of plants at 6dpi',
       created_at: generate_random_time(my_modules[1].created_at, 3.days),
       file_name: '6dpi_height.JPG'
@@ -541,6 +547,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[2].protocol.steps.where('position = 1').take,
       current_user: user,
+      current_team: team,
       file_name: 'RNeasy-Plant-Mini-Kit-EN.pdf'
     )
 
@@ -559,6 +566,7 @@ module FirstTimeDataGenerator
     )
     temp_result.table = Table.new(
       created_by: user,
+      team: team,
       contents: tab_content['module3']['nanodrop']
     )
     temp_result.save
@@ -581,6 +589,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[2],
       current_user: user,
+      current_team: team,
       result_name: 'Agarose gel electrophoresis of totRNA samples',
       created_at: generate_random_time(my_modules[2].created_at, 3.days),
       file_name: 'totRNA_gel.jpg'
@@ -599,6 +608,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[3].protocol.steps.where('position = 0').take,
       current_user: user,
+      current_team: team,
       file_name: 'G2938-90034_KitRNA6000Nano_ebook.pdf'
     )
 
@@ -606,6 +616,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[3],
       current_user: user,
+      current_team: team,
       result_name: 'Result of RNA integrity',
       created_at: generate_random_time(my_modules[3].created_at, 2.days),
       file_name: 'Bioanalyser_result.JPG'
@@ -671,24 +682,28 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[5].protocol.steps.where('position = 0').take,
       current_user: user,
+      current_team: team,
       file_name: 'sample_preparation.JPG'
     )
 
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[5].protocol.steps.where('position = 1').take,
       current_user: user,
+      current_team: team,
       file_name: 'reaction_setup.JPG'
     )
 
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[5].protocol.steps.where('position = 2').take,
       current_user: user,
+      current_team: team,
       file_name: 'cycling_conditions.JPG'
     )
 
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[5].protocol.steps.where('position = 3').take,
       current_user: user,
+      current_team: team,
       file_name: '96plate.doc'
     )
 
@@ -702,6 +717,7 @@ module FirstTimeDataGenerator
     )
     temp_result.table = Table.new(
       created_by: user,
+      team: team,
       contents: tab_content['module6']['distribution'] % {
         sample0: samples_to_assign[0].name,
         sample1: samples_to_assign[1].name,
@@ -729,6 +745,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[5],
       current_user: user,
+      current_team: team,
       result_name: 'Mixtures and plate setup',
       created_at: generate_random_time(my_modules[5].created_at, 2.days),
       file_name: 'Mixes_Templats.xls'
@@ -737,6 +754,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[5],
       current_user: user,
+      current_team: team,
       result_name: 'Raw data from ABI 7300',
       created_at: generate_random_time(my_modules[5].created_at, 3.days),
       file_name: 'BootCamp-Experiment-results-20122.sds'
@@ -745,6 +763,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[5],
       current_user: user,
+      current_team: team,
       result_name: 'All results - curves',
       created_at: generate_random_time(my_modules[5].created_at, 4.days),
       file_name: 'curves.JPG'
@@ -791,6 +810,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).add_step_asset(
       step: my_modules[7].protocol.steps.where('position = 0').take,
       current_user: user,
+      current_team: team,
       file_name: 'ddCq-quantification_diagnostics-template.xls'
     )
 
@@ -798,6 +818,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[7],
       current_user: user,
+      current_team: team,
       result_name: 'Results of ddCq method',
       created_at: generate_random_time(my_modules[7].created_at, 1.days),
       file_name: 'ddCq-quantification_diagnostics-results.xls'
@@ -806,6 +827,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[7],
       current_user: user,
+      current_team: team,
       result_name: 'Dilution curve and efficiency',
       created_at: generate_random_time(my_modules[7].created_at, 2.days),
       file_name: 'dilution_curve-efficiency.JPG'
@@ -814,6 +836,7 @@ module FirstTimeDataGenerator
     DelayedUploaderTutorial.delay(queue: :tutorial).generate_result_asset(
       my_module: my_modules[7],
       current_user: user,
+      current_team: team,
       result_name: 'Relative quantification results',
       created_at: generate_random_time(my_modules[7].created_at, 3.days),
       file_name: 'result-ddCq.JPG'

From 239a44c26bd1a3f7c8c8b1d6eee46ff935e2a119 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Fri, 24 Mar 2017 16:25:50 +0100
Subject: [PATCH 19/19] change send to public_send

---
 app/helpers/reports_helper.rb | 2 +-
 app/models/report_element.rb  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/helpers/reports_helper.rb b/app/helpers/reports_helper.rb
index d66f6eeda..9c15582b7 100644
--- a/app/helpers/reports_helper.rb
+++ b/app/helpers/reports_helper.rb
@@ -44,7 +44,7 @@ module ReportsHelper
     # ReportExtends is located in config/initializers/extends/report_extends.rb
 
     ReportElement.type_ofs.keys.each do |type|
-      next unless element.send("#{type}?")
+      next unless element.public_send("#{type}?")
       local_sym = type.split('_').last.to_sym
       local_sym = type
                   .split('_')
diff --git a/app/models/report_element.rb b/app/models/report_element.rb
index 14cba7cf1..398a69883 100644
--- a/app/models/report_element.rb
+++ b/app/models/report_element.rb
@@ -56,7 +56,7 @@ class ReportElement < ActiveRecord::Base
     ReportExtends::SET_ELEMENT_REFERENCES_LIST.each do |el_ref|
       check = el_ref.check(self)
       next unless check
-      self.send("#{el_ref.element}=", ref_id)
+      public_send("#{el_ref.element}=", ref_id)
       break
     end
   end