From 11b2ef311249a674042690e6c3924a9bac55f400 Mon Sep 17 00:00:00 2001
From: Zanz2 <zan.zagar@hotmail.com>
Date: Mon, 25 Sep 2017 13:53:32 +0200
Subject: [PATCH]  Made code nicer, hopefully not unintentionally breaking
 something

---
 app/controllers/protocols_controller.rb       | 325 ++++++++-------
 .../_import_json_protocol_modal.html.erb      |  18 +-
 ...mport_json_protocol_preview_modal.html.erb | 389 ++++++++++--------
 app/views/protocols/index.html.erb            |   8 -
 config/routes.rb                              |   4 -
 5 files changed, 389 insertions(+), 355 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index 62ec530e0..05c55fad1 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -600,176 +600,189 @@ class ProtocolsController < ApplicationController
     end
   end
 
-def protocolsio_import_create
-  @protocolsio_too_big=false
-  file_size=(File.size(params[:json_file].path))
+  def protocolsio_import_create
+    @protocolsio_too_big = false
+    file_size = File.size(params[:json_file].path)
 
-  if(file_size/1000>Constants::FILE_MAX_SIZE_MB)
-    @protocolsio_too_big=true
+    if file_size / 1000 > Constants::FILE_MAX_SIZE_MB
+      @protocolsio_too_big = true
+      respond_to do |format|
+        format.js {}
+        # if file is too big, default to the js.erb file,
+        # named the same as this controller
+        # where a javascript alert is called
+      end
+    end
+    json_file_contents = File.read(params[:json_file].path)
+    json_file_contents.gsub! '\"', "'"
+    # escaped double quotes too stressfull, html works with single quotes too
+    # json double quotes dont get escaped since they dont match \"
+    @json_object = JSON.parse(json_file_contents)
+    @protocol = Protocol.new
     respond_to do |format|
-      format.js {} #if file is too big, default to the js.erb file named the same as this controller
-      # where a javascript alert is called
+      format.js {} # go to the js.erb file named the same as this controller,
+      # where a preview modal is rendered,
+      # and some modals get closed and opened
     end
   end
-  json_file_contents=File.read(params[:json_file].path)
-  json_file_contents.gsub! '\"', "'" #escaped double quotes too stressfull, html works with single quotes too
-  #json double quotes dont get escaped since they dont match \", they are just "
-  @json_object=JSON.parse(json_file_contents)
-  @protocol=Protocol.new
-  respond_to do |format|
-    format.js {}  # go to the js.erb file named the same as this controller, where a preview modal is rendered, and
-    # some modals get closed and opened
-  end
-end
 
-
-def protocolsio_import_save
-  @json_object=JSON.parse(params["json_object"])
-  @import_object=Hash.new
-  @import_object["name"]=params["protocol"]["name"]
-  # since scinote only has description field, while protocols.io has many many others, here i am basically
-  #putting everything important from protocols.io into description
-  description_array = [ "before_start","warning","guidelines","manuscript_citation","publish_date","created_on","vendor_name","vendor_link","keywords","tags","link" ]
-  description_string=params["protocol"]["description"]
-  description_array.each do |element|
-    if(element=="created_on")
-      if(@json_object[element]&&@json_object[element]!="")
-        new_element = element.slice(0,1).capitalize + element.slice(1..-1)
-        new_element= new_element.gsub("_"," ")
-        description_string=description_string+new_element.to_s+":  "+Sanitize.clean(params["protocol"]["created_at"].to_s)+"\n"
+  def protocolsio_import_save
+    @json_object = JSON.parse(params['json_object'])
+    @import_object = {}
+    @import_object['name'] = params['protocol']['name']
+    # since scinote only has description field, and protocols.io has many others
+    # ,here i am putting everything important from protocols.io into description
+    description_array = %w[
+      (before_start warning guidelines manuscript_citation publish_date
+      created_on vendor_name vendor_link keywords tags link)
+    ]
+    description_string = Sanitize.clean(params['protocol']['description'])
+    description_array.each do |element|
+    if element == 'created_on'
+      if @json_object[element] && @json_object[element] != ''
+        new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
+        new_element = new_element.tr('_', ' ')
+        description_string =
+          description_string +
+          new_element.to_s + ':  ' +
+          Sanitize.clean(params['protocol']['created_at'].to_s) + "\n"
       end
     else
-      if(element=="tags")
-        if(@json_object[element].any?&&@json_object[element]!="")
-          new_element = element.slice(0,1).capitalize + element.slice(1..-1)
-          new_element= new_element.gsub("_"," ")
-          description_string=description_string+new_element.to_s+": "
+      if element == 'tags'
+        if @json_object[element].any? && @json_object[element] != ''
+          new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
+          new_element = new_element.tr('_', ' ')
+          description_string = description_string + new_element.to_s + ': '
           @json_object[element].each do |tag|
-            description_string=description_string+Sanitize.clean(tag["tag_name"])+" , "
+            description_string =
+              description_string +
+              Sanitize.clean(tag['tag_name']) + ' , '
           end
-          description_string=description_string+"\n"
+          description_string += "\n"
         end
-      #Since protocols description field doesnt show html, i just remove it here because its even messier Otherwise
-      #what this does is basically appends "FIELD NAME: "+" FIELD VALUE" to description for various fields
+      # Since protocols description field doesnt show html,i just remove it here
+      # because its even messier Otherwise
+      # what this does is basically appends "FIELD NAME: "+" FIELD VALUE"
+      # to description for various fields
       else
-        if(@json_object[element]&&@json_object[element]!="")
-          new_element = element.slice(0,1).capitalize + element.slice(1..-1)
-          new_element= new_element.gsub("_"," ")
-          description_string=description_string+new_element.to_s+":  "+Sanitize.clean(@json_object[element].to_s)+"\n"
+        if @json_object[element] && @json_object[element] != ''
+          new_element = element.slice(0, 1).capitalize + element.slice(1..-1)
+          new_element = new_element.tr('_', ' ')
+          description_string +=
+            new_element.to_s + ':  ' +
+            Sanitize.clean(@json_object[element].to_s) + "\n"
         end
       end
     end
-  end
-  @import_object["authors"]=params["protocol"]["authors"]
-  @import_object["created_at"]=params["protocol"]["created_at"]
-  @import_object["updated_at"]=params["protocol"]["last_modified"]
-  @import_object["description"]=description_string
-  @import_object["steps"]=Hash.new
-  counter=0
-  step_pos=-1
-  #these whitelists are there to not let some useless step components trough, that always have data set to null (data doesnt get imported over to json)
-  whitelist_simple=["1","6","17"] #(simple to map) id 1= step description, id 6= section (title), id 17= expected result
-  whitelist_complex=["8","9","15","18","19","20"] #(complex mapping with nested hashes) id 8 = software package, id 9 = dataset, id 15 = command, id 18 = attached sub protocol
-  # id 19= safety information ,id 20= regents (materials, like scinote samples kind of)
-  @json_object["steps"].each do |step|
-        step_pos+=1
-        counter+=1
-        @import_object["steps"][step_pos.to_s]=Hash.new
-        @import_object["steps"][step_pos.to_s]["position"]=step_pos
+    end
+    @import_object['authors'] = params['protocol']['authors']
+    @import_object['created_at'] = params['protocol']['created_at']
+    @import_object['updated_at'] = params['protocol']['last_modified']
+    @import_object['description'] = description_string
+    @import_object['steps'] = {}
+    counter = 0
+    step_pos = -1
+    # these whitelists are there to not let some useless step components trough,
+    # that always have data set to null (data doesnt get imported over to json)
+    whitelist_simple = %w(1 6 17)
+    # (simple to map) id 1= step description, id 6= section (title),
+    # id 17= expected result
+    whitelist_complex = %w(8 9 15 18 19 20)
+    # (complex mapping with nested hashes) id 8 = software package,
+    # id 9 = dataset, id 15 = command, id 18 = attached sub protocol
+    # id 19= safety information ,
+    # id 20= regents (materials, like scinote samples kind of)
+    @json_object['steps'].each do |step|
+    step_pos += 1
+    counter += 1
+    @import_object['steps'][step_pos.to_s] = {}
+    @import_object['steps'][step_pos.to_s]['position'] = step_pos
 
-        step["components"].each do |key,value|
-          element_string=nil
-          if counter<=1 #here i made an if to distinguish the first step from the others, because the first step
-            #sometimes has index values as keys instead of hashes, for no good reason
-             if value.class==Hash
-             key=value
-             end
-           end
-       if whitelist_simple.include?(key["component_type_id"])
+    step['components'].each do |key,value|
+    element_string = nil
+    if counter <= 1
+      # here i made an if to distinguish the first step from the others,
+      # because the first step
+      # sometimes has index values as keys instead of hashes, for no good reason
+      key = value if value.class == Hash
+    end
+    if whitelist_simple.include?(key['component_type_id'])
 
-         case key["component_type_id"]
-         when "1"
-           if !key["data"].nil? && key["data"]!=""
-
-             element_string="<br>"+(key["data"])+"<br>"
-              if(@import_object["steps"][step_pos.to_s]["description"])
-                @import_object["steps"][step_pos.to_s]["description"]<<element_string
-              else
-                @import_object["steps"][step_pos.to_s]["description"]=element_string
-              end
-            else
-              @import_object["steps"][step_pos.to_s]["description"]||="Description missing!"
-            end
-         when "6"
-           if !key["data"].nil? && key["data"]!=""
-          @import_object["steps"][step_pos.to_s]["name"]=key["data"]
+      case key['component_type_id']
+      when '1'
+        if !key['data'].nil? && key['data'] != ''
+          element_string = '<br>' + (key['data']) + '<br>'
+          if @import_object['steps'][step_pos.to_s]['description']
+            @import_object['steps'][step_pos.to_s]['description'] << element_string
           else
-          @import_object["steps"][step_pos.to_s]["name"]="Step"
-        end
-         when "17"
-           if !key["data"].nil? && key["data"]!=""
-
-             element_string="<br><strong>Expected result: </strong>"+(key["data"])+"<br>"
-             @import_object["steps"][step_pos.to_s]["description"]<<element_string
+            @import_object['steps'][step_pos.to_s]['description'] = element_string
           end
         else
+          @import_object['steps'][step_pos.to_s]['description'] ||= 'Description missing!'
+        end
+      when '6'
+        if !key['data'].nil? && key['data'] != ''
+          @import_object['steps'][step_pos.to_s]['name'] = key['data']
+        else
+          @import_object['steps'][step_pos.to_s]['name'] = 'Step'
+        end
+      when '17'
+        if !key['data'].nil? && key['data'] != ''
+          element_string = '<br><strong>Expected result: </strong>' + (key['data']) + '<br>'
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
 
-        end#(complex mapping with nested hashes) id 8 = software package, id 9 = dataset,
-        #id 15 = command, id 18 = attached sub protocol
-        # id 19= safety information ,id 20= regents (materials, like scinote samples kind of)
+        end
+      end
+      # (complex mapping with nested hashes)
+      # id 8 = software package, id 9 = dataset,
+      # id 15 = command, id 18 = attached sub protocol
+      # id 19= safety information ,
+      # id 20= regents (materials, like scinote samples kind of)
 
-      elsif key && whitelist_complex.include?(key["component_type_id"])
-        case key["component_type_id"]
-        when "8"
-          if(key["source_data"]["name"]&&key["source_data"]["developer"]&&key["source_data"]["version"]&&key["source_data"]["link"]&&key["source_data"]["repository"]&&key["source_data"]["os_name"]&&key["source_data"]["os_version"])
-          element_string="<br><strong>Software package: </strong>"+(key["source_data"]["name"])+"<br>Developer: "+(key["source_data"]["developer"])+"<br>Version: "+(key["source_data"]["version"])+"<br>Link: "+(key["source_data"]["link"])+"<br>Repository: "+(key["source_data"]["repository"])+"<br> OS name , OS version: "+(key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"])
-          @import_object["steps"][step_pos.to_s]["description"]<<element_string
-          end
-        when "9"
-          if(key["source_data"]["name"]&&key["source_data"]["link"])
-          element_string="<br><strong>Dataset: </strong>"+(key["source_data"]["name"])+"<br>Link: "+(key["source_data"]["link"])
-          @import_object["steps"][step_pos.to_s]["description"]<<element_string
-          end
-         when "15"
-           if(key["source_data"]["name"]&&key["source_data"]["description"]&&key["source_data"]["os_name"]&&key["source_data"]["os_version"])
-           element_string="<br><strong>Command: </strong>"+(key["source_data"]["name"])+"<br>Description: "+(key["source_data"]["description"])+"<br>OS name , OS version: "+(key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"])
-           @import_object["steps"][step_pos.to_s]["description"]<<element_string
-          end
-         when "18"
-           if(key["source_data"]["protocol_name"]&&key["source_data"]["full_name"]&&key["source_data"]["link"])
-           element_string="<br><strong>This protocol also contains an attached sub-protocol: </strong>"+(key["source_data"]["protocol_name"])+"<br>Author: "+(key["source_data"]["full_name"])+"<br>Link: "+(key["source_data"]["link"])
-           @import_object["steps"][step_pos.to_s]["description"]<<element_string
+    elsif key && whitelist_complex.include?(key['component_type_id'])
+      case key['component_type_id']
+      when '8'
+        if key['source_data']['name'] && key['source_data']['developer'] && key['source_data']['version'] && key['source_data']['link'] && key['source_data']['repository'] && key['source_data']['os_name'] && key['source_data']['os_version']
+          element_string = '<br><strong>Software package: </strong>' + (key['source_data']['name']) + '<br>Developer: ' + (key['source_data']['developer']) + '<br>Version: ' + (key['source_data']['version']) + '<br>Link: ' + (key['source_data']['link']) + '<br>Repository: ' + (key['source_data']['repository']) + '<br> OS name , OS version: ' + (key['source_data']['os_name']) + ' , ' + (key['source_data']['os_version'])
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
+        end
+      when '9'
+        if key['source_data']['name'] && key['source_data']['link']
+          element_string='<br><strong>Dataset: </strong>' + (key['source_data']['name']) + '<br>Link: ' + (key['source_data']['link'])
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
+        end
+      when '15'
+        if key['source_data']['name'] && key['source_data']['description'] && key['source_data']['os_name'] && key['source_data']['os_version']
+          element_string = '<br><strong>Command: </strong>' + (key['source_data']['name']) + '<br>Description: ' + (key['source_data']['description']) + '<br>OS name , OS version: ' + (key['source_data']['os_name']) + ' , ' + (key['source_data']['os_version'])
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
+        end
+      when '18'
+        if key['source_data']['protocol_name'] && key['source_data']['full_name'] && key['source_data']['link']
+          element_string = '<br><strong>This protocol also contains an attached sub-protocol: </strong>' + (key['source_data']['protocol_name']) + '<br>Author: ' + (key['source_data']['full_name']) + '<br>Link: ' + (key['source_data']['link'])
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
 
-          end
-         #if key["source_data"]["link"]&&key["source_data"]["link"]!=""
-         #end
-         when "19"
-           if(key["source_data"]["body"]&&key["source_data"]["link"])
-           element_string="<br><strong>Safety information: </strong>"+(key["source_data"]["body"])+"<br>Link: "+(key["source_data"]["link"])
-           @import_object["steps"][step_pos.to_s]["description"]<<element_string
-         end
-         when "20"
-         else
+        end
+      when '19'
+        if key['source_data']['body'] && key['source_data']['link']
+          element_string = '<br><strong>Safety information: </strong>' + (key['source_data']['body'])+'<br>Link: '+(key['source_data']['link'])
+          @import_object['steps'][step_pos.to_s]['description'] << element_string
+        end
+        # when '20' placeholder za materiale
+      end
+    end # finished step component iteration
+    end # finished looping over step components
+    end # steps
 
-         end
-       end #finished step component iteration
-
-
-    end #finished looping over step components
-  end #steps
-
-  protocol = nil
-  respond_to do |format|
+    protocol = nil
+    respond_to do |format|
     transaction_error = false
-    #@steps_object=JSON.parse(params["steps"]["steps_object"])
-    @protocolsio_general_error=false
+    @protocolsio_general_error = false
     Protocol.transaction do
       begin
-
+        # pass the import_object we made, current team,user
+        # and the type (private,public)
         protocol = import_new_protocol(@import_object, current_team, params[:type].to_sym, current_user)
-
       rescue Exception
-
         transaction_error = true
         raise ActiveRecord:: Rollback
       end
@@ -783,31 +796,25 @@ def protocolsio_import_save
       end
 
     if transaction_error
+      @protocolsio_general_error = true
+      #  format.json {
+      #    render json: { name: p_name, status: :bad_request },
+      # status: :bad_request
+      #  }
 
-      @protocolsio_general_error=true
-    #  format.json {
-    #    render json: { name: p_name, status: :bad_request }, status: :bad_request
-    #  }
-      format.js{}
-
-      #:location => root_url
-        #  protocolsDatatable.ajax.reload();
-        #  $('#modal-import-json-protocol-preview').modal('hide');
     else
-      @protocolsio_general_error=false
+      # General something went wrong, upload to db failed error
+      @protocolsio_general_error = false
       format.json {
-        render json: {
-          name: p_name, new_name: protocol.name, status: :ok
-        },
+        render json:
+       { name: p_name, new_name: protocol.name, status: :ok },
         status: :ok
       }
-      format.js{}
+    end
+    format.js {}
     end
   end
-end
 
-
-#
   def export
     # Make a zip output stream and send it to the client
     respond_to do |format|
diff --git a/app/views/protocols/import_export/_import_json_protocol_modal.html.erb b/app/views/protocols/import_export/_import_json_protocol_modal.html.erb
index 9caf6750e..cc82e9d53 100644
--- a/app/views/protocols/import_export/_import_json_protocol_modal.html.erb
+++ b/app/views/protocols/import_export/_import_json_protocol_modal.html.erb
@@ -1,21 +1,29 @@
-<div class="modal fade" id="modal-import-json-protocol" tabindex="-1" role="dialog" >
+<div
+  class="modal fade"
+  id="modal-import-json-protocol"
+  tabindex="-1"
+  role="dialog">
   <div class="modal-dialog" role="document">
     <div class="modal-content">
       <div class="modal-header">
-        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+          <span aria-hidden="true">&times;</span>
+        </button>
         <h4 class="modal-title"><%= t('protocols.index.modal_import_json_title') %></h4>
         <%= t("protocols.index.modal_import_json_notice") %>
       </div>
-                             <%= form_tag({ action: "protocolsio_import_create"}, id:"protocols_io_form", format: :json, multipart: true,remote: true,:method => "post") do %>
+      <%= form_tag({ action: "protocolsio_import_create"}, id:"protocols_io_form",
+      format: :json, multipart: true,remote: true,:method => "post") do %>
 
       <div class="modal-body">
 
-           <%= file_field_tag 'json_file', accept: '.txt' %>
+        <%= file_field_tag 'json_file', accept: '.txt' %>
 
       </div>
       <div class="modal-footer">
         <button type="button" class="btn btn-default" data-dismiss="modal"><%= t('general.cancel')%></button>
-        <%= submit_tag t("protocols.index.modal_import_json_submit"), class: "btn btn-default" %>
+        <%= submit_tag t("protocols.index.modal_import_json_submit"), class: "btn
+        btn-default" %>
       </div>
       <% end %>
 
diff --git a/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb b/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
index 6bf7ffa68..8a479cc19 100644
--- a/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
+++ b/app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
@@ -1,52 +1,59 @@
-<%= form_for(@protocol, :url => url_for(:controller => 'protocols', :action => 'protocolsio_import_save'),method: :post,format: :javascript,remote: true,:html => { :id => "protocolsio-import-form" }) do |f| %>
+<%= form_for(@protocol, :url => url_for(:controller => 'protocols', :action =>'protocolsio_import_save'),method: :post,format: :javascript,remote: true,:html=> { :id => "protocolsio-import-form" }) do |f| %>
 
-  <%= hidden_field_tag :json_object, JSON.generate(@json_object) %>
-  <%= hidden_field_tag :type, CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
-
-<div id="modal-import-json-protocol-preview" class="modal fade" role="dialog" tabindex="-1">
+<%= hidden_field_tag :json_object, JSON.generate(@json_object) %>
+<%= hidden_field_tag :type,
+CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
+<!--Get the type of protocol to import (private, public) from the url -->
+<div
+  id="modal-import-json-protocol-preview"
+  class="modal fade"
+  role="dialog"
+  tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">
       <div class="modal-header">
         <button type="button" class="close" data-dismiss="modal">&times;</button>
-        <h4 class="modal-title" data-role="header-import-into-protocol_protocols_io"><%= t("protocols.import_export.import_modal.title_import_into_protocol_protocols_io") %></h4>
+        <h4 class="modal-title" data-role="header-import-into-protocol_protocols_io"><%=
+          t("protocols.import_export.import_modal.title_import_into_protocol_protocols_io")
+          %></h4>
       </div>
       <div class="modal-body">
-        
-
 
         <!-- General protocol info -->
         <div class="form-group">
 
           <label><%= t("protocols.import_export.import_modal.name_label") %></label>
 
-       <%= f.text_field :name, :value => @json_object['protocol_name'], class: "form-control"  %>
+          <%= f.text_field :name, :value => @json_object['protocol_name'], class:
+          "form-control" %>
         </div>
         <div class="form-group">
           <label>
             <span class="glyphicon glyphicon-user"></span>&nbsp;<%= t("protocols.import_export.import_modal.authors_label") %>
           </label>
-          <%= f.text_field :authors, :value => @json_object['full_name'], class: "form-control"  %>
-
+          <%= f.text_field :authors, :value => @json_object['full_name'], class:
+          "form-control" %>
 
         </div>
         <div class="form-group">
           <label><%= t("protocols.import_export.import_modal.description_label") %></label>
 
-      <%= f.text_area :description, :value => @json_object['description'], class: "form-control"  %>
+          <%= f.text_area :description, :value => @json_object['description'], class:
+          "form-control" %>
         </div>
         <div class="form-group">
           <div class="row">
             <div class="col-xs-4">
               <label><%= t("protocols.import_export.import_modal.created_at_label") %></label>
 
-          <% display_created_at=Time.at(@json_object['created_on'].to_i) %>
-            <%= f.text_field :created_at, :value => display_created_at.to_s+" (Protocols.io value)",readonly: true, class: "form-control"  %>
+              <% display_created_at=Time.at(@json_object['created_on'].to_i) %>
+              <%= f.text_field :created_at, :value => display_created_at.to_s+"(Protocols.io value)",readonly: true, class: "form-control" %>
             </div>
             <div class="col-xs-4">
               <label><%= t("protocols.import_export.import_modal.updated_at_label") %></label>
 
               <% display_last_modified=Time.at(@json_object['last_modified'].to_i) %>
-            <%= f.text_field :last_modified, :value => display_last_modified.to_s+" (Protocols.io value)",readonly: true, class: "form-control"  %>
+              <%= f.text_field :last_modified, :value => display_last_modified.to_s+"(Protocols.io value)",readonly: true, class: "form-control" %>
             </div>
           </div>
         </div>
@@ -59,170 +66,189 @@
 
         <!-- Preview scroller -->
 
+        <div
+          class="import-protocols-modal-preview-container-json"
+          data-role="preview-container">
+          <hr>
 
-          <div class="import-protocols-modal-preview-container-json" data-role="preview-container">
+          <% if @json_object["before_start"]&&@json_object["before_start"]!="" %>
+
+          <strong>Before starting protocol information:</strong><br>
+          <%= (@json_object["before_start"]) %><br>
+
+          <% end %>
+          <% if @json_object["warning"]&&@json_object["warning"]!="" %>
+
+          <strong>Protocol warning:</strong><br>
+          <%= (@json_object["warning"]) %><br>
+
+          <% end %>
+          <% if @json_object["guidelines"]&&@json_object["guidelines"]!="" %>
+
+          <strong>Guidelines:</strong><br>
+          <%= (@json_object["guidelines"]) %><br>
+
+          <% end %>
+
+          <% if @json_object["link"]&&@json_object["link"]!="" %>
+
+          <br>
+          <strong>Supplied link:</strong><br>
+          <%= (@json_object["link"]) %>
+
+          <% end %>
+
+          <%  counter=0 %>
+          <%  whitelist_simple=["1","6","17"] %>
+          <%  whitelist_complex=["8","9","15","18","19","20"]%>
+          <% @json_object["steps"].each do |step| %>
+          <div style="display: block;">
             <hr>
-
-              <% if @json_object["before_start"]&&@json_object["before_start"]!="" %>
-
-                    <strong>Before starting protocol information:</strong><br>
-                    <%= (@json_object["before_start"]) %><br>
-
-
-                <% end %>
-              <% if @json_object["warning"]&&@json_object["warning"]!="" %>
-
-                    <strong>Protocol warning:</strong><br>
-                    <%= (@json_object["warning"]) %><br>
-
-
-              <% end %>
-              <% if @json_object["guidelines"]&&@json_object["guidelines"]!="" %>
-
-                    <strong>Guidelines:</strong><br>
-                    <%= (@json_object["guidelines"]) %><br>
-
-              <% end %>
-
-              <% if @json_object["link"]&&@json_object["link"]!="" %>
-
-                    <br><strong>Supplied link:</strong><br>
-                    <%= (@json_object["link"]) %>
-
-              <% end %>
-
-                <%  counter=0 %>
-                <%  whitelist_simple=["1","6","17"] %>
-                <%  whitelist_complex=["8","9","15","18","19","20"]%>
-            <% @json_object["steps"].each do |step| %>
-                  <div style="display: block;">
-                    <hr>
-                    <td>
-                      <div class="badge-num">
-                        <span class="badge-preview bg-primary size-digit-1">
-                          <b data-val="position"><%= (counter+=1) %></b>
-                        </span>
-                        &nbsp;
-                        &nbsp;
-                        <span class="step-panel-collapse-link" data-toggle="collapse">
-                          <span class="glyphicon collapse-step-icon glyphicon-collapse-up"></span>
-
-
-                    <%#=   Step guid (Protocols.io) :%><%#= step["guid"] %>
-                      <%# if counter>1  #only steps after the first one have previous step guid field valid%>
-                      <%#=Guid of previous step (Protocols.io) :%><%#= step["previous_guid"] %>
-                       <%# end %>
-                       <% title=nil %>
-            <% step["components"].each do |key1,value1| #finding section (title of step) %>
+            <td>
+              <div class="badge-num">
+                <span class="badge-preview bg-primary size-digit-1">
+                  <b data-val="position"><%= (counter+=1) %></b>
+                </span>
+                &nbsp; &nbsp;
+                <span class="step-panel-collapse-link" data-toggle="collapse">
+                  <span class="glyphicon collapse-step-icon glyphicon-collapse-up"></span>
+                  <%# this guid attributes were ommited because they didnt seem relevenat %>
+                  <%#=   Step guid (Protocols.io) :%><%#= step["guid"] %>
+                  <%# if counter>1 #only steps after the first one have previous step guid field
+                  valid%>
+                  <%#=Guid of previous step (Protocols.io) :%><%#= step["previous_guid"] %>
+                  <%# end %>
+                  <% title=nil %>
+                  <% step["components"].each do |key1,value1| #finding section (title of step) %>
 
                   <% if counter <=1 %>
-                    <% if value1.class==Hash %>
-                    <% key1=value1 %>
-                    <% end %>
-                    <% end %>
-                    <%  if(key1["component_type_id"]=="6") %>
-                      <% if(!key1["data"].nil? && key1["data"]!="") %>
-                      <%# byebug %>
-                        <% title ||=key1["data"] %>
-                      <% end %>
-                    <% end %>
+                  <% if value1.class==Hash %>
+                  <% key1=value1 %>
+                  <% end %>
+                  <% end %>
+                  <%  if(key1["component_type_id"]=="6") %>
+                  <% if(!key1["data"].nil? && key1["data"]!="") %>
+                  <% title ||=key1["data"] %>
+                  <% end %>
+                  <% end %>
 
-                    <% end %>
-          <% if title.nil? %>
-          <%# byebug %>
-          <% title ="Step" %>
-          <% end %>
-                <strong data-val="name"><%= title %></strong>
+                  <% end %>
+                  <% if title.nil? %>
+                  <% title ="Step" %>
+                  <% end %>
+                  <strong data-val="name"><%= title %></strong>
                 </span>
               </div>
               <br>
 
               <div class="tab-content">
-    <div class="tab-pane active" role="tabpanel">
-      <div data-val="description" class="ql-editor">
+                <div class="tab-pane active" role="tabpanel">
+                  <div data-val="description" class="ql-editor">
 
-
-            <% step["components"].each do |key,value|  %>
-                  <% if counter<=1 #here i made an if to distinguish the first step from the others, because the first step
-                    #sometimes has index values as keys instead of hashes
-                    %>
+                    <% step["components"].each do |key,value|  %>
+                    <% if counter<=1 %>
+                    <%#here i made an if to distinguish the first step from the
+                    others, because the first step #sometimes has index values as keys instead of
+                    hashes, you might see this elsewhere %>
                     <% if value.class==Hash %>
                     <% key=value %>
                     <% end %>
-                  <% end %>
-
-
+                    <% end %>
+                    <% # the below blocks of code output the various attributes if they exist and arent null or "" from the json object %>
                     <% if whitelist_simple.include?(key["component_type_id"]) && key["data"]!="" && key["data"] %>
                     <br>
                     <% case key["component_type_id"]%>
                     <% when "1" %>
-                <br><strong>Description: </strong> <%=key["data"]%><br>
+                    <br>
+                    <strong>Description:
+                    </strong>
+                    <%=key["data"]%><br>
                     <% when "17" %>
-                  <br><strong>Expected result: </strong> <%=key["data"]%><br>
-                    <% else %>
+                    <br>
+                    <strong>Expected result:
+                    </strong>
+                    <%=key["data"]%><br>
+                  <% else %>
                     <% end %>
                     <% elsif key && whitelist_complex.include?(key["component_type_id"]) %>
 
-                      <% case key["component_type_id"]%>
-                      <% when "8"%>
-                      <br>
-                      <strong><%= key["name"]+": " %></strong>  <%= (key["source_data"]["name"]) %>
-                      <br>
-                      Developer: <%= (key["source_data"]["developer"]) %>
-                      <br>
-                      Version: <%= (key["source_data"]["version"]) %>
-                      <br>
-                      Link: <%= (key["source_data"]["link"]) %>
-                      <br>
-                      Repository: <%= (key["source_data"]["repository"]) %>
-                      <br>
-                      OS name , OS version: <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
+                    <% case key["component_type_id"]%>
+                    <% when "8"%>
+                    <br>
+                    <strong><%= key["name"]+": " %></strong>
+                    <%= (key["source_data"]["name"]) %>
+                    <br>
+                    Developer:
+                    <%= (key["source_data"]["developer"]) %>
+                    <br>
+                    Version:
+                    <%= (key["source_data"]["version"]) %>
+                    <br>
+                    Link:
+                    <%= (key["source_data"]["link"]) %>
+                    <br>
+                    Repository:
+                    <%= (key["source_data"]["repository"]) %>
+                    <br>
+                    OS name , OS version:
+                    <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
 
-                      <% when "9"%>
-                      <br>
-                      <strong><%= key["name"]+": " %></strong>    <%= key["source_data"]["name"] %>
-                      <br>
-                      Link : <%= (key["source_data"]["link"]) %>
+                    <% when "9"%>
+                    <br>
+                    <strong><%= key["name"]+": " %></strong>
+                    <%= key["source_data"]["name"] %>
+                    <br>
+                    Link :
+                    <%= (key["source_data"]["link"]) %>
 
+                    <% when "15"%>
+                    <br>
+                    <strong><%= key["name"]+": " %></strong>
+                    <%=  key["source_data"]["name"] %>
+                    <br>
+                    Description:
+                    <%= (key["source_data"]["description"]) %>
+                    <br>
+                    OS name , OS version:
+                    <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
 
-                      <% when "15"%>
-                      <br>
-                      <strong><%= key["name"]+": " %></strong> <%=  key["source_data"]["name"] %>
-                      <br>
-                      Description: <%= (key["source_data"]["description"]) %>
-                      <br>
-                      OS name , OS version: <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
+                    <% when "18"%>
+                    <br>
+                    <strong>This protocol also contains an attached sub-protocol:
+                    </strong>
+                    <%= (key["source_data"]["protocol_name"]) %>
+                    <br>
+                    Author:
+                    <%= (key["source_data"]["full_name"]) %>
+                    <br>
+                    <% if key["source_data"]["link"]&&key["source_data"]["link"]!="" %>
+                    Link:
+                    <%= (key["source_data"]["link"]) %>
+                    <% end %>
+                    <% when "19"%>
+                    <br>
+                    <strong><%= key["name"]+": " %></strong>
+                    <%= key["source_data"]["body"] %>
+                    <br>
+                    Link:
+                    <%= (key["source_data"]["link"]) %>
 
-                      <% when "18"%>
-                      <br>
-                      <strong>This protocol also contains an attached sub-protocol: </strong> <%= (key["source_data"]["protocol_name"]) %>
-                      <br>
-                      Author: <%= (key["source_data"]["full_name"]) %>
-                      <br>
-                      <% if key["source_data"]["link"]&&key["source_data"]["link"]!="" %>
-                      Link: <%= (key["source_data"]["link"]) %>
-                      <% end %>
-                      <% when "19"%>
-                      <br>
-                      <strong><%= key["name"]+": " %></strong>  <%= key["source_data"]["body"] %>
-                      <br>
-                      Link: <%= (key["source_data"]["link"]) %>
+                    <% when "20"%>
 
+                  <% else %>
 
-                      <% when "20"%>
-
-                      <% else %>
-
-                      <% end #case if%>
+                    <% end #case if%>
 
                     <% end #inner if%>
 
+                    <% end #step component loop %>
 
-              <% end #step component loop %>
+                  </div>
+                  <hr>
+                  <!-- This could be implemented later maybe,i believe this is different styling
+                  for scinotes own rich text format tables
 
-            </div>
-            <hr>
-        <!--    <div class="row">
+                     <div class="row">
               <div data-toggle="tables" class="col-xs-12" style="display: none;">
                 <div data-hold="tables"> </div>
               </div>
@@ -235,71 +261,76 @@
                 <div data-hold="checklists"></div>
               </div>
             </div> -->
-          </div>
-        </div>
+                </div>
+              </div>
+
+            </div>
 
-      </div> <%# block div%>
             <% end  #step loop%>
 
+            <% if
+            @json_object["manuscript_citation"]&&@json_object["manuscript_citation"]!="" %>
 
-
-            <% if @json_object["manuscript_citation"]&&@json_object["manuscript_citation"]!="" %>
-
-                  <br><strong>Manuscript citation:</strong><br>
-                  <%= (@json_object["manuscript_citation"]) %>
+            <br>
+            <strong>Manuscript citation:</strong><br>
+            <%= (@json_object["manuscript_citation"]) %>
 
             <% end %>
             <% if @json_object["publish_date"]&&@json_object["publish_date"]!="" %>
 
-                  <br><strong>Publish date:</strong><br>
-                  <%= (@json_object["publish_date"]) %>
+            <br>
+            <strong>Publish date:</strong><br>
+            <%= (@json_object["publish_date"]) %>
 
             <% end %>
             <% if @json_object["vendor_name"]&&@json_object["vendor_name"]!="" %>
 
-                  <br><strong>Vendor name:</strong><br>
-                  <%= (@json_object["vendor_name"]) %>
+            <br>
+            <strong>Vendor name:</strong><br>
+            <%= (@json_object["vendor_name"]) %>
 
             <% end %>
             <% if @json_object["vendor_link"]&&@json_object["vendor_link"]!="" %>
 
-                  <br><strong>Vendor link:</strong><br>
-                  <%= (@json_object["vendor_link"]) %>
+            <br>
+            <strong>Vendor link:</strong><br>
+            <%= (@json_object["vendor_link"]) %>
 
             <% end %>
             <% if @json_object["keywords"]&&@json_object["keywords"]!="" %>
 
-                  <br><strong>Keywords:</strong><br>
-                  <%= (@json_object["keywords"]) %>
+            <br>
+            <strong>Keywords:</strong><br>
+            <%= (@json_object["keywords"]) %>
 
             <% end %>
             <% if @json_object["tags"]&&@json_object["tags"]!="" %>
 
-                  <br><strong>Tags:</strong><br>
-                  <%  @json_object["tags"].each do |tag| %>
-                 <%= (tag["tag_name"])+" , " %>
-                 <% end %>
+            <br>
+            <strong>Tags:</strong><br>
+            <%  @json_object["tags"].each do |tag| %>
+            <%= (tag["tag_name"])+" , " %>
+            <% end %>
 
             <% end %>
             <hr>
           </div>
 
-
-      </div>
-      <div class="modal-footer">
+        </div>
+        <div class="modal-footer">
           <button type="button" class="btn btn-default" data-dismiss="modal"><%= t("general.cancel") %></button>
 
-            <%= f.submit t("protocols.import_export.import_modal.import"),class: "btn btn-primary" %>
-            <% end %>
+          <%= f.submit t("protocols.import_export.import_modal.import"),class: "btn
+          btn-primary" %>
+          <% end %>
 
+        </div>
       </div>
     </div>
   </div>
-</div>
-
-
-<script>
- $('#modal-import-json-protocol-preview').on('hide.bs.modal',function(){
-   $('#protocols_io_form').trigger("reset");
- })
-</script>
+<% # the below script resets all the fields after you decide not to import the file (cancel (modal hide)) %>
+  <script>
+    $('#modal-import-json-protocol-preview').on('hide.bs.modal', function () {
+      $('#protocols_io_form').trigger("reset");
+    })
+  </script>
diff --git a/app/views/protocols/index.html.erb b/app/views/protocols/index.html.erb
index 388e110b3..518505a45 100644
--- a/app/views/protocols/index.html.erb
+++ b/app/views/protocols/index.html.erb
@@ -53,7 +53,6 @@
 
           <ul class="dropdown-menu">
             <li>
-
               <a class="btn-link-alt btn-default-link btn-open-file" <%= can_import_protocols(@current_team) ? 'data-action="import"' : 'disabled="disabled"' %>>
                 <span class="glyphicon glyphicon-file"></span>
                 <span class="hidden-xs"><%= t("protocols.index.import_alt") %></span>
@@ -61,20 +60,13 @@
                 data-team-id="<%= @current_team.id %>"
                 data-type="<%= @type %>" data-import-url="<%= import_protocols_path %>"
                 <%= 'disabled="disabled"' unless can_import_protocols(@current_team) %>>
-
               </a>
-
             </li>
-
             <li>
-
-
             <%= link_to "#modal-import-json-protocol", "data-toggle" => "modal" do %>
             <span class="glyphicon glyphicon-file"></span>
             <span class="hidden-xs"><%= t("protocols.index.import_json") %></span>
             <% end %>
-
-
             </li>
 
           </ul>
diff --git a/config/routes.rb b/config/routes.rb
index 96a9f8ee9..98bfbde5b 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -417,12 +417,8 @@ Rails.application.routes.draw do
         post 'archive', to: 'protocols#archive'
         post 'restore', to: 'protocols#restore'
         post 'import', to: 'protocols#import'
-        ##
-        ##-tule gre tvoje json_import match
         post 'protocolsio_import_create', to: 'protocols#protocolsio_import_create'
         post 'protocolsio_import_save', to: 'protocols#protocolsio_import_save'
-        #get 'testcontroller', to: 'protocols#testcontroller'
-        ##
         get 'export', to: 'protocols#export'
       end
     end