protocol importing into database works, still need to decide how to add other fields from protocols.io to step description and protocol description, but that can be added easily, and need to make it refresh after submit

app/controllers/protocols_controller.rb

@@ -66,6 +66,7 @@ class ProtocolsController < ApplicationController
   before_action :check_import_permissions, only: [ :import ]
   before_action :check_export_permissions, only: [ :export ]
 
+
   def index
   end
 
@@ -629,53 +630,224 @@ def protocolsio_import_save
   @import_object["name"]=params["protocol"]["name"]
 
   @import_object["description"]=params["protocol"]["description"]
-  #v description bo treba velik drugih stvari še spravit
+  # will have to fit various things in here (guidelines, manuscript citations etc etc)
 
   @import_object["authors"]=params["protocol"]["authors"]
   @import_object["created_at"]=params["protocol"]["created_at"]
   @import_object["updated_at"]=params["protocol"]["last_modified"]
-  @import_object["steps"]
-  byebug
+  #@import_object["steps"]
+
+
+  @import_object["steps"]=Hash.new
+  counter=0
+  step_pos=-1
+  #these whitelists are there to not let some useless step components true, 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|
+    #@import_object["steps"][step_pos.to_s]=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
+
+
+        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 weird nesting that requires different handling
+
+
+
+
+       if whitelist_simple.include?(key["component_type_id"])
+
+         case key["component_type_id"]
+         when "1"
+           if !key["data"].nil? && key["data"]!=""
+             @import_object["steps"][step_pos.to_s]["description"]=key["data"]
+            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"]="Protocols.io"
+        end
+         when "17"
+
+        else
+
+
+        end
+
+         elsif key && whitelist_complex.include?(key["component_type_id"])
+         case key["component_type_id"]
+         when "8"
+
+        # "-"+(key["name"])+" : "+(key["source_data"]["name"])
+        #Developer : <%= (key["source_data"]["developer"])
+        #Version : (key["source_data"]["version"])
+        #Link :  (key["source_data"]["link"])
+        # Repository : (key["source_data"]["repository"])
+        #OS name , OS version : (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"])
+
+      when "9"
+
+        # "-"+(key["name"])+" : "+(key["source_data"]["name"])
+        # Link :  (key["source_data"]["link"])
+
+         when "15"
+
+        # "-"+(key["name"])+" : "+(key["source_data"]["name"])
+        # Description :  (key["source_data"]["description"])
+        # OS name , OS version :  (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"])
+
+         when "18"
+
+        #-This protocol also contains an attached sub-protocol:  (key["source_data"]["protocol_name"])
+        #Author: (key["source_data"]["full_name"])
+
+         if key["source_data"]["link"]&&key["source_data"]["link"]!=""
+        #Link:  (key["source_data"]["link"])
+         end
+         when "19"
+
+        # "-"+(key["name"])+" : "+(key["source_data"]["body"])
+        #Link :  (key["source_data"]["link"])
+
+         when "20"
+
+         else
+
+         end
+
+       end #finished step component loop
+
+     else #it is first step
+
+       unless value
+       value=key #some json files have random empty arrays in beggining of step components
+       end
+
+         if whitelist_simple.include?(value["component_type_id"])
+
+           case value["component_type_id"]
+           when "1"
+             if !value["data"].nil? && value["data"]!=""
+               @import_object["steps"][step_pos.to_s]["description"]=value["data"]
+              else
+                @import_object["steps"][step_pos.to_s]["description"]="Description missing!"
+              end
+           when "6"
+             if !value["data"].nil? && value["data"]!=""
+            @import_object["steps"][step_pos.to_s]["name"]=value["data"]
+            else
+            @import_object["steps"][step_pos.to_s]["name"]="Protocols.io"
+          end
+           when "17"
+
+          else
+
+          end
+
+         elsif value && whitelist_complex.include?(value["component_type_id"])
+         case value["component_type_id"]
+         when "8"
+
+        # "-"+(value["name"])+" : "+(value["source_data"]["name"])
+        # Developer :  (value["source_data"]["developer"])
+        # Version :  (value["source_data"]["version"])
+        # Link :  (value["source_data"]["link"])
+        # Repository :  (value["source_data"]["repository"])
+        # OS name , OS version :  (value["source_data"]["os_name"])+" , "+(value["source_data"]["os_version"])
+
+         when "9"
+
+        # "-"+(value["name"])+" : "+(value["source_data"]["name"])
+        #Link :  (value["source_data"]["link"])
+
+         when "15"
+
+        # "-"+(value["name"])+" : "+(value["source_data"]["name"])
+        # Description :  (value["source_data"]["description"])
+        # OS name , OS version :  (value["source_data"]["os_name"])+" , "+(value["source_data"]["os_version"])
+
+         when "18"
+
+        # -This protocol also contains an attached sub-protocol:  (value["source_data"]["protocol_name"])
+        # Author:  (value["source_data"]["full_name"])
+
+         if value["source_data"]["link"]&&value["source_data"]["link"]!=""
+
+        #Link:  (value["source_data"]["link"])
+         end
+         when "19"
+
+        # "-"+(value["name"])+" : "+(value["source_data"]["body"])
+        # Link :  (value["source_data"]["link"])
+
+         when "20"
+
+         else
+
+          end
+
+        end #if statement to check if its first step or not
+
+      end #finished step component looping, onto next step component
+
+
+    end #finished looping over step components
+
+
+
+  end #steps
+
   protocol = nil
   respond_to do |format|
     transaction_error = false
-    @steps_object=JSON.parse(params["steps"]["steps_object"])
-    byebug
+    #@steps_object=JSON.parse(params["steps"]["steps_object"])
+
     Protocol.transaction do
       begin
+        #byebug
+        protocol = import_new_protocol(@import_object, current_team, params[:type].to_sym, current_user)
 
-
-        protocol = import_new_protocol(@protocol_json, @team, @type, current_user)
       rescue Exception
+
         transaction_error = true
         raise ActiveRecord:: Rollback
       end
     end
 
     p_name =
-      if @protocol_json['name'].present? && !@protocol_json['name'].empty?
-        escape_input(@protocol_json['name'])
+      if @import_object['name'].present? && !@import_object['name'].empty?
+        escape_input(@import_object['name'])
       else
         t('protocols.index.no_protocol_name')
       end
+
     if transaction_error
       format.json {
         render json: { name: p_name, status: :bad_request }, status: :bad_request
       }
+      #:location => root_url
     else
       format.json {
         render json: {
           name: p_name, new_name: protocol.name, status: :ok
-        },
+        },redirect_to: @protocol,
         status: :ok
       }
     end
   end
 end
 
-def protocolsio_temp_params
-  params.require(:json_file)
-end
+
 #
   def export
     # Make a zip output stream and send it to the client

app/utilities/protocols_importer.rb

@@ -3,7 +3,7 @@ module ProtocolsImporter
 
   def import_new_protocol(protocol_json, team, type, user) # .eln import
     remove_empty_inputs(protocol_json)
-    byebug
+
     protocol = Protocol.new(
       name: protocol_json["name"],
       description: protocol_json["description"],
@@ -42,18 +42,12 @@ module ProtocolsImporter
     protocol
   end
 
-  def import_new_protocols_io_json()
 
-
-
-
-  end
   private
 
 
   def populate_protocol(protocol, protocol_json, user, team)
     protocol.reload
-
     asset_ids = []
     step_pos = 0
     # Check if protocol has steps

app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb

@@ -9,9 +9,9 @@
    %>
 
   <%= hidden_field_tag :json_object, JSON.generate(@json_object) %>
+  <%= hidden_field_tag :type, CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
 
-
-  <%# end %>
+  <%# #CGI.parse(URI.parse(request.referrer).query).fetch("type") %>
 <div id="modal-import-json-protocol-preview" class="modal fade" role="dialog" tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">

app/views/protocols/index.html.erb

@@ -54,7 +54,7 @@
           <ul class="dropdown-menu">
             <li>
 
-              <a class="btn-link btn-default-link btn-open-file" <%= can_import_protocols(@current_team) ? 'data-action="import"' : 'disabled="disabled"' %>>
+              <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>
                 <input type="file" value="" accept=".eln" data-role="import-file-input"