scinote-eln/scinote-web
1
1
Fork 0
mirror of https://github.com/scinote-eln/scinote-web.git synced 2024-09-21 07:26:15 +08:00
Code Issues Packages Projects Releases Wiki Activity

Added all the fields into description of protocol steps and protocol itself, need to make protocols description format nicer

Browse source
This commit is contained in:
Zanz2 2017-09-21 16:05:33 +02:00
parent df8cbc2741
commit 1dbb03e22d
2 changed files with 129 additions and 68 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

160
app/controllers/protocols_controller.rb
View file

@ -629,12 +629,45 @@ def protocolsio_import_save
@import_object=Hash.new
@import_object["name"]=params["protocol"]["name"]
@import_object["description"]=params["protocol"]["description"]
# will have to fit various things in here (guidelines, manuscript citations etc etc)
#"before_start","warning","guidelines","manuscript_citation","publish_date","created_on"
#"vendor_name","vendor_link","keywords","tags"
description_array = [ "before_start","warning","guidelines","manuscript_citation","publish_date","created_on","vendor_name","vendor_link","keywords","tags" ]
description_string=params["protocol"]["description"]
#@import_object["description"]=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+": "+params["protocol"]["created_at"].to_s+"\n"
end
else
if(element=="tags")
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+": "
@json_object[element].each do |tag|
description_string=description_string+tag["tag_name"]+" , "
end
description_string=description_string+"\n"
end
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+": "+@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"]
@ -652,9 +685,9 @@ def protocolsio_import_save
@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|
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 weird nesting that requires different handling
if whitelist_simple.include?(key["component_type_id"])
@ -662,9 +695,15 @@ def protocolsio_import_save
case key["component_type_id"]
when "1"
if !key["data"].nil? && key["data"]!=""
@import_object["steps"][step_pos.to_s]["description"]=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!"
@import_object["steps"][step_pos.to_s]["description"]||="Description missing!"
end
when "6"
if !key["data"].nil? && key["data"]!=""
@ -673,83 +712,106 @@ def protocolsio_import_save
@import_object["steps"][step_pos.to_s]["name"]="Protocols.io"
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
else
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"
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
when "9"
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
when "15"
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
when "18"
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"]
if key["source_data"]["link"]&&key["source_data"]["link"]!=""
end
#if key["source_data"]["link"]&&key["source_data"]["link"]!=""
#end
when "19"
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
when "20"
else
end
end #finished step component loop
end #finished step component iteration
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"])
if whitelist_simple.include?(value["component_type_id"])
case value["component_type_id"]
when "8"
when "1"
if !value["data"].nil? && value["data"]!=""
when "9"
element_string="<br>"+value["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 !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"
if !value["data"].nil? && value["data"]!=""
element_string="<br><strong>Expected result: </strong>"+value["data"]+"<br>"
@import_object["steps"][step_pos.to_s]["description"]<<element_string
end
else
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 value && whitelist_complex.include?(value["component_type_id"])
case value["component_type_id"]
when "8"
element_string="<br><strong>Software package: </strong>"+value["source_data"]["name"]+"<br>Developer: "+value["source_data"]["developer"]+"<br>Version: "+value["source_data"]["version"]+"<br>Link: "+value["source_data"]["link"]+"<br>Repository: "+value["source_data"]["repository"]+"<br> OS name , OS version: "+value["source_data"]["os_name"]+" , "+value["source_data"]["os_version"]
@import_object["steps"][step_pos.to_s]["description"]<<element_string
when "9"
element_string="<br><strong>Dataset: </strong>"+value["source_data"]["name"]+"<br>Link: "+value["source_data"]["link"]
@import_object["steps"][step_pos.to_s]["description"]<<element_string
when "15"
element_string="<br><strong>Command: </strong>"+value["source_data"]["name"]+"<br>Description: "+value["source_data"]["description"]+"<br>OS name , OS version: "+value["source_data"]["os_name"]+" , "+value["source_data"]["os_version"]
@import_object["steps"][step_pos.to_s]["description"]<<element_string
when "18"
element_string="<br><strong>This protocol also contains an attached sub-protocol: </strong>"+value["source_data"]["protocol_name"]+"<br>Author: "+value["source_data"]["full_name"]+"<br>Link: "+value["source_data"]["link"]
if value["source_data"]["link"]&&value["source_data"]["link"]!=""
end
#if key["source_data"]["link"]&&key["source_data"]["link"]!=""
#end
when "19"
element_string="<br><strong>Safety information</strong>"+value["source_data"]["body"]+"<br>Link: "+value["source_data"]["link"]
@import_object["steps"][step_pos.to_s]["description"]<<element_string
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
end #finished step component iteration
end #if statement to check if its first step or not
end #finished looping over step components
end #steps

37
app/views/protocols/import_export/_import_json_protocol_preview_modal.html.erb
View file

@ -44,13 +44,13 @@
<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)", class: "form-control" %>
<%= 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)", 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>
@ -65,26 +65,26 @@
<div class="import-protocols-modal-preview-container-json" data-role="preview-container">
<hr>
<% if @json_object["before_start"]&&@json_object["before_start"]!="" %>
<br><strong>Before starting protocol information:</strong><br>
<%= (@json_object["before_start"]) %>
<strong>Before starting protocol information:</strong><br>
<%= (@json_object["before_start"]) %><br>
<% end %>
<% if @json_object["warning"]&&@json_object["warning"]!="" %>
<br><strong>Protocol warning:</strong><br>
<%= (@json_object["warning"]) %>
<strong>Protocol warning:</strong><br>
<%= (@json_object["warning"]) %><br>
<% end %>
<% if @json_object["guidelines"]&&@json_object["guidelines"]!="" %>
<br><strong>Guidelines:</strong><br>
<%= (@json_object["guidelines"]) %>
<strong>Guidelines:</strong><br>
<%= (@json_object["guidelines"]) %><br>
<% end %>
@ -150,7 +150,6 @@
<% 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 makes the below outputs not work
%>
<% #byebug %>
<% if whitelist_simple.include?(key["component_type_id"]) && key["data"]!="" && key["data"] %>
<br>
<% case key["component_type_id"]%>
@ -169,15 +168,15 @@
<br>
<strong><%= key["name"]+": " %></strong> <%= (key["source_data"]["name"]) %>
<br>
Developer : <%= (key["source_data"]["developer"]) %>
Developer: <%= (key["source_data"]["developer"]) %>
<br>
Version : <%= (key["source_data"]["version"]) %>
Version: <%= (key["source_data"]["version"]) %>
<br>
Link : <%= (key["source_data"]["link"]) %>
Link: <%= (key["source_data"]["link"]) %>
<br>
Repository : <%= (key["source_data"]["repository"]) %>
Repository: <%= (key["source_data"]["repository"]) %>
<br>
OS name , OS version : <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
OS name , OS version: <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
<% when "9"%>
<br>
@ -190,9 +189,9 @@
<br>
<strong><%= key["name"]+": " %></strong> <%= key["source_data"]["name"] %>
<br>
Description : <%= (key["source_data"]["description"]) %>
Description: <%= (key["source_data"]["description"]) %>
<br>
OS name , OS version : <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
OS name , OS version: <%= (key["source_data"]["os_name"])+" , "+(key["source_data"]["os_version"]) %>
<% when "18"%>
<br>
@ -207,7 +206,7 @@
<br>
<strong><%= key["name"]+": " %></strong> <%= key["source_data"]["body"] %>
<br>
Link : <%= (key["source_data"]["link"]) %>
Link: <%= (key["source_data"]["link"]) %>
<% when "20"%>
@ -354,7 +353,7 @@
<% end %>
<% end %>
<hr>
</div>