rbbt-views 1.0.1 → 2.0.0

data/share/views/layout.haml

@@ -1,114 +1,24 @@
+- title = $title || "Workflow Explorer"
 !!!
 !!! XML
 !!! Strict
 %html{ :xmlns => "http://www.w3.org/1999/xhtml", :lang => "en", 'xml:lang' => "en" }
   %head
-    - if defined? @rbbt_refresh and Fixnum === @rbbt_refresh and @rbbt_refresh > 0
-      %meta(http-equiv="refresh" content=@rbbt_refresh)
+    = workflow_partial('partials/layout/_head', :title => title)
 
-    - if defined? step and Step === step
-      - title = "#{step.task.name} [#{step.status}]"
-    - else
-      - title = $title || "Workflow Explorer"
-    %title
-      = title
-    %link{:rel => "shortcut icon", :type => "image/png", :href => "/favicon.gif"}/
-
-
-    %meta{'http-equiv'=>"Content-Type", :content=>"text/html; charset=UTF-8"}/
-    %meta{'http-equiv'=>"Content-Language", :content=>"en-us"}/
-
-
-    %link{:href=>"/stylesheets/layout.css", :rel=>"stylesheet", :type=>"text/css"}/
-    %link{:href=>"/stylesheets/app.css", :rel=>"stylesheet", :type=>"text/css"}/
-
-    %script{:src => '/plugins/jquery/js/jquery-1.6.2.min.js', :type => 'text/javascript'}
-    %script{:src => '/plugins/jquery/js/jquery.form.js', :type => 'text/javascript'}
-    %script{:src => '/plugins/jquery/js/jquery.cookie.js', :type => 'text/javascript'}
-    %script{:src => '/plugins/jmol/Jmol.js', :type => 'text/javascript'}
-
-    -# %link{:href=>"/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css", :rel=>"stylesheet", :type=>"text/css"}/
-    -# %script{:src => '/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js', :type => 'text/javascript'}
-
-    %script{:src => '/js/app.js', :type => 'text/javascript'}
   %body
-    #header
-      %h1
-        %a(href="/")= title
-        %span.login
-          - if session[:user]
-            ==Logged in as: 
-            %span.user== #{session[:user]}
-            \. 
-            %a(href="/logout") logout
-          - else
-            Not logged in
-            %a(href="/login") login
-        %span.list_dropdown
-          %a(href='#lists') Loaded Entity Lists
+    = workflow_partial('partials/layout/_header', :title => title)
  
     - unless $nomenu
-      #menu
-        - if session.include?(:context) and Hash === session[:context] and session[:context].collect{|w,t| t.values}.flatten.any?
-          #context
-            %h2 Context Jobs
-            = workflow_partial('partials/_context_control', nil, nil, locals)
-
-          %h2 Workflows
-
-        - WorkflowREST.workflows.each do |workflow|
-          %h3.workflow_title(target=workflow)= workflow.to_s
-          %div.workflow_menu(id=workflow)
-            %a.replace(href="/#{workflow.to_s}")
-        #footer
-          %p Structural Computational Biology Group
+      = workflow_partial('partials/layout/_menu')
 
-          %p Structural Biology and BioComputing Programme
-
-          %p Spanish National Cancer Research Centre (CNIO). C/ Melchor Fernández Almagro, 3, E-28029 Madrid Spain 
-
-    #content{:style => ($nomenu ? "width:100%" : "")}
+    #content{:style => ($nomenu ? "width:100%" : "float:left")}
+      #lists
       #main
         = yield
-      #details_controls
-        %ul
-          %li
-            %a.button(href="#" id="hide_details") hide
-          %li
-            %a.button(href="#" id="toggle_expand_details") toggle
-          %li
-            %a.button(href="#" id="back_details") back
-      #details
-
-    #lists
-
-:javascript        
-
-  $('h3.workflow_title').click(function(){
-    var target = $(this).attr('target');
-    $('div#' + target).toggle();
-  })
-
-  rbbt_action_setup();
-
-  hide_details();
- 
-  $('#hide_details').click(hide_details);
-  $('#toggle_expand_details').click(toggle_expand_details);
-  $('#back_details').click(back_details);
-
-  var details_history = [];
-  
-  $('span.list_dropdown > a').click(function(){ $('#lists').toggle(); return false})
+      = workflow_partial('partials/layout/_details')
 
-  var _saved_lists = saved_lists();
-  if (_saved_lists == null){ _saved_lists = []; }
+    = workflow_partial('partials/layout/_coda')
 
-  update_list_viewer();
 
-  $.each(_saved_lists, function(type, lists){
-    $.each(lists, function(id, list){
-      add_entity_list(type, list)
-    })
-  })
 

data/share/views/notes.haml

@@ -0,0 +1,15 @@
+:markdown
+
+  Notes use [Markdown](http://daringfireball.net/projects/markdown/syntax) 
+  see [this link](http://support.mashery.com/docs/customizing_your_portal/Markdown_Cheat_Sheet/) for
+  a cheat sheet.
+
+  Additionally you can write 'Gene GENENAME' to make a link to that gene, or 'KEGG:"Pathway name"' for a link
+  to a given pathway in KEGG. 
+
+%form(method='post')
+  #markup
+    - text = preserve do
+      =  markup
+    %textarea(name="markup" style="width:80%;height:300px")= text
+  %input(type='submit')

data/share/views/partials/_form.haml

@@ -1,6 +1,15 @@
 - input_descriptions ||= {}
 - input_defaults ||= {}
 - input_types ||= {}
+- input_labels ||= {}
+- input_options ||= {}
+
+- if defined? select_options
+  - input_options = {}
+  - select_options.each do |t,o|
+    - input_options[t] ||= {}
+    - input_options[t][:select_options] = o
+
 - values ||= {}
 - jobname ||= false
 - email ||= false
@@ -9,23 +18,26 @@
 - action ||= ''
 - klass ||= ''
 - enctype = method == 'post' ? "multipart/form-data" : ""
-- id ||= ""
+-# input_html_options ||= {}
+- id ||= nil
 
 %form(class=klass action=action method=method id=id enctype=enctype)
   - if inputs.empty?
     %input(type="hidden" name="noinputs" value="noinputs")
 
   - inputs.each do |name|
-    - input_id = File.join(id, name.to_s)
+    - input_id = (id and not id.empty?) ? [id, name.to_s] * "_" : nil
     - input_type = input_types[name]
+    - input_label = input_labels[name]
     - default = input_defaults[name]
-    - value = values[name] || default
+    - value = values[name]  
+    - value = default if value.nil?
     - description = input_descriptions[name]
-    - select_options = defined?(input_options)? input_options[name] : nil
+    - options = input_options.nil? ? nil : input_options[name]
     - hide = hide_inputs.include? name
-    = input(input_type, name, :id => input_id, :value => value, :default => default, :description => description, :select_options => select_options, :default => default, :hide => hide)
+    = form_input(input_type, name, :id => input_id, :input_options => options, :label => input_label, :value => value, :default => default, :description => description, :default => default, :hide => hide)
 
-  %div.submit_job
+  %div.form_submit
     - if jobname
       %span.jobname(id="jobname_#{id}")
         Optional Job Name
@@ -34,5 +46,8 @@
         Email
         %input(class="email" name="email" id="email_#{id}")
 
-    %input(type="submit" id="submit_#{id}")
+    - if id and not id.empty?
+      %input(type="submit" id="submit_#{id}")
+    - else
+      %input(type="submit")
 

data/share/views/partials/_job_control.haml

@@ -1,17 +1,17 @@
 %ul.job_control
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}")= clean_jobname jobname
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}")= clean_jobname jobname
   %li
-    %a.POST(href="/context/#{[workflow, task, jobname] * "/"}") context
+    %a.POST(href="/context/#{[workflow.to_s, task, jobname] * "/"}") context
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}?_format=raw") raw
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}?_format=raw") raw
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}?_format=json") json
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}?_format=json") json
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}/info") info
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}/info") info
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}/files") files
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}/files") files
   %li
-    %a(href="/#{[workflow, task, jobname] * "/"}/dependencies") dependencies
+    %a(href="/#{[workflow.to_s, task, jobname] * "/"}/dependencies") dependencies
   %li
-    %a.DELETE(href="/#{[workflow, task, jobname] * "/"}") delete
+    %a.DELETE(href="/#{[workflow.to_s, task, jobname] * "/"}") delete

data/share/views/partials/_list_control.haml

@@ -0,0 +1,32 @@
+%ul.list_control
+  %li
+    %a.load_entity_list(href='#load_entity_list' attr-list=id attr-list-type=entity_type)== load
+  %li
+    %a.edit_entity_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/edit/#{ id }" attr-list=id attr-list-type=entity_type)== edit
+
+  - if ! locals[:saved_already]
+    %li
+      %a.POST.save_entity_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/copy/#{ id }?new_id=#{ id }" attr-list=id attr-list-type=entity_type)== save
+
+  %li
+    %a.DELETE.delete_entity_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/#{ id }" attr-list=id attr-list-type=entity_type)== delete
+  %li
+    \---
+  %li
+    %a.json_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/#{ id }?_format=json" attr-list=id attr-list-type=entity_type)== json
+  %li
+    %a.tsv_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/#{ id }?_format=tsv " attr-list=id attr-list-type=entity_type)== tsv
+  %li
+    %a.literal_list(href="/entity_list/#{ format ? [entity_type, format] * ":" : entity_type }/#{ id }?_format=literal " attr-list=id attr-list-type=entity_type)== literal
+
+  %li
+    \---
+
+  %li
+    %a.compare_list(href="#" attr-list=id attr-list-type=entity_type)== compare
+
+  %li
+    %a.rename_list(href="#" attr-list=id attr-list-type=entity_type)== rename
+    %input.rename_list(attr-list=id)
+
+

data/share/views/partials/_list_header.haml

@@ -0,0 +1,6 @@
+.list_header
+  %header
+    == List:
+    %span.list_id= id
+
+  = workflow_partial('partials/_list_control', workflow, task, locals)

data/share/views/partials/_note_list.haml

@@ -0,0 +1,64 @@
+- entity_types = {}
+- news = nil
+- notes.each do |note, url|
+  - type_of_page, format, *rest = note.sub(/^shared\//, '').split('/')
+  - if format.nil?
+    - news = [note,url]
+    - next
+  - entity_type, format = format.split(":")
+  - entity_types[entity_type] ||= {}
+  - entity_types[entity_type][type_of_page] ||= []
+  - entity_types[entity_type][type_of_page] << [note, url, rest]
+
+
+- shared_notes = shared_notes(user)
+%dl.notes
+  - if news
+    %div.news
+      - note, url = news
+      - path, param_string = url.split(/\?/)
+      - param_string ||= ""
+      - params = Misc.GET_params2hash(param_string)
+      - if not shared
+        %ul.note_controls(shared='#{shared_notes.include? note}')
+          %li.share
+            %a.share_note(href="#{url.sub("/notes", "/notes/share")}") share
+          %li.unshare
+            %a.unshare_note(href="#{url.sub("/notes", "/notes/unshare")}") unshare
+      %a(href=url)
+        == News
+      %div.sneak_peek= get_notes_markup(path.sub('/notes','').sub(/shared\/\w+\//,'/'), params, (shared ? shared_user : user), shared).gsub(/[^\w,.!?:\s]/,'')
+ 
+  - entity_types.each do |entity_type, types_of_pages|
+    %dt= entity_type
+    %dd
+      %ul.note_list
+        - types_of_pages.each do |type_of_page, list|
+          - list.each do |note, url, rest|
+            %li
+              - path, param_string = url.split(/\?/)
+              - param_string ||= ""
+              - params = Misc.GET_params2hash(param_string)
+              - if not shared
+                %ul.note_controls(shared='#{shared_notes.include? note}')
+                  %li.share
+                    %a.share_note(href="#{url.sub("/notes", "/notes/share")}") share
+                  %li.unshare
+                    %a.unshare_note(href="#{url.sub("/notes", "/notes/unshare")}") unshare
+              %a(href=url)
+                - case type_of_page.to_s
+                - when "entity"
+                  - entity = rest.first.sub(/\?.*/,'')
+                  - type_of_page, format, *rest = note.split('/')
+                  - format = format.split(":").last 
+                  - Misc.prepare_entity(entity, format.gsub('+', ' '), params)
+                  == Entity '#{entity.respond_to?(:name)? entity.name : entity }'
+                - when "entity_list_action"
+                  == List Action '#{rest.first}': #{rest[1..-1].join("/").sub(/\?.*/,'')}
+                - when "entity_action"
+                  == Action '#{rest.first}': #{rest[1..-1].join("/").sub(/\?.*/,'')}
+                - when "entity_list"
+                  == List: #{rest.join("/").sub(/\?.*/,'')}
+              %span.note= CGI.unescape(param_string.gsub('&', ', '))
+              %div.sneak_peek= get_notes_markup(path.sub('/notes','').sub(/shared\/\w+\//,'/'), params, (shared ? shared_user : user), shared).gsub(/[^\w,.!?:\s]/,'')
+                  

data/share/views/partials/_result_table.haml

@@ -1,18 +1,23 @@
 - id = locals.include?(:task) ? "results_tsv_table_#{locals[:task]}" : "NONE"
 - klass = "results_tsv_table"
+
+- locals[:result] = locals[:step].run if (not locals.include? :result and locals.include? :step)
+- result = locals[:result]
+
 - rows, total = process_result(result, locals)
 
 - if result.key_field == "ID"
   - header = result.fields
 - else
   - header = result.all_fields
-  - case
-  - when rows.type == :single
-    - rows = rows.collect{|k,v| [k, NamedArray.setup([k].push(v), header, k, result.namespace)]}
-  - when rows.type == :flat
-    - rows = rows.collect{|k,v| [k, NamedArray.setup([k].push([v]), header, k, result.namespace)]}
-  - else
-    - rows = rows.collect{|k,v| [k, NamedArray.setup([k].concat(v), header, k, result.namespace)]}
+  - locals[:add_id] = true
+- case
+- when result.type == :single
+  - rows = rows.collect{|k,v| [k, NamedArray.setup([v], result.fields, k, result.entity_options)]}
+- when result.type == :flat
+  - rows = rows.collect{|k,v| [k, NamedArray.setup([v], result.fields, k, result.entity_options)]}
+- else
+  - rows = rows.collect{|k,v| [k, NamedArray.setup(v, result.fields, k, result.entity_options)]}
 
 
 = workflow_partial('partials/_table', workflow, task, locals.merge(:header => header, :id => id, :klass => klass, :rows => rows, :total => total))         

data/share/views/partials/_result_table_controls.haml

@@ -1,23 +1,29 @@
 
+- key_field = header.first
+
 - if locals.include? :_page and not locals[:_page].nil?
   - pfield, page, size = parse_page(locals[:_page])
 - else
-  - pfield, page, size = [result.key_field, 1, 25]
+  - pfield, page, size = [key_field, 1, 25]
 
 - if locals.include? :_filter and not locals[:_filter].nil?
   - ffield, query = locals[:_filter].split "~"
 - else
-  - ffield, query = [result.key_field, ""]
+  - ffield, query = [key_field, ""]
 
 - total ||= result.size
 - max = total / size.to_i + 1
 - page = page.to_i
 - page = max if page > max
 - page = - max if page < - max
+- page_params ||= {}
 
 %form.table_controls(method='get')
+  - page_params.each do |key,value|
+    %input(type="hidden" name=key value=value)
 
-  %p
+  
+  .input_section
     %h3 Subset
     Query:
     %input.fquery(name="_fquery" value=query)
@@ -29,7 +35,7 @@
         - else
           %option(value=f)= f
 
-  %p
+  .input_section
     %h3 Sort
     Field:
     %select.pfield(name='_pfield')
@@ -42,7 +48,7 @@
     %input.change_page(type='submit' value="Desc" name="_paginate")
     %input.change_page(type='submit' value="Asc"  name="_paginate")
 
-  %p
+  .input_section
     %h3 Navigate
     Page:
     %input.pnum(name="_pnum" value=page)

data/share/views/partials/_table.haml

@@ -1,8 +1,19 @@
-- klass = locals[:klass]
+- klass = locals[:klass] || locals[:class]
 - id = locals[:id]
 - header = locals[:header]
 - rows = locals[:rows]
 - total = locals[:total]
+- add_id = locals[:add_id]
+- paginate = locals[:paginate]
+- paginate = true if paginate.nil? and locals.include? :result
+
+- if locals.include? :step
+  - step = locals[:step]
+  - rows ||= step.load
+  - if add_id
+    - header ||= rows.all_fields
+  - else
+    - header ||= rows.fields
 
 %table(class=klass id=id)
 
@@ -12,19 +23,25 @@
       - header.each do |field|
         %th(class=field)= field
 
-
   -# BODY
   %tbody
-    - rows.each do |id, values|
+    - rows.each do |id,values|
       %tr(id=id)
         - if Array === values
+          - if add_id
+            - values.unshift id
+            - values.fields = [header.first] + values.fields  if values.respond_to?(:fields) and not values.fields.nil?
+
           - values.each do |value|
-            - value = value.link if value.respond_to? :link
+            - value = value.link if Annotated === value and value.respond_to? :rbbt_id and value.respond_to? :link and not (Array === value and not (Annotated === value.first))
             - type = value.respond_to?(:format)? value.format : ""
             - if Array === value
               %td(class=type)= value * ", "
             - else
               %td(class=type)= value
+          - if add_id
+            - values.shift
+            - values.fields = values.fields[1..-1] if values.respond_to?(:fields)
         - else
           - value = value.link if value.respond_to? :link
           - type = value.respond_to?(:format)? value.format : ""
@@ -32,8 +49,9 @@
           
             
   -# FOOT (paginate)
-  - if locals.include? :step
+  - if paginate
     %tfoot
       %tr
         %th(colspan="#{header.length}") 
-          = workflow_partial('partials/_result_table_controls', workflow, task,  locals.merge(:fields => header, :total => total))         
+
+          = workflow_partial('partials/_result_table_controls', workflow, task,  locals.merge(:fields => header, :total => total, :page_params => locals[:page_params]))