rbbt-views 1.0.1 → 2.0.0

data/share/views/compass/lists.sass

@@ -0,0 +1,128 @@
+a.entity_list
+  text-decoration: none
+
+select.loaded_lists
+  max-width: 300px
+
+#lists
+  display: none
+  position: absolute
+  top: 2.3em
+  right: 27px
+  width: auto
+  min-width: 300px
+  padding: 20px
+  padding-left: 30px
+  background-color: #fefefe
+  border: solid 1px $bit_darker
+  z-index: 10
+
+  #entity_list_menu
+    a
+      +button_link()
+
+  h5.loaded_lists
+    margin: 5px 0px
+    font-style: italic
+
+  ul.entity_list
+    li
+      display: block
+
+  a.remove_list, a.select_list
+    font-size: 0.7em
+    +button_link
+
+  a.view_list
+    margin-left: 10px
+    text-decoration: none
+
+
+.list_header
+  margin-bottom: 20px
+  header
+    font-size: 1.7em
+    margin-bottom: 20px
+    span.list_id
+      font-style: italic
+
+.list_control
+  +clean_list
+  display: inline
+  li
+    a
+      +button_link()
+
+dl.user_lists
+  dd
+    margin-top: $vspace
+    
+ul.user_list
+  +clean_list(false)
+  & > li
+    +clear_floats
+    margin-top: $vspace / 2
+    margin-left: $indent
+     
+    ul.list_control
+      +clear_floats
+      float: right
+      display: inline
+      li
+        position: relative
+        top: -3px
+
+//{{{
+
+.edit_list_forms
+  margin-left: $indent
+  form
+    margin-top: $vspace
+    input, select
+      float: right
+      min-width: 270px
+    input[type=submit]
+      min-width: 0px
+      width: 150px
+      margin-right: $indent
+  margin-bottom: $vspace * 2
+
+.list_info
+  margin-left: $indent
+  
+ul.entity_list_elements
+  +clean_list(false)
+  margin-left: $indent
+  & > li
+    margin-top: $indent
+  ul.entity_controls
+    float: right
+
+div.compare_list
+  +border_radius(4px, 4px)
+  position: absolute
+  top: - 2 * $vspace
+  left: $indent
+  background-color: white
+  border: solid 1px $bit_darker
+  padding: $indent $vspace
+  a.close_compare_list
+    +button_link()
+    position: absolute
+    top: $vspace
+    right: $indent
+    font-size: 0.7em
+
+  ul
+    +clean_list(false)
+    li
+      margin-top: $indent
+      span
+        margin-left: $indent
+      a
+        margin-right: $indent
+        font-size: 0.7em
+        float: left
+        +button_link()
+
+

data/share/views/compass/menu.sass

@@ -0,0 +1,35 @@
+#menu
+  padding: 5px
+  font-size: 0.9em
+  overflow: auto
+  overflow-x: hidden
+  +column(5)
+  ul
+    +clean_list
+    li
+      display: block
+
+  .workflow_menu
+    margin-bottom: 20px
+
+  .embedded
+    margin-top: $vspace
+
+ul.context_control
+  +clean_list(true)
+  height: 2em
+  li
+    float: left
+    padding: 3px
+    margin-left: 5px
+
+
+ul.job_control
+  +clean_list(true)
+  height: 2em
+  li
+    float: right
+    padding: 3px
+    margin-right: 15px
+
+

data/share/views/compass/notes.sass

@@ -0,0 +1,52 @@
+a.edit_note, a.back_note, a.delete_note
+  +button_link()
+
+dl.notes
+  margin-left: $indent
+
+div.note
+  margin-top: $vspace
+
+ul.note_list
+  +clean_list()
+  li
+    display: block
+    margin-left: $indent
+    margin-top: $vspace
+    margin-bottom: $vspace
+    span.note
+      margin-left: $indent
+  a
+    text-decoration: none
+
+ul.note_controls
+  +clean_list()
+  display: inline
+  li
+  &[shared=true]
+    li.share
+      display: none
+    li.unshare
+      display: visible
+  &[shared=false]
+    li.share
+      display: visible
+    li.unshare
+      display: none
+
+
+  a
+    +button_link()
+
+div.sneak_peek
+  margin-top: $vspace / 2
+  font-family: serif
+  border: solid 1px gray
+  text-overflow: ellipsis
+  overflow: hidden
+  padding: 0.5em
+  max-height: 1.2em
+
+div.news
+  margin-top: $vspace
+  margin-bottom: $vspace

data/share/views/compass/sizes.sass

@@ -0,0 +1,8 @@
+$screen_size: 1024px
+$scroll_padding: 22px
+$indent: 12px
+$vspace: 1.2em
+$body_size: $screen_size
+$content_size: $screen_size - $scroll_padding - $indent * 4
+
+$font_size: 12px

data/share/views/compass/tables.sass

@@ -0,0 +1,22 @@
+table tfoot 
+  text-align: left
+  h3
+    display: inline-block
+    margin: 0
+    margin-top: $vspace / 2
+    width: 8em
+  input, select
+    margin-left: 1em
+    margin-right: 1em
+    &.pnum, &.psize
+      width: 3em
+
+table td
+  word-spacing: 5px
+
+thead th
+  color: white
+  background: black
+
+table.sortable thead th
+  cursor: pointer

data/share/views/compass/wait.sass

@@ -0,0 +1,9 @@
+span.status
+  margin-right: $indent
+
+ul.messages
+  margin: auto
+  +clean_list(false)
+  li.message
+    margin-left: $indent
+    color: gray

data/share/views/edit_list.haml

@@ -1,39 +1,50 @@
-%a(href="/entity_list/#{ type }/#{ id }") View
-
-%form(action="#{File.join('/entity_list', type, 'copy', id)}" method='post')
-  %label Copy as:
-  %input(name='new_id')
-  %input(type='submit')
-
-%form(action="#{File.join('/entity_list', type, 'add', id)}" method='post')
-  %label Add other list:
-  %select.loaded_lists(name="other_list" type=type)
-  %input(type='submit')
-
-%form(action="#{File.join('/entity_list', type, 'subset', id)}" method='post')
-  %label Subset other list:
-  %select.loaded_lists(name="other_list" type=type)
-  %input(type='submit')
-
-%form(action="#{File.join('/entity_list', type, 'remove', id)}" method='post')
-  %label Remove other list:
-  %select.loaded_lists(name="other_list" type=type)
-  %input(type='submit')
-
-
-%ul.entity_list
+%header
+  %a.entity_list(href="/entity_list/#{ entity_type }/#{ id }")= id
+
+.edit_list_forms
+  %form(action="#{File.join('/entity_list', entity_type, 'copy', id)}" method='post')
+    %label Copy as:
+    %input(name='new_id')
+    %input(type='submit')
+
+  %form(action="#{File.join('/entity_list', entity_type, 'add', id)}" method='post')
+    %label Add other list:
+    %select.loaded_lists(name="other_list" type=entity_type)
+    %input(type='submit')
+
+  %form(action="#{File.join('/entity_list', entity_type, 'subset', id)}" method='post')
+    %label Subset other list:
+    %select.loaded_lists(name="other_list" type=entity_type)
+    %input(type='submit')
+
+  %form(action="#{File.join('/entity_list', entity_type, 'remove', id)}" method='post')
+    %label Remove other list:
+    %select.loaded_lists(name="other_list" type=entity_type)
+    %input(type='submit')
+
+%ul.entity_list_elements
   - list.each do |entity|
-    - values = {}
-    - types = {}
-    - entity.info.each{|k,v| values[k] = String === v ? v : v.to_json; types[k] = :string }
-
     %li(id="#{entity.id}")
       = entity.respond_to?(:link) ? entity.link : entity
-      \.
-      %a.DELETE.remove_entity_from_list(rel="#{entity.id}" href="/entity_list/#{ type }/#{ entity }/#{ id }") remove
+
+      %ul.entity_controls
+        %li
+          %a.DELETE.remove_entity_from_list(rel="#{entity.id}" href="/entity_list/#{ entity_type }/#{ entity }/#{ id }") remove
+
+      -# values = {}
+      -# types = {}
+      -# entity.info.each{|k,v| values[k] = String === v ? v : v.to_json; types[k] = :string }
       -#- form_id = "edit_entity_#{id}_#{entity.to_s}".gsub(/\s/, '_')
       -#%a.open_edit_controls(href="#edit_controls" ref=form_id) edit
       -#.edit_controls
       -#  - action = File.join("/entity_list", type, entity, id)
       -#  = workflow_partial('partials/_form', workflow, :values => values, :inputs => values.keys, :input_types => types, :action => action, :method => "post", :id => form_id)
 
+.list_info
+
+  %h4 Additional annotation information
+  %p
+    - info = list.info
+    = info.to_json
+
+

data/share/views/entity/GOTerm.haml

@@ -10,6 +10,7 @@
 - term_genes = Organism.gene_go_bp(organism).tsv(:persist => true, :key_field => "GO ID", :fields => ["Ensembl Gene ID"], :type => :flat, :merge =>  true)[entity]
 - Gene.setup(term_genes, "Ensembl Gene ID", organism)
 %dl
-
-  %dt All genes
-  %dd= term_genes.link * ", "
+  %dt
+    All Genes in pathway
+    == (#{ term_genes.ensembl.list_link :length, "Genes for GO term #{entity.name}"})
+  %dd= term_genes.from_kegg.link * ", "

data/share/views/entity/Gene.haml

@@ -7,7 +7,14 @@
   %dt Description
   %dd= entity.description
 
-%a(href="http://jun2011.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=#{entity.to "Ensembl Gene ID"}")= entity.to "Ensembl Gene ID"
+  %dd Isoforms
+  - isoforms = entity.transcripts.protein.compact
+  - if isoforms.respond_to? :link
+    %dd= isoforms.link * ", "
+  - else
+    %dd= isoforms * ", "
 
+
+%a(href="http://#{Misc.ensembl_server(entity.organism)}/Homo_sapiens/Gene/Summary?g=#{entity.to "Ensembl Gene ID"}")= entity.to "Ensembl Gene ID"
 %a(href="http://www.ncbi.nlm.nih.gov/gene/#{entity.to "Entrez Gene ID"}")= entity.to "Entrez Gene ID"
 

data/share/views/entity/GenomicMutation.haml

@@ -1,3 +1,6 @@
+- raise "No organism code defined. Try Hsa for current human build; add '?organism=Hsa' to your url." if entity.organism.nil? or (String === entity.organism and entity.organism.empty?)
+
+
 %h3= entity
 
 %p== reference base: #{entity.reference}
@@ -9,7 +12,7 @@
 %a(href="#{entity.ensembl_browser}") Ensembl Browser
 
 %ul
-  - (entity.mutated_isoforms || []).select{|mi| mi.consequence != "SYNONYMOUS"}.each do |mi|
+  - (entity.mutated_isoforms || []).reject{|mi| mi.synonymous}.each do |mi|
     %li
       = mi.link
       %span.note

data/share/views/entity/KeggPathway.haml

@@ -9,7 +9,7 @@
   %dt 
     All Genes in pathway
     == (#{ genes_in_pathway.ensembl.list_link :length, "Genes in pathway #{entity.name}"})
-  %dd= genes_in_pathway.from_kegg.link * ", "
+  %dd= genes_in_pathway.from_kegg.compact.link * ", "
 
 %img(src='http://www.genome.jp/kegg/pathway/hsa/#{entity}.png' style='width:100%;float:left;margin-right:10px;margin-botton:10px;' title='Click to see KEGG entry')
 

data/share/views/entity/MutatedIsoform.haml

@@ -1,15 +1,72 @@
-%h1= entity
-= entity.action_link 'marked_svg', "Protein overview", :link_options => {:extra_classes => "replace"}
+- if entity =~ /ENST/
+  %header== #{entity} (#{entity.transcript.gene.link})
+- else
+  %header== #{entity} (#{entity.protein.gene.link})
 
-%dl
-  %dt MutationAssesor prediction
-  %dd= entity.damage_scores([:mutation_assessor])
+  %dl
 
-  %dt SIFT prediction
-  %dd= entity.damage_scores([:sift])
+    - if entity.protein.gene.description
+      %dt Description
+      %dd= entity.protein.gene.description
 
+    %dt Length
+    %dd= entity.protein.sequence.length
+
+    - pos = entity.position
+    - if entity.truncated
+      - ablated_domains = entity.ablated_domain_positions
+      - if ablated_domains.any?
+        %dt Ablated IntePro domains
+        %dd
+          %ul
+            - ablated_domains.each do |domain,s,e|
+              %li
+                - InterProDomain.setup(domain, entity.organism)
+                - pfam = domain.pfam
+                - if pfam
+                  == #{domain.link} (#{pfam.link pfam}) [#{s} - #{e}]
+                - else
+                  == #{domain.link} [#{s} - #{e}]
+   
+
+    - else
+      - affected_domains =  entity.affected_domain_positions
+      - if affected_domains.any?
+        %dt Affected IntePro domain
+        %dd
+          %ul
+            - affected_domains.each do |domain,pos,s,e|
+              %li
+                - InterProDomain.setup(domain, entity.organism)
+                - pfam = domain.pfam
+                - if pfam
+                  == #{domain.link} (#{pfam.link pfam}) [Aprox. AA number #{ pos } in range #{s} #{e}]
+                - else
+                  == #{domain.link} [Aprox. AA number #{ pos } in range #{s} #{e}]
+   
+    %dt MutationAssesor prediction
+    %dd= entity.damage_scores([:mutation_assessor])
+
+    %dt SIFT prediction
+    %dd= entity.damage_scores([:sift])
+   
+    %dt Sequence
+    %dd(style='font-family: Andale Mono, monospace')
+      - dec = 0
+      = ((1..10).to_a * 5).collect{|i| i == 10 ? "<span style='color:red'>#{ dec += 1 }</span>" : i} * ""
+      %br
+      %br
+      - sequence = "" 
+      - entity.protein.sequence.scan(/.{1,50}/).each_with_index do |line, i|
+        - if i == entity.position / 50
+          - line[entity.position % 50 - 1] = "<span style='color:red'>#{line[entity.position % 50 - 1]}</span>"
+        - sequence += "<span class='line'>" + line + "</span><span class='line_count' style='margin-left: 5px'>#{i + 1}</span><br/>"
+      %span.sequence= sequence
+
+  = entity.action_link 'marked_svg', "Protein overview", :link_options => {:extra_classes => "replace"}
+
+  - if entity.pdbs and entity.pdbs.any?
+    = entity.action_link 'pdbs', "Mutation over pdbs", :link_options => {:extra_classes => "replace"}
+  - else
+    %p No pdbs found
 
-- if entity.pdbs and entity.pdbs.any?
-  = entity.action_link 'pdbs', "Mutation over pdbs", :link_options => {:extra_classes => "replace"}
-- else
-  No pdbs found