rbbt-rest 1.8.136 → 1.8.142

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8291911f0473d9d30956ea5989996c626736f5406bc4e6a09478c2a7ada771fb
-  data.tar.gz: 9ca33ac6c0b51b927b3d6041aced32a732646414772ba6aa46df8a48190ad7ae
+  metadata.gz: 41d4cc31577331447eb862dab40cfa0579535cebe63f5a8a18fa15faf0e52903
+  data.tar.gz: 9df9b6195d6c3c7cb67f3d36055013c1024c197584a59a25321804d58b8b1575
 SHA512:
-  metadata.gz: 2ae762c95a7d407c3c90c5e242ae3370f2c2083fc90181bbe63bc5e80159e68196beba7d128c1e6c415a87287efbba132f3d0b452c5f0564019fea4a4660cced
-  data.tar.gz: 2625b47931d49c18711718846760db4c62c5f5ab0c451a459ddbca96960ddbccd0345605a4994752a7d81af9ee0769c3ea6343593fb58902e18e9c649d57ad1b
+  metadata.gz: 90c5a597c253cf60af21c149c0671973a3b1c0d1012b592f300f87e7fb84dedae70989ef632740dcb9f0cca5dfa8198c44268012393e6c7ecf9aa1b71122e4e0
+  data.tar.gz: f4019b6940791f2a2b54a7a70aad1ec7c1eb27c135f516362fd6289b7ff7785ae2c236321d6f403dc6017275aae36c03ed12a23bfecbb29d0f04abb3dec763a3

data/lib/rbbt/rest/common/cache.rb

@@ -153,6 +153,7 @@ module RbbtRESTHelpers
           header "Location", Entity::REST.entity_list_url(list_id, type)
           url = Entity::REST.entity_list_url(list_id, type)
           url = url + '?_layout=false' unless @layout
+          url = URI.encode(url)
           redirect to(url)
         when "map"
           raw_tsv, tsv_options = load_tsv(fragment_file)
@@ -174,6 +175,7 @@ module RbbtRESTHelpers
           Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
           url = Entity::REST.entity_map_url(map_id, type, column)
           url = url + '?_layout=false' unless @layout
+          url = URI.encode(url)
           redirect to(url)
         when "excel"
           require 'rbbt/tsv/excel'
@@ -223,7 +225,8 @@ data = NULL
 
           if mime.nil?
             txt = Open.read(fragment_file)
-            if txt =~ /<([^> ]+)[^>]*>.*<\/\1>/sm
+
+            if txt =~ /<([^> ]+)[^>]*>.*?<\/\1>/m
               mime = "text/html"
             else
               begin

data/lib/rbbt/rest/common/misc.rb

@@ -59,8 +59,13 @@ module RbbtRESTHelpers
     @ajax = request.xhr?
     @ajax_url = headers["AJAX-URL"]
 
-    @fullpath = request.fullpath
     @uri = request.env["REQUEST_URI"]
+    @path = request.env["PATH_INFO"]
+    @query = request.env["QUERY_STRING"]
+
+    #@fullpath = request.fullpath
+    @fullpath = (@query && ! @query.empty?) ? @path + "?" + @query : @path
+    @fullpath = remove_GET_param(@fullpath, ["_update", "_"])
 
     @layout = consume_parameter(:_layout)
 

data/lib/rbbt/rest/common/render.rb

@@ -166,9 +166,10 @@ module RbbtRESTHelpers
         }
         Open.write(pid_file, pid.to_s)
 
-        url = @uri
+        url = @fullpath 
         url = remove_GET_param(url, "_update")
         url = remove_GET_param(url, "_")
+
         fragment_url = add_GET_param(url, "_fragment", fragment_code)
         if link.nil?
           html_tag('a', "", :href => fragment_url, :class => 'fragment', "data-text" => text)
@@ -226,7 +227,7 @@ module RbbtRESTHelpers
     filename = Misc.sanitize_filename(Misc.name2basename(filename))
 
     if @step
-      url = add_GET_param(remove_GET_param(@uri, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
+      url = add_GET_param(remove_GET_param(@fullpath, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
       f = @step.file(:html_resources)[filename].find
     else
       url = "/files/#{ filename }"

data/lib/rbbt/rest/common/table.rb

@@ -402,7 +402,7 @@ module RbbtRESTHelpers
     if @step
       table_file = @step.file(table_code) if @step
 
-      url = add_GET_param(@uri, "_fragment", File.basename(table_file))
+      url = add_GET_param(@fullpath, "_fragment", File.basename(table_file))
       url = remove_GET_param(url, "_update")
       url = remove_GET_param(url, "_layout")
       url = remove_GET_param(url, "_")

data/lib/rbbt/rest/entity/rest.rb

@@ -14,11 +14,11 @@ module Entity
     #{{{ MISC
     
     def self.clean_element(elem)
-      elem.gsub('/', '-..-').gsub("|", '-...-').gsub('%', 'o-o').gsub('[','(.-(').gsub(']',').-)')
+      elem.gsub('&', '--AND--').gsub('/', '-..-').gsub("|", '-...-').gsub('%', 'o-o').gsub('[','(.-(').gsub(']',').-)')
     end
  
     def self.restore_element(elem)
-      CGI.unescape(CGI.unescape(elem.gsub('-..-', '/').gsub('-...-', '|').gsub('o-o', '%').gsub('(.-(','[').gsub(').-)',']')))
+      CGI.unescape(CGI.unescape(elem.gsub('--AND--', '&').gsub('-..-', '/').gsub('-...-', '|').gsub('o-o', '%').gsub('(.-(','[').gsub(').-)',']')))
     end
 
     def self.setup(mod)
@@ -146,6 +146,12 @@ module Entity
       rescue
         text = self
       end
+
+      begin
+        attributes[:title] ||= self.respond_to?(:title)? self.title || self : self 
+      rescue
+      end
+
       attributes[:title] = text if attributes[:title].nil?
 
       Misc.html_tag('a', text, attributes)

data/share/views/compass/card_templates.sass

@@ -1,4 +1,13 @@
 
+.action_controller
+  display:flex !important
+  & > .action_progress
+    flex-width: 100%
+  & > .ui.buttons > .button
+    flex-height: 3em
+  & > .ui.buttons.controls > .button
+    max-height: 3em
+
 .action_parameters, .filter_controls
   form
     &:after
@@ -41,3 +50,8 @@
       width: 7em !important
 
 
+.card_sidebar, .card_sidebar > *, .card_sidebar > * > *
+  text-overflow: ellipsis
+  overflow-x: auto
+  max-width: 100%
+      

data/share/views/compass/layout.sass

@@ -2,6 +2,8 @@
 .preload * 
   +animation-duration(0s !important)
         
+html, body
+  scroll-padding-top: 60px
 body
   background: none repeat scroll 0% 0% #F7F7F7
   margin: 0 !important

data/share/views/compass/misc.sass

@@ -278,3 +278,18 @@ ul.tasks
 
 .table > .table_url
   display: none
+
+dl.flex_dl
+  display: flex
+  flex-flow: row wrap
+  & > dt
+    flex-basis: 20%
+    text-align: right
+    padding-right: 2em
+    max-width: 20%
+    text-overflow: ellipsis
+  & > dd
+    flex-basis: 80%
+    flex-grow: 1
+    margin: 0
+

data/share/views/entity_partials/action_controller.haml

@@ -39,6 +39,6 @@
             = entity.action_link action, text, params.merge(:class => 'ui item button')
           - last_resource = resource
 
-      .action_progress.ui.info.message
+    .action_progress.ui.info.message
 
     .action_loader.ui.very.basic.segment<

data/share/views/entity_partials/entity_card.haml

@@ -2,21 +2,31 @@
 - entity_id = "entity__" + entity.id
 - default = entity.respond_to?(:default)? entity.default || entity.to_s : entity.to_s
 
+:sass
+  .card_sidebar, .card_sidebar > *, .card_sidebar > * > *
+    text-overflow: ellipsis
+    overflow-x: auto
+    max-width: 100%
       
 .entity_card.ui.grid(data-entity=entity data-entity-id=default data-entity-type="#{entity.base_type}" data-entity-format="#{entity.respond_to?(:format) ? entity.format : ""}" data-entity-info="#{entity.info.to_json}")
   /-- card_sidebar --
-  .ui.four.wide.column.vertical.card_sidebar.menu
+  .ui.four.wide.column.vertical.card_sidebar.menu.hidden
+    - empty = true
     - if card.sections.any?
+      - empty = false
       %h3 Sections
       - card.sections.each do |name,section|
         %a.item(href="##{Misc.snake_case(name)}")= Misc.humanize(name)
-      %a.item(href="#entity_actions") Entity actions
+      - if card.action_controller
+        %a.item(href="#entity_actions") Entity actions
 
     - info = card.entity.info
+    - info.delete :annotation_types
     - if info.any? or card.meta or card.list_container
-      %h3 Meta data
+      - empty = false
       .meta
         - if info.any?
+          %h3 Meta data
           .entity_info
             = hash2dl(info)
 
@@ -28,10 +38,16 @@
           = fragment :meta, &card.meta
 
     - if card.list_container
+      - empty = false
       %h3 Related lists
       .list_container
         = list_container_render(card.list_container)
 
+    - if ! empty
+      .show_opened
+    - else
+      .delete_empty
+
 
   .ui.twelve.wide.column.content
     .ui.header.basic.segment

data/share/views/entity_partials/entity_list_card.haml

@@ -3,7 +3,9 @@
 
 .entity_list_card.ui.grid(id="#{ list_id.gsub(/\s/,'_') }_card" data-list=list_id data-list-type="#{list.base_type}")
   .ui.four.wide.column.vertical.card_sidebar.menu.hidden
+    - empty = true
     - if card.sections.any?
+      - empty = false
       %h3 Sections
       - card.sections.each do |name,section|
         %a.item(href="##{Misc.snake_case(name)}")= Misc.humanize(name)
@@ -22,7 +24,10 @@
       %a.edit_list.ui.button(href="#") Edit
 
     - info = card.list.info
+    - info.delete :annotation_types
+    - info.delete :annotated_array
     - if info.any? or card.meta or card.list_container
+      - empty = false
       /-- sidebar --
       %h3 Meta data
       .meta
@@ -55,10 +60,14 @@
                   %li= link
  
     - if card.list_container
+      - empty = false
       %h3 Related lists
       .list_container
         = list_container_render(card.list_container)
 
+    - if ! empty
+      .show_opened
+
   .ui.twelve.wide.column.content
     .ui.header.basic.segment
       .content

data/share/views/entity_partials/entity_map_card.haml

@@ -21,7 +21,7 @@
               %input(type='submit')
 
           - if (%w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values) & map.fields.first.downcase.split(/\s+/)).any? and map.fields.first.downcase !~ /score$/
-            - url = add_GET_param(@uri, '_format', 'pvalue_score')
+            - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
             %a.ui.small.button(href=url) Pvalue score
 
             = reveal "QQ-plot", nil, :class => 'ui small button plot' do
@@ -56,16 +56,16 @@
 
           - if Gene == Entity.formats[map.key_field]
             - if map.key_field != "Ensembl Gene ID"
-              - url = add_GET_param(@uri, '_format', 'ensembl')
+              - url = add_GET_param(@fullpath, '_format', 'ensembl')
               %a.ensembl.ui.small.button(href=url) Ensembl
             - if map.key_field != "Associated Gene Name"
-              - url = add_GET_param(@uri, '_format', 'name')
+              - url = add_GET_param(@fullpath, '_format', 'name')
               %a.name.ui.small.button(href=url) Name
           - if "Rank" == map.fields.first
-            - url = add_GET_param(@uri, '_format', 'invert_ranks')
+            - url = add_GET_param(@fullpath, '_format', 'invert_ranks')
             %a.invert_ranks.ui.small.button(href=url) Invert ranks
           - else
-            - url = add_GET_param(@uri, '_format', 'ranks')
+            - url = add_GET_param(@fullpath, '_format', 'ranks')
             %a.ranks.ui.small.button(href=url) Ranks
           - if NumericValue == Entity.formats[map.fields.first] or (map.entity_templates[map.fields.first] and map.entity_templates[map.fields.first].annotation_types.include? NumericValue)
             - $page_entity_base_type = page_entity_base_type 

data/share/views/job_result/array.haml

@@ -1,4 +1,7 @@
 %ul
   - result.each do |elem|
-    %li= elem
+    - if elem.respond_to?(:link)
+      %li= elem.link
+    - else
+      %li= elem
  

data/share/views/layout/footer.haml

@@ -37,24 +37,11 @@
       a 
         width: 100%
 
-.ui.segment.stackable.bottom.attached.grid.three.column
+.ui.segment.stackable.bottom.attached.grid.two.column
   .ui.column
     = partial_render('partials/footers/bsc')
+-#
   .ui.column
     = partial_render('partials/footers/ntnu')
   .ui.column
     = partial_render('partials/footers/cnio')
--#.ui.segment
-  .image
-    %a(href="http://www.cnio.es/")
-      %img(src="/file/cnio.png" height='115px' width='241px')
-  .content
-    .ui.header
-      CNIO. Centro Nacional de Investigaciones Oncologicas (Spanish National Cancer Research Center)
-    .description
-      %span.group Structural Computational Biology Group
-      %br/
-      %span.address   C/ Melchor Fernandez Almagro, 3, E-28029 Madrid
-    .meta.contact
-      %span.who miguel.vazquez
-      %span.where cnio.es

data/share/views/partials/footers/bsc.haml

@@ -2,19 +2,19 @@
   %a(href="http://www.bsc.es/")
     %img(src="/file/bsc.svg")
 .content
-  .ui.header
+  -#.ui.header
     :sass
       span.bsc
         font-weight: bold
       span.cns
         font-style: italic
         font-weight: normal
-        
+  -#      
     %span.bsc Barcelona Supercomputing Center
     %span.cns Centro Nacional de Supercomputación
 
   .description
-    %span.group Genome Informatics Unit
+    %span.group Genome Informatics Unit. Life sciences Department.
     %span.address  Nexus II Building. C/ Jordi Girona, 29. 08034 Barcelona (Spain)
 
   .meta.contact

data/share/views/partials/tabs.haml

@@ -2,23 +2,26 @@
 - id = "tab_menu_"  + rand(1000).to_s unless defined? id and not id.nil?
 - active = false unless defined? active and not active.nil?
 - active = headers.first if TrueClass === active
-.ui.top.attached.tabular.stackable.menu(id=id)
+.tabs(id=id)
+  .ui.top.attached.tabular.stackable.menu
+    - headers.each do |header|
+      - code = codes[header] ||= Misc.digest([header, id]*"-")
+      - tab_active = (active and active == header) ? 'active' : ''
+      .ui.item(data-tab=code class=tab_active)= header
+
   - headers.each do |header|
-    - code = codes[header] ||= Misc.digest([header, id]*"-")
+    - code = codes[header] 
+    - next if content[header].nil?
     - tab_active = (active and active == header) ? 'active' : ''
-    .ui.item(data-tab=code class=tab_active)= header
-
-- headers.each do |header|
-  - code = codes[header] 
-  - next if content[header].nil?
-  - tab_active = (active and active == header) ? 'active' : ''
-  .ui.tab.bottom.attached.segment.content(data-tab=code class=tab_active)
-    = content[header]
+    .ui.tab.bottom.attached.segment.content(data-tab=code class=tab_active)
+      = content[header]
 
 :deferjs
-  $("##{id} > .item[data-tab]").tab()
+  //$("##{id} > .item[data-tab]").tab()
+
+  $("##{id} > .menu > .item[data-tab]").tab({"context": "##{id}"})
 
-  $('##{id} > .item[data-tab=close]').click(function(item){
+  $('##{id} > .menu > .item[data-tab=close]').click(function(item){
     var tool = $(this).parents('.cytoscape_tool').first()
     tool.find('.tab.active, .item.active').removeClass('active')
     return false

data/share/views/public/js/app.js

@@ -39,6 +39,19 @@ if (typeof user === 'undefined') user = 'none'
 
 $(function(){
 
+  register_dom_update('.card_sidebar > .show_opened', function(elem){
+    elem.parent('.card_sidebar').removeClass('hidden')
+    elem.remove()
+  })
+
+  register_dom_update('.card_sidebar > .delete_empty', function(elem){
+    console.log('delete')
+    elem.parent('.card_sidebar').siblings('.content').find('.controls > .card_sidebar_open').remove()
+    elem.parent('.card_sidebar').remove()
+  })
+
+
+
   register_dom_update('.reload_workflow', function(elem){
    elem.click(function(){
      console.log('WR')

data/share/views/public/js/helpers/helpers.js

@@ -48,11 +48,11 @@ function remove_parameter(url, parameter){
 }
 
 function clean_element(elem){
- return elem.replace(/\//g, '-..-').replace(/%/g,'o-o').replace(/\[/g,'(.-(').replace(/\]/g,').-)')
+ return elem.replace('&','--AND--').replace(/\//g, '-..-').replace(/%/g,'o-o').replace(/\[/g,'(.-(').replace(/\]/g,').-)')
 }
 
 function restore_element(elem){
- return unescape(elem.replace(/-\.\.-/g, '/').replace(/o-o/g,'%')).replace(/\(\.-\(/g,'[').replace(/\)\.-\)/g,']');
+ return unescape(elem.replace('--AND--','&').replace(/-\.\.-/g, '/').replace(/o-o/g,'%')).replace(/\(\.-\(/g,'[').replace(/\)\.-\)/g,']');
 }
 
 function parse_parameters(params){

data/share/views/public/js/rbbt.basic.js

@@ -160,7 +160,7 @@ rbbt.post = function(url, data, params){
 // Cookies
 
 rbbt.set_cookie = function(name,value){
-  Cookies.set(name, value)
+  Cookies.set(name, value, { sameSite: 'strict'})
 }
 
 rbbt.get_cookie = function(name){
@@ -171,7 +171,7 @@ rbbt.get_cookie = function(name){
 }
 
 rbbt.remove_cookie = function(name){
-  Cookies.remove(name)
+  Cookies.remove(name, { sameSite: 'strict'})
 }
 
 // LocalStorage

data/share/views/public/js/rbbt.plots/rbbt.plots.graph.adapters.js

@@ -66,6 +66,7 @@ rbbt.plots.graph.build_cytoscapejs = function(graph_model){
   forArray(model.edges, function(edge){
     var clean = clean_hash(edge)
     if (undefined === clean.id) clean.id = clean.code
+    clean.id = clean.code + "@" +  clean.database
     edges.push({data: clean})
   })
 
@@ -100,6 +101,10 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
     style: { 'shape': 'data(shape)' }
   },
 
+  {
+    selector: 'edge',
+    style: { 'curve-style': 'bezier'}
+  },
   {
     selector: 'edge[color]',
     style: { 'line-color': 'data(color)',
@@ -113,18 +118,35 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
     selector: 'edge[width]',
     style: { 'width': 'data(width)'}
   },
-  {
-    selector: 'edge[target-arrow-shape]',
-    style: { 'target-arrow-shape': 'data(target-arrow-shape)'}
-  },
-  {
-    selector: 'edge[target-arrow-color]',
-    style: { 'target-arrow-color': 'data(target-arrow-color)'}
-  }
+  //{
+  //  selector: 'edge[target-arrow-shape]',
+  //  style: { 'target-arrow-shape': 'data(target-arrow-shape)'}
+  //},
+  //{
+  //  selector: 'edge[target-arrow-color]',
+  //  style: { 'target-arrow-color': 'data(target-arrow-color)'}
+  //}
 
   ]
 
-  var default_layout = { name: 'cose' }
+  var default_layout = {
+              name: 'cose',
+              idealEdgeLength: 100,
+              nodeOverlap: 20,
+              refresh: 20,
+              fit: true,
+              padding: 30,
+              randomize: false,
+              componentSpacing: 100,
+              nodeRepulsion: 400000,
+              edgeElasticity: 100,
+              nestingFactor: 5,
+              gravity: 80,
+              numIter: 1000,
+              initialTemp: 200,
+              coolingFactor: 0.95,
+              minTemp: 1.0
+            }
 
   if (undefined === style) style = default_style
   if (undefined === layout) layout = default_layout
@@ -139,6 +161,7 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
         container: elem,
         elements: cy_model.elements,
         style: style,
+        layout: layout,
       }
 
       if (undefined !== extra) forHash(extra, function(k,v){ cy_params[k,v] })
@@ -147,7 +170,7 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
 
       cy.layout(layout)
 
-      cy.one('layoutready', function(){
+      cy.one('layoutstop', function(){
         deferred.resolve(this)
       })
     })
@@ -238,7 +261,6 @@ rbbt.plots.graph.update_cytoscape = function(graph_model, elem){
 
 rbbt.plots.graph.view_d3js_graph = function(graph_model, elem, node_obj){
   rbbt.plots.graph.update(graph_model).then(function(updated_model){
-    console.log(updated_model)
     var dataset = rbbt.plots.graph.build_d3(updated_model)
 
     if (undefined === node_obj){