rbbt-rest 1.8.135 → 1.8.140

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b24d5bf255e99819325d04fd31b37eea707de16cb7bf686eb0c688df20271e21
-  data.tar.gz: 53d1400862b7970a92dbdab18f047b9d2e48554bbf555bac689f69aa53463b41
+  metadata.gz: 6e5a50362fab94b2e7e8536e08cd547e14a537e3ef9ea74d845b39f7e07f1ec6
+  data.tar.gz: 5d1cb0b86d12a2b2ef88432a1c0a6c59cce7981122866e29d6758bde77a1053a
 SHA512:
-  metadata.gz: bd77cb58c1ca6f69f222f4ce3e68fdf888f6c11bb270fef9faff6ba2ea8b278cc782426fc3ace48ad8e3fbdb9ee370f25fe5d0a15e3552559cbedeed7ccc5704
-  data.tar.gz: e36647d2e36eaf9103a07fc08b7ca0362387e9a680ff5ca94263c30b8cac487555ee545590be38d371ba910d00a4320d81e53425aa32dc06ccb973a3e2dc6674
+  metadata.gz: 7ad5e6f0c6a576017f4b70e729e567d39b61f30acbd821ed6a1c9229501868328f9127e50530e2d17864489d6853ae322d1d672fa5b68e96978e548b337e263a
+  data.tar.gz: a052ddbe5362be74bb1a2b2b76f9098b1d9c546e681f8b6491247c3ca8b9c9edc0c59e688b7d1297136684eca17ba948580bc93a3f90ab8938066e84a7ee6c41

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/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/dependencies.haml

@@ -7,9 +7,15 @@
     - dep_workflow ||= dep.task.workflow if dep.task
     - dep_workflow ||= File.basename(File.dirname(File.dirname(dep.path)))
     - str = [dep_workflow, dep.task_name, dep.name].compact * " - "
-    - dep_status = "done" if dep.path.exists?
+    - remote = true if Open.remote?(dep.path) || Open.ssh?(dep.path)
+
+    - if remote
+      - dep_status = "done" if dep.done?
+    - else
+      - dep_status = "done" if dep.path.exists?
+
     - dep_status ||= dep.status
-    - if dep.file(:progress).exists?
+    - if ! remote && dep.file(:progress).exists?
       - pgr = dep.file(:progress).yaml
       - if pgr and pgr[:last_percent]
         - start = pgr[:start]
@@ -57,8 +63,8 @@
         - elsif Module === dep_workflow
           - wf = dep_workflow
 
-        - if Open.remote? dep.path
-          - url = path.split("?").first
+        - if Open.remote?(dep.path)
+          - url = dep.path.split("?").first
           %a(href=url) #{ name }  
 
         - elsif wf and Sinatra::RbbtRESTWorkflow::WORKFLOWS.include?(wf) and wf.task_exports.include? dep.task_name.to_sym
@@ -71,7 +77,7 @@
 
       %span.status(class="#{dep_status}") [#{status}]
 
-      - if dep.dependencies.any?
+      - if dep.dependencies && dep.dependencies.any?
         - if cache[dep.path]
           = reveal "(deps)", nil, :title => "Dependencies already shown above", "attr-reveal_title" => "#{[dep_workflow, dep.task_name, dep.name] * " # "}"  do
             = cache[dep.path]

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){