rbbt-rest 1.8.4 → 1.8.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6e2b9ecf9c546f18c529e7deffa7d8829339b943
-  data.tar.gz: 1121811f2ea813adf3164fa8676b42c50eb4cc2e
+  metadata.gz: 3cf37f751208e4d5cbfc407fd164ae7e49022f17
+  data.tar.gz: 773c970644b6f15df0ad6bfed8b0f1893d74362b
 SHA512:
-  metadata.gz: a1c5060636cb7383184b48de8b948cc67fc15ef7aba1961736b31d5ec8ed8ad069f04bd80de3f455a839d219dea07dfacd04ae8656cef49dd724248efecc280e
-  data.tar.gz: dd39e56e9aedb3096d1ce1b1cb96d89a7682be237c23e458756baaf61d097d052187040e14189b6bf3b9d1339b6b9c39c06411c09de43f35b449177fefdb8280
+  metadata.gz: 1988193658bd442876356d325a0f1ac0e17aa69ee872d9f0600a18959dbffddf89761ed78c311be91298cca71c2596e03d567d3ccee58be0f7f34d499fc5abd4
+  data.tar.gz: 00d4e4a8a07de772cbc0e2ef145b52609710011f902a769113d30f1fa043c5ca28ff60d632410ce22da17bd345204a1be5489030a079e33340032b03a5fb3d10

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

@@ -244,8 +244,8 @@ module RbbtRESTHelpers
   def hash2dl(hash, options = {})
     entries = hash.collect{|k,v|
       v = v * ", " if Array === v
-      html_tag(:dt, k) +
-      html_tag(:dd, v)
+      v = hash2dl(v) if Hash === v
+      html_tag(:dt, k) + html_tag(:dd, v)
     } * "\n"
     html_tag(:dl, entries, options)
   end

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

@@ -283,6 +283,7 @@ module RbbtRESTHelpers
 
     Misc.prepare_entity(value, type, entity_options) if Entity.formats[type] and not options[:unnamed]
 
+    orig_value = value
     value = value.link if value.respond_to? :link and not options[:unnamed]
 
     if Array === value and value.length > 100
@@ -294,7 +295,7 @@ module RbbtRESTHelpers
           when true, "true", :true
             Array === value ? value.collect{|v| "<span class='table_value'>#{v.to_s}</span>"} * ", " : "<span class='table_value'>#{value}</span>"
           when :long, "long"
-            Array === value ? value.collect{|v| "<span class='table_value long'>#{v.to_s}</span>"} * " " : "<span class='table_value long'>#{value}</span>"
+            Array === value ? value.zip(orig_value).collect{|v,ov| "<span class='table_value long' title='#{URI.escape(ov.to_s)}'>#{v.to_s}</span>"} * " " : "<span class='table_value long' title='#{URI.escape(orig_value)}'>#{value}</span>"
           else
             Array === value ? value.collect{|v| v.to_s} * ", " : value
           end

data/lib/rbbt/rest/knowledge_base/helpers.rb

@@ -47,6 +47,10 @@ module KnowledgeBaseRESTHelpers
                              kb.syndicate name, new
                            end if KnowledgeBaseRESTHelpers.syndications.any?
 
+                           user_studies[user].each do |study|
+                             kb.syndicate study, study.knowledge_base
+                           end
+
                            kb
                          end
   end

data/share/views/compass/app.sass

@@ -56,12 +56,3 @@ table > caption
 .filters + p
   margin-top: 2em
 
-.table_value
-  white-space: nowrap
-  &.strip
-    font-weight: bold
-  &.long
-    overflow: hidden
-    text-overflow: ellipsis
-    float: left
-    clear: left

data/share/views/compass/layout.sass

@@ -114,11 +114,35 @@ body
   #footer
     display: none
 
+table 
+  td:after
+    content: ""
+    clear: both
+    display: block
+    
+.table_value
+  white-space: nowrap
+  &.strip
+    font-weight: bold
+  &.long
+    max-width: 40em
+    overflow: hidden
+    text-overflow: ellipsis
+    float: left
+    clear: left
+
 =small_screen
   table:not(.collapsing)
     caption
       width: 100%
 
+  .table_value.long
+    float: left
+    clear: none
+    margin-left: 0.5em
+    &:not(:last-child):after
+      content: ', '
+    
 
   form.workflow_task
     .input.field.submit

data/share/views/compass/misc.sass

@@ -187,7 +187,7 @@ label[title]
   clear: both
 
 
-.action_menu.ui.buttons
+.action_menu.ui.buttons, .map_management.ui.buttons
   flex-wrap: wrap
 
 .flex-wrap

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.message
+      .action_progress.ui.info.message
 
     .action_loader.ui.very.basic.segment<

data/share/views/entity_partials/entity_map_card.haml

@@ -24,6 +24,35 @@
             - 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
+              - pvalue = map.values.flatten.collect{|v| v.nil? or (String === v and v.empty?) ? nil : v.to_f}.compact.flatten
+              - pvalue = pvalue[0..100]
+              = resource map_id + '.qqplot.png', nil, :image do |file|
+                = fragment do
+                  - FileUtils.mkdir_p File.dirname(file) unless File.exists? File.dirname(file)
+                  :ruby
+                    script =<<-EOF
+                      library(ggplot2)
+                      p = #{R.ruby2R pvalue}
+                      ggd.qqplot = function(pvector, main=NULL, ...) {
+                          Observed = -log10(sort(pvector,decreasing=F))
+                          Expected = -log10( 1:length(Observed)/length(Observed) )
+                          plot(Expected,Observed,pch=19,cex=1, ...,
+                              xlim=c(0,max(Expected)), ylim=c(0,max(Observed))) 
+                          lines(Expected,Expected,col="red")
+                      }
+                      png(filename=#{R.ruby2R file})
+                      ggd.qqplot(p)
+                      #ggsave(file=#{R.ruby2R file}, plot, width=width, height=height);
+                    EOF
+
+
+                  - R.run script
+
+              
+              
+
+
           - if Gene == Entity.formats[map.key_field]
             - if map.key_field != "Ensembl Gene ID"
               - url = add_GET_param(@fullpath, '_format', 'ensembl')

data/share/views/partials/table.haml

@@ -6,7 +6,7 @@
 - table_class = table_options[:table_class]  unless defined? table_class and table_class
 - header      = table_options[:header]  unless defined? header and header
 - row_ids     = table_options[:row_ids]  unless defined? row_ids and row_ids
-- row_ids     = consume if row_ids and row_ids.to_s == "false"
+- row_ids     = :consume if row_ids and row_ids.to_s == "false"
 - table_url   = table_options[:url]  unless defined? table_url and table_url
 - total_size  = table_options[:total_size]   unless defined? total_size and total_size
 - filters     = table_options[:filters]   unless defined? filters and filters

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.4
+  version: 1.8.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-30 00:00:00.000000000 Z
+date: 2016-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake