rbbt-rest 1.8.53 → 1.8.55

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2c9a1692ddc71512f10e55f78e92351df7f4467e
-  data.tar.gz: d82b4f419488fabdec95fda1bad0ddddec457e65
+  metadata.gz: 6716eb64f85a3f3e6d72310e9d09f1a684f5721a
+  data.tar.gz: cb0a0bc5263652ac50cd0b00937184b32208b560
 SHA512:
-  metadata.gz: 6bbdf93ba911ca609933389d2108a3f538113645fa1283aed8f0c3945683083724050992ee5f0fc0aecccad71a75f18043052c3100c55b1cd9782b3b2afda6a0
-  data.tar.gz: 453460f37c3594853499a226e38582a4e415647189b8f867090fa433a6001a07a30454c5174c607dd01f99e775acbf4a1c3a868a6d44a515615b4be80fa56e99
+  metadata.gz: f0a5df5ee5734f0fb8df1c03ec7b3b957cf7fb0e317134ead50cb60950dccad225bbfba96437683c7808fc4b022c5ce981dd7463152357a8d444667eb9507cdc
+  data.tar.gz: 3f5b0455920ee70bc8000e6e124c4a65ae6def0638dd4f4dbe7619a61f9517296606a828106fe3bb0afa3a6491b87880bdcbc7c810134dc79efaf9ddd175126b

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

@@ -78,9 +78,20 @@ module NumericValue
 
   self.format =(<<-EOF
 p-value
+p-value
 p.value
 P-value
 P.value
+p-value score
+p-value score
+p.value score
+P-value score
+P.value score
+p-value Score
+p-value Score
+p.value Score
+P-value Score
+P.value Score
 p-values
 p.values
 P-values

data/share/views/compass/misc.sass

@@ -82,10 +82,13 @@ table, table.responsive
 .entity_list
   width: auto !important
   clear: both
-  span.title
+  .title
     border: none !important
-    > a 
-      padding: 0.5em
+    & > a
+      display: inline-block
+      padding: 0.5em 1em
+    span.title
+      border: none !important
 
 table
   .caption, .title

data/share/views/job_result/job_control.haml

@@ -11,7 +11,20 @@
 
   - if files.any?
     %dt.ui.header Files
-    %dd.job_files
+    %dd.job_files.ui.basic.segment
+      - files_by_dir = {}
+      - files.each do |file|
+        - dir = File.dirname(file)
+        - files_by_dir[dir] ||= []
+        - files_by_dir[dir]  << file
       .ui.buttons
-        - files.sort.each do |file|
+        - (files_by_dir["."] || []).sort.each do |file|
           %a.small.ui.button(href="/#{[workflow.to_s, task, jobname, "file", file] * "/"}")= file
+      - (files_by_dir.keys - ["."]).each do |dir|
+        %dl
+          %dt.ui.header #{dir}/
+          %dd
+            .ui.buttons
+              - files_by_dir[dir].each do |file|
+                %a.small.ui.button(href="/#{[workflow.to_s, task, jobname, "file", file] * "/"}")= File.basename(file)
+             

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

@@ -8,6 +8,7 @@ rbbt.exception.report = function(err){
   console.log(err)
   console.log("Error: " + err)
   var stack = err.stack
+  console.log("Error: " + stack)
   if(undefined === stack) stack = "No stack trace"
   if (rbbt.modal){
     stack = "<ul class='stacktrace'><li>" + stack.replace(/\n/g, '</li><li>') + '<li/></ul>'

data/share/views/public/js/rbbt.plots/rbbt.plots.aes.js

@@ -26,7 +26,7 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
       return get_sign_gradient(aes, 'red', 'grey', 'green')
     case 'map':
       if (typeof aes == 'object')
-        return aes.map(function(value){ return map_obj[value.toString()] })
+        return aes.map(function(value){ if (value !== undefined && value != null ) value = value.toString(); return map_obj[value] })
      else
         return map_obj[aes]
     case 'function':

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

@@ -78,29 +78,42 @@ rbbt.plots.graph.build_cytoscapejs = function(graph_model){
 rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, extra){
 
   var default_style = [ // the stylesheet for the graph
+  // Default values
   {
     selector: 'node',
     style: { 'background-color': 'blue', 'label': 'data(id)' }
   },
-  
+  {
+    selector: 'edge',
+    style: { 'width': 1, 'line-color': 'grey', 'target-arrow-color': '#ccc', 'target-arrow-shape': 'triangle' }
+  },
   {
     selector: 'node[label]',
     style: {'label': 'data(label)' }
   },
-
   {
     selector: 'node[color]',
     style: { 'background-color': 'data(color)' }
   },
-
   {
-    selector: 'edge',
-    style: { 'width': 1, 'line-color': 'grey', 'target-arrow-color': '#ccc', 'target-arrow-shape': 'triangle' }
+    selector: 'node[shape]',
+    style: { 'shape': 'data(shape)' }
   },
+
   {
     selector: 'edge[color]',
-    style: { 'line-color': 'data(color)'}
+    style: { 'line-color': 'data(color)',
+             'target-arrow-color': 'data(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' }
@@ -113,22 +126,24 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
   rbbt.plots.graph.update(graph_model).then(function(updated_model){
     var cy_model = rbbt.plots.graph.build_cytoscapejs(updated_model)
 
-    console.log(cy_model)
     require_js(['/plugins/cytoscapejs/cytoscape.js'], function(){
       var cy_params = {
         container: elem,
         elements: cy_model.elements,
         style: style,
-        layout: layout,
       }
 
-      if (undefined !== extra) forHash(extra,function(k,v){ cy_params[k,v] })
+      if (undefined !== extra) forHash(extra, function(k,v){ cy_params[k,v] })
 
       var cy = cytoscape(cy_params)
 
-      deferred.resolve(cy)
+      cy.layout(default_layout)
+
+      cy.one('layoutready', function(){
+        deferred.resolve(this)
+      })
     })
-  },rbbt.exception.report)
+  }, rbbt.exception.report)
 
   return deferred.promise
 }

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

@@ -37,6 +37,9 @@ rbbt.plots.graph.get_entities = function(graph_model){
 }
 
 rbbt.plots.aes.complete_source_target = function(list){
+  if (undefined === list.aes) list.aes = {}
+  if (undefined === list.properties) list.properties = {}
+
   if (undefined === list.aes.source && undefined === list.aes.source){
     if (undefined === list.properties.source && undefined === list.properties.source){
       var source = [];

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.53
+  version: 1.8.55
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-02-10 00:00:00.000000000 Z
+date: 2017-03-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake