rbbt-rest 1.8.2 → 1.8.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9db115f33017c66595437648ad05997d452733a6
-  data.tar.gz: abda02054f71c7d38d6024524d755bcc2fb1dff6
+  metadata.gz: 8bc8c84dbe3d17dfa0f63f7a513da1d52ed7e150
+  data.tar.gz: fc73cf5e1d13d176ab35fa2e5f065d9756033cc7
 SHA512:
-  metadata.gz: ea5dbd2c6b35d1de6975818ac8916a2ea7430680ad5a17bf73be7b5d01c5b3136360a2ff138654593a7cefe97d51120fa1b87972265f8bb7d7b7cfdb3331546d
-  data.tar.gz: 15a3cbed98f5c0b531df9aa0b56936c644dca35b17676bb88bab6f0ea61ef8b4e8b7838c551f78f674ac25e2aa8d5d4a44d77c592dc91143d9c2fdfae555b02b
+  metadata.gz: 384ceaf737b835b8cba9e49b631b78f2d4b8b2d16c0f1d74b9cb532912daf6599491e22f67d63ddd6c6eb276501d43eb323233daf0c17d54f4544fe632a9b610
+  data.tar.gz: e96e260ef7ee2bfc4f78d46367c3a2a6f1785991a4978dab3b974ebf92a954472d57fa2bcfd72ed847cc46a398b35daff9c9ab3b38a075b7dd940774db740c15

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

@@ -54,8 +54,10 @@ module KnowledgeBaseRESTHelpers
   def get_knowledge_base(name=:user, namespace = nil)
     kb = case name.to_s
            when 'step'
-             dir = cookies[:step_path] + '.files/knowledge_base'
-             iii dir
+             step_path = cookies[:step_path]
+             step_path = params[:step_path] if step_path.nil?
+             raise "No step_path" if step_path.nil?
+             dir = step_path + '.files/knowledge_base'
              KnowledgeBase.load(dir)
            when "user"
              user_kb(user)

data/share/views/error.haml

@@ -1,20 +1,33 @@
-.error
-  %h5 Error on #{format_name File.basename(job.name)}
+.error.ui.segment.error.message
+  %h5.ui.header Error on #{format_name File.basename(job.name)}
   - if job.messages and job.messages.any?
-    %span.error_message
-      %pre= CGI.escapeHTML(job.messages[-1] || "")
+    %pre.error_message.ui.basic.segment.content
+      = CGI.escapeHTML(job.messages[-1] || "")
 
 
   - if defined? job.info_file and File.exists? job.info_file and request.env["REQUEST_URI"].include? job.name
     - clean_url = add_GET_param(request.env["REQUEST_URI"], "_update", "clean")
-    %a(href=clean_url) Clean
+    %a.ui.button.blue(href=clean_url) Clean
   - else
     - clean_url = add_GET_param(request.env["REQUEST_URI"], "_update", "reload")
-    %a(href=clean_url) Reload
+    %a.ui.blue.button(href=clean_url) Reload
 
-  - backtrace = job.info[:backtrace]
-  - if backtrace and backtrace.any?
-    %hr
-    %ul.error_backtrace.clean_list
+- backtrace = job.info[:backtrace]
+- if backtrace and backtrace.any?
+
+  %ul.error_backtrace.clean_list.ui.segment
+    .ui.header Backtrace
+    %pre.ui.content
+      - require 'rbbt/util/colorize'
+      - pallete = {}
+      - matches = %w(views workflows rbbt).collect{|w| /\/#{w}/ }
+      - colors = Colorize.distinct(matches)
       - backtrace.each do |line|
-        %li= line
+        - color = nil
+        - matches.each_with_index do |m,i|
+          - if m.match(line)
+            - color = colors[i].darken(0.3).to_s 
+            - break
+
+        - style = color ? ';color:'+color : ""
+        %li(style="font-size:0.9em;font-family:monospace#{style}")= line.sub('`',"'")

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

@@ -18,12 +18,15 @@ rbbt.exception.report = function(err){
   }
 }
 
-rbbt.try = function(func){
+rbbt.try = function(func, catch_function){
   var f = function(){
     try {
       return func.apply(this, arguments)
     }catch(err){
-      rbbt.exception.report(err)
+      if (catch_function)
+        catch_function(err)
+      else
+        rbbt.exception.report(err)
     }
   }
   return f

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

@@ -52,7 +52,7 @@ rbbt.plots.aes.get_properties = function(list, rules){
       eval('extract='+extract)
     }
     
-    if (rule.entity_type && rule.entity_type != list.type) return 
+    if (rule.entity_type && rule.entity_type != list.type && rule.entity_type != list.format) return 
 
     if (rule.info){
       var property = rule.property
@@ -66,6 +66,14 @@ rbbt.plots.aes.get_properties = function(list, rules){
 
       deferred.resolve(value)
       promise = deferred.promise
+      if (extract){ 
+        promise = promise.then(function(res){ 
+          if (typeof res == 'object')
+            return res.map(function(elem){ return extract.call(null, elem)}) 
+          else
+            return extract.call(null, res) 
+        }) 
+      }
     }
 
     if (rule.value){
@@ -79,8 +87,15 @@ rbbt.plots.aes.get_properties = function(list, rules){
       var property = rule.property
       var args = rule.args
       if (undefined === name) name = property
-      promise = rbbt.entity_array.property(list.codes, list.type, list.info, property, args)
-      if (extract){ promise = promise.then(function(res){ return res.map(extract)}) }
+
+      var deferred = m.deferred()
+      var tmp_promise = rbbt.entity_array.property(list.codes, list.type, list.info, property, args)
+
+      if (extract){ tmp_promise = tmp_promise.then(function(res){ return res.map(extract)}) }
+
+      tmp_promise.then(deferred.resolve, function(){ deferred.resolve(undefined)})
+
+      promise = deferred.promise
     }
 
     if (rule.workflow){
@@ -163,7 +178,7 @@ rbbt.plots.aes.get_properties = function(list, rules){
       }
     }
 
-    promises.push(promise.then(function(res){list.properties[name] = res}))
+    promises.push(promise.then(function(res){ if (undefined !== res) list.properties[name] = res}))
   })
 
   return m.sync(promises)

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

@@ -137,7 +137,7 @@ rbbt.plots.graph.view_cytoscape = function(graph_model, elem, style, layout, ext
     var dataset = rbbt.plots.graph.build_cytoscape(updated_model)
 
     require_js(['/js/cytoscape/js/src/AC_OETags.js', '/js/cytoscape/js/src/cytoscapeweb.js', '/js/cytoscape'], function(){
-      var tool = $('#plot').cytoscape_tool({
+      var tool = $(elem).cytoscape_tool({
         knowledge_base: 'user',
         namespace: 'Hsa/feb2014',
         entities: dataset.nodes,
@@ -159,7 +159,8 @@ rbbt.plots.graph.view_cytoscape = function(graph_model, elem, style, layout, ext
 
           var url = target.data.url;
 
-          rbbt.modal.controller.show_url(url)
+          if (url)
+            rbbt.modal.controller.show_url(url)
           return(false)
         },
 

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

@@ -11,12 +11,14 @@ rbbt.plots.graph.get_entities = function(graph_model){
     source_entities.codes = unique(list.info.source)
     source_entities.info = list.source_info
     source_entities.type = list.source_type
+    source_entities.format = list.source_format
 
     var target_type = list.target_type
     var target_entities = {}
     target_entities.codes = unique(list.info.target)
     target_entities.info = list.target_info
     target_entities.type = list.target_type
+    target_entities.format = list.target_format
 
     if (entities[source_entities.type])
       entities[source_entities.type].codes = unique(entities[source_entities.type].codes.concat(source_entities.codes))

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

@@ -11,8 +11,14 @@ rbbt.plots.graph.prepare_associations = function(db, associations, info){
   var edges = {}
   edges.codes = []
   edges.database = db
-  edges.source_type = info.source
-  edges.target_type = info.target
+
+  edges.source_type = info.source_type
+  edges.target_type = info.target_type
+  edges.source_format = info.source
+  edges.target_format = info.target
+  if (undefined === edges.source_type || null === edges.source_type) edges.source_type = edges.source_format
+  if (undefined === edges.target_type || null === edges.target_type) edges.target_type = edges.target_format
+
   edges.source_info = info.source_entity_options
   edges.target_info = info.target_entity_options
   edges.info = {}

data/share/views/wait.haml

@@ -1,32 +1,33 @@
 - @reload_page = true
 
-.wait
-  %h5 Waiting on #{format_name File.basename(job.name)}
+.wait.ui.segment.info.message
+  %h3.ui.header Waiting on #{format_name File.basename(job.name)}
 
-  %span.status= job.status
+  %span.ui.basic.segment.content.status= job.status
 
 
   - if job.file(:progress).exists?
-    - progress = job.file(:progress).yaml
-    - if progress[:last_percent]
-      .ui.teal.step.percent.progress.indicating(data-percent="#{progress[:last_percent]}" data-total=100)
-        .bar
-          .progress
-        .label= progress[:desc]
-        :deferjs
-          $('.step.progress').progress()
-    - else
-      - ticks = progress[:ticks]
-      - max_ticks = ticks  * 1.2
-      .ui.teal.step.progress(data-value=ticks data-total=max_ticks data-percent="#{ticks.to_f * 100.0 / max_ticks}")
-        .bar
-          .progress
-        .label= progress[:desc]
-        :deferjs
-          $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
-  - else
-    %hr
+    .footer.ui.basic.segment
+      - progress = job.file(:progress).yaml
+      - if progress[:last_percent]
+        .ui.teal.step.percent.progress.indicating.meta(data-percent="#{progress[:last_percent]}" data-total=100)
+          .bar
+            .progress
+          .label= progress[:desc]
+          :deferjs
+            $('.step.progress').progress()
+      - else
+        - ticks = progress[:ticks]
+        - max_ticks = ticks  * 1.2
+        .ui.teal.step.progress.meta(data-value=ticks data-total=max_ticks data-percent="#{ticks.to_f * 100.0 / max_ticks}")
+          .bar
+            .progress
+          .label= progress[:desc]
+          :deferjs
+            $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
 
+.ui.segment
+  %h3.ui.header Log
   %ul.step_messages.clean_list
     - job.messages.reverse.each do |line|
       - next if line.nil? or line.strip.empty?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.2
+  version: 1.8.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-28 00:00:00.000000000 Z
+date: 2016-03-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake