rbbt-rest 1.8.20 → 1.8.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a7bac229be773bd504edf30ebe5bf36b1efd8eb6
-  data.tar.gz: 9935e8de06b0853d2561876e82e1420a4f5a624f
+  metadata.gz: 185572829398c880b3d6cb1e2a6d4dea0ae6ca9f
+  data.tar.gz: bb37ea54b1cefc0c4802b3d8c45d0ad350ad8cde
 SHA512:
-  metadata.gz: 149647ea41453e9d8c2fac83fb6ca1588a173e27fc3364c76c1cfbe39c57f703817a6ef223ac6124c5ebfa2f85c1f8e0c2b686ae306aed0c4e32549c4e85d4c1
-  data.tar.gz: 0623b16dcf724e4cdbf0d5c101523b8094b5034ea46a2dc5bd5af524dfacb358c2b755f9e66ee1f5fb544810d667a92fe402faac4c71b1bd5c3b2a646c7b9cbc
+  metadata.gz: fafe374d7bbc2f9100c39d7a9981ae89bd855c29262696c25fc325eadc157a17e443aa2cab0f448f8211d6cefca7ae0115f24607ed4fc32fe4b14325f05c7a92
+  data.tar.gz: 3ded826d68949dbb5e61b9690825ffec277ccbbd488f3dbbbad35a5166c454ecb24ae6198e445d8257ee4235e86937de2f045d3f154ba48f0d781745a90c022c

data/lib/rbbt/rest/main.rb

@@ -187,7 +187,6 @@ module Sinatra
           template_render(template, params, name, :cache_type => :asynchronous)
         end
 
-
         get '/help/?:section?' do
           if params[:section]
             section = params[:section]

data/lib/rbbt/rest/workflow.rb

@@ -109,6 +109,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         task_parameters = consume_task_parameters(workflow, task, params)
         
         task_parameters[:jobname] = jobname
@@ -126,6 +128,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         task_parameters = consume_task_parameters(workflow, task, params)
 
         issue_job(workflow, task, jobname, task_parameters)
@@ -137,6 +141,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         job = workflow.load_id(File.join(task, job))
 
         clean_job(workflow, job) and halt 200 if update.to_s == "clean"
@@ -176,6 +182,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         job = workflow.load_id(File.join(task, job))
 
         begin
@@ -211,6 +219,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         job = workflow.load_id(File.join(task, job))
 
         case format
@@ -231,6 +241,8 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
+        execution_type = execution_type(workflow, task)
+
         job = workflow.load_id(File.join(task, job))
 
         require 'mimemagic'

data/lib/rbbt/rest/workflow/jobs.rb

@@ -37,7 +37,7 @@ module WorkflowRESTHelpers
     when workflow.asynchronous_exports.include?(task)
       :asynchronous
     else
-      raise "No known export type for #{ workflow } #{ task }. Accesses denied"
+      raise "Access denied: no known export type for #{ workflow }##{ task }."
     end
   end
 
@@ -171,6 +171,8 @@ module WorkflowRESTHelpers
   end
 
   def issue_job(workflow, task, jobname = nil, params = {})
+    execution_type = execution_type(workflow, task)
+
     inputs = prepare_job_inputs(workflow, task, params)
     job = workflow.job(task, jobname, inputs)
 
@@ -179,8 +181,6 @@ module WorkflowRESTHelpers
     clean_job(workflow, job) and clean = true if update.to_s == "clean"
     recursive_clean_job(workflow, job) and clean = true if update.to_s == "recursive_clean"
 
-    execution_type = execution_type(workflow, task)
-
     case execution_type.to_sym
     when :exec
       show_exec_result job.exec(:stream), workflow, task

data/share/views/error.haml

@@ -6,10 +6,10 @@
 
 
   - 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")
+    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "clean")
     %a.ui.button.blue.clean(href=clean_url) Clean
   - else
-    - clean_url = add_GET_param(request.env["REQUEST_URI"], "_update", "reload")
+    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
 - backtrace = job.info[:backtrace]

data/share/views/job_info.haml

@@ -9,9 +9,12 @@
     - task_exports = workflow.synchronous_exports + workflow.asynchronous_exports
     - task_exports = task_exports.collect{|t| t.to_s}
     - info[:dependencies].each do |task,name,path|
-      - url = "/" + [workflow.to_s, task.to_s, name.to_s] * "/"
+      - if Open.remote? path
+        - url = path.split("?").first
+      - else
+        - url = "/" + [workflow.to_s, task.to_s, name.to_s] * "/"
       %li
-        (#{workflow} #{task}) 
+        (#{workflow}##{task}) 
         - if task_exports.include? task.to_s
           %a(href=url) #{ name }  
         - else

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

@@ -29,7 +29,7 @@ rbbt.entity_array.property = function(codes, type, info, name, args){
 }
 
 rbbt.entity_array.property = function(codes, type, info, name, args){
-  if (info.format && ! type.indexOf(":") < 0){
+  if (undefined !== info && info.format && ! type.indexOf(":") < 0){
     type = type + ':' + info.format
   }
   var url = "/entity_list_property/" + name + "/" + type

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

@@ -41,9 +41,26 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
   }
 }
 
-rbbt.plots.aes.get_properties = function(list, rules){
+rbbt.plots.aes.get_properties = function(list, rules, type, namespace){
+  if (undefined !== list.type) type = list.type
   if (undefined === rules) rules == []
   if (undefined === list.properties) list.properties = {}
+
+  if (undefined !== list.info){
+    info = list.info
+  }else{
+    info = {}
+  }
+
+  if (list.namespace && undefined === namespace){
+    namespace = list.namespace
+  }
+
+  if (undefined !== namespace && undefined === list.organism){
+    info.organism = namespace
+    info.namespace = namespace
+  }
+
   var promises = []
   forArray(rules, function(rule){
     var name = rule.name
@@ -52,7 +69,7 @@ rbbt.plots.aes.get_properties = function(list, rules){
       eval('extract='+extract)
     }
     
-    if (rule.entity_type && rule.entity_type != list.type && rule.entity_type != list.format) return 
+    if (rule.entity_type && rule.entity_type != type && rule.entity_type != list.format) return 
 
     if (rule.info){
       var property = rule.property
@@ -60,8 +77,8 @@ rbbt.plots.aes.get_properties = function(list, rules){
       var entry = rule.info
       if (undefined === name) name = entry
 
-      var value = list.info[entry]
-      if (undefined === value && entry == 'type') value = list.type
+      var value = info[entry]
+      if (undefined === value && entry == 'type') value = type
       if (undefined === value && entry == 'code') value = list.codes
 
       deferred.resolve(value)
@@ -89,7 +106,7 @@ rbbt.plots.aes.get_properties = function(list, rules){
       if (undefined === name) name = property
 
       var deferred = m.deferred()
-      var tmp_promise = rbbt.entity_array.property(list.codes, list.type, list.info, property, args)
+      var tmp_promise = rbbt.entity_array.property(list.codes, type, info, property, args)
 
       if (extract){ tmp_promise = tmp_promise.then(function(res){ return res.map(extract)}) }
 
@@ -115,13 +132,13 @@ rbbt.plots.aes.get_properties = function(list, rules){
         var database = rule.parents
         if (undefined === name) name = database
 
-        promise = rbbt.entity_array.parents(list.codes, list.type, database)
+        promise = rbbt.entity_array.parents(list.codes, type, database)
       }else{
         kb_type = 'children'
         var database = rule.children
         if (undefined === name) name = database
 
-        promise = rbbt.entity_array.children(list.codes, list.type, database)
+        promise = rbbt.entity_array.children(list.codes, type, database)
       }
 
       if (rule.field){
@@ -184,11 +201,12 @@ rbbt.plots.aes.get_properties = function(list, rules){
   return m.sync(promises)
 }
 
-rbbt.plots.aes.set_aes = function(list, aes_rules){
+rbbt.plots.aes.set_aes = function(list, aes_rules, type){
+  if (undefined !== list.type) type = list.type
   if (undefined === list.aes) list.aes = {}
   forArray(aes_rules, function(rule){
 
-    if (rule.entity_type && rule.entity_type != list.type) return 
+    if (rule.entity_type && rule.entity_type != type) return 
 
 
     var name = rule.name
@@ -202,9 +220,9 @@ rbbt.plots.aes.set_aes = function(list, aes_rules){
       return 
     }
 
-    if (undefined === property && list.info[name]) property = list.info[name]
-    if (undefined === property && name == 'type') property = list.type
-    if (undefined === property && name == 'code') property = list.codes
+    if (undefined === property && undefined !== info && info[name]) property = info[name]
+    if (undefined === property && name == 'type') property = type
+    if (undefined === property && name == 'code') property = list.codes.slice()
     if (undefined === property) return
 
     var aes_values = rbbt.plots.aes.map_aesthetic(property, mapper, mapper_obj)

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

@@ -36,14 +36,32 @@ rbbt.plots.graph.get_entities = function(graph_model){
   return graph_model
 }
 
+rbbt.plots.aes.complete_source_target = function(list){
+  if (undefined === list.aes.source && undefined === list.aes.source){
+    if (undefined === list.properties.source && undefined === list.properties.source){
+      var source = [];
+      var target = [];
+      forArray(list.codes, function(elem){
+        var parts = elem.split("~")
+        source.push(parts[0])
+        target.push(parts[1])
+      })
+      list.properties.source = source
+      list.properties.target = target
+    }
+   list.aes.source = list.properties.source
+   list.aes.target = list.properties.target
+  }
+}
+
 rbbt.plots.graph.update_aes = function(graph_model){
   var data_promises = []
   forHash(graph_model.entities, function(type, list){
     data_promises.push(
 
-      rbbt.plots.aes.get_properties(list, graph_model.rules).
+      rbbt.plots.aes.get_properties(list, graph_model.rules, type, graph_model.namespace).
         then(function(){
-      rbbt.plots.aes.set_aes(list, graph_model.aes_rules)
+      rbbt.plots.aes.set_aes(list, graph_model.aes_rules, type)
         })
 
     )
@@ -55,6 +73,8 @@ rbbt.plots.graph.update_aes = function(graph_model){
       rbbt.plots.aes.get_properties(list, graph_model.edge_rules).
         then(function(){
       rbbt.plots.aes.set_aes(list, graph_model.edge_aes_rules)
+        }).then(function(){
+      rbbt.plots.aes.complete_source_target(list)
         })
 
     )

data/share/views/tools/nvd3/pie.haml

@@ -4,8 +4,14 @@
 - resolution ||= 250
 - title ||= "Piechart"
 
-- data.to_single if data.respond_to? :to_single and data.type != :single
-- values = data.collect{|k,v| {:key => k, :y => v} }
+-# data.to_single if data.respond_to? :to_single and data.type != :single
+-# values = data.collect{|k,v| {:key => k, :y => v} }
+
+- data.to_single if data.respond_to? :to_single and data.type != :single and data.fields.length == 1
+- if not data.respond_to? :type or data.type == :single
+  - values = data.collect{|k,v| {:key => k, :y => v} }
+- else
+  - values = data.collect{|k,vs| i = {:key => k}; vs.zip(data.fields).each{|v,f| i[f] = v}; i }
 
 - plot_data = values
 
@@ -15,10 +21,20 @@
     var graph = nv.models.pieChart()
         .x(function(d) { return d.key })
         .y(function(d) { return d.y })
-        .color(d3.scale.category10().range())
+
+        #{if data.respond_to? :fields and data.fields.include? 'color' 
+          "graph.color(function(d){ return d.color } )"
+          else
+            "graph.color(d3.scale.category10().range())"
+          end
+         }
+
+        #{if data.respond_to? :fields and data.fields.include? 'url' 
+          "graph.pie.dispatch.on('elementClick', function(d){ window.location = d.data.url})"
+          end
+        }
 
         graph.tooltip.enabled(true)
   EOF
 
 = partial_render('tools/nvd3/chart', locals.merge(:plot_data => plot_data, :id => id, :resolution => resolution, :setup => setup))
-

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.20
+  version: 1.8.21
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-01 00:00:00.000000000 Z
+date: 2016-07-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake