rbbt-rest 1.8.62 → 1.8.63

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e6d91a32b4426c4b8be4988e10eca7540db94676
-  data.tar.gz: 888c9c6f5dd89be6ce380c42a3a007775671cf56
+  metadata.gz: 575bc1891fa7c9dcc1334107cd7523c6583254be
+  data.tar.gz: 6b6c79f02c11e216ce8d5ee6ec0242b25ac21529
 SHA512:
-  metadata.gz: 4bbfa4d37fdd5079a03d5f58f989bbf9681c273c3823b51c7e84aee9e4cb820bb43de36f614bff0cf0e86021d303348ab6097e123d079b98486cc3b7eb3d7a7c
-  data.tar.gz: ec91cee052738256cf508596a813e0d076ce25bd3b2f21d0138cc37ba2a6c9e067ea5de8633dcc370e76ed0e309237ddaebd275d5cb2d8fed352b327cf1e473f
+  metadata.gz: bae019d9ac143210c65952a3d3ca74d7c64d9326a19618c530cd7599743dd6b50a7f125ed736e8c85c2383eba09a742a98fe4f8e7f5ca16fa6bfbc33d58176c5
+  data.tar.gz: 3e5b7aecef6c228e73525868c3cbc7b0284b9ea159f598b831d0bc80217f8b0c513346135785c41cd7112d09d16d3746e1003ec91eebaa08d7dc81fa3f22e2d9

data/lib/rbbt/rest/web_tool.rb

@@ -1,9 +1,11 @@
 
 module Sinatra
   module RbbtToolHelper
-    def tool(toolname, options = {})
+    def tool(toolname, options = {}, &block)
       options[:id] ||= toolname.to_s + "_#{rand(10000)}"
 
+      options[:block] = block if block_given?
+
       template_file = locate_template("tools/#{toolname}")
       Log.debug "Loading tool #{toolname} from: #{template_file}"
       content = Tilt::HamlTemplate.new(template_file, :filename => template_file).render(self, options)

data/lib/rbbt/rest/workflow.rb

@@ -37,6 +37,10 @@ module Sinatra
       add_workflow_resource(workflow, add_resource == :priority) if add_resource
       workflow.documentation
 
+      if ENV["RBBT_WORKFLOW_EXPORT_ALL"] == "true"
+        workflow.export *workflow.tasks.keys
+      end
+
 
       self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if workflow.respond_to?(:libdir) and  File.exists? workflow.libdir.lib['sinatra.rb']
 
@@ -201,7 +205,7 @@ module Sinatra
 
         case format
         when :html
-          workflow_render('job_info', workflow, task, :info => job.info)
+          workflow_render('job_info', workflow, task, :job => job, :info => job.info)
         when :json
           content_type "application/json"
           info_json = {}

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

@@ -65,7 +65,7 @@ module WorkflowRESTHelpers
 
     task_inputs = {}
     inputs.each do |input|
-      stream = input_options.include?(input) and input_options[input][:stream]
+      stream = input_options.include?(input) && input_options[input][:stream]
       value = prepare_input(params, input, input_types[input], stream)
       task_inputs[input] = value
     end
@@ -112,7 +112,8 @@ module WorkflowRESTHelpers
   end
 
   def show_result(job, workflow, task, params = nil)
-    return show_result_html nil, workflow, task, job.name, job if @fragment
+    #return show_result_html nil, workflow, task, job.name, job if @fragment
+    return show_result_html nil, workflow, task, job.name, job, params if @fragment
 
     case format.to_sym
     when :html

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

@@ -28,7 +28,10 @@ module WorkflowRESTHelpers
       server_key = $app_name
       html_dir = job.file('.html')
       FileUtils.mkdir_p html_dir.find unless File.exists? html_dir.find
-      cache_file = html_dir[server_key]
+      other_params = params.dup
+      other_params.delete_if{|k,v| k[0] == "_"}
+      other_params.delete :result
+      cache_file = html_dir[server_key + "_" << Misc.obj2digest(other_params)]
       cache_type = false if params[:cache] == FalseClass
       render(template_file, locals, layout_file, [task,workflow,job.name] * "-", :cache_type => cache_type, :cache_file => cache_file)
     else

data/share/views/job_info.haml

@@ -4,18 +4,27 @@
 
 - if info[:dependencies] and info[:dependencies].any?
   %h3 Dependencies
-  %ul
+  = partial_render('partials/dependencies', :job => job)
+  -#%ul
 
     - task_exports = workflow.synchronous_exports + workflow.asynchronous_exports
     - task_exports = task_exports.collect{|t| t.to_s}
-    - info[:dependencies].each do |task,name,path|
-      - if Open.remote? path
-        - url = path.split("?").first
-      - else
-        - url = "/" + [workflow.to_s, task.to_s, name.to_s] * "/"
+    -# info[:dependencies].each do |task,name,path|
+      - dep = Step.new path
+      - d_workflow = dep.workflow || "Unknown Workflow"
+      - wf = workflow if d_workflow.nil? || d_workflow.to_s == workflow.to_s
+      - if wf.nil? and d_workflow
+        - wf ||= begin
+          - Kernel.const_get d_workflow
+          - rescue
+
       %li
-        (#{workflow}##{task}) 
-        - if task_exports.include? task.to_s
+        (#{d_workflow}##{task}) 
+        - if Open.remote? path
+          - url = path.split("?").first
+          %a(href=url) #{ name }  
+        - elsif wf and wf.task_exports.include? task
+          - url = "/" + [d_workflow.to_s, task.to_s, name.to_s] * "/"
           %a(href=url) #{ name }  
         - else
           = name 

data/share/views/partials/dependencies.haml

@@ -0,0 +1,39 @@
+
+%ul.dependencies
+  - job.dependencies.each do |dep|
+    - dep_workflow = dep.workflow 
+    - 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 * " - "
+    - if dep.file(':progress').exists?
+      - status = dep.status + " - " + dep.file(:progress).yaml[:last_percent] + "%"
+    - else
+      - status = dep.status
+    - name = dep.name
+    %li
+      %span.workflow= dep_workflow
+      %span.task= dep.task_name
+      %span.name
+        - if String === dep_workflow
+          - wf ||= begin
+            - Kernel.const_get dep_workflow
+            - rescue
+        - elsif Module === dep_workflow
+          - wf = dep_workflow
+
+        - if Open.remote? dep.path
+          - url = path.split("?").first
+          %a(href=url) #{ name }  
+
+        - elsif wf and wf.task_exports.include? dep.task_name.to_sym
+          - url = "/" + [dep_workflow.to_s, dep.task_name.to_s, dep.name.to_s] * "/"
+          %a(href=url) #{ name }  
+
+        - else
+          = name 
+
+
+      %span.status(class="#{dep.status}") [#{status}]
+
+      - if dep.dependencies.any?
+        = partial_render('partials/dependencies', :job => dep)

data/share/views/public/js/helpers/helpers.js

@@ -266,12 +266,12 @@ function get_sign_gradient(values, color1, color0, color2){
   forArray(values, function(value){
     if (typeof value == 'string') value = parseFloat(value)
     if (typeof value == 'number'){
-      if (value > 0){
+      if (value >= 0){
         var a = value/max
-        colors.push(color0.blend(color1, a).toString())
+        colors.push(color0.blend(color2, a).toString())
       }else{
         var a = value/min
-        colors.push(color0.blend(color2, a).toString())
+        colors.push(color0.blend(color1, a).toString())
       }
     }else{
       colors.push(undefined)

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

@@ -15,6 +15,7 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
           aes = map_obj[aes]
         }
       }
+      aes.push(0)
       return get_gradient(aes, '#EABD5D', '#40324F')
     case 'sign-gradient':
       if (map_obj){
@@ -72,6 +73,29 @@ rbbt.plots.aes.get_properties = function(list, rules, type, namespace){
     
     if (rule.entity_type && rule.entity_type != type && rule.entity_type != list.format) return 
 
+    if (rule.map){
+      var deferred = m.deferred()
+      var entry = rule.map
+      var obj = rule.mapper_obj
+      if (undefined === name) name = entry
+
+      var keys = info[entry]
+      if (undefined === value && entry == 'type') keys = type
+      if (undefined === value && entry == 'code') keys = list.codes
+
+      var value = keys.map(function(k){ return obj[k]})
+      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.info){
       var property = rule.property
       var deferred = m.deferred()
@@ -262,6 +286,7 @@ rbbt.plots.aes.set_aes = function(list, aes_rules, type){
     if (undefined === property && name == 'code') property = list.codes.slice()
     if (undefined === property) return
 
+    console.log([property, mapper, mapper_obj])
     var aes_values = rbbt.plots.aes.map_aesthetic(property, mapper, mapper_obj)
 
     if (undefined === list.aes[aes]){

data/share/views/tools/Rpng.haml

@@ -0,0 +1,12 @@
+- filename = 'R-png_' << rand(10000).to_s unless defined? filename and filename
+- text = filename unless defined? text and text
+
+- width = 500 unless defined? width and width
+- height = 500 unless defined? height and height
+- plot = block.call unless (defined? plot and plot) or not defined? block
+
+- filename += '.png' unless filename =~ /\.png$/i
+= resource filename, text, :image do |filename|
+  - CSBC.ic50.tsv.transpose.R "png.file = '#{filename}';\n" + plot
+
+

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

@@ -6,7 +6,8 @@
 
 - extra = "" unless defined? extra
 
-- url = @step.instance_variable_get(:@url_path)
+- url = @fullpath
+
 %svg(id=id)
 
 :ruby

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

@@ -2,14 +2,29 @@
 - id ||= title || ("scatter-" << (1000 * rand).to_i.to_s)
 - title ||= "Scatter Plot"
 
-- size ||= "size"
-- x ||= "x"
-- y ||= "y"
+- if data.fields.length == 1
+  - y ||= data.fields.first
+  - x_values = Hash[*data.keys.zip((0..data.length-1).to_a).flatten]
+  - size_values = Hash[*data.keys.zip([1] * data.length).flatten]
+
+- if data.fields.length == 2
+  - x ||= data.fields.first
+  - y ||= data.fields.last
+  - size_values = Hash[*data.keys.zip([1] * data.length).flatten]
+
+- if data.fields.length == 3
+  - x ||= data.fields.first
+  - y ||= data.fields[1]
+  - size ||= data.fields.last
+  - size_values = Hash[*data.keys.zip([1] * data.length).flatten]
 
 - data_values = []
 - data.through do |key,values|
   - label = key.respond_to?(:name)? key.name || key : key
-  - data_values << {:label => label, :x => values[x], :y => values[y], :size => values[size]}
+  - y_value = (defined?(y) and y) ? values[y] : y_values[y].to_f
+  - x_value = (defined?(x) and x) ? values[x] : x_values[key].to_f
+  - size_value = (defined?(size) and size) ? values[size] : size_values[key].to_f
+  - data_values << {:label => label, :x => x_value, :y => y_value, :size => size_value}
 
 - plot_data = [{:key => "Group", :values => data_values}]
 

data/share/views/wait.haml

@@ -3,9 +3,23 @@
 :sass
   span.progress_time
     color: grey
-  .wait.ui.segment
-    overflow: auto
-    text-overflow: ellipsis
+  .dependencies
+    .wait.ui.segment
+      overflow: auto
+      text-overflow: ellipsis
+    .status
+      color: grey
+    .status.done
+      color: green
+    .status.error
+      color: red
+    .status.dependencies
+      color: orange
+    .workflow
+      font-weight: bold
+    .task
+      font-style: italic
+
 .wait.ui.segment.info.message
   %h3.ui.header Waiting on #{format_name File.basename(job.name)}
 
@@ -58,4 +72,9 @@
       - next if line.nil? or line.strip.empty?
       %li= line
 
-
+- if job.dependencies.any?
+  
+  .ui.segment
+    %h3.ui.header Dependencies
+    .content
+      = partial_render('partials/dependencies', :job => job)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.62
+  version: 1.8.63
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-07-05 00:00:00.000000000 Z
+date: 2017-08-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -255,6 +255,7 @@ files:
 - share/views/main.haml
 - share/views/monitor/jobs.haml
 - share/views/monitor/locks.haml
+- share/views/partials/dependencies.haml
 - share/views/partials/form.haml
 - share/views/partials/table.haml
 - share/views/partials/table/column.haml
@@ -1825,6 +1826,7 @@ files:
 - share/views/public/plugins/underscore/js/underscore.js
 - share/views/public/robots.txt
 - share/views/tasks.haml
+- share/views/tools/Rpng.haml
 - share/views/tools/nvd3.haml
 - share/views/tools/nvd3/chart.haml
 - share/views/tools/nvd3/histogram.haml