rbbt-rest 1.3.3 → 1.3.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b556674b8552bf64d8680def41f2316821743b64
-  data.tar.gz: 3f1fb6faa193e793870d65706e3ca828b7de897f
+  metadata.gz: 149f96d6cd3121af4c1948eb970b3ef15caa2ff9
+  data.tar.gz: c9c8e18ecbda7f195325212a64f5ae9ccbb1a631
 SHA512:
-  metadata.gz: 8329fbef77bc84d70921839a9648e988a1d587a33de739c23dd1255e90bddbe33794a12dee8e51dc6e4bede70b7118690ea1afb5a1022ddc35dc995401303b4b
-  data.tar.gz: 233769daa035553e3a1d294f2cf1cb426bbc779605b24e1c357a65d6d3693f831c9d72014d1cf845ebe00c6f0b770d31a68810e47daa384e613dfd164709993b
+  metadata.gz: 634d3acb1114b6baaeaf19d104465c5765ec6d075c08168181584c10b9688e7d076bda718e89a3ba4b75976f42edce43726637fe9378d4dca0e551730e6afc50
+  data.tar.gz: 5440ddd934f2a1ef148f7a2c0f2c95f81d2341f9d0cbdcd3a4cb0ddbe8501d54f33694bb4eee638711190e85be93c3a40522f70a8896c38412b2e9481c8f1147

data/lib/rbbt/rest/client/get.rb

@@ -18,6 +18,7 @@ class WorkflowRESTClient
     begin
       yield
     rescue Exception => e
+      raise $! unless e.respond_to? :response
       klass, message = e.response.split " => "
       begin
         klass = Kernel.const_get klass

data/lib/rbbt/rest/client/step.rb

@@ -1,27 +1,14 @@
 class WorkflowRESTClient
   class RemoteStep < Step
 
-    attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :exec
+    attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :is_exec
 
-    def initialize(base_url, task = nil, name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
-      if task.nil?
-        @url = base_url
-      else
-        @base_url, @task, @name, @inputs, @result_type, @result_description = base_url, task, name, inputs, result_type, result_description
-        if exec
-          @url = [File.join(base_url, task.to_s), inputs]
-        else
-          self.fork 
-        end
-      end
-    end
-
-    def initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
-      @base_url, @task, @base_name, @inputs, @result_type, @result_description, @exec = base_url, task, base_name, inputs, result_type, result_description, exec
+    def initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, is_exec = false)
+      @base_url, @task, @base_name, @inputs, @result_type, @result_description, @is_exec = base_url, task, base_name, inputs, result_type, result_description, is_exec
     end
 
     def name
-      return nil if exec
+      return nil if @is_exec
       (Array === @url ? @url.first : @url).split("/").last
     end
 
@@ -30,6 +17,7 @@ class WorkflowRESTClient
     end
 
     def info
+      init_job unless url
       info = WorkflowRESTClient.get_json(File.join(url, 'info'))
       info = WorkflowRESTClient.fix_hash(info)
       info[:status] = info[:status].to_sym if String === info[:status]
@@ -76,6 +64,7 @@ class WorkflowRESTClient
     end
 
     def get
+      params ||= {}
       params = params.merge(:_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json )
       begin
         WorkflowRESTClient.get_raw(url, params) 
@@ -93,17 +82,27 @@ class WorkflowRESTClient
       res = WorkflowRESTClient.capture_exception do
         RestClient.post(URI.encode(File.join(base_url, task.to_s)), inputs.merge(:_cache_type => :exec, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json))
       end
-      load_res res
+      loaded = load_res res
+      exit
+      loaded
     end
 
     def fork
-      init_job
+      init_job(:asynchronous)
+    end
+
+    def running?
+      ! %w(done error aborted).include? status.to_s
+    end
+
+    def path
+      url
     end
 
     def run(noload = false)
-      return exec_job if exec
+      return exec_job if @is_exec
       init_job(:synchronous)
-      noload ? name : self.load
+      noload ? @name : self.load
     end
 
     def exec
@@ -116,7 +115,7 @@ class WorkflowRESTClient
     end
 
     def clean
-      WorkflowRESTClient.get_raw(url, :_update => :clean) unless exec
+      WorkflowRESTClient.get_raw(url, :_update => :clean) unless @is_exec
       self
     end
   end

data/share/views/compass/workflow.sass

@@ -18,10 +18,14 @@ ul.tasks > li
       width: 5em
       float: right
 
-dd.job_control
+dd.job_control, dd.job_files
+  +clearfix
   ul
-    +rbbt_button_list($color_bg: $base3)
+    +rbbt_button_list($color_bg: $color_menu_bg)
+    +clearfix
+    background-color: $color_top_menu
     width: auto
+    float: left
     li a
 
 

data/share/views/form.haml

@@ -14,3 +14,44 @@
   .form
     = partial_render('partials/form', :id => id, :action => action, :method => 'post', 
       :enctype => "multipart/form-data", :info => task_info, :klass => 'workflow_task')
+  
+  - if workflow.libdir.examples[task.to_s].exist? 
+    .examples
+
+      %p
+        Click the links bellow to load example data:
+        
+      :javascript
+        example_inputs = [];
+      %ul
+        - workflow.libdir.examples[task.to_s].glob('*').each do |example_dir|
+          - name = File.basename(example_dir)
+          - task_info = workflow.task_info task
+          - inputs = Workflow.load_inputs(example_dir, task_info[:inputs], task_info[:input_types])
+          - inputs.each{ |k,v| v.replace Open.read(v) if String === v and File.exists? v }
+          :javascript
+            example_inputs["#{ name }"] = #{inputs.to_json}
+          %li
+            %a.load_example(href="#" task=task name=name)= name
+
+      :javascript
+        deffer(function(){
+          $("a.load_example").click(function(){
+            var link = $(this);
+            var name = $(link).attr('name');
+            var inputs = example_inputs[name];
+            var form = link.parents('.workflow_task').find('.form')
+
+            for (var input in inputs){
+              var value = inputs[input]
+              var input = form.find('[name=' + input + ']')
+              if (input.is('[type=checkbox]')){
+                input.prop('checked', value)
+              }else{
+                input.val(value)
+              }
+            }
+            form.find('[name=jobname]').val(name)
+            return false
+          })
+        })

data/share/views/job_result/job_control.haml

@@ -11,7 +11,7 @@
 
   - if job.files.any?
     %dt Files
-    %dd
+    %dd.job_files
       %ul
         - job.files.each do |file|
           %li

data/share/views/job_result/tsv.haml

@@ -1,8 +1,12 @@
 - table_id = [workflow.to_s, task, jobname] * "_"
 - table_class = 'workflow_tsv_result'
-- rows, total_size = tsv_rows(result)
+- begin
+  - page = result.size > 50 ? "1" : nil
+- rescue
+  - page = "1" 
+
+- rows, total_size = tsv_rows(result, page)
 - header = result.all_fields
-- page = total_size > 50 ? "1" : nil
 
 = workflow_partial('partials/table', workflow, task, 
-  locals.merge(:table_id => table_id, :page => page, :table_class => table_class, :rows => rows, :total_size => total_size, :header => result.all_fields, :row_ids => :use, :table_url => File.join('/', workflow.to_s, task, jobname)))
+  locals.merge(:table_id => table_id, :page => page, :table_class => table_class, :rows => rows, :total_size => total_size, :header => result.all_fields, :row_ids => :use, :table_url => jobname ? File.join('/', workflow.to_s, task, jobname) : nil))

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.3
+  version: 1.3.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-18 00:00:00.000000000 Z
+date: 2014-03-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -1128,7 +1128,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces