rbbt-rest 1.3.4 → 1.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: c9c8e18ecbda7f195325212a64f5ae9ccbb1a631
+  metadata.gz: 08aa70a66616d766753916da78c7439a4ec800c5
+  data.tar.gz: 29ce9753938dcaf1890744d51a0b65bc694721c6
 SHA512:
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-  data.tar.gz: 5440ddd934f2a1ef148f7a2c0f2c95f81d2341f9d0cbdcd3a4cb0ddbe8501d54f33694bb4eee638711190e85be93c3a40522f70a8896c38412b2e9481c8f1147
+  metadata.gz: 4d24e26e939eedc02ebb6c7f60651d1404f4da0900a5cc97e06809885efbfd3d292dff3006fc98dc2d5c26ca4808123ea30a5e50594a082e8b046a54191b10cc
+  data.tar.gz: 6562147f6e34262b00f5ebf4105e404ab10a37e169a4510844d4c3921b353dc2c2a7f237a6355613c1b57bebe921449e46340b77c6c1c89d22c0c1115b851fd3

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

@@ -18,14 +18,15 @@ class WorkflowRESTClient
     begin
       yield
     rescue Exception => e
-      raise $! unless e.respond_to? :response
-      klass, message = e.response.split " => "
+      raise e unless e.respond_to? :response
       begin
+        klass, message = e.response.to_s.split " => "
         klass = Kernel.const_get klass
+        raise klass.new message
       rescue
-        raise message
+        raise e
       end
-      raise klass.new message
+      raise $!
     end
   end
 

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

@@ -17,15 +17,21 @@ 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]
-      info
+      @info ||= begin
+                  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]
+                  info
+                end
     end
     
     def status
-      info[:status]
+      begin
+        info[:status]
+      ensure
+        @info = nil
+      end
     end
 
     def done?
@@ -58,6 +64,8 @@ class WorkflowRESTClient
         TSV.open(StringIO.new(res))
       when :annotations
         Annotated.load_tsv(TSV.open(StringIO.new(res)))
+      when :array
+        res.split("\n")
       else
         JSON.parse res
       end
@@ -65,9 +73,9 @@ class WorkflowRESTClient
 
     def get
       params ||= {}
-      params = params.merge(:_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json )
+      params = params.merge(:_format => [:string, :boolean, :tsv, :annotations,:array].include?(result_type.to_sym) ? :raw : :json )
       begin
-        WorkflowRESTClient.get_raw(url, params) 
+        WorkflowRESTClient.get_raw(url, params)
       rescue => e
         raise e.response
       end
@@ -82,9 +90,7 @@ 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
-      loaded = load_res res
-      exit
-      loaded
+      load_res res
     end
 
     def fork
@@ -114,8 +120,21 @@ class WorkflowRESTClient
       self
     end
 
+    def recursive_clean
+      init_job unless url
+      begin
+        WorkflowRESTClient.get_raw(url, :_update => :recursive_clean) unless @is_exec
+      rescue Exception
+      end
+      self
+    end
+
     def clean
-      WorkflowRESTClient.get_raw(url, :_update => :clean) unless @is_exec
+      init_job unless url
+      begin
+        WorkflowRESTClient.get_raw(url, :_update => :clean) unless @is_exec
+      rescue Exception
+      end
       self
     end
   end

data/lib/rbbt/rest/main.rb

@@ -138,6 +138,7 @@ module Sinatra
         end
 
         error Exception do |e|
+          raise e unless @format == :html
           halt 500, [e.class.to_s, e.message] * " => "
         end
       end

data/lib/rbbt/rest/workflow.rb

@@ -39,6 +39,7 @@ module Sinatra
       Log.debug "Adding #{ workflow } to REST server" 
 
       add_workflow_resource(workflow) if add_resource
+      workflow.documentation
 
 
       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']
@@ -138,6 +139,7 @@ module Sinatra
         job = workflow.load_id(File.join(task, job))
 
         clean_job(workflow, job) if update == :clean
+        recursive_clean_job(workflow, job) if update == :recursive_clean
 
         begin
           started = job.info.any?

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

@@ -34,7 +34,7 @@ module WorkflowRESTHelpers
     when workflow.asynchronous_exports.include?(task)
       :asynchronous
     else
-      raise "No known export type for #{ workflow } #{ task }"
+      raise "No known export type for #{ workflow } #{ task }. Accesses denied"
     end
   end
 
@@ -147,6 +147,7 @@ module WorkflowRESTHelpers
     job = workflow.job(task, jobname, inputs)
 
     job.clean if update == :clean
+    job.recursive_clean if update == :recursive_clean
 
     execution_type = execution_type(workflow, task)
     case execution_type
@@ -175,6 +176,15 @@ module WorkflowRESTHelpers
     end
   end
 
+  def recursive_clean_job(workflow, job)
+    job.recursive_clean
+
+    if ajax
+      halt 200
+    else
+      redirect to(File.join("/", workflow.to_s, job.task_name.to_s))
+    end
+  end
   def clean_job(workflow, job)
     job.clean
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.4
+  version: 1.3.5
 platform: ruby
 authors:
 - Miguel Vazquez