rbbt-util 5.20.15 → 5.20.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8acdb68bc077ef40aa93cc0bd822e2a03e634d7f
-  data.tar.gz: 5aeb1004ef167478f65659794dbc2c93d294cd10
+  metadata.gz: f8ff80d80e35fa0ba2bbdc6fb626a00ae0097973
+  data.tar.gz: eae7437a6901578f908d32bdadf109c339be8794
 SHA512:
-  metadata.gz: c5bb2dc2c484251bc7d41b88d3869eeea5d179724bf4ff46403fdd7e3c84be1c28bb31c8bd5d4412f51027221e3fd41139acd1b444fbb1829adcd8baa49560e6
-  data.tar.gz: 1c82abfa22a27807250e030c22f03a586327d10cee8baea5bc70644275e71ad7f69cff72c4327df9ff4f6f0f05b8e788a5c1ff28b949bdae1ab9d5791f519672
+  metadata.gz: caf52df7da1aac95ec53d5883c1a49f26170bdb95f09b039321e435078b74969abdcbecb594b12e736d9a9640aebf0eb73d902a308242fc734dd537c650a0a42
+  data.tar.gz: 76592f03fe4bcfe0881a8c8e0e2e943829cda0ae03116b8c4410ee350119c9499dd829c6f407a6d2d461d33e921d650bed2b5eb68129d7784deaf54583410f39

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

@@ -90,6 +90,7 @@ class WorkflowRESTClient
     params = params.merge({ :_format => 'jobname' })
     params = fix_params params
 
+    params = WorkflowRESTClient.__prepare_inputs_for_restclient(params)
     name = capture_exception do
       RestClient.post(URI.encode(url), params)
     end

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

@@ -1,4 +1,27 @@
 class WorkflowRESTClient
+
+  def self.__prepare_inputs_for_restclient(inputs)
+
+    new = IndiferentHash.setup({})
+    inputs.each do |k,v|
+      if v.respond_to? :path and not v.respond_to? :original_filename
+        class << v
+          def original_filename
+            File.expand_path(path)
+          end
+        end
+      end
+
+      if Array === v and v.empty?
+        new[k] = "EMPTY_ARRAY"
+      else
+        new[k] = v
+      end
+    end
+
+    new
+  end
+
   class RemoteStep < Step
 
     attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :is_exec, :stream_input
@@ -89,7 +112,6 @@ class WorkflowRESTClient
     end
 
     def status
-      return nil unless url or started?
       return :done if @done
       return :streaming if @streaming
       begin
@@ -181,7 +203,9 @@ class WorkflowRESTClient
       end
       sleep 0.2 unless self.done?
       sleep 1 unless self.done?
-      sleep 3 while not self.done?
+      while not self.done?
+        sleep 3
+      end
       self
     end
 
@@ -231,11 +255,12 @@ class WorkflowRESTClient
       params = {}
       load_res get
     end
-    
+
     def _run_job(cache_type = :async)
       get_streams
       if cache_type == :stream or cache_type == :exec and stream_input and inputs[stream_input]
         task_url = URI.encode(File.join(base_url, task.to_s))
+        inputs = WorkflowRESTClient.__prepare_inputs_for_restclient(inputs)
         task_params = inputs.merge(:_cache_type => cache_type, :jobname => base_name, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json)
         @streaming = true
         io =  WorkflowRESTClient.stream_job(task_url, task_params, stream_input, cache_type) 
@@ -256,19 +281,6 @@ class WorkflowRESTClient
 
       WorkflowRESTClient.capture_exception do
         @url = URI.encode(File.join(base_url, task.to_s))
-        inputs.each do |k,v|
-          if v.respond_to? :path
-            class << v
-              def original_filename
-                File.expand_path(path)
-              end
-            end
-          end
-
-          if Array === v and v.empty?
-            inputs[k] = "EMPTY_ARRAY"
-          end
-        end
         task_params = inputs.merge(:_cache_type => cache_type, :jobname => base_name, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json)
 
         sout, sin = Misc.pipe

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.20.15
+  version: 5.20.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-20 00:00:00.000000000 Z
+date: 2016-06-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake