rbbt-util 5.17.58 → 5.17.59

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 4928e05c224b503008194c134ba51a67b1071376
+  metadata.gz: 849b316f4dfa60ed5c29ef8da518739f1e367f5b
+  data.tar.gz: ae52b18f5d3ad480fabd97b1d6c335ec6d761015
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+  metadata.gz: 71e1e58112898babac4e3314fe5cd6199b8401f77724d1282eb91915fd1c5399dcb2acd0bd5c2d4e8928f6530536bbce7186b44117a71abc567b827ffca9a2e6
+  data.tar.gz: ee609ff5e22ce8d218416af0e3a4c958dc58b63033f70eecec04b1f89961643a98197ee7d6815712d7ece7ef4b7edab2f240dff502818ccd21b7c2fd039bd03e

data/lib/rbbt/rest/client.rb

@@ -33,6 +33,7 @@ class WorkflowRESTClient
       if TSV === v
         fixed_inputs[k] = v.to_s
       else
+        next if input_types[k].nil?
         case input_types[k].to_sym
         when :tsv, :array, :file, :text
           fixed_inputs[k] = (String === v and Open.exists?(v)) ? Open.open(v) : v

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

@@ -11,6 +11,7 @@ class WorkflowRESTClient
         end
       end
     end
+
     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
       @mutex = Mutex.new
@@ -23,10 +24,12 @@ class WorkflowRESTClient
     end
 
     def task_name
+      init_job
       (Array === @url ? @url.first : @url).split("/")[-2]
     end
 
     def info(check_lock=false)
+      @info = nil unless @info and @info[:status] and @info[:status].to_sym == :done
       @info ||= begin
                   init_job unless url
                   info = WorkflowRESTClient.get_json(File.join(url, 'info'))
@@ -58,8 +61,10 @@ class WorkflowRESTClient
 
     #{{{ MANAGEMENT
     
-    def init_job(cache_type = :asynchronous)
-      @name ||= Persist.memory("RemoteSteps", :jobname => @name, :inputs => inputs) do
+    def init_job(cache_type = nil)
+      cache_type = :asynchronous if cache_type.nil? and not @is_exec
+      cache_type = :exec if cache_type.nil?
+      @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
         WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name||@base_name, :_cache_type => cache_type))
       end
       @url = File.join(base_url, task.to_s, @name)
@@ -118,7 +123,8 @@ class WorkflowRESTClient
     end
 
     def path
-      url
+      init_job
+      @url + '?_format=raw'
     end
 
     def run(noload = false)

data/lib/rbbt/util/misc/omics.rb

@@ -222,6 +222,9 @@ module Misc
     end
   end
 
+  def self.sort_genomic_locations(stream)
+    sort_stream(stream, '#', '-k1,1 -k2,2n -t:')
+  end
 
   def self.intersect_streams_read(io, sep=":")
     line = io.gets.strip

data/lib/rbbt/workflow/accessor.rb

@@ -279,7 +279,7 @@ class Step
   end
 
   def dirty?
-    rec_dependencies.collect{|dependency| dependency.path }.uniq.reject{|path| path.exists?}.any?
+    rec_dependencies.collect{|dependency| dependency.path }.uniq.reject{|path| not Path === path or path.exists?}.any?
   end
 
   def done?
@@ -545,7 +545,9 @@ module Workflow
         options.each{|i,v|
           case v
           when Symbol
-            rec_dependency = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies}).flatten.compact.uniq.select{|d| d.task.name.to_sym == v }.first
+            all_d = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
+            rec_dependency = all_d.select{|d| d.task_name.to_sym == v }.first
+
             if rec_dependency.nil?
               _inputs[i] = v
             else

data/lib/rbbt/workflow/definition.rb

@@ -55,7 +55,7 @@ module Workflow
       DependencyBlock.setup block, dependency if dependency.any?
       @dependencies << block
     else
-      if Module === dependency.first
+      if Module === dependency.first or (defined? WorkflowRESTClient and WorkflowRESTClient === dependency.first)
         @dependencies << dependency
       else
         @dependencies.concat dependency

data/lib/rbbt/workflow/step.rb

@@ -230,7 +230,7 @@ class Step
 
     # A step result with no info_file means that it was manually
     # placed. In that case, do not consider its dependencies
-    return [] if Open.exists?(self.path.to_s) and not Open.exists? self.info_file
+    return [] if not WorkflowRESTClient::RemoteStep === self and Open.exists?(self.path.to_s) and not Open.exists? self.info_file
 
     return [] if dependencies.nil? or dependencies.empty?
 

data/lib/rbbt/workflow/step/run.rb

@@ -96,7 +96,7 @@ class Step
   end
 
   def checks
-    rec_dependencies.collect{|dependency| dependency.path }.uniq
+    rec_dependencies.collect{|dependency| (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency) ? nil : dependency.path }.compact.uniq
   end
   
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.58
+  version: 5.17.59
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-13 00:00:00.000000000 Z
+date: 2015-07-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake