rbbt-util 5.17.27 → 5.17.28

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 9dae7037fe6214447e7bd555a5e67745a6ba435a
+  metadata.gz: b62b4d3d3b46cfcf8e631a471daf1cc574843cc8
+  data.tar.gz: 5b284a5ef7ade80f035ece5978a3cd31c5ea1d03
 SHA512:
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-  data.tar.gz: 493e6552a59d2b035e4c4efc426a75ca436f5d0d2cba1ebfe26d700ef2639c50792e4288507ce8c751b317d0d1c8a91dc47838be305f505edad7358ce0c142bc
+  metadata.gz: a85420b0c5ad7ac41d5f6cd46add0d49bd1841658849acba2e06c5f4f57a3f854a93916789afbaa4794137ee4855a63e88cdf4a430cb8e5df5fcda868d8f2e39
+  data.tar.gz: f36d892b81611a5e2fffc95c50ca5fb0cb6121aca61552a74d60e9c20ede3daf1d1bb1422b8f00b8c84414773e41b534ef71747e5ddcd2391ea0a2f6d729d23f

data/lib/rbbt/association/database.rb

@@ -140,6 +140,11 @@ module Association
 
   def self.database(file,  options = {})
     database = case file
+               when Step
+                 file.clean if file.error? or file.aborted? or file.dirty?
+                 file.run(true) unless file.done? or file.started?
+                 file.join unless file.done?
+                 open_stream(TSV.get_stream(file), options.dup)
                when TSV
                  file = file.to_double unless file.type == :double
                  reorder_tsv(file, options.dup)

data/lib/rbbt/tsv/stream.rb

@@ -18,7 +18,7 @@ module TSV
  
   def self.paste_streams(streams, options = {})
     options = Misc.add_defaults options, :sep => "\t", :sort => true
-    sort, sep, preamble, same_fields = Misc.process_options options, :sort, :sep, :preamble, :same_fields
+    sort, sep, preamble, header, same_fields, fix_flat = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat
 
     out = Misc.open_pipe do |sin|
 
@@ -63,7 +63,11 @@ module TSV
         input_options << parser.options
         preambles     << parser.preamble      if preamble and not parser.preamble.empty?
 
-        parser.stream
+        if fix_flat and parser.type == :flat
+          TSV.stream_flat2double(parser.stream).stream
+        else
+          parser.stream
+        end
       end
 
       key_field = key_fields.compact.first
@@ -74,6 +78,7 @@ module TSV
       end
       options = options.merge(input_options.first)
       options[:type] = :list if options[:type] == :single
+      options[:type] = :double if fix_flat
 
       preamble_txt = case preamble
                      when TrueClass
@@ -88,7 +93,7 @@ module TSV
                        nil
                      end
 
-      header = TSV.header_lines(key_field, fields, options.merge(:preamble => preamble_txt))
+      header ||= TSV.header_lines(key_field, fields, options.merge(:preamble => preamble_txt))
       sin.puts header
 
       empty_pos = empty.collect{|stream| streams.index stream }
@@ -210,6 +215,7 @@ module TSV
     dumper = TSV::Dumper.new dumper_options
     dumper.init
     TSV.traverse parser, :into => dumper do |key,values|
+      key = key.first if Array === key
       [key, [values]]
     end
     dumper

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

@@ -3,20 +3,16 @@ module Misc
     if use
       Log.medium "Activating lockfile ids"
       Lockfile.dont_use_lock_id = false
-      #Lockfile.refresh = 20 
-      #Lockfile.max_age = 60
-      #Lockfile.suspend = 2
+      Lockfile.refresh = 2 
+      Lockfile.max_age = 30
+      Lockfile.suspend = 4
     else
       Log.medium "De-activating lockfile ids"
       Lockfile.dont_use_lock_id = true
-      #Lockfile.refresh = 5
-      #Lockfile.max_age = 60 * 10
-      #Lockfile.suspend = 5
+      Lockfile.refresh = 4
+      Lockfile.max_age = 60
+      Lockfile.suspend = 8
     end
-
-    Lockfile.refresh = 10
-    Lockfile.max_age = 60
-    Lockfile.suspend = 2
   end
 
   self.use_lock_id = ENV["RBBT_NO_LOCKFILE_ID"] != "true"

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

@@ -462,4 +462,23 @@ module Misc
     out
   end
 
+  def self.intercalate_streams(streams)
+    Misc.open_pipe do |sin|
+      continue = true
+      while continue
+        line1 = streams.first.gets unless streams.first.eof?
+        line2 = streams.last.gets unless streams.first.eof?
+        continue = false if line1.nil? and line2.nil?
+        sin.puts line1.strip if line1
+        sin.puts line2.strip if line2
+        line1 = nil
+        line2 = nil
+      end
+      streams.each do |stream| 
+        stream.join if stream.respond_to? :join
+        stream.close if stream.respond_to? :close and not stream.closed?
+      end
+    end
+  end
+
 end

data/lib/rbbt/workflow/definition.rb

@@ -80,7 +80,8 @@ module Workflow
       :inputs             => consume_inputs,
       :description        => consume_description,
       :input_types        => consume_input_types,
-      :result_type        => (Array === type ? type.to_sym : type),
+      :result_type        => (String === type ? type.to_sym : type),
+      :result_description => consume_result_description,
       :input_defaults     => consume_input_defaults,
       :input_descriptions => consume_input_descriptions,
       :extension          => consume_extension,

data/lib/rbbt/workflow/step.rb

@@ -94,8 +94,8 @@ class Step
     self
   end
 
-  def prepare_result(value, description = nil, info = {})
-    case 
+  def prepare_result(value, description = nil, entity_info = nil)
+    res = case 
     when IO === value
       begin
         res = case @task.result_type
@@ -127,13 +127,44 @@ class Step
       value
     when Annotated === value
       annotations = value.annotations
-      info.each do |k,v|
+      entity_info ||= begin 
+                        entity_info = info.dup
+                        entity_info.merge! info[:inputs] if info[:inputs]
+                        entity_info
+                      end
+      entity_info.each do |k,v|
         value.send("#{h}=", v) if annotations.include? k
       end
+                        
       value
     else
-      Entity.formats[description].setup(value, info.merge(:format => description))
+      entity_info ||= begin 
+                        entity_info = info.dup
+                        entity_info.merge! info[:inputs] if info[:inputs]
+                        entity_info
+                      end
+      Entity.formats[description].setup(value, entity_info.merge(:format => description))
     end
+
+    if Annotated === res
+      dep_hash = nil
+      res.annotations.each do |a|
+        a = a.to_s
+        varname = "@" + a
+        next unless res.instance_variable_get(varname).nil? 
+
+        dep_hash ||= begin
+                       h = {}
+                       rec_dependencies.each{|dep| h[dep.task.name.to_s] ||= dep }
+                       h
+                     end
+        dep = dep_hash[a]
+        next if dep.nil?
+        res.send(a.to_s+"=", dep.load)
+      end 
+    end
+
+    res
   end
 
 
@@ -152,10 +183,20 @@ class Step
 
 
   def load
-    return prepare_result @result, @task.result_description if @result and not @path == @result
-    join if not done?
-    return Persist.load_file(@path, @task.result_type) if @path.exists?
-    exec
+    res = if @result and not @path == @result
+            res = @result
+          else
+            join if not done?
+            @path.exists? ? Persist.load_file(@path, @task.result_type) : exec
+          end
+
+    if @task.result_description
+      entity_info = info.dup
+      entity_info.merge! info[:inputs] if info[:inputs]
+      res = prepare_result res, @task.result_description, entity_info 
+    end
+
+    res
   end
 
   def self.clean(path)

data/test/rbbt/workflow/test_step.rb

@@ -204,14 +204,18 @@ class TestStep < Test::Unit::TestCase
           end
         end
         Step.wait_for_jobs(jobs)
-        #jobs.each do |job|
-        #  while not job.done?
-        #    sleep 1
-        #  end
-        #end
       ensure
         RbbtSemaphore.delete_semaphore(semaphore)
       end
     end
   end
+
+  def __test_load_return_description
+    require 'rbbt/workflow'
+    Workflow.require_workflow "Study"
+    study = Study.setup("LICA-FR")
+    job = study.recurrent_mutations(:job)
+    iii job.load.organism
+    iii study.recurrent_mutations.organism
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.27
+  version: 5.17.28
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-21 00:00:00.000000000 Z
+date: 2015-05-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake