rbbt-util 5.9.8 → 5.9.10

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 619c854df951805baf6f4320ba2f9586debf4ef0
+  metadata.gz: 1b01c7fe766ec84aa4005a1454ba37c116cdab5e
+  data.tar.gz: fbdc4ffcdc4eecde849214ebbb2cb34c5707a133
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+  data.tar.gz: eae2392ac690150d68bbc3a2d8b0f9d1bc64f4956f32016feede48833cad7e72c0cefff1a91e08b5329b32e6f75a3ed251f193a4a40b6b2d8af0c8113e447faa

data/lib/rbbt/tsv/attach/util.rb

@@ -23,7 +23,10 @@ module TSV
             when other.type == :single
               new_values = [other[key]]
             else
-              new_values = other[key].values_at *field_positions
+              other_values = other[key]
+              new_values = field_positions.collect do |pos|
+                pos == :key ? key : other_values[pos]
+              end
             end
 
             new_values.collect!{|v| [v]}     if     type == :double and not other.type == :double

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -162,5 +162,6 @@ module TSV
         traverse_cpus cpus, obj, options, &block
       end
     end
+    into
   end
 end

data/lib/rbbt/tsv/util.rb

@@ -83,11 +83,25 @@ module TSV
     case
     when Path === file
       file.open(open_options)
+    when file.respond_to?(:gets)
+      file.rewind if file.respond_to?(:rewind) and file.eof?
+      file
     when String === file
       Open.open(file, open_options)
-    when file.respond_to?(:gets)
+    else
+      raise "Cannot get stream from: #{file.inspect}"
+    end
+  end
+  def self.get_stream(file, open_options = {})
+    case file
+    when Path
+      file.open(open_options)
+    when IO, StringIO
       file.rewind if file.respond_to?(:rewind) and file.eof?
       file
+    when String
+      raise "Could not open file given by String: #{Misc.fingerprint file}" unless File.exists? file
+      Open.open(file, open_options)
     else
       raise "Cannot get stream from: #{file.inspect}"
     end

data/lib/rbbt/workflow/step.rb

@@ -123,14 +123,13 @@ class Step
           raise $!
         end
       }
-      
-      Log.info{"#{Log.color :magenta, "Starting task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ Log.color :blue, path }"}
-      set_info :status, :started
 
-      set_info :started, (start_time = Time.now)
-      
       set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, @inputs)) unless task.inputs.nil?
 
+      #Log.info{"#{Log.color :magenta, "Starting task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ Log.color :blue, path }"}
+      set_info :started, (start_time = Time.now)
+      log :started, "#{Log.color :magenta, "Starting task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]"
+
       res = begin
               exec
             rescue Aborted
@@ -162,10 +161,9 @@ class Step
               raise $!
             end
 
-      set_info :status, :done
       set_info :done, (done_time = Time.now)
-      set_info :time_elapsed, done_time - start_time
-      Log.info{"#{Log.color :magenta, "Completed task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ Log.color :blue, path }"}
+      set_info :time_elapsed, (time_elapsed = done_time - start_time)
+      log :done, "#{Log.color :magenta, "Completed task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}] +#{time_elapsed.to_i}"
 
       res
     end

data/share/rbbt_commands/stat/abs

@@ -12,7 +12,7 @@ Take absolute value
 
 $ rbbt stat density <file>
 
-Display summary information. Works with Tokyocabinet HDB and DBD as well.
+Display summary information. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/stat/density

@@ -12,7 +12,7 @@ Calculate density
 
 $ rbbt stat density <file>
 
-Display summary information. Works with Tokyocabinet HDB and DBD as well.
+Display summary information. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/stat/log

@@ -12,7 +12,7 @@ Take logs
 
 $ rbbt stat density <file>
 
-Display summary information. Works with Tokyocabinet HDB and DBD as well.
+Display summary information. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/tsv/info

@@ -10,7 +10,7 @@ Inspect a TSV file
 
 $ rbbt tsv info [options] file.tsv
 
-Display summary information. Works with Tokyocabinet HDB and DBD as well.
+Display summary information. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/tsv/slice

@@ -10,7 +10,7 @@ Slice column from tsv
 
 $ rbbt tsv slice [options] file.tsv -f "Field 1"
 
-Display summary informations. Works with Tokyocabinet HDB and DBD as well.
+Display summary informations. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/tsv/subset

@@ -10,7 +10,7 @@ Subset entries in a tsv
 
 $ rbbt tsv subset [options] file.tsv --subset key1,key2,key3
 
-Subsets entries from a TSV file from a given list. Works with Tokyocabinet HDB and DBD as well.
+Subsets entries from a TSV file from a given list. Works with Tokyocabinet HDB and BDB as well.
 
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB

data/share/rbbt_commands/workflow/task

@@ -224,8 +224,6 @@ workflow.workdir = Path.setup(File.expand_path(options.delete(:workdir))) if opt
 
 #- get job
 
-ddd job_options["watson"]
-
 job = workflow.job(task.name, name, job_options)
 
 # clean job

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.8
+  version: 5.9.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-21 00:00:00.000000000 Z
+date: 2014-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake