rbbt-util 5.13.7 → 5.13.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a7fb14a033052fa9f9e469e40ab600e40dfa6f90
-  data.tar.gz: 38a1246aae816a12634ee5681954c11beac3c9af
+  metadata.gz: e7281b74a41b34bf9cc71d351b6ca175a40f8aeb
+  data.tar.gz: 6f31f788281e74e00b594e9ff0303ccf0cddb491
 SHA512:
-  metadata.gz: f55bd2c2fbdd1815df354e7b6bf56c6ef5ec2383acc5ead9fba128ba23048c979bf54a8a1c90392c6982c99e80beebf2a45f5c4f7fef8832aa4a3853292afacc
-  data.tar.gz: f515c4276f796c56826412ffffc23856b221d76be923dc8655234dc1e0cb92781028cc9b0d1e2c92b049724aaaa889b61e4eb79d7e27cca8451fd8749a521051
+  metadata.gz: 7faad521cd49f6079fc8db95d49ad2d60dfda58f0ba99ee2f7249dcc519b3967df2c1a8cbe09f6de6af8d31c219233b3181ca7b70b859383885f335d7e13d80d
+  data.tar.gz: c218eb43aaaee50d7fb41c08d55b99b5615243e7c9f38bf6d1c499ee1766486c0f4e1cd21edd01389525747714f50669c35d6a120aab7e01c1011dd1410fd216

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

@@ -28,7 +28,7 @@ module TSV
       when Path
         CMD.cmd("wc -l '#{obj.find}'").read.to_i
       end
-    rescue
+    rescue Exception
       nil
     end
   end

data/lib/rbbt/tsv/parser.rb

@@ -496,7 +496,6 @@ module TSV
           desc = monitor[:desc] if monitor.include? :desc 
           step = monitor[:step] if monitor.include? :step 
         end
-        #progress_monitor = Progress::Bar.new(size, 0, step, desc)
         progress_monitor = Log::ProgressBar.new(size, :desc => desc)
       else
         progress_monitor = nil

data/lib/rbbt/workflow/accessor.rb

@@ -207,7 +207,7 @@ class Step
   end
 
   def started?
-    Open.exists? info_file
+    Open.exists? info_file or Open.exists? path
   end
 
   def done?

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

@@ -15,7 +15,7 @@ class Step
           Log.medium "Not duplicating stream #{ Misc.fingerprint(stream) }"
           STREAM_CACHE[stream] = stream
         when File
-          if true or current.closed?
+          if Open.exists? current.filename 
             Log.medium "Reopening file #{ Misc.fingerprint(current) }"
             Open.open(current.filename)
           else
@@ -136,7 +136,7 @@ class Step
     @seen.each do |dependency| 
       next if dependency == self
       next unless dependencies.include? dependency
-      Log.info "#{Log.color :magenta, "Checking dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} -- #{Log.color :blue, dependency.path}"
+      Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} -- #{Log.color :blue, dependency.path}"
       begin
         if dependency.streaming? 
           next if dependency.running?
@@ -184,7 +184,7 @@ class Step
 
           Open.rm info_file if Open.exists? info_file
 
-          log :setup, "#{Log.color :green, "Task"} #{Log.color :yellow, task.name.to_s || ""}"
+          log :setup, "#{Log.color :magenta, "Task"} #{Log.color :yellow, task.name.to_s || ""}"
 
           merge_info({
             :pid => Process.pid,
@@ -234,12 +234,12 @@ class Step
           case result
           when IO
 
-            log :streaming, "#{Log.color :magenta, "Streaming task result IO"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]"
+            log :streaming, "#{Log.color :magenta, "Streaming IO"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]"
             ConcurrentStream.setup result do
               begin
                 set_info :done, (done_time = Time.now)
                 set_info :time_elapsed, (time_elapsed = done_time - start_time)
-                log :done, "#{Log.color :red, "Completed task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}] +#{time_elapsed.to_i} -- #{path}"
+                log :done, "#{Log.color :red, "Completed"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}] +#{time_elapsed.to_i} -- #{path}"
               rescue
                 Log.exception $!
               ensure
@@ -256,7 +256,7 @@ class Step
               end
             end
           when TSV::Dumper
-            log :streaming, "#{Log.color :magenta, "Streaming task result TSV::Dumper"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]"
+            log :streaming, "#{Log.color :magenta, "Streaming TSV::Dumper"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]"
             ConcurrentStream.setup result.stream do
               begin
                 set_info :done, (done_time = Time.now)

data/share/rbbt_commands/tsv/read

@@ -0,0 +1,64 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.setup <<EOF
+Read a TSV file and dump it
+
+$ rbbt tsv read [options] <filename.tsv|->
+
+Use - to read from STDIN
+
+-k--key_field* Key field
+-f--fields* Fields
+-t--type* Type
+-m--merge* Merge from multiple rows
+-h--help Print this help
+
+EOF
+rbbt_usage and exit 0 if options[:help]
+
+file = ARGV.shift
+
+file = STDIN if file == '-'
+
+parser = TSV::Parser.new TSV.get_stream(file), options
+
+dumper = TSV::Dumper.new parser.options
+
+options[:merge] = false if options[:merge] == "false"
+
+Thread.new do
+  line = parser.first_line
+  bar = Log::ProgressBar.new
+  while line 
+    bar.tick
+
+    line = Misc.fixutf8(line)
+    line = parser.process line
+    raise SKIP_LINE if line.empty?
+    parts = parser.chop_line line
+    key, values = parser.get_values parts
+    values = parser.cast_values values if parser.cast?
+
+    if Array === key
+      key.each do |k|
+        dumper.add k, values
+      end
+      line = parser.stream.gets
+    else
+      dumper.add key, values
+      line = parser.stream.gets
+    end
+  end
+  dumper.close
+end
+
+dumper.init
+stream = dumper.stream
+stream = TSV.collapse_stream(dumper.stream).stream if options[:merge]
+
+while line = stream.gets
+  puts line
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.7
+  version: 5.13.8
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-08 00:00:00.000000000 Z
+date: 2014-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -250,6 +250,7 @@ files:
 - share/rbbt_commands/tsv/get
 - share/rbbt_commands/tsv/info
 - share/rbbt_commands/tsv/json
+- share/rbbt_commands/tsv/read
 - share/rbbt_commands/tsv/slice
 - share/rbbt_commands/tsv/sort
 - share/rbbt_commands/tsv/subset