rbbt-util 5.23.36 → 5.23.37

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: e5ddc970668f140bd1923ce200b2754d352c8e61
+  metadata.gz: 206746628d7fcc049b1e322ac9b7869199855c61
+  data.tar.gz: 77bb05fbe30fd9e912a119460afe1d4a40ebb613
 SHA512:
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+  metadata.gz: f74c4c63ee0590f18de5b405dc74eba69fc9f936cd49dec989407c576c203ebdd199ee338884e9992dd3cc1302215bae4b16a75d54976098687003c1479732f4
+  data.tar.gz: 7407802c1cf02b75a8fe2dfaa162d66cc878efc23a2517e3f1ee0b70332ab2adce1428d4ecf85ff45e3d7e998e92d0ddc3bd39c9a6900664a17e62494bcbe4da

data/lib/rbbt/util/open.rb

@@ -13,6 +13,18 @@ module Open
   REMOTE_CACHEDIR = File.join(ENV["HOME"], "/tmp/open_cache")
   FileUtils.mkdir_p REMOTE_CACHEDIR unless File.exist? REMOTE_CACHEDIR
 
+  GREP_CMD = begin
+               if ENV["GREP_CMD"] 
+                 ENV["GREP_CMD"]
+               elsif File.exists?('/bin/grep')
+                 "/bin/grep"
+               elsif File.exists?('/usr/bin/grep')
+                 "/usr/bin/grep"
+               else
+                 "grep"
+               end
+             end
+
   class << self
     attr_accessor :repository_dirs
 
@@ -127,14 +139,13 @@ module Open
   # Grep
   
   def self.grep(stream, grep, invert = false)
-    grep_cmd = ENV["GREP_CMD"] || "/bin/grep"
     case 
     when Array === grep
       TmpFile.with_file(grep * "\n", false) do |f|
-        CMD.cmd("#{grep_cmd} #{invert ? '-v' : ''} -", "-w" => true, "-F" => true, "-f" => f, :in => stream, :pipe => true, :post => proc{FileUtils.rm f})
+        CMD.cmd("#{GREP_CMD} #{invert ? '-v' : ''} -", "-w" => true, "-F" => true, "-f" => f, :in => stream, :pipe => true, :post => proc{FileUtils.rm f})
       end
     else
-      CMD.cmd("#{grep_cmd} #{invert ? '-v ' : ''} '#{grep}' -", :in => stream, :pipe => true, :post => proc{begin stream.force_close; rescue Exception; end if stream.respond_to?(:force_close)})
+      CMD.cmd("#{GREP_CMD} #{invert ? '-v ' : ''} '#{grep}' -", :in => stream, :pipe => true, :post => proc{begin stream.force_close; rescue Exception; end if stream.respond_to?(:force_close)})
     end
   end
 
@@ -386,11 +397,11 @@ module Open
     repo_target = get_repo_from_dir(dir_sub_path_target[0])
 
     content = repo_source.read_and_close do
-      repo_target[dir_sub_path_target[1]]
+      repo_source[dir_sub_path_source[1]]
     end
 
     repo_target.write_and_close do
-      repo_source[dir_sub_path_source[1]] = content
+      repo_target[dir_sub_path_target[1]] = content
     end
 
     return nil
@@ -405,7 +416,7 @@ module Open
       tmp_target = File.join(File.dirname(target), '.tmp_mv.' + File.basename(target))
       FileUtils.mv source, tmp_target
       FileUtils.mv tmp_target, target
-      return
+      return nil
     end
 
     if dir_sub_path_source.nil?
@@ -422,11 +433,11 @@ module Open
     repo_target = get_repo_from_dir(dir_sub_path_target[0])
 
     content = repo_source.read_and_close do
-      repo_target[dir_sub_path_target[1]]
+      repo_source[dir_sub_path_target[1]]
     end
 
     repo_target.write_and_close do
-      repo_source[dir_sub_path_source[1]] = content
+      repo_target[dir_sub_path_source[1]] = content
     end
 
     repo_source.write_and_close do

data/lib/rbbt/workflow.rb

@@ -505,7 +505,6 @@ module Workflow
   end
     
   def self.fast_load_step(path)
-    return load_step(path)
     step = Step.new path
     step.dependencies = nil
     class << step
@@ -533,6 +532,7 @@ module Workflow
       def dirty?
         false
       end
+
       def updated?
         true
       end

data/share/rbbt_commands/tsv/read

@@ -38,7 +38,8 @@ end
 
 parser = TSV::Parser.new TSV.get_stream(file), options
 
-dumper = TSV::Dumper.new parser.options
+dumper = TSV::Dumper.new parser.options.merge(:sep => "\t", :sep2 => '|')
+dumper.init
 
 options[:merge] = false if options[:merge] == "false"
 
@@ -68,7 +69,6 @@ Thread.new do
   dumper.close
 end
 
-dumper.init
 stream = dumper.stream
 stream = TSV.collapse_stream(dumper.stream).stream if options[:merge]
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.36
+  version: 5.23.37
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-29 00:00:00.000000000 Z
+date: 2018-12-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake