rbbt-util 5.34.22 → 5.34.24

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: fd625b45572be4a158bc9f08007225e284659ec9ef26fbe66a2e9ae7fb84ce9f
+  metadata.gz: 7359f3a8ce8bde23107f23515557f47eb7bb65ee094c64419ba5542378af1c8c
+  data.tar.gz: 0a030eb0b6f9648a60c11abaac383fe33b24845c288ddd7a28eb8e9aa8d8ac1c
 SHA512:
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+  metadata.gz: dce1b81193d5d0d7ad86140e7287228b4a9d83fe99f08c4a431e34491d3c2a6057054cc9d80a76be9d4ac34b422c8203470d53579c4ba84bee8a804b6f12a2dd
+  data.tar.gz: 5b1d4e2aa040b183a92ea7b3ccb45fef2e3467a7d94203fd5214a366cbc87bfd6944095888f68c0ca6c8da6d2442cd0f6685b381e4be2e5b68c07bc68365ae72

data/lib/rbbt/util/log.rb

@@ -131,6 +131,30 @@ module Log
     end
   end
 
+  def self._ignore_stdout
+    begin
+      File.open('/dev/null', 'w') do |f|
+        backup_stdout = STDOUT.dup
+        STDOUT.reopen(f)
+        begin
+          yield
+        ensure
+          STDOUT.reopen backup_stdout
+          backup_stdout.close
+        end
+      end
+    rescue Errno::ENOENT
+      yield
+    end
+  end
+
+
+  def self.ignore_stdout(&block)
+    LOG_MUTEX.synchronize do
+      _ignore_stdout &block
+    end
+  end
+
   def self.get_level(level)
     case level
     when Numeric

data/lib/rbbt/workflow/dependencies.rb

@@ -72,7 +72,7 @@ module Workflow
   def setup_override_dependency(dep, workflow, task_name)
     return [] if dep == :skip || dep == 'skip'
 
-    if ! Step === dep
+    if not Step === dep
       located = Open.exists?(dep)
       dep = Workflow.load_step(dep)
     end

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

@@ -577,20 +577,20 @@ class Step
 
     return [] if dependencies.nil? or dependencies.empty?
 
-    new_dependencies = []
     if self.overriden?
       archived_deps = []
     else
       archived_deps = self.info[:archived_info] ? self.info[:archived_info].keys : []
     end
 
+    new_dependencies = []
     dependencies.each{|step| 
       #next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
       next if archived_deps.include? step.path
-      next if seen.include? step.path
+      next if seen.include? step
       next if self.done? && connected && ! updatable?
 
-      r = step.rec_dependencies(connected, new_dependencies.collect{|d| d.path})
+      r = step.rec_dependencies(connected, new_dependencies)
       new_dependencies.concat r
       new_dependencies << step
     }

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

@@ -96,7 +96,12 @@ module Workflow
           Log.debug "Opening tsv #{ input } from #{file}"
           inputs[input.to_sym]  = TSV.open(file)
         when :boolean
-          inputs[input.to_sym]  = (file.read.strip == 'true')
+          case file.read.strip.downcase
+          when 'true'
+            inputs[input.to_sym]  = true
+          when 'false'
+            inputs[input.to_sym]  = false
+          end
         when :integer
           inputs[input.to_sym]  = file.read.to_i
         when :float

data/share/Rlib/util.R

@@ -185,9 +185,17 @@ rbbt.tsv <- function(filename, sep = "\t", comment.char ="#", row.names=1, check
   }
 
   columns = rbbt.tsv.columns(filename, sep, comment.char=comment.char)
+  if (! is.null(comment.char))
+      columns[1] = substring(columns[1],length(comment.char) + 1)
+
   if (! is.null(columns)){
-      names(data) <- columns[2:length(columns)];
-      attributes(data)$key.field = substring(columns[1],2);
+      #names(data) <- columns[2:length(columns)];
+      if (! is.null(row.names)){
+          names(data) <- columns[c(-row.names)];
+      }else{
+          names(data) <- columns
+      }
+      attributes(data)$key.field = columns[1];
   }
 
   return(data);

data/share/rbbt_commands/tsv/read

@@ -37,6 +37,8 @@ when options[:tokyocabinet_bd]
   exit
 end
 
+options[:fields] = options[:fields].split(/,\s*/) if options[:fields]
+
 parser = TSV::Parser.new TSV.get_stream(file), options
 
 dumper = TSV::Dumper.new parser.options.merge(:sep => "\t", :sep2 => '|')

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.22
+  version: 5.34.24
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-11-28 00:00:00.000000000 Z
+date: 2022-12-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake