rbbt-util 5.34.23 → 5.34.25

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: c8a029debfd1ee7c820185aa1dead29575ecd173a1868692751c6a01dc7be01a
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data/lib/rbbt/hpc/batch.rb

@@ -101,6 +101,11 @@ module HPC
 
       task = Symbol === job.overriden ? job.overriden : job.task_name
 
+      #override_deps = job.overriden_deps.collect do |dep| 
+      #  name = [dep.workflow.to_s, dep.task_name] * "#"
+      #  [name, dep.path] * "="  
+      #end.uniq * ","
+
       if job.overriden?
         #override_deps = job.rec_dependencies.
         #  select{|dep| Symbol === dep.overriden }.
@@ -568,7 +573,7 @@ env > #{batch_options[:fenv]}
         Misc.add_defaults options, 
           :batch_dir => batch_dir, 
           :inputs_dir => File.join(batch_dir, "inputs_dir"),
-          :workflows => workflows_to_load.uniq * ","
+          :workflows => workflows_to_load.any? ? workflows_to_load.uniq * "," : nil
 
         options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath
 

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

@@ -73,8 +73,10 @@ module Workflow
     return [] if dep == :skip || dep == 'skip'
 
     if not Step === dep
-      located = Open.exists?(dep)
+      located = Open.exists?(dep) || Open.exists?(dep + '.info')
       dep = Workflow.load_step(dep)
+    else
+      located = true
     end
 
     dep.original_workflow ||= dep.workflow if dep.workflow

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

@@ -527,7 +527,7 @@ class Step
 
   def overriden?
     return true if @overriden
-    return true if dependencies && dependencies.select{|dep| dep.overriden? }.any?
+    return true if dependencies && dependencies.select{|dep| TrueClass === dep.overriden }.any?
     info[:archived_info].each do |f,i|
       next if Symbol === i
       return true if i[:overriden] || i["overriden"]
@@ -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

@@ -31,6 +31,8 @@ module Workflow
 
         type = :step_array if file.split(".").last == 'as_step_array'
 
+        type = :number_array if file.split(".").last == 'as_number_array'
+
         type = :step_file if file.split(".").last == 'as_step_file'
 
         type = :step_file_array if file.split(".").last == 'as_step_file_array'
@@ -57,6 +59,9 @@ module Workflow
         when :step_array
           steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
           inputs[input.to_sym] = steps
+        when :number_array
+          numbers = Open.read(file).strip.split("\n").collect{|num| num.to_f }
+          inputs[input.to_sym] = numbers
         when :step
           steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
           inputs[input.to_sym] = steps.first
@@ -176,6 +181,8 @@ class Step
       when Step
         path = path + '.as_step_array'
         value = value.collect{|s| s.path }
+      when Numeric
+        path = path + '.as_number_array'
       end
 
       value = value * "\n"

data/lib/rbbt/workflow.rb

@@ -437,8 +437,8 @@ module Workflow
       jobname_input = nil 
     end
 
-    if jobname_input && jobname && inputs[jobname_input].nil?
-      inputs[jobname_input] = jobname
+    if jobname_input && inputs[jobname_input].nil?
+      inputs[jobname_input] = jobname || DEFAULT_NAME
     end
 
     real_inputs = {}
@@ -503,7 +503,7 @@ module Workflow
     when :not_overriden_dep
       job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
     else
-      job.overriden = true if has_overriden_inputs || overriden_deps.any?
+      job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
     end
 
     job.real_inputs = real_inputs.keys

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/hpc/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

data/share/rbbt_commands/lsf/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

data/share/rbbt_commands/slurm/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

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: 5.34.23
+  version: 5.34.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-11-30 00:00:00.000000000 Z
+date: 2022-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake