rbbt-util 5.26.26 → 5.26.27

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1e656caf6f822514da2a5b9bf3b951ea4c5f6178cd8fd6da6059b4a940d7835b
-  data.tar.gz: e27dfec559b548efcd10dd9fa676168c330b085b50cdc7628b19c1308ee175fe
+  metadata.gz: d6047c6e75852ae9b3ec91c8950e3298a5d6005b9049adfe25d6edf7c4e36fa6
+  data.tar.gz: 91615cb7a2e9778cac5724c39d587a629db56d4ecdd340e904396e24b3becfe3
 SHA512:
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-  data.tar.gz: 6b84830391a26b793a531452b76c96e57fc9b00dc937087eec1269ed6f312dfa7aa0ef07aa48930600cc57c8fe1eab63a48a393ff576abe499ad5563f157a582
+  metadata.gz: 2e7b18ac930414fa922f5e52cf203e7ce733983f7ba31e79ba45e8537a5cf0804a271789575c1eef232110f652d2f8814d07f5d11e61abfb5fc595e9f3c75a8a
+  data.tar.gz: 514ff881334cbdb4faeba6f09038fd27fa2fbe5242582b85c1626c78731e9b836d6fd64f7b468e714d3091d16c0e63e48dfe3ea6c0a88f2e387550f855807fac

data/bin/rbbt

@@ -224,6 +224,7 @@ $previous_commands = []
 
 cmd_alias
 
+exit_status = 0
 begin
   while ARGV.any?
     $command = ARGV.shift
@@ -234,38 +235,45 @@ begin
     when dir[$command].exists?
       if locate
         puts dir[$command].find
-        exit 0
+        exit_status = 0
+        exit exit_status
       else
         load dir[$command].find
-        exit 0
+        exit_status = 0
+        exit exit_status
       end
     when File.exist?($command)
       load $command
-      exit 0
+      exit_status = 0
+      exit exit_status
     else
       error = "Command '#{$command }' not understood"
       rbbt_usage($previous_commands)
       print_error(error)
-      exit -1
+      exit_status = -1
+      exit exit_status
     end
   end
 
   rbbt_usage($previous_commands)
-  exit 0
+  exit_status = 0
+  exit exit_status
 
 rescue ParameterException
   puts
   rbbt_usage
   print_error($!.message, $!.backtrace)
   puts
-  exit -1
+  exit_status = -1
+  exit exit_status
 rescue SystemExit
 rescue CmdStop
   exit_status = $!.exit_status
   exit exit_status
 rescue Exception
   Log.exception $!
-  exit -1
+  exit_status = -1
+  exit exit_status
 ensure
   if options[:profile]
     result = RubyProf.stop
@@ -273,3 +281,5 @@ ensure
     printer.print(STDOUT, :min_percent => 10)
   end
 end
+
+exit exit_status

data/lib/rbbt/hpc.rb

@@ -178,7 +178,7 @@ echo "/scratch/tmp/rbbt/projects/rbbt/workflows/" > $CONTAINER_DIR/.rbbt/etc/wor
           env +=<<EOF
 
 # Copy image
-rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img"
+rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img" 1>&2
 SINGULARITY_IMG="$CONTAINER_DIR/rbbt.singularity.img"
 EOF
         end
@@ -426,9 +426,13 @@ EOF
         options[:slurm_basedir] ||= File.join(tmp_directory, 'workdir')
         slurm_basedir = options[:slurm_basedir]
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
-        Step.save_job_inputs(job, inputs_dir)
-        options[:inputs_dir] = inputs_dir
-        cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
+        saved = Step.save_job_inputs(job, inputs_dir, options)
+        if saved
+          options[:inputs_dir] = inputs_dir
+          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
+        else
+          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--log', (options[:log] || Log.severity).to_s]
+        end
 
 
         template = self.template(cmd, options)

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

@@ -86,8 +86,16 @@ module TSV
                   [source_key]
                 else
                   if other.include? source_key
-                    v = other.type == :flat ?  other[source_key] : other[source_key][pos]
-                    Array === v ? v : [v]
+                    v = case other.type
+                        when :flat
+                          other[source_key] 
+                        when :single
+                          [other[source_key]]
+                        when :double
+                          other[source_key][pos]
+                        when :list
+                          [other[source_key][pos]]
+                        end
                   else
                     [nil]
                   end

data/lib/rbbt/workflow/accessor.rb

@@ -84,7 +84,8 @@ class Step
     end
   end
 
-  def self.save_job_inputs(job, dir)
+  def self.save_job_inputs(job, dir, options = nil)
+    options = IndiferentHash.setup options.dup if options
 
     task_name = job.task_name
     workflow = job.workflow
@@ -92,9 +93,13 @@ class Step
     task_info = workflow.task_info(task_name)
     input_types = task_info[:input_types]
     task_inputs = task_info[:inputs]
+
+    saved = false
     job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
       next unless task_inputs.include? name.to_sym
+      next if options and ! options.include?(name)
       next if value.nil?
+      saved = true
       path = File.join(dir, name.to_s)
       type = input_types[name].to_s
       Log.debug "Saving job input #{name} (#{type}) into #{path}"
@@ -113,6 +118,8 @@ class Step
         Open.write(path, value.to_s)
       end
     end
+
+    saved
   end
 
   def name

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.26
+  version: 5.26.27
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-08 00:00:00.000000000 Z
+date: 2019-07-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake