rbbt-util 5.41.0 → 5.42.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5f8c020988e2d5df3aa710ce88fe4d92a2a754363d924a580fcc31b138330258
-  data.tar.gz: b6ee155b7bfb819baa21fac27c8561a3e1332bd9677a081abbe811bbb45c7973
+  metadata.gz: 8b23de77e3900d1a81e8ffa349ab9f88a4283f30bb2cec62c04bff4539243170
+  data.tar.gz: 494b18d5e2ba4802225617a03b2f69255ec9deab173e8d18e06654a7b415325c
 SHA512:
-  metadata.gz: 16d876542942fd0a0e1982dee1e7bf94ccd7bf8c8f4e3bb5310588a2f4587a3abe6d56fb101e1e1352c12225de507d46c18fa6b9109b2328079a999142479fa9
-  data.tar.gz: 6d135e37aa6151b68552a5c9f32f3cc1f1fef20a3f26695c9a033a09e0541a31a60de9b2fac33aea4c69e89a1acff54296264ba8435e9fecdaed5dcd5ee868fb
+  metadata.gz: d57bd3bc7ff84a4e8101dd907f98ef20923dbcab95c3187523e6b84eba6774d900f269ed2457fd6e1a81821edf3e2d1f11fcbdd5863f791282d549bcf83a48a5
+  data.tar.gz: a4857d82292ab4234cf10fbf2fcb242b466e6400f9476cb4de4bc625ff808542a690f27fbd9dede4ff692a82644561ebfc086ccdf953102cb4f7a0020b094849

data/lib/rbbt/hpc/batch.rb

@@ -15,6 +15,7 @@ module HPC
     when 'pbs'
       HPC::PBS
     when 'auto'
+      $previous_commands = [] if $previous_commands.nil?
       case $previous_commands.last
       when 'slurm'
         HPC::SLURM
@@ -735,7 +736,7 @@ env > #{batch_options[:fenv]}
     end
 
     def job_queued(job)
-      job_status(job).split(/\s+/).include?(job.to_s)
+      job_status(job).split(/[\s\.]+/).include?(job.to_s)
     end
 
     def wait_for_job(batch_dir, time = 1)

data/lib/rbbt/tsv/change_id.rb

@@ -8,8 +8,8 @@ module TSV
 
     identifiers, persist_input = Misc.process_options options, :identifiers, :persist_input
 
-    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
-
+    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
+      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
 
     if ! tsv.fields.include?(format)
       new = {}
@@ -58,7 +58,10 @@ module TSV
 
     identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
     identifiers = tsv.identifier_files.first if identifiers.nil?
-    identifiers = Organism.identifiers(tsv.namespace) if defined?(Organism) && identifiers.nil? && tsv.namespace && Organism.identifiers(tsv.namespace).exists?
+
+    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
+      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
+
     identifiers.namespace ||= tsv.namespace
 
     fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 

data/lib/rbbt/tsv.rb

@@ -69,6 +69,7 @@ module TSV
     options = TSV.str2options(options) if String === options and options.include? "~"
     options ||= {}
     options[:type] ||= type unless type.nil?
+    options[:zipped] = true if options[:one2one]
 
     persist_options = Misc.pull_keys options, :persist
 

data/lib/rbbt/util/R.rb

@@ -50,7 +50,7 @@ source('#{UTIL}');
           Log.debug "R: " <<  line
         end
       end
-      nil
+      io.join if io.respond_to? :join
     else
       CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => options[:xvfb]))
     end

data/lib/rbbt/util/config.rb

@@ -18,7 +18,7 @@ module Rbbt::Config
     Log.debug "Loading config file: #{ file }"
     TSV.traverse file, :type => :array do |line|
       next if line =~ /^#/
-      key, value, *tokens = line.strip.split(/\s/)
+      key, value, *tokens = line.strip.split(/\s+/)
 
       self.add_entry(key, value, tokens) if key
     end

data/lib/rbbt/util/log.rb

@@ -399,6 +399,10 @@ module Log
         end
       end
     end
+    LOG_MUTEX.synchronize do
+      Log::LAST.replace "log"
+    end
+    nil
   end
 
   def self.stack(stack)

data/lib/rbbt/util/named_array.rb

@@ -203,7 +203,7 @@ module NamedArray
 
   def report
     fields.zip(self).collect do |field,value|
-      "#{ field }: #{ Array === value ? value * "|" : value }"
+      "#{Log.color(:magenta, field) }: #{ Array === value ? value * "|" : value }"
     end * "\n"
   end
 

data/lib/rbbt/util/open.rb

@@ -101,7 +101,6 @@ module Open
 
       CMD.cmd("wget '#{ url }'", wget_options)
     rescue
-     STDERR.puts $!.backtrace.inspect
      raise OpenURLError, "Error reading remote url: #{ url }.\n#{$!.message}"
     end
   end
@@ -654,7 +653,12 @@ module Open
   end
 
   def self.download(url, path)
-    Open.wget(url, "--output-document" => path, :pipe => false)
+    begin
+      Open.wget(url, "--output-document" => path, :pipe => false)
+    rescue Exception
+      Open.rm(path) if Open.exist?(path)
+      raise $!
+    end
   end
 
   def self.can_open?(file)

data/lib/rbbt/workflow/definition.rb

@@ -129,6 +129,8 @@ module Workflow
     end
   end
 
+  alias task_alias dep_task
+
   def task(name, &block)
     if Hash === name
       type = name.first.last

data/lib/rbbt/workflow/integration/nextflow.rb

@@ -1,4 +1,47 @@
 module Workflow
+
+  OUTPUT_FIELDS=%w(outdir output)
+
+  def self.parse_nextflow_schema(file)
+    doc = Open.open(file){|f| JSON.parse(f.read) }
+    description = doc["description"]
+
+    properties = {}
+    required = []
+
+    properties[nil] = doc["properties"] if doc["properties"]
+    required.concat doc["required"] if doc["required"]
+
+    doc["definitions"].each do |section,section_info|
+      next unless section_info["properties"]
+      name = section_info["title"] || section
+      properties[name] = section_info["properties"]
+      required.concat section_info["required"] if section_info["required"] if section_info["required"]
+    end if doc["definitions"]
+
+    required = required.compact.flatten
+
+    parameters = {}
+    properties.each do |section,param_info|
+      param_info.each do |name,info|
+        input_options = {}
+        type = info["type"]
+        format = info["format"]
+        input_desc = info["description"]
+        input_section = info["description"]
+        input_required = required.include?(name)
+        input_options[:required] = true if input_required && ! OUTPUT_FIELDS.include?(name)
+        if info.include?("enum")
+          type = 'select'
+          input_options[:select_options] = info["enum"]
+        end
+        parameters[name] = {type: type, format: format, description: input_desc, options: input_options, section: section}
+      end
+    end
+
+    [description, parameters]
+  end
+
   def self.nextflow_file_params(file)
     Open.read(file).scan(/params\.\w+/).collect{|p| p.split(".").last}.uniq
   end
@@ -16,8 +59,11 @@ module Workflow
       included_file += '.nf' unless File.exist?(included_file) || ! File.exist?(included_file + '.nf')
       name_str.split(";").each do |name|
         name = name.strip
-        include_params = nextflow_recursive_params(included_file).collect{|p| [p,name] * "-"}
-        params += include_params
+        begin
+          include_params = nextflow_recursive_params(included_file).collect{|p| [p,name] * "-"}
+          params += include_params
+        rescue
+        end
       end
       params
     end
@@ -32,22 +78,31 @@ module Workflow
       result = :text
     end
 
+    dir = Path.setup(File.dirname(file))
+
+    nextflow_schema = dir['nextflow_schema.json']
+
+    description, params = Workflow.parse_nextflow_schema(nextflow_schema) if nextflow_schema.exists?
+
     file = file + '.nf' unless File.exist?(file) || ! File.exist?(file + '.nf')
     file = File.expand_path(file)
     name ||= File.basename(file).sub(/\.nf$/,'').gsub(/\s/,'_')
-    params = Workflow.nextflow_recursive_params(file)
-
-    params.each do |param|
+    Workflow.nextflow_recursive_params(file).each do |param|
       p,_sep, section = param.partition("-")
-      if section.nil? || section.empty?
-        input param, :string, "Nextflow param #{p}", nil, :nofile => true
-      else
-        input param, :string, "Nextflow param #{p} from import #{section}", nil, :nofile => true
+      if ! params.include?(p)
+        params[p] = {type: :string, description: "Undocumented"}
       end
     end
+
+    used_params = []
+    desc description
+    params.each do |name,info|
+      input name.to_sym, info[:type], info[:description], nil, info[:options].merge(:noload => true)
+    end
     task name => result do 
       work = file('work')
       profile = config :profile, :nextflow
+      resume = config :resume, :nextflow
       config_file = config :config, :nextflow
 
       nextflow_inputs = {}
@@ -68,9 +123,17 @@ module Workflow
           name = f
         end
           
-        nextflow_inputs[name] = v
+        case name.to_s
+        when 'outdir'
+          output = nextflow_inputs[name] = v || output || file('output')
+        when 'output'
+          output = nextflow_inputs[name] = v || output || self.tmp_path
+        else
+          nextflow_inputs[name] = v
+        end
       end
-      
+
+      current_pwd = FileUtils.pwd
       Misc.in_dir file('stage') do
 
         cmd = "nextflow "
@@ -83,19 +146,26 @@ module Workflow
 
         cmd += " -profile #{profile}" if profile
 
+        cmd += " -resume" if resume == 'true'
+
+        Dir.glob(current_pwd + "/*").each do |file|
+          target = File.basename(file)
+          Open.ln_s file, target unless File.exist?(target)
+        end
 
         cmd("#{cmd} #{file}", nextflow_inputs.merge('add_option_dashes' => true))
       end
 
-      output_file = file(output).glob.first if output
-      output_file = work[File.join('*', '*', output)].glob.first if output && output_file.nil?
-
-      if output_file.nil?
-        work[File.join("*", "*", "*")].glob * "\n"
+      if output && Open.exists?(output)
+        if File.directory?(output)
+          Dir.glob(output + "/**/*") * "\n"
+        else
+          output_file = output
+          Open.link output, self.tmp_path
+          nil
+        end
       else
-        Open.link output_file, self.tmp_path
-        #Open.rm_rf file('work')
-        nil
+        work[File.join("*", "*", "*")].glob * "\n"
       end
     end
   end
@@ -105,11 +175,19 @@ module Workflow
     nextflow_file main, File.basename(path), output
   end
 
+  def nextflow_project(project, *args)
+    CMD.cmd_log("nextflow pull #{project}")
+    directory = File.join(ENV["HOME"], '.nextflow/assets', project)
+    nextflow_dir directory, *args
+  end
+
   def nextflow(path, *args)
     if File.directory?(path)
       nextflow_dir path, *args
-    else
+    elsif File.exist?(path)
       nextflow_file path, *args
+    else
+      nextflow_project path, *args
     end
   end
 end

data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb

@@ -136,33 +136,33 @@ STDOUT.write job.path
       Misc.ssh_run(server, script)
     end
 
-    def self.run_slurm_job(url, input_id, jobname = nil, slurm_options = {})
+    def self.run_batch_job(url, input_id, jobname = nil, batch_options = {})
       server, path = parse_url(url)
 
       script = path_script(path)
       script += job_script(input_id, jobname)
       script +=<<-EOF
 require 'rbbt/hpc'
-HPC::BATCH_MODULE = HPC.batch_system "SLURM"
-slurm_options = JSON.parse(%q(#{slurm_options.to_json}))
+HPC::BATCH_MODULE = HPC.batch_system 
+batch_options = JSON.parse(%q(#{batch_options.to_json}))
 job.clean if job.error? and job.recoverable_error?
-HPC::BATCH_MODULE.run_job(job, slurm_options) unless job.done? || job.error?
+HPC::BATCH_MODULE.run_job(job, batch_options) unless job.done? || job.error?
 STDOUT.write job.path
       EOF
       Misc.ssh_run(server, script)
     end
 
-    def self.orchestrate_slurm_job(url, input_id, jobname = nil, slurm_options = {})
+    def self.orchestrate_batch_job(url, input_id, jobname = nil, batch_options = {})
       server, path = parse_url(url)
 
       script = path_script(path)
       script += job_script(input_id, jobname)
       script +=<<-EOF
 require 'rbbt/hpc'
-HPC::BATCH_MODULE = HPC.batch_system "SLURM"
-slurm_options = JSON.parse(%q(#{slurm_options.to_json}))
+HPC::BATCH_MODULE = HPC.batch_system
+batch_options = JSON.parse(%q(#{batch_options.to_json}))
 job.clean if job.error? and job.recoverable_error?
-HPC::BATCH_MODULE.orchestrate_job(job, slurm_options) unless job.done? || job.error?
+HPC::BATCH_MODULE.orchestrate_job(job, batch_options) unless job.done? || job.error?
 STDOUT.write job.path
       EOF
       Misc.ssh_run(server, script)
@@ -268,8 +268,8 @@ job.clean
     end
 
     def self.relay_job(job, server, options = {})
-      migrate, produce, produce_dependencies, search_path, run_type, slurm_options = Misc.process_options options.dup,
-        :migrate, :produce, :produce_dependencies, :search_path, :run_type, :slurm_options
+      migrate, produce, produce_dependencies, search_path, run_type, batch_options = Misc.process_options options.dup,
+        :migrate, :produce, :produce_dependencies, :search_path, :run_type, :batch_options
 
       search_path ||= 'user'
 
@@ -287,7 +287,7 @@ job.clean
       rjob.override_dependencies = override_dependencies
 
       rjob.run_type = run_type
-      rjob.slurm_options = slurm_options || {}
+      rjob.batch_options = batch_options || {}
 
       if options[:migrate]
         rjob.produce
@@ -298,8 +298,8 @@ job.clean
     end
 
     def self.relay_job_list(job_list, server, options = {})
-      migrate, produce, produce_dependencies, search_path, run_type, slurm_options = Misc.process_options options.dup,
-        :migrate, :produce, :produce_dependencies, :search_path, :run_type, :slurm_options
+      migrate, produce, produce_dependencies, search_path, run_type, batch_options = Misc.process_options options.dup,
+        :migrate, :produce, :produce_dependencies, :search_path, :run_type, :batch_options
 
       search_path ||= 'user'
 
@@ -320,7 +320,7 @@ job.clean
         rjob.override_dependencies = override_dependencies
 
         rjob.run_type = run_type
-        rjob.slurm_options = slurm_options || {}
+        rjob.batch_options = batch_options || {}
 
         rjob.run(true)
 
@@ -330,7 +330,6 @@ job.clean
       if options[:migrate]
         rjobs_job.each do |rjob,job|
           rjob.produce
-          iif [:migrate, job]
           Step.migrate(Rbbt.identify(job.path), 'user', :source => server) 
         end
       end

data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb

@@ -1,6 +1,6 @@
 class RemoteStep
   module SSH
-    attr_accessor :override_dependencies, :run_type, :slurm_options, :produce_dependencies
+    attr_accessor :override_dependencies, :run_type, :batch_options, :produce_dependencies
 
     def init_job(cache_type = nil, other_params = {})
       return self if @url
@@ -22,7 +22,7 @@ class RemoteStep
 
       RemoteWorkflow::SSH.upload_inputs(@server, inputs, @input_types, @input_id)
 
-      @remote_path ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
+      @remote_path ||= Persist.memory("RemoteStep", :workflow => self.workflow, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
         Misc.insist do
           input_types = {}
           RemoteWorkflow::SSH.post_job(File.join(base_url, task.to_s), @input_id, @base_name)
@@ -56,13 +56,13 @@ class RemoteStep
       RemoteWorkflow::SSH.run_job(File.join(base_url, task.to_s), @input_id, @base_name)
     end
 
-    def _run_slurm
+    def _run_batch
       RemoteWorkflow::SSH.upload_dependencies(self, @server, 'user', @produce_dependencies)
-      RemoteWorkflow::SSH.run_slurm_job(File.join(base_url, task.to_s), @input_id, @base_name, @slurm_options || {})
+      RemoteWorkflow::SSH.run_batch_job(File.join(base_url, task.to_s), @input_id, @base_name, @batch_options || {})
     end
 
-    def _orchestrate_slurm
-      RemoteWorkflow::SSH.orchestrate_slurm_job(File.join(base_url, task.to_s), @input_id, @base_name, @slurm_options || {})
+    def _orchestrate_batch
+      RemoteWorkflow::SSH.orchestrate_batch_job(File.join(base_url, task.to_s), @input_id, @base_name, @batch_options || {})
     end
 
     def issue
@@ -71,10 +71,10 @@ class RemoteStep
       @remote_path = case @run_type
                      when 'run', :run, nil
                        _run
-                     when 'slurm', :slurm
-                       _run_slurm
+                     when 'batch', :batch
+                       _run_batch
                      when 'orchestrate', :orchestrate
-                       _orchestrate_slurm
+                       _orchestrate_batch
                      end
       @started = true
     end

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

@@ -219,7 +219,7 @@ class Step
     Step.log_progress(status, options, file(:progress), &block)
   end
 
-  def progress_bar(msg = "Progress", options = nil)
+  def progress_bar(msg = "Progress", options = nil, &block)
     if Hash === msg and options.nil?
       options = msg
       msg = nil
@@ -227,7 +227,16 @@ class Step
     options = {} if options.nil?
 
     max = options[:max]
-    Log::ProgressBar.new_bar(max, {:desc => msg, :file => (@exec ? nil : file(:progress))}.merge(options))
+    bar = Log::ProgressBar.new_bar(max, {:desc => msg, :file => (@exec ? nil : file(:progress))}.merge(options))
+
+    if block_given?
+      bar.init
+      res = yield bar
+      bar.remove
+      res
+    else
+      bar
+    end
   end
 
   def self.log(status, message, path, &block)

data/lib/rbbt/workflow.rb

@@ -496,7 +496,7 @@ module Workflow
     end
 
     #overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?
-    overriden = true if dependencies.select{|d| Symbol === d.overriden }.any?
+    overriden = true if not_overriden && dependencies.select{|d| Symbol === d.overriden }.any?
 
     input_values = task.take_input_values(inputs)
     if real_inputs.empty? && Workflow::TAG != :inputs && ! overriden #&& ! dependencies.select{|d| d.overriden && d.clean_name != d.name }.any?

data/share/Rlib/util.R

@@ -646,10 +646,8 @@ rbbt.pheatmap <- function(filename, data, width=800, height=800, take_log=FALSE,
 }
 
 rbbt.heatmap <- function(filename, data, width=800, height=800, take_log=FALSE, stdize=FALSE, ...){
+    rbbt.require('gplots')
     opar = par()
-    png(filename=filename, width=width, height=height);
-
-    #par(cex.lab=0.5, cex=0.5, ...)
 
     data = as.matrix(data)
     data[is.nan(data)] = NA
@@ -657,6 +655,22 @@ rbbt.heatmap <- function(filename, data, width=800, height=800, take_log=FALSE,
     #data = data[rowSums(!is.na(data))!=0, colSums(!is.na(data))!=0]
     data = data[rowSums(is.na(data))==0, ]
 
+    key.size = 150
+    label.size = 200
+    block.size = 12
+    
+    if (height == 'auto'){
+        height = max(c(dim(data)[1], 30)) * block.size + key.size + label.size
+    }
+
+    if (width == 'auto'){
+        width = max(c(dim(data)[2], 30)) * block.size + key.size + label.size
+    }
+
+    png(filename=filename, width=width, height=height);
+
+    #par(cex.lab=0.5, cex=0.5, ...)
+
     if (take_log){
         for (study in colnames(data)){
             skip = sum(data[, study] <= 0) != 0
@@ -673,7 +687,11 @@ rbbt.heatmap <- function(filename, data, width=800, height=800, take_log=FALSE,
         data = stdize(data)
     }
 
-    heatmap.2(data, scale='column', ...)
+    lwid = key.size / (width)
+    lhei = key.size / (height)
+    str(dim(data))
+    str(c(height, lhei, width, lwid))
+    heatmap.2(data, scale='column', lwid = c(lwid, 1-lwid), lhei = c(lhei, 1-lhei), ...)
 
     dev.off();
     par(opar)

data/share/config.ru

@@ -44,7 +44,7 @@ app_eval app, Rbbt.etc['app.d/remote_workflow_tasks.rb'].find_all
 app_eval app, Rbbt.etc['app.d/base.rb'].find
 
 #{{{ SINATRA
-load_file Rbbt.lib['sinatra.rb'].find_all
+app_eval app, Rbbt.lib['sinatra.rb'].find_all
 
 #{{{ RESOURCES
 load_file Rbbt.etc['app.d/resources.rb'].find

data/share/rbbt_commands/resource/find

@@ -30,7 +30,7 @@ if options[:help]
 end
 
 resource, path = ARGV
-path, resource = resource, nil
+path, resource = resource, nil if path.nil?
 
 raise MissingParameterException.new(:path) if path.nil?
 

data/share/rbbt_commands/tsv/get

@@ -7,9 +7,10 @@ options = SOPT.setup <<EOF
 
 Query a TSV value
 
-$ rbbt tsv get [options] <filename.tsv|-> <key>
+$ rbbt tsv get [options] <filename.tsv|-> [<key>]
 
-Use - to read from STDIN
+Use - to read from STDIN, 'key' can be the key string or a number representing
+its position. If not specified 'key' defaults to 0, the first entry.
 
 -tch--tokyocabinet File is a tokyocabinet hash database
 -tcb--tokyocabinet_bd File is a tokyocabinet B database
@@ -26,7 +27,7 @@ rbbt_usage and exit 0 if options[:help]
 
 file, key = ARGV
 
-raise ParameterException, "Please specify file and key" if key.nil?
+raise ParameterException, "Please specify file" if file.nil?
 
 file = STDIN if file == '-'
 
@@ -48,7 +49,15 @@ key_field = options[:key_field]
 fields = fields.split(/[,|]/, -1) unless fields.nil?
 
 if TSV === tsv
+  case key
+  when nil
+    key = tsv.keys.first if key.nil?
+  when /^\d+$/
+    key = tsv.keys[key.to_i] unless tsv.include?(key)
+  end
+
   v = tsv[key]
+
   fields ||= tsv.fields
   puts Log.color(:blue, "Key: #{ key }")
   if fields
@@ -72,8 +81,15 @@ end
 parser = TSV::Parser.new tsv, :key_field => key_field,  :fields => fields, :type => options[:type], :header_hash => options[:header_hash], :sep => options[:sep]
 fields ||= parser.fields
 
+i = 0
 TSV.traverse(parser) do |k,v|
-  next unless k.include? key
+  if key== "#{i}"
+    key = k.first
+  elsif key.nil?
+    key = k.first
+  end
+  i += 1
+  next unless k.include?(key)
   k = k.first if Array === k
   puts Log.color(:blue, "Key: #{ k }")
   if fields

data/share/rbbt_commands/workflow/task

@@ -221,7 +221,7 @@ The `recursive_clean` cleans all the job dependency steps recursively.
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
 -PERF--procpath_performance* Measure performance using procpath
 --relay* Relay job to SSH server
---slurm_relay* Relay job to SSH SLURM server
+--batch_relay* Relay job to SSH BATCH server (SLURM, PBS, etc.)
 -rdep--relay_dependencies* Relay dependencies instead of main job
 -pdr--produce_dependencies_for_relay Prepare dependencies previous to relay jobs
 EOF
@@ -493,9 +493,9 @@ begin
     replace_relayed_jobs(jobs_to_relay, server, produce_dependencies_for_relay, :run)
   end
 
-  if server = options.delete(:slurm_relay)
+  if server = options.delete(:batch_relay)
     require 'rbbt/workflow/remote_workflow'
-    relay_dependencies = options.delete(:relay_dependencies).split(",")
+    relay_dependencies = options.include?(:relay_dependencies) ? options.delete(:relay_dependencies).split(",") : nil
     produce_dependencies_for_relay = options.delete(:produce_dependencies_for_relay)
     jobs_to_relay = relay_dependencies ?  match_dependencies(relay_dependencies, job.rec_dependencies) : [job]
     jobs_to_relay.reject!{|d| d.done? }

data/share/workflow_config.ru

@@ -46,7 +46,6 @@ app.get '/' do
   begin
     template_render('main', params, 'main', :cache_type => :asynchronous)
   rescue TemplateMissing
-    Log.exception $!
     redirect to(File.join('/', wf.to_s))
   end
 end

data/test/rbbt/resource/test_path.rb

@@ -38,8 +38,8 @@ class TestTSV < Test::Unit::TestCase
     assert_equal Path.setup(File.join('doc', path)).find(:lib), path.find(:lib).doc_file
 
     assert_equal "lib/rbbt/resource.rb", path.doc_file.source_for_doc_file
-    assert_equal path.find, path.doc_file.find(:lib).source_for_doc_file
-    assert_equal path.find, path.doc_file.source_for_doc_file.find
+    assert_equal File.realpath(path.find), File.realpath(path.doc_file.find(:lib).source_for_doc_file)
+    assert_equal File.realpath(path.find), File.realpath(path.doc_file.source_for_doc_file.find)
 
     assert_equal "doc/lib/rbbt/resource.rb.doc", path.doc_file.set_extension('doc')
     #assert_equal "lib/rbbt/resource.rb", path.doc_file.set_extension('doc').source_for_doc_file

data/test/rbbt/tsv/test_accessor.rb

@@ -74,6 +74,25 @@ row2    A    B    Id3
     end
   end
   
+  def test_to_s_no_preable
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    target =<<-EOF
+Id,ValueA,ValueB,OtherID
+row1,a|aa|aaa,b,Id1|Id2
+row2,A,B,Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      assert_equal tsv.to_s(preamble: false, header_hash: '').gsub(/\t/, ','), target
+    end
+  end
+  
   def test_entries
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID

data/test/rbbt/util/test_open.rb

@@ -187,5 +187,14 @@ class TestOpen < Test::Unit::TestCase
 
   end
 
+  def test_download_fails
+    TmpFile.with_file do |tmp|
+      assert_raise do
+        Open.download("http:fake-host/some_path", tmp)
+      end
+      refute Open.exists?(tmp)
+    end
+  end
+
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.41.0
+  version: 5.42.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-12-21 00:00:00.000000000 Z
+date: 2024-02-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake