rbbt-util 5.33.8 → 5.33.12

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: b8a2a233686ec2f229ed79bb19d87d8eb79ad945142305f7b61dcdb11f5f7912
+  metadata.gz: 729b93bb0b82b05a03eb9cdf99728b4793ecd002ab06a92c08dc899341d26810
+  data.tar.gz: 568b263ae5bbc16e18383bd0fc5fb42054d2954b674bb1df97f80280ade9e7b2
 SHA512:
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-  data.tar.gz: ac7c01fa7e8fccdff8dfc861b82f28889a68f77886c198ff55b09558b36857ec9c29a8bae979bc7d088f311ad81515676bc7a4cc30097fd6c4b7586e6838c0e3
+  metadata.gz: 1c56e3f171523bb412b391899b93ba88d80038a2a201ed4573897c3039526fbf1f05d2a2bcb81b837d6cb9ad31672c7c5a67572d7baa3789c10f3fc3929db274
+  data.tar.gz: b178ecce6c10f7933bdafd3cf495e3a185d6f0005b5111ed6b86f79f70b9608d613c837d7141c6ca42bf4504d352f46102d2ac628bc19d6e9a2001dbcc081284

data/lib/rbbt/hpc/batch.rb

@@ -88,8 +88,8 @@ module HPC
     def rbbt_job_exec_cmd(job, options)
 
       jobname  = job.clean_name
-      workflow = job.workflow
-      task     = job.task_name
+      workflow = job.original_workflow || job.workflow
+      task     = job.original_task_name || job.task_name
 
       Misc.add_defaults options, :jobname => jobname
 
@@ -535,8 +535,8 @@ env > #{batch_options[:fenv]}
         :batch_base_dir, :clean_batch_job, :remove_batch_dir, :batch_procpath, :tail, :batch_dependencies, :dry_run,
         :batch_base_dir => File.expand_path(File.join('~/rbbt-batch')) 
 
-      workflow = job.workflow
-      task_name = job.task_name
+      workflow = job.original_workflow ||job.workflow
+      task_name = job.original_task_name || job.task_name
 
       workflows_to_load = job.rec_dependencies.select{|d| Step === d}.collect{|d| d.workflow }.compact.collect(&:to_s) - [workflow.to_s]
 

data/lib/rbbt/hpc/orchestrate/batches.rb

@@ -101,7 +101,9 @@ module HPC
 
       batches.each do |batch|
         job_rules = batch[:jobs].inject(nil) do |acc,job|
-          task_rules = task_specific_rules(rules, job.workflow, job.task_name)
+          workflow = job.original_workflow || job.workflow
+          task_name = job.original_task_name || job.task_name
+          task_rules = task_specific_rules(rules, workflow, task_name)
           acc = accumulate_rules(acc, task_rules.dup)
         end
 
@@ -120,13 +122,16 @@ module HPC
         end
 
         batches.each do |batch|
+          next if batch[:top_level].overriden?
           next unless batch[:rules][:skip]
           batch[:rules].delete :skip
           next if batch[:deps].nil?
 
           if batch[:deps].any?
+            batch_dep_jobs = batch[:top_level].rec_dependencies
             target = batch[:deps].select do |target|
-              (batch[:deps] - [target] - target[:deps]).empty?
+              batch_dep_jobs.include?(target[:top_level]) && # Don't piggyback batches that are an input dependency, only real dependencies
+                (batch[:deps] - [target] - target[:deps]).empty?
             end.first
             next if target.nil?
             target[:jobs] = batch[:jobs] + target[:jobs]

data/lib/rbbt/hpc/orchestrate/chains.rb

@@ -4,8 +4,10 @@ module HPC
       return [] if Symbol === job.overriden
       matches = []
       chains.each do |name, chain|
-        next unless chain[:tasks].include?(job.workflow.to_s)
-        next unless chain[:tasks][job.workflow.to_s].include?(job.task_name.to_s)
+        workflow = job.original_workflow || job.workflow
+        task_name = job.original_task_name || job.task_name
+        next unless chain[:tasks].include?(workflow.to_s)
+        next unless chain[:tasks][workflow.to_s].include?(task_name.to_s)
         matches << name
       end
       matches
@@ -38,46 +40,50 @@ module HPC
     end
 
     def self.job_chains(rules, job)
-      chains = self.parse_chains(rules)
-
-      matches = check_chains(chains, job)
-
-      dependencies = job_dependencies(job)
-
-      job_chains = []
-      new_job_chains = {}
-      dependencies.each do |dep|
-        dep_matches = check_chains(chains, dep)
-        common = matches & dep_matches
-
-        dep_chains = job_chains(rules, dep)
-        found = []
-        dep_chains.each do |match,info|
-          if common.include?(match)
-            found << match
-            new_info = new_job_chains[match] ||= {}
-            new_info[:jobs] ||= []
-            new_info[:jobs].concat info[:jobs]
-            new_info[:top_level] = job
-          else
+      @@job_chains ||= {}
+      @@job_chains[Misc.digest([rules, job.path].inspect)] ||= 
+        begin
+          chains = self.parse_chains(rules)
+
+          matches = check_chains(chains, job)
+
+          dependencies = job_dependencies(job)
+
+          job_chains = []
+          new_job_chains = {}
+          dependencies.each do |dep|
+            dep_matches = check_chains(chains, dep)
+            common = matches & dep_matches
+
+            dep_chains = job_chains(rules, dep)
+            found = []
+            dep_chains.each do |match,info|
+              if common.include?(match)
+                found << match
+                new_info = new_job_chains[match] ||= {}
+                new_info[:jobs] ||= []
+                new_info[:jobs].concat info[:jobs]
+                new_info[:top_level] = job
+              else
+                job_chains << [match, info]
+              end
+            end
+
+            (common - found).each do |match|
+              info = {}
+              info[:jobs] = [job, dep]
+              info[:top_level] = job
+              job_chains << [match, info]
+            end
+          end
+
+          new_job_chains.each do |match,info|
+            info[:jobs].prepend job
             job_chains << [match, info]
           end
-        end
 
-        (common - found).each do |match|
-          info = {}
-          info[:jobs] = [job, dep]
-          info[:top_level] = job
-          job_chains << [match, info]
+          job_chains
         end
-      end
-
-      new_job_chains.each do |match,info|
-        info[:jobs].prepend job
-        job_chains << [match, info]
-      end
-
-      job_chains
     end
 
   end

data/lib/rbbt/hpc/orchestrate.rb

@@ -30,6 +30,7 @@ module HPC
       options.delete "printpath"
       options.delete "detach"
       options.delete "jobname"
+      options.delete "load_inputs"
 
       Log.high "Prepare for exec"
       prepare_for_execution(job)
@@ -81,7 +82,7 @@ module HPC
 
         if options[:dry_run]
           puts Log.color(:magenta, "Manifest: ") + Log.color(:blue, job_options[:manifest] * ", ") + " - tasks: #{job_options[:task_cpus] || 1} - time: #{job_options[:time]} - config: #{job_options[:config_keys]}"
-          puts Log.color(:magenta, "Deps: ") + Log.color(:blue, job_options[:batch_dependencies]*", ")
+          puts Log.color(:yellow, "Deps: ") + Log.color(:blue, job_options[:batch_dependencies]*", ")
           puts Log.color(:yellow, "Path: ") + top[:top_level].path
           puts Log.color(:yellow, "Options: ") + job_options.inspect
           batch_ids[top] = top[:top_level].task_signature

data/lib/rbbt/hpc/slurm.rb

@@ -94,8 +94,8 @@ export BATCH_SYSTEM=SLURM
 
       return if Open.exists?(fexit)
 
-      STDERR.puts Log.color(:magenta, "Issuing SLURM file: #{fcmd}")
-      STDERR.puts Open.read(fcmd)
+      Log.info "Issuing SLURM file: #{fcmd}"
+      Log.debug Open.read(fcmd)
 
       if File.exists?(fjob)
         job = Open.read(fjob).to_i

data/lib/rbbt/util/misc/communication.rb

@@ -0,0 +1,79 @@
+module Misc
+  PUSHBULLET_KEY=begin
+                   if ENV["PUSHBULLET_KEY"]
+                     ENV["PUSHBULLET_KEY"]
+                   else
+                     config_api = File.join(ENV['HOME'], 'config/apps/pushbullet/apikey')
+                     if File.exist? config_api
+                       File.read(config_api).strip
+                     else
+                       nil
+                     end
+                   end
+                 end
+
+  def self.notify(description, event='notification', key = nil)
+    if PUSHBULLET_KEY.nil? and key.nil?
+      Log.warn "Could not notify, no PUSHBULLET_KEY"
+      return
+    end
+
+    Thread.new do
+      application = 'rbbt'
+      event ||= 'notification'
+      key ||= PUSHBULLET_KEY
+      `curl -s --header "Authorization: Bearer #{key}" -X POST https://api.pushbullet.com/v2/pushes --header 'Content-Type: application/json' --data-binary '{"type": "note", "title": "#{event}", "body": "#{description}"}'`
+    end
+  end
+
+  def self.send_email_old(from, to, subject, message, options = {})
+    IndiferentHash.setup(options)
+    options = Misc.add_defaults options, :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login
+
+    server, port, user, pass, from_alias, to_alias, auth = Misc.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth
+
+    msg = <<-END_OF_MESSAGE
+From: #{from_alias} <#{from}>
+To: #{to_alias} <#{to}>
+Subject: #{subject}
+
+#{message}
+END_OF_MESSAGE
+
+    Net::SMTP.start(server, port, server, user, pass, auth) do |smtp|
+      smtp.send_message msg, from, to
+    end
+  end
+
+  def self.send_email(from, to, subject, message, options = {})
+    require 'mail'
+
+    IndiferentHash.setup(options)
+    options = Misc.add_defaults options, :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login, :files => []
+
+    server, port, user, pass, from_alias, to_alias, auth, files = Misc.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth, :files
+
+    files = [] if files.nil?
+    files = [files] unless Array === files
+
+    Mail.defaults do
+      delivery_method :smtp, address: server, port: port, user_name: user, password: pass
+    end
+
+    mail = Mail.deliver do 
+      from  "#{from_alias} <#{from}>"
+      to "#{to_alias} <#{to}>"
+      subject subject
+
+      text_part do 
+        body message
+      end
+
+      files.each do |file|
+        file = file.find if Path === file
+        file = file.path if Step === file
+      end
+    end
+  end
+
+end

data/lib/rbbt/util/misc/development.rb

@@ -385,32 +385,6 @@ def self.add_libdir(dir=nil)
     `ps -o rss -p #{pid || $$}`.strip.split.last.to_i
   end
 
-  PUSHBULLET_KEY=begin
-                   if ENV["PUSHBULLET_KEY"]
-                     ENV["PUSHBULLET_KEY"]
-                   else
-                     config_api = File.join(ENV['HOME'], 'config/apps/pushbullet/apikey')
-                     if File.exist? config_api
-                       File.read(config_api).strip
-                     else
-                       nil
-                     end
-                   end
-                 end
-
-  def self.notify(description, event='notification', key = nil)
-    if PUSHBULLET_KEY.nil? and key.nil?
-      Log.warn "Could not notify, no PUSHBULLET_KEY"
-      return
-    end
-
-    Thread.new do
-      application = 'rbbt'
-      event ||= 'notification'
-      key ||= PUSHBULLET_KEY
-      `curl -s --header "Authorization: Bearer #{key}" -X POST https://api.pushbullet.com/v2/pushes --header 'Content-Type: application/json' --data-binary '{"type": "note", "title": "#{event}", "body": "#{description}"}'`
-    end
-  end
 
   def self.unzip_in_dir(file, dir)
     raise "Target is not a directory: #{file}" if File.exist?(dir) and not File.directory?(dir)

data/lib/rbbt/util/misc/inspect.rb

@@ -355,7 +355,7 @@ module Misc
               "<IO:" << obj.path << "--" << mtime_str(obj.path) << ">"
             end
           when (defined? Step and Step)
-            "<IO:" << obj.short_path << ">"
+            "<IO:" << obj.short_path_real << ">"
           when IO
             if obj.respond_to? :filename and obj.filename
               if defined?(Step) && Open.exists?(Step.info_file(obj.filename))

data/lib/rbbt/util/misc/system.rb

@@ -16,25 +16,6 @@ module Misc
     end
   end
 
-  def self.send_email(from, to, subject, message, options = {})
-    IndiferentHash.setup(options)
-    options = Misc.add_defaults options, :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login
-
-    server, port, user, pass, from_alias, to_alias, auth = Misc.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth
-
-    msg = <<-END_OF_MESSAGE
-From: #{from_alias} <#{from}>
-To: #{to_alias} <#{to}>
-Subject: #{subject}
-
-#{message}
-END_OF_MESSAGE
-
-Net::SMTP.start(server, port, server, user, pass, auth) do |smtp|
-  smtp.send_message msg, from, to
-end
-  end
-
   def self.env_add(var, value, sep = ":", prepend = true)
     ENV[var] ||= ""
     return if ENV[var] =~ /(#{sep}|^)#{Regexp.quote value}(#{sep}|$)/
@@ -113,9 +94,10 @@ end
   end
 
   def self.is_filename?(string, need_to_exists = true)
+    return false if string.nil?
     return true if defined? Path and Path === string
     return true if string.respond_to? :exists
-    return true if String === string and string.length < 265 and (File.exist?(string) || ! need_to_exists)
+    return true if String === string and string.split("/").select{|p| p.length > 265}.empty? and (! need_to_exists || File.exist?(string))
     return false
   end
 

data/lib/rbbt/util/misc.rb

@@ -20,6 +20,7 @@ require 'rbbt/util/misc/options'
 require 'rbbt/util/misc/system'
 require 'rbbt/util/misc/objects'
 require 'rbbt/util/misc/manipulation'
+require 'rbbt/util/misc/communication'
 
 require 'to_regexp'
 

data/lib/rbbt/util/open.rb

@@ -678,7 +678,14 @@ module Open
       if Open.exists? notification_file
         key = Open.read(notification_file).strip
         key = nil if key.empty?
-        Misc.notify("Wrote " << file, nil, key)
+        if key.include?("@")
+          to = from = key
+          subject = "Wrote " << file
+          message = "Content attached"
+          Misc.send_email(from, to, subject, message, :files => [file])
+        else
+          Misc.notify("Wrote " << file, nil, key)
+        end
         Open.rm notification_file
       end
     rescue

data/lib/rbbt/workflow/dependencies.rb

@@ -72,9 +72,12 @@ module Workflow
   def setup_override_dependency(dep, workflow, task_name)
     return [] if dep == :skip || dep == 'skip'
     dep = Step === dep ? dep.dup : Workflow.load_step(dep)
+
+    dep.original_workflow ||= dep.workflow if dep.workflow
+    dep.original_task_name ||= dep.task_name if dep.workflow
+
     dep.workflow = workflow
     dep.info[:name] = dep.name
-    dep.original_task_name ||= dep.task_name if dep.workflow
 
 
     begin

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

@@ -96,6 +96,10 @@ class Step
     [task_name, name] * "/"
   end
 
+  def short_path_real
+    [(Symbol === overriden ? overriden : task_name).to_s, name] * "/"
+  end
+
   def workflow_short_path
     return short_path unless workflow
     workflow.to_s + "#" + short_path

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

@@ -510,7 +510,7 @@ class Step
 
   def overriden?
     return true if @overriden
-    return true if dependencies.select{|dep| dep.overriden? }.any?
+    return true if dependencies && dependencies.select{|dep| dep.overriden? }.any?
     info[:archived_info].each do |f,i|
       next if Symbol === i
       return true if i[:overriden] || i["overriden"]

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

@@ -1,4 +1,5 @@
 module Workflow
+
   def self.load_inputs(dir, input_names, input_types)
     inputs = {}
     if File.exists?(dir) && ! File.directory?(dir)
@@ -20,21 +21,59 @@ module Workflow
         Log.debug "Trying #{ input }: #{file}"
         next unless file and (File.symlink?(file) || file.exists?)
 
-        type = input_types[input]
+        type = orig_type = input_types[input]
 
         type = :io if file.split(".").last == 'as_io'
 
+        type = :io_array if file.split(".").last == 'as_io_array'
+
+        type = :step if file.split(".").last == 'as_step'
+
+        type = :step_array if file.split(".").last == 'as_step_array'
+
+        type = :step_file if file.split(".").last == 'as_step_file'
+
+        type = :step_file_array if file.split(".").last == 'as_step_file_array'
+
         type = :path if file.split(".").last == 'as_path'
 
+        type = :path_array if file.split(".").last == 'as_path_array'
+
+        type = :filename if file.split(".").last == 'as_filename'
+
         type = :nofile if file.split(".").last == 'nofile'
 
         case type
         when :nofile
           inputs[input.to_sym]  = Open.realpath(file)
+        when :path_array
+          inputs[input.to_sym]  = Open.read(file).strip.split("\n")
         when :path
-          inputs[input.to_sym]  = Open.realpath(Open.read(file).strip)
+          inputs[input.to_sym]  = Open.read(file).strip.split("\n").first
+        when :io
+          inputs[input.to_sym] = Open.open(Open.realpath(file)).split("\n")
         when :io
-          inputs[input.to_sym] = Open.open(Open.realpath(file))
+          inputs[input.to_sym] = Open.realpath(file).split("\n").collect{|f| Open.open(f)}
+        when :step_array
+          steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
+          inputs[input.to_sym] = steps
+        when :step
+          steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
+          inputs[input.to_sym] = steps.first
+        when :step_file
+          path = Open.read(file).strip
+          path.extend Path
+          step_path = path.match(/(.*)\.files/)[1]
+          path.resource = Step.new step_path
+          inputs[input.to_sym] = path
+        when :step_file_array
+          paths = Open.read(file).split("\n")
+          paths.each do |path| 
+            path.extend Path
+            step_path = path.match(/(.*)\.files/)[1]
+            path.resource = Step.new step_path
+          end
+          inputs[input.to_sym] = paths
         when :file, :binary
           Log.debug "Pointing #{ input } to #{file}"
           if file =~ /\.yaml/
@@ -87,60 +126,149 @@ module Workflow
     job(task_name, jobname, inputs)
   end
 
+  #def self.load_inputs_old(dir, input_names, input_types)
+  #  inputs = {}
+  #  if File.exists?(dir) && ! File.directory?(dir)
+  #    Log.debug "Loading inputs from #{dir}, not a directory trying as tar.gz"
+  #    tarfile = dir
+  #    digest = CMD.cmd("md5sum '#{tarfile}'").read.split(" ").first
+  #    tmpdir = Rbbt.tmp.input_bundle[digest].find
+  #    Misc.untar(tarfile, tmpdir) unless File.exists? tmpdir
+  #    files = tmpdir.glob("*")
+  #    if files.length == 1 && File.directory?(files.first)
+  #      tmpdir = files.first
+  #    end
+  #    load_inputs(tmpdir, input_names, input_types)
+  #  else
+  #    dir = Path.setup(dir.dup)
+  #    input_names.each do |input|
+  #      file = dir[input].find
+  #      file = dir.glob(input.to_s + ".*").reject{|f| f =~ /\.md5$/}.first if file.nil? or not (File.symlink?(file) || file.exists?)
+  #      Log.debug "Trying #{ input }: #{file}"
+  #      next unless file and (File.symlink?(file) || file.exists?)
+
+  #      type = input_types[input]
+
+  #      type = :io if file.split(".").last == 'as_io'
+
+  #      type = :path if file.split(".").last == 'as_path'
+
+  #      type = :filename if file.split(".").last == 'as_filename'
+
+  #      type = :nofile if file.split(".").last == 'nofile'
+
+  #      case type
+  #      when :nofile
+  #        inputs[input.to_sym]  = Open.realpath(file)
+  #      when :path
+  #        inputs[input.to_sym]  = Open.realpath(Open.read(file).strip)
+  #      when :io
+  #        inputs[input.to_sym] = Open.open(Open.realpath(file))
+  #      when :file, :binary
+  #        Log.debug "Pointing #{ input } to #{file}"
+  #        if file =~ /\.yaml/
+  #          inputs[input.to_sym]  = YAML.load(Open.read(file))
+  #        else
+  #          if File.symlink?(file)
+  #            link_target = File.expand_path(File.readlink(file), File.dirname(file))
+  #            inputs[input.to_sym]  = link_target
+  #          else
+  #            inputs[input.to_sym]  = Open.realpath(file)
+  #          end
+  #        end
+  #      when :text
+  #        Log.debug "Reading #{ input } from #{file}"
+  #        inputs[input.to_sym]  = Open.read(file)
+  #      when :array
+  #        Log.debug "Reading array #{ input } from #{file}"
+  #        inputs[input.to_sym]  = Open.read(file).split("\n")
+  #      when :tsv
+  #        Log.debug "Opening tsv #{ input } from #{file}"
+  #        inputs[input.to_sym]  = TSV.open(file)
+  #      when :boolean
+  #        inputs[input.to_sym]  = (file.read.strip == 'true')
+  #      else
+  #        Log.debug "Loading #{ input } from #{file}"
+  #        inputs[input.to_sym]  = file.read.strip
+  #      end
+
+  #    end
+  #    inputs = IndiferentHash.setup(inputs)
+
+  #    dir.glob("*#*").each do |od|
+  #      name = File.basename(od)
+  #      value = Open.read(od)
+  #      Log.debug "Loading override dependency #{ name } as #{value}"
+  #      inputs[name] = value.chomp
+  #    end
+
+  #    inputs
+  #  end
+  #end
 end
 
 class Step
-  def self.save_inputs(inputs, input_types, input_options, dir)
-    inputs.each do |name,value|
-      type = input_types[name]
-      type = type.to_s if type
-      path = File.join(dir, name.to_s)
-
-      path = path + '.as_io' if (IO === value || Step === value) && ! (input_options[name] && input_options[name][:nofile])
-      Log.debug "Saving job input #{name} (#{type}) into #{path}"
-
-      case
-      when IO === value
-        Open.write(path, value.to_s)
-      when Step === value
-        Open.ln_s(value.path, path)
-      when type.to_s == "binary"
-        if String === value && File.exists?(value)
-          value = File.expand_path(value)
-          Open.ln_s(value, path)
-        elsif String === value && Misc.is_filename?(value, false)
-          Open.write(path + '.as_path' , value)
-        else
-          Open.write(path, value, :mode => 'wb')
-        end
-      when type.to_s == "file"
-        if String === value && File.exists?(value)
-          value = File.expand_path(value)
-          Open.ln_s(value, path)
+  def self.save_input(name, value, type, dir)
+    path = File.join(dir, name.to_s)
+
+    case value
+    when Path
+      if Step === value.resource
+        path = path + '.as_step_file'
+      else
+        path = path + '.as_path'
+      end
+    when String
+      if Misc.is_filename?(value, false)
+        value = value.dup
+        value.extend Path
+        return save_input(name, value, type, dir)
+      end
+    when IO
+      path = path + '.as_io'
+    when Step
+      value = value.path
+      path = path + '.as_step'
+    when Array
+      case value.first
+      when Path
+        if Step === value.first.resource
+          path = path + '.as_step_file_array'
         else
-          value = value.collect{|v| v = "#{v}" if Path === v; v } if Array === value
-          value = "#{value}" if Path === value
-          Open.write(path + '.yaml', value.to_yaml)
+          path = path + '.as_path_array'
         end
-      when Array === value
-        Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
-      when IO === value
-        if value.filename && String === value.filename && File.exists?(value.filename)
-          Open.ln_s(value.filename, path)
-        else
-          Open.write(path, value)
+      when String
+        if Misc.is_filename?(value.first, false)
+          path = path + '.as_path_array'
         end
-      else
-        Open.write(path, value.to_s)
+      when IO
+        path = path + '.as_io_array'
+      when Step
+        path = path + '.as_step_array'
+        value = value.collect{|s| s.path }
       end
+
+      value = value * "\n"
+    end
+
+    Log.debug "Saving job input #{name} (#{type}) into #{path}"
+    Open.write(path, value.to_s)
+  end
+
+  def self.save_inputs(inputs, input_types, input_options, dir)
+    inputs.each do |name,value|
+      type = input_types[name]
+      type = type.to_s if type
+
+      save_input(name, value, type, dir)
     end.any?
   end
 
   def self.save_job_inputs(job, dir, options = nil)
     options = IndiferentHash.setup options.dup if options
 
-    task_name = Symbol === job.overriden ? job.overriden : job.task_name
-    workflow = job.workflow
+    task_name = job.original_task_name || job.task_name
+    workflow = job.original_workflow || job.workflow
     workflow = Kernel.const_get workflow if String === workflow
     if workflow
       task_info = IndiferentHash.setup(workflow.task_info(task_name))
@@ -176,4 +304,60 @@ class Step
 
     inputs.keys
   end
+
+  #def self.save_inputs_old(inputs, input_types, input_options, dir)
+  #  inputs.each do |name,value|
+  #    type = input_types[name]
+  #    type = type.to_s if type
+  #    path = File.join(dir, name.to_s)
+
+  #    if (IO === value || Step === value) && ! (input_options[name] && input_options[name][:nofile])
+  #      path = path + '.as_io' 
+  #    elsif Misc.is_filename?(value, false)
+  #      path = path + '.as_filename'
+  #    end
+
+  #    Log.debug "Saving job input #{name} (#{type}) into #{path}"
+
+  #    case
+  #    when IO === value
+  #      Open.write(path, value.to_s)
+  #    when Step === value
+  #      Open.ln_s(value.path, path)
+  #    when type.to_s == "binary"
+  #      if String === value && File.exists?(value)
+  #        value = File.expand_path(value)
+  #        Open.ln_s(value, path)
+  #      elsif String === value && Misc.is_filename?(value, false)
+  #        Open.write(path + '.as_path' , value)
+  #      else
+  #        Open.write(path, value, :mode => 'wb')
+  #      end
+  #    when TSV === value
+  #      Open.write(path, value.to_s)
+  #    when Array === value
+  #      Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
+  #    when %w(file tsv array).include?(type.to_s)
+  #      if String === value && File.exists?(value)
+  #        value = File.expand_path(value)
+  #        Open.ln_s(value, path)
+  #      elsif String === value && Misc.is_filename?(value, false)
+  #        Open.write(path + '.as_path' , value)
+  #      else
+  #        value = value.collect{|v| v = "#{v}" if Path === v; v } if Array === value
+  #        value = "#{value}" if Path === value
+  #        Open.write(path + '.yaml', value.to_yaml)
+  #      end
+  #    when IO === value
+  #      if value.filename && String === value.filename && File.exists?(value.filename)
+  #        Open.ln_s(value.filename, path)
+  #      else
+  #        Open.write(path, value)
+  #      end
+  #    else
+  #      Open.write(path, value.to_s)
+  #    end
+  #  end.any?
+  #end
+
 end

data/lib/rbbt/workflow/step.rb

@@ -15,7 +15,7 @@ class Step
   attr_accessor :exec
   attr_accessor :relocated
   attr_accessor :result, :mutex, :seen
-  attr_accessor :real_inputs, :original_task_name
+  attr_accessor :real_inputs, :original_task_name, :original_workflow
 
   RBBT_DEBUG_CLEAN = ENV["RBBT_DEBUG_CLEAN"] == 'true'
 
@@ -376,9 +376,9 @@ class Step
                        }
                        raise "Dependency step not found: #{ name }" if deps.empty?
                        if (deps & self.dependencies).any?
-                         (deps & self.dependencies).first
+                         (deps & self.dependencies).last
                        else
-                         deps.first
+                         deps.last
                        end
                      end
   end

data/share/rbbt_commands/hpc/list

@@ -141,7 +141,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    rescue
      nodes = []
    end
- elsif job_nodes[id]
+ elsif job_nodes && job_nodes[id]
    nodes = job_nodes[id].reject{|n| n.include? "("}
  else
    nodes = []
@@ -209,7 +209,9 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          if j.file(:progress).exists?
            bar = Log::ProgressBar.new 
            bar.load(j.file(:progress).yaml)
-           prog_rep << bar.report_msg.split("·")[0..1]
+           rep = bar.report_msg.split("·")[1]
+           rep = rep.sub(/.*?(\d+%)/, Log.color(:blue,'\1')).sub(/\-.*/,'')
+           prog_rep << [rep]
          end
        end
      end
@@ -340,7 +342,10 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          has_bar = true
        end
      end
-     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
+     step_status = step.status
+     step_status = Log.color :red, step_status if step_status.to_s == 'cleaned'
+     step_status = Log.color :green, step_status if step_status.to_s == 'done'
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step_status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/hpc/orchestrate

@@ -60,5 +60,6 @@ class Step
     end
 end
 
-ARGV.concat ["-W", $slurm_options[:workflows], '--detach'] if $slurm_options[:workflows]
+ARGV.concat ['--detach']
+ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
 load Rbbt.share.rbbt_commands.workflow.task.find

data/share/rbbt_commands/hpc/tail

@@ -57,6 +57,7 @@ else
   step_path = nil
 end
 
+puts Log.color(:magenta, "Directory: ") + directory if directory
 puts Log.color(:magenta, "Step path: ") + step_path if step_path
 
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/lsf/list

@@ -141,7 +141,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    rescue
      nodes = []
    end
- elsif job_nodes[id]
+ elsif job_nodes && job_nodes[id]
    nodes = job_nodes[id].reject{|n| n.include? "("}
  else
    nodes = []
@@ -209,7 +209,9 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          if j.file(:progress).exists?
            bar = Log::ProgressBar.new 
            bar.load(j.file(:progress).yaml)
-           prog_rep << bar.report_msg.split("·")[0..1]
+           rep = bar.report_msg.split("·")[1]
+           rep = rep.sub(/.*?(\d+%)/, Log.color(:blue,'\1')).sub(/\-.*/,'')
+           prog_rep << [rep]
          end
        end
      end
@@ -340,7 +342,10 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          has_bar = true
        end
      end
-     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
+     step_status = step.status
+     step_status = Log.color :red, step_status if step_status.to_s == 'cleaned'
+     step_status = Log.color :green, step_status if step_status.to_s == 'done'
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step_status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/lsf/orchestrate

@@ -60,5 +60,6 @@ class Step
     end
 end
 
-ARGV.concat ["-W", $slurm_options[:workflows], '--detach'] if $slurm_options[:workflows]
+ARGV.concat ['--detach']
+ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
 load Rbbt.share.rbbt_commands.workflow.task.find

data/share/rbbt_commands/lsf/tail

@@ -57,6 +57,7 @@ else
   step_path = nil
 end
 
+puts Log.color(:magenta, "Directory: ") + directory if directory
 puts Log.color(:magenta, "Step path: ") + step_path if step_path
 
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/slurm/list

@@ -141,7 +141,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    rescue
      nodes = []
    end
- elsif job_nodes[id]
+ elsif job_nodes && job_nodes[id]
    nodes = job_nodes[id].reject{|n| n.include? "("}
  else
    nodes = []
@@ -209,7 +209,9 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          if j.file(:progress).exists?
            bar = Log::ProgressBar.new 
            bar.load(j.file(:progress).yaml)
-           prog_rep << bar.report_msg.split("·")[0..1]
+           rep = bar.report_msg.split("·")[1]
+           rep = rep.sub(/.*?(\d+%)/, Log.color(:blue,'\1')).sub(/\-.*/,'')
+           prog_rep << [rep]
          end
        end
      end
@@ -340,7 +342,10 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
          has_bar = true
        end
      end
-     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
+     step_status = step.status
+     step_status = Log.color :red, step_status if step_status.to_s == 'cleaned'
+     step_status = Log.color :green, step_status if step_status.to_s == 'done'
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step_status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/slurm/orchestrate

@@ -60,5 +60,6 @@ class Step
     end
 end
 
-ARGV.concat ["-W", $slurm_options[:workflows], '--detach'] if $slurm_options[:workflows]
+ARGV.concat ['--detach']
+ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
 load Rbbt.share.rbbt_commands.workflow.task.find

data/share/rbbt_commands/slurm/tail

@@ -57,6 +57,7 @@ else
   step_path = nil
 end
 
+puts Log.color(:magenta, "Directory: ") + directory if directory
 puts Log.color(:magenta, "Step path: ") + step_path if step_path
 
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/workflow/task

@@ -76,6 +76,16 @@ def fix_options(workflow, task, job_options)
     type = input_types[name]
     type = type.to_sym if type
 
+    if Step === value
+        job_options_cleaned[name] = value
+        next
+    end
+
+    if Path === value && Step === value.resource
+        job_options_cleaned[name] = value
+        next
+    end
+
     value = case type
             when nil
                 value
@@ -148,6 +158,7 @@ def fix_options(workflow, task, job_options)
             else
               value
             end
+
     job_options_cleaned[name] = value
   end
 

data/test/rbbt/util/misc/test_communication.rb

@@ -0,0 +1,11 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/misc/communication'
+
+class TestCommunication < Test::Unit::TestCase
+  def test_send_email
+    to = from = 'mvazque2@localhost'
+    subject = message = "Test"
+    iii Misc.send_email(to, from, subject, message)
+  end
+end
+

data/test/rbbt/workflow/step/test_save_load_inputs.rb

@@ -26,11 +26,26 @@ module TestSaveLoadWF
   task :prefix => :array do
     step(:reverse).run.collect{|e| "A-#{e}" }
   end
+
+  input :integer, :integer
+  input :float, :float
+  input :file, :file
+  input :file_no_file, :file, "", nil, :nofile => true
+  input :string, :string
+  input :select, :select
+  input :array, :array
+  input :array_no_file, :array, "", nil, :nofile => true
+  input :tsv, :tsv, "", nil, :nofile => true
+  input :tsv_no_file, :tsv, "", nil, :nofile => true
+  input :binary, :binary, "", nil, :nofile => true
+  input :binary_no_file, :tsv, "", nil, :nofile => true
+  task :save_test => :string do
+    "DONE"
+  end
 end
 
 class TestSaveLoad < Test::Unit::TestCase
   def test_save
-    Log.with_severity 0 do
     job = TestSaveLoadWF.job(:prefix)
     job.recursive_clean
     job = TestSaveLoadWF.job(:prefix)
@@ -40,6 +55,81 @@ class TestSaveLoad < Test::Unit::TestCase
       newjob = TestSaveLoadWF.job_for_directory_inputs(:reverse, directory)
       assert_equal job.rec_dependencies.last.path, newjob.path
     end
+  end
+
+  def test_save_all_normal
+    tsv = TSV.setup({}, "Key~Value#:type=:single")
+    tsv["key"] = "value"
+    options = {
+      :float => 0.5,
+      :integer => 15,
+      :string => "STRING",
+      :select => "option",
+      :array => [0,1,2,3],
+      :tsv => tsv,
+    }
+    Log.with_severity 0 do
+      Misc.with_env "RBBT_DEBUG_JOB_HASH", "true" do
+        job = TestSaveLoadWF.job(:save_test, nil, options)
+        TmpFile.with_file do |directory|
+          Step.save_job_inputs(job, directory)
+          newjob = TestSaveLoadWF.job_for_directory_inputs(:save_test, directory)
+          assert_equal job.path, newjob.path
+        end
+      end
+    end
+  end
+
+  def test_save_all_file
+    tsv = TSV.setup({}, "Key~Value#:type=:single")
+    tsv["key"] = "value"
+    Log.with_severity 0 do
+      Misc.with_env "RBBT_DEBUG_JOB_HASH", "true" do
+        TmpFile.with_file do |input_file|
+          Path.setup(input_file)
+          options = {
+            :float => input_file.float,
+            :integer => input_file.integer,
+            :string => input_file.string,
+            :select => input_file.select,
+            :array => input_file.array,
+            :tsv => input_file.tsv_file,
+          }
+          job = TestSaveLoadWF.job(:save_test, nil, options)
+          TmpFile.with_file do |directory|
+            Step.save_job_inputs(job, directory)
+            newjob = TestSaveLoadWF.job_for_directory_inputs(:save_test, directory)
+            assert_equal job.path, newjob.path
+          end
+        end
+      end
+    end
+  end
+
+  def test_save_all_job_file
+    tsv = TSV.setup({}, "Key~Value#:type=:single")
+    tsv["key"] = "value"
+    Log.with_severity 0 do
+      Misc.with_env "RBBT_DEBUG_JOB_HASH", "true" do
+        TmpFile.with_file do |input_file|
+          Path.setup(input_file)
+          options = {
+            :float => input_file.float,
+            :integer => input_file.integer,
+            :string => input_file.string,
+            :select => input_file.select,
+            :array => TestSaveLoadWF.job(:list),
+            :binary => TestSaveLoadWF.job(:list).file('binary'),
+            :tsv => input_file.tsv_file,
+          }
+          job = TestSaveLoadWF.job(:save_test, nil, options)
+          TmpFile.with_file do |directory|
+            Step.save_job_inputs(job, directory)
+            newjob = TestSaveLoadWF.job_for_directory_inputs(:save_test, directory)
+            assert_equal job.path, newjob.path
+          end
+        end
+      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.8
+  version: 5.33.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-03-14 00:00:00.000000000 Z
+date: 2022-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -292,6 +292,7 @@ files:
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/misc/annotated_module.rb
 - lib/rbbt/util/misc/bgzf.rb
+- lib/rbbt/util/misc/communication.rb
 - lib/rbbt/util/misc/concurrent_stream.rb
 - lib/rbbt/util/misc/development.rb
 - lib/rbbt/util/misc/exceptions.rb
@@ -531,6 +532,7 @@ files:
 - test/rbbt/util/concurrency/test_threads.rb
 - test/rbbt/util/log/test_progress.rb
 - test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_communication.rb
 - test/rbbt/util/misc/test_development.rb
 - test/rbbt/util/misc/test_format.rb
 - test/rbbt/util/misc/test_lock.rb
@@ -611,6 +613,7 @@ test_files:
 - test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/misc/test_format.rb
+- test/rbbt/util/misc/test_communication.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb