Module: Workflow

Includes:
InputModule
Included in:
RemoteWorkflow
Defined in:
lib/rbbt/workflow.rb,
lib/rbbt/workflow/doc.rb,
lib/rbbt/workflow/usage.rb,
lib/rbbt/workflow/accessor.rb,
lib/rbbt/workflow/examples.rb,
lib/rbbt/workflow/util/data.rb,
lib/rbbt/workflow/definition.rb,
lib/rbbt/workflow/util/trace.rb,
lib/rbbt/workflow/dependencies.rb,
lib/rbbt/workflow/util/orchestrator.rb,
lib/rbbt/workflow/integration/cromwell.rb,
lib/rbbt/workflow/integration/nextflow.rb,
lib/rbbt/workflow/step/save_load_inputs.rb

Defined Under Namespace

Modules: Data, DependencyBlock Classes: Orchestrator, TaskNotFoundException

Constant Summary collapse

TAG = 
ENV["RBBT_INPUT_JOBNAME"] == "true" ? :inputs : :hash
DEBUG_JOB_HASH = 
ENV["RBBT_DEBUG_JOB_HASH"] == 'true'
DEFAULT_NAME =

{{{ JOB MANAGEMENT

"Default"
FORGET_DEP_TASKS = 
ENV["RBBT_FORGET_DEP_TASKS"] == "true"
REMOVE_DEP_TASKS = 
ENV["RBBT_REMOVE_DEP_TASKS"] == "true"
OUTPUT_FIELDS = 
%w(outdir output)

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from InputModule

#input

Class Attribute Details

.autoinstall ⇒ Object

Returns the value of attribute autoinstall.



26
27
28
 
# File 'lib/rbbt/workflow.rb', line 26

def autoinstall
  @autoinstall
end

.main ⇒ Object

Returns the value of attribute main.



26
27
28
 
# File 'lib/rbbt/workflow.rb', line 26

def main
  @main
end

.workflow_dir ⇒ Object

Returns the value of attribute workflow_dir.



26
27
28
 
# File 'lib/rbbt/workflow.rb', line 26

def workflow_dir
  @workflow_dir
end

.workflows ⇒ Object

Returns the value of attribute workflows.



26
27
28
 
# File 'lib/rbbt/workflow.rb', line 26

def workflows
  @workflows
end

Instance Attribute Details

#asynchronous_exports ⇒ Object

Returns the value of attribute asynchronous_exports.



229
230
231
 
# File 'lib/rbbt/workflow.rb', line 229

def asynchronous_exports
  @asynchronous_exports
end

#complete_name ⇒ Object

{{{ ATTR DEFAULTS



237
238
239
 
# File 'lib/rbbt/workflow.rb', line 237

def complete_name
  @complete_name
end

#description ⇒ Object

Returns the value of attribute description.



225
226
227
 
# File 'lib/rbbt/workflow.rb', line 225

def description
  @description
end

#documentation ⇒ Object

Returns the value of attribute documentation.



71
72
73
 
# File 'lib/rbbt/workflow/doc.rb', line 71

def documentation
  @documentation
end

#example_dir ⇒ Object

Returns the value of attribute example_dir.



2
3
4
 
# File 'lib/rbbt/workflow/examples.rb', line 2

def example_dir
  @example_dir
end

#exec_exports ⇒ Object

Returns the value of attribute exec_exports.



229
230
231
 
# File 'lib/rbbt/workflow.rb', line 229

def exec_exports
  @exec_exports
end

#helpers ⇒ Object

Returns the value of attribute helpers.



227
228
229
 
# File 'lib/rbbt/workflow.rb', line 227

def helpers
  @helpers
end

#last_task ⇒ Object

Returns the value of attribute last_task.



228
229
230
 
# File 'lib/rbbt/workflow.rb', line 228

def last_task
  @last_task
end

#libdir ⇒ Object

Returns the value of attribute libdir.



226
227
228
 
# File 'lib/rbbt/workflow.rb', line 226

def libdir
  @libdir
end

#load_step_cache ⇒ Object

Returns the value of attribute load_step_cache.



231
232
233
 
# File 'lib/rbbt/workflow.rb', line 231

def load_step_cache
  @load_step_cache
end

#relay_tasks ⇒ Object

Returns the value of attribute relay_tasks.



233
234
235
 
# File 'lib/rbbt/workflow.rb', line 233

def relay_tasks
  @relay_tasks
end

#remote_tasks ⇒ Object

Returns the value of attribute remote_tasks.



232
233
234
 
# File 'lib/rbbt/workflow.rb', line 232

def remote_tasks
  @remote_tasks
end

#step_cache ⇒ Object

Returns the value of attribute step_cache.



230
231
232
 
# File 'lib/rbbt/workflow.rb', line 230

def step_cache
  @step_cache
end

#stream_exports ⇒ Object

Returns the value of attribute stream_exports.



229
230
231
 
# File 'lib/rbbt/workflow.rb', line 229

def stream_exports
  @stream_exports
end

#synchronous_exports ⇒ Object

Returns the value of attribute synchronous_exports.



229
230
231
 
# File 'lib/rbbt/workflow.rb', line 229

def synchronous_exports
  @synchronous_exports
end

#task_dependencies ⇒ Object

Returns the value of attribute task_dependencies.



228
229
230
 
# File 'lib/rbbt/workflow.rb', line 228

def task_dependencies
  @task_dependencies
end

#task_description ⇒ Object

Returns the value of attribute task_description.



228
229
230
 
# File 'lib/rbbt/workflow.rb', line 228

def task_description
  @task_description
end

#tasks ⇒ Object

Returns the value of attribute tasks.



227
228
229
 
# File 'lib/rbbt/workflow.rb', line 227

def tasks
  @tasks
end

#workdir ⇒ Object

Returns the value of attribute workdir.



226
227
228
 
# File 'lib/rbbt/workflow.rb', line 226

def workdir
  @workdir
end

Class Method Details

.__load_step(path) ⇒ Object 



661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
 
# File 'lib/rbbt/workflow.rb', line 661

def self.__load_step(path)
  if Open.remote?(path) || Open.ssh?(path)
    require 'rbbt/workflow/remote_workflow'
    return RemoteWorkflow.load_path path
  end
  step = Step.new path
  relocated = false
  dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
    dep_path = task if dep_path.nil?
    if Open.exists?(dep_path) || Open.exists?(dep_path + '.info') || Open.remote?(dep_path) || Open.ssh?(dep_path)
      Workflow._load_step dep_path
    else
      new_path = relocate(path, dep_path)
      relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
      Workflow._load_step new_path
    end
  end
  step.instance_variable_set("@dependencies", dependencies)
  step.relocated = relocated
  step.load_inputs_from_info
  step
end

._load_step(path) ⇒ Object 



736
737
738
739
740
 
# File 'lib/rbbt/workflow.rb', line 736

def self._load_step(path)
  Persist.memory("STEP", :path => path, :repo => load_step_cache) do
    __load_step(path)
  end
end

.complete_name ⇒ Object 



239
240
241
 
# File 'lib/rbbt/workflow.rb', line 239

def self.complete_name
  @complete_name ||= self.to_s
end

.doc_parse_chunks(str, pattern) ⇒ Object 



21
22
23
24
25
26
27
 
# File 'lib/rbbt/workflow/doc.rb', line 21

def self.doc_parse_chunks(str, pattern)
  parts = str.split(pattern)
  return {} if parts.length < 2
  tasks = Hash[*parts[1..-1].collect{|v| v.strip}]
  tasks.delete_if{|t,d| d.empty?}
  tasks
end

.doc_parse_first_line(str) ⇒ Object 



3
4
5
6
7
8
9
10
 
# File 'lib/rbbt/workflow/doc.rb', line 3

def self.doc_parse_first_line(str)
  if str.match(/^([^\n]*)\n\n(.*)/sm)
    str.replace $2
    $1
  else
    ""
  end
end

.doc_parse_up_to(str, pattern, keep = false) ⇒ Object 



12
13
14
15
16
17
18
19
 
# File 'lib/rbbt/workflow/doc.rb', line 12

def self.doc_parse_up_to(str, pattern, keep = false)
  pre, _pat, _post = str.partition pattern
  if _pat
    [pre, (keep ? _pat << _post : _post)]
  else
    _post
  end
end

.extended(base) ⇒ Object 



35
36
37
38
39
40
 
# File 'lib/rbbt/workflow.rb', line 35

def self.extended(base)
  self.workflows << base
  libdir = Path.caller_lib_dir
  return if libdir.nil?
  base.libdir = Path.setup(libdir).tap{|p| p.resource = base}
end

.fast_load_step(path) ⇒ Object 



684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
 
# File 'lib/rbbt/workflow.rb', line 684

def self.fast_load_step(path)
  if Open.remote?(path) || Open.ssh?(path)
    require 'rbbt/workflow/remote_workflow'
    return RemoteWorkflow.load_path path
  end

  step = Step.new path
  step.dependencies = nil
  class << step
    def dependencies
      @dependencies ||= (self.info[:dependencies] || []).collect do |task,name,dep_path|
        dep = if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
                relocate = false
                Workflow.fast_load_step dep_path
              else
                new_path = Workflow.relocate(path, dep_path)
                relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
                Workflow.fast_load_step new_path
              end
        dep.relocated = relocated
        dep
      end
      @dependencies
    end

    def inputs
      self.load_inputs_from_info unless @inputs
      @inputs
    end

    def dirty?
      false
    end

    def updated?
      true
    end
  end

  if ! Open.exists?(step.info_file)
    begin
      workflow = step.path.split("/")[-3]
      task_name = step.path.split("/")[-2]
      workflow = Kernel.const_get workflow
      step.task = workflow.tasks[task_name.to_sym]
    rescue
      Log.exception $!
    end
  end
  step
end

.get_SOPT(workflow, task) ⇒ Object 



282
283
284
285
286
 
# File 'lib/rbbt/workflow/usage.rb', line 282

def self.get_SOPT(workflow, task)
  workflow = Workflow.require_workflow workflow if String === workflow
  task = workflow.tasks[task.to_sym] if String === task || Symbol === task
  workflow.get_SOPT(task)
end

.init_relay_tasks ⇒ Object 



48
49
50
51
52
 
# File 'lib/rbbt/workflow.rb', line 48

def self.init_relay_tasks
  return if defined? @@init_relay_tasks and @@init_relay_tasks
  @@init_relay_tasks = true
  load_relay_tasks(Rbbt.root.etc.relay_tasks.find) if Rbbt.root.etc.relay_tasks.exists?
end

.init_remote_tasks ⇒ Object 



42
43
44
45
46
 
# File 'lib/rbbt/workflow.rb', line 42

def self.init_remote_tasks
  return if defined? @@init_remote_tasks and @@init_remote_tasks
  @@init_remote_tasks = true
  load_remote_tasks(Rbbt.root.etc.remote_tasks.find) if Rbbt.root.etc.remote_tasks.exists?
end

.installed_workflows ⇒ Object 



87
88
89
90
91
 
# File 'lib/rbbt/workflow.rb', line 87

def self.installed_workflows
  self.workflow_dir['**/workflow.rb'].glob_all.collect do |file|
    File.basename(File.dirname(file))
  end
end

.job_path?(path) ⇒ Boolean

Returns:

  • (Boolean) 


19
20
21
 
# File 'lib/rbbt/workflow/accessor.rb', line 19

def self.job_path?(path)
  path.split("/")[-4] == "jobs"
end

.load_inputs(dir, input_names, input_types) ⇒ Object 



3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
 
# File 'lib/rbbt/workflow/step/save_load_inputs.rb', line 3

def self.load_inputs(dir, input_names, input_types)
  inputs = {}
  if File.exist?(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.exist? 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 = 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 = :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'

      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").collect{|p| Path.setup(p) }
      when :path
        inputs[input.to_sym]  = Path.setup(Open.read(file).strip.split("\n").first)
      when :io
        inputs[input.to_sym] = Open.open(Open.realpath(file))
      when :io_array
        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 :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
      when :step_file
        path = Open.read(file).strip
        step_path, relative = path.match(/(.*)\.files\/(.*)/).values_at 1, 2
        step = Step.new Path.setup(step_path).find
        path = step.file(relative)
        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/
          inputs[input.to_sym]  = Misc.load_yaml(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
        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
        inputs[input.to_sym]  = file.read.to_f
      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)
      name.sub!(/\.as_path$/,'')
      value = Open.read(od)
      Log.debug "Loading override dependency #{ name } as #{value}"
      inputs[name] = value.chomp
    end

    inputs
  end
end

.load_relay_tasks(filename) ⇒ Object 



878
879
880
881
 
# File 'lib/rbbt/workflow.rb', line 878

def self.load_relay_tasks(filename)
  relay_workflow_tasks = Misc.load_yaml(filename)
  Workflow.process_relay_tasks(relay_workflow_tasks)
end

.load_remote_tasks(filename) ⇒ Object 



854
855
856
857
 
# File 'lib/rbbt/workflow.rb', line 854

def self.load_remote_tasks(filename)
  remote_workflow_tasks = Misc.load_yaml(filename)
  Workflow.process_remote_tasks(remote_workflow_tasks)
end

.load_step(path) ⇒ Object 



742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
 
# File 'lib/rbbt/workflow.rb', line 742

def self.load_step(path)
  path = Path.setup(path.dup) unless Path === path

  if ! (Path === path ? path.exists? : File.exist?(path)) && path.split("/").length == 3 
    new_path = Rbbt.var.jobs[path]
    if new_path.exists? || new_path.set_extension('info').exists?
      path = new_path
    end
  end

  path = path.find if Path === path

  begin
    _load_step(path)
  ensure
    load_step_cache.clear
  end
end

.load_step_cache ⇒ Object 



338
339
340
 
# File 'lib/rbbt/workflow.rb', line 338

def self.load_step_cache
  Thread.current[:load_step_cache] ||= {}
end

.load_workflow_file(filename) ⇒ Object 



69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
 
# File 'lib/rbbt/workflow.rb', line 69

def self.load_workflow_file(filename)
  begin

    load_workflow_libdir(filename)

    filename = File.expand_path(filename)

    Rbbt.add_version(filename)

    require filename
    Log.debug{"Workflow loaded from: #{ filename }"}
    return true
  rescue Exception
    Log.warn{"Error loading workflow: #{ filename }"}
    raise $!
  end
end

.load_workflow_libdir(filename) ⇒ Object 



61
62
63
64
65
66
67
 
# File 'lib/rbbt/workflow.rb', line 61

def self.load_workflow_libdir(filename)
  workflow_lib_dir = File.join(File.dirname(File.expand_path(filename)), 'lib')
  if File.directory? workflow_lib_dir
    Log.debug "Adding workflow lib directory to LOAD_PATH: #{workflow_lib_dir}"
    $LOAD_PATH.unshift(workflow_lib_dir)
  end
end

.local_workflow_filename(wf_name) ⇒ Object 



109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
 
# File 'lib/rbbt/workflow.rb', line 109

def self.local_workflow_filename(wf_name)
  filename = nil

  if Path === wf_name
    case
      # Points to workflow file
    when ((File.exist?(wf_name.find) and not File.directory?(wf_name.find)) or File.exist?(wf_name.find + '.rb')) 
      filename = wf_name.find

      # Points to workflow dir
    when (File.exist?(wf_name.find) and File.directory?(wf_name.find) and File.exist?(File.join(wf_name.find, 'workflow.rb')))
      filename = wf_name['workflow.rb'].find
    end

  else
    if ((File.exist?(wf_name) and not File.directory?(wf_name)) or File.exist?(wf_name + '.rb'))
      filename = (wf_name =~ /\.?\//) ? wf_name : "./" << wf_name 
    else
      filename = workflow_dir[wf_name]['workflow.rb'].find
    end
  end

  if filename.nil? or not File.exist?(filename)
    wf_name_snake = Misc.snake_case(wf_name)
    return local_workflow_filename(wf_name_snake) if wf_name_snake != wf_name
  end

  filename
end

.nextflow_file_params(file) ⇒ Object 



45
46
47
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 45

def self.nextflow_file_params(file)
  Open.read(file).scan(/params\.\w+/).collect{|p| p.split(".").last}.uniq
end

.nextflow_includes(file) ⇒ Object 



49
50
51
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 49

def self.nextflow_includes(file)
  Open.read(file).scan(/^include\s*{\s*([^\s]*?)\s+.*?}\s*from\s+["'](.*?)["'](?:\s*params.*)?/).collect{|p| p}.uniq
end

.nextflow_recursive_params(file) ⇒ Object 



53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 53

def self.nextflow_recursive_params(file)
  params = nextflow_file_params(file)
  dir = File.dirname(file)
  nextflow_includes(file).inject(params) do |params,info|
    name_str, included_file = info
    included_file = File.join(dir, included_file)
    included_file += '.nf' unless File.exist?(included_file) || ! File.exist?(included_file + '.nf')
    name_str.split(";").each do |name|
      name = name.strip
      begin
        include_params = nextflow_recursive_params(included_file).collect{|p| [p,name] * "-"}
        params += include_params
      rescue
      end
    end
    params
  end
end

.parse_nextflow_schema(file) ⇒ Object 



5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 5

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

.parse_workflow_doc(doc) ⇒ Object 



29
30
31
32
33
34
35
 
# File 'lib/rbbt/workflow/doc.rb', line 29

def self.parse_workflow_doc(doc)
  title = doc_parse_first_line doc
  description, task_info = doc_parse_up_to doc, /^# Tasks/i
  task_description, tasks = doc_parse_up_to task_info, /^##/, true
  tasks = doc_parse_chunks tasks, /^## (.*)/ 
  {:title => title.strip, :description => description.strip, :task_description => task_description.strip, :tasks => tasks}
end

.plot_trace_job_times(data, plot, width = 800, height = 800) ⇒ Object 



82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
 
# File 'lib/rbbt/workflow/util/trace.rb', line 82

def self.plot_trace_job_times(data, plot, width=800, height=800)
  data.R <<-EOF, [:svg]
rbbt.require('dplyr')
rbbt.require('tidyr')
rbbt.require('ggplot2')

names(data) <- make.names(names(data))
data$id = data$Code
data$content = data$Task
data$start = data$Start
data$end = data$End
data$Project = data$Workflow

tasks = data

#theme_gantt <- function(base_size=11, base_family="Source Sans Pro Light") {
theme_gantt <- function(base_size=11, base_family="Sans Serif") {
ret <- theme_bw(base_size, base_family) %+replace%
  theme(panel.background = element_rect(fill="#ffffff", colour=NA),
        axis.title.x=element_text(vjust=-0.2), axis.title.y=element_text(vjust=1.5),
        title=element_text(vjust=1.2, family="Source Sans Pro Semibold"),
        panel.border = element_blank(), axis.line=element_blank(),
        panel.grid.minor=element_blank(),
        panel.grid.major.y = element_blank(),
        panel.grid.major.x = element_line(size=0.5, colour="grey80"),
        axis.ticks=element_blank(),
        legend.position="bottom", 
        axis.title=element_text(size=rel(1.2), family="Source Sans Pro Semibold"),
        strip.text=element_text(size=rel(1.5), family="Source Sans Pro Semibold"),
        strip.background=element_rect(fill="#ffffff", colour=NA),
        panel.spacing.y=unit(1.5, "lines"),
        legend.key = element_blank())

ret
}

tasks.long <- tasks %>%
gather(date.type, task.date, -c(Code,Project, Task, id, Start.second, End.second)) %>%
arrange(date.type, task.date) %>%
mutate(id = factor(id, levels=rev(unique(id)), ordered=TRUE))

x.breaks <- seq(length(tasks$Task) + 0.5 - 3, 0, by=-3)

timeline <- ggplot(tasks.long, aes(y=id, yend=id, x=Start.second, xend=End.second, colour=Task)) + 
geom_segment() + 
geom_vline(xintercept=x.breaks, colour="grey80", linetype="dotted") + 
guides(colour=guide_legend(title=NULL)) +
labs(x=NULL, y=NULL) + 
theme_gantt() + theme(axis.text.x=element_text(angle=45, hjust=1))

rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, pointsize=6)
  EOF
end

.process_relay_tasks(relay_tasks) ⇒ Object 



859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
 
# File 'lib/rbbt/workflow.rb', line 859

def self.process_relay_tasks(relay_tasks)
  require 'rbbt/workflow/remote_workflow'
  relay_tasks.each do |workflow, servers|
    wf = Workflow.require_workflow workflow
    wf.relay_tasks ||= {}
    IndiferentHash.setup wf.relay_tasks
    servers.each do |server, tasks|
      case tasks
      when Array
        tasks.each do |task|
          wf.relay_tasks[task.to_sym] = [server, {:migrate => :true}]
        end
      else
        wf.relay_tasks[tasks.to_sym] = [server, {:migrate => :true}]
      end
    end
  end
end

.process_remote_tasks(remote_tasks) ⇒ Object 



838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
 
# File 'lib/rbbt/workflow.rb', line 838

def self.process_remote_tasks(remote_tasks)
  require 'rbbt/workflow/remote_workflow'
  remote_tasks.each do |workflow, info|
    wf = Workflow.require_workflow workflow
    wf.remote_tasks ||= {}
    IndiferentHash.setup wf.remote_tasks
    info.each do |remote, tasks|
      remote_wf = RemoteWorkflow.new remote, workflow
      tasks.each do |task|
        Log.debug "Add remote task #{task} in #{wf} using #{remote_wf.url}"
        wf.remote_tasks[task.to_sym] = remote_wf
      end
    end
  end
end

.relocate(real, other) ⇒ Object 



640
641
642
643
644
645
646
647
 
# File 'lib/rbbt/workflow.rb', line 640

def  self.relocate(real, other)
  preal = real.split(/\/+/)
  pother = other.split(/\/+/)
  end_part = pother[-3..-1] * "/"
  new_path = preal[0..-4] * "/" << "/" << end_part
  return new_path if File.exist?(new_path) || File.exist?(new_path + '.info')
  Rbbt.var.jobs[end_part].find
end

.relocate_array(real, list) ⇒ Object 



625
626
627
628
629
630
631
632
633
634
635
636
637
638
 
# File 'lib/rbbt/workflow.rb', line 625

def  self.relocate_array(real, list)
  preal = real.split(/\/+/)
  prefix = preal[0..-4] * "/" 
  list.collect do |other|
    pother = other.split(/\/+/)
    end_part = pother[-3..-1] * "/"
    new_path = prefix + "/" << end_part
    if File.exist? new_path
      new_path 
    else
      Rbbt.var.jobs[end_part].find
    end
  end
end

.relocate_dependency(main, dep) ⇒ Object 



649
650
651
652
653
654
655
656
657
658
659
 
# File 'lib/rbbt/workflow.rb', line 649

def self.relocate_dependency(main, dep)
  dep_path = dep.path
  path = main.path
  if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
    dep
  else
    new_path = relocate(path, dep_path)
    relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
    Workflow._load_step new_path
  end
end

.require_local_workflow(wf_name) ⇒ Object 



139
140
141
142
143
144
145
146
147
148
 
# File 'lib/rbbt/workflow.rb', line 139

def self.require_local_workflow(wf_name)

  filename = local_workflow_filename(wf_name)

  if filename and File.exist?(filename)
    load_workflow_file filename
  else
    return false
  end
end

.require_remote_workflow(wf_name, url) ⇒ Object 



56
57
58
59
 
# File 'lib/rbbt/workflow.rb', line 56

def self.require_remote_workflow(wf_name, url)
  require 'rbbt/workflow/remote_workflow'
  eval "Object::#{wf_name.split("+").first} = RemoteWorkflow.new '#{ url }', '#{wf_name}'"
end

.require_workflow(wf_name, force_local = false) ⇒ Object 



150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
 
# File 'lib/rbbt/workflow.rb', line 150

def self.require_workflow(wf_name, force_local=false)
  Workflow.init_remote_tasks
  Workflow.init_relay_tasks
  # Already loaded
  begin
    workflow = Misc.string2const wf_name
    Log.debug{"Workflow #{ wf_name } already loaded"}
    return workflow
  rescue Exception
  end

  # Load remotely
  if not force_local and Rbbt.etc.remote_workflows.exists?
    remote_workflows = Rbbt.etc.remote_workflows.yaml
    if Hash === remote_workflows and remote_workflows.include?(wf_name)
      url = remote_workflows[wf_name]
      begin
        return require_remote_workflow(wf_name, url)
      ensure
        Log.debug{"Workflow #{ wf_name } loaded remotely: #{ url }"}
      end
    end
  end

  if Open.remote?(wf_name) or Open.ssh?(wf_name)
    url = wf_name

    if Open.ssh?(wf_name)
      wf_name = File.basename(url.split(":").last)
    else
      wf_name = File.basename(url)
    end

    begin
      return require_remote_workflow(wf_name, url)
    ensure
      Log.debug{"Workflow #{ wf_name } loaded remotely: #{ url }"}
    end
  end

  # Load locally

  if wf_name =~ /::\w+$/
    clean_name = wf_name.sub(/::.*/,'')  
    Log.info{"Looking for '#{wf_name}' in '#{clean_name}'"}
    require_workflow clean_name
    workflow = Misc.string2const Misc.camel_case(wf_name)
    workflow.load_documentation
    return workflow
  end

  Log.high{"Loading workflow #{wf_name}"}

  first = nil
  wf_name.split("+").each do |wf_name|
    self.main = nil
    require_local_workflow(wf_name) or 
      (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")

    workflow = begin
                 Misc.string2const Misc.camel_case(wf_name)
               rescue
                 self.main || Workflow.workflows.last 
               end
    workflow.load_documentation


    first ||= workflow
  end

  first.complete_name = wf_name

  return first
end

.resolve_locals(inputs) ⇒ Object 



386
387
388
389
390
391
392
393
394
395
396
397
 
# File 'lib/rbbt/workflow.rb', line 386

def self.resolve_locals(inputs)
  inputs.each do |name, value|
    if (String === value and value =~ /^local:(.*?):(.*)/) or 
      (Array === value and value.length == 1 and value.first =~ /^local:(.*?):(.*)/) or
      (TSV === value and value.size == 1 and value.keys.first =~ /^local:(.*?):(.*)/)
      task_name = $1
      jobname = $2
      value = load_id(File.join(task_name, jobname)).load
      inputs[name] = value
    end
  end 
end

.trace(seed_jobs, options = {}) ⇒ Object 



187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
 
# File 'lib/rbbt/workflow/util/trace.rb', line 187

def self.trace(seed_jobs, options = {})
  jobs = []
  seed_jobs.each do |step|
    jobs += step.rec_dependencies + [step]
    step.info[:archived_info].each do |path,ainfo|
      next unless Hash === ainfo
      archived_step = Step.new path

      archived_step.define_singleton_method :info do
        ainfo
      end

      #class << archived_step
      #  self
      #end.define_method :info do
      #  ainfo
      #end

      jobs << archived_step
    end if step.info[:archived_info]

  end

  jobs = jobs.uniq.sort_by{|job| [job, job.info]; t = job.info[:started] || Open.mtime(job.path) || Time.now; Time === t ? t : Time.parse(t) }

  data = trace_job_times(jobs, options[:fix_gap])

  report_keys = options[:report_keys] || ""
  report_keys = report_keys.split(/,\s*/) if String === report_keys
  summary = trace_job_summary(jobs, report_keys)

  raise "No jobs to process" if data.size == 0

  plot, size, width, height = options.values_at :plot, :size, :width, :height

  size = 800 if size.nil?
  width = size.to_i * 2 if width.nil?
  height = size  if height.nil?

  plot_trace_job_times(data, plot, width, height) if plot

  if options[:plot_data]
    data
  else
    summary
  end

end

.trace_job_summary(jobs, report_keys = []) ⇒ Object 



136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
 
# File 'lib/rbbt/workflow/util/trace.rb', line 136

def self.trace_job_summary(jobs, report_keys = [])
  tasks_info = {}

  report_keys = report_keys.collect{|k| k.to_s}

  jobs.each do |dep|
    next unless dep.info[:done]
    task = [dep.workflow, dep.task_name].compact.collect{|s| s.to_s} * "#"
    info = tasks_info[task] ||= IndiferentHash.setup({})
    dep_info = IndiferentHash.setup(dep.info)

    ddone = dep_info[:done]
    started = dep_info[:started]

    started = Time.parse started if String === started
    ddone = Time.parse ddone if String === ddone

    time = ddone - started
    info[:time] ||= []
    info[:time] << time

    report_keys.each do |key|
      info[key] = dep_info[key] 
    end

    dep.info[:config_keys].each do |kinfo| 
      key, value, tokens = kinfo

      info[key.to_s] = value if report_keys.include? key.to_s
    end if dep.info[:config_keys]
  end

  summary = TSV.setup({}, "Task~Calls,Avg. Time,Total Time#:type=:list")

  tasks_info.each do |task, info|
    time_lists = info[:time]
    avg_time = Misc.mean(time_lists).to_i
    total_time = Misc.sum(time_lists).to_i
    calls = time_lists.length
    summary[task] = [calls, avg_time, total_time]
  end

  report_keys.each do |key|
    summary.add_field Misc.humanize(key) do |task|
      tasks_info[task][key]
    end
  end if Array === report_keys && report_keys.any?

  summary
end

.trace_job_times(jobs, fix_gap = false) ⇒ Object 



4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
 
# File 'lib/rbbt/workflow/util/trace.rb', line 4

def self.trace_job_times(jobs, fix_gap = false)
  data = TSV.setup({}, "Job~Code,Workflow,Task,Start,End#:type=:list")
  min_start = nil
  max_done = nil
  jobs.each do |job|
    next unless job.info[:done]
    started = job.info[:started]
    ddone = job.info[:done]

    started = Time.parse started if String === started
    ddone = Time.parse ddone if String === ddone

    code = [job.workflow, job.task_name].compact.collect{|s| s.to_s} * " · "
    code = job.name + " - " + code

    data[job.path] = [code,job.workflow.to_s, job.task_name, started, ddone]
    if min_start.nil?
      min_start = started
    else
      min_start = started if started < min_start
    end

    if max_done.nil?
      max_done = ddone
    else
      max_done = ddone if ddone > max_done
    end
  end

  data.add_field "Start.second" do |k,value|
    value["Start"] - min_start
  end

  data.add_field "End.second" do |k,value|
    value["End"] - min_start
  end

  if fix_gap
    ranges = []
    data.through do |k,values|
      start, eend = values.values_at "Start.second", "End.second"

      ranges << (start..eend)
    end

    gaps = {}
    last = nil
    Misc.collapse_ranges(ranges).each do |range|
      start = range.begin
      eend = range.end
      if last
        gaps[last] = start - last
      end
      last = eend
    end

    data.process "End.second" do |value,k,values|
      gap = Misc.sum(gaps.select{|pos,size| pos < values["Start.second"]}.collect{|pos,size| size})
      value - gap
    end

    data.process "Start.second" do |value,k,values|
      gap = Misc.sum(gaps.select{|pos,size| pos < values["Start.second"]}.collect{|pos,size| size})
      value - gap
    end

    total_gaps = Misc.sum(gaps.collect{|k,v| v})
    Log.info "Total gaps: #{total_gaps} seconds"
  end

  start = data.column("Start.second").values.flatten.collect{|v| v.to_f}.min
  eend = data.column("End.second").values.flatten.collect{|v| v.to_f}.max
  total = eend - start unless eend.nil? || start.nil?
  Log.info "Total time elapsed: #{total} seconds" if total

  data
end

.transplant(listed, real, other) ⇒ Object 



605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
 
# File 'lib/rbbt/workflow.rb', line 605

def self.transplant(listed, real, other)
  if listed.nil?
    parts = real.split("/")
    other_parts = other.split("/")
    listed = (other_parts[0..-4] + parts[-3..-1]) * "/"
  end

  sl = listed.split("/", -1)
  so = other.split("/", -1)
  sr = real.split("/", -1)
  prefix = [] 
  while true
    break if sl[0] != so[0]
    cl = sl.shift
    co = so.shift
    prefix << cl
  end
  File.join(sr - sl + so)
end

.workdir ⇒ Object 



248
249
250
251
252
253
254
 
# File 'lib/rbbt/workflow.rb', line 248

def self.workdir
  @@workdir ||= if defined? Rbbt
                  Rbbt.var.jobs
                else
                  Path.setup('var/jobs')
                end
end

.workdir=(path) ⇒ Object 



243
244
245
246
 
# File 'lib/rbbt/workflow.rb', line 243

def self.workdir=(path)
  path = Path.setup path.dup unless Path === path
  @@workdir = path
end

.workflow_for(path) ⇒ Object 



204
205
206
207
208
209
210
 
# File 'lib/rbbt/workflow/accessor.rb', line 204

def self.workflow_for(path)
  begin
    Kernel.const_get File.dirname(File.dirname(path))
  rescue
    nil
  end
end

Instance Method Details

#__job(taskname, jobname = nil, inputs = {}) ⇒ Object 



412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
 
# File 'lib/rbbt/workflow.rb', line 412

def __job(taskname, jobname = nil, inputs = {})
  taskname = taskname.to_sym
  return remote_tasks[taskname].job(taskname, jobname, inputs) if remote_tasks and remote_tasks.include? taskname

  task = tasks[taskname]
  raise "Task not found: #{ taskname }" if task.nil?

  inputs = IndiferentHash.setup(inputs)

  not_overriden = inputs.delete :not_overriden 
  if not_overriden
    inputs[:not_overriden] = :not_overriden_dep
  end

  Workflow.resolve_locals(inputs)

  task_info = task_info(taskname)
  task_inputs = task_info[:inputs]
  #defaults = IndiferentHash.setup(task_info[:input_defaults]).merge(task.input_defaults)
  all_defaults = IndiferentHash.setup(task_info[:input_defaults])
  defaults = IndiferentHash.setup(task.input_defaults)

  missing_inputs = []
  task.required_inputs.each do |input|
    missing_inputs << input if inputs[input].nil?
  end if task.required_inputs

  if missing_inputs.length == 1
    raise ParameterException, "Input '#{missing_inputs.first}' is required but was not provided or is nil"
  end

  if missing_inputs.length > 1
    raise ParameterException, "Inputs #{Misc.humanize_list(missing_inputs)} are required but were not provided or are nil"
  end

  # jobname => true sets the value of the input to the name of the job
  if task.input_options
    jobname_input = task.input_options.select{|i,o| o[:jobname] }.collect{|i,o| i }.first
  else
    jobname_input = nil 
  end

  if jobname_input && inputs[jobname_input].nil?
    inputs[jobname_input] = jobname || DEFAULT_NAME
  end

  real_inputs = {}

  inputs.each do |k,v|
    next unless (task_inputs.include?(k.to_sym) or task_inputs.include?(k.to_s))
    default = all_defaults[k]
    next if default == v 
    next if (String === default and Symbol === v and v.to_s == default)
    next if (Symbol === default and String === v and v == default.to_s)
    real_inputs[k.to_sym] = v 
  end

  jobname_input_value = inputs[jobname_input] || all_defaults[jobname_input]
  if jobname_input && jobname.nil? && String === jobname_input_value && ! jobname_input_value.include?('/')
    jobname = jobname_input_value
  end

  jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?

  dependencies, overriden = real_dependencies(task, jobname, defaults.merge(inputs), task_dependencies[taskname] || [])

  #overriden_deps        = dependencies.select{|d| Symbol === d.overriden }
  #overriden_target_deps = overriden_deps.select{|d| TrueClass === d.overriden }

  extension = task.extension

  if extension == :dep_task
    extension = nil
    if dependencies.any?
      dep_basename = File.basename(dependencies.last.path)
      if dep_basename.include? "."
        parts = dep_basename.split(".")
        extension = [parts.pop]
        while parts.length > 1 && parts.last.length <= 4
          extension << parts.pop
        end
        extension = extension.reverse * "."
      end
    end
  end

  #overriden = true if dependencies.select{|d| d.overriden && d.clean_name != d.name }.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?
    step_path = step_path taskname, jobname, [], [], extension
  else
    step_path = step_path taskname, jobname, input_values, dependencies, extension
  end

  job = get_job_step step_path, task, input_values, dependencies
  job.workflow = self
  job.overriden = overriden if job.overriden.nil?
  job.clean_name = jobname

  #iif [job, not_overriden]
  #case not_overriden 
  #when TrueClass
  #  job.overriden = false
  #when :not_overriden_dep
  #  job.overriden = true if overriden_target_deps.any?
  #else
  #  job.overriden = true if overriden_deps.any?
  #end

  job.real_inputs = real_inputs.keys
  job
end

#_job(taskname, jobname = nil, inputs = {}) ⇒ Object 



527
528
529
530
531
532
533
534
535
536
 
# File 'lib/rbbt/workflow.rb', line 527

def _job(taskname, jobname = nil, inputs = {})

  task_info = task_info(taskname)
  task_inputs = task_info[:inputs]
  persist_inputs = inputs.values_at(*task_inputs)
  persist_inputs += inputs.values_at(*inputs.keys.select{|k| String === k && k.include?("#") }.sort)
  Persist.memory("STEP", :workflow => self.to_s, :taskname => taskname, :jobname => jobname, :inputs => persist_inputs, :repo => step_cache) do
    __job(taskname, jobname, inputs)
  end
end

#_prov_tasks(tree) ⇒ Object 



100
101
102
103
104
105
106
107
108
109
110
111
 
# File 'lib/rbbt/workflow/usage.rb', line 100

def _prov_tasks(tree)
  tasks = [] 
  heap = [tree]
  while heap.any?
    t = heap.pop
    t.each do |k,v|
      tasks << k
      heap << v
    end
  end
  tasks
end

#add_remote_tasks(remote_tasks) ⇒ Object 



830
831
832
833
834
835
836
 
# File 'lib/rbbt/workflow.rb', line 830

def add_remote_tasks(remote_tasks)
  remote_tasks.each do |remote, tasks|
    tasks.each do |task|
      self.remote_tasks[task.to_f] = remote
    end
  end
end

#all_exports ⇒ Object 



375
376
377
 
# File 'lib/rbbt/workflow.rb', line 375

def all_exports
  @all_exports ||= asynchronous_exports + synchronous_exports + exec_exports + stream_exports
end

#assign_dep_inputs(_inputs, options, all_d, task_info) ⇒ Object 



106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
 
# File 'lib/rbbt/workflow/dependencies.rb', line 106

def assign_dep_inputs(_inputs, options, all_d, task_info)
  IndiferentHash.setup(_inputs)

  options.each{|i,v|
    next if i == :compute or i == "compute"
    case v
    when :compute
      compute = v
    when Symbol
      rec_dependency = all_d.flatten.select{|d| d.task_name.to_sym == v }.first

      if rec_dependency.nil?
        if _inputs.include?(v)
          #_inputs[i] = _inputs.delete(v)
          _inputs[i] = _inputs[v] unless _inputs.include? i #_inputs.delete(v)
        else
          _inputs[i] = v unless _inputs.include? i
        end
      else
        input_options = task_info[:input_options][i] || {}

        #ToDo why was this always true?
        if input_options[:stream] or true
          #rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
          _inputs[i] = rec_dependency
        else
          rec_dependency.abort if rec_dependency.streaming? and not rec_dependency.running?
          rec_dependency.clean if rec_dependency.error? or rec_dependency.aborted?
          if rec_dependency.streaming? and rec_dependency.running?
            _inputs[i] = rec_dependency.join.load
          else
            rec_dependency.run(true)
            rec_dependency.join
            _inputs[i] = rec_dependency.load
          end
        end
      end
    else
      _inputs[i] = v
    end
  } if options

  _inputs
end

#dep(*dependency, &block) ⇒ Object 



50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
 
# File 'lib/rbbt/workflow/definition.rb', line 50

def dep(*dependency, &block)
  @dependencies ||= []
  dependency = [tasks.keys.last] if dependency.empty? && ! block_given?
  if block_given?
    if dependency.any?

      wf, task_name, options = dependency
      options, task_name = task_name, nil if Hash === task_name
      options, wf = wf, nil if Hash === wf
      task_name, wf = wf, self if task_name.nil?

      DependencyBlock.setup block, [wf, task_name, options] 
    end
    @dependencies << block
  else
    if Module === dependency.first or 
      (defined? RemoteWorkflow and RemoteWorkflow === dependency.first) or
      Hash === dependency.last

      dependency = ([self] + dependency) unless Module === dependency.first || (defined?(RemoteWorkflow) && RemoteWorkflow === dependency.first)
      @dependencies << dependency
    else
      @dependencies.concat dependency
    end
  end
end

#dep_task(name, workflow, oname, *rest, &block) ⇒ Object Also known as: task_alias 



79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
 
# File 'lib/rbbt/workflow/definition.rb', line 79

def dep_task(name, workflow, oname, *rest, &block)
  dep(workflow, oname, *rest, &block) 
  extension :dep_task unless @extension
  returns workflow.tasks[oname].result_description if workflow.tasks.include?(oname) unless @result_description 
  task name do
    raise RbbtException, "dep_task does not have any dependencies" if dependencies.empty?
    Step.wait_for_jobs dependencies.select{|d| d.streaming? }
    dep = dependencies.last
    dep.join
    raise dep.get_exception if dep.error?
    raise Aborted, "Aborted dependency #{dep.path}" if dep.aborted?
    set_info :result_type, dep.info[:result_type]
    forget = config :forget_dep_tasks, "forget_dep_tasks", :default => FORGET_DEP_TASKS
    if forget
      remove = config :remove_dep_tasks, "remove_dep_tasks", :default => REMOVE_DEP_TASKS

      self.archive_deps
      self.copy_files_dir
      self.dependencies = self.dependencies - [dep]
      Open.rm_rf self.files_dir if Open.exist? self.files_dir
      FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist?(dep.files_dir)

      if dep.overriden || ! Workflow.job_path?(dep.path)
        Open.link dep.path, self.tmp_path
      else
        Open.ln_h dep.path, self.tmp_path

        case remove.to_s
        when 'true'
          dep.clean
        when 'recursive'
          (dep.dependencies + dep.rec_dependencies).uniq.each do |d|
            next if d.overriden
            d.clean unless config(:remove_dep, d.task_signature, d.task_name, d.workflow.to_s, :default => true).to_s == 'false'
          end
          dep.clean unless config(:remove_dep, dep.task_signature, dep.task_name, dep.workflow.to_s, :default => true).to_s == 'false'
        end 
      end
    else
      if Open.exists?(dep.files_dir)
        Open.rm_rf self.files_dir 
        Open.link dep.files_dir, self.files_dir
      end
      if defined?(RemoteStep) && RemoteStep === dep
        Open.write(self.tmp_path, Open.read(dep.path))
      else
        Open.link dep.path, self.path
      end
    end
    nil
  end
end

#dep_tree(name, seen = []) ⇒ Object 



72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
 
# File 'lib/rbbt/workflow/usage.rb', line 72

def dep_tree(name, seen = [])
  @dep_tree ||= {}
  @dep_tree[name] ||= begin
                      dep_tree = {}
                      self.task_dependencies[name.to_sym].reverse.each do |dep|
                        next if seen.include? dep
                        seen << dep
                        dep = dep.first if Array === dep && dep.length == 1
                        dep = dep.dependency if DependencyBlock === dep

                        workflow, task = case dep
                                         when Array
                                           dep.values_at 0, 1
                                         when Symbol, String
                                           [self, dep]
                                         else
                                           next
                                         end


                        key = [workflow, task]

                        dep_tree[key] = workflow.dep_tree(task, seen)
                      end if name && self.task_dependencies[name.to_sym]
                      dep_tree
                    end
end

#desc(description) ⇒ Object 



34
35
36
 
# File 'lib/rbbt/workflow/definition.rb', line 34

def desc(description)
  @description = description
end

#doc(task = nil, abridge = false) ⇒ Object 



163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
 
# File 'lib/rbbt/workflow/usage.rb', line 163

def doc(task = nil, abridge = false)

  if task.nil?
    puts Log.color :magenta, self.to_s 
    puts Log.color :magenta, "=" * self.to_s.length

    if self.documentation[:title] and not self.documentation[:title].empty?
      puts
      puts Misc.format_paragraph self.documentation[:title] 
    end

    if self.documentation[:description] and not self.documentation[:description].empty?
      puts
      puts Misc.format_paragraph self.documentation[:description] 
    end
    puts

    puts Log.color :magenta, "## TASKS"
    if self.documentation[:task_description] and not self.documentation[:task_description].empty?
      puts
      puts Misc.format_paragraph self.documentation[:task_description] 
    end
    puts

    final = Set.new
    not_final = Set.new
    tasks.each do |name,task|
      tree = dep_tree(name)
      not_final += tree.keys
      final << name unless not_final.include?(name)
    end

    not_final.each do |p|
      final -= [p.last]
    end

    tasks.each do |name,task|
      description = task.description || ""
      description = description.split("\n\n").first

      next if abridge && ! final.include?(name)
      puts Misc.format_definition_list_item(name.to_s, description, Log.tty_size || 80, 30, :yellow)

      prov_string = prov_string(dep_tree(name))
      puts Misc.format_paragraph Log.color(:blue, "->" + prov_string) if prov_string && ! prov_string.empty?
    end

  else

    if Task === task
      task_name = task.name
    else
      task_name = task
      task = self.tasks[task_name]
    end

    #dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name[1].to_sym] : self.tasks[dep_name.to_sym]}
    task.doc(self, self.rec_dependencies(task_name))

    dep_tree = {[self, task_name] => dep_tree(task_name)}
    prov_tree = prov_tree(dep_tree)
    if prov_tree && ! prov_tree.empty? && prov_tree.split("\n").length > 2

      puts Log.color :magenta, "## DEPENDENCY GRAPH (abridged)"
      puts
      prov_tree.split("\n").each do |line|
        next if line.strip.empty?
        if m = line.match(/^( *)(\w+?)#(\w*)/i)
            offset, workflow, task_name =  m.values_at 1, 2, 3
          puts [offset, Log.color(:magenta, workflow), "#", Log.color(:yellow, task_name)] * ""
        else
          puts Log.color :blue, line 
        end
      end
      puts
    end

    if self.examples.include? task_name
      self.examples[task_name].each do |example|

        puts Log.color(:magenta, "Example ") << Log.color(:green, example) + " -- " + Log.color(:blue, example_dir[task_name][example])

        inputs = self.example(task_name, example)

        inputs.each do |input, type, file|
          case type
          when :tsv, :array, :text, :file
            lines = file.read.split("\n")
            head = lines[0..5].compact * "\n\n"
            head = head[0..500]
            puts Misc.format_definition_list_item(input, head, 1000, -1, :blue).gsub(/\n\s*\n/,"\n") 
            puts '...' if lines.length > 6
          else
            puts Misc.format_definition_list_item(input, file.read, Log.tty_size, 20, :blue)
          end
        end
        puts
      end
    end
  end
end

#documentation_markdown ⇒ Object 



37
38
39
40
41
42
43
44
45
46
 
# File 'lib/rbbt/workflow/doc.rb', line 37

def documentation_markdown
  return "" if @libdir.nil?
  file = @libdir['workflow.md'].find
  file = @libdir['README.md'].find unless file.exists?
  if file.exists?
    file.read
  else
    ""
  end
end

#documented_tasks ⇒ Object 



379
380
381
 
# File 'lib/rbbt/workflow.rb', line 379

def documented_tasks
  tasks.select{|k,v| v.description && ! v.description.empty? }.collect{|k,v| k }
end

#example(task_name, example) ⇒ Object 



21
22
23
24
25
26
 
# File 'lib/rbbt/workflow/examples.rb', line 21

def example(task_name, example)
  task_info(task_name.to_sym)[:input_types].collect do |input,type|
    next unless example_dir[task_name][example][input].exists?
    [input, type, example_dir[task_name][example][input].find]
  end.compact
end

#example_inputs(task_name, example) ⇒ Object

case type

  when :tsv, :array, :text
    Log.debug "Pointing #{ input } to #{file}"
    inputs[input.to_sym]  = 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

end



47
48
49
50
51
 
# File 'lib/rbbt/workflow/examples.rb', line 47

def example_inputs(task_name, example)
  dir = example_dir[task_name][example]
  info = self.task_info(task_name)
  Workflow.load_inputs(dir, info[:inputs], info[:input_types])
end

#example_step(task_name, example = "Example", new_inputs = {}) ⇒ Object 



53
54
55
56
57
58
59
60
61
62
 
# File 'lib/rbbt/workflow/examples.rb', line 53

def example_step(task_name, example="Example", new_inputs = {})
  inputs = example_inputs(task_name, example)

  if new_inputs and new_inputs.any?
    IndiferentHash.setup(new_inputs)
    inputs = inputs.merge(new_inputs)
  end

  self.job(task_name, example, inputs)
end

#examples ⇒ Object 



8
9
10
11
12
13
14
15
16
17
18
19
 
# File 'lib/rbbt/workflow/examples.rb', line 8

def examples
  return {} unless self.libdir.examples.exists?
  examples = {}
  example_dir.glob("*/*").each do |example_dir|
    example = File.basename(example_dir)
    task_name = File.basename(File.dirname(example_dir))
    examples[task_name] ||= []
    examples[task_name] << example
  end
  IndiferentHash.setup examples
  examples
end

#export_asynchronous(*names) ⇒ Object Also known as: export 



207
208
209
210
211
212
 
# File 'lib/rbbt/workflow/definition.rb', line 207

def export_asynchronous(*names)
  unexport *names
  asynchronous_exports.concat names
  asynchronous_exports.uniq!
  asynchronous_exports
end

#export_exec(*names) ⇒ Object 



193
194
195
196
197
198
 
# File 'lib/rbbt/workflow/definition.rb', line 193

def export_exec(*names)
  unexport *names
  exec_exports.concat names
  exec_exports.uniq!
  exec_exports
end

#export_stream(*names) ⇒ Object 



214
215
216
217
218
219
 
# File 'lib/rbbt/workflow/definition.rb', line 214

def export_stream(*names)
  unexport *names
  stream_exports.concat names
  stream_exports.uniq!
  stream_exports
end

#export_synchronous(*names) ⇒ Object 



200
201
202
203
204
205
 
# File 'lib/rbbt/workflow/definition.rb', line 200

def export_synchronous(*names)
  unexport *names
  synchronous_exports.concat names
  synchronous_exports.uniq!
  synchronous_exports
end

#extension(extension) ⇒ Object 



38
39
40
 
# File 'lib/rbbt/workflow/definition.rb', line 38

def extension(extension)
  @extension = extension
end

#fast_load_id(id) ⇒ Object 



773
774
775
776
777
778
779
780
781
782
 
# File 'lib/rbbt/workflow.rb', line 773

def fast_load_id(id)
  path = if Path === workdir
           workdir[id].find
         else
           File.join(workdir, id)
         end
  task = task_for path
  return remote_tasks[task].load_id(id) if remote_tasks && remote_tasks.include?(task)
  return Workflow.fast_load_step path
end

#get_job_step(step_path, task = nil, input_values = nil, dependencies = nil) ⇒ Object

{{{ LOAD FROM FILE



565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
 
# File 'lib/rbbt/workflow.rb', line 565

def get_job_step(step_path, task = nil, input_values = nil, dependencies = nil)
  step_path = step_path.call if Proc === step_path
  persist = input_values.nil? ? false : true
  persist = false

  if ! (Path === step_path ? step_path.find : File.exist?(step_path)) && 
      step_path.split("/").length == 3 && 
      File.exist?(new_path = Rbbt.var.jobs[step_path].find)

    step_path = new_path
  end
  
  key = Path === step_path ? step_path.find : step_path

  if ! File.exist?(step_path) && step_path.split("/").length == 3 && File.exist?(new_path = Rbbt.var.jobs[step_path].find)
    step_path = new_path
  end

  step = Step.new step_path, task, input_values, dependencies

  set_step_dependencies(step) unless dependencies

  step.extend step_module

  step.task ||= task
  step.inputs ||= input_values
  step.dependencies = dependencies if dependencies and (step.dependencies.nil? or step.dependencies.length < dependencies.length)

  step
end

#get_SOPT(task) ⇒ Object 



277
278
279
280
 
# File 'lib/rbbt/workflow/usage.rb', line 277

def get_SOPT(task)
  sopt_option_string = self.SOPT_str(task)
  SOPT.get sopt_option_string
end

#helper(name, *args, &block) ⇒ Object 



25
26
27
28
29
30
31
32
 
# File 'lib/rbbt/workflow/definition.rb', line 25

def helper(name, *args, &block)
  if block_given?
    helpers[name] = block
  else
    raise RbbtException, "helper #{name} unkown in #{self} workflow" unless helpers[name]
    helpers[name].call(*args)
  end
end

#id_for(path) ⇒ Object 



195
196
197
198
199
200
201
202
 
# File 'lib/rbbt/workflow/accessor.rb', line 195

def id_for(path)
  if workdir.respond_to? :find
    workdir_find = workdir.find 
  else
    workdir_find = workdir
  end
  Misc.path_relative_to workdir_find, path
end

#import(source, *args) ⇒ Object 



223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
 
# File 'lib/rbbt/workflow/definition.rb', line 223

def import(source, *args)
  if args.empty?
    tasks = source.tasks.collect{|n,t| n} + source.helpers.collect{|n,h| n }
  else
    tasks = args.flatten
  end

  tasks.each do |task|
    Log.high "Task #{task} from #{source.to_s} is already present in #{self.to_s} and will be cloacked" if self.tasks.include? task.to_sym
    self.tasks[task.to_sym] = source.tasks[task.to_sym] if source.tasks.include? task.to_sym
    self.task_dependencies[task.to_sym] = source.task_dependencies[task.to_sym] if source.tasks.include? task.to_sym
    self.task_description[task.to_sym] = source.task_description[task.to_sym] if source.tasks.include? task.to_sym
    self.helpers[task.to_sym] = source.helpers[task.to_sym] if source.helpers.include? task.to_sym
  end
end

#import_task(workflow, orig, new) ⇒ Object 



298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
 
# File 'lib/rbbt/workflow.rb', line 298

def import_task(workflow, orig, new)
  orig_task = workflow.tasks[orig]
  new_task = orig_task.dup
  options = {}
  orig_task.singleton_methods.
    select{|method| method.to_s[-1] != "="[0]}.each{|method|
    if orig_task.respond_to?(method.to_s + "=") 
      options[method.to_s] = orig_task.send(method.to_s)
    end
  }

  Task.setup(options, &new_task)
  new_task.workflow = self
  new_task.name = new
  tasks[new] = new_task
  task_dependencies[new] = workflow.task_dependencies[orig]
  task_description[new] = workflow.task_description[orig]
end

#job(taskname, jobname = nil, inputs = {}) ⇒ Object 



538
539
540
541
542
543
544
545
 
# File 'lib/rbbt/workflow.rb', line 538

def job(taskname, jobname = nil, inputs = {})
  inputs, jobname = jobname, nil if Hash === jobname
  begin
    _job(taskname, jobname, inputs)
  ensure
    step_cache.clear
  end
end

#job_for_directory_inputs(task_name, directory, jobname = nil) ⇒ Object 



139
140
141
142
 
# File 'lib/rbbt/workflow/step/save_load_inputs.rb', line 139

def job_for_directory_inputs(task_name, directory, jobname = nil)
  inputs = task_inputs_from_directory(task_name, directory)
  job(task_name, jobname, inputs)
end

#jobs(taskname, query = nil) ⇒ Object

}}} LOAD FROM FILE



793
794
795
796
797
798
799
800
801
 
# File 'lib/rbbt/workflow.rb', line 793

def jobs(taskname, query = nil)
  task_dir = File.join(File.expand_path(workdir.find), taskname.to_s)
  pattern = File.join(File.expand_path(task_dir), '**/*')
  job_info_files = Dir.glob(Step.info_file(pattern)).collect{|f| Misc.path_relative_to task_dir, f }
  job_info_files = job_info_files.select{|f| f.index(query) == 0 } if query
  job_info_files.collect{|f|
    job_name = Step.job_name_for_info_file(f, tasks[taskname].extension)
  }
end

#load_cromwell(file) ⇒ Object 



18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
 
# File 'lib/rbbt/workflow/integration/cromwell.rb', line 18

def load_cromwell(file)
  jar = Rbbt.software.opt.jar["wdltool.jar"].produce.find
  inputs = JSON.load(CMD.cmd("java -jar '#{jar}' inputs '#{file}'"))

  workflow_inputs = {}
  inputs.each do |input,input_type|
    workflow, task, input_name = input.split(".")
    workflow_inputs[workflow] ||= {}

    if input_name.nil?
      input_name = task
    else
      input_name = [task, input_name] * "."
    end

    workflow_inputs[workflow][input_name] = input_type
  end

  workflow_inputs.each do |workflow,input_list|
    input_list.each do |input_name,input_type|

      input_type = input_type.split(" ").last.sub('?','')
      input_type_fixed = case input_type
                          when "File", "file"
                            :file
                          when "Int"
                            :integer
                          when /Array/
                            :array
                          else
                            input_type.downcase.to_sym
                          end

      desc = [workflow, input_name] * "."
      default = nil
      input input_name, input_type_fixed, desc, default, :nofile => true
    end

    task workflow => :string do |*args|
      cromwell = file
      options = {}
      Misc.in_dir(self.files_dir) do
        options["metadata-output"] = file('metadata.json')
        options["inputs"] = file('inputs')

        cromwell_inputs = {}
        self.inputs.to_hash.each do |input, value|
          next if value.nil?
          key = [workflow.to_s, input] * "."
          cromwell_inputs[key] = value
        end

        Open.write(file('inputs'), cromwell_inputs.to_json )
        Cromwell.run_cromwell(cromwell, self.files_dir, options)
      end
      Open.read(Dir.glob(File.join(files_dir, "/cromwell-executions/#{workflow}/*/call-*/execution/stdout")).first)
    end

  end
end

#load_documentation ⇒ Object 



48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
 
# File 'lib/rbbt/workflow/doc.rb', line 48

def load_documentation
  return if @documentation
  @documentation ||= Workflow.parse_workflow_doc documentation_markdown
  @documentation[:tasks].each do |task, description|
    if task.include? "#"
      workflow, task = task.split("#")
      workflow = begin
                   Kernel.const_get workflow
                 rescue
                   next
                 end
    else
      workflow = self
    end

    if workflow.tasks.include? task.to_sym
      workflow.tasks[task.to_sym].description = description
    else
      Log.low "Documentation for #{ task }, but not a #{ workflow.to_s } task" 
    end
  end
end

#load_id(id) ⇒ Object 



761
762
763
764
765
766
767
768
769
770
 
# File 'lib/rbbt/workflow.rb', line 761

def load_id(id)
  path = if Path === workdir
           workdir[id].find
         else
           File.join(workdir, id)
         end
  task = task_for path
  return remote_tasks[task].load_id(id) if remote_tasks && remote_tasks.include?(task)
  return Workflow.load_step path
end

#load_name(task, name) ⇒ Object 



784
785
786
787
788
789
 
# File 'lib/rbbt/workflow.rb', line 784

def load_name(task, name)
  return remote_tasks[task].load_step(path) if remote_tasks and remote_tasks.include? task
  task = tasks[task.to_sym] if String === task or Symbol === task
  path = step_path task.name, name, [], [], task.extension
  get_job_step path, task
end

#load_step(path) ⇒ Object 



596
597
598
599
600
601
602
603
 
# File 'lib/rbbt/workflow.rb', line 596

def load_step(path)
  task = task_for path
  if task
    get_job_step path, tasks[task.to_sym]
  else
    get_job_step path
  end
end

#local_persist_setup ⇒ Object

{{{ Make workflow resources local



804
805
806
807
808
809
 
# File 'lib/rbbt/workflow.rb', line 804

def local_persist_setup
  class << self
    include LocalPersist
  end
  self.local_persist_dir = Rbbt.var.cache.persistence.find :lib
end

#local_workdir_setup ⇒ Object 



811
812
813
 
# File 'lib/rbbt/workflow.rb', line 811

def local_workdir_setup
  self.workdir = Rbbt.var.jobs.find :lib
end

#log(status, message = nil, &block) ⇒ Object 



23
24
25
 
# File 'lib/rbbt/workflow/accessor.rb', line 23

def log(status, message = nil, &block)
  Step.log(status, message, nil, &block)
end

#make_local ⇒ Object 



815
816
817
818
 
# File 'lib/rbbt/workflow.rb', line 815

def make_local
  local_persist_setup
  local_workdir_setup
end

#nextflow(path, *args) ⇒ Object 



184
185
186
187
188
189
190
191
192
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 184

def nextflow(path, *args)
  if File.directory?(path)
    nextflow_dir path, *args
  elsif File.exist?(path)
    nextflow_file path, *args
  else
    nextflow_project path, *args
  end
end

#nextflow_dir(path, output = nil) ⇒ Object 



173
174
175
176
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 173

def nextflow_dir(path, output = nil)
  main = File.join(path, 'main.nf')
  nextflow_file main, File.basename(path), output
end

#nextflow_file(file, name = nil, output = nil) ⇒ Object 



72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 72

def nextflow_file(file, name = nil, output = nil)
  name, output = nil, name if Hash === name

  if Hash === output
    result, output = output.collect.first
  else
    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/,'_')
  Workflow.nextflow_recursive_params(file).each do |param|
    p,_sep, section = param.partition("-")
    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 = {}

    inputs.zip(inputs.fields).collect do |v,f|
      v = if String === v && m = v.match(/^JOB_FILE:(.*)/)
            file(m[1]) 
          elsif v.nil?
            Rbbt::Config.get(['nextflow', f] * "_", 'default', f)
          else
            v
          end

      if f.to_s.include?("-") 
        p,_sep, section = f.to_s.partition("-")
        name = [section, p] * "."
      else
        name = f
      end
        
      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 "

      cmd += " -C #{config_file}" if config_file

      cmd += " run"

      cmd += " -work-dir #{work} -ansi-log false"

      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

    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
      work[File.join("*", "*", "*")].glob * "\n"
    end
  end
end

#nextflow_project(project, *args) ⇒ Object 



178
179
180
181
182
 
# File 'lib/rbbt/workflow/integration/nextflow.rb', line 178

def nextflow_project(project, *args)
  CMD.cmd_log("nextflow pull #{project}")
  directory = File.join(ENV["HOME"], '.nextflow/assets', project)
  nextflow_dir directory, *args
end

#override_dependencies(inputs) ⇒ Object 



58
59
60
61
62
63
64
65
66
67
68
69
70
 
# File 'lib/rbbt/workflow/dependencies.rb', line 58

def override_dependencies(inputs)
  override_dependencies = IndiferentHash.setup({})
  return override_dependencies if inputs.nil?
  inputs.each do |key,value|
    if String === key && m = key.match(/(.*)#(.*)/)
      workflow, task = m.values_at 1, 2
      workflow = self.to_s if workflow.empty?
      override_dependencies[workflow] ||= IndiferentHash.setup({})
      override_dependencies[workflow][task] = value
    end
  end
  override_dependencies
end

#prov_string(tree) ⇒ Object 



113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
 
# File 'lib/rbbt/workflow/usage.rb', line 113

def prov_string(tree)
  description = ""

  last = nil
  seen = Set.new

  tasks = _prov_tasks(tree)
  tasks.each do |workflow,task_name|

    next if seen.include?([workflow,task_name])

    child = last && last.include?([workflow, task_name])
    first = last.nil?
    last = _prov_tasks(workflow.dep_tree(task_name))

    break if child

    if child
      description << "->" << task_name.to_s
    elsif first
      description << "" << task_name.to_s
    else
      description << ";" << task_name.to_s
    end
    
    seen << [workflow, task_name]
  end
  description
end

#prov_tree(tree, offset = 0, seen = []) ⇒ Object 



143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
 
# File 'lib/rbbt/workflow/usage.rb', line 143

def prov_tree(tree, offset = 0, seen = [])

  return "" if tree.empty?

  lines = []

  offset_str = " " * offset

  lines << offset_str 

  tree.each do |p,dtree| 
    next if seen.include?(p)
    seen.push(p)
    workflow, task = p
    lines << offset_str + [workflow.to_s, task.to_s] * "#" + "\n" + workflow.prov_tree(dtree, offset + 1, seen)
  end

  lines * "\n"
end

#real_dependencies(task, orig_jobname, inputs, dependencies) ⇒ Object 



151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
 
# File 'lib/rbbt/workflow/dependencies.rb', line 151

def real_dependencies(task, orig_jobname, inputs, dependencies)
  real_dependencies = []
  path_deps = {}

  override_dependencies = override_dependencies(inputs)

  overriden = false
  dependencies.each do |dependency|
    _inputs = IndiferentHash.setup(inputs.dup)
    jobname = orig_jobname
    jobname = _inputs[:jobname] if _inputs.include? :jobname

    real_dep = case dependency
               when Array
                 workflow, dep_task, options = dependency

                 if override_dependencies[workflow.to_s] && value = override_dependencies[workflow.to_s][dep_task]
                   overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                   #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                   setup_override_dependency(value, workflow, dep_task)
                 else

                   compute = options[:compute] if options
                   if options && options[:canfail]
                     compute = case compute
                               when nil
                                 :canfail
                               when Array
                                 compute + [:canfail]
                               else
                                 [compute, :canfail]
                               end
                   end

                   all_d = (real_dependencies + real_dependencies.flatten.collect{|d| d.rec_dependencies} ).flatten.compact.uniq

                   _inputs = assign_dep_inputs(_inputs, options, all_d, workflow.task_info(dep_task))
                   jobname = _inputs.delete :jobname if _inputs.include? :jobname

                   job = workflow._job(dep_task, jobname, _inputs)
                   ComputeDependency.setup(job, compute) if compute

                   overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])

                   job
                 end
               when Step
                 job = dependency
                 overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                 job
               when Symbol
                 if override_dependencies[self.to_s] && value = override_dependencies[self.to_s][dependency]
                   overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                   #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                   setup_override_dependency(value, self, dependency)
                 else
                   job = _job(dependency, jobname, _inputs)
                   overriden = true if Symbol === job.overriden && (options.nil? || ! options[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])

                   job
                 end
               when Proc
                 if DependencyBlock === dependency
                   orig_dep = dependency.dependency 
                   wf, task_name, options = orig_dep

                   if override_dependencies[wf.to_s] && value = override_dependencies[wf.to_s][task_name]
                     overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                     #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                     dep = setup_override_dependency(value, wf, task_name)
                   else

                     options = {} if options.nil?
                     compute = options[:compute]
                     if options[:canfail]
                       compute = case compute
                                 when nil
                                   :canfail
                                 when Array
                                   compute + [:canfail]
                                 else
                                   [compute, :canfail]
                                 end
                     end

                     options = IndiferentHash.setup(options.dup)
                     dep = dependency.call jobname, _inputs.merge(options), real_dependencies

                     dep = [dep] unless Array === dep

                     new_=[]
                     dep.each{|d| 
                       next if d.nil?
                       if Hash === d
                         d = d.merge(options)
                         d[:workflow] ||= wf 
                         d[:task] ||= task_name
                         _override_dependencies = override_dependencies.merge(override_dependencies(d[:inputs] || {}))
                         d = if _override_dependencies[d[:workflow].to_s] && value = _override_dependencies[d[:workflow].to_s][d[:task]]
                               overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                               #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                               setup_override_dependency(value, d[:workflow], d[:task])
                             else
                               task_info = d[:workflow].task_info(d[:task])

                               _inputs = assign_dep_inputs({}, options.merge(d[:inputs] || {}), real_dependencies, task_info) 
                               _jobname = d.include?(:jobname) ? d[:jobname] : jobname
                               job = d[:workflow]._job(d[:task], _jobname, _inputs) 
                               overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                               job
                             end
                       end
                       ComputeDependency.setup(d, compute) if compute
                       new_ << d
                     }
                     dep = new_
                   end
                 else
                   _inputs = IndiferentHash.setup(_inputs.dup)
                   dep = dependency.call jobname, _inputs, real_dependencies
                   if Hash === dep
                     dep[:workflow] ||= wf || self
                     _override_dependencies = override_dependencies.merge(override_dependencies(dep[:inputs] || {}))
                     if _override_dependencies[dep[:workflow].to_s] && value = _override_dependencies[dep[:workflow].to_s][dep[:task]]
                       overriden = true if (inputs.nil? || ! inputs[:not_overriden]) && (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                       #overriden = true if (options.nil? || ! options[:not_overriden]) && ! unlocated_override?(value)
                       setup_override_dependency(value, dep[:workflow], dep[:task])
                     else
                       task_info = (dep[:task] && dep[:workflow]) ? dep[:workflow].task_info(dep[:task]) : nil
                       _inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, task_info)
                       _jobname = dep.include?(:jobname) ? dep[:jobname] : jobname
                       job = dep[:workflow]._job(dep[:task], _jobname, _inputs)
                       overriden = true if Symbol === job.overriden? && (d.nil? || ! d[:not_overriden]) && (inputs.nil? || ! inputs[:not_overriden])
                       job
                     end
                   end
                 end

                 dep
               else
                 raise "Dependency for #{task.name} not understood: #{Misc.fingerprint dependency}"
               end

    real_dependencies << real_dep
  end
  [real_dependencies.flatten.compact, overriden]
end

#rec_dependencies(taskname, seen = []) ⇒ Object 



2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
 
# File 'lib/rbbt/workflow/dependencies.rb', line 2

def rec_dependencies(taskname, seen = [])
  @rec_dependencies ||= {}
  @rec_dependencies[taskname] ||= [] unless task_dependencies.include?(taskname)
  @rec_dependencies[taskname] ||= begin

                                    deps = task_dependencies[taskname]

                                    all_deps = []
                                    deps.each do |dep| 
                                      next if seen.include?(dep)
                                      if DependencyBlock === dep
                                        all_deps << dep.dependency if dep.dependency
                                      else
                                        all_deps << dep unless Proc === dep
                                      end

                                      begin
                                        case dep
                                        when Array
                                          wf, t, o = dep

                                          wf.rec_dependencies(t.to_sym, seen + [dep]).each do |d|
                                            if Array === d
                                              new = d.dup
                                            else
                                              new = [dep.first, d]
                                            end

                                            if Hash === o and not o.empty? 
                                              if Hash === new.last
                                                hash = new.last.dup
                                                o.each{|k,v| hash[k] ||= v}
                                                new[new.length-1] = hash
                                              else
                                                new.push o.dup
                                              end
                                            end

                                            all_deps << new
                                          end if wf && t

                                        when String, Symbol
                                          rec_deps = rec_dependencies(dep.to_sym, seen + [dep])
                                          all_deps.concat rec_deps
                                        when DependencyBlock
                                          dep = dep.dependency
                                          raise TryAgain
                                        end
                                      rescue TryAgain
                                        retry
                                      end
                                    end
                                    all_deps.uniq
                                  end
end

#rec_input_defaults(taskname) ⇒ Object 



82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
 
# File 'lib/rbbt/workflow/accessor.rb', line 82

def rec_input_defaults(taskname)
  rec_inputs = rec_inputs(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject(IndiferentHash.setup({})){|acc, tn|
    if Array === tn and tn[0] and tn[1]
      new = tn.first.tasks[tn[1].to_sym].input_defaults
    elsif Symbol === tn
      new = tasks[tn.to_sym].input_defaults
    else
      next acc
    end
    acc = new.merge(acc) 
    acc.delete_if{|input,defaults| not rec_inputs.include? input}
    acc
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_descriptions(taskname) ⇒ Object 



143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
 
# File 'lib/rbbt/workflow/accessor.rb', line 143

def rec_input_descriptions(taskname)
  rec_inputs = rec_inputs(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    if Array === tn and tn[0] and tn[1]
      new = tn.first.tasks[tn[1].to_sym].input_descriptions
    elsif Symbol === tn
      new = tasks[tn.to_sym].input_descriptions
    else
      next acc
    end
    acc = new.merge(acc) 
    acc.delete_if{|input,defaults| not rec_inputs.include? input}
    acc
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_options(taskname) ⇒ Object 



159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
 
# File 'lib/rbbt/workflow/accessor.rb', line 159

def rec_input_options(taskname)
  rec_inputs = rec_inputs(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    if Array === tn and tn[0] and tn[1]
      new = tn.first.tasks[tn[1].to_sym].input_options
    elsif Symbol === tn
      new = tasks[tn.to_sym].input_options
    else
      next acc
    end
    acc = new.merge(acc) 
    acc = acc.delete_if{|input,defaults| not rec_inputs.include? input}
    acc
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_types(taskname) ⇒ Object 



98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
 
# File 'lib/rbbt/workflow/accessor.rb', line 98

def rec_input_types(taskname)
  rec_inputs = rec_inputs(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    if Array === tn and tn[0] and tn[1]
      new = tn.first.tasks[tn[1].to_sym].input_types
    elsif Symbol === tn
      new = tasks[tn.to_sym].input_types
    else
      next acc
    end
    acc = new.merge(acc) 
    acc.delete_if{|input,defaults| not rec_inputs.include? input}
    acc
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_use(taskname) ⇒ Object 



114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
 
# File 'lib/rbbt/workflow/accessor.rb', line 114

def rec_input_use(taskname)
  task = task_from_dep(taskname)
  deps = rec_dependencies(taskname)
  inputs = {}
  task.inputs.each do |input|
    name = task.name
    workflow = (task.workflow || self).to_s

    inputs[input] ||= {}
    inputs[input][workflow] ||= []
    inputs[input][workflow]  << name
  end

  dep_inputs = Task.dep_inputs deps, self

  dep_inputs.each do |dep,is|
    name = dep.name
    workflow = dep.workflow

    is.each do |input|
      inputs[input] ||= {}
      inputs[input][workflow] ||= []
      inputs[input][workflow]  << name
    end
  end

  inputs
end

#rec_inputs(taskname) ⇒ Object 



75
76
77
78
79
80
 
# File 'lib/rbbt/workflow/accessor.rb', line 75

def rec_inputs(taskname)
  task = task_from_dep(taskname)
  deps = rec_dependencies(taskname)
  dep_inputs = task.dep_inputs deps, self
  task.inputs + dep_inputs.values.flatten
end

#resumable ⇒ Object 



42
43
44
 
# File 'lib/rbbt/workflow/definition.rb', line 42

def resumable
  @resumable = true
end

#returns(description) ⇒ Object 



46
47
48
 
# File 'lib/rbbt/workflow/definition.rb', line 46

def returns(description)
  @result_description = description
end

#set_step_dependencies(step) ⇒ Object 



548
549
550
551
552
553
554
555
556
557
558
559
560
561
 
# File 'lib/rbbt/workflow.rb', line 548

def set_step_dependencies(step)
  if step.info[:dependencies]
    Misc.insist do
      step.dependencies = step.info[:dependencies].collect do |task, job, path|
        next if job.nil?
        if Open.exists?(path)
          load_step(path) 
        else
          Workflow.load_step(path)
        end
      end
    end
  end
end

#setup_override_dependency(dep, workflow, task_name) ⇒ Object 



72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
 
# File 'lib/rbbt/workflow/dependencies.rb', line 72

def setup_override_dependency(dep, workflow, task_name)
  return [] if dep == :skip || dep == 'skip'

  unlocated = unlocated_override?(dep)
  dep = Workflow.load_step(dep) if not Step === dep

  dep.original_workflow ||= dep.workflow if dep.workflow
  dep.original_task_name ||= dep.task_name if dep.task_name

  dep.original_task_name ||= dep.path.split("/")[-3]
  dep.original_task_name ||= dep.path.split("/")[-2]

  dep.workflow = workflow
  dep.info[:name] = dep.name

  begin
    workflow = Kernel.const_get workflow if String === workflow
    dep.task = workflow.tasks[task_name] if dep.task.nil? && workflow.tasks.include?(task_name)
  rescue
    Log.exception $!
  end

  dep.task_name = task_name
  dep.overriden = dep.original_task_name.to_sym if dep.original_task_name && dep.original_task_name.to_s != task_name.to_s || ! unlocated

  dep.extend step_module

  dep
end

#SOPT_str(task) ⇒ Object 



265
266
267
268
269
270
271
272
273
274
275
 
# File 'lib/rbbt/workflow/usage.rb', line 265

def SOPT_str(task)
  sopt_options = []
  self.rec_inputs(task.name).each do |name|
    short = name.to_s.chars.first
    boolean = self.rec_input_types(task.name)[name].to_sym == :boolean

    sopt_options << "-#{short}--#{name}#{boolean ? "" : "*"}"
  end

  sopt_options * ":"
end

#step_module ⇒ Object 



399
400
401
402
403
404
405
406
407
408
409
410
 
# File 'lib/rbbt/workflow.rb', line 399

def step_module
  @_m ||= begin
            m = Module.new

            helpers.each do |name,block|
              m.send(:define_method, name, &block)
            end

            m
          end
  @_m
end

#step_path(taskname, jobname, inputs, dependencies, extension = nil) ⇒ Object 



258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
 
# File 'lib/rbbt/workflow.rb', line 258

def step_path(taskname, jobname, inputs, dependencies, extension = nil)
  raise "Jobname makes an invalid path: #{ jobname }" if jobname.include? '..'
  if inputs.length > 0 or dependencies.any?
    tagged_jobname = case TAG
                     when :hash
                       clean_inputs = Annotated.purge(inputs)
                       clean_inputs = clean_inputs.collect{|i| Symbol === i ? i.to_s : i }
                       deps_str = dependencies.collect{|d| (Step === d || (defined?(RemoteStep) && RemoteStep === d)) ? "Step: " << (Symbol === d.overriden ? d.path : d.short_path) : d }
                       key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
                       key_str = Misc.obj2str(key_obj)
                       hash_str = Misc.digest(key_str)
                       Log.debug "Hash for '#{[taskname, jobname] * "/"}' #{hash_str} for #{key_str}" if DEBUG_JOB_HASH
                       jobname + '_' << hash_str
                     when :inputs
                       all_inputs = {}
                       inputs.zip(self.task_info(taskname)[:inputs]) do |i,f|
                         all_inputs[f] = i
                       end
                       dependencies.each do |dep|
                         ri = dep.recursive_inputs
                         ri.zip(ri.fields).each do |i,f|
                           all_inputs[f] = i
                         end
                       end

                       all_inputs.any? ? jobname + '_' << Misc.obj2str(all_inputs) : jobname
                     else
                       jobname
                     end
  else
    tagged_jobname = jobname
  end

  if extension and not extension.empty?
    tagged_jobname = tagged_jobname + ('.' << extension.to_s)
  end

  workdir[taskname][tagged_jobname].find
end

#task(name, &block) ⇒ Object 



134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
 
# File 'lib/rbbt/workflow/definition.rb', line 134

def task(name, &block)
  if Hash === name
    type = name.first.last
    name = name.first.first
  else
    result_type = consume_result_type || :marshal
  end

  name = name.to_sym
 
  block = self.method(name) unless block_given?

  task_info = {
    :name               => name,
    :inputs             => consume_inputs,
    :description        => consume_description,
    :input_types        => consume_input_types,
    :result_type        => (String === type ? type.to_sym : type),
    :result_description => consume_result_description,
    :input_defaults     => consume_input_defaults,
    :input_descriptions => consume_input_descriptions,
    :required_inputs    => consume_required_inputs,
    :extension          => consume_extension,
    :resumable          => consume_resumable,
    :input_options      => consume_input_options
  }
   
  task_info[:extension] = case task_info[:result_type].to_s
                          when "tsv"
                            "tsv"
                          when "yaml"
                            "yaml"
                          when "marshal"
                            "marshal"
                          when "json"
                            "json"
                          else
                            nil
                          end if task_info[:extension].nil?

  task = Task.setup(task_info, &block)

  last_task = task

  tasks[name] = task
  task_dependencies[name] = consume_dependencies

  task
end

#task_exports ⇒ Object 



229
230
231
 
# File 'lib/rbbt/workflow/accessor.rb', line 229

def task_exports
  [exec_exports, synchronous_exports, asynchronous_exports, stream_exports].compact.flatten.uniq
end

#task_for(path) ⇒ Object 



212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
 
# File 'lib/rbbt/workflow/accessor.rb', line 212

def task_for(path)
  if workdir.respond_to? :find
    workdir_find = workdir.find 
  else
    workdir_find = workdir
  end

  workdir_find = File.expand_path(workdir_find)
  path = File.expand_path(path)
  dir = File.dirname(path)
  begin
    Misc.path_relative_to(workdir_find, dir).sub(/([^\/]+)\/.*/,'\1')
  rescue
    nil
  end
end

#task_from_dep(dep) ⇒ Object 



176
177
178
179
180
181
182
183
184
185
186
187
 
# File 'lib/rbbt/workflow/accessor.rb', line 176

def task_from_dep(dep)
  task = case dep
         when Array
           dep.first.tasks[dep[1]] 
         when String
           tasks[dep.to_sym]
         when Symbol
           tasks[dep.to_sym]
         end
  raise "Unknown dependency: #{Misc.fingerprint dep}" if task.nil?
  task
end

#task_info(name) ⇒ Object 



27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
 
# File 'lib/rbbt/workflow/accessor.rb', line 27

def task_info(name)
  name = name.to_sym
  task = tasks[name]
  raise "No '#{name}' task in '#{self.to_s}' Workflow" if task.nil?
  id = File.join(self.to_s, name.to_s)
  @task_info ||= {}
  @task_info[id] ||= begin 
                       description = task.description
                       result_description = task.result_description
                       result_type = task.result_type
                       inputs = rec_inputs(name).uniq
                       input_types = rec_input_types(name)
                       input_descriptions = rec_input_descriptions(name)
                       input_use = rec_input_use(name)
                       input_defaults = rec_input_defaults(name)
                       input_options = rec_input_options(name)
                       extension = task.extension
                       export = case
                                when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
                                  :synchronous
                                when (asynchronous_exports.include?(name.to_sym) or asynchronous_exports.include?(name.to_s))
                                  :asynchronous
                                when (exec_exports.include?(name.to_sym) or exec_exports.include?(name.to_s))
                                  :exec
                                when (stream_exports.include?(name.to_sym) or stream_exports.include?(name.to_s))
                                  :stream
                                else
                                  :none
                                end

                       dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
                       { :id => id,
                         :description => description,
                         :export => export,
                         :inputs => inputs,
                         :input_types => input_types,
                         :input_descriptions => input_descriptions,
                         :input_defaults => input_defaults,
                         :input_options => input_options,
                         :input_use => input_use,
                         :result_type => result_type,
                         :result_description => result_description,
                         :dependencies => dependencies,
                         :extension => extension
                       }
                     end
end

#task_inputs_from_directory(task_name, directory) ⇒ Object 



134
135
136
137
 
# File 'lib/rbbt/workflow/step/save_load_inputs.rb', line 134

def task_inputs_from_directory(task_name, directory)
  task_info = self.task_info(task_name)
  Workflow.load_inputs(directory, task_info[:inputs], task_info[:input_types])
end

#unexport(*names) ⇒ Object 



184
185
186
187
188
189
190
191
 
# File 'lib/rbbt/workflow/definition.rb', line 184

def unexport(*names)
  names = names.collect{|n| n.to_s} + names.collect{|n| n.to_sym}
  names.uniq!
  exec_exports.replace exec_exports - names if exec_exports
  synchronous_exports.replace synchronous_exports - names if synchronous_exports
  asynchronous_exports.replace asynchronous_exports - names if asynchronous_exports
  stream_exports.replace stream_exports - names if stream_exports
end

#unlocated_override?(dep) ⇒ Boolean

Returns:

  • (Boolean) 


102
103
104
 
# File 'lib/rbbt/workflow/dependencies.rb', line 102

def unlocated_override?(dep)
  String === dep && ! (Open.exists?(dep) || Open.exists?(dep + '.info'))
end

#with_workdir(workdir) ⇒ Object 



820
821
822
823
824
825
826
827
828
 
# File 'lib/rbbt/workflow.rb', line 820

def with_workdir(workdir)
  saved = self.workdir
  begin
    self.workdir = Path.setup(File.expand_path(workdir))
    yield
  ensure
    self.workdir = saved
  end
end