Module: Workflow

Includes:
InputModule
Included in:
WorkflowRESTClient
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/definition.rb

Defined Under Namespace

Modules: DependencyBlock Classes: TaskNotFoundException

Constant Summary collapse

STEP_CACHE = 
{}
DEFAULT_NAME =

{{{ JOB MANAGEMENT

"Default"
TAG = 
ENV["RBBT_INPUT_JOBNAME"] == "true" ? :inputs : :hash

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.



24
25
26
 
# File 'lib/rbbt/workflow.rb', line 24

def autoinstall
  @autoinstall
end

.workflow_dir ⇒ Object

Returns the value of attribute workflow_dir.



24
25
26
 
# File 'lib/rbbt/workflow.rb', line 24

def workflow_dir
  @workflow_dir
end

.workflows ⇒ Object

Returns the value of attribute workflows.



24
25
26
 
# File 'lib/rbbt/workflow.rb', line 24

def workflows
  @workflows
end

Instance Attribute Details

#asynchronous_exports ⇒ Object

Returns the value of attribute asynchronous_exports.



192
193
194
 
# File 'lib/rbbt/workflow.rb', line 192

def asynchronous_exports
  @asynchronous_exports
end

#description ⇒ Object

Returns the value of attribute description.



188
189
190
 
# File 'lib/rbbt/workflow.rb', line 188

def description
  @description
end

#documentation ⇒ Object

Returns the value of attribute documentation.



54
55
56
 
# File 'lib/rbbt/workflow/doc.rb', line 54

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.



192
193
194
 
# File 'lib/rbbt/workflow.rb', line 192

def exec_exports
  @exec_exports
end

#helpers ⇒ Object

Returns the value of attribute helpers.



190
191
192
 
# File 'lib/rbbt/workflow.rb', line 190

def helpers
  @helpers
end

#last_task ⇒ Object

Returns the value of attribute last_task.



191
192
193
 
# File 'lib/rbbt/workflow.rb', line 191

def last_task
  @last_task
end

#libdir ⇒ Object

Returns the value of attribute libdir.



189
190
191
 
# File 'lib/rbbt/workflow.rb', line 189

def libdir
  @libdir
end

#remote_tasks ⇒ Object

Returns the value of attribute remote_tasks.



194
195
196
 
# File 'lib/rbbt/workflow.rb', line 194

def remote_tasks
  @remote_tasks
end

#step_cache ⇒ Object

Returns the value of attribute step_cache.



193
194
195
 
# File 'lib/rbbt/workflow.rb', line 193

def step_cache
  @step_cache
end

#stream_exports ⇒ Object

Returns the value of attribute stream_exports.



192
193
194
 
# File 'lib/rbbt/workflow.rb', line 192

def stream_exports
  @stream_exports
end

#synchronous_exports ⇒ Object

Returns the value of attribute synchronous_exports.



192
193
194
 
# File 'lib/rbbt/workflow.rb', line 192

def synchronous_exports
  @synchronous_exports
end

#task_dependencies ⇒ Object

Returns the value of attribute task_dependencies.



191
192
193
 
# File 'lib/rbbt/workflow.rb', line 191

def task_dependencies
  @task_dependencies
end

#task_description ⇒ Object

Returns the value of attribute task_description.



191
192
193
 
# File 'lib/rbbt/workflow.rb', line 191

def task_description
  @task_description
end

#tasks ⇒ Object

Returns the value of attribute tasks.



190
191
192
 
# File 'lib/rbbt/workflow.rb', line 190

def tasks
  @tasks
end

#workdir ⇒ Object

Returns the value of attribute workdir.



189
190
191
 
# File 'lib/rbbt/workflow.rb', line 189

def workdir
  @workdir
end

Class Method Details

.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 



33
34
35
36
 
# File 'lib/rbbt/workflow.rb', line 33

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

.init_remote_tasks ⇒ Object 



38
39
40
41
42
 
# File 'lib/rbbt/workflow.rb', line 38

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 



73
74
75
76
77
 
# File 'lib/rbbt/workflow.rb', line 73

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

.load_inputs(dir, input_names, input_types) ⇒ Object 



28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
 
# File 'lib/rbbt/workflow/examples.rb', line 28

def self.load_inputs(dir, input_names, input_types)
  inputs = {}
  dir = Path.setup(dir.dup)
  input_names.each do |input|
    file = dir[input].find
    file = dir.glob(input.to_s + ".*").first if file.nil? or not file.exists?
    Log.debug "Trying #{ input }: #{file}"
    next unless file and file.exists?

    case input_types[input]
    when :tsv, :array, :text, :file
      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
  IndiferentHash.setup(inputs)
end

.load_remote_tasks(filename) ⇒ Object 



474
475
476
477
478
 
# File 'lib/rbbt/workflow.rb', line 474

def self.load_remote_tasks(filename)
  yaml_text = Open.read(filename)
  remote_workflow_tasks = YAML.load(yaml_text)
  Workflow.process_remote_tasks(remote_workflow_tasks)
end

.load_workflow_file(filename) ⇒ Object 



57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
 
# File 'lib/rbbt/workflow.rb', line 57

def self.load_workflow_file(filename)
  begin

    load_workflow_libdir(filename)

    filename = File.expand_path(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 



49
50
51
52
53
54
55
 
# File 'lib/rbbt/workflow.rb', line 49

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 



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
 
# File 'lib/rbbt/workflow.rb', line 95

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

.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

.process_remote_tasks(remote_tasks) ⇒ Object 



459
460
461
462
463
464
465
466
467
468
469
470
471
472
 
# File 'lib/rbbt/workflow.rb', line 459

def self.process_remote_tasks(remote_tasks)
  require 'rbbt/rest/client'
  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 = WorkflowRESTClient.new remote, workflow
      tasks.each do |task|
        wf.remote_tasks[task.to_sym] = remote_wf
      end
    end
  end
end

.require_local_workflow(wf_name) ⇒ Object 



125
126
127
128
129
130
131
132
133
 
# File 'lib/rbbt/workflow.rb', line 125

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 



44
45
46
47
 
# File 'lib/rbbt/workflow.rb', line 44

def self.require_remote_workflow(wf_name, url)
  require 'rbbt/rest/client'
  eval "Object::#{wf_name} = WorkflowRESTClient.new '#{ url }', '#{wf_name}'"
end

.require_workflow(wf_name, force_local = false) ⇒ Object 



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
183
184
185
186
 
# File 'lib/rbbt/workflow.rb', line 135

def self.require_workflow(wf_name, force_local=false)
  Workflow.init_remote_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
    url = wf_name
    wf_name = File.basename(url)
    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
    return Misc.string2const Misc.camel_case(wf_name)
  end

  Log.info{"Loading workflow #{wf_name}"}
  require_local_workflow(wf_name) or 
  (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)}` and require_local_workflow(Misc.snake_case(wf_name))) or
  raise("Workflow not found or could not be loaded: #{ wf_name }")
  begin
    Misc.string2const Misc.camel_case(wf_name)
  rescue
    Workflow.workflows.last || true
  end
end

.resolve_locals(inputs) ⇒ Object 



271
272
273
274
275
276
277
278
279
280
281
282
 
# File 'lib/rbbt/workflow.rb', line 271

def self.resolve_locals(inputs)
  inputs.each do |name, value|
    if 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

.workdir ⇒ Object 



203
204
205
206
207
208
209
 
# File 'lib/rbbt/workflow.rb', line 203

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

.workdir=(path) ⇒ Object

{{{ ATTR DEFAULTS



198
199
200
201
 
# File 'lib/rbbt/workflow.rb', line 198

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

Instance Method Details

#add_remote_tasks(remote_tasks) ⇒ Object 



451
452
453
454
455
456
457
 
# File 'lib/rbbt/workflow.rb', line 451

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 



264
265
266
 
# File 'lib/rbbt/workflow.rb', line 264

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

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



720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
 
# File 'lib/rbbt/workflow/accessor.rb', line 720

def assign_dep_inputs(_inputs, options, all_d, task_info)
  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)
        else
          _inputs[i] = v unless _inputs.include? i
        end
      else
        input_options = task_info[:input_options][i] || {}
        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 



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

def dep(*dependency, &block)
  @dependencies ||= []
  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? WorkflowRESTClient and WorkflowRESTClient === dependency.first) or
      Hash === dependency.last

      dependency = ([self] + dependency) unless Module === dependency.first or (defined? WorkflowRESTClient and WorkflowRESTClient === dependency.first)
      @dependencies << dependency
    else
      @dependencies.concat dependency
    end
  end
end

#desc(description) ⇒ Object 



28
29
30
 
# File 'lib/rbbt/workflow/definition.rb', line 28

def desc(description)
  @description = description
end

#doc(task = nil) ⇒ Object 



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
 
# File 'lib/rbbt/workflow/usage.rb', line 62

def doc(task = nil)

  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

    tasks.each do |name,task|
      description = task.description || ""
      description = description.split("\n\n").first
      puts Misc.format_definition_list_item(name.to_s, description, 80, 30, :yellow)
    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))

    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
                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, 80, 20, :blue)
              end
          end
          puts
        end
      end
    end
end

#documentation_markdown ⇒ Object 



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

def documentation_markdown
  file = @libdir['workflow.md'].find
  if file.exists?
    file.read
  else
    ""
  end
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_step(task_name, example) ⇒ Object 



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

def example_step(task_name, example)
  inputs = {}
  example(task_name, example).each do |input,type,file|

    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
  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 



123
124
125
126
127
128
 
# File 'lib/rbbt/workflow/definition.rb', line 123

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

#export_exec(*names) ⇒ Object 



109
110
111
112
113
114
 
# File 'lib/rbbt/workflow/definition.rb', line 109

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

#export_stream(*names) ⇒ Object 



130
131
132
133
134
135
 
# File 'lib/rbbt/workflow/definition.rb', line 130

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

#export_synchronous(*names) ⇒ Object 



116
117
118
119
120
121
 
# File 'lib/rbbt/workflow/definition.rb', line 116

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

#extension(extension) ⇒ Object 



32
33
34
 
# File 'lib/rbbt/workflow/definition.rb', line 32

def extension(extension)
  @extension = extension
end

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

{{{ LOAD FROM FILE



366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
 
# File 'lib/rbbt/workflow.rb', line 366

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

  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

#helper(name, &block) ⇒ Object 



24
25
26
 
# File 'lib/rbbt/workflow/definition.rb', line 24

def helper(name, &block)
  helpers[name] = block
end

#id_for(path) ⇒ Object 



867
868
869
870
871
872
873
874
 
# File 'lib/rbbt/workflow/accessor.rb', line 867

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

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



297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
 
# File 'lib/rbbt/workflow.rb', line 297

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

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

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

  inputs = IndiferentHash.setup(inputs)

  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)

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

  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

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

  real_inputs = {}
  recursive_inputs = rec_inputs(taskname)

  inputs.each do |k,v|
    default = defaults[k]
    next unless (task_inputs.include?(k.to_sym) or task_inputs.include?(k.to_s))
    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] = v 
  end

  if real_inputs.empty? and not Workflow::TAG == :inputs
    step_path = step_path taskname, jobname, [], [], task.extension
    input_values = task.take_input_values(inputs)
  else
    input_values = task.take_input_values(inputs)
    step_path = step_path taskname, jobname, input_values, dependencies, task.extension
  end

  job = get_job_step step_path, task, input_values, dependencies
  job.workflow = self
  job.clean_name = jobname
  job
end

#jobs(taskname, query = nil) ⇒ Object

}}} LOAD FROM FILE



414
415
416
417
418
419
420
421
422
 
# File 'lib/rbbt/workflow.rb', line 414

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_documentation ⇒ Object 



46
47
48
49
50
51
52
 
# File 'lib/rbbt/workflow/doc.rb', line 46

def load_documentation
  @documentation = Workflow.parse_workflow_doc documentation_markdown
  @documentation[:tasks].each do |task, description|
    raise "Documentation for #{ task }, but not a #{ self.to_s } task" unless tasks.include? task.to_sym
    tasks[task.to_sym].description = description
  end
end

#load_id(id) ⇒ Object 



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

def load_id(id)
  path = File.join(workdir, id)
  task = task_for path
  return remote_tasks[task].load_id(id) if remote_tasks and remote_tasks.include? task
  step = Step.new path, tasks[task.to_sym]
  step.load_inputs_from_info
  set_step_dependencies(step)
  step
end

#load_name(task, name) ⇒ Object 



405
406
407
408
409
410
 
# File 'lib/rbbt/workflow.rb', line 405

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 



396
397
398
399
400
401
402
403
 
# File 'lib/rbbt/workflow.rb', line 396

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



425
426
427
428
429
430
 
# File 'lib/rbbt/workflow.rb', line 425

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

#local_workdir_setup ⇒ Object 



432
433
434
 
# File 'lib/rbbt/workflow.rb', line 432

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

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



527
528
529
 
# File 'lib/rbbt/workflow/accessor.rb', line 527

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

#make_local ⇒ Object 



436
437
438
439
 
# File 'lib/rbbt/workflow.rb', line 436

def make_local
  local_persist_setup
  local_workdir_setup
end

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



760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
 
# File 'lib/rbbt/workflow/accessor.rb', line 760

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

                 compute = options[:compute] if options

                 all_d = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
                 
                 _inputs = assign_dep_inputs(_inputs, options, all_d, workflow.task_info(dep_task))
                 jobname = _inputs[:jobname] if _inputs.include? :jobname

                 job = workflow.job(dep_task, jobname, _inputs)
                 ComputeDependency.setup(job, compute) if compute
                 job
               when Step
                 dependency
               when Symbol
                 job(dependency, jobname, _inputs)
               when Proc
                 if DependencyBlock === dependency
                   orig_dep = dependency.dependency 
                   wf, task_name, options = orig_dep

                   options = {} if options.nil?
                   compute = options[:compute]

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

                   dep = [dep] unless Array === dep

                   new_=[]
                   dep.each{|d| 
                     if Hash === d
                       d[:workflow] ||= wf 
                       d[:task] = task_name
                       inputs = assign_dep_inputs({}, options.merge(d[:inputs] || {}), real_dependencies, d[:workflow].task_info(d[:task])) 
                       d = d[:workflow].job(d[:task], d[:jobname], inputs) 
                     end
                     ComputeDependency.setup(d, compute) if compute
                     new_ << d
                   }
                   dep = new_
                 else
                   _inputs = IndiferentHash.setup(_inputs.dup)
                   dep = dependency.call jobname, _inputs, real_dependencies
                   if Hash === dep
                     dep[:workflow] ||= wf  || self
                     task_info = (dep[:task] && dep[:workflow]) ? dep[:workflow].task_info(dep[:task]) : nil
                     inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, task_info)
                     dep = dep[:workflow].job(dep[:task], dep[:jobname], inputs)
                   end
                 end

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

    real_dependencies << real_dep
  end
  real_dependencies.flatten.compact
end

#rec_dependencies(taskname) ⇒ Object 



572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
 
# File 'lib/rbbt/workflow/accessor.rb', line 572

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

                            deps = task_dependencies[taskname]

                            #all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}

                            all_deps = []
                            deps.each do |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).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

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

#rec_input_defaults(taskname) ⇒ Object 



656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
 
# File 'lib/rbbt/workflow/accessor.rb', line 656

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 



688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
 
# File 'lib/rbbt/workflow/accessor.rb', line 688

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 



704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
 
# File 'lib/rbbt/workflow/accessor.rb', line 704

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 



672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
 
# File 'lib/rbbt/workflow/accessor.rb', line 672

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_inputs(taskname) ⇒ Object

def rec_inputs(taskname)

[taskname].concat(rec_dependencies(taskname)).inject([]){|acc, tn| acc.concat(task_from_dep(tn).inputs) }.uniq

end



649
650
651
652
653
654
 
# File 'lib/rbbt/workflow/accessor.rb', line 649

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

#returns(description) ⇒ Object 



36
37
38
 
# File 'lib/rbbt/workflow/definition.rb', line 36

def returns(description)
  @result_description = description
end

#set_step_dependencies(step) ⇒ Object 



355
356
357
358
359
360
361
362
 
# File 'lib/rbbt/workflow.rb', line 355

def set_step_dependencies(step)
  if step.info.include? :dependencies
    step.dependencies = step.info[:dependencies].collect do |task, job, path|
      next if job.nil?
      load_step(path) 
    end
  end
end

#step_module ⇒ Object 



284
285
286
287
288
289
290
291
292
293
294
295
 
# File 'lib/rbbt/workflow.rb', line 284

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 



833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
 
# File 'lib/rbbt/workflow/accessor.rb', line 833

def step_path(taskname, jobname, inputs, dependencies, extension = nil)
  raise "Jobname makes an invalid path: #{ jobname }" if jobname =~ /\.\./
  if inputs.length > 0 or dependencies.any?
    tagged_jobname = case TAG
                     when :hash
                       hash_str = Misc.obj2digest({:inputs => inputs, :dependencies => dependencies})
                       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 



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
 
# File 'lib/rbbt/workflow/definition.rb', line 66

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,
    :input_options      => consume_input_options
  }
  
  task = Task.setup(task_info, &block)

  last_task = task

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

#task_exports ⇒ Object 



893
894
895
 
# File 'lib/rbbt/workflow/accessor.rb', line 893

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

#task_for(path) ⇒ Object 



876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
 
# File 'lib/rbbt/workflow/accessor.rb', line 876

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 



632
633
634
635
636
637
638
639
640
641
642
643
 
# File 'lib/rbbt/workflow/accessor.rb', line 632

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 



531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
 
# File 'lib/rbbt/workflow/accessor.rb', line 531

def task_info(name)
  name = name.to_sym
  task = tasks[name]
  raise "No '#{name}' task in '#{self.to_s}' Workflow" if task.nil?
  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_defaults = rec_input_defaults(name)
  input_options = rec_input_options(name)
  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 => File.join(self.to_s, name.to_s),
    :description => description,
    :export => export,
    :inputs => inputs,
    :input_types => input_types,
    :input_descriptions => input_descriptions,
    :input_defaults => input_defaults,
    :input_options => input_options,
    :result_type => result_type,
    :result_description => result_description,
    :dependencies => dependencies
  }
end

#unexport(*names) ⇒ Object 



100
101
102
103
104
105
106
107
 
# File 'lib/rbbt/workflow/definition.rb', line 100

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

#with_workdir(workdir) ⇒ Object 



441
442
443
444
445
446
447
448
449
 
# File 'lib/rbbt/workflow.rb', line 441

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