Module: Workflow

Includes:
AnnotatedModule
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 = 
:hash

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from AnnotatedModule

add_consummable_annotation, #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.



164
165
166
 
# File 'lib/rbbt/workflow.rb', line 164

def asynchronous_exports
  @asynchronous_exports
end

#description ⇒ Object

Returns the value of attribute description.



160
161
162
 
# File 'lib/rbbt/workflow.rb', line 160

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.



164
165
166
 
# File 'lib/rbbt/workflow.rb', line 164

def exec_exports
  @exec_exports
end

#helpers ⇒ Object

Returns the value of attribute helpers.



162
163
164
 
# File 'lib/rbbt/workflow.rb', line 162

def helpers
  @helpers
end

#last_task ⇒ Object

Returns the value of attribute last_task.



163
164
165
 
# File 'lib/rbbt/workflow.rb', line 163

def last_task
  @last_task
end

#libdir ⇒ Object

Returns the value of attribute libdir.



161
162
163
 
# File 'lib/rbbt/workflow.rb', line 161

def libdir
  @libdir
end

#step_cache ⇒ Object

Returns the value of attribute step_cache.



165
166
167
 
# File 'lib/rbbt/workflow.rb', line 165

def step_cache
  @step_cache
end

#synchronous_exports ⇒ Object

Returns the value of attribute synchronous_exports.



164
165
166
 
# File 'lib/rbbt/workflow.rb', line 164

def synchronous_exports
  @synchronous_exports
end

#task_dependencies ⇒ Object

Returns the value of attribute task_dependencies.



163
164
165
 
# File 'lib/rbbt/workflow.rb', line 163

def task_dependencies
  @task_dependencies
end

#task_description ⇒ Object

Returns the value of attribute task_description.



163
164
165
 
# File 'lib/rbbt/workflow.rb', line 163

def task_description
  @task_description
end

#tasks ⇒ Object

Returns the value of attribute tasks.



162
163
164
 
# File 'lib/rbbt/workflow.rb', line 162

def tasks
  @tasks
end

#workdir ⇒ Object

Returns the value of attribute workdir.



161
162
163
 
# File 'lib/rbbt/workflow.rb', line 161

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 



32
33
34
35
 
# File 'lib/rbbt/workflow.rb', line 32

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

.installed_workflows ⇒ Object 



57
58
59
60
61
 
# File 'lib/rbbt/workflow.rb', line 57

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
 
# 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
    Log.debug "Trying #{ input }: #{file}"
    next unless file.exists?

    case input_types[input]
    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
  IndiferentHash.setup(inputs)
end

.load_workflow_file(filename) ⇒ Object 



42
43
44
45
46
47
48
49
50
51
52
53
54
55
 
# File 'lib/rbbt/workflow.rb', line 42

def self.load_workflow_file(filename)
  begin
    $LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))

    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

.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

.require_local_workflow(wf_name) ⇒ Object 



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
 
# File 'lib/rbbt/workflow.rb', line 78

def self.require_local_workflow(wf_name)
  filename = nil

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

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

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

  if filename and File.exists? filename
    load_workflow_file filename
  else
    return false
  end
end

.require_remote_workflow(wf_name, url) ⇒ Object 



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

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) ⇒ Object 



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
 
# File 'lib/rbbt/workflow.rb', line 107

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

  # Load remotely
  if 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 
  require_local_workflow(Misc.snake_case(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 



227
228
229
230
231
232
233
234
235
236
237
238
 
# File 'lib/rbbt/workflow.rb', line 227

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

Instance Method Details

#all_exports ⇒ Object 



220
221
222
 
# File 'lib/rbbt/workflow.rb', line 220

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

#dep(*dependency, &block) ⇒ Object 



37
38
39
40
41
42
43
44
45
46
47
48
49
 
# File 'lib/rbbt/workflow/definition.rb', line 37

def dep(*dependency_list, &block)
  @dependencies ||= []
  if Module === dependency_list.first or Hash === dependency_list.last
    @dependencies << dependency_list
  else
    @dependency_list ||= []
    if block_given?
      dependency_list.unshift self if dependency_list.length == 1
      dependency_list << block 
    end
    dependencies.concat dependency_list
  end
end

#desc(description) ⇒ Object 



25
26
27
 
# File 'lib/rbbt/workflow/definition.rb', line 25

def desc(description)
  @description = description
end

#doc(task = nil) ⇒ Object 



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
 
# File 'lib/rbbt/workflow/usage.rb', line 46

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[: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 



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

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 



104
105
106
107
108
 
# File 'lib/rbbt/workflow/definition.rb', line 104

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

#export_exec(*names) ⇒ Object 



98
99
100
101
102
 
# File 'lib/rbbt/workflow/definition.rb', line 98

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

#export_synchronous(*names) ⇒ Object 



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

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

#extension(extension) ⇒ Object 



29
30
31
 
# File 'lib/rbbt/workflow/definition.rb', line 29

def extension(extension)
  @extension = extension
end

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



253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
 
# File 'lib/rbbt/workflow.rb', line 253

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


  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 



21
22
23
 
# File 'lib/rbbt/workflow/definition.rb', line 21

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

#id_for(path) ⇒ Object 



558
559
560
561
562
563
564
565
 
# File 'lib/rbbt/workflow/accessor.rb', line 558

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 



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
298
299
300
301
302
303
304
305
306
307
 
# File 'lib/rbbt/workflow.rb', line 270

def job(taskname, jobname = nil, inputs = {})
  taskname = taskname.to_sym
  jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?

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

  IndiferentHash.setup(inputs)

  Workflow.resolve_locals(inputs)

  task_inputs = task_info(taskname)[:inputs]
  defaults = IndiferentHash.setup(task_info(taskname)[:input_defaults])

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

  real_inputs = {}

  inputs.each do |k,v|
    default = defaults[k]
    if (task_inputs.include?(k.to_sym) or task_inputs.include?(k.to_s)) and 
      (defaults[k].to_s != v.to_s and not (FalseClass === v and defaults[k].nil?))
      real_inputs[k] = v 
    end
  end

  if real_inputs.empty?
    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.clean_name = jobname
  job
end

#jobs(taskname, query = nil) ⇒ Object 



333
334
335
336
337
338
339
340
341
 
# File 'lib/rbbt/workflow.rb', line 333

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 



314
315
316
317
318
319
320
321
322
323
324
325
 
# File 'lib/rbbt/workflow.rb', line 314

def load_id(id)
  path = File.join(workdir, id)
  task = task_for path
  step = Step.new path, tasks[task.to_sym]
  step.info
  if step.info.include? :dependencies
    step.dependencies = step.info[:dependencies].collect do |task, job|
      load_id(File.join(task.to_s, job))
    end
  end
  step
end

#load_name(task, name) ⇒ Object 



327
328
329
330
331
 
# File 'lib/rbbt/workflow.rb', line 327

def load_name(task, name)
  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 



309
310
311
312
 
# File 'lib/rbbt/workflow.rb', line 309

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

#local_persist_setup ⇒ Object

{{{ Make workflow resources local



344
345
346
347
348
349
 
# File 'lib/rbbt/workflow.rb', line 344

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

#local_workdir_setup ⇒ Object 



351
352
353
 
# File 'lib/rbbt/workflow.rb', line 351

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

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



378
379
380
 
# File 'lib/rbbt/workflow/accessor.rb', line 378

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

#make_local ⇒ Object 



355
356
357
358
 
# File 'lib/rbbt/workflow.rb', line 355

def make_local
  local_persist_setup
  local_workdir_setup
end

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



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
526
527
528
529
530
 
# File 'lib/rbbt/workflow/accessor.rb', line 498

def real_dependencies(task, jobname, inputs, dependencies)
  real_dependencies = []
  dependencies.each do |dependency|
    real_dependencies << case dependency
    when Array
      inputs = inputs.dup
      workflow, task, options = dependency
      options = dependency.last if Hash === dependency.last
      options.each{|i,v|
        case v
        when Symbol
          rec_dependency = real_dependencies.collect{|d| [d, d.rec_dependencies].compact.flatten}.flatten.select{|d| d.task.name == v }.first
          if (dependency.first.tasks[dependency[1]].input_options[i] || {})[:stream]
            inputs[i] = rec_dependency.run(true).grace.join.path 
          else
            inputs[i] = rec_dependency.run(true).join.load
          end
        else
          inputs[i] = v
        end
      } if options
      res = dependency.first.job(dependency[1], jobname, inputs)
      res
    when Step
      dependency
    when Symbol
      job(dependency, jobname, inputs)
    when Proc
      dependency.call jobname, inputs, real_dependencies
    end
  end
  real_dependencies.flatten.compact
end

#rec_dependencies(taskname) ⇒ Object 



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
 
# File 'lib/rbbt/workflow/accessor.rb', line 421

def rec_dependencies(taskname)
  if task_dependencies.include? taskname
    deps = task_dependencies[taskname]
    all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}
    deps.each do |dep| 
      case dep
      when Array
        dep.first.rec_dependencies(dep.last).each do |d|
          if Array === d
            all_deps << d
          else
            all_deps << [dep.first, d]
          end
        end
      when String, Symbol
        all_deps.concat rec_dependencies(dep.to_sym)
      when DependencyBlock
        all_deps << dep.dependency
      end
    end
    all_deps.uniq
  else
    []
  end
end

#rec_input_defaults(taskname) ⇒ Object 



470
471
472
473
474
475
 
# File 'lib/rbbt/workflow/accessor.rb', line 470

def rec_input_defaults(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject(IndiferentHash.setup({})){|acc, tn|
    new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_defaults
    acc = new.merge(acc) 
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_descriptions(taskname) ⇒ Object 



484
485
486
487
488
489
 
# File 'lib/rbbt/workflow/accessor.rb', line 484

def rec_input_descriptions(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_descriptions
    acc = new.merge(acc) 
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_options(taskname) ⇒ Object 



491
492
493
494
495
496
 
# File 'lib/rbbt/workflow/accessor.rb', line 491

def rec_input_options(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_options
    acc = new.merge(acc) 
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_input_types(taskname) ⇒ Object 



477
478
479
480
481
482
 
# File 'lib/rbbt/workflow/accessor.rb', line 477

def rec_input_types(taskname)
  [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
    new = (Array === tn ? tn.first.tasks[tn[1].to_sym] : tasks[tn.to_sym]).input_types
    acc = new.merge(acc) 
  }.tap{|h| IndiferentHash.setup(h)}
end

#rec_inputs(taskname) ⇒ Object 



460
461
462
 
# File 'lib/rbbt/workflow/accessor.rb', line 460

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

#returns(description) ⇒ Object 



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

def returns(description)
  @result_description = description
end

#step_module ⇒ Object 



240
241
242
243
244
245
246
247
248
249
250
251
 
# File 'lib/rbbt/workflow.rb', line 240

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 



533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
 
# File 'lib/rbbt/workflow/accessor.rb', line 533

def step_path(taskname, jobname, inputs, dependencies, extension = nil)
  #Proc.new{
    raise "Jobname makes an invalid path: #{ jobname }" if jobname =~ /\.\./
    if inputs.any? or dependencies.any?
      tagged_jobname = case TAG
                       when :hash
                         input_str = ""
                         input_str << inputs.collect{|i| Misc.fingerprint(i) } * "," 
                         input_str << ";" << dependencies.collect{|dep| dep.name } * "\n"
                         jobname + '_' << Misc.digest(input_str)
                       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
 
# 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        => (Array === type ? type.to_sym : type),
    :input_defaults     => consume_input_defaults,
    :input_descriptions => consume_input_descriptions,
    :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_for(path) ⇒ Object 



567
568
569
570
571
572
573
574
575
576
577
578
 
# File 'lib/rbbt/workflow/accessor.rb', line 567

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)
  Misc.path_relative_to(workdir_find, dir).sub(/([^\/]+)\/.*/,'\1')
end

#task_from_dep(dep) ⇒ Object 



447
448
449
450
451
452
453
454
455
456
457
458
 
# File 'lib/rbbt/workflow/accessor.rb', line 447

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 



382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
 
# File 'lib/rbbt/workflow/accessor.rb', line 382

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
           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

#with_workdir(workdir) ⇒ Object 



360
361
362
363
364
365
366
367
368
 
# File 'lib/rbbt/workflow.rb', line 360

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