Module: WorkflowRESTHelpers

Included in:
StreamWorkflowTask
Defined in:
lib/rbbt/rest/workflow/jobs.rb,
lib/rbbt/rest/workflow/locate.rb,
lib/rbbt/rest/workflow/render.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#workflow_resourcesObject

Returns the value of attribute workflow_resources.



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

def workflow_resources
  @workflow_resources
end

Class Method Details

.workflow_resourcesObject



4
5
6
# File 'lib/rbbt/rest/workflow/locate.rb', line 4

def self.workflow_resources
  @workflow_resources ||= [Rbbt.share.views.find(:lib)]
end

Instance Method Details

#clean_job(workflow, job) ⇒ Object



262
263
264
265
266
267
268
269
270
271
272
273
# File 'lib/rbbt/rest/workflow/jobs.rb', line 262

def clean_job(workflow, job)
  job.clean


  if format == :jobname
    halt 200, job.name
  elsif ajax
    halt 200
  else
    redirect to(File.join("/", workflow.to_s, job.task_name.to_s))
  end
end

#complete_input_set(workflow, task, inputs) ⇒ Object



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

def complete_input_set(workflow, task, inputs)
  (inputs.keys.sort - [:jobname]) === workflow.task_info(task.to_sym)[:inputs].sort
end

#consume_task_parameters(workflow, task, params = nil) ⇒ Object



6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
# File 'lib/rbbt/rest/workflow/jobs.rb', line 6

def consume_task_parameters(workflow, task, params = nil)
  task_inputs = workflow.task_info(task.to_sym)[:inputs]

  task_parameters = {}
  task_inputs.each do |input|

    input_val = consume_parameter(input, params)
    input_val = input_val.strip if String === input_val 
    input_val = [] if input_val == "EMPTY_ARRAY"

    task_parameters[input] = input_val  unless input_val.nil?

    # Param files
    input_val = consume_parameter(input.to_s + '__param_file', params)
    task_parameters[input.to_s + '__param_file'] = input_val unless input_val.nil?
  end

  task_parameters
end

#execution_type(workflow, task) ⇒ Object



44
45
46
47
48
49
50
# File 'lib/rbbt/rest/workflow/jobs.rb', line 44

def execution_type(workflow, task)
  export = type_of_export(workflow, task)
  return cache_type if cache_type
  return :sync if export == :exec and format == :html
  return export if export == :exec 
  return :asynchronous
end

#issue_job(workflow, task, jobname = nil, params = {}) ⇒ Object



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
# File 'lib/rbbt/rest/workflow/jobs.rb', line 173

def issue_job(workflow, task, jobname = nil, params = {})
  execution_type = execution_type(workflow, task)

  inputs = prepare_job_inputs(workflow, task, params)
  job = workflow.job(task, jobname, inputs)

  job.clean if job.aborted?

  clean_job(workflow, job) and clean = true if update.to_s == "clean"
  recursive_clean_job(workflow, job) and clean = true if update.to_s == "recursive_clean"

  case execution_type.to_sym
  when :exec
    show_exec_result job.exec(:stream), workflow, task
  when :stream
    if update == :reload
      job.abort
      job.clean 
    end

    job_url = File.join("/", workflow.to_s, task, job.name)

    stream_job(job, job_url)

  when :synchronous, :sync
    if update == :reload
      job.abort
      job.clean 
    end

    begin
      job_url = to(File.join("/", workflow.to_s, task, job.name)) 
      job_url += "?_format=#{@format}" if @format

      if not job.started?
        job.run
        job.join
      end

      if format == :jobname
        job.name
      else
        redirect job_url
      end
    rescue Exception
      Log.exception $!
      halt 500, $!.message
    end
  when :asynchronous, :async, nil
    if update == :reload
      job.abort
      job.clean 
    end

    begin
      job.fork unless job.started?

      job_url = to(File.join("/", workflow.to_s, task, job.name)) 
      job_url += "?_format=#{@format}" if @format
      if format == :jobname
        while not File.exists? job.info_file
          sleep 1
        end
        content_type :text
        job.name
      else
        job.soft_grace
        redirect job_url
      end
    rescue Exception
      Log.exception $!
    end
  else
    raise "Unsupported execution_type: #{ execution_type }"
  end
end

#locate_workflow_template(template, workflow = nil, task = nil) ⇒ Object



27
28
29
30
31
32
33
34
35
36
37
38
39
40
# File 'lib/rbbt/rest/workflow/locate.rb', line 27

def locate_workflow_template(template, workflow = nil, task = nil)

  if workflow
    path = locate_workflow_template_from_resource(workflow.libdir.www.views.find, template, workflow, task)
    return path if path and path.exists?
  end

  workflow_resources.each do |resource|
    path = locate_workflow_template_from_resource(resource, template, workflow, task)
    return path if path and path.exists?
  end

  raise "Template not found: [#{ template }, #{workflow}, #{ task }]"
end

#locate_workflow_template_from_resource(resource, template, workflow = nil, task = nil) ⇒ Object



12
13
14
15
16
17
18
19
20
21
22
23
24
25
# File 'lib/rbbt/rest/workflow/locate.rb', line 12

def locate_workflow_template_from_resource(resource, template, workflow = nil, task = nil)
  template += '.haml' unless template =~ /.+\..+/

  paths = []
  paths << resource[workflow][task][template] if task and workflow
  paths << resource[workflow][template] if workflow
  paths << resource[template]

  paths.each do |path|
    return path.find if path.exists?
  end 

  nil
end

#prepare_job_inputs(workflow, task, params) ⇒ Object



52
53
54
55
56
57
58
59
60
61
62
63
64
# File 'lib/rbbt/rest/workflow/jobs.rb', line 52

def prepare_job_inputs(workflow, task, params)
  inputs = workflow.task_info(task)[:inputs]
  input_types = workflow.task_info(task)[:input_types]
  input_options = workflow.task_info(task)[:input_options]

  task_inputs = {}
  inputs.each do |input|
    stream = input_options.include?(input) and input_options[input][:stream]
    task_inputs[input] = prepare_input(params, input, input_types[input], stream)
  end

  task_inputs
end

#recursive_clean_job(workflow, job) ⇒ Object



250
251
252
253
254
255
256
257
258
259
260
# File 'lib/rbbt/rest/workflow/jobs.rb', line 250

def recursive_clean_job(workflow, job)
  job.recursive_clean

  if format == :jobname
    halt 200, job.name
  elsif ajax
    halt 200
  else
    redirect to(File.join("/", workflow.to_s, job.task_name.to_s))
  end
end

#show_exec_result(result, workflow, task) ⇒ Object



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
# File 'lib/rbbt/rest/workflow/jobs.rb', line 73

def show_exec_result(result, workflow, task)
  case format.to_sym
  when :html
    show_result_html result, workflow, task, nil
  when :json
    content_type "application/json"
    halt 200, result.to_json
  when :tsv
    content_type "text/tab-separated-values"
    result = result.to_s unless String === result or result.respond_to? :gets
    halt 200, result
  when :literal, :raw
    content_type "text/plain"
    case workflow.task_info(task)[:result_type]
    when :array
      halt 200, result * "\n"
    else
      result = result.to_s unless String === result or result.respond_to? :gets
      halt 200, result
    end
  when :binary
    content_type "application/octet-stream"
    result = result.to_s unless String === result or result.respond_to? :gets
    halt 200, result.to_s
  when :jobname
    halt 200, nil
  else
    raise "Unsupported format: #{ format }"
  end
end

#show_result(job, workflow, task, params = nil) ⇒ Object



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
# File 'lib/rbbt/rest/workflow/jobs.rb', line 104

def show_result(job, workflow, task, params = nil)
  return show_result_html nil, workflow, task, job.name, job if @fragment

  case format.to_sym
  when :html
    show_result_html job.load, workflow, task, job.name, job, params
  when :table
    halt 200, tsv2html(job.path, :url => "/" << [workflow.to_s, task, job.name] * "/")
  when :entities
    tsv = tsv_process(load_tsv(job.path).first)
    list = tsv.column_values(tsv.fields.first).flatten
    if not AnnotatedArray === list and Annotated === list.first
      list.first.annotate list 
      list.extend AnnotatedArray
    end
    type = list.annotation_types.last
    list_id = "TMP #{type} in #{ [workflow.to_s, task, job.name] * " - " }"
    Entity::List.save_list(type.to_s, list_id, list, user)
    redirect to(Entity::REST.entity_list_url(list_id, type))
  when :map
    tsv = tsv_process(load_tsv(job.path).first)
    type = tsv.keys.annotation_types.last
    column = tsv.fields.first
    map_id = "MAP #{type}-#{column} in #{ [workflow.to_s, task, job.name] * " - " }"
    Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
    redirect to(Entity::REST.entity_map_url(map_id, type, column))
  when :json
    content_type "application/json"
    halt 200, job.load.to_json
  when :tsv
    content_type "text/tab-separated-values"
    job.path ? send_file(job.path) : halt(200, job.load.to_s)
  when :literal, :raw
    content_type "text/plain"
    job.path ? send_file(job.path) : halt(200, job.load.to_s)
  when :binary
    content_type "application/octet-stream"
    job.path ? send_file(job.path) : halt(200, job.load.to_s)
  when :excel
    require 'rbbt/tsv/excel'
    data = nil
    excel_file = TmpFile.tmp_file
    result = job.load
    result.excel(excel_file, :name => @excel_use_name,:sort_by => @excel_sort_by, :sort_by_cast => @excel_sort_by_cast, :remove_links => true)
    send_file excel_file, :type => 'application/vnd.ms-excel', :filename => job.clean_name + '.xls'
  else
    raise "Unsupported format: #{ format }"
  end
end

#show_result_html(result, workflow, task, jobname = nil, job = nil, params = nil) ⇒ Object



66
67
68
69
70
71
# File 'lib/rbbt/rest/workflow/jobs.rb', line 66

def show_result_html(result, workflow, task, jobname = nil, job = nil, params = nil)
  params ||= {}
  result_type = workflow.task_info(task)[:result_type]
  result_description = workflow.task_info(task)[:result_description]
  workflow_render('job_result', workflow, task, {:result => result, :type => result_type, :description => result_description, :jobname => jobname, :job => job}.merge(params))
end

#stream_job(job, job_url = nil) ⇒ Object



154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
# File 'lib/rbbt/rest/workflow/jobs.rb', line 154

def stream_job(job, job_url = nil)
  unless job.started? or job.done?
    job.run(:stream) 
    job.soft_grace
  end

  raise job.messages.last if job.error?

  s = TSV.get_stream job

  sout, sin = Misc.pipe

  Misc.consume_stream(s, true, sin)

  headers "RBBT-STREAMING-JOB-URL" =>  job_url if job_url

  halt 200, sout
end

#type_of_export(workflow, task) ⇒ Object



30
31
32
33
34
35
36
37
38
39
40
41
42
# File 'lib/rbbt/rest/workflow/jobs.rb', line 30

def type_of_export(workflow, task)
  task = task.to_sym
  case
  when workflow.exec_exports.include?(task)
    :exec
  when workflow.synchronous_exports.include?(task)
    :synchronous
  when workflow.asynchronous_exports.include?(task)
    :asynchronous
  else
    raise "Access denied: no known export type for #{ workflow }##{ task }."
  end
end

#workflow_partial(template, workflow = nil, task = nil, params = {}) ⇒ Object



35
36
37
38
39
40
41
42
43
44
45
46
# File 'lib/rbbt/rest/workflow/render.rb', line 35

def workflow_partial(template, workflow = nil, task = nil, params = {})
  workflow = consume_parameter(:workflow, params) if workflow.nil?
  task     = consume_parameter(:task, params) if workflow.nil?

  template_file = locate_workflow_template(template, workflow, task)

  locals = params.dup
  locals[:workflow] = workflow if workflow
  locals[:task]     = task if task

  render_partial(template_file, locals)
end

#workflow_render(template, workflow = nil, task = nil, params = {}) ⇒ Object



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
# File 'lib/rbbt/rest/workflow/render.rb', line 6

def workflow_render(template, workflow = nil, task = nil, params = {})
  workflow = consume_parameter(:workflow, params) if workflow.nil?
  task     = consume_parameter(:task, params) if workflow.nil?
  job      = consume_parameter(:job, params) if job.nil?

  template_file = locate_workflow_template(template, workflow, task)

  locals = params.dup
  locals[:workflow] = workflow if workflow
  locals[:task]     = task if task

  if layout
    layout_file = workflow.libdir.www.views[workflow.to_s]["layout.haml"] if workflow.libdir
    layout_file = locate_template("layout") unless layout_file and layout_file.exists?
  else
    layout_file = nil
  end

  if job 
    locals[:job] = job 
    @step = job
    cache_type = execution_type(workflow, task)
    cache_file = job.file('html')
    render(template_file, locals, layout_file, [task,workflow,job.name] * "-", :cache_type => cache_type, :cache_file => cache_file)
  else
    render(template_file, locals, layout_file, [workflow, task, template_file].compact * "-", :cache_type => :async )
  end
end