rbbt-rest 1.3.2 → 1.3.3
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- checksums.yaml +4 -4
- data/lib/rbbt/rest/client.rb +8 -329
- data/lib/rbbt/rest/client/adaptor.rb +66 -0
- data/lib/rbbt/rest/client/get.rb +83 -0
- data/lib/rbbt/rest/client/step.rb +123 -0
- data/lib/rbbt/rest/common/misc.rb +1 -1
- data/lib/rbbt/rest/main.rb +4 -4
- data/lib/rbbt/rest/workflow.rb +18 -0
- metadata +4 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: b556674b8552bf64d8680def41f2316821743b64
|
4
|
+
data.tar.gz: 3f1fb6faa193e793870d65706e3ca828b7de897f
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 8329fbef77bc84d70921839a9648e988a1d587a33de739c23dd1255e90bddbe33794a12dee8e51dc6e4bede70b7118690ea1afb5a1022ddc35dc995401303b4b
|
7
|
+
data.tar.gz: 233769daa035553e3a1d294f2cf1cb426bbc779605b24e1c357a65d6d3693f831c9d72014d1cf845ebe00c6f0b770d31a68810e47daa384e613dfd164709993b
|
data/lib/rbbt/rest/client.rb
CHANGED
@@ -4,174 +4,12 @@ require 'rbbt/workflow'
|
|
4
4
|
require 'rbbt/workflow/step'
|
5
5
|
require 'rbbt/util/misc'
|
6
6
|
|
7
|
-
|
7
|
+
require 'rbbt/rest/client/get'
|
8
|
+
require 'rbbt/rest/client/adaptor'
|
9
|
+
require 'rbbt/rest/client/step'
|
8
10
|
|
9
|
-
|
10
|
-
|
11
|
-
hash.each do |key, value|
|
12
|
-
fixed[key.to_sym] = case
|
13
|
-
when Hash === value
|
14
|
-
fix_hash(value)
|
15
|
-
when (fix_values and String === value)
|
16
|
-
value.to_sym
|
17
|
-
else
|
18
|
-
value
|
19
|
-
end
|
20
|
-
end
|
21
|
-
fixed
|
22
|
-
end
|
23
|
-
|
24
|
-
def self.get_raw(url, params = {})
|
25
|
-
Log.debug{ "RestClient get_raw: #{ url } - #{Misc.fingerprint params}" }
|
26
|
-
params = params.merge({ :_format => 'raw' })
|
27
|
-
Misc.insist(2, 0.5) do
|
28
|
-
RestClient.get(URI.encode(url), :params => params)
|
29
|
-
end
|
30
|
-
end
|
31
|
-
|
32
|
-
def self.post_jobname(url, params = {})
|
33
|
-
Log.debug{ "RestClient post_jobname: #{ url } - #{Misc.fingerprint params}" }
|
34
|
-
params = params.merge({ :_format => 'jobname' })
|
35
|
-
RestClient.post(URI.encode(url), params)
|
36
|
-
end
|
37
|
-
|
38
|
-
def self.get_json(url, params = {})
|
39
|
-
Log.debug{ "RestClient get_json: #{ url } - #{Misc.fingerprint params }" }
|
40
|
-
params = params.merge({ :_format => 'json' })
|
41
|
-
begin
|
42
|
-
res = RestClient.get(URI.encode(url), :params => params)
|
43
|
-
rescue => e
|
44
|
-
raise JSON.parse(e.response)["message"]
|
45
|
-
end
|
46
|
-
begin
|
47
|
-
JSON.parse(res)
|
48
|
-
rescue
|
49
|
-
res
|
50
|
-
end
|
51
|
-
end
|
52
|
-
|
53
|
-
def self.post_json(url, params = {})
|
54
|
-
if url =~ /_cache_type=:exec/
|
55
|
-
JSON.parse(Open.open(url, :nocache => true))
|
56
|
-
else
|
57
|
-
params = params.merge({ :_format => 'json' })
|
58
|
-
res = RestClient.post(URI.encode(url), params)
|
59
|
-
begin
|
60
|
-
JSON.parse(res)
|
61
|
-
rescue
|
62
|
-
res
|
63
|
-
end
|
64
|
-
end
|
65
|
-
end
|
66
|
-
|
67
|
-
class RemoteStep < Step
|
68
|
-
|
69
|
-
attr_accessor :url, :base_url, :task, :name, :inputs, :result_type, :result_description
|
70
|
-
|
71
|
-
def name
|
72
|
-
(Array === @url ? @url.first : @url).split("/").last
|
73
|
-
end
|
74
|
-
|
75
|
-
def task_name
|
76
|
-
(Array === @url ? @url.first : @url).split("/")[-2]
|
77
|
-
end
|
78
|
-
|
79
|
-
def info
|
80
|
-
info = WorkflowRESTClient.get_json(File.join(url, 'info'))
|
81
|
-
info = WorkflowRESTClient.fix_hash(info)
|
82
|
-
info[:status] = info[:status].to_sym if String === info[:status]
|
83
|
-
info
|
84
|
-
end
|
85
|
-
|
86
|
-
def done?
|
87
|
-
status.to_s == 'done'
|
88
|
-
end
|
89
|
-
|
90
|
-
def fork
|
91
|
-
@name = WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name, :_cache_type => :asynchronous))
|
92
|
-
@url = File.join(base_url, task.to_s, @name)
|
93
|
-
self
|
94
|
-
end
|
95
|
-
|
96
|
-
def initialize(base_url, task = nil, name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
|
97
|
-
if task.nil?
|
98
|
-
@url = base_url
|
99
|
-
else
|
100
|
-
@base_url, @task, @name, @inputs, @result_type, @result_description = base_url, task, name, inputs, result_type, result_description
|
101
|
-
if exec
|
102
|
-
@url = [File.join(base_url, task.to_s), inputs]
|
103
|
-
else
|
104
|
-
self.fork
|
105
|
-
end
|
106
|
-
end
|
107
|
-
end
|
108
|
-
|
109
|
-
def _exec(noload = false)
|
110
|
-
if Array === @url
|
111
|
-
url, params = @url
|
112
|
-
else
|
113
|
-
url, params = @url, {:_cache_type => :synchronous}
|
114
|
-
end
|
115
|
-
|
116
|
-
params[:jobname] = @name if @name
|
117
|
-
|
118
|
-
if noload and %w(boolean string tsv).include? result_type
|
119
|
-
WorkflowRESTClient.get_raw(url, params)
|
120
|
-
else
|
121
|
-
case result_type
|
122
|
-
when :string
|
123
|
-
WorkflowRESTClient.get_raw(url, params)
|
124
|
-
when :boolean
|
125
|
-
WorkflowRESTClient.get_raw(url, params) == "true"
|
126
|
-
when :tsv
|
127
|
-
TSV.open(StringIO.new(WorkflowRESTClient.get_raw(url, params)))
|
128
|
-
when :annotations
|
129
|
-
Annotated.load_tsv(TSV.open(StringIO.new(WorkflowRESTClient.get_raw(url, params))))
|
130
|
-
else
|
131
|
-
WorkflowRESTClient.get_json(url, params)
|
132
|
-
end
|
133
|
-
end
|
134
|
-
end
|
135
|
-
|
136
|
-
def exec
|
137
|
-
res = _exec
|
138
|
-
prepare_result(res, result_type)
|
139
|
-
end
|
140
|
-
|
141
|
-
def run(noload = false)
|
142
|
-
if noload
|
143
|
-
_exec(noload)
|
144
|
-
else
|
145
|
-
exec
|
146
|
-
end
|
147
|
-
end
|
148
|
-
|
149
|
-
def load
|
150
|
-
exec
|
151
|
-
end
|
152
|
-
|
153
|
-
def join
|
154
|
-
exec
|
155
|
-
self
|
156
|
-
end
|
157
|
-
|
158
|
-
def status
|
159
|
-
info[:status]
|
160
|
-
end
|
161
|
-
|
162
|
-
def clean
|
163
|
-
WorkflowRESTClient.get_raw(url, :_update => :clean)
|
164
|
-
self
|
165
|
-
end
|
166
|
-
|
167
|
-
def files
|
168
|
-
WorkflowRESTClient.get_json(File.join(url, 'files'))
|
169
|
-
end
|
170
|
-
|
171
|
-
def file(file)
|
172
|
-
WorkflowRESTClient.get_json(File.join(url, 'file', file))
|
173
|
-
end
|
174
|
-
end
|
11
|
+
class WorkflowRESTClient
|
12
|
+
include Workflow
|
175
13
|
|
176
14
|
attr_accessor :url, :name, :exec_exports, :asynchronous_exports, :synchronous_exports
|
177
15
|
|
@@ -185,103 +23,6 @@ class WorkflowRESTClient
|
|
185
23
|
name
|
186
24
|
end
|
187
25
|
|
188
|
-
def workflow_description
|
189
|
-
WorkflowRESTClient.get_raw(File.join(url, 'description'))
|
190
|
-
end
|
191
|
-
|
192
|
-
def documentation
|
193
|
-
@documention ||= IndiferentHash.setup(WorkflowRESTClient.get_json(File.join(url, "documentation"),{}))
|
194
|
-
end
|
195
|
-
|
196
|
-
def task_info(task)
|
197
|
-
@task_info ||= {}
|
198
|
-
@task_info[task]
|
199
|
-
|
200
|
-
if @task_info[task].nil?
|
201
|
-
task_info = WorkflowRESTClient.get_json(File.join(url, task.to_s, 'info'))
|
202
|
-
task_info = WorkflowRESTClient.fix_hash(task_info)
|
203
|
-
|
204
|
-
task_info[:result_type] = task_info[:result_type].to_sym
|
205
|
-
task_info[:export] = task_info[:export].to_sym
|
206
|
-
task_info[:input_types] = WorkflowRESTClient.fix_hash(task_info[:input_types], true)
|
207
|
-
task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym }
|
208
|
-
|
209
|
-
@task_info[task] = task_info
|
210
|
-
end
|
211
|
-
@task_info[task]
|
212
|
-
end
|
213
|
-
|
214
|
-
def exported_tasks
|
215
|
-
(@asynchronous_exports + @synchronous_exports + @exec_exports).compact.flatten
|
216
|
-
end
|
217
|
-
|
218
|
-
def tasks
|
219
|
-
@tasks ||= Hash.new do |hash,task_name|
|
220
|
-
info = task_info(task_name)
|
221
|
-
task = Task.setup info do |*args|
|
222
|
-
raise "This is a remote task"
|
223
|
-
end
|
224
|
-
task.name = task_name.to_sym
|
225
|
-
hash[task_name] = task
|
226
|
-
end
|
227
|
-
end
|
228
|
-
|
229
|
-
def load_tasks
|
230
|
-
exported_tasks.each{|name| tasks[name]}
|
231
|
-
nil
|
232
|
-
end
|
233
|
-
|
234
|
-
def task_dependencies
|
235
|
-
@task_dependencies ||= Hash.new do |hash,task|
|
236
|
-
hash[task] = if exported_tasks.include? task
|
237
|
-
WorkflowRESTClient.get_json(File.join(url, task.to_s, 'dependencies'))
|
238
|
-
else
|
239
|
-
[]
|
240
|
-
end
|
241
|
-
end
|
242
|
-
end
|
243
|
-
|
244
|
-
def rec_dependencies(taskname)
|
245
|
-
if task_dependencies.include? taskname
|
246
|
-
deps = task_dependencies[taskname].select{|dep| String === dep or Symbol === dep}
|
247
|
-
deps.concat deps.collect{|dep| rec_dependencies(dep)}.compact.flatten
|
248
|
-
deps.uniq
|
249
|
-
else
|
250
|
-
[]
|
251
|
-
end
|
252
|
-
end
|
253
|
-
|
254
|
-
def rec_inputs(taskname)
|
255
|
-
[taskname].concat(rec_dependencies(taskname)).inject([]){|acc, tn| acc.concat tasks[tn.to_sym].inputs}
|
256
|
-
end
|
257
|
-
|
258
|
-
def rec_input_defaults(taskname)
|
259
|
-
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_defaults}.
|
260
|
-
tap{|h| IndiferentHash.setup(h) }
|
261
|
-
end
|
262
|
-
|
263
|
-
def rec_input_types(taskname)
|
264
|
-
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_types}.
|
265
|
-
tap{|h| IndiferentHash.setup(h) }
|
266
|
-
end
|
267
|
-
|
268
|
-
def rec_input_descriptions(taskname)
|
269
|
-
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_descriptions}.
|
270
|
-
tap{|h| IndiferentHash.setup(h) }
|
271
|
-
end
|
272
|
-
|
273
|
-
def rec_input_options(taskname)
|
274
|
-
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_options}.
|
275
|
-
tap{|h| IndiferentHash.setup(h) }
|
276
|
-
end
|
277
|
-
|
278
|
-
def init_remote_tasks
|
279
|
-
task_exports = WorkflowRESTClient.get_json(url)
|
280
|
-
@asynchronous_exports = task_exports["asynchronous"].collect{|task| task.to_sym }
|
281
|
-
@synchronous_exports = task_exports["synchronous"].collect{|task| task.to_sym }
|
282
|
-
@exec_exports = task_exports["exec"].collect{|task| task.to_sym }
|
283
|
-
end
|
284
|
-
|
285
26
|
def job(task, name, inputs)
|
286
27
|
task_info = task_info(task)
|
287
28
|
fixed_inputs = {}
|
@@ -293,78 +34,16 @@ class WorkflowRESTClient
|
|
293
34
|
v
|
294
35
|
end
|
295
36
|
end
|
37
|
+
|
296
38
|
RemoteStep.new(url, task, name, fixed_inputs, task_info[:result_type], task_info[:result_description], @exec_exports.include?(task))
|
297
39
|
end
|
298
40
|
|
299
41
|
def load_id(id)
|
300
42
|
task, name = id.split("/")
|
301
|
-
step = RemoteStep.new
|
43
|
+
step = RemoteStep.new url, task, nil
|
44
|
+
step.name = name
|
302
45
|
step.result_type = task_info(task)[:result_type]
|
303
46
|
step.result_description = task_info(task)[:result_description]
|
304
47
|
step
|
305
48
|
end
|
306
|
-
|
307
|
-
def doc(task = nil)
|
308
|
-
|
309
|
-
if task.nil?
|
310
|
-
puts self.to_s
|
311
|
-
puts "=" * self.to_s.length
|
312
|
-
puts
|
313
|
-
|
314
|
-
puts "## TASKS"
|
315
|
-
puts
|
316
|
-
tasks.each do |name,task|
|
317
|
-
puts " * #{ name }:"
|
318
|
-
puts " " << task.description if task.description and not task.description.empty?
|
319
|
-
puts
|
320
|
-
end
|
321
|
-
else
|
322
|
-
|
323
|
-
if Task === task
|
324
|
-
task_name = task.name
|
325
|
-
else
|
326
|
-
task_name = task
|
327
|
-
task = self.tasks[task_name]
|
328
|
-
end
|
329
|
-
dependencies = self.rec_dependencies(task_name).collect{|dep_name| self.tasks[dep_name.to_sym]}
|
330
|
-
|
331
|
-
task.doc(dependencies)
|
332
|
-
end
|
333
|
-
end
|
334
|
-
|
335
|
-
def doc(task = nil)
|
336
|
-
|
337
|
-
if task.nil?
|
338
|
-
puts Log.color :magenta, self.to_s
|
339
|
-
puts Log.color :magenta, "=" * self.to_s.length
|
340
|
-
if self.documentation[:description] and not self.documentation[:description].empty?
|
341
|
-
puts
|
342
|
-
puts Misc.format_paragraph self.documentation[:description]
|
343
|
-
end
|
344
|
-
puts
|
345
|
-
|
346
|
-
puts Log.color :magenta, "## TASKS"
|
347
|
-
if self.documentation[:task_description] and not self.documentation[:task_description].empty?
|
348
|
-
puts
|
349
|
-
puts Misc.format_paragraph self.documentation[:task_description]
|
350
|
-
end
|
351
|
-
puts
|
352
|
-
|
353
|
-
tasks.each do |name,task|
|
354
|
-
puts Misc.format_definition_list_item(name.to_s, task.description || "", 80, 30, :yellow)
|
355
|
-
end
|
356
|
-
|
357
|
-
else
|
358
|
-
|
359
|
-
if Task === task
|
360
|
-
task_name = task.name
|
361
|
-
else
|
362
|
-
task_name = task
|
363
|
-
task = self.tasks[task_name]
|
364
|
-
end
|
365
|
-
dependencies = self.rec_dependencies(task_name).collect{|dep_name| self.tasks[dep_name.to_sym]}
|
366
|
-
|
367
|
-
task.doc(dependencies)
|
368
|
-
end
|
369
|
-
end
|
370
49
|
end
|
@@ -0,0 +1,66 @@
|
|
1
|
+
class WorkflowRESTClient
|
2
|
+
|
3
|
+
def workflow_description
|
4
|
+
WorkflowRESTClient.get_raw(File.join(url, 'description'))
|
5
|
+
end
|
6
|
+
|
7
|
+
def documentation
|
8
|
+
@documention ||= IndiferentHash.setup(WorkflowRESTClient.get_json(File.join(url, "documentation"),{}))
|
9
|
+
end
|
10
|
+
|
11
|
+
def task_info(task)
|
12
|
+
@task_info ||= {}
|
13
|
+
@task_info[task]
|
14
|
+
|
15
|
+
if @task_info[task].nil?
|
16
|
+
task_info = WorkflowRESTClient.get_json(File.join(url, task.to_s, 'info'))
|
17
|
+
task_info = WorkflowRESTClient.fix_hash(task_info)
|
18
|
+
|
19
|
+
task_info[:result_type] = task_info[:result_type].to_sym
|
20
|
+
task_info[:export] = task_info[:export].to_sym
|
21
|
+
task_info[:input_types] = WorkflowRESTClient.fix_hash(task_info[:input_types], true)
|
22
|
+
task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym }
|
23
|
+
|
24
|
+
@task_info[task] = task_info
|
25
|
+
end
|
26
|
+
@task_info[task]
|
27
|
+
end
|
28
|
+
|
29
|
+
def exported_tasks
|
30
|
+
(@asynchronous_exports + @synchronous_exports + @exec_exports).compact.flatten
|
31
|
+
end
|
32
|
+
|
33
|
+
def tasks
|
34
|
+
@tasks ||= Hash.new do |hash,task_name|
|
35
|
+
info = task_info(task_name)
|
36
|
+
task = Task.setup info do |*args|
|
37
|
+
raise "This is a remote task"
|
38
|
+
end
|
39
|
+
task.name = task_name.to_sym
|
40
|
+
hash[task_name] = task
|
41
|
+
end
|
42
|
+
end
|
43
|
+
|
44
|
+
def load_tasks
|
45
|
+
exported_tasks.each{|name| tasks[name]}
|
46
|
+
nil
|
47
|
+
end
|
48
|
+
|
49
|
+
def task_dependencies
|
50
|
+
@task_dependencies ||= Hash.new do |hash,task|
|
51
|
+
hash[task] = if exported_tasks.include? task
|
52
|
+
WorkflowRESTClient.get_json(File.join(url, task.to_s, 'dependencies'))
|
53
|
+
else
|
54
|
+
[]
|
55
|
+
end
|
56
|
+
end
|
57
|
+
end
|
58
|
+
|
59
|
+
def init_remote_tasks
|
60
|
+
task_exports = WorkflowRESTClient.get_json(url)
|
61
|
+
@asynchronous_exports = task_exports["asynchronous"].collect{|task| task.to_sym }
|
62
|
+
@synchronous_exports = task_exports["synchronous"].collect{|task| task.to_sym }
|
63
|
+
@exec_exports = task_exports["exec"].collect{|task| task.to_sym }
|
64
|
+
nil
|
65
|
+
end
|
66
|
+
end
|
@@ -0,0 +1,83 @@
|
|
1
|
+
class WorkflowRESTClient
|
2
|
+
def self.fix_hash(hash, fix_values = false)
|
3
|
+
fixed = {}
|
4
|
+
hash.each do |key, value|
|
5
|
+
fixed[key.to_sym] = case
|
6
|
+
when Hash === value
|
7
|
+
fix_hash(value)
|
8
|
+
when (fix_values and String === value)
|
9
|
+
value.to_sym
|
10
|
+
else
|
11
|
+
value
|
12
|
+
end
|
13
|
+
end
|
14
|
+
fixed
|
15
|
+
end
|
16
|
+
|
17
|
+
def self.capture_exception
|
18
|
+
begin
|
19
|
+
yield
|
20
|
+
rescue Exception => e
|
21
|
+
klass, message = e.response.split " => "
|
22
|
+
begin
|
23
|
+
klass = Kernel.const_get klass
|
24
|
+
rescue
|
25
|
+
raise message
|
26
|
+
end
|
27
|
+
raise klass.new message
|
28
|
+
end
|
29
|
+
end
|
30
|
+
|
31
|
+
def self.get_raw(url, params = {})
|
32
|
+
Log.debug{ "RestClient get_raw: #{ url } - #{Misc.fingerprint params}" }
|
33
|
+
params = params.merge({ :_format => 'raw' })
|
34
|
+
capture_exception do
|
35
|
+
Misc.insist(2, 0.5) do
|
36
|
+
RestClient.get(URI.encode(url), :params => params)
|
37
|
+
end
|
38
|
+
end
|
39
|
+
end
|
40
|
+
|
41
|
+
def self.post_jobname(url, params = {})
|
42
|
+
Log.debug{ "RestClient post_jobname: #{ url } - #{Misc.fingerprint params}" }
|
43
|
+
params = params.merge({ :_format => 'jobname' })
|
44
|
+
|
45
|
+
capture_exception do
|
46
|
+
RestClient.post(URI.encode(url), params)
|
47
|
+
end
|
48
|
+
end
|
49
|
+
|
50
|
+
def self.get_json(url, params = {})
|
51
|
+
Log.debug{ "RestClient get_json: #{ url } - #{Misc.fingerprint params }" }
|
52
|
+
params = params.merge({ :_format => 'json' })
|
53
|
+
|
54
|
+
res = capture_exception do
|
55
|
+
RestClient.get(URI.encode(url), :params => params)
|
56
|
+
end
|
57
|
+
|
58
|
+
begin
|
59
|
+
JSON.parse(res)
|
60
|
+
rescue
|
61
|
+
res
|
62
|
+
end
|
63
|
+
end
|
64
|
+
|
65
|
+
def self.post_json(url, params = {})
|
66
|
+
if url =~ /_cache_type=:exec/
|
67
|
+
JSON.parse(Open.open(url, :nocache => true))
|
68
|
+
else
|
69
|
+
params = params.merge({ :_format => 'json' })
|
70
|
+
|
71
|
+
res = capture_exception do
|
72
|
+
RestClient.post(URI.encode(url), params)
|
73
|
+
end
|
74
|
+
|
75
|
+
begin
|
76
|
+
JSON.parse(res)
|
77
|
+
rescue
|
78
|
+
res
|
79
|
+
end
|
80
|
+
end
|
81
|
+
end
|
82
|
+
|
83
|
+
end
|
@@ -0,0 +1,123 @@
|
|
1
|
+
class WorkflowRESTClient
|
2
|
+
class RemoteStep < Step
|
3
|
+
|
4
|
+
attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :exec
|
5
|
+
|
6
|
+
def initialize(base_url, task = nil, name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
|
7
|
+
if task.nil?
|
8
|
+
@url = base_url
|
9
|
+
else
|
10
|
+
@base_url, @task, @name, @inputs, @result_type, @result_description = base_url, task, name, inputs, result_type, result_description
|
11
|
+
if exec
|
12
|
+
@url = [File.join(base_url, task.to_s), inputs]
|
13
|
+
else
|
14
|
+
self.fork
|
15
|
+
end
|
16
|
+
end
|
17
|
+
end
|
18
|
+
|
19
|
+
def initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
|
20
|
+
@base_url, @task, @base_name, @inputs, @result_type, @result_description, @exec = base_url, task, base_name, inputs, result_type, result_description, exec
|
21
|
+
end
|
22
|
+
|
23
|
+
def name
|
24
|
+
return nil if exec
|
25
|
+
(Array === @url ? @url.first : @url).split("/").last
|
26
|
+
end
|
27
|
+
|
28
|
+
def task_name
|
29
|
+
(Array === @url ? @url.first : @url).split("/")[-2]
|
30
|
+
end
|
31
|
+
|
32
|
+
def info
|
33
|
+
info = WorkflowRESTClient.get_json(File.join(url, 'info'))
|
34
|
+
info = WorkflowRESTClient.fix_hash(info)
|
35
|
+
info[:status] = info[:status].to_sym if String === info[:status]
|
36
|
+
info
|
37
|
+
end
|
38
|
+
|
39
|
+
def status
|
40
|
+
info[:status]
|
41
|
+
end
|
42
|
+
|
43
|
+
def done?
|
44
|
+
status.to_s == 'done'
|
45
|
+
end
|
46
|
+
|
47
|
+
def files
|
48
|
+
WorkflowRESTClient.get_json(File.join(url, 'files'))
|
49
|
+
end
|
50
|
+
|
51
|
+
def file(file)
|
52
|
+
WorkflowRESTClient.get_raw(File.join(url, 'file', file))
|
53
|
+
end
|
54
|
+
|
55
|
+
#{{{ MANAGEMENT
|
56
|
+
|
57
|
+
def init_job(cache_type = :asynchronous)
|
58
|
+
@name = WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name, :_cache_type => cache_type))
|
59
|
+
@url = File.join(base_url, task.to_s, @name)
|
60
|
+
nil
|
61
|
+
end
|
62
|
+
|
63
|
+
def load_res(res)
|
64
|
+
case result_type
|
65
|
+
when :string
|
66
|
+
res
|
67
|
+
when :boolean
|
68
|
+
res == "true"
|
69
|
+
when :tsv
|
70
|
+
TSV.open(StringIO.new(res))
|
71
|
+
when :annotations
|
72
|
+
Annotated.load_tsv(TSV.open(StringIO.new(res)))
|
73
|
+
else
|
74
|
+
JSON.parse res
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
def get
|
79
|
+
params = params.merge(:_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json )
|
80
|
+
begin
|
81
|
+
WorkflowRESTClient.get_raw(url, params)
|
82
|
+
rescue => e
|
83
|
+
raise e.response
|
84
|
+
end
|
85
|
+
end
|
86
|
+
|
87
|
+
def load
|
88
|
+
params = {}
|
89
|
+
load_res get
|
90
|
+
end
|
91
|
+
|
92
|
+
def exec_job
|
93
|
+
res = WorkflowRESTClient.capture_exception do
|
94
|
+
RestClient.post(URI.encode(File.join(base_url, task.to_s)), inputs.merge(:_cache_type => :exec, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json))
|
95
|
+
end
|
96
|
+
load_res res
|
97
|
+
end
|
98
|
+
|
99
|
+
def fork
|
100
|
+
init_job
|
101
|
+
end
|
102
|
+
|
103
|
+
def run(noload = false)
|
104
|
+
return exec_job if exec
|
105
|
+
init_job(:synchronous)
|
106
|
+
noload ? name : self.load
|
107
|
+
end
|
108
|
+
|
109
|
+
def exec
|
110
|
+
exec_job
|
111
|
+
end
|
112
|
+
|
113
|
+
def join
|
114
|
+
self.load
|
115
|
+
self
|
116
|
+
end
|
117
|
+
|
118
|
+
def clean
|
119
|
+
WorkflowRESTClient.get_raw(url, :_update => :clean) unless exec
|
120
|
+
self
|
121
|
+
end
|
122
|
+
end
|
123
|
+
end
|
data/lib/rbbt/rest/main.rb
CHANGED
@@ -26,6 +26,8 @@ module Sinatra
|
|
26
26
|
|
27
27
|
set :public_folder, Rbbt.share.views.public.find
|
28
28
|
|
29
|
+
set :environment, ENV["RACK_ENV"].to_sym if ENV["RACK_ENV"]
|
30
|
+
|
29
31
|
attr_accessor :ajax, :layout, :format, :size, :update, :cache_type, :_, :profile
|
30
32
|
|
31
33
|
if production?
|
@@ -135,10 +137,8 @@ module Sinatra
|
|
135
137
|
halt 404, e.message
|
136
138
|
end
|
137
139
|
|
138
|
-
|
139
|
-
|
140
|
-
halt 404, e.message
|
141
|
-
end
|
140
|
+
error Exception do |e|
|
141
|
+
halt 500, [e.class.to_s, e.message] * " => "
|
142
142
|
end
|
143
143
|
end
|
144
144
|
end
|
data/lib/rbbt/rest/workflow.rb
CHANGED
@@ -69,6 +69,8 @@ module Sinatra
|
|
69
69
|
get "/#{workflow.to_s}/:task/info" do
|
70
70
|
task = consume_parameter(:task)
|
71
71
|
|
72
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
73
|
+
|
72
74
|
case format
|
73
75
|
when :html
|
74
76
|
workflow_render('task_info', workflow)
|
@@ -83,6 +85,8 @@ module Sinatra
|
|
83
85
|
get "/#{workflow.to_s}/:task/dependencies" do
|
84
86
|
task = consume_parameter(:task)
|
85
87
|
|
88
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
89
|
+
|
86
90
|
case format
|
87
91
|
when :html
|
88
92
|
workflow_render('task_dependencies', workflow)
|
@@ -103,6 +107,8 @@ module Sinatra
|
|
103
107
|
task = consume_parameter(:task)
|
104
108
|
jobname = consume_parameter(:jobname)
|
105
109
|
|
110
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
111
|
+
|
106
112
|
task_parameters = consume_task_parameters(workflow, task, params)
|
107
113
|
|
108
114
|
if complete_input_set(workflow, task, task_parameters) or format != :html
|
@@ -116,6 +122,8 @@ module Sinatra
|
|
116
122
|
task = consume_parameter(:task)
|
117
123
|
jobname = consume_parameter(:jobname)
|
118
124
|
|
125
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
126
|
+
|
119
127
|
task_parameters = consume_task_parameters(workflow, task, params)
|
120
128
|
|
121
129
|
issue_job(workflow, task, jobname, task_parameters)
|
@@ -125,6 +133,8 @@ module Sinatra
|
|
125
133
|
task = consume_parameter(:task)
|
126
134
|
job = consume_parameter(:job)
|
127
135
|
|
136
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
137
|
+
|
128
138
|
job = workflow.load_id(File.join(task, job))
|
129
139
|
|
130
140
|
clean_job(workflow, job) if update == :clean
|
@@ -160,6 +170,8 @@ module Sinatra
|
|
160
170
|
task = consume_parameter(:task)
|
161
171
|
job = consume_parameter(:job)
|
162
172
|
|
173
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
174
|
+
|
163
175
|
job = workflow.load_id(File.join(task, job))
|
164
176
|
|
165
177
|
case format
|
@@ -177,6 +189,8 @@ module Sinatra
|
|
177
189
|
task = consume_parameter(:task)
|
178
190
|
job = consume_parameter(:job)
|
179
191
|
|
192
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
193
|
+
|
180
194
|
job = workflow.load_id(File.join(task, job))
|
181
195
|
|
182
196
|
case format
|
@@ -195,6 +209,8 @@ module Sinatra
|
|
195
209
|
job = consume_parameter(:job)
|
196
210
|
filename = params[:splat].first
|
197
211
|
|
212
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
213
|
+
|
198
214
|
job = workflow.load_id(File.join(task, job))
|
199
215
|
|
200
216
|
send_file job.file(filename)
|
@@ -205,6 +221,8 @@ module Sinatra
|
|
205
221
|
job = consume_parameter(:job)
|
206
222
|
job = workflow.load_id(File.join(task, job))
|
207
223
|
|
224
|
+
raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
|
225
|
+
|
208
226
|
clean_job(workflow, job)
|
209
227
|
end
|
210
228
|
end
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-rest
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.3.
|
4
|
+
version: 1.3.3
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
@@ -175,6 +175,9 @@ files:
|
|
175
175
|
- Rakefile
|
176
176
|
- config.ru
|
177
177
|
- lib/rbbt/rest/client.rb
|
178
|
+
- lib/rbbt/rest/client/adaptor.rb
|
179
|
+
- lib/rbbt/rest/client/get.rb
|
180
|
+
- lib/rbbt/rest/client/step.rb
|
178
181
|
- lib/rbbt/rest/common/cache.rb
|
179
182
|
- lib/rbbt/rest/common/forms.rb
|
180
183
|
- lib/rbbt/rest/common/locate.rb
|