arvados-cli 0.1.20140513124920 → 0.1.20140513131358
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/bin/arv-run-pipeline-instance +29 -17
- metadata +2 -2
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: af2790ca4c3acf7859b5a681e98d678400801e4b
|
|
4
|
+
data.tar.gz: bc485942263396f534edb805c5a4cde6d09b8796
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: a3ddee95b6bab6a8b04ed2da17f30a214216a38da8bf2bebcc34e8d650ce7c2dc73950faed84c882bcaf4efba0599dbc7076b39738aab34eb92d630a30bc6f3b
|
|
7
|
+
data.tar.gz: e9bb843f22e3f5e6fefcea14736dd4a591de4a1204c6c70f5044e2faa5d85b90dc361c3504324f2c17c1915902f53e9eea138852f8f4a06b6f15ffaf907f3f4c
|
|
@@ -226,10 +226,10 @@ class PipelineInstance
|
|
|
226
226
|
:parameters => {
|
|
227
227
|
:uuid => uuid
|
|
228
228
|
},
|
|
229
|
-
:
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
229
|
+
:authenticated => false,
|
|
230
|
+
:headers => {
|
|
231
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
232
|
+
})
|
|
233
233
|
j = JSON.parse result.body, :symbolize_names => true
|
|
234
234
|
unless j.is_a? Hash and j[:uuid]
|
|
235
235
|
debuglog "Failed to get pipeline_instance: #{j[:errors] rescue nil}", 0
|
|
@@ -242,10 +242,12 @@ class PipelineInstance
|
|
|
242
242
|
def self.create(attributes)
|
|
243
243
|
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
|
|
244
244
|
:body => {
|
|
245
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
246
245
|
:pipeline_instance => attributes
|
|
247
246
|
},
|
|
248
|
-
:authenticated => false
|
|
247
|
+
:authenticated => false,
|
|
248
|
+
:headers => {
|
|
249
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
250
|
+
})
|
|
249
251
|
j = JSON.parse result.body, :symbolize_names => true
|
|
250
252
|
unless j.is_a? Hash and j[:uuid]
|
|
251
253
|
abort "Failed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
|
|
@@ -259,10 +261,12 @@ class PipelineInstance
|
|
|
259
261
|
:uuid => @pi[:uuid]
|
|
260
262
|
},
|
|
261
263
|
:body => {
|
|
262
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
263
264
|
:pipeline_instance => @attributes_to_update.to_json
|
|
264
265
|
},
|
|
265
|
-
:authenticated => false
|
|
266
|
+
:authenticated => false,
|
|
267
|
+
:headers => {
|
|
268
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
269
|
+
})
|
|
266
270
|
j = JSON.parse result.body, :symbolize_names => true
|
|
267
271
|
unless j.is_a? Hash and j[:uuid]
|
|
268
272
|
debuglog "Failed to save pipeline_instance: #{j[:errors] rescue nil}", 0
|
|
@@ -291,20 +295,24 @@ class JobCache
|
|
|
291
295
|
@cache ||= {}
|
|
292
296
|
result = $client.execute(:api_method => $arvados.jobs.get,
|
|
293
297
|
:parameters => {
|
|
294
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
295
298
|
:uuid => uuid
|
|
296
299
|
},
|
|
297
|
-
:authenticated => false
|
|
300
|
+
:authenticated => false,
|
|
301
|
+
:headers => {
|
|
302
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
303
|
+
})
|
|
298
304
|
@cache[uuid] = JSON.parse result.body, :symbolize_names => true
|
|
299
305
|
end
|
|
300
306
|
def self.where(conditions)
|
|
301
307
|
result = $client.execute(:api_method => $arvados.jobs.list,
|
|
302
308
|
:parameters => {
|
|
303
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
304
309
|
:limit => 10000,
|
|
305
310
|
:where => conditions.to_json
|
|
306
311
|
},
|
|
307
|
-
:authenticated => false
|
|
312
|
+
:authenticated => false,
|
|
313
|
+
:headers => {
|
|
314
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
315
|
+
})
|
|
308
316
|
list = JSON.parse result.body, :symbolize_names => true
|
|
309
317
|
if list and list[:items].is_a? Array
|
|
310
318
|
list[:items]
|
|
@@ -315,11 +323,13 @@ class JobCache
|
|
|
315
323
|
def self.create(job, create_params)
|
|
316
324
|
@cache ||= {}
|
|
317
325
|
result = $client.execute(:api_method => $arvados.jobs.create,
|
|
318
|
-
:
|
|
319
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
326
|
+
:body => {
|
|
320
327
|
:job => job.to_json
|
|
321
328
|
}.merge(create_params),
|
|
322
|
-
:authenticated => false
|
|
329
|
+
:authenticated => false,
|
|
330
|
+
:headers => {
|
|
331
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
332
|
+
})
|
|
323
333
|
j = JSON.parse result.body, :symbolize_names => true
|
|
324
334
|
if j.is_a? Hash and j[:uuid]
|
|
325
335
|
@cache[j[:uuid]] = j
|
|
@@ -348,10 +358,12 @@ class WhRunPipelineInstance
|
|
|
348
358
|
else
|
|
349
359
|
result = $client.execute(:api_method => $arvados.pipeline_templates.get,
|
|
350
360
|
:parameters => {
|
|
351
|
-
:api_token => ENV['ARVADOS_API_TOKEN'],
|
|
352
361
|
:uuid => template
|
|
353
362
|
},
|
|
354
|
-
:authenticated => false
|
|
363
|
+
:authenticated => false,
|
|
364
|
+
:headers => {
|
|
365
|
+
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
|
|
366
|
+
})
|
|
355
367
|
@template = JSON.parse result.body, :symbolize_names => true
|
|
356
368
|
if !@template[:uuid]
|
|
357
369
|
abort "#{$0}: fatal: failed to retrieve pipeline template #{template} #{@template[:errors].inspect rescue nil}"
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: arvados-cli
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.1.
|
|
4
|
+
version: 0.1.20140513131358
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Arvados Authors
|
|
@@ -146,7 +146,7 @@ dependencies:
|
|
|
146
146
|
- - "~>"
|
|
147
147
|
- !ruby/object:Gem::Version
|
|
148
148
|
version: '0.8'
|
|
149
|
-
description: This is the Arvados SDK CLI gem, git revision
|
|
149
|
+
description: This is the Arvados SDK CLI gem, git revision 67f17818338153fc6f7b0c65f51e97bbb16f0cc7
|
|
150
150
|
email: gem-dev@curoverse.com
|
|
151
151
|
executables:
|
|
152
152
|
- arv
|