sequencescape-client-api 0.3.10 → 0.4.0.pre.rc1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.rubocop.yml +44 -0
- data/.rubocop_todo.yml +338 -0
- data/.ruby-version +1 -0
- data/Gemfile +1 -1
- data/README.markdown +13 -0
- data/lib/sequencescape-api.rb +1 -1
- data/lib/sequencescape-api/actions.rb +9 -8
- data/lib/sequencescape-api/associations.rb +8 -6
- data/lib/sequencescape-api/associations/base.rb +1 -1
- data/lib/sequencescape-api/associations/base/instance_methods.rb +10 -8
- data/lib/sequencescape-api/associations/belongs_to.rb +4 -4
- data/lib/sequencescape-api/associations/has_many.rb +14 -13
- data/lib/sequencescape-api/associations/has_many/json.rb +1 -1
- data/lib/sequencescape-api/associations/has_many/validation.rb +1 -1
- data/lib/sequencescape-api/composition.rb +11 -7
- data/lib/sequencescape-api/connection_factory.rb +6 -5
- data/lib/sequencescape-api/connection_factory/actions.rb +17 -12
- data/lib/sequencescape-api/core.rb +12 -7
- data/lib/sequencescape-api/core_ext/array.rb +1 -1
- data/lib/sequencescape-api/core_ext/hash.rb +3 -3
- data/lib/sequencescape-api/errors.rb +2 -2
- data/lib/sequencescape-api/finder_methods.rb +16 -11
- data/lib/sequencescape-api/rails.rb +8 -7
- data/lib/sequencescape-api/resource/active_model.rb +1 -1
- data/lib/sequencescape-api/resource/attribute_groups.rb +11 -7
- data/lib/sequencescape-api/resource/attributes.rb +8 -8
- data/lib/sequencescape-api/resource/instance_methods.rb +17 -9
- data/lib/sequencescape-api/resource/json.rb +18 -15
- data/lib/sequencescape-api/resource/modifications.rb +20 -11
- data/lib/sequencescape-api/resource_model_proxy.rb +7 -5
- data/lib/sequencescape-api/version.rb +1 -1
- data/lib/sequencescape.rb +1 -2
- data/lib/sequencescape/bait_library.rb +1 -1
- data/lib/sequencescape/bait_library_layout.rb +2 -2
- data/lib/sequencescape/barcoded_asset.rb +1 -1
- data/lib/sequencescape/batch.rb +6 -6
- data/lib/sequencescape/behaviour/qced.rb +3 -4
- data/lib/sequencescape/behaviour/receptacle.rb +3 -3
- data/lib/sequencescape/behaviour/state_driven.rb +4 -4
- data/lib/sequencescape/bulk_transfer.rb +1 -1
- data/lib/sequencescape/comment.rb +0 -2
- data/lib/sequencescape/extraction_attribute.rb +1 -1
- data/lib/sequencescape/library_event.rb +1 -1
- data/lib/sequencescape/library_tube.rb +1 -1
- data/lib/sequencescape/lot.rb +0 -1
- data/lib/sequencescape/lot_type.rb +1 -2
- data/lib/sequencescape/order_template.rb +1 -2
- data/lib/sequencescape/pipeline.rb +1 -1
- data/lib/sequencescape/plate.rb +19 -15
- data/lib/sequencescape/plate/pooling.rb +9 -3
- data/lib/sequencescape/plate/well_structure.rb +6 -6
- data/lib/sequencescape/plate_conversion.rb +3 -3
- data/lib/sequencescape/plate_creation.rb +3 -3
- data/lib/sequencescape/plate_purpose.rb +3 -3
- data/lib/sequencescape/plate_template.rb +0 -2
- data/lib/sequencescape/pooled_plate_creation.rb +3 -3
- data/lib/sequencescape/project.rb +2 -1
- data/lib/sequencescape/qc_decision.rb +0 -1
- data/lib/sequencescape/qc_file.rb +0 -3
- data/lib/sequencescape/qcable.rb +0 -3
- data/lib/sequencescape/qcable_creator.rb +0 -3
- data/lib/sequencescape/request.rb +3 -3
- data/lib/sequencescape/search.rb +10 -8
- data/lib/sequencescape/specific_tube_creation.rb +2 -2
- data/lib/sequencescape/stamp.rb +0 -1
- data/lib/sequencescape/state_change.rb +2 -2
- data/lib/sequencescape/study.rb +1 -1
- data/lib/sequencescape/submission.rb +1 -2
- data/lib/sequencescape/tag2_layout.rb +3 -3
- data/lib/sequencescape/tag2_layout_template.rb +2 -2
- data/lib/sequencescape/tag_group.rb +0 -1
- data/lib/sequencescape/tag_layout.rb +3 -3
- data/lib/sequencescape/tag_layout_template.rb +4 -4
- data/lib/sequencescape/transfer.rb +2 -2
- data/lib/sequencescape/transfer_request.rb +4 -5
- data/lib/sequencescape/transfer_template.rb +2 -2
- data/lib/sequencescape/tube.rb +3 -3
- data/lib/sequencescape/tube_creation.rb +3 -3
- data/lib/sequencescape/tube_from_tube_creation.rb +3 -3
- data/lib/sequencescape/tube_purpose.rb +3 -3
- data/lib/sequencescape/user.rb +2 -2
- data/lib/sequencescape/volume_update.rb +1 -1
- data/lib/sequencescape/well.rb +0 -2
- data/lib/sequencescape/work_completion.rb +1 -1
- data/sequencescape-api.gemspec +18 -17
- data/spec/sequencescape-api/associations_spec.rb +4 -2
- data/spec/sequencescape-api/finding_methods_spec.rb +3 -1
- data/spec/sequencescape-api/modifications_spec.rb +17 -16
- data/spec/sequencescape-api/root_spec.rb +11 -6
- data/spec/spec_helper.rb +3 -1
- data/spec/support/contract_helper.rb +18 -10
- data/spec/support/namespaces.rb +9 -9
- data/spec/support/shared_examples.rb +2 -0
- metadata +53 -35
- data/.rvmrc +0 -52
checksums.yaml
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- 'lib/sequencescape/order.rb'
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- 'lib/sequencescape/order_template.rb'
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- 'lib/sequencescape/project.rb'
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- 'lib/sequencescape/qc_decision.rb'
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- 'lib/sequencescape/robot.rb'
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- 'lib/sequencescape/sample.rb'
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- 'lib/sequencescape/search.rb'
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- 'lib/sequencescape/specific_tube_creation.rb'
|
|
162
|
+
- 'lib/sequencescape/stamp.rb'
|
|
163
|
+
- 'lib/sequencescape/state_change.rb'
|
|
164
|
+
- 'lib/sequencescape/study.rb'
|
|
165
|
+
- 'lib/sequencescape/submission.rb'
|
|
166
|
+
- 'lib/sequencescape/submission_pool.rb'
|
|
167
|
+
- 'lib/sequencescape/tag.rb'
|
|
168
|
+
- 'lib/sequencescape/tag2_layout.rb'
|
|
169
|
+
- 'lib/sequencescape/tag2_layout_template.rb'
|
|
170
|
+
- 'lib/sequencescape/tag_group.rb'
|
|
171
|
+
- 'lib/sequencescape/tag_layout.rb'
|
|
172
|
+
- 'lib/sequencescape/tag_layout_template.rb'
|
|
173
|
+
- 'lib/sequencescape/template.rb'
|
|
174
|
+
- 'lib/sequencescape/transfer.rb'
|
|
175
|
+
- 'lib/sequencescape/transfer_request.rb'
|
|
176
|
+
- 'lib/sequencescape/transfer_request_collection.rb'
|
|
177
|
+
- 'lib/sequencescape/transfer_template.rb'
|
|
178
|
+
- 'lib/sequencescape/tube.rb'
|
|
179
|
+
- 'lib/sequencescape/tube_creation.rb'
|
|
180
|
+
- 'lib/sequencescape/tube_from_tube_creation.rb'
|
|
181
|
+
- 'lib/sequencescape/tube_purpose.rb'
|
|
182
|
+
- 'lib/sequencescape/user.rb'
|
|
183
|
+
- 'lib/sequencescape/volume_update.rb'
|
|
184
|
+
- 'lib/sequencescape/well.rb'
|
|
185
|
+
- 'lib/sequencescape/work_completion.rb'
|
|
186
|
+
|
|
187
|
+
# Offense count: 6
|
|
188
|
+
# Cop supports --auto-correct.
|
|
189
|
+
Style/EmptyCaseCondition:
|
|
190
|
+
Exclude:
|
|
191
|
+
- 'lib/sequencescape-api/associations/base/instance_methods.rb'
|
|
192
|
+
- 'lib/sequencescape-api/associations/belongs_to.rb'
|
|
193
|
+
- 'lib/sequencescape-api/associations/has_many.rb'
|
|
194
|
+
- 'lib/sequencescape-api/connection_factory/actions.rb'
|
|
195
|
+
- 'lib/sequencescape-api/resource/modifications.rb'
|
|
196
|
+
|
|
197
|
+
# Offense count: 1
|
|
198
|
+
# Cop supports --auto-correct.
|
|
199
|
+
# Configuration parameters: EnforcedStyle.
|
|
200
|
+
# SupportedStyles: empty, nil, both
|
|
201
|
+
Style/EmptyElse:
|
|
202
|
+
Exclude:
|
|
203
|
+
- 'lib/sequencescape-api/resource/json.rb'
|
|
204
|
+
|
|
205
|
+
# Offense count: 11
|
|
206
|
+
Style/EvalWithLocation:
|
|
207
|
+
Exclude:
|
|
208
|
+
- 'lib/sequencescape-api/actions.rb'
|
|
209
|
+
- 'lib/sequencescape-api/associations.rb'
|
|
210
|
+
- 'lib/sequencescape-api/composition.rb'
|
|
211
|
+
- 'lib/sequencescape-api/finder_methods.rb'
|
|
212
|
+
- 'lib/sequencescape-api/resource/attributes.rb'
|
|
213
|
+
- 'lib/sequencescape/batch.rb'
|
|
214
|
+
- 'lib/sequencescape/behaviour/state_driven.rb'
|
|
215
|
+
- 'lib/sequencescape/search.rb'
|
|
216
|
+
|
|
217
|
+
# Offense count: 104
|
|
218
|
+
# Cop supports --auto-correct.
|
|
219
|
+
# Configuration parameters: EnforcedStyle.
|
|
220
|
+
# SupportedStyles: always, always_true, never
|
|
221
|
+
Style/FrozenStringLiteralComment:
|
|
222
|
+
Exclude:
|
|
223
|
+
- 'Gemfile'
|
|
224
|
+
- 'Rakefile'
|
|
225
|
+
- 'lib/sequencescape-api.rb'
|
|
226
|
+
- 'lib/sequencescape-api/actions.rb'
|
|
227
|
+
- 'lib/sequencescape-api/associations.rb'
|
|
228
|
+
- 'lib/sequencescape-api/associations/base.rb'
|
|
229
|
+
- 'lib/sequencescape-api/associations/base/instance_methods.rb'
|
|
230
|
+
- 'lib/sequencescape-api/associations/belongs_to.rb'
|
|
231
|
+
- 'lib/sequencescape-api/associations/has_many.rb'
|
|
232
|
+
- 'lib/sequencescape-api/associations/has_many/json.rb'
|
|
233
|
+
- 'lib/sequencescape-api/associations/has_many/validation.rb'
|
|
234
|
+
- 'lib/sequencescape-api/capabilities.rb'
|
|
235
|
+
- 'lib/sequencescape-api/composition.rb'
|
|
236
|
+
- 'lib/sequencescape-api/connection_factory.rb'
|
|
237
|
+
- 'lib/sequencescape-api/connection_factory/actions.rb'
|
|
238
|
+
- 'lib/sequencescape-api/connection_factory/helpers.rb'
|
|
239
|
+
- 'lib/sequencescape-api/core.rb'
|
|
240
|
+
- 'lib/sequencescape-api/core_ext.rb'
|
|
241
|
+
- 'lib/sequencescape-api/core_ext/array.rb'
|
|
242
|
+
- 'lib/sequencescape-api/core_ext/hash.rb'
|
|
243
|
+
- 'lib/sequencescape-api/error_handling.rb'
|
|
244
|
+
- 'lib/sequencescape-api/errors.rb'
|
|
245
|
+
- 'lib/sequencescape-api/finder_methods.rb'
|
|
246
|
+
- 'lib/sequencescape-api/rails.rb'
|
|
247
|
+
- 'lib/sequencescape-api/resource.rb'
|
|
248
|
+
- 'lib/sequencescape-api/resource/active_model.rb'
|
|
249
|
+
- 'lib/sequencescape-api/resource/attribute_groups.rb'
|
|
250
|
+
- 'lib/sequencescape-api/resource/attributes.rb'
|
|
251
|
+
- 'lib/sequencescape-api/resource/instance_methods.rb'
|
|
252
|
+
- 'lib/sequencescape-api/resource/json.rb'
|
|
253
|
+
- 'lib/sequencescape-api/resource/modifications.rb'
|
|
254
|
+
- 'lib/sequencescape-api/resource_model_proxy.rb'
|
|
255
|
+
- 'lib/sequencescape-api/version.rb'
|
|
256
|
+
- 'lib/sequencescape.rb'
|
|
257
|
+
- 'lib/sequencescape/asset.rb'
|
|
258
|
+
- 'lib/sequencescape/asset_audit.rb'
|
|
259
|
+
- 'lib/sequencescape/asset_group.rb'
|
|
260
|
+
- 'lib/sequencescape/bait_library.rb'
|
|
261
|
+
- 'lib/sequencescape/bait_library_layout.rb'
|
|
262
|
+
- 'lib/sequencescape/barcode_printer.rb'
|
|
263
|
+
- 'lib/sequencescape/barcoded_asset.rb'
|
|
264
|
+
- 'lib/sequencescape/batch.rb'
|
|
265
|
+
- 'lib/sequencescape/behaviour/barcoded.rb'
|
|
266
|
+
- 'lib/sequencescape/behaviour/labeled.rb'
|
|
267
|
+
- 'lib/sequencescape/behaviour/qced.rb'
|
|
268
|
+
- 'lib/sequencescape/behaviour/receptacle.rb'
|
|
269
|
+
- 'lib/sequencescape/behaviour/state_driven.rb'
|
|
270
|
+
- 'lib/sequencescape/bulk_transfer.rb'
|
|
271
|
+
- 'lib/sequencescape/comment.rb'
|
|
272
|
+
- 'lib/sequencescape/custom_metadatum_collection.rb'
|
|
273
|
+
- 'lib/sequencescape/extraction_attribute.rb'
|
|
274
|
+
- 'lib/sequencescape/lane.rb'
|
|
275
|
+
- 'lib/sequencescape/library_event.rb'
|
|
276
|
+
- 'lib/sequencescape/library_tube.rb'
|
|
277
|
+
- 'lib/sequencescape/lot.rb'
|
|
278
|
+
- 'lib/sequencescape/lot_type.rb'
|
|
279
|
+
- 'lib/sequencescape/multiplexed_library_tube.rb'
|
|
280
|
+
- 'lib/sequencescape/order.rb'
|
|
281
|
+
- 'lib/sequencescape/order_template.rb'
|
|
282
|
+
- 'lib/sequencescape/pipeline.rb'
|
|
283
|
+
- 'lib/sequencescape/plate.rb'
|
|
284
|
+
- 'lib/sequencescape/plate/pooling.rb'
|
|
285
|
+
- 'lib/sequencescape/plate/well_structure.rb'
|
|
286
|
+
- 'lib/sequencescape/plate_conversion.rb'
|
|
287
|
+
- 'lib/sequencescape/plate_creation.rb'
|
|
288
|
+
- 'lib/sequencescape/plate_purpose.rb'
|
|
289
|
+
- 'lib/sequencescape/plate_template.rb'
|
|
290
|
+
- 'lib/sequencescape/pooled_plate_creation.rb'
|
|
291
|
+
- 'lib/sequencescape/project.rb'
|
|
292
|
+
- 'lib/sequencescape/qc_decision.rb'
|
|
293
|
+
- 'lib/sequencescape/qc_file.rb'
|
|
294
|
+
- 'lib/sequencescape/qcable.rb'
|
|
295
|
+
- 'lib/sequencescape/qcable_creator.rb'
|
|
296
|
+
- 'lib/sequencescape/request.rb'
|
|
297
|
+
- 'lib/sequencescape/robot.rb'
|
|
298
|
+
- 'lib/sequencescape/sample.rb'
|
|
299
|
+
- 'lib/sequencescape/sample_tube.rb'
|
|
300
|
+
- 'lib/sequencescape/search.rb'
|
|
301
|
+
- 'lib/sequencescape/specific_tube_creation.rb'
|
|
302
|
+
- 'lib/sequencescape/stamp.rb'
|
|
303
|
+
- 'lib/sequencescape/state_change.rb'
|
|
304
|
+
- 'lib/sequencescape/study.rb'
|
|
305
|
+
- 'lib/sequencescape/submission.rb'
|
|
306
|
+
- 'lib/sequencescape/submission_pool.rb'
|
|
307
|
+
- 'lib/sequencescape/tag.rb'
|
|
308
|
+
- 'lib/sequencescape/tag2_layout.rb'
|
|
309
|
+
- 'lib/sequencescape/tag2_layout_template.rb'
|
|
310
|
+
- 'lib/sequencescape/tag_group.rb'
|
|
311
|
+
- 'lib/sequencescape/tag_layout.rb'
|
|
312
|
+
- 'lib/sequencescape/tag_layout_template.rb'
|
|
313
|
+
- 'lib/sequencescape/template.rb'
|
|
314
|
+
- 'lib/sequencescape/transfer.rb'
|
|
315
|
+
- 'lib/sequencescape/transfer_request.rb'
|
|
316
|
+
- 'lib/sequencescape/transfer_request_collection.rb'
|
|
317
|
+
- 'lib/sequencescape/transfer_template.rb'
|
|
318
|
+
- 'lib/sequencescape/tube.rb'
|
|
319
|
+
- 'lib/sequencescape/tube_creation.rb'
|
|
320
|
+
- 'lib/sequencescape/tube_from_tube_creation.rb'
|
|
321
|
+
- 'lib/sequencescape/tube_purpose.rb'
|
|
322
|
+
- 'lib/sequencescape/user.rb'
|
|
323
|
+
- 'lib/sequencescape/volume_update.rb'
|
|
324
|
+
- 'lib/sequencescape/well.rb'
|
|
325
|
+
- 'lib/sequencescape/work_completion.rb'
|
|
326
|
+
- 'sequencescape-api.gemspec'
|
|
327
|
+
|
|
328
|
+
# Offense count: 2
|
|
329
|
+
Style/MethodMissingSuper:
|
|
330
|
+
Exclude:
|
|
331
|
+
- 'lib/sequencescape-api/associations/belongs_to.rb'
|
|
332
|
+
- 'lib/sequencescape-api/resource_model_proxy.rb'
|
|
333
|
+
|
|
334
|
+
# Offense count: 2
|
|
335
|
+
Style/MissingRespondToMissing:
|
|
336
|
+
Exclude:
|
|
337
|
+
- 'lib/sequencescape-api/associations/belongs_to.rb'
|
|
338
|
+
- 'lib/sequencescape-api/core.rb'
|
data/.ruby-version
ADDED
|
@@ -0,0 +1 @@
|
|
|
1
|
+
ruby-2.5.8
|
data/Gemfile
CHANGED
data/README.markdown
CHANGED
|
@@ -1,4 +1,17 @@
|
|
|
1
1
|
Sequencescape Client API
|
|
2
2
|
========================
|
|
3
|
+
|
|
3
4
|
This is the Ruby client library for the Sequencescape API.
|
|
4
5
|
Documentation can be found [on the wiki](https://github.com/sanger/sequencescape-client-api/wiki).
|
|
6
|
+
|
|
7
|
+
Version Guides
|
|
8
|
+
--------------
|
|
9
|
+
|
|
10
|
+
- 0.2.x Supports older versions of Rails.
|
|
11
|
+
- 0.3.x Supports Rails 3.2.x to 5.1.x
|
|
12
|
+
- 0.4.x Supports Rails 5.0 and up
|
|
13
|
+
|
|
14
|
+
- master currently corresponds to 0.4.x
|
|
15
|
+
|
|
16
|
+
Rails 6 appears to be supported judging by Specs, but haven't used it in anger
|
|
17
|
+
yet.
|
data/lib/sequencescape-api.rb
CHANGED
|
@@ -13,4 +13,4 @@ require 'sequencescape-api/resource'
|
|
|
13
13
|
require 'sequencescape-api/rails'
|
|
14
14
|
|
|
15
15
|
# Ensure that the I18n stuff has been properly configured
|
|
16
|
-
I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w
|
|
16
|
+
I18n.config.load_path << File.expand_path(File.join(File.dirname(__FILE__), %w[sequencescape-api locale en.yml]))
|
|
@@ -9,9 +9,10 @@ module Sequencescape::Api::Actions
|
|
|
9
9
|
module ClassActionHelpers
|
|
10
10
|
# Defines a method that is available on the resource model itself, rather than on an instance of
|
|
11
11
|
# the resource model.
|
|
12
|
-
def has_class_create_action(*args)
|
|
13
|
-
action_module
|
|
14
|
-
|
|
12
|
+
def has_class_create_action(*args) # rubocop:todo Metrics/MethodLength
|
|
13
|
+
action_module = Module.new
|
|
14
|
+
line = __LINE__ + 1
|
|
15
|
+
action_module.module_eval(%{
|
|
15
16
|
def initialize_class_actions(proxy)
|
|
16
17
|
super
|
|
17
18
|
|
|
@@ -31,7 +32,7 @@ module Sequencescape::Api::Actions
|
|
|
31
32
|
end
|
|
32
33
|
|
|
33
34
|
module InstanceActionHelpers
|
|
34
|
-
def has_create_action(*args)
|
|
35
|
+
def has_create_action(*args) # rubocop:todo Metrics/MethodLength
|
|
35
36
|
options = args.extract_options!
|
|
36
37
|
name = args.first || :create!
|
|
37
38
|
|
|
@@ -40,7 +41,7 @@ module Sequencescape::Api::Actions
|
|
|
40
41
|
result_class = "api.#{options[:resource]}" if options[:resource]
|
|
41
42
|
|
|
42
43
|
line = __LINE__ + 1
|
|
43
|
-
class_eval(%
|
|
44
|
+
class_eval(%{
|
|
44
45
|
def #{name}(attributes = nil)
|
|
45
46
|
url = actions.try(#{action.to_sym.inspect}) or
|
|
46
47
|
raise Sequencescape::Api::Error, "Cannot perform #{action} without an URL"
|
|
@@ -54,14 +55,14 @@ module Sequencescape::Api::Actions
|
|
|
54
55
|
|
|
55
56
|
def has_update_action(name, options = {})
|
|
56
57
|
api_method = options[:verb] == :create ? :create : :update
|
|
57
|
-
skip_json = options[:skip_json]||false
|
|
58
|
+
skip_json = options[:skip_json] || false
|
|
58
59
|
action = options[:action] || :update
|
|
59
60
|
|
|
60
61
|
line = __LINE__ + 1
|
|
61
|
-
class_eval(%
|
|
62
|
+
class_eval(%{
|
|
62
63
|
def #{name}(body = nil)
|
|
63
64
|
update_from_json(body || {}, false)
|
|
64
|
-
modify!(:
|
|
65
|
+
modify!(action: #{action.to_sym.inspect}, http_verb: #{api_method.to_sym.inspect}, skip_json: #{skip_json})
|
|
65
66
|
end
|
|
66
67
|
}, __FILE__, line)
|
|
67
68
|
end
|