labimotion 2.3.0 → 2.4.0.rc11

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.
Files changed (70) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +25 -1
  3. data/lib/labimotion/apis/generic_dataset_api.rb +93 -3
  4. data/lib/labimotion/apis/generic_element_api.rb +198 -8
  5. data/lib/labimotion/apis/generic_klass_api.rb +74 -8
  6. data/lib/labimotion/apis/klass_share_api.rb +648 -0
  7. data/lib/labimotion/apis/labimotion_ai_api.rb +252 -0
  8. data/lib/labimotion/apis/labimotion_api.rb +4 -0
  9. data/lib/labimotion/apis/labimotion_doi_api.rb +24 -10
  10. data/lib/labimotion/apis/labimotion_template_browse_api.rb +13 -1
  11. data/lib/labimotion/apis/ontology_root_api.rb +74 -0
  12. data/lib/labimotion/apis/segment_api.rb +77 -10
  13. data/lib/labimotion/apis/user_klass_settings_api.rb +93 -0
  14. data/lib/labimotion/conf.rb +5 -0
  15. data/lib/labimotion/constants.rb +64 -0
  16. data/lib/labimotion/entities/application_entity.rb +8 -0
  17. data/lib/labimotion/entities/eln_element_entity.rb +6 -0
  18. data/lib/labimotion/entities/generic_klass_entity.rb +126 -0
  19. data/lib/labimotion/entities/klass_share_entity.rb +48 -0
  20. data/lib/labimotion/entities/properties_entity.rb +78 -2
  21. data/lib/labimotion/entities/segment_entity.rb +8 -0
  22. data/lib/labimotion/entities/user_klass_setting_entity.rb +10 -0
  23. data/lib/labimotion/helpers/cover_image_helpers.rb +181 -0
  24. data/lib/labimotion/helpers/dataset_helpers.rb +187 -1
  25. data/lib/labimotion/helpers/element_helpers.rb +282 -6
  26. data/lib/labimotion/helpers/exporter_helpers.rb +17 -2
  27. data/lib/labimotion/helpers/generic_helpers.rb +293 -4
  28. data/lib/labimotion/helpers/param_helpers.rb +105 -0
  29. data/lib/labimotion/helpers/sample_association_helpers.rb +7 -0
  30. data/lib/labimotion/helpers/segment_helpers.rb +102 -4
  31. data/lib/labimotion/libs/ai_egress_guard.rb +99 -0
  32. data/lib/labimotion/libs/ai_klass_queue.rb +88 -0
  33. data/lib/labimotion/libs/ai_klass_validator.rb +74 -0
  34. data/lib/labimotion/libs/ai_models.rb +201 -0
  35. data/lib/labimotion/libs/ai_template.rb +2285 -0
  36. data/lib/labimotion/libs/converter.rb +5 -43
  37. data/lib/labimotion/libs/data/datacite/labimotion_template.html.erb +67 -0
  38. data/lib/labimotion/libs/export_element.rb +128 -13
  39. data/lib/labimotion/libs/file_extractor.rb +210 -0
  40. data/lib/labimotion/libs/linked_element.rb +313 -0
  41. data/lib/labimotion/libs/ontology_store.rb +226 -0
  42. data/lib/labimotion/libs/ontology_terms.rb +227 -0
  43. data/lib/labimotion/libs/owner_resolver.rb +50 -0
  44. data/lib/labimotion/libs/ownership_audit.rb +73 -0
  45. data/lib/labimotion/libs/sample_association.rb +52 -1
  46. data/lib/labimotion/libs/share_notifier.rb +114 -0
  47. data/lib/labimotion/libs/share_resolver.rb +373 -0
  48. data/lib/labimotion/libs/user_ai_settings.rb +129 -0
  49. data/lib/labimotion/models/cellline.rb +47 -0
  50. data/lib/labimotion/models/concerns/datasetable.rb +3 -0
  51. data/lib/labimotion/models/concerns/matrice_labimotion.rb +124 -0
  52. data/lib/labimotion/models/concerns/segmentable.rb +2 -0
  53. data/lib/labimotion/models/concerns/template_doi.rb +133 -0
  54. data/lib/labimotion/models/dataset_klass.rb +1 -1
  55. data/lib/labimotion/models/element_klass.rb +1 -1
  56. data/lib/labimotion/models/klass_share.rb +129 -0
  57. data/lib/labimotion/models/segment_klass.rb +1 -1
  58. data/lib/labimotion/models/user_klass_setting.rb +58 -0
  59. data/lib/labimotion/models/user_setting.rb +60 -0
  60. data/lib/labimotion/usecases/build_template_doi_xml.rb +69 -23
  61. data/lib/labimotion/usecases/release_template_doi.rb +42 -17
  62. data/lib/labimotion/usecases/template_doi_helpers.rb +28 -6
  63. data/lib/labimotion/usecases/update_template_publication_metadata.rb +71 -2
  64. data/lib/labimotion/utils/export_utils.rb +1 -0
  65. data/lib/labimotion/utils/import_utils.rb +20 -3
  66. data/lib/labimotion/utils/serializer.rb +27 -0
  67. data/lib/labimotion/utils/units.rb +32 -67
  68. data/lib/labimotion/version.rb +1 -1
  69. data/lib/labimotion.rb +27 -0
  70. metadata +45 -3
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: labimotion
3
3
  version: !ruby/object:Gem::Version
4
- version: 2.3.0
4
+ version: 2.4.0.rc11
5
5
  platform: ruby
6
6
  authors:
7
7
  - Chia-Lin Lin
@@ -25,6 +25,20 @@ dependencies:
25
25
  - - "~>"
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  - !ruby/object:Gem::Version
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  version: '4.0'
28
+ - !ruby/object:Gem::Dependency
29
+ name: pdf-reader
30
+ requirement: !ruby/object:Gem::Requirement
31
+ requirements:
32
+ - - "~>"
33
+ - !ruby/object:Gem::Version
34
+ version: '2.11'
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+ type: :runtime
36
+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
38
+ requirements:
39
+ - - "~>"
40
+ - !ruby/object:Gem::Version
41
+ version: '2.11'
28
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  - !ruby/object:Gem::Dependency
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  name: rails
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  requirement: !ruby/object:Gem::Requirement
@@ -77,15 +91,19 @@ files:
77
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  - lib/labimotion/apis/generic_dataset_api.rb
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  - lib/labimotion/apis/generic_element_api.rb
79
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  - lib/labimotion/apis/generic_klass_api.rb
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+ - lib/labimotion/apis/klass_share_api.rb
95
+ - lib/labimotion/apis/labimotion_ai_api.rb
80
96
  - lib/labimotion/apis/labimotion_api.rb
81
97
  - lib/labimotion/apis/labimotion_doi_api.rb
82
98
  - lib/labimotion/apis/labimotion_hub_api.rb
83
99
  - lib/labimotion/apis/labimotion_template_browse_api.rb
84
100
  - lib/labimotion/apis/mtt_api.rb
101
+ - lib/labimotion/apis/ontology_root_api.rb
85
102
  - lib/labimotion/apis/segment_api.rb
86
103
  - lib/labimotion/apis/standard_api.rb
87
104
  - lib/labimotion/apis/standard_layer_api.rb
88
105
  - lib/labimotion/apis/user_api.rb
106
+ - lib/labimotion/apis/user_klass_settings_api.rb
89
107
  - lib/labimotion/apis/vocabulary_api.rb
90
108
  - lib/labimotion/apis/wellplate_api.rb
91
109
  - lib/labimotion/collection/export.rb
@@ -104,14 +122,17 @@ files:
104
122
  - lib/labimotion/entities/generic_klass_entity.rb
105
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  - lib/labimotion/entities/generic_public_entity.rb
106
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  - lib/labimotion/entities/klass_revision_entity.rb
125
+ - lib/labimotion/entities/klass_share_entity.rb
107
126
  - lib/labimotion/entities/labimotion_template_doi_entity.rb
108
127
  - lib/labimotion/entities/properties_entity.rb
109
128
  - lib/labimotion/entities/segment_entity.rb
110
129
  - lib/labimotion/entities/segment_klass_entity.rb
111
130
  - lib/labimotion/entities/segment_revision_entity.rb
112
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  - lib/labimotion/entities/user_entity.rb
132
+ - lib/labimotion/entities/user_klass_setting_entity.rb
113
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  - lib/labimotion/entities/vocabulary_entity.rb
114
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  - lib/labimotion/helpers/converter_helpers.rb
135
+ - lib/labimotion/helpers/cover_image_helpers.rb
115
136
  - lib/labimotion/helpers/dataset_helpers.rb
116
137
  - lib/labimotion/helpers/element_helpers.rb
117
138
  - lib/labimotion/helpers/exporter_helpers.rb
@@ -123,8 +144,14 @@ files:
123
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  - lib/labimotion/helpers/search_helpers.rb
124
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  - lib/labimotion/helpers/segment_helpers.rb
125
146
  - lib/labimotion/helpers/vocabulary_helpers.rb
147
+ - lib/labimotion/libs/ai_egress_guard.rb
148
+ - lib/labimotion/libs/ai_klass_queue.rb
149
+ - lib/labimotion/libs/ai_klass_validator.rb
150
+ - lib/labimotion/libs/ai_models.rb
151
+ - lib/labimotion/libs/ai_template.rb
126
152
  - lib/labimotion/libs/attachment_handler.rb
127
153
  - lib/labimotion/libs/converter.rb
154
+ - lib/labimotion/libs/data/datacite/labimotion_template.html.erb
128
155
  - lib/labimotion/libs/data/mapper/Chemwiki.json
129
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  - lib/labimotion/libs/data/mapper/Source.json
130
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  - lib/labimotion/libs/data/vocab/Standard.json
@@ -135,14 +162,24 @@ files:
135
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  - lib/labimotion/libs/export_dataset.rb
136
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  - lib/labimotion/libs/export_element.rb
137
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  - lib/labimotion/libs/export_element_variations.rb
165
+ - lib/labimotion/libs/file_extractor.rb
138
166
  - lib/labimotion/libs/import_element_variations.rb
167
+ - lib/labimotion/libs/linked_element.rb
139
168
  - lib/labimotion/libs/nmr_mapper.rb
169
+ - lib/labimotion/libs/ontology_store.rb
170
+ - lib/labimotion/libs/ontology_terms.rb
171
+ - lib/labimotion/libs/owner_resolver.rb
172
+ - lib/labimotion/libs/ownership_audit.rb
140
173
  - lib/labimotion/libs/properties_handler.rb
141
174
  - lib/labimotion/libs/sample_association.rb
175
+ - lib/labimotion/libs/share_notifier.rb
176
+ - lib/labimotion/libs/share_resolver.rb
142
177
  - lib/labimotion/libs/template_hub.rb
143
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  - lib/labimotion/libs/template_matcher.rb
179
+ - lib/labimotion/libs/user_ai_settings.rb
144
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  - lib/labimotion/libs/vocabulary_handler.rb
145
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  - lib/labimotion/libs/xlsx_exporter.rb
182
+ - lib/labimotion/models/cellline.rb
146
183
  - lib/labimotion/models/collections_element.rb
147
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  - lib/labimotion/models/concerns/attachment_converter.rb
148
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  - lib/labimotion/models/concerns/datasetable.rb
@@ -152,8 +189,10 @@ files:
152
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  - lib/labimotion/models/concerns/generic_revisions.rb
153
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  - lib/labimotion/models/concerns/klass_revision.rb
154
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  - lib/labimotion/models/concerns/linked_properties.rb
192
+ - lib/labimotion/models/concerns/matrice_labimotion.rb
155
193
  - lib/labimotion/models/concerns/metadata_validation.rb
156
194
  - lib/labimotion/models/concerns/segmentable.rb
195
+ - lib/labimotion/models/concerns/template_doi.rb
157
196
  - lib/labimotion/models/concerns/workflow.rb
158
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  - lib/labimotion/models/dataset.rb
159
198
  - lib/labimotion/models/dataset_klass.rb
@@ -171,6 +210,7 @@ files:
171
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  - lib/labimotion/models/elements_sample.rb
172
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  - lib/labimotion/models/elements_wellplate.rb
173
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  - lib/labimotion/models/hub_log.rb
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+ - lib/labimotion/models/klass_share.rb
174
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  - lib/labimotion/models/reaction.rb
175
215
  - lib/labimotion/models/research_plan.rb
176
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  - lib/labimotion/models/sample.rb
@@ -182,6 +222,8 @@ files:
182
222
  - lib/labimotion/models/std_layer.rb
183
223
  - lib/labimotion/models/std_layers_revision.rb
184
224
  - lib/labimotion/models/template_submission.rb
225
+ - lib/labimotion/models/user_klass_setting.rb
226
+ - lib/labimotion/models/user_setting.rb
185
227
  - lib/labimotion/models/vocabulary.rb
186
228
  - lib/labimotion/models/wellplate.rb
187
229
  - lib/labimotion/usecases/build_template_doi_xml.rb
@@ -222,9 +264,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
222
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  version: '3.4'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
225
- - - ">="
267
+ - - ">"
226
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  - !ruby/object:Gem::Version
227
- version: '0'
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+ version: 1.3.1
228
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  requirements: []
229
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  rubygems_version: 3.1.6
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  signing_key: