cdisc-rules-engine 1.0.0__135-py3-none-any.whl

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Files changed (273) hide show
  1. cdisc_rules_engine/__init__.py +4 -0
  2. cdisc_rules_engine/check_operators/__init__.py +0 -0
  3. cdisc_rules_engine/check_operators/dataframe_operators.py +2331 -0
  4. cdisc_rules_engine/check_operators/helpers.py +464 -0
  5. cdisc_rules_engine/config/__init__.py +3 -0
  6. cdisc_rules_engine/config/config.py +47 -0
  7. cdisc_rules_engine/constants/__init__.py +14 -0
  8. cdisc_rules_engine/constants/adam_products.py +9 -0
  9. cdisc_rules_engine/constants/cache_constants.py +1 -0
  10. cdisc_rules_engine/constants/classes.py +15 -0
  11. cdisc_rules_engine/constants/data_structures.py +9 -0
  12. cdisc_rules_engine/constants/define_xml_constants.py +2 -0
  13. cdisc_rules_engine/constants/domains.py +1 -0
  14. cdisc_rules_engine/constants/metadata_columns.py +3 -0
  15. cdisc_rules_engine/constants/permissibility.py +5 -0
  16. cdisc_rules_engine/constants/rule_constants.py +2 -0
  17. cdisc_rules_engine/constants/use_cases.py +108 -0
  18. cdisc_rules_engine/dataset_builders/__init__.py +5 -0
  19. cdisc_rules_engine/dataset_builders/base_dataset_builder.py +263 -0
  20. cdisc_rules_engine/dataset_builders/content_metadata_dataset_builder.py +17 -0
  21. cdisc_rules_engine/dataset_builders/contents_dataset_builder.py +31 -0
  22. cdisc_rules_engine/dataset_builders/contents_define_dataset_builder.py +47 -0
  23. cdisc_rules_engine/dataset_builders/contents_define_variables_dataset_builder.py +38 -0
  24. cdisc_rules_engine/dataset_builders/contents_define_vlm_dataset_builder.py +88 -0
  25. cdisc_rules_engine/dataset_builders/contents_library_variables_dataset_builder.py +33 -0
  26. cdisc_rules_engine/dataset_builders/dataset_builder_factory.py +119 -0
  27. cdisc_rules_engine/dataset_builders/dataset_metadata_define_dataset_builder.py +178 -0
  28. cdisc_rules_engine/dataset_builders/dataset_metadata_values_builder.py +30 -0
  29. cdisc_rules_engine/dataset_builders/define_variables_with_library_metadata.py +58 -0
  30. cdisc_rules_engine/dataset_builders/domain_list_dataset_builder.py +18 -0
  31. cdisc_rules_engine/dataset_builders/domain_list_with_define_builder.py +43 -0
  32. cdisc_rules_engine/dataset_builders/json_schema_check_dataset_builder.py +210 -0
  33. cdisc_rules_engine/dataset_builders/jsonata_dataset_builder.py +30 -0
  34. cdisc_rules_engine/dataset_builders/values_dataset_builder.py +35 -0
  35. cdisc_rules_engine/dataset_builders/variables_metadata_dataset_builder.py +140 -0
  36. cdisc_rules_engine/dataset_builders/variables_metadata_values_dataset_builder.py +36 -0
  37. cdisc_rules_engine/dataset_builders/variables_metadata_with_define_and_library_dataset_builder.py +106 -0
  38. cdisc_rules_engine/dataset_builders/variables_metadata_with_define_dataset_builder.py +49 -0
  39. cdisc_rules_engine/dataset_builders/variables_metadata_with_library_metadata.py +77 -0
  40. cdisc_rules_engine/dummy_models/__init__.py +0 -0
  41. cdisc_rules_engine/dummy_models/dummy_dataset.py +49 -0
  42. cdisc_rules_engine/dummy_models/dummy_variable.py +7 -0
  43. cdisc_rules_engine/enums/__init__.py +0 -0
  44. cdisc_rules_engine/enums/base_enum.py +11 -0
  45. cdisc_rules_engine/enums/dataformat_types.py +11 -0
  46. cdisc_rules_engine/enums/dataset_title_case.py +6 -0
  47. cdisc_rules_engine/enums/default_file_paths.py +26 -0
  48. cdisc_rules_engine/enums/domain_presence_values.py +7 -0
  49. cdisc_rules_engine/enums/excel_test_sheets.py +8 -0
  50. cdisc_rules_engine/enums/execution_status.py +21 -0
  51. cdisc_rules_engine/enums/join_types.py +6 -0
  52. cdisc_rules_engine/enums/library_endpoints.py +30 -0
  53. cdisc_rules_engine/enums/optional_condition_parameters.py +25 -0
  54. cdisc_rules_engine/enums/progress_parameter_options.py +8 -0
  55. cdisc_rules_engine/enums/report_types.py +7 -0
  56. cdisc_rules_engine/enums/rule_types.py +30 -0
  57. cdisc_rules_engine/enums/sensitivity.py +8 -0
  58. cdisc_rules_engine/enums/standard_types.py +20 -0
  59. cdisc_rules_engine/enums/variable_roles.py +11 -0
  60. cdisc_rules_engine/exceptions/__init__.py +49 -0
  61. cdisc_rules_engine/exceptions/custom_exceptions.py +135 -0
  62. cdisc_rules_engine/interfaces/__init__.py +23 -0
  63. cdisc_rules_engine/interfaces/cache_service_interface.py +56 -0
  64. cdisc_rules_engine/interfaces/condition_interface.py +28 -0
  65. cdisc_rules_engine/interfaces/config_interface.py +15 -0
  66. cdisc_rules_engine/interfaces/data_reader_interface.py +34 -0
  67. cdisc_rules_engine/interfaces/data_service_interface.py +136 -0
  68. cdisc_rules_engine/interfaces/dictionary_term_interface.py +14 -0
  69. cdisc_rules_engine/interfaces/factory_interface.py +12 -0
  70. cdisc_rules_engine/interfaces/logger_interface.py +87 -0
  71. cdisc_rules_engine/interfaces/representation_interface.py +14 -0
  72. cdisc_rules_engine/interfaces/terms_factory_interface.py +31 -0
  73. cdisc_rules_engine/models/__init__.py +0 -0
  74. cdisc_rules_engine/models/actions.py +529 -0
  75. cdisc_rules_engine/models/base_validation_entity.py +10 -0
  76. cdisc_rules_engine/models/dataset/__init__.py +10 -0
  77. cdisc_rules_engine/models/dataset/dask_dataset.py +396 -0
  78. cdisc_rules_engine/models/dataset/dataset_interface.py +270 -0
  79. cdisc_rules_engine/models/dataset/pandas_dataset.py +297 -0
  80. cdisc_rules_engine/models/dataset_metadata.py +19 -0
  81. cdisc_rules_engine/models/dataset_types.py +7 -0
  82. cdisc_rules_engine/models/dataset_variable.py +25 -0
  83. cdisc_rules_engine/models/define/__init__.py +5 -0
  84. cdisc_rules_engine/models/define/value_level_metadata.py +286 -0
  85. cdisc_rules_engine/models/dictionaries/__init__.py +14 -0
  86. cdisc_rules_engine/models/dictionaries/abstract_factory.py +48 -0
  87. cdisc_rules_engine/models/dictionaries/base_dictionary_validator.py +82 -0
  88. cdisc_rules_engine/models/dictionaries/base_external_dictionary.py +26 -0
  89. cdisc_rules_engine/models/dictionaries/dictionary_types.py +14 -0
  90. cdisc_rules_engine/models/dictionaries/get_dictionary_terms.py +17 -0
  91. cdisc_rules_engine/models/dictionaries/loinc/__init__.py +10 -0
  92. cdisc_rules_engine/models/dictionaries/loinc/loinc_term.py +10 -0
  93. cdisc_rules_engine/models/dictionaries/loinc/loinc_terms_factory.py +74 -0
  94. cdisc_rules_engine/models/dictionaries/loinc/loinc_validator.py +67 -0
  95. cdisc_rules_engine/models/dictionaries/meddra/__init__.py +10 -0
  96. cdisc_rules_engine/models/dictionaries/meddra/meddra_file_names.py +14 -0
  97. cdisc_rules_engine/models/dictionaries/meddra/meddra_terms_factory.py +208 -0
  98. cdisc_rules_engine/models/dictionaries/meddra/meddra_validator.py +131 -0
  99. cdisc_rules_engine/models/dictionaries/meddra/meddra_variables.py +16 -0
  100. cdisc_rules_engine/models/dictionaries/meddra/terms/__init__.py +0 -0
  101. cdisc_rules_engine/models/dictionaries/meddra/terms/meddra_term.py +43 -0
  102. cdisc_rules_engine/models/dictionaries/meddra/terms/term_types.py +13 -0
  103. cdisc_rules_engine/models/dictionaries/medrt/__init__.py +10 -0
  104. cdisc_rules_engine/models/dictionaries/medrt/term.py +15 -0
  105. cdisc_rules_engine/models/dictionaries/medrt/terms_factory.py +116 -0
  106. cdisc_rules_engine/models/dictionaries/medrt/validator.py +62 -0
  107. cdisc_rules_engine/models/dictionaries/snomed/__init__.py +10 -0
  108. cdisc_rules_engine/models/dictionaries/snomed/term.py +21 -0
  109. cdisc_rules_engine/models/dictionaries/snomed/terms_factory.py +74 -0
  110. cdisc_rules_engine/models/dictionaries/snomed/validator.py +59 -0
  111. cdisc_rules_engine/models/dictionaries/unii/__init__.py +10 -0
  112. cdisc_rules_engine/models/dictionaries/unii/term.py +4 -0
  113. cdisc_rules_engine/models/dictionaries/unii/terms_factory.py +61 -0
  114. cdisc_rules_engine/models/dictionaries/unii/validator.py +54 -0
  115. cdisc_rules_engine/models/dictionaries/whodrug/__init__.py +15 -0
  116. cdisc_rules_engine/models/dictionaries/whodrug/atc_classification.py +32 -0
  117. cdisc_rules_engine/models/dictionaries/whodrug/atc_text.py +33 -0
  118. cdisc_rules_engine/models/dictionaries/whodrug/base_whodrug_term.py +33 -0
  119. cdisc_rules_engine/models/dictionaries/whodrug/drug_dict.py +32 -0
  120. cdisc_rules_engine/models/dictionaries/whodrug/whodrug_file_names.py +12 -0
  121. cdisc_rules_engine/models/dictionaries/whodrug/whodrug_record_types.py +11 -0
  122. cdisc_rules_engine/models/dictionaries/whodrug/whodrug_terms_factory.py +99 -0
  123. cdisc_rules_engine/models/dictionaries/whodrug/whodrug_validator.py +67 -0
  124. cdisc_rules_engine/models/dictionaries/whodrug/whodrug_variable_names.py +11 -0
  125. cdisc_rules_engine/models/external_dictionaries_container.py +49 -0
  126. cdisc_rules_engine/models/failed_validation_entity.py +23 -0
  127. cdisc_rules_engine/models/library_metadata_container.py +141 -0
  128. cdisc_rules_engine/models/operation_params.py +66 -0
  129. cdisc_rules_engine/models/rule.py +208 -0
  130. cdisc_rules_engine/models/rule_conditions/__init__.py +7 -0
  131. cdisc_rules_engine/models/rule_conditions/allowed_conditions_keys.py +11 -0
  132. cdisc_rules_engine/models/rule_conditions/condition_composite.py +109 -0
  133. cdisc_rules_engine/models/rule_conditions/condition_composite_factory.py +54 -0
  134. cdisc_rules_engine/models/rule_conditions/not_condition_composite.py +66 -0
  135. cdisc_rules_engine/models/rule_conditions/single_condition.py +50 -0
  136. cdisc_rules_engine/models/rule_validation_result.py +67 -0
  137. cdisc_rules_engine/models/sdtm_dataset_metadata.py +105 -0
  138. cdisc_rules_engine/models/validation_args.py +34 -0
  139. cdisc_rules_engine/models/validation_error_container.py +35 -0
  140. cdisc_rules_engine/models/validation_error_entity.py +57 -0
  141. cdisc_rules_engine/models/variable_metadata_container.py +25 -0
  142. cdisc_rules_engine/operations/__init__.py +3 -0
  143. cdisc_rules_engine/operations/base_operation.py +327 -0
  144. cdisc_rules_engine/operations/codelist_extensible.py +78 -0
  145. cdisc_rules_engine/operations/codelist_terms.py +174 -0
  146. cdisc_rules_engine/operations/dataset_column_order.py +20 -0
  147. cdisc_rules_engine/operations/dataset_names.py +9 -0
  148. cdisc_rules_engine/operations/day_data_validator.py +59 -0
  149. cdisc_rules_engine/operations/define_dictionary_version_validator.py +44 -0
  150. cdisc_rules_engine/operations/define_variable_metadata.py +50 -0
  151. cdisc_rules_engine/operations/define_xml_extensible_codelists.py +35 -0
  152. cdisc_rules_engine/operations/distinct.py +108 -0
  153. cdisc_rules_engine/operations/domain_is_custom.py +14 -0
  154. cdisc_rules_engine/operations/domain_label.py +20 -0
  155. cdisc_rules_engine/operations/expected_variables.py +24 -0
  156. cdisc_rules_engine/operations/extract_metadata.py +16 -0
  157. cdisc_rules_engine/operations/get_codelist_attributes.py +223 -0
  158. cdisc_rules_engine/operations/get_dataset_filtered_variables.py +21 -0
  159. cdisc_rules_engine/operations/get_library_class_domains.py +29 -0
  160. cdisc_rules_engine/operations/get_model_filtered_variables.py +32 -0
  161. cdisc_rules_engine/operations/get_xhtml_errors.py +168 -0
  162. cdisc_rules_engine/operations/intersect.py +52 -0
  163. cdisc_rules_engine/operations/label_referenced_variable_metadata.py +22 -0
  164. cdisc_rules_engine/operations/library_column_order.py +42 -0
  165. cdisc_rules_engine/operations/library_model_column_order.py +21 -0
  166. cdisc_rules_engine/operations/map.py +18 -0
  167. cdisc_rules_engine/operations/max_date.py +48 -0
  168. cdisc_rules_engine/operations/maximum.py +12 -0
  169. cdisc_rules_engine/operations/mean.py +23 -0
  170. cdisc_rules_engine/operations/meddra_code_references_validator.py +39 -0
  171. cdisc_rules_engine/operations/meddra_code_term_pairs_validator.py +132 -0
  172. cdisc_rules_engine/operations/meddra_term_references_validator.py +39 -0
  173. cdisc_rules_engine/operations/min_date.py +49 -0
  174. cdisc_rules_engine/operations/minimum.py +12 -0
  175. cdisc_rules_engine/operations/minus.py +86 -0
  176. cdisc_rules_engine/operations/name_referenced_variable_metadata.py +23 -0
  177. cdisc_rules_engine/operations/operations_factory.py +197 -0
  178. cdisc_rules_engine/operations/parent_library_model_column_order.py +61 -0
  179. cdisc_rules_engine/operations/permissible_variables.py +21 -0
  180. cdisc_rules_engine/operations/record_count.py +193 -0
  181. cdisc_rules_engine/operations/referenced_domain_variable_names.py +52 -0
  182. cdisc_rules_engine/operations/related_domain_is_custom.py +16 -0
  183. cdisc_rules_engine/operations/required_variables.py +21 -0
  184. cdisc_rules_engine/operations/split_by.py +13 -0
  185. cdisc_rules_engine/operations/standard_domains.py +9 -0
  186. cdisc_rules_engine/operations/study_domains.py +11 -0
  187. cdisc_rules_engine/operations/valid_codelist_dates.py +59 -0
  188. cdisc_rules_engine/operations/valid_external_dictionary_code.py +61 -0
  189. cdisc_rules_engine/operations/valid_external_dictionary_code_term_pair.py +74 -0
  190. cdisc_rules_engine/operations/valid_external_dictionary_value.py +59 -0
  191. cdisc_rules_engine/operations/variable_count.py +44 -0
  192. cdisc_rules_engine/operations/variable_exists.py +6 -0
  193. cdisc_rules_engine/operations/variable_is_null.py +19 -0
  194. cdisc_rules_engine/operations/variable_names.py +16 -0
  195. cdisc_rules_engine/operations/variable_value_count.py +57 -0
  196. cdisc_rules_engine/operations/whodrug_hierarchy_validator.py +56 -0
  197. cdisc_rules_engine/operations/whodrug_references_validator.py +27 -0
  198. cdisc_rules_engine/plugin_loader.py +53 -0
  199. cdisc_rules_engine/rules_engine.py +657 -0
  200. cdisc_rules_engine/serializers/__init__.py +20 -0
  201. cdisc_rules_engine/serializers/base_serializer.py +22 -0
  202. cdisc_rules_engine/serializers/dataset_metadata_serializer.py +49 -0
  203. cdisc_rules_engine/serializers/rule_serializer.py +59 -0
  204. cdisc_rules_engine/serializers/term_serializers/__init__.py +11 -0
  205. cdisc_rules_engine/serializers/term_serializers/atc_classification_serializer.py +28 -0
  206. cdisc_rules_engine/serializers/term_serializers/atc_text_serializer.py +30 -0
  207. cdisc_rules_engine/serializers/term_serializers/base_whodrug_term_serializer.py +15 -0
  208. cdisc_rules_engine/serializers/term_serializers/drug_dictionary_serializer.py +28 -0
  209. cdisc_rules_engine/serializers/term_serializers/meddra_term_serializer.py +35 -0
  210. cdisc_rules_engine/services/__init__.py +4 -0
  211. cdisc_rules_engine/services/adam_variable_reader.py +53 -0
  212. cdisc_rules_engine/services/cache/__init__.py +9 -0
  213. cdisc_rules_engine/services/cache/cache_populator_service.py +697 -0
  214. cdisc_rules_engine/services/cache/cache_service_factory.py +38 -0
  215. cdisc_rules_engine/services/cache/in_memory_cache_service.py +136 -0
  216. cdisc_rules_engine/services/cache/redis_cache_service.py +107 -0
  217. cdisc_rules_engine/services/cdisc_library_service.py +720 -0
  218. cdisc_rules_engine/services/csv_metadata_reader.py +187 -0
  219. cdisc_rules_engine/services/data_readers/__init__.py +6 -0
  220. cdisc_rules_engine/services/data_readers/csv_reader.py +121 -0
  221. cdisc_rules_engine/services/data_readers/data_reader_factory.py +76 -0
  222. cdisc_rules_engine/services/data_readers/dataset_json_reader.py +60 -0
  223. cdisc_rules_engine/services/data_readers/dataset_ndjson_reader.py +69 -0
  224. cdisc_rules_engine/services/data_readers/json_reader.py +46 -0
  225. cdisc_rules_engine/services/data_readers/parquet_reader.py +36 -0
  226. cdisc_rules_engine/services/data_readers/xpt_reader.py +53 -0
  227. cdisc_rules_engine/services/data_services/__init__.py +16 -0
  228. cdisc_rules_engine/services/data_services/base_data_service.py +363 -0
  229. cdisc_rules_engine/services/data_services/data_service_factory.py +153 -0
  230. cdisc_rules_engine/services/data_services/dummy_data_service.py +168 -0
  231. cdisc_rules_engine/services/data_services/excel_data_service.py +273 -0
  232. cdisc_rules_engine/services/data_services/local_data_service.py +254 -0
  233. cdisc_rules_engine/services/data_services/usdm_data_service.py +462 -0
  234. cdisc_rules_engine/services/datasetjson_metadata_reader.py +150 -0
  235. cdisc_rules_engine/services/datasetndjson_metadata_reader.py +175 -0
  236. cdisc_rules_engine/services/datasetxpt_metadata_reader.py +190 -0
  237. cdisc_rules_engine/services/define_xml/base_define_xml_reader.py +637 -0
  238. cdisc_rules_engine/services/define_xml/define_xml_reader_2_0.py +62 -0
  239. cdisc_rules_engine/services/define_xml/define_xml_reader_2_1.py +148 -0
  240. cdisc_rules_engine/services/define_xml/define_xml_reader_factory.py +131 -0
  241. cdisc_rules_engine/services/logging/__init__.py +7 -0
  242. cdisc_rules_engine/services/logging/console_logger.py +91 -0
  243. cdisc_rules_engine/services/logging/logging_service_factory.py +45 -0
  244. cdisc_rules_engine/services/reporting/__init__.py +7 -0
  245. cdisc_rules_engine/services/reporting/base_report.py +50 -0
  246. cdisc_rules_engine/services/reporting/base_report_data.py +87 -0
  247. cdisc_rules_engine/services/reporting/csv_report.py +43 -0
  248. cdisc_rules_engine/services/reporting/excel_report.py +108 -0
  249. cdisc_rules_engine/services/reporting/excel_writer.py +53 -0
  250. cdisc_rules_engine/services/reporting/json_report.py +81 -0
  251. cdisc_rules_engine/services/reporting/report_factory.py +91 -0
  252. cdisc_rules_engine/services/reporting/report_metadata_item.py +8 -0
  253. cdisc_rules_engine/services/reporting/sdtm_report_data.py +452 -0
  254. cdisc_rules_engine/services/reporting/usdm_report_data.py +307 -0
  255. cdisc_rules_engine/utilities/__init__.py +0 -0
  256. cdisc_rules_engine/utilities/data_processor.py +485 -0
  257. cdisc_rules_engine/utilities/dataset_preprocessor.py +581 -0
  258. cdisc_rules_engine/utilities/decorators.py +91 -0
  259. cdisc_rules_engine/utilities/jsonata_processor.py +130 -0
  260. cdisc_rules_engine/utilities/progress_displayers.py +80 -0
  261. cdisc_rules_engine/utilities/rule_processor.py +708 -0
  262. cdisc_rules_engine/utilities/sdtm_utilities.py +531 -0
  263. cdisc_rules_engine/utilities/utils.py +441 -0
  264. cdisc_rules_engine-1.0.0.dist-info/METADATA +453 -0
  265. cdisc_rules_engine-1.0.0.dist-info/RECORD +273 -0
  266. cdisc_rules_engine-1.0.0.dist-info/WHEEL +6 -0
  267. cdisc_rules_engine-1.0.0.dist-info/licenses/LICENSE +21 -0
  268. cdisc_rules_engine-1.0.0.dist-info/top_level.txt +4 -0
  269. docs/PYPI.md +412 -0
  270. resources/schema/USDM.yaml +138 -0
  271. resources/schema/dataset-ndjson-schema.json +270 -0
  272. resources/schema/dataset.schema.json +307 -0
  273. version.py +1 -0
cdisc_rules_engine/__init__.py ADDED
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+ from .plugin_loader import PluginLoader
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+ loader = PluginLoader()
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+ loader.load()
cdisc_rules_engine/check_operators/__init__.py ADDED
File without changes