clinicedc 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

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  1. {clinicedc-2.0.0.dist-info → clinicedc-2.0.2.dist-info}/METADATA +15 -22
  2. {clinicedc-2.0.0.dist-info → clinicedc-2.0.2.dist-info}/RECORD +895 -792
  3. {clinicedc-2.0.0.dist-info → clinicedc-2.0.2.dist-info}/WHEEL +1 -1
  4. edc_action_item/action.py +13 -32
  5. edc_action_item/action_with_notification.py +1 -2
  6. edc_action_item/admin/action_item_admin.py +2 -6
  7. edc_action_item/admin_site.py +1 -3
  8. edc_action_item/auths.py +1 -3
  9. edc_action_item/create_or_update_action_type.py +1 -3
  10. edc_action_item/data_fixers.py +7 -20
  11. edc_action_item/forms/action_item_form.py +1 -3
  12. edc_action_item/management/commands/inspect_action_items.py +3 -9
  13. edc_action_item/migrations/0001_initial.py +4 -5
  14. edc_action_item/migrations/0003_auto_20180116_1528.py +2 -1
  15. edc_action_item/migrations/0006_auto_20180707_1659.py +3 -4
  16. edc_action_item/migrations/0007_auto_20180707_1715.py +1 -3
  17. edc_action_item/migrations/0008_auto_20180809_0303.py +2 -1
  18. edc_action_item/migrations/0014_auto_20181121_1738.py +2 -6
  19. edc_action_item/migrations/0015_auto_20190114_0250.py +4 -3
  20. edc_action_item/migrations/0021_auto_20190628_2113.py +1 -3
  21. edc_action_item/migrations/0022_auto_20190628_2136.py +2 -6
  22. edc_action_item/migrations/0030_edcpermissions.py +1 -1
  23. edc_action_item/migrations/0033_alter_actionitem_managers.py +1 -0
  24. edc_action_item/migrations/0034_alter_actionitem_device_created_and_more.py +13 -37
  25. edc_action_item/migrations/0038_alter_actionitem_revision_alter_actiontype_revision_and_more.py +86 -0
  26. edc_action_item/models/action_item.py +2 -6
  27. edc_action_item/models/action_model_mixin.py +5 -16
  28. edc_action_item/models/action_type.py +1 -3
  29. edc_action_item/models/reference.py +1 -2
  30. edc_action_item/models/signals.py +3 -9
  31. edc_action_item/site_action_items.py +4 -12
  32. edc_action_item/templatetags/action_item_extras.py +1 -3
  33. edc_action_item/view_utils/action_item_button.py +1 -3
  34. edc_action_item/view_utils/action_item_popover_list_item.py +1 -2
  35. edc_adherence/migrations/0002_nonadherencereasons_plural_name.py +1 -3
  36. edc_adherence/model_admin_mixin.py +1 -3
  37. edc_adverse_event/action_items/ae_followup_action.py +2 -6
  38. edc_adverse_event/action_items/ae_initial_action.py +3 -7
  39. edc_adverse_event/auth_objects.py +2 -6
  40. edc_adverse_event/constants.py +1 -3
  41. edc_adverse_event/form_validator_mixins/death_report_form_validator.py +1 -3
  42. edc_adverse_event/form_validator_mixins/requires_death_report_form_validator_mixin.py +2 -7
  43. edc_adverse_event/form_validators/hospitalization.py +1 -3
  44. edc_adverse_event/migrations/0003_auto_20191026_2231.py +3 -9
  45. edc_adverse_event/migrations/0008_auto_20220825_0451.py +1 -1
  46. edc_adverse_event/migrations/0009_auto_20220907_0157.py +1 -1
  47. edc_adverse_event/migrations/0010_auto_20220913_2139.py +4 -12
  48. edc_adverse_event/migrations/0013_alter_aeactionclassification_device_created_and_more.py +11 -31
  49. edc_adverse_event/migrations/0015_alter_aeactionclassification_revision_and_more.py +74 -0
  50. edc_adverse_event/model_mixins/ae_followup/ae_followup_fields_model_mixin.py +1 -3
  51. edc_adverse_event/model_mixins/ae_followup/ae_followup_model_mixin.py +1 -5
  52. edc_adverse_event/model_mixins/ae_initial/ae_initial_ae_model_mixin.py +1 -3
  53. edc_adverse_event/model_mixins/ae_initial/ae_initial_fields_model_mixin.py +1 -3
  54. edc_adverse_event/model_mixins/ae_initial/ae_initial_susar_model_mixin.py +1 -2
  55. edc_adverse_event/model_mixins/ae_special_interest/aesi_model_mixin.py +1 -5
  56. edc_adverse_event/model_mixins/ae_susar/ae_susar_model_mixin.py +1 -5
  57. edc_adverse_event/model_mixins/ae_tmg/ae_tmg_fields_model_mixin.py +2 -6
  58. edc_adverse_event/model_mixins/ae_tmg/ae_tmg_model_mixin.py +1 -5
  59. edc_adverse_event/model_mixins/death_report/death_report_extra_fields_model_mixin.py +1 -2
  60. edc_adverse_event/model_mixins/death_report/death_report_model_mixin.py +2 -5
  61. edc_adverse_event/model_mixins/death_report/death_report_tmg_model_mixin.py +2 -7
  62. edc_adverse_event/model_mixins/death_report/simple_death_report_model_mixin.py +1 -3
  63. edc_adverse_event/modeladmin_mixins/ae_tmg_admin_mixin.py +1 -3
  64. edc_adverse_event/modeladmin_mixins/death_report_admin_mixin.py +6 -10
  65. edc_adverse_event/modelform_mixins/ae_tmg_modelform_mixin.py +1 -3
  66. edc_adverse_event/models/signals.py +3 -9
  67. edc_adverse_event/pdf_reports/ae_pdf_report.py +6 -18
  68. edc_adverse_event/pdf_reports/death_pdf_report.py +3 -9
  69. edc_adverse_event/templatetags/edc_adverse_event_extras.py +5 -15
  70. edc_adverse_event/utils.py +2 -6
  71. edc_adverse_event/view_mixins/ae/ae_listboard_view_mixin.py +1 -3
  72. edc_adverse_event/view_mixins/ae/death_report_listboard_view_mixin.py +1 -3
  73. edc_adverse_event/view_mixins/tmg/tmg_ae_listboard_view_mixin.py +2 -6
  74. edc_adverse_event/view_utils/tmg_button.py +2 -6
  75. edc_adverse_event/views/home_view.py +1 -3
  76. edc_adverse_event/views/tmg/death_listboard_view.py +1 -3
  77. edc_adverse_event/views/tmg/home_view.py +2 -6
  78. edc_adverse_event/views/tmg/summary_listboard_view.py +1 -3
  79. edc_appconfig/apps.py +3 -2
  80. edc_appointment/admin/appointment_admin.py +1 -3
  81. edc_appointment/admin/list_filters.py +1 -3
  82. edc_appointment/admin_site.py +1 -3
  83. edc_appointment/analytics/dataframes/get_appointment_df.py +2 -6
  84. edc_appointment/appointment_reason_updater.py +2 -5
  85. edc_appointment/appointment_status_updater.py +1 -4
  86. edc_appointment/constants.py +1 -3
  87. edc_appointment/creators/appointment_creator.py +4 -10
  88. edc_appointment/creators/appointments_creator.py +3 -2
  89. edc_appointment/creators/unscheduled_appointment_creator.py +3 -7
  90. edc_appointment/creators/utils.py +4 -0
  91. edc_appointment/form_validator_mixins/next_appointment_crf_form_validator_mixin.py +3 -10
  92. edc_appointment/form_validator_mixins/window_period_form_validator_mixin.py +3 -9
  93. edc_appointment/form_validators/appointment_form_validator.py +11 -37
  94. edc_appointment/form_validators/next_appointment_crf_form_validator.py +1 -3
  95. edc_appointment/form_validators/utils.py +1 -3
  96. edc_appointment/managers.py +2 -6
  97. edc_appointment/migrations/0002_auto_20161126_1156.py +5 -8
  98. edc_appointment/migrations/0003_auto_20161127_2226.py +7 -16
  99. edc_appointment/migrations/0006_auto_20170106_2118.py +2 -1
  100. edc_appointment/migrations/0008_auto_20171115_1601.py +3 -4
  101. edc_appointment/migrations/0014_auto_20180116_1411.py +2 -1
  102. edc_appointment/migrations/0024_auto_20200911_0425.py +1 -1
  103. edc_appointment/migrations/0034_appointmenttype_alter_appointment_appt_type_and_more.py +2 -4
  104. edc_appointment/migrations/0036_auto_20230124_1822.py +2 -6
  105. edc_appointment/migrations/0040_appointment_appt_type_other_and_more.py +1 -0
  106. edc_appointment/migrations/0042_alter_appointment_device_created_and_more.py +5 -13
  107. edc_appointment/migrations/0046_infosources.py +1 -3
  108. edc_appointment/migrations/0047_alter_appointment_options_and_more.py +1 -3
  109. edc_appointment/migrations/0049_alter_appointment_revision_and_more.py +38 -0
  110. edc_appointment/model_mixins/appointment_methods_model_mixin.py +1 -5
  111. edc_appointment/model_mixins/appointment_model_mixin.py +7 -12
  112. edc_appointment/model_mixins/next_appointment_crf_model_mixin.py +1 -3
  113. edc_appointment/modeladmin_mixins/next_appointment_crf_modeladmin_mixin.py +1 -3
  114. edc_appointment/modelform_mixins/next_appointment_crf_modelform_mixins.py +1 -5
  115. edc_appointment/models/signals.py +5 -17
  116. edc_appointment/utils.py +11 -33
  117. edc_appointment/view_mixins/appointment_view_mixin.py +2 -6
  118. edc_auth/admin/list_filters.py +2 -6
  119. edc_auth/admin/role_admin.py +1 -3
  120. edc_auth/admin/user_admin.py +4 -12
  121. edc_auth/admin/user_profile_admin.py +2 -5
  122. edc_auth/auth_updater/auth_updater.py +1 -3
  123. edc_auth/forms.py +1 -3
  124. edc_auth/get_app_codenames.py +1 -3
  125. edc_auth/import_users.py +3 -9
  126. edc_auth/management/commands/export_users.py +1 -3
  127. edc_auth/management/commands/reset_password.py +1 -3
  128. edc_auth/migrations/0001_squashed_0033_alter_userprofile_is_multisite_viewer.py +4 -12
  129. edc_auth/migrations/0015_auto_20191026_2149.py +1 -3
  130. edc_auth/migrations/0016_auto_20191026_2153.py +1 -3
  131. edc_auth/migrations/0025_permissions.py +1 -1
  132. edc_auth/migrations/0029_alter_edcpermissions_device_created_and_more.py +5 -13
  133. edc_auth/migrations/0034_alter_edcpermissions_revision_alter_role_revision.py +38 -0
  134. edc_auth/models/__init__.py +1 -3
  135. edc_auth/models/signals.py +2 -6
  136. edc_auth/models/user_profile.py +1 -3
  137. edc_auth/password_setter.py +1 -3
  138. edc_auth/system_checks.py +1 -5
  139. edc_auth/urls_for_accounts.py +1 -3
  140. edc_auth/utils.py +3 -9
  141. edc_consent/actions.py +3 -9
  142. edc_consent/consent_definition.py +5 -8
  143. edc_consent/consent_definition_extension.py +4 -12
  144. edc_consent/field_mixins/citizen_fields_mixin.py +2 -4
  145. edc_consent/field_mixins/identity_fields_mixin.py +1 -2
  146. edc_consent/field_mixins/personal_fields_mixin.py +8 -3
  147. edc_consent/field_mixins/site_fields_mixin.py +1 -2
  148. edc_consent/form_validators/subject_consent_form_validator.py +4 -8
  149. edc_consent/migrations/0001_initial.py +1 -1
  150. edc_consent/migrations/0002_alter_edcpermissions_device_created_and_more.py +3 -7
  151. edc_consent/migrations/0005_alter_edcpermissions_revision.py +26 -0
  152. edc_consent/model_mixins/consent_extension_model_mixin.py +2 -3
  153. edc_consent/model_mixins/consent_model_mixin.py +3 -9
  154. edc_consent/modeladmin_mixins/consent_model_admin_mixin.py +7 -17
  155. edc_consent/modelform_mixins/consent_modelform_mixin/consent_modelform_validation_mixin.py +6 -10
  156. edc_consent/modelform_mixins/requires_consent_modelform_mixin.py +1 -3
  157. edc_consent/models/signals.py +3 -6
  158. edc_consent/site_consents.py +6 -17
  159. edc_consent/system_checks.py +3 -9
  160. edc_consent/validators.py +1 -2
  161. edc_consent/view_mixins/consent_view_mixins.py +3 -5
  162. edc_crf/crf_form_validator.py +4 -7
  163. edc_crf/crf_form_validator_mixins.py +2 -6
  164. edc_crf/migrations/0004_alter_crfstatus_device_created_and_more.py +3 -7
  165. edc_crf/migrations/0008_alter_crfstatus_revision.py +26 -0
  166. edc_crf/utils.py +1 -3
  167. edc_dashboard/management/commands/update_search_slugs.py +1 -3
  168. edc_dashboard/migrations/0001_initial.py +1 -1
  169. edc_dashboard/migrations/0003_alter_edcpermissions_device_created_and_more.py +3 -7
  170. edc_dashboard/migrations/0005_alter_edcpermissions_revision.py +26 -0
  171. edc_dashboard/templatetags/edc_dashboard_extras.py +2 -6
  172. edc_dashboard/view_mixins/administration_view_mixin.py +1 -3
  173. edc_dashboard/view_mixins/edc_view_mixin.py +1 -3
  174. edc_dashboard/views/administration_view.py +1 -3
  175. edc_data_manager/action_items.py +1 -3
  176. edc_data_manager/admin/actions.py +3 -9
  177. edc_data_manager/admin/data_query_admin.py +4 -12
  178. edc_data_manager/admin/query_rule_admin.py +4 -13
  179. edc_data_manager/auths.py +1 -3
  180. edc_data_manager/forms/data_query.py +2 -6
  181. edc_data_manager/forms/query_rule.py +1 -3
  182. edc_data_manager/get_longitudinal_value.py +2 -5
  183. edc_data_manager/handlers/handlers.py +2 -6
  184. edc_data_manager/migrations/0001_initial.py +4 -3
  185. edc_data_manager/migrations/0003_auto_20190806_1749.py +2 -6
  186. edc_data_manager/migrations/0004_auto_20190806_1750.py +1 -3
  187. edc_data_manager/migrations/0025_edcpermissions.py +1 -1
  188. edc_data_manager/migrations/0027_alter_dataquery_dm_user.py +1 -1
  189. edc_data_manager/migrations/0028_alter_dataquery_options_alter_queryrule_options_and_more.py +2 -1
  190. edc_data_manager/migrations/0029_alter_dataquery_managers.py +2 -1
  191. edc_data_manager/migrations/0030_alter_datadictionary_device_created_and_more.py +15 -43
  192. edc_data_manager/migrations/0039_alter_datadictionary_revision_and_more.py +101 -0
  193. edc_data_manager/models/model_mixins.py +1 -3
  194. edc_data_manager/populate_data_dictionary.py +1 -2
  195. edc_data_manager/post_migrate_signals.py +1 -3
  196. edc_data_manager/site_data_manager.py +1 -3
  197. edc_document_status/model_mixins.py +1 -3
  198. edc_egfr/__init__.py +1 -0
  199. edc_egfr/admin/__init__.py +1 -0
  200. edc_egfr/admin/egfr_drop_notification_admin_mixin.py +73 -0
  201. edc_egfr/apps.py +5 -0
  202. edc_egfr/calculators/__init__.py +4 -0
  203. edc_egfr/calculators/base_egrfr.py +56 -0
  204. edc_egfr/calculators/egfr_ckd_epi.py +68 -0
  205. edc_egfr/calculators/egfr_cockcroft_gault.py +63 -0
  206. edc_egfr/calculators/percent_change.py +7 -0
  207. edc_egfr/constants.py +1 -0
  208. edc_egfr/egfr.py +237 -0
  209. edc_egfr/form_validator_mixins/__init__.py +4 -0
  210. edc_egfr/form_validator_mixins/egfr_form_validator_mixins.py +55 -0
  211. edc_egfr/get_drop_notification_model.py +10 -0
  212. edc_egfr/get_egfr_for_subject.py +31 -0
  213. edc_egfr/model_mixins/__init__.py +2 -0
  214. edc_egfr/model_mixins/egfr_drop_notification_model_mixin.py +63 -0
  215. edc_egfr/model_mixins/egfr_model_mixin.py +120 -0
  216. edc_export/archive_exporter.py +2 -6
  217. edc_export/exportables.py +2 -6
  218. edc_export/files_emailer.py +1 -3
  219. edc_export/management/commands/import_receipts.py +1 -3
  220. edc_export/managers.py +3 -9
  221. edc_export/migrations/0001_initial.py +15 -36
  222. edc_export/migrations/0005_exportdata_importdata.py +1 -3
  223. edc_export/migrations/0006_auto_20200512_0208.py +2 -6
  224. edc_export/migrations/0010_auto_20210910_1636.py +2 -6
  225. edc_export/migrations/0013_edcpermissions.py +1 -1
  226. edc_export/migrations/0015_alter_datarequest_managers_and_more.py +2 -1
  227. edc_export/migrations/0016_alter_datarequest_device_created_and_more.py +27 -79
  228. edc_export/migrations/0017_alter_datarequest_options_and_more.py +2 -6
  229. edc_export/migrations/0020_remove_datarequesthistory_edc_export__exporte_ba8050_idx_and_more.py +2 -6
  230. edc_export/migrations/0021_alter_datarequest_revision_and_more.py +173 -0
  231. edc_export/model_exporter/model_exporter.py +4 -15
  232. edc_export/model_exporter/object_history_helpers.py +1 -3
  233. edc_export/model_exporter/value_getter.py +5 -14
  234. edc_export/models/signals.py +1 -3
  235. edc_export/models/upload_export_receipt_file.py +1 -3
  236. edc_export/utils.py +1 -4
  237. edc_export/views/export_selected_models_view.py +6 -17
  238. edc_facility/default_definitions.py +1 -3
  239. edc_facility/facility.py +4 -14
  240. edc_facility/import_holidays.py +1 -3
  241. edc_facility/migrations/0005_healthfacility_healthfacilitytypes_and_more.py +4 -6
  242. edc_facility/migrations/0006_alter_healthfacility_health_facility_type.py +1 -1
  243. edc_facility/migrations/0008_alter_healthfacility_device_created_and_more.py +5 -13
  244. edc_facility/migrations/0015_alter_healthfacility_revision_and_more.py +38 -0
  245. edc_facility/models/holiday.py +1 -3
  246. edc_facility/utils.py +1 -3
  247. edc_fieldsets/fieldsets_modeladmin_mixin.py +1 -3
  248. edc_form_describer/form_describer.py +3 -9
  249. edc_form_describer/make_forms_reference.py +1 -3
  250. edc_form_describer/management/commands/make_forms_reference.py +1 -3
  251. edc_form_runners/admin/issue_admin.py +2 -6
  252. edc_form_runners/form_runner.py +4 -13
  253. edc_form_runners/form_runner_by_scr_id.py +1 -3
  254. edc_form_runners/get_form_runner.py +1 -3
  255. edc_form_runners/get_form_runner_by_src_id.py +3 -3
  256. edc_form_runners/management/commands/run_form_runners.py +1 -3
  257. edc_form_runners/migrations/0001_initial.py +2 -4
  258. edc_form_runners/migrations/0004_alter_issue_revision.py +26 -0
  259. edc_form_runners/run_form_runners.py +1 -3
  260. edc_form_runners/utils.py +1 -3
  261. edc_form_validators/applicable_field_validator.py +6 -17
  262. edc_form_validators/base_form_validator.py +1 -3
  263. edc_form_validators/date_range_validator.py +4 -12
  264. edc_form_validators/date_validator.py +3 -9
  265. edc_form_validators/many_to_many_field_validator.py +1 -3
  266. edc_form_validators/other_specify_field_validator.py +3 -7
  267. edc_form_validators/range_field_validator.py +1 -3
  268. edc_form_validators/required_field_validator.py +5 -18
  269. edc_glucose/__init__.py +0 -0
  270. edc_glucose/apps.py +6 -0
  271. edc_glucose/constants.py +3 -0
  272. edc_glucose/fieldsets.py +14 -0
  273. edc_glucose/form_validators/__init__.py +6 -0
  274. edc_glucose/form_validators/fasting_form_validator.py +12 -0
  275. edc_glucose/form_validators/fbg_form_validator_mixin.py +32 -0
  276. edc_glucose/form_validators/fbg_ogtt_form_validator_mixin.py +47 -0
  277. edc_glucose/form_validators/glucose_form_validator.py +44 -0
  278. edc_glucose/form_validators/glucose_form_validator_mixin.py +53 -0
  279. edc_glucose/form_validators/ogtt_form_validator_mixin.py +91 -0
  280. edc_glucose/list_filters.py +42 -0
  281. edc_glucose/migrations/__init__.py +0 -0
  282. edc_glucose/model_mixin_factories/__init__.py +4 -0
  283. edc_glucose/model_mixin_factories/fasting_model_mixin_factory.py +63 -0
  284. edc_glucose/model_mixin_factories/fbg_model_mixin_factory.py +48 -0
  285. edc_glucose/model_mixin_factories/glucose_model_mixin_factory.py +49 -0
  286. edc_glucose/model_mixin_factories/ogtt_model_mixin_factory.py +71 -0
  287. edc_glucose/model_mixins/__init__.py +5 -0
  288. edc_glucose/model_mixins/fasting_model_mixin.py +15 -0
  289. edc_glucose/model_mixins/fbg_model_mixin.py +10 -0
  290. edc_glucose/model_mixins/glucose_model_mixin.py +17 -0
  291. edc_glucose/model_mixins/hba1c_model_mixin.py +42 -0
  292. edc_glucose/model_mixins/ogtt_model_mixin.py +10 -0
  293. edc_glucose/models.py +0 -0
  294. edc_glucose/utils.py +42 -0
  295. edc_identifier/admin_site.py +1 -3
  296. edc_identifier/identifier.py +1 -3
  297. edc_identifier/migrations/0001_initial.py +3 -4
  298. edc_identifier/migrations/0001_squashed_0018_auto_20180128_1054.py +3 -2
  299. edc_identifier/migrations/0005_alter_identifiermodel_managers.py +2 -1
  300. edc_identifier/migrations/0005_historicalidentifierhistory_historicalidentifiertracker_historicalsubjectidentifier.py +4 -5
  301. edc_identifier/migrations/0006_auto_20161127_2226.py +16 -43
  302. edc_identifier/migrations/0007_alter_identifiermodel_device_created_and_more.py +3 -7
  303. edc_identifier/migrations/0007_auto_20161204_2227.py +4 -7
  304. edc_identifier/migrations/0009_auto_20161221_2323.py +1 -0
  305. edc_identifier/migrations/0010_alter_identifiermodel_revision.py +26 -0
  306. edc_identifier/migrations/0010_auto_20170112_0602.py +2 -1
  307. edc_identifier/migrations/0012_auto_20171116_1606.py +2 -1
  308. edc_identifier/migrations/0013_auto_20171230_1316.py +3 -9
  309. edc_identifier/research_identifier.py +3 -11
  310. edc_identifier/short_identifier.py +5 -9
  311. edc_identifier/utils.py +1 -3
  312. edc_lab/admin/modeladmin_mixins.py +2 -8
  313. edc_lab/aliquot_types.py +1 -3
  314. edc_lab/form_validators/requisition_form_validator_mixin.py +1 -3
  315. edc_lab/forms/box_type_form.py +4 -6
  316. edc_lab/lab/aliquot_type.py +2 -6
  317. edc_lab/lab/manifest.py +2 -6
  318. edc_lab/lab/primary_aliquot.py +1 -3
  319. edc_lab/lab/requisition_panel.py +1 -3
  320. edc_lab/lab/requisition_panel_group.py +2 -6
  321. edc_lab/lab/specimen.py +1 -3
  322. edc_lab/labels/aliquot_label.py +4 -6
  323. edc_lab/labels/manifest_label.py +1 -3
  324. edc_lab/migrations/0001_initial.py +12 -29
  325. edc_lab/migrations/0002_auto_20170305_1939.py +4 -12
  326. edc_lab/migrations/0007_auto_20170321_1119.py +2 -6
  327. edc_lab/migrations/0008_auto_20170921_0719.py +2 -1
  328. edc_lab/migrations/0010_auto_20171127_1541.py +3 -2
  329. edc_lab/migrations/0012_auto_20180114_1438.py +2 -1
  330. edc_lab/migrations/0013_auto_20180117_1438.py +2 -1
  331. edc_lab/migrations/0022_auto_20211210_1839.py +1 -0
  332. edc_lab/migrations/0024_alter_manifestitem_managers.py +2 -1
  333. edc_lab/migrations/0027_alter_aliquot_managers_alter_box_managers_and_more.py +1 -1
  334. edc_lab/migrations/0028_alter_aliquot_device_created_and_more.py +43 -127
  335. edc_lab/migrations/0035_alter_aliquot_revision_alter_box_revision_and_more.py +266 -0
  336. edc_lab/model_mixins/aliquot/aliquot_label_mixin.py +1 -3
  337. edc_lab/model_mixins/aliquot/aliquot_model_mixin.py +4 -12
  338. edc_lab/model_mixins/requisition/requisition_identifier_mixin.py +1 -3
  339. edc_lab/model_mixins/shipping/manifest_model_mixin.py +1 -3
  340. edc_lab/models/box_item.py +1 -3
  341. edc_lab/models/box_type.py +1 -3
  342. edc_lab/models/manifest/manifest.py +3 -9
  343. edc_lab/models/manifest/manifest_item.py +1 -3
  344. edc_lab/models/order.py +1 -3
  345. edc_lab/models/signals.py +1 -3
  346. edc_lab/patterns.py +1 -3
  347. edc_lab/pdf_reports/manifest_pdf_report.py +9 -27
  348. edc_lab/post_migrate_signals.py +1 -3
  349. edc_lab/site_labs.py +4 -10
  350. edc_lab_dashboard/migrations/0001_initial.py +1 -1
  351. edc_lab_dashboard/migrations/0002_alter_edcpermissions_device_created_and_more.py +3 -7
  352. edc_lab_dashboard/migrations/0004_alter_edcpermissions_revision.py +26 -0
  353. edc_lab_dashboard/view_mixins/box_view_mixin.py +1 -3
  354. edc_lab_dashboard/view_mixins/manifest_view_mixin.py +4 -12
  355. edc_lab_dashboard/views/action_views/receive_view.py +1 -3
  356. edc_lab_dashboard/views/action_views/verify_box_item_view.py +1 -3
  357. edc_lab_dashboard/views/listboard_filters/aliquot_listboard_view_filters.py +2 -6
  358. edc_lab_dashboard/views/listboard_filters/manifest_listboard_filters.py +1 -3
  359. edc_lab_dashboard/views/listboard_views/base_box_item_listboard_view.py +1 -3
  360. edc_lab_dashboard/views/listboard_views/manifest_listboard_view.py +1 -3
  361. edc_lab_dashboard/views/listboard_views/process_listboard_view.py +2 -6
  362. edc_lab_dashboard/views/listboard_views/receive_listboard_view.py +2 -6
  363. edc_lab_dashboard/views/listboard_views/requisition_listboard_view.py +2 -6
  364. edc_lab_results/action_items.py +1 -3
  365. edc_lab_results/form_validator_mixins/blood_results_fbg_form_validator_mixin.py +2 -4
  366. edc_lab_results/form_validator_mixins/blood_results_form_validator_mixin.py +1 -3
  367. edc_lab_results/get_summary.py +3 -5
  368. edc_lab_results/model_mixin_factories/__init__.py +10 -0
  369. edc_lab_results/{model_mixin_factory → model_mixin_factories}/field_attrs.py +8 -8
  370. edc_lab_results/{model_mixin_factory → model_mixin_factories}/reportable_result_model_mixin_factory.py +2 -0
  371. edc_lab_results/{model_mixin_factory → model_mixin_factories}/result_model_mixin_factory.py +2 -0
  372. edc_lab_results/model_mixins/blood_result_model_mixin.py +2 -5
  373. edc_lab_results/model_mixins/electrolytes_model_mixins.py +1 -1
  374. edc_lab_results/model_mixins/fbc_model_mixins.py +1 -1
  375. edc_lab_results/model_mixins/fbg_model_mixin.py +6 -3
  376. edc_lab_results/model_mixins/glucose_model_mixin.py +2 -2
  377. edc_lab_results/model_mixins/hba1c_model_mixin.py +2 -28
  378. edc_lab_results/model_mixins/insulin_model_mixin.py +5 -11
  379. edc_lab_results/model_mixins/lft_model_mixins.py +1 -1
  380. edc_lab_results/model_mixins/lipid_model_mixins.py +1 -1
  381. edc_lab_results/model_mixins/proteinuria_model_mixin.py +1 -1
  382. edc_lab_results/model_mixins/rft_model_mixins.py +1 -1
  383. edc_label/apps.py +1 -2
  384. edc_label/migrations/0001_initial.py +1 -1
  385. edc_label/migrations/0003_alter_zpllabeltemplates_device_created_and_more.py +3 -7
  386. edc_label/migrations/0006_alter_zpllabeltemplates_revision.py +29 -0
  387. edc_label/printer.py +2 -6
  388. edc_label/printers_mixin.py +1 -3
  389. edc_label/urls.py +1 -3
  390. edc_label/view_mixins.py +1 -3
  391. edc_label/views/print_label_view.py +1 -3
  392. edc_list_data/model_mixins.py +1 -3
  393. edc_list_data/preload_data.py +2 -6
  394. edc_list_data/site_list_data.py +1 -3
  395. edc_listboard/migrations/0001_initial.py +1 -1
  396. edc_listboard/migrations/0003_alter_listboard_device_created_and_more.py +3 -7
  397. edc_listboard/migrations/0006_alter_listboard_revision.py +29 -0
  398. edc_listboard/view_mixins/listboard_filter_view_mixin.py +5 -15
  399. edc_listboard/view_mixins/search_listboard_view_mixin.py +2 -6
  400. edc_listboard/views/listboard_view.py +2 -6
  401. edc_listboard/views/screen/screening_listboard_view.py +1 -3
  402. edc_listboard/views/subject/subject_listboard_view.py +1 -3
  403. edc_locator/forms/subject_locator_form_validator.py +4 -12
  404. edc_locator/migrations/0001_initial.py +3 -2
  405. edc_locator/migrations/0003_auto_20180103_1351.py +2 -1
  406. edc_locator/migrations/0004_auto_20180106_2148.py +2 -1
  407. edc_locator/migrations/0007_auto_20180117_1819.py +2 -1
  408. edc_locator/migrations/0011_auto_20181007_0053.py +1 -1
  409. edc_locator/migrations/0013_auto_20181007_0054.py +2 -3
  410. edc_locator/migrations/0014_auto_20181009_0545.py +1 -0
  411. edc_locator/migrations/0032_alter_subjectlocator_managers.py +1 -1
  412. edc_locator/migrations/0034_alter_historicalsubjectlocator_device_created_and_more.py +5 -13
  413. edc_locator/migrations/0039_alter_historicalsubjectlocator_revision_and_more.py +38 -0
  414. edc_locator/modeladmin_mixins.py +1 -3
  415. edc_locator/view_mixins/subject_locator_view_mixins.py +1 -3
  416. edc_ltfu/admin.py +1 -3
  417. edc_ltfu/forms/ltfu_form.py +1 -3
  418. edc_ltfu/forms/ltfu_form_validator_mixin.py +1 -2
  419. edc_ltfu/modelform_mixins.py +3 -8
  420. edc_metadata/admin/modeladmin_mixins.py +2 -8
  421. edc_metadata/management/commands/validate_entry_status.py +1 -3
  422. edc_metadata/metadata/metadata.py +12 -41
  423. edc_metadata/metadata/metadata_getter.py +2 -9
  424. edc_metadata/metadata/requisition_metadata_getter.py +1 -3
  425. edc_metadata/metadata_handler.py +3 -9
  426. edc_metadata/metadata_helper/metadata_helper_mixin.py +1 -3
  427. edc_metadata/metadata_mixins/source_model_metadata_mixin.py +3 -9
  428. edc_metadata/metadata_refresher.py +3 -9
  429. edc_metadata/metadata_rules/crf/crf_rule_group.py +2 -5
  430. edc_metadata/metadata_rules/persistant_singleton_mixin.py +3 -3
  431. edc_metadata/metadata_rules/requisition/requisition_rule_group.py +1 -2
  432. edc_metadata/metadata_rules/rule_evaluator.py +1 -3
  433. edc_metadata/metadata_rules/rule_group.py +2 -6
  434. edc_metadata/metadata_rules/rule_group_meta_options.py +1 -3
  435. edc_metadata/metadata_updater.py +1 -3
  436. edc_metadata/metadata_wrappers/metadata_wrapper.py +1 -3
  437. edc_metadata/migrations/0001_initial.py +2 -1
  438. edc_metadata/migrations/0002_auto_20161127_2226.py +6 -13
  439. edc_metadata/migrations/0005_auto_20170112_0602.py +2 -1
  440. edc_metadata/migrations/0007_auto_20170810_1032.py +2 -1
  441. edc_metadata/migrations/0009_auto_20180116_1528.py +2 -1
  442. edc_metadata/migrations/0014_auto_20190707_0002.py +1 -1
  443. edc_metadata/migrations/0015_auto_20190709_0009.py +3 -5
  444. edc_metadata/migrations/0021_alter_crfmetadata_managers_and_more.py +1 -1
  445. edc_metadata/migrations/0023_alter_crfmetadata_device_created_and_more.py +5 -13
  446. edc_metadata/migrations/0030_alter_crfmetadata_revision_and_more.py +38 -0
  447. edc_metadata/model_mixins/creates/creates_metadata_model_mixin.py +1 -3
  448. edc_metadata/model_mixins/updates/updates_metadata_model_mixin.py +1 -3
  449. edc_metadata/models/crf_metadata_model_mixin.py +2 -6
  450. edc_metadata/next_form_getter.py +1 -3
  451. edc_metadata/requisition/requisition_metadata_handler.py +3 -2
  452. edc_metadata/requisition/requisition_metadata_updater.py +1 -3
  453. edc_metadata/update_metadata_on_schedule_change.py +7 -14
  454. edc_model/models/fields/initials_field.py +1 -3
  455. edc_model/models/signals.py +1 -3
  456. edc_model/system_checks.py +1 -3
  457. edc_model/validators/duration.py +1 -3
  458. edc_model_admin/admin_site.py +1 -3
  459. edc_model_admin/changelist_buttons/model_admin_changelist_button_mixin.py +4 -12
  460. edc_model_admin/changelist_buttons/model_admin_changelist_model_button_mixin.py +1 -3
  461. edc_model_admin/dashboard/model_admin_crf_dashboard_mixin.py +1 -3
  462. edc_model_admin/dashboard/model_admin_dashboard_mixin.py +1 -3
  463. edc_model_admin/mixins/base_model_admin_redirect_mixin.py +2 -6
  464. edc_model_admin/mixins/inlines/limited_admin_inline_mixin.py +1 -3
  465. edc_model_admin/mixins/model_admin_bypass_default_form_cls_mixin.py +4 -12
  466. edc_model_admin/mixins/model_admin_form_auto_number_mixin.py +2 -6
  467. edc_model_admin/mixins/model_admin_form_instructions_mixin.py +2 -6
  468. edc_model_admin/mixins/model_admin_next_url_redirect_mixin.py +3 -9
  469. edc_model_admin/mixins/model_admin_protect_pii_mixin.py +1 -3
  470. edc_model_admin/mixins/model_admin_redirect_all_to_changelist_mixin.py +2 -6
  471. edc_model_admin/mixins/model_admin_redirect_on_delete_mixin.py +1 -3
  472. edc_model_admin/templatetags/edc_admin_modify.py +3 -9
  473. edc_model_fields/fields/initials_field.py +1 -3
  474. edc_model_form/mixins/inline_model_form_mixin.py +5 -9
  475. edc_model_to_dataframe/model_to_dataframe.py +15 -46
  476. edc_navbar/get_default_navbar.py +1 -3
  477. edc_navbar/migrations/0004_auto_20220825_0451.py +1 -1
  478. edc_navbar/migrations/0006_alter_edcpermissions_device_created_and_more.py +3 -7
  479. edc_navbar/migrations/0008_alter_edcpermissions_revision.py +26 -0
  480. edc_navbar/navbar.py +1 -3
  481. edc_navbar/navbar_item.py +1 -3
  482. edc_navbar/site_navbars.py +2 -6
  483. edc_navbar/templatetags/edc_navbar_extras.py +1 -3
  484. edc_notification/admin_site.py +1 -3
  485. edc_notification/mailing_list_manager.py +5 -15
  486. edc_notification/migrations/0001_initial.py +2 -1
  487. edc_notification/migrations/0008_alter_notification_device_created_and_more.py +3 -7
  488. edc_notification/migrations/0010_alter_notification_revision.py +26 -0
  489. edc_notification/modeladmin_mixins.py +1 -3
  490. edc_notification/models/notification.py +1 -3
  491. edc_notification/models/signals.py +3 -10
  492. edc_notification/notification/model_notification.py +3 -9
  493. edc_notification/notification/notification.py +4 -12
  494. edc_notification/site_notifications.py +5 -14
  495. edc_offstudy/migrations/0001_initial.py +2 -1
  496. edc_offstudy/migrations/0002_auto_20180921_0434.py +4 -3
  497. edc_offstudy/migrations/0008_auto_20191102_0033.py +2 -1
  498. edc_offstudy/migrations/0015_auto_20220925_0032.py +1 -1
  499. edc_offstudy/migrations/0016_auto_20220929_1742.py +1 -0
  500. edc_offstudy/migrations/0018_alter_subjectoffstudy_managers.py +2 -1
  501. edc_offstudy/migrations/0019_alter_historicalsubjectoffstudy_device_created_and_more.py +5 -13
  502. edc_offstudy/migrations/0022_alter_historicalsubjectoffstudy_revision_and_more.py +41 -0
  503. edc_offstudy/model_mixins/offstudy_model_mixin.py +3 -3
  504. edc_offstudy/modelform_mixins/crf/offstudy_crf_modelform_mixin.py +2 -6
  505. edc_offstudy/templatetags/edc_offstudy_extras.py +2 -6
  506. edc_offstudy/utils.py +1 -3
  507. edc_pdf_reports/admin/modeladmin_mixins.py +1 -3
  508. edc_pdf_reports/crf_pdf_report.py +3 -9
  509. edc_pdf_reports/flowables/textbox.py +1 -3
  510. edc_pdf_reports/report.py +6 -18
  511. edc_pdf_reports/utils.py +1 -3
  512. edc_pdf_reports/views/pdf_intermediate_view.py +1 -3
  513. edc_pdf_reports/views/print_pdf_report_view.py +2 -6
  514. edc_pdutils/actions.py +4 -12
  515. edc_pdutils/choices.py +1 -4
  516. edc_pdutils/database.py +1 -3
  517. edc_pdutils/df_exporters/csv_crf_inline_tables_exporter.py +4 -12
  518. edc_pdutils/df_exporters/csv_exporter.py +7 -22
  519. edc_pdutils/df_handlers/crf_df_handler.py +3 -9
  520. edc_pdutils/df_handlers/df_handler.py +1 -3
  521. edc_pdutils/df_handlers/registered_subject_df_handler.py +1 -3
  522. edc_pdutils/management/commands/export_models.py +2 -6
  523. edc_pdutils/migrations/0001_initial.py +6 -9
  524. edc_pdutils/site.py +2 -6
  525. edc_pdutils/site_values_mappings.py +3 -9
  526. edc_pdutils/tables/aliquot.py +2 -9
  527. edc_pdutils/tables/consent.py +2 -6
  528. edc_pdutils/tables/crf.py +4 -12
  529. edc_pdutils/tables/requisition.py +4 -12
  530. edc_pdutils/tables/visit.py +1 -3
  531. edc_pdutils/utils/convert_dates_from_model.py +3 -9
  532. edc_pdutils/utils/convert_numerics_from_model.py +1 -3
  533. edc_pdutils/utils/convert_timedelta_from_model.py +1 -3
  534. edc_pdutils/utils/missing_subject_identifiers.py +1 -3
  535. edc_pharmacy/admin/actions/confirm_stock.py +2 -6
  536. edc_pharmacy/admin/actions/delete_order_items.py +1 -3
  537. edc_pharmacy/admin/actions/delete_receive_items.py +1 -3
  538. edc_pharmacy/admin/actions/print_stock_report.py +1 -3
  539. edc_pharmacy/admin/list_filters.py +5 -17
  540. edc_pharmacy/admin/model_admin_mixin.py +1 -3
  541. edc_pharmacy/admin/prescription/rx_admin.py +2 -6
  542. edc_pharmacy/admin/prescription/rx_refill_admin.py +1 -3
  543. edc_pharmacy/admin/reports/stock_availability_admin.py +1 -5
  544. edc_pharmacy/admin/stock/allocation_admin.py +5 -15
  545. edc_pharmacy/admin/stock/allocation_proxy_admin.py +1 -3
  546. edc_pharmacy/admin/stock/confirmation_admin.py +1 -3
  547. edc_pharmacy/admin/stock/confirmation_at_site_admin.py +4 -12
  548. edc_pharmacy/admin/stock/confirmation_at_site_item_admin.py +5 -17
  549. edc_pharmacy/admin/stock/dispense_admin.py +3 -11
  550. edc_pharmacy/admin/stock/dispense_item_admin.py +4 -14
  551. edc_pharmacy/admin/stock/order_admin.py +1 -3
  552. edc_pharmacy/admin/stock/order_item_admin.py +5 -15
  553. edc_pharmacy/admin/stock/receive_admin.py +4 -12
  554. edc_pharmacy/admin/stock/receive_item_admin.py +4 -12
  555. edc_pharmacy/admin/stock/repack_request_admin.py +2 -6
  556. edc_pharmacy/admin/stock/stock_adjustment_admin.py +1 -3
  557. edc_pharmacy/admin/stock/stock_admin.py +8 -24
  558. edc_pharmacy/admin/stock/stock_proxy_admin.py +1 -5
  559. edc_pharmacy/admin/stock/stock_request_admin.py +5 -4
  560. edc_pharmacy/admin/stock/stock_request_item_admin.py +10 -19
  561. edc_pharmacy/admin/stock/stock_transfer_admin.py +4 -12
  562. edc_pharmacy/admin/stock/stock_transfer_item_admin.py +6 -18
  563. edc_pharmacy/admin/stock/storage_bin_admin.py +3 -11
  564. edc_pharmacy/admin/stock/storage_bin_item_admin.py +4 -14
  565. edc_pharmacy/analytics/dataframes/get_next_scheduled_visit_for_subjects_df.py +1 -1
  566. edc_pharmacy/analytics/dataframes/in_stock_for_subjects_df.py +2 -6
  567. edc_pharmacy/analytics/dataframes/stock_for_subjects.py +1 -3
  568. edc_pharmacy/form_validators/crf/study_medication_form_validator.py +9 -27
  569. edc_pharmacy/forms/stock/container_form.py +2 -6
  570. edc_pharmacy/forms/stock/receive_item_form.py +2 -6
  571. edc_pharmacy/forms/stock/repack_request_form.py +4 -11
  572. edc_pharmacy/forms/stock/stock_request_form.py +1 -0
  573. edc_pharmacy/forms/stock/stock_request_item_form.py +1 -3
  574. edc_pharmacy/labels/draw_bulk_stock_label_code128.py +1 -3
  575. edc_pharmacy/labels/draw_bulk_stock_label_code39.py +3 -9
  576. edc_pharmacy/labels/draw_patient_stock_label_code128.py +1 -3
  577. edc_pharmacy/migrations/0001_initial.py +7 -15
  578. edc_pharmacy/migrations/0005_alter_rx_managers.py +2 -1
  579. edc_pharmacy/migrations/0015_auto_20220913_2139.py +9 -22
  580. edc_pharmacy/migrations/0016_auto_20220929_1742.py +2 -1
  581. edc_pharmacy/migrations/0018_alter_rxrefill_managers.py +1 -1
  582. edc_pharmacy/migrations/0020_alter_box_device_created_alter_box_device_modified_and_more.py +71 -211
  583. edc_pharmacy/migrations/0021_alter_box_options_alter_container_options_and_more.py +1 -1
  584. edc_pharmacy/migrations/0023_remove_rx_edc_pharmac_modifie_986021_idx_and_more.py +1 -3
  585. edc_pharmacy/migrations/0024_allocation_assignment_containerunits_dispense_and_more.py +40 -104
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  876. edc_vitals/form_validators/__init__.py +5 -0
  877. edc_vitals/form_validators/blood_pressure_form_validator_mixin.py +40 -0
  878. edc_vitals/form_validators/bmi_form_validator_mixin.py +19 -0
  879. edc_vitals/form_validators/weight_height_with_bmi_form_validator_mixin.py +13 -0
  880. edc_vitals/migrations/__init__.py +0 -0
  881. edc_vitals/model_mixins/__init__.py +5 -0
  882. edc_vitals/model_mixins/blood_pressure_model_mixin.py +80 -0
  883. edc_vitals/model_mixins/weight_height_bmi_model_mixin.py +42 -0
  884. edc_vitals/models/__init__.py +10 -0
  885. edc_vitals/models/fields/__init__.py +7 -0
  886. edc_vitals/models/fields/blood_pressure.py +36 -0
  887. edc_vitals/models/fields/heart_rate.py +22 -0
  888. edc_vitals/models/fields/height.py +26 -0
  889. edc_vitals/models/fields/respiratory_rate.py +22 -0
  890. edc_vitals/models/fields/temperature.py +26 -0
  891. edc_vitals/models/fields/waist_circumference.py +23 -0
  892. edc_vitals/models/fields/weight.py +26 -0
  893. edc_vitals/utils.py +51 -0
  894. edc_vitals/validators.py +5 -0
  895. edc_lab_results/model_mixin_factory/__init__.py +0 -2
  896. {clinicedc-2.0.0.dist-info → clinicedc-2.0.2.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,63 @@
1
+ from __future__ import annotations
2
+
3
+ from decimal import Decimal
4
+
5
+ from edc_constants.constants import FEMALE
6
+ from edc_reportable import MICROMOLES_PER_LITER
7
+
8
+ from .base_egrfr import BaseEgfr, EgfrCalculatorError
9
+
10
+
11
+ class EgfrCockcroftGault(BaseEgfr):
12
+ """Reference https://www.mdcalc.com/creatinine-clearance-cockcroft-gault-equation
13
+
14
+ Cockcroft-Gault
15
+
16
+ eGFR (mL/min) = { (140 – age (years)) x weight (kg) x constant*} /
17
+ serum creatinine (μmol/L)
18
+ *constant = 1.23 for males and 1.05 for females
19
+
20
+ Cockcroft-Gault CrCl, mL/min =
21
+ (140 – age) × (weight, kg) × (0.85 if female) / (72 × SCr(mg/dL))
22
+
23
+ or:
24
+
25
+ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763564/
26
+
27
+ GFR = 141 × min(Scr/κ, 1)α × max(Scr/κ, 1)-1.209 × 0.993Age
28
+ """
29
+
30
+ def __init__(self, weight: int | float | Decimal = None, **kwargs):
31
+ self.weight = float(weight) if weight else None
32
+ super().__init__(**kwargs)
33
+
34
+ @property
35
+ def value(self) -> float:
36
+ """Returns the eGFR value or raises.
37
+
38
+ eGFR (mL/min) = { (140 – age (years)) x weight (kg) x constant*} /
39
+ serum creatinine (μmol/L)
40
+
41
+ *constant = 1.23 for males and 1.05 for females
42
+ """
43
+ if (
44
+ self.gender
45
+ and self.age_in_years
46
+ and self.weight
47
+ and self.scr.get(MICROMOLES_PER_LITER)
48
+ ):
49
+ gender_factor = 1.05 if self.gender == FEMALE else 1.23
50
+ adjusted_age = 140.00 - self.age_in_years
51
+ value = (adjusted_age * self.weight * gender_factor) / float(
52
+ self.scr.get(MICROMOLES_PER_LITER)
53
+ )
54
+ return value
55
+ opts = dict(
56
+ gender=self.gender,
57
+ age_in_years=self.age_in_years,
58
+ weight=self.weight,
59
+ scr=self.scr.get(MICROMOLES_PER_LITER),
60
+ )
61
+ raise EgfrCalculatorError(
62
+ f"Unable to calculate egfr_value. Insufficient information. Got {opts}."
63
+ )
@@ -0,0 +1,7 @@
1
+ def egfr_percent_change(egfr_value: float, baseline_egfr_value: float) -> float:
2
+ """Returns the percent change from baseline"""
3
+ if egfr_value and baseline_egfr_value:
4
+ return 100 * (
5
+ (float(baseline_egfr_value) - float(egfr_value)) / float(baseline_egfr_value)
6
+ )
7
+ return 0.0
edc_egfr/constants.py ADDED
@@ -0,0 +1 @@
1
+ EGFR_DROP_NOTIFICATION_ACTION = "egfr_notification_action"
edc_egfr/egfr.py ADDED
@@ -0,0 +1,237 @@
1
+ from __future__ import annotations
2
+
3
+ from datetime import date, datetime
4
+ from decimal import Decimal
5
+ from typing import TYPE_CHECKING, Any, Optional
6
+ from zoneinfo import ZoneInfo
7
+
8
+ from dateutil.relativedelta import relativedelta
9
+ from django.core.exceptions import ObjectDoesNotExist
10
+ from django.db import transaction
11
+
12
+ from edc_constants.constants import NEW
13
+ from edc_reportable.models import ReferenceRangeCollection
14
+ from edc_reportable.units import EGFR_UNITS, PERCENT
15
+ from edc_reportable.utils import get_grade_for_value
16
+ from edc_utils import age, get_utcnow
17
+
18
+ from .calculators import EgfrCkdEpi, EgfrCockcroftGault, egfr_percent_change
19
+ from .get_drop_notification_model import get_egfr_drop_notification_model_cls
20
+
21
+ if TYPE_CHECKING:
22
+ from edc_visit_tracking.typing_stubs import RelatedVisitProtocol
23
+
24
+
25
+ class EgfrError(Exception):
26
+ pass
27
+
28
+
29
+ class Egfr:
30
+ calculators: dict = {"ckd-epi": EgfrCkdEpi, "cockcroft-gault": EgfrCockcroftGault}
31
+
32
+ def __init__(
33
+ self,
34
+ baseline_egfr_value: Decimal | float | None = None,
35
+ gender: str | None = None,
36
+ ethnicity: str | None = None,
37
+ age_in_years: int | None = None,
38
+ dob: date | None = None,
39
+ weight_in_kgs: Decimal | float | None = None,
40
+ report_datetime: datetime | None = None,
41
+ creatinine_value: Decimal | float | None = None,
42
+ creatinine_units: str | None = None,
43
+ formula_name: str | None = None,
44
+ value_threshold: Decimal | float | None = None,
45
+ percent_drop_threshold: Decimal | float | None = None,
46
+ reference_range_collection: ReferenceRangeCollection | None = None,
47
+ reference_range_collection_name: str | None = None,
48
+ calling_crf: Any | None = None,
49
+ related_visit: RelatedVisitProtocol | None = None,
50
+ assay_datetime: datetime | None = None,
51
+ egfr_drop_notification_model: str | None = None,
52
+ ):
53
+ self._egfr_value: Decimal | None = None
54
+ self._egfr_grade = None
55
+ self._egfr_drop_value: Decimal | None = None
56
+ self._egfr_drop_grade = None
57
+ self.assay_date: date | None = None
58
+ self.related_visit = None
59
+
60
+ self.baseline_egfr_value = baseline_egfr_value
61
+ if formula_name not in self.calculators:
62
+ raise EgfrError(
63
+ f"Invalid formula_name. Expected one of {list(self.calculators.keys())}. "
64
+ f"Got {formula_name}."
65
+ )
66
+ else:
67
+ self.calculator_cls = self.calculators.get(formula_name)
68
+ self.age_in_years = age_in_years
69
+ self.dob = dob
70
+ self.weight_in_kgs = weight_in_kgs
71
+ self.egfr_drop_notification_model = egfr_drop_notification_model
72
+ self.egfr_drop_units = PERCENT
73
+ self.egfr_units = EGFR_UNITS
74
+ self.ethnicity = ethnicity
75
+ self.gender = gender
76
+ if not reference_range_collection:
77
+ try:
78
+ self.reference_range_collection = ReferenceRangeCollection.objects.get(
79
+ name=reference_range_collection_name
80
+ )
81
+ except ObjectDoesNotExist as e:
82
+ raise ObjectDoesNotExist(f"{e} Got {reference_range_collection_name}")
83
+ else:
84
+ self.reference_range_collection = reference_range_collection
85
+ self.report_datetime = report_datetime
86
+ self.value_threshold = value_threshold
87
+ self.percent_drop_threshold = percent_drop_threshold
88
+
89
+ if self.dob:
90
+ self.age_in_years = age(
91
+ born=self.dob,
92
+ reference_dt=self.report_datetime.astimezone(ZoneInfo("UTC")),
93
+ ).years
94
+ elif not self.dob and self.age_in_years:
95
+ self.dob = (
96
+ self.report_datetime.astimezone(ZoneInfo("UTC"))
97
+ - relativedelta(years=self.age_in_years)
98
+ ).date()
99
+ else:
100
+ raise EgfrError("Expected `age_in_years` or `dob`. Got None for both.")
101
+
102
+ if calling_crf:
103
+ self.creatinine_units = calling_crf.creatinine_units
104
+ self.creatinine_value = calling_crf.creatinine_value
105
+ self.percent_drop_threshold = calling_crf.percent_drop_threshold
106
+ self.related_visit = calling_crf.related_visit
107
+ self.report_datetime = calling_crf.report_datetime
108
+ self.assay_date = calling_crf.assay_datetime.astimezone(ZoneInfo("UTC")).date()
109
+ else:
110
+ self.creatinine_units = creatinine_units
111
+ self.creatinine_value = creatinine_value
112
+ self.percent_drop_threshold = percent_drop_threshold
113
+ self.related_visit = related_visit
114
+ self.report_datetime = report_datetime
115
+ if assay_datetime:
116
+ self.assay_date = assay_datetime.astimezone(ZoneInfo("UTC")).date()
117
+
118
+ if self.percent_drop_threshold is not None and self.percent_drop_threshold < 1.0:
119
+ raise EgfrError(
120
+ "Attr `percent_drop_threshold` should be a percentage. "
121
+ f"Got {self.percent_drop_threshold}"
122
+ )
123
+
124
+ self.on_value_threshold_reached()
125
+
126
+ self.on_percent_drop_threshold_reached()
127
+
128
+ def on_value_threshold_reached(self) -> None:
129
+ """A hook to respond if egfr value is at or beyond the value
130
+ threshold.
131
+ """
132
+ pass
133
+
134
+ def on_percent_drop_threshold_reached(self) -> None:
135
+ """A hook to respond if egfr percent drop from baseline
136
+ is at or beyond the percent drop threshold.
137
+ """
138
+ if self.egfr_drop_value and self.percent_drop_threshold is not None:
139
+ if self.egfr_drop_value >= self.percent_drop_threshold:
140
+ self.create_or_update_egfr_drop_notification()
141
+
142
+ @property
143
+ def egfr_value(self) -> float:
144
+ if self._egfr_value is None:
145
+ self._egfr_value = self.calculator_cls(
146
+ gender=self.gender,
147
+ ethnicity=self.ethnicity,
148
+ age_in_years=self.age_in_years,
149
+ creatinine_value=self.creatinine_value,
150
+ creatinine_units=self.creatinine_units,
151
+ weight=self.get_weight_in_kgs(),
152
+ ).value
153
+ return self._egfr_value
154
+
155
+ @property
156
+ def egfr_grade(self) -> Optional[int]:
157
+ if self._egfr_grade is None:
158
+ grading_data, _ = get_grade_for_value(
159
+ self.reference_range_collection,
160
+ value=self.egfr_value,
161
+ label="egfr",
162
+ gender=self.gender,
163
+ dob=self.dob,
164
+ report_datetime=self.report_datetime,
165
+ units=self.egfr_units,
166
+ age_units="years",
167
+ )
168
+ if grading_data:
169
+ self._egfr_grade = grading_data.grade
170
+ return self._egfr_grade
171
+
172
+ @property
173
+ def egfr_drop_value(self) -> float:
174
+ if self._egfr_drop_value is None:
175
+ if self.baseline_egfr_value:
176
+ egfr_drop_value = egfr_percent_change(
177
+ float(self.egfr_value), float(self.baseline_egfr_value)
178
+ )
179
+ else:
180
+ egfr_drop_value = 0.0000
181
+ self._egfr_drop_value = 0.0000 if egfr_drop_value < 0.0000 else egfr_drop_value
182
+ return self._egfr_drop_value
183
+
184
+ @property
185
+ def egfr_drop_grade(self) -> Optional[int]:
186
+ if self._egfr_drop_grade is None:
187
+ grading_data, _ = get_grade_for_value(
188
+ self.reference_range_collection,
189
+ value=self.egfr_drop_value,
190
+ label="egfr_drop",
191
+ gender=self.gender,
192
+ dob=self.dob,
193
+ report_datetime=self.report_datetime,
194
+ units=self.egfr_drop_units,
195
+ age_units="years",
196
+ )
197
+ if grading_data:
198
+ self._egfr_drop_grade = grading_data.grade
199
+ return self._egfr_drop_grade
200
+
201
+ def get_weight_in_kgs(self) -> Optional[float]:
202
+ return self.weight_in_kgs
203
+
204
+ def create_or_update_egfr_drop_notification(self):
205
+ """Creates or updates the `eGFR notification model`"""
206
+ with transaction.atomic():
207
+ try:
208
+ obj = self.egfr_drop_notification_model_cls.objects.get(
209
+ subject_visit__id=self.related_visit.id
210
+ )
211
+ except ObjectDoesNotExist:
212
+ obj = self.egfr_drop_notification_model_cls.objects.create(
213
+ subject_visit_id=self.related_visit.id,
214
+ report_datetime=self.report_datetime,
215
+ egfr_value=self.egfr_value,
216
+ creatinine_date=self.assay_date,
217
+ creatinine_value=self.creatinine_value,
218
+ creatinine_units=self.creatinine_units,
219
+ weight=self.get_weight_in_kgs(),
220
+ egfr_percent_change=self.egfr_drop_value,
221
+ report_status=NEW,
222
+ site_id=self.related_visit.site.id,
223
+ )
224
+ else:
225
+ obj.egfr_value = self.egfr_value
226
+ obj.creatinine_value = self.creatinine_value
227
+ obj.weight = self.get_weight_in_kgs()
228
+ obj.egfr_percent_change = self.egfr_drop_value
229
+ obj.creatinine_date = self.assay_date
230
+ obj.modified = get_utcnow()
231
+ obj.save()
232
+ obj.refresh_from_db()
233
+ return obj
234
+
235
+ @property
236
+ def egfr_drop_notification_model_cls(self):
237
+ return get_egfr_drop_notification_model_cls()
@@ -0,0 +1,4 @@
1
+ from .egfr_form_validator_mixins import (
2
+ EgfrCkdEpiFormValidatorMixin,
3
+ EgfrCockcroftGaultFormValidatorMixin,
4
+ )
@@ -0,0 +1,55 @@
1
+ from django import forms
2
+
3
+ from edc_form_validators import INVALID_ERROR
4
+ from edc_reportable import ConversionNotHandled
5
+ from edc_vitals.calculators import CalculatorError
6
+
7
+ from ..calculators import EgfrCalculatorError, EgfrCkdEpi, EgfrCockcroftGault
8
+
9
+
10
+ class EgfrCkdEpiFormValidatorMixin:
11
+ def validate_egfr(
12
+ self,
13
+ gender: str = None,
14
+ age_in_years: int = None,
15
+ weight_in_kgs: float = None,
16
+ ethnicity: str = None,
17
+ baseline_egfr_value: float | None = None,
18
+ ):
19
+ opts = dict(
20
+ gender=gender,
21
+ age_in_years=age_in_years,
22
+ weight=weight_in_kgs,
23
+ ethnicity=ethnicity,
24
+ creatinine_value=self.cleaned_data.get("creatinine_value"),
25
+ creatinine_units=self.cleaned_data.get("creatinine_units"),
26
+ baseline_egfr_value=baseline_egfr_value,
27
+ )
28
+ try:
29
+ value = EgfrCkdEpi(**opts).value
30
+ except (EgfrCalculatorError, CalculatorError, ConversionNotHandled) as e:
31
+ raise forms.ValidationError(e)
32
+ return value
33
+
34
+
35
+ class EgfrCockcroftGaultFormValidatorMixin:
36
+ def validate_egfr(
37
+ self,
38
+ gender: str = None,
39
+ age_in_years: int = None,
40
+ weight_in_kgs: float = None,
41
+ ethnicity: str = None,
42
+ ):
43
+ opts = dict(
44
+ gender=gender,
45
+ age_in_years=age_in_years,
46
+ weight=weight_in_kgs,
47
+ ethnicity=ethnicity,
48
+ creatinine_value=self.cleaned_data.get("creatinine_value"),
49
+ creatinine_units=self.cleaned_data.get("creatinine_units"),
50
+ )
51
+ try:
52
+ value = EgfrCockcroftGault(**opts).value
53
+ except (EgfrCalculatorError, CalculatorError, ConversionNotHandled) as e:
54
+ self.raise_validation_error({"__all__": str(e)}, INVALID_ERROR)
55
+ return value
@@ -0,0 +1,10 @@
1
+ from django.apps import apps as django_apps
2
+ from django.conf import settings
3
+
4
+
5
+ def get_egfr_drop_notification_model():
6
+ return getattr(settings, "EDC_EGFR_DROP_NOTIFICATION_MODEL")
7
+
8
+
9
+ def get_egfr_drop_notification_model_cls():
10
+ return django_apps.get_model(get_egfr_drop_notification_model())
@@ -0,0 +1,31 @@
1
+ from datetime import date, datetime
2
+
3
+ from .egfr import Egfr
4
+
5
+
6
+ def get_egfr_for_subject(
7
+ creatinine_value: float = None,
8
+ creatinine_units: str = None,
9
+ assay_datetime: datetime = None,
10
+ dob: date = None,
11
+ gender: str = None,
12
+ ethnicity: str = None,
13
+ report_datetime: datetime = None,
14
+ baseline_egfr_value: float | None = None,
15
+ value_threshold: float | None = None,
16
+ percent_drop_threshold: float | None = None,
17
+ ):
18
+ return Egfr(
19
+ percent_drop_threshold=percent_drop_threshold or 20.0000,
20
+ dob=dob,
21
+ gender=gender,
22
+ ethnicity=ethnicity,
23
+ value_threshold=value_threshold or 45.0000,
24
+ report_datetime=report_datetime,
25
+ baseline_egfr_value=baseline_egfr_value,
26
+ formula_name="ckd-epi",
27
+ reference_range_collection_name="meta",
28
+ creatinine_units=creatinine_units,
29
+ creatinine_value=creatinine_value,
30
+ assay_datetime=assay_datetime,
31
+ )
@@ -0,0 +1,2 @@
1
+ from .egfr_drop_notification_model_mixin import EgfrDropNotificationModelMixin
2
+ from .egfr_model_mixin import EgfrModelMixin
@@ -0,0 +1,63 @@
1
+ from django.db import models
2
+
3
+ from edc_constants.constants import COMPLETE, INCOMPLETE, NEW, OPEN
4
+ from edc_lab.choices import SERUM_CREATININE_UNITS
5
+ from edc_lab_results.model_mixin_factories import reportable_result_model_mixin_factory
6
+ from edc_model import REPORT_STATUS
7
+ from edc_reportable.units import EGFR_UNITS, MICROMOLES_PER_LITER
8
+ from edc_vitals.models import WeightField
9
+
10
+
11
+ class EgfrDropNotificationModelMixin(
12
+ reportable_result_model_mixin_factory(
13
+ utest_id="egfr",
14
+ verbose_name="eGFR",
15
+ decimal_places=4,
16
+ default_units=EGFR_UNITS,
17
+ max_digits=8,
18
+ units_choices=((EGFR_UNITS, EGFR_UNITS),),
19
+ exclude_attrs_for_reportable=True,
20
+ ),
21
+ reportable_result_model_mixin_factory(
22
+ utest_id="creatinine",
23
+ verbose_name="Serum creatinine",
24
+ decimal_places=2,
25
+ default_units=MICROMOLES_PER_LITER,
26
+ max_digits=8,
27
+ units_choices=((SERUM_CREATININE_UNITS, SERUM_CREATININE_UNITS),),
28
+ exclude_attrs_for_reportable=True,
29
+ ),
30
+ models.Model,
31
+ ):
32
+ creatinine_date = models.DateField(verbose_name="Serum creatinine date")
33
+
34
+ weight = WeightField(null=True, blank=True)
35
+
36
+ egfr_percent_change = models.DecimalField(
37
+ verbose_name="Percent change from baseline",
38
+ max_digits=10,
39
+ decimal_places=2,
40
+ null=True,
41
+ blank=True,
42
+ help_text="Copied from RFT result eGFR section.",
43
+ )
44
+
45
+ narrative = models.TextField(
46
+ verbose_name="Narrative",
47
+ null=True,
48
+ blank=True,
49
+ )
50
+
51
+ report_status = models.CharField(max_length=15, choices=REPORT_STATUS, default=NEW)
52
+
53
+ def save(self, *args, **kwargs):
54
+ if self.report_status == OPEN:
55
+ self.crf_status = INCOMPLETE
56
+ else:
57
+ self.crf_status = COMPLETE
58
+ super().save(*args, **kwargs)
59
+
60
+ class Meta:
61
+ verbose_name = "eGFR Drop Notification"
62
+ verbose_name_plural = "eGFR Drop Notifications"
63
+ abstract = True
@@ -0,0 +1,120 @@
1
+ from __future__ import annotations
2
+
3
+ from decimal import Decimal
4
+
5
+ from django.core.exceptions import ObjectDoesNotExist
6
+ from django.db import models, transaction
7
+
8
+ from edc_lab_results.model_mixin_factories import reportable_result_model_mixin_factory
9
+ from edc_registration.models import RegisteredSubject
10
+ from edc_reportable.units import EGFR_UNITS, PERCENT
11
+ from edc_reportable.utils import get_reference_range_collection
12
+
13
+ from ..calculators import EgfrCalculatorError
14
+ from ..egfr import Egfr
15
+
16
+
17
+ class EgfrModelMixin(
18
+ reportable_result_model_mixin_factory(
19
+ utest_id="egfr",
20
+ verbose_name="eGFR",
21
+ decimal_places=4,
22
+ default_units=EGFR_UNITS,
23
+ max_digits=8,
24
+ units_choices=((EGFR_UNITS, EGFR_UNITS),),
25
+ ),
26
+ reportable_result_model_mixin_factory(
27
+ utest_id="egfr_drop",
28
+ verbose_name="eGFR Drop",
29
+ decimal_places=4,
30
+ default_units=PERCENT,
31
+ max_digits=10,
32
+ units_choices=((PERCENT, PERCENT),),
33
+ ),
34
+ models.Model,
35
+ ):
36
+ """Declared with a bloodresult RFT CRF model.
37
+
38
+ As a lab result CRF, expects subject_visit, requisition
39
+ and report_datetime.
40
+
41
+ See edc_lab_result, edc_crf.
42
+ """
43
+
44
+ percent_drop_threshold: float = 20.0
45
+ baseline_timepoint: int = 0
46
+ egfr_formula_name: str = None
47
+ egfr_cls = Egfr
48
+
49
+ def save(self, *args, **kwargs):
50
+ if self.creatinine_value:
51
+ self.set_egfr_value_or_raise()
52
+ super().save(*args, **kwargs)
53
+
54
+ def set_egfr_value_or_raise(self) -> None:
55
+ egfr = self.egfr_cls(**self.egfr_options)
56
+ try:
57
+ self.egfr_value = egfr.egfr_value
58
+ except EgfrCalculatorError:
59
+ if self.creatinine_value:
60
+ raise
61
+ self.egfr_value = None
62
+ self.egfr_units = None
63
+ self.egfr_grade = None
64
+ self.egfr_drop_value = None
65
+ self.egfr_drop_units = None
66
+ self.egfr_drop_grade = None
67
+ else:
68
+ self.egfr_units = egfr.egfr_units
69
+ self.egfr_grade = egfr.egfr_grade
70
+ self.egfr_drop_value = egfr.egfr_drop_value
71
+ self.egfr_drop_units = egfr.egfr_drop_units
72
+ self.egfr_drop_grade = egfr.egfr_drop_grade
73
+
74
+ @property
75
+ def egfr_options(self) -> dict:
76
+ rs = RegisteredSubject.objects.get(
77
+ subject_identifier=self.related_visit.subject_identifier
78
+ )
79
+ return dict(
80
+ calling_crf=self,
81
+ dob=rs.dob,
82
+ gender=rs.gender,
83
+ ethnicity=rs.ethnicity,
84
+ weight_in_kgs=self.get_weight_in_kgs_for_egfr(),
85
+ percent_drop_threshold=self.percent_drop_threshold,
86
+ value_threshold=45.0000,
87
+ report_datetime=self.report_datetime,
88
+ baseline_egfr_value=self.get_baseline_egfr_value(),
89
+ formula_name=self.egfr_formula_name,
90
+ reference_range_collection=get_reference_range_collection(self),
91
+ )
92
+
93
+ def get_baseline_egfr_value(self) -> float | None:
94
+ """Returns a baseline or reference eGFR value.
95
+
96
+ Expects a longitudinal / CRF model with attrs `subject_visit`.
97
+ """
98
+ egfr_value = None
99
+ with transaction.atomic():
100
+ baseline_visit = self.related_visit.__class__.objects.get(
101
+ appointment__subject_identifier=self.related_visit.subject_identifier,
102
+ appointment__visit_schedule_name=self.related_visit.visit_schedule_name,
103
+ appointment__schedule_name=self.related_visit.schedule_name,
104
+ appointment__timepoint=self.baseline_timepoint,
105
+ visit_code_sequence=0,
106
+ )
107
+ with transaction.atomic():
108
+ try:
109
+ egfr_value = self.__class__.objects.get(
110
+ subject_visit=baseline_visit
111
+ ).egfr_value
112
+ except ObjectDoesNotExist:
113
+ pass
114
+ return egfr_value
115
+
116
+ def get_weight_in_kgs_for_egfr(self) -> Decimal | None:
117
+ return None
118
+
119
+ class Meta:
120
+ abstract = True
@@ -64,9 +64,7 @@ class ArchiveExporter:
64
64
  )
65
65
  self.exported.append(csv_exporter.to_csv())
66
66
  if not self.exported:
67
- raise ArchiveExporterNothingExported(
68
- f"Nothing exported. Got models={models}."
69
- )
67
+ raise ArchiveExporterNothingExported(f"Nothing exported. Got models={models}.")
70
68
  else:
71
69
  if archive:
72
70
  archiver = self.files_archiver_cls(
@@ -92,6 +90,4 @@ class ArchiveExporter:
92
90
  else:
93
91
  self.emailed_to = user.email
94
92
  self.emailed_datetime = get_utcnow()
95
- self.exported_datetime = (
96
- self.exported_datetime or self.emailed_datetime
97
- )
93
+ self.exported_datetime = self.exported_datetime or self.emailed_datetime
edc_export/exportables.py CHANGED
@@ -69,9 +69,7 @@ class Exportable(OrderedDict):
69
69
  for site in sites.all_sites:
70
70
  for model_cls, admin_site in site._registry.items():
71
71
  for inline_cls in admin_site.inlines:
72
- model_opts = ModelOptions(
73
- model=inline_cls.model._meta.label_lower
74
- )
72
+ model_opts = ModelOptions(model=inline_cls.model._meta.label_lower)
75
73
  try:
76
74
  self._inlines[model_cls._meta.app_label].append(model_opts)
77
75
  except KeyError:
@@ -105,9 +103,7 @@ class Exportables(OrderedDict):
105
103
  try:
106
104
  user.groups.get(name=self.export_group_name)
107
105
  except ObjectDoesNotExist:
108
- messages.error(
109
- request, "You do not have sufficient permissions to export data."
110
- )
106
+ messages.error(request, "You do not have sufficient permissions to export data.")
111
107
  else:
112
108
  for app_config in app_configs:
113
109
  self.update({app_config.name: Exportable(app_config=app_config)})
@@ -70,9 +70,7 @@ class FilesEmailer:
70
70
  try:
71
71
  email_message.send()
72
72
  except socket.gaierror:
73
- raise FilesEmailerError(
74
- "Unable to connect to email server.", code="gaierror"
75
- )
73
+ raise FilesEmailerError("Unable to connect to email server.", code="gaierror")
76
74
 
77
75
  def email_files(self) -> None:
78
76
  email_message = self.get_email_message()
@@ -72,9 +72,7 @@ class Command(BaseCommand):
72
72
  try:
73
73
  app_label1, app_label2 = self.app_labe1.split("_")
74
74
  error_filename = (
75
- "_".join(
76
- ["error", app_label1, app_label2, self.object_name, self.timestamp]
77
- )
75
+ "_".join(["error", app_label1, app_label2, self.object_name, self.timestamp])
78
76
  + "."
79
77
  + self.extension
80
78
  )