meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl

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Files changed (411) hide show
  1. meta_ae/action_items.py +2 -2
  2. meta_ae/migrations/0017_auto_20221130_2257.py +12 -7
  3. meta_ae/tests/holidays.csv +1 -1
  4. meta_analytics/README.rst +17 -0
  5. meta_analytics/dataframes/__init__.py +19 -0
  6. meta_analytics/dataframes/constants.py +33 -0
  7. meta_analytics/dataframes/enrolled/__init__.py +1 -0
  8. meta_analytics/dataframes/enrolled/get_glucose_df.py +122 -0
  9. meta_analytics/dataframes/get_eos_df.py +26 -0
  10. meta_analytics/dataframes/get_last_imp_visits_df.py +101 -0
  11. meta_analytics/dataframes/glucose_endpoints/__init__.py +2 -0
  12. meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py +183 -0
  13. meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py +531 -0
  14. meta_analytics/dataframes/screening/__init__.py +2 -0
  15. meta_analytics/dataframes/screening/get_glucose_tested_only_df.py +20 -0
  16. meta_analytics/dataframes/screening/get_screening_df.py +163 -0
  17. meta_analytics/dataframes/utils.py +65 -0
  18. meta_analytics/get_tables.py +81 -0
  19. meta_analytics/tables/__init__.py +2 -0
  20. meta_analytics/tables/eligible.py +106 -0
  21. meta_analytics/tables/enrolled/__init__.py +0 -0
  22. meta_analytics/tables/enrolled/glucose.py +28 -0
  23. meta_analytics/tables/has_dm.py +61 -0
  24. meta_analytics/tests/__init__.py +0 -0
  25. meta_analytics/tests/test_endpoints_by_date.py +94 -0
  26. meta_auth/auth_objects.py +32 -3
  27. meta_auth/auths.py +18 -3
  28. meta_consent/action_items.py +18 -1
  29. meta_consent/admin/__init__.py +1 -0
  30. meta_consent/admin/subject_consent_v1_ext_admin.py +45 -0
  31. meta_consent/baker_recipes.py +5 -4
  32. meta_consent/consents.py +21 -2
  33. meta_consent/constants.py +1 -0
  34. meta_consent/forms/__init__.py +1 -0
  35. meta_consent/forms/subject_consent_v1_ext_form.py +16 -0
  36. meta_consent/locale/lg/LC_MESSAGES/django.po +69 -0
  37. meta_consent/locale/sw/LC_MESSAGES/django.po +12 -12
  38. meta_consent/migrations/0025_alter_historicalsubjectconsent_first_name_and_more.py +151 -0
  39. meta_consent/migrations/0026_historicalsubjectconsentv1ext_subjectconsentv1ext.py +544 -0
  40. meta_consent/migrations/0027_auto_20250111_0344.py +30 -0
  41. meta_consent/models/__init__.py +1 -0
  42. meta_consent/models/signals.py +34 -13
  43. meta_consent/models/subject_consent_v1.py +1 -3
  44. meta_consent/models/subject_consent_v1_ext.py +29 -0
  45. meta_consent/tests/holidays.csv +1 -1
  46. meta_consent/tests/tests/test_form_validators.py +1 -1
  47. meta_dashboard/locale/lg/LC_MESSAGES/django.po +30 -0
  48. meta_dashboard/locale/sw/LC_MESSAGES/django.po +11 -2
  49. meta_dashboard/navbars.py +3 -1
  50. meta_dashboard/templates/meta_dashboard/bootstrap3/buttons/eligibility_button.html +1 -1
  51. meta_dashboard/templates/meta_dashboard/bootstrap3/buttons/screening_button.html +1 -1
  52. meta_dashboard/templates/meta_dashboard/bootstrap3/screening/listboard.html +4 -4
  53. meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard/sidebar.html +24 -0
  54. meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard.html +3 -0
  55. meta_dashboard/templates/meta_dashboard/bootstrap3/subject/listboard.html +1 -2
  56. meta_dashboard/templatetags/meta_dashboard_extras.py +1 -1
  57. meta_dashboard/tests/holidays.csv +1 -1
  58. meta_dashboard/tests/urls.py +0 -1
  59. meta_dashboard/view_utils/__init__.py +6 -0
  60. meta_dashboard/view_utils/subject_screening_button.py +2 -2
  61. meta_dashboard/views/subject/dashboard/dashboard_view.py +38 -0
  62. meta_edc/__init__.py +7 -0
  63. meta_edc/celery.py +4 -13
  64. meta_edc/celery_live.py +18 -0
  65. meta_edc/celery_uat.py +24 -0
  66. meta_edc/management/commands/update_forms_reference.py +6 -2
  67. meta_edc/migrations/__init__.py +0 -0
  68. meta_edc/navbars.py +2 -1
  69. meta_edc/settings/debug.py +17 -9
  70. meta_edc/settings/defaults.py +82 -60
  71. meta_edc/settings/live.py +1 -9
  72. meta_edc/settings/uat.py +1 -14
  73. meta_edc/templates/meta_edc/bootstrap3/home.html +13 -7
  74. meta_edc/tests/tests/test_endpoints.py +22 -19
  75. meta_edc/urls.py +5 -2
  76. meta_edc/wsgi.py +1 -1
  77. meta_edc/wsgi_live.py +1 -1
  78. meta_edc/wsgi_uat.py +1 -1
  79. meta_edc-0.3.50.dist-info/AUTHORS +0 -0
  80. meta_edc-0.3.50.dist-info/METADATA +766 -0
  81. {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/RECORD +400 -157
  82. {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/WHEEL +1 -1
  83. {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/top_level.txt +1 -0
  84. meta_pharmacy/admin/__init__.py +2 -0
  85. meta_pharmacy/admin/rx_admin.py +75 -0
  86. meta_pharmacy/admin/substitutions_admin.py +67 -0
  87. meta_pharmacy/admin_site.py +9 -0
  88. meta_pharmacy/apps.py +5 -0
  89. meta_pharmacy/constants.py +10 -0
  90. meta_pharmacy/forms/__init__.py +2 -0
  91. meta_pharmacy/forms/rx_form.py +16 -0
  92. meta_pharmacy/forms/substitutions_form.py +54 -0
  93. meta_pharmacy/label_configs.py +30 -0
  94. meta_pharmacy/labels/__init__.py +5 -0
  95. meta_pharmacy/labels/draw_label_for_subject_with_barcode.py +62 -0
  96. meta_pharmacy/labels/draw_label_for_subject_with_code128.py +14 -0
  97. meta_pharmacy/labels/draw_label_with_test_data.py +26 -0
  98. meta_pharmacy/labels/label_data.py +14 -0
  99. meta_pharmacy/labels/print_sheets.py +97 -0
  100. meta_pharmacy/list_data.py +8 -0
  101. meta_pharmacy/management/__init__.py +0 -0
  102. meta_pharmacy/management/commands/__init__.py +0 -0
  103. meta_pharmacy/management/commands/update_initial_pharmacy_data.py +10 -0
  104. meta_pharmacy/migrations/0002_initial.py +695 -0
  105. meta_pharmacy/migrations/0003_auto_20240909_2335.py +64 -0
  106. meta_pharmacy/migrations/0004_alter_historicalsubstitutions_report_datetime_and_more.py +23 -0
  107. meta_pharmacy/migrations/0005_auto_20240911_0352.py +17 -0
  108. meta_pharmacy/migrations/0006_lotnumber_label.py +289 -0
  109. meta_pharmacy/migrations/0007_lotnumber_medication.py +24 -0
  110. meta_pharmacy/migrations/0008_remove_lotnumber_medication_and_more.py +390 -0
  111. meta_pharmacy/migrations/0009_remove_historicalrx_slug.py +17 -0
  112. meta_pharmacy/models/__init__.py +3 -0
  113. meta_pharmacy/models/label_data.py +38 -0
  114. meta_pharmacy/models/rx.py +18 -0
  115. meta_pharmacy/models/rx_label.py +39 -0
  116. meta_pharmacy/models/substitutions.py +88 -0
  117. meta_pharmacy/urls.py +8 -0
  118. meta_pharmacy/utils/__init__.py +1 -0
  119. meta_pharmacy/utils/update_initial_pharmacy_data.py +146 -0
  120. meta_prn/action_items.py +52 -2
  121. meta_prn/admin/__init__.py +3 -0
  122. meta_prn/admin/dm_referral_admin.py +49 -0
  123. meta_prn/admin/offschedule_dm_referral_admin.py +47 -0
  124. meta_prn/admin/onschedule_dm_referral_admin.py +39 -0
  125. meta_prn/admin/pregnancy_notification_admin.py +6 -2
  126. meta_prn/baker_recipes.py +8 -1
  127. meta_prn/choices.py +2 -1
  128. meta_prn/constants.py +4 -1
  129. meta_prn/forms/__init__.py +2 -0
  130. meta_prn/forms/dm_referral_form.py +40 -0
  131. meta_prn/forms/offschedule_dm_referral_form.py +35 -0
  132. meta_prn/forms/offschedule_form.py +6 -0
  133. meta_prn/migrations/0034_auto_20220630_1110.py +3 -3
  134. meta_prn/migrations/0035_auto_20220630_1140.py +59 -56
  135. meta_prn/migrations/0057_historicalonscheduledmreferral_and_more.py +1156 -0
  136. meta_prn/migrations/0058_dmreferral_referral_note_and_more.py +29 -0
  137. meta_prn/migrations/0059_alter_historicaloffstudymedication_reason_and_more.py +53 -0
  138. meta_prn/models/__init__.py +13 -2
  139. meta_prn/models/dm_referral.py +39 -0
  140. meta_prn/models/offschedule.py +15 -1
  141. meta_prn/models/onschedule.py +6 -0
  142. meta_prn/models/signals.py +41 -1
  143. meta_prn/tests/tests/test_dm_referral.py +203 -0
  144. meta_reports/__init__.py +1 -0
  145. meta_reports/admin/__init__.py +15 -0
  146. meta_reports/admin/dbviews/__init__.py +14 -0
  147. meta_reports/admin/dbviews/glucose_summary_admin.py +116 -0
  148. meta_reports/admin/dbviews/imp_substitutions_admin.py +101 -0
  149. meta_reports/admin/dbviews/missing_screening_ogtt_admin/__init__.py +2 -0
  150. meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py +53 -0
  151. meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py +84 -0
  152. meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py +1 -0
  153. meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py +13 -0
  154. meta_reports/admin/dbviews/on_study_missing_values_admin/__init__.py +1 -0
  155. meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py +13 -0
  156. meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py +58 -0
  157. meta_reports/admin/dbviews/unattended_three_in_row2_admin.py +47 -0
  158. meta_reports/admin/dbviews/unattended_three_in_row_admin.py +35 -0
  159. meta_reports/admin/dbviews/unattended_two_in_row_admin.py +34 -0
  160. meta_reports/admin/endpoints_admin.py +14 -0
  161. meta_reports/admin/endpoints_all_admin.py +13 -0
  162. meta_reports/admin/last_imp_refill_admin.py +181 -0
  163. meta_reports/admin/list_filters.py +30 -0
  164. meta_reports/admin/modeladmin_mixins.py +112 -0
  165. meta_reports/admin_site.py +5 -0
  166. meta_reports/apps.py +1 -16
  167. meta_reports/forms/__init__.py +1 -0
  168. meta_reports/forms/missing_ogtt_note_form.py +33 -0
  169. meta_reports/management/__init__.py +0 -0
  170. meta_reports/management/commands/__init__.py +0 -0
  171. meta_reports/management/commands/generate_endpoints.py +13 -0
  172. meta_reports/migrations/0001_initial.py +87 -0
  173. meta_reports/migrations/0002_patienthistorymissingbaselinecd4_and_more.py +64 -0
  174. meta_reports/migrations/0003_auto_20240618_0505.py +12 -0
  175. meta_reports/migrations/0004_alter_patienthistorymissingbaselinecd4_table.py +17 -0
  176. meta_reports/migrations/0005_endpoints.py +47 -0
  177. meta_reports/migrations/0006_endpoints_baseline_datetime.py +18 -0
  178. meta_reports/migrations/0007_alter_endpoints_endpoint_label_and_more.py +43 -0
  179. meta_reports/migrations/0008_alter_endpoints_endpoint_label.py +18 -0
  180. meta_reports/migrations/0009_alter_endpoints_options.py +21 -0
  181. meta_reports/migrations/0010_alter_patienthistorymissingbaselinecd4_options_and_more.py +49 -0
  182. meta_reports/migrations/0011_auto_20240813_0156.py +54 -0
  183. meta_reports/migrations/0012_auto_20240813_1516.py +48 -0
  184. meta_reports/migrations/0013_auto_20240813_1516.py +48 -0
  185. meta_reports/migrations/0014_auto_20240813_1517.py +48 -0
  186. meta_reports/migrations/0015_alter_endpoints_site.py +22 -0
  187. meta_reports/migrations/0016_missingscreeningogtt.py +47 -0
  188. meta_reports/migrations/0017_auto_20240819_1711.py +166 -0
  189. meta_reports/migrations/0018_auto_20240819_1713.py +54 -0
  190. meta_reports/migrations/0019_auto_20240819_1721.py +54 -0
  191. meta_reports/migrations/0020_auto_20240819_1811.py +54 -0
  192. meta_reports/migrations/0021_auto_20240819_1817.py +54 -0
  193. meta_reports/migrations/0022_auto_20240819_1832.py +54 -0
  194. meta_reports/migrations/0023_endpoints_meta_report_subject_a56b22_idx.py +20 -0
  195. meta_reports/migrations/0024_glucosesummary.py +38 -0
  196. meta_reports/migrations/0025_auto_20240822_0115.py +87 -0
  197. meta_reports/migrations/0026_auto_20240822_0120.py +54 -0
  198. meta_reports/migrations/0027_auto_20240822_0140.py +54 -0
  199. meta_reports/migrations/0028_alter_glucosesummary_options.py +22 -0
  200. meta_reports/migrations/0029_auto_20240822_0149.py +54 -0
  201. meta_reports/migrations/0030_auto_20240822_1637.py +54 -0
  202. meta_reports/migrations/0031_endpointsproxy.py +25 -0
  203. meta_reports/migrations/0032_alter_endpointsproxy_options.py +21 -0
  204. meta_reports/migrations/0033_auto_20240823_0012.py +54 -0
  205. meta_reports/migrations/0034_auto_20240823_1642.py +54 -0
  206. meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py +457 -0
  207. meta_reports/migrations/0036_historicalmissingogttnote_fasting_and_more.py +86 -0
  208. meta_reports/migrations/0037_historicalmissingogttnote_result_status_and_more.py +51 -0
  209. meta_reports/migrations/0038_alter_historicalmissingogttnote_fasting_and_more.py +33 -0
  210. meta_reports/migrations/0039_onstudymissingvalues.py +44 -0
  211. meta_reports/migrations/0040_auto_20240824_0412.py +282 -0
  212. meta_reports/migrations/0041_auto_20240828_2229.py +14 -0
  213. meta_reports/migrations/0042_onstudymissinglabvalues.py +43 -0
  214. meta_reports/migrations/0043_auto_20240828_2309.py +88 -0
  215. meta_reports/migrations/0044_auto_20240828_2323.py +93 -0
  216. meta_reports/migrations/0045_auto_20240829_0248.py +54 -0
  217. meta_reports/migrations/0046_auto_20240829_0250.py +54 -0
  218. meta_reports/migrations/0047_impsubstitutions.py +56 -0
  219. meta_reports/migrations/0048_auto_20240909_2338.py +48 -0
  220. meta_reports/migrations/0049_auto_20240911_0327.py +54 -0
  221. meta_reports/migrations/0050_alter_endpoints_created.py +19 -0
  222. meta_reports/migrations/0051_remove_endpoints_baseline_datetime_and_more.py +40 -0
  223. meta_reports/migrations/0052_lastimpvisit.py +57 -0
  224. meta_reports/migrations/0053_rename_lastimpvisit_lastimprefill_and_more.py +31 -0
  225. meta_reports/models/__init__.py +16 -0
  226. meta_reports/models/dbviews/README +14 -0
  227. meta_reports/models/dbviews/__init__.py +9 -0
  228. meta_reports/models/dbviews/glucose_summary/__init__.py +2 -0
  229. meta_reports/models/dbviews/glucose_summary/unmanaged_model.py +35 -0
  230. meta_reports/models/dbviews/glucose_summary/view_definition.py +28 -0
  231. meta_reports/models/dbviews/imp_substitutions/__init__.py +1 -0
  232. meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py +41 -0
  233. meta_reports/models/dbviews/imp_substitutions/view_definition.py +21 -0
  234. meta_reports/models/dbviews/missing_screening_ogtt/__init__.py +2 -0
  235. meta_reports/models/dbviews/missing_screening_ogtt/note_model.py +57 -0
  236. meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py +41 -0
  237. meta_reports/models/dbviews/missing_screening_ogtt/view_definition.py +20 -0
  238. meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py +1 -0
  239. meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py +53 -0
  240. meta_reports/models/dbviews/on_study_missing_lab_values/unmanged_model.py +20 -0
  241. meta_reports/models/dbviews/on_study_missing_lab_values/view_definition.py +17 -0
  242. meta_reports/models/dbviews/on_study_missing_values/__init__.py +1 -0
  243. meta_reports/models/dbviews/on_study_missing_values/qa_cases.py +54 -0
  244. meta_reports/models/dbviews/on_study_missing_values/unmanged_model.py +20 -0
  245. meta_reports/models/dbviews/on_study_missing_values/view_definition.py +17 -0
  246. meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py +1 -0
  247. meta_reports/models/dbviews/patient_history_missing_baseline_cd4/unmanaged_model.py +31 -0
  248. meta_reports/models/dbviews/patient_history_missing_baseline_cd4/view_definition.py +21 -0
  249. meta_reports/models/dbviews/unattended_three_in_row/__init__.py +1 -0
  250. meta_reports/models/dbviews/unattended_three_in_row/unmanaged_model.py +29 -0
  251. meta_reports/models/dbviews/unattended_three_in_row/view_definition.py +31 -0
  252. meta_reports/models/dbviews/unattended_three_in_row2/__init__.py +1 -0
  253. meta_reports/models/dbviews/unattended_three_in_row2/unmanaged_model.py +29 -0
  254. meta_reports/models/dbviews/unattended_three_in_row2/view_definition.py +50 -0
  255. meta_reports/models/dbviews/unattended_two_in_row/__init__.py +1 -0
  256. meta_reports/models/dbviews/unattended_two_in_row/unmanaged_model.py +27 -0
  257. meta_reports/models/dbviews/unattended_two_in_row/view_definition.py +30 -0
  258. meta_reports/models/endpoints.py +31 -0
  259. meta_reports/models/endpoints_proxy.py +11 -0
  260. meta_reports/models/last_imp_refill.py +34 -0
  261. meta_reports/tasks.py +12 -0
  262. meta_reports/templates/meta_reports/columns/subject_identifier_column.html +1 -0
  263. meta_reports/templates/meta_reports/endpoints_all_change_list_note.html +12 -0
  264. meta_reports/templates/meta_reports/endpoints_change_list_note.html +12 -0
  265. meta_reports/tests/test_sql_gen.py +5 -0
  266. meta_reports/urls.py +8 -0
  267. meta_reports/utils.py +0 -0
  268. meta_screening/admin/subject_screening_admin.py +1 -0
  269. meta_screening/form_validators/screening_part_two.py +1 -1
  270. meta_screening/migrations/0062_remove_icpreferral_site_and_more.py +27 -0
  271. meta_screening/migrations/0063_alter_historicalscreeningpartone_fasting_duration_str_and_more.py +184 -0
  272. meta_screening/migrations/0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more.py +126 -0
  273. meta_screening/migrations/0065_auto_20240516_0352.py +31 -0
  274. meta_screening/migrations/0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more.py +103 -0
  275. meta_screening/migrations/0067_alter_historicalscreeningpartone_report_datetime_and_more.py +84 -0
  276. meta_screening/models/__init__.py +1 -1
  277. meta_screening/tests/holidays.csv +1 -1
  278. meta_screening/tests/meta_test_case_mixin.py +17 -2
  279. meta_screening/tests/options.py +3 -3
  280. meta_sites/__init__.py +0 -1
  281. meta_sites/sites.py +8 -7
  282. meta_sites/tests/test_sites.py +1 -1
  283. meta_subject/action_items.py +25 -2
  284. meta_subject/admin/__init__.py +2 -1
  285. meta_subject/admin/birth_outcome_admin.py +4 -3
  286. meta_subject/admin/blood_results/__init__.py +1 -1
  287. meta_subject/admin/blood_results/{blood_results_lipid_admin.py → blood_results_lipids_admin.py} +7 -7
  288. meta_subject/admin/delivery_admin.py +0 -1
  289. meta_subject/admin/diabetes/__init__.py +2 -0
  290. meta_subject/admin/diabetes/dm_endpoint_admin.py +35 -0
  291. meta_subject/admin/{dm_referral_followup_admin.py → diabetes/dm_followup_admin.py} +15 -8
  292. meta_subject/admin/glucose_admin.py +1 -1
  293. meta_subject/admin/glucose_fbg_admin.py +38 -8
  294. meta_subject/admin/other_arv_regimens_admin.py +2 -0
  295. meta_subject/admin/study_medication_admin.py +10 -0
  296. meta_subject/admin/subject_visit_admin.py +4 -1
  297. meta_subject/baker_recipes.py +6 -0
  298. meta_subject/choices.py +8 -0
  299. meta_subject/constants.py +2 -1
  300. meta_subject/form_validators/__init__.py +2 -1
  301. meta_subject/form_validators/dm_endpoint_form_validator.py +35 -0
  302. meta_subject/form_validators/{dm_referral_followup_form_validator.py → dm_followup_form_validator.py} +41 -2
  303. meta_subject/forms/__init__.py +2 -1
  304. meta_subject/forms/blood_results/__init__.py +1 -1
  305. meta_subject/forms/blood_results/{blood_results_lipid_form.py → blood_results_lipids_form.py} +5 -5
  306. meta_subject/forms/diabetes/__init__.py +2 -0
  307. meta_subject/forms/diabetes/dm_endpoint_form.py +13 -0
  308. meta_subject/forms/diabetes/dm_followup_form.py +25 -0
  309. meta_subject/forms/glucose_fbg_form.py +38 -16
  310. meta_subject/forms/study_medication_form.py +35 -0
  311. meta_subject/forms/subject_visit_form.py +16 -0
  312. meta_subject/locale/lg/LC_MESSAGES/django.po +470 -0
  313. meta_subject/locale/sw/LC_MESSAGES/django.po +191 -89
  314. meta_subject/metadata_rules/metadata_rules.py +21 -0
  315. meta_subject/metadata_rules/predicates.py +67 -8
  316. meta_subject/migrations/0107_auto_20220415_0043.py +28 -22
  317. meta_subject/migrations/0126_auto_20220719_2142.py +4 -4
  318. meta_subject/migrations/0131_auto_20220722_0411.py +28 -23
  319. meta_subject/migrations/0132_auto_20220722_1825.py +10 -6
  320. meta_subject/migrations/0135_auto_20220722_2212.py +39 -35
  321. meta_subject/migrations/0150_auto_20220914_0039.py +15 -11
  322. meta_subject/migrations/0181_dmreferralfollowup_action_identifier_and_more.py +143 -0
  323. meta_subject/migrations/0182_rename_dmreferralfollowup_dmfollowup_and_more.py +54 -0
  324. meta_subject/migrations/0183_alter_dmfollowup_on_dm_medications_and_more.py +31 -0
  325. meta_subject/migrations/0184_alter_glucose_options_and_more.py +31 -0
  326. meta_subject/migrations/0185_alter_bloodresultsins_fasting_duration_str_and_more.py +82 -0
  327. meta_subject/migrations/0186_healtheconomicsupdate_singleton_field_and_more.py +55 -0
  328. meta_subject/migrations/0187_dmdiagnosis_historicaldmdiagnosis_dmdxresult_and_more.py +451 -0
  329. meta_subject/migrations/0188_historicaldmdxresult_dmdxresult.py +403 -0
  330. meta_subject/migrations/0189_alter_dmdxresult_options_and_more.py +116 -0
  331. meta_subject/migrations/0190_dmdiagnosis_dx_no_tmg_reason_and_more.py +65 -0
  332. meta_subject/migrations/0191_alter_dmdiagnosis_dx_no_tmg_reason_and_more.py +70 -0
  333. meta_subject/migrations/0192_rename_glucose_quantifier_glucosefbg_fbg_quantifier_and_more.py +44 -0
  334. meta_subject/migrations/0193_alter_glucosefbg_fbg_value_and_more.py +44 -0
  335. meta_subject/migrations/0194_remove_glucosefbg_assay_datetime_and_more.py +166 -0
  336. meta_subject/migrations/0195_alter_glucosefbg_fbg_datetime_and_more.py +27 -0
  337. meta_subject/migrations/0196_glucosefbg_fbg_not_performed_reason_and_more.py +49 -0
  338. meta_subject/migrations/0197_glucosefbg_fasting_duration_estimated_and_more.py +33 -0
  339. meta_subject/migrations/0198_alter_glucosefbg_fasting_duration_estimated_and_more.py +33 -0
  340. meta_subject/migrations/0199_auto_20240516_0247.py +18 -0
  341. meta_subject/migrations/0200_rename_fasting_duration_minutes_bloodresultsins_fasting_duration_delta_and_more.py +43 -0
  342. meta_subject/migrations/0201_alter_bloodresultsins_fasting_duration_delta_and_more.py +58 -0
  343. meta_subject/migrations/0202_auto_20240516_0315.py +32 -0
  344. meta_subject/migrations/0203_alter_bloodresultsins_fasting_duration_delta_and_more.py +67 -0
  345. meta_subject/migrations/0204_glucosefbg_repeat_fbg_date_and_more.py +27 -0
  346. meta_subject/migrations/0205_historicalsubjectrequisition_crf_status_and_more.py +80 -0
  347. meta_subject/migrations/0206_bloodresultsfbc_crf_status_and_more.py +62 -0
  348. meta_subject/migrations/0207_alter_historicalphysicalexam_waist_circumference_and_more.py +46 -0
  349. meta_subject/migrations/0208_birthoutcomes_crf_status_and_more.py +62 -0
  350. meta_subject/migrations/0209_remove_historicaldmdxresult_dm_diagnosis_and_more.py +37 -0
  351. meta_subject/migrations/0210_remove_dmdxresult_dm_diagnosis_and_more.py +123 -0
  352. meta_subject/migrations/0211_dmendpoint_endpoint_reached_and_more.py +45 -0
  353. meta_subject/migrations/0212_auto_20240827_2222.py +23 -0
  354. meta_subject/migrations/0213_rename_bloodresultslipid_bloodresultslipids_and_more.py +35 -0
  355. meta_subject/migrations/0214_historicalstudymedication_stock_codes_and_more.py +44 -0
  356. meta_subject/migrations/0215_alter_historicalstudymedication_stock_codes_and_more.py +46 -0
  357. meta_subject/model_mixins/arv_history_model_mixin.py +3 -3
  358. meta_subject/models/__init__.py +3 -2
  359. meta_subject/models/birth_outcomes.py +6 -1
  360. meta_subject/models/blood_results/__init__.py +1 -1
  361. meta_subject/models/blood_results/blood_results_fbc.py +3 -2
  362. meta_subject/models/blood_results/blood_results_hba1c.py +2 -0
  363. meta_subject/models/blood_results/blood_results_ins.py +2 -0
  364. meta_subject/models/blood_results/blood_results_lft.py +2 -0
  365. meta_subject/models/blood_results/{blood_results_lipid.py → blood_results_lipids.py} +5 -3
  366. meta_subject/models/blood_results/blood_results_rft.py +2 -0
  367. meta_subject/models/diabetes/__init__.py +2 -0
  368. meta_subject/models/diabetes/dm_endpoint.py +61 -0
  369. meta_subject/models/{dm_referral_followup.py → diabetes/dm_followup.py} +18 -6
  370. meta_subject/models/glucose.py +7 -14
  371. meta_subject/models/glucose_fbg.py +40 -51
  372. meta_subject/models/health_economics/health_economics_update.py +2 -0
  373. meta_subject/models/physical_exam.py +1 -0
  374. meta_subject/models/signals.py +19 -0
  375. meta_subject/models/subject_requisition.py +3 -4
  376. meta_subject/models/todo.txt +1 -1
  377. meta_subject/static/meta_subject/slider.css +1 -1
  378. meta_subject/templates/meta_subject/endpoint_review_instructions.html +1 -1
  379. meta_subject/templates/meta_subject/widgets/slider.html +0 -1
  380. meta_subject/tests/holidays.csv +1 -1
  381. meta_subject/tests/tests/test_egfr.py +6 -5
  382. meta_subject/tests/tests/test_medication_adherence.py +5 -1
  383. meta_subject/tests/tests/test_metadata_rules.py +34 -4
  384. meta_subject/tests/tests/test_mnsi.py +212 -121
  385. meta_subject/tests/tests/test_sf12.py +0 -12
  386. meta_visit_schedule/constants.py +7 -1
  387. meta_visit_schedule/tests/tests/test_schedule.py +4 -0
  388. meta_visit_schedule/visit_schedules/phase_three/crfs.py +87 -14
  389. meta_visit_schedule/visit_schedules/phase_three/requisitions.py +12 -0
  390. meta_visit_schedule/visit_schedules/phase_three/schedule.py +65 -2
  391. meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py +60 -0
  392. meta_visit_schedule/visit_schedules/phase_three/visit_schedule.py +2 -0
  393. tests/etc/randomization_list.csv +1 -1
  394. {meta_edc/tests → tests}/etc/randomization_list_phase_three.csv +4 -4
  395. tests/holidays.csv +1 -1
  396. tests/test_settings.py +186 -0
  397. meta_edc/tests/etc/user-aes-local.key +0 -1
  398. meta_edc/tests/etc/user-aes-restricted.key +0 -0
  399. meta_edc/tests/etc/user-rsa-local-private.pem +0 -27
  400. meta_edc/tests/etc/user-rsa-local-public.pem +0 -9
  401. meta_edc/tests/etc/user-rsa-restricted-private.pem +0 -27
  402. meta_edc/tests/etc/user-rsa-restricted-public.pem +0 -9
  403. meta_edc/tests/etc/user-salt-local.key +0 -0
  404. meta_edc/tests/etc/user-salt-restricted.key +0 -0
  405. meta_edc-0.3.7.dist-info/METADATA +0 -87
  406. meta_reports/tests/holidays.csv +0 -15
  407. meta_subject/forms/dm_referral_followup.py +0 -18
  408. /meta_edc-0.3.7.dist-info/AUTHORS → /meta_analytics/__init__.py +0 -0
  409. /meta_pharmacy/models.py → /meta_analytics/constants.py +0 -0
  410. /meta_reports/models.py → /meta_analytics/notebooks/cleaning/__init__.py +0 -0
  411. {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/LICENSE +0 -0
@@ -12,14 +12,18 @@ from edc_visit_schedule.constants import (
12
12
  MONTH1,
13
13
  MONTH3,
14
14
  MONTH6,
15
+ MONTH12,
15
16
  MONTH18,
16
17
  MONTH24,
17
18
  MONTH30,
18
19
  MONTH36,
20
+ MONTH48,
19
21
  WEEK2,
20
22
  )
21
23
  from edc_visit_schedule.utils import is_baseline
22
24
 
25
+ from meta_visit_schedule.constants import MONTH39, MONTH42, MONTH45
26
+
23
27
 
24
28
  def hba1c_crf_required_at_baseline(visit):
25
29
  model_name = "meta_subject.bloodresultshba1c"
@@ -67,8 +71,14 @@ class Predicates(PersistantSingletonMixin):
67
71
 
68
72
  @staticmethod
69
73
  def glucose_required(visit, **kwargs):
70
- if visit.report_datetime >= datetime(2023, 11, 24, tzinfo=ZoneInfo("UTC")):
71
- if visit.visit_code in [MONTH6, MONTH18, MONTH24, MONTH30, MONTH36]:
74
+ if visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]:
75
+ return True
76
+ return False
77
+
78
+ @staticmethod
79
+ def glucose_fbg_required(visit, **kwargs):
80
+ if visit.report_datetime >= datetime(2024, 3, 4, tzinfo=ZoneInfo("UTC")):
81
+ if visit.visit_code in [MONTH6, MONTH18, MONTH30, MONTH42]:
72
82
  return True
73
83
  return False
74
84
 
@@ -173,15 +183,50 @@ class Predicates(PersistantSingletonMixin):
173
183
  required = True
174
184
  return required
175
185
 
186
+ def health_economics_update_required(self, visit, **kwargs) -> bool:
187
+ """Returns true if `healtheconomicsupdate` was not completed at
188
+ month 3 or ever.
189
+
190
+ `healtheconomicsupdate` is a singleton CRF.
191
+ """
192
+ required = False
193
+ model_cls = django_apps.get_model(f"{self.app_label}.healtheconomicsupdate")
194
+ try:
195
+ obj = model_cls.objects.get(
196
+ subject_visit__subject_identifier=visit.subject_identifier,
197
+ )
198
+ except ObjectDoesNotExist:
199
+ obj = None
200
+ if (
201
+ not obj
202
+ and visit.appointment.visit_code_sequence == 0
203
+ and visit.appointment.visit_code not in [DAY1, WEEK2, MONTH1]
204
+ ):
205
+ required = True
206
+ return required
207
+
176
208
  def mnsi_required(self, visit, **kwargs) -> bool:
177
- """Returns True if MNSI assessment was not performed at the
178
- 1M, 3M or 6M visits.
209
+ """Returns True if:
210
+ - MNSI assessment not performed in the 1, 3 or 6M visits
211
+ - MNSI assessment not performed in the 36, 39, 42, 45M visits
212
+ - MNSI assessment not performed in the 48M visit
179
213
  """
214
+ model_cls = django_apps.get_model(f"{self.app_label}.mnsi")
180
215
  required = True
181
- if (
182
- visit.appointment.visit_code in [MONTH1, MONTH3, MONTH6]
183
- ) and visit.appointment.visit_code_sequence == 0:
184
- model_cls = django_apps.get_model(f"{self.app_label}.mnsi")
216
+ if visit.visit_code_sequence != 0:
217
+ required = False
218
+ elif visit.visit_code not in [
219
+ MONTH1,
220
+ MONTH3,
221
+ MONTH6,
222
+ MONTH36,
223
+ MONTH39,
224
+ MONTH42,
225
+ MONTH45,
226
+ MONTH48,
227
+ ]:
228
+ required = False
229
+ elif visit.visit_code in [MONTH1, MONTH3, MONTH6]:
185
230
  objs = model_cls.objects.filter(
186
231
  subject_visit__subject_identifier=visit.subject_identifier,
187
232
  subject_visit__visit_code__in=[MONTH1, MONTH3, MONTH6],
@@ -191,16 +236,30 @@ class Predicates(PersistantSingletonMixin):
191
236
  if obj.mnsi_performed == YES:
192
237
  required = False
193
238
  break
239
+ elif visit.visit_code in [MONTH36, MONTH39, MONTH42, MONTH45]:
240
+ objs = model_cls.objects.filter(
241
+ subject_visit__subject_identifier=visit.subject_identifier,
242
+ subject_visit__visit_code__in=[MONTH36, MONTH39, MONTH42, MONTH45],
243
+ subject_visit__visit_code_sequence=0,
244
+ )
245
+ for obj in objs:
246
+ if obj.mnsi_performed == YES:
247
+ required = False
248
+ break
194
249
  return required
195
250
 
196
251
  def sf12_required(self, visit, **kwargs):
197
252
  model = f"{self.app_label}.sf12"
253
+ if visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
254
+ return True
198
255
  return self.persistant_singleton_required(
199
256
  visit, model=model, exclude_visit_codes=[DAY1]
200
257
  )
201
258
 
202
259
  def eq5d3l_required(self, visit, **kwargs):
203
260
  model = f"{self.app_label}.eq5d3l"
261
+ if visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
262
+ return True
204
263
  return self.persistant_singleton_required(
205
264
  visit, model=model, exclude_visit_codes=[DAY1]
206
265
  )
@@ -1,5 +1,5 @@
1
1
  # Generated by Django 3.2.11 on 2022-04-14 21:43
2
-
2
+ from django.core.exceptions import ObjectDoesNotExist
3
3
  from django.db import migrations
4
4
  from django.db.migrations import RunPython
5
5
  from edc_consent.utils import get_consent_model_name
@@ -10,28 +10,34 @@ from meta_pharmacy.constants import METFORMIN
10
10
 
11
11
 
12
12
  def func(apps, schema_editor):
13
- medication = apps.get_model("edc_pharmacy.medication")._default_manager.get(name=METFORMIN)
14
- site_model_cls = apps.get_model("sites.site")
15
- subject_identifiers = [
16
- tpl[0]
17
- for tpl in apps.get_model("edc_pharmacy.rx")._default_manager.values_list(
18
- "subject_identifier"
19
- )
20
- ]
21
- for subject_consent in apps.get_model(get_consent_model_name())._default_manager.exclude(
22
- subject_identifier__in=subject_identifiers
23
- ):
24
- site = site_model_cls.objects.get(id=subject_consent.site.id)
25
- create_prescription(
26
- subject_identifier=subject_consent.subject_identifier,
27
- report_datetime=subject_consent.consent_datetime,
28
- randomizer_name=get_meta_version(),
29
- medications=[METFORMIN],
30
- site_id=site.id,
13
+ try:
14
+ medication = apps.get_model("edc_pharmacy.medication")._default_manager.get(
15
+ name=METFORMIN
31
16
  )
32
- for obj in apps.get_model("edc_pharmacy.rx")._default_manager.all():
33
- obj.medications.clear()
34
- obj.medications.add(medication)
17
+ except ObjectDoesNotExist:
18
+ pass
19
+ else:
20
+ site_model_cls = apps.get_model("sites.site")
21
+ subject_identifiers = [
22
+ tpl[0]
23
+ for tpl in apps.get_model("edc_pharmacy.rx")._default_manager.values_list(
24
+ "subject_identifier"
25
+ )
26
+ ]
27
+ for subject_consent in apps.get_model(
28
+ get_consent_model_name()
29
+ )._default_manager.exclude(subject_identifier__in=subject_identifiers):
30
+ site = site_model_cls.objects.get(id=subject_consent.site.id)
31
+ create_prescription(
32
+ subject_identifier=subject_consent.subject_identifier,
33
+ report_datetime=subject_consent.consent_datetime,
34
+ randomizer_name=get_meta_version(),
35
+ medications=[METFORMIN],
36
+ site_id=site.id,
37
+ )
38
+ for obj in apps.get_model("edc_pharmacy.rx")._default_manager.all():
39
+ obj.medications.clear()
40
+ obj.medications.add(medication)
35
41
 
36
42
 
37
43
  class Migration(migrations.Migration):
@@ -4,11 +4,11 @@ from django.db import migrations
4
4
 
5
5
 
6
6
  def update_egfr_drop_action(apps, schema_editor):
7
- action_item_model_cls = apps.get_model("edc_action_item.actionitem")
7
+ # action_item_model_cls = apps.get_model("edc_action_item.actionitem")
8
8
  crf_metadata_model_cls = apps.get_model("edc_metadata.crfmetadata")
9
- action_item_model_cls.objects.filter(
10
- reference_model="meta_subject.egfrnotification"
11
- ).update(reference_model="meta_subject.egfrdropnotification")
9
+ # action_item_model_cls.objects.filter(
10
+ # reference_model="meta_subject.egfrnotification"
11
+ # ).update(reference_model="meta_subject.egfrdropnotification")
12
12
  crf_metadata_model_cls.objects.filter(model="meta_subject.egfrnotification").update(
13
13
  model="meta_subject.egfrdropnotification"
14
14
  )
@@ -1,5 +1,5 @@
1
1
  # Generated by Django 3.2.11 on 2022-07-22 01:11
2
-
2
+ from django.core.exceptions import ObjectDoesNotExist
3
3
  from django.db import migrations
4
4
  from edc_action_item.identifiers import ActionIdentifier
5
5
  from edc_constants.constants import CLOSED, HIGH_PRIORITY
@@ -13,28 +13,33 @@ def update_missing_action_items_for_missed_visits(apps, schema_editor):
13
13
  actionitem_model_cls = apps.get_model("edc_action_item.actionitem")
14
14
  subjectvisitmissed_model_cls = apps.get_model("meta_subject.subjectvisitmissed")
15
15
  subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
16
- action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
17
-
18
- total = subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True).count()
19
- for obj in tqdm(
20
- subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
21
- total=total,
22
- ):
23
- subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
24
- action_item = actionitem_model_cls.objects.create(
25
- subject_identifier=subject_visit.subject_identifier,
26
- action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
27
- report_datetime=subject_visit.report_datetime,
28
- action_type=action_type,
29
- reference_model="meta_subject.subjectvisitmissed",
30
- linked_to_reference=True,
31
- priority=HIGH_PRIORITY,
32
- status=CLOSED,
33
- auto_created=True,
34
- site_id=subject_visit.site_id,
35
- )
36
- obj.action_identifier = action_item.action_identifier
37
- obj.save_base(update_fields=["action_identifier"])
16
+ try:
17
+ action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
18
+ except ObjectDoesNotExist:
19
+ pass
20
+ else:
21
+ total = subjectvisitmissed_model_cls.objects.filter(
22
+ action_identifier__isnull=True
23
+ ).count()
24
+ for obj in tqdm(
25
+ subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
26
+ total=total,
27
+ ):
28
+ subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
29
+ action_item = actionitem_model_cls.objects.create(
30
+ subject_identifier=subject_visit.subject_identifier,
31
+ action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
32
+ report_datetime=subject_visit.report_datetime,
33
+ action_type=action_type,
34
+ reference_model="meta_subject.subjectvisitmissed",
35
+ linked_to_reference=True,
36
+ priority=HIGH_PRIORITY,
37
+ status=CLOSED,
38
+ auto_created=True,
39
+ site_id=subject_visit.site_id,
40
+ )
41
+ obj.action_identifier = action_item.action_identifier
42
+ obj.save_base(update_fields=["action_identifier"])
38
43
 
39
44
 
40
45
  class Migration(migrations.Migration):
@@ -1,5 +1,5 @@
1
1
  # Generated by Django 3.2.11 on 2022-07-22 15:25
2
-
2
+ from django.core.exceptions import ObjectDoesNotExist
3
3
  from django.db import migrations
4
4
  from tqdm import tqdm
5
5
 
@@ -9,11 +9,15 @@ from meta_pharmacy.constants import METFORMIN
9
9
  def update_rx_missing_medication(apps, schema_editor):
10
10
  medication_model_cls = apps.get_model("edc_pharmacy.medication")
11
11
  rx_model_cls = apps.get_model("edc_pharmacy.rx")
12
- medication = medication_model_cls.objects.get(name=METFORMIN)
13
- total = rx_model_cls.objects.filter(medications__isnull=True).count()
14
- for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
15
- if not obj.medications.all().exists():
16
- obj.medications.add(medication)
12
+ try:
13
+ medication = medication_model_cls.objects.get(name=METFORMIN)
14
+ except ObjectDoesNotExist:
15
+ pass
16
+ else:
17
+ total = rx_model_cls.objects.filter(medications__isnull=True).count()
18
+ for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
19
+ if not obj.medications.all().exists():
20
+ obj.medications.add(medication)
17
21
 
18
22
 
19
23
  class Migration(migrations.Migration):
@@ -9,42 +9,46 @@ from tqdm import tqdm
9
9
  def update_revised_egrf(apps, schema_editor):
10
10
  bloodresultrft_model_cls = apps.get_model("meta_subject.bloodresultsrft")
11
11
  subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
12
- subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
13
- total = bloodresultrft_model_cls.objects.all().count()
14
- for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
15
- subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
16
- subject_screening = subjectscreening_model_cls.objects.get(
17
- subject_identifier=subject_visit.subject_identifier
18
- )
19
- try:
20
- baseline_obj = bloodresultrft_model_cls.objects.get(
21
- subject_visit__subject_identifier=subject_visit.subject_identifier,
22
- subject_visit__visit_code=DAY1,
23
- subject_visit__visit_code_sequence=0,
24
- )
25
- except ObjectDoesNotExist:
26
- pass
27
- else:
28
- obj.old_egfr_value = obj.egfr_value
29
- obj.old_egfr_drop_value = obj.egfr_drop_value
30
- obj.egfr_value = EgfrCkdEpi(
31
- gender=subject_screening.gender,
32
- ethnicity=subject_screening.ethnicity,
33
- age_in_years=subject_screening.age_in_years,
34
- creatinine_value=obj.creatinine_value,
35
- creatinine_units=obj.creatinine_units,
36
- ).value
37
- obj.egfr_drop_value = egfr_percent_change(
38
- float(obj.egfr_value), float(baseline_obj.egfr_value)
39
- )
40
- obj.save_base(
41
- update_fields=[
42
- "egfr_value",
43
- "egfr_drop_value",
44
- "old_egfr_value",
45
- "old_egfr_drop_value",
46
- ]
12
+ try:
13
+ subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
14
+ except LookupError:
15
+ pass
16
+ else:
17
+ total = bloodresultrft_model_cls.objects.all().count()
18
+ for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
19
+ subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
20
+ subject_screening = subjectscreening_model_cls.objects.get(
21
+ subject_identifier=subject_visit.subject_identifier
47
22
  )
23
+ try:
24
+ baseline_obj = bloodresultrft_model_cls.objects.get(
25
+ subject_visit__subject_identifier=subject_visit.subject_identifier,
26
+ subject_visit__visit_code=DAY1,
27
+ subject_visit__visit_code_sequence=0,
28
+ )
29
+ except ObjectDoesNotExist:
30
+ pass
31
+ else:
32
+ obj.old_egfr_value = obj.egfr_value
33
+ obj.old_egfr_drop_value = obj.egfr_drop_value
34
+ obj.egfr_value = EgfrCkdEpi(
35
+ gender=subject_screening.gender,
36
+ ethnicity=subject_screening.ethnicity,
37
+ age_in_years=subject_screening.age_in_years,
38
+ creatinine_value=obj.creatinine_value,
39
+ creatinine_units=obj.creatinine_units,
40
+ ).value
41
+ obj.egfr_drop_value = egfr_percent_change(
42
+ float(obj.egfr_value), float(baseline_obj.egfr_value)
43
+ )
44
+ obj.save_base(
45
+ update_fields=[
46
+ "egfr_value",
47
+ "egfr_drop_value",
48
+ "old_egfr_value",
49
+ "old_egfr_drop_value",
50
+ ]
51
+ )
48
52
 
49
53
 
50
54
  class Migration(migrations.Migration):
@@ -5,18 +5,22 @@ from tqdm import tqdm
5
5
 
6
6
  def update_rs_missing_ethnicity(apps, schema_editor):
7
7
  register_subject_model_cls = apps.get_model("edc_registration.registeredsubject")
8
- subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
9
8
  subject_consent_model_cls = apps.get_model("meta_consent.subjectconsent")
10
- total = subject_consent_model_cls.objects.all().count()
11
- for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
12
- subject_screening = subject_screening_model_cls.objects.get(
13
- subject_identifier=subject_consent.subject_identifier
14
- )
15
- register_subject = register_subject_model_cls.objects.get(
16
- subject_identifier=subject_consent.subject_identifier
17
- )
18
- register_subject.ethnicity = subject_screening.ethnicity
19
- register_subject.save(update_fields=["ethnicity"])
9
+ try:
10
+ subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
11
+ except LookupError:
12
+ pass
13
+ else:
14
+ total = subject_consent_model_cls.objects.all().count()
15
+ for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
16
+ subject_screening = subject_screening_model_cls.objects.get(
17
+ subject_identifier=subject_consent.subject_identifier
18
+ )
19
+ register_subject = register_subject_model_cls.objects.get(
20
+ subject_identifier=subject_consent.subject_identifier
21
+ )
22
+ register_subject.ethnicity = subject_screening.ethnicity
23
+ register_subject.save(update_fields=["ethnicity"])
20
24
 
21
25
 
22
26
  class Migration(migrations.Migration):
@@ -0,0 +1,143 @@
1
+ # Generated by Django 4.2.11 on 2024-04-03 19:45
2
+
3
+ from django.db import migrations, models
4
+ import django.db.models.deletion
5
+
6
+
7
+ class Migration(migrations.Migration):
8
+
9
+ dependencies = [
10
+ ("edc_action_item", "0037_remove_actionitem_reference_model_and_more"),
11
+ ("meta_subject", "0180_dmreferralfollowup_missed_referral_reasons_and_more"),
12
+ ]
13
+
14
+ operations = [
15
+ migrations.AddField(
16
+ model_name="dmreferralfollowup",
17
+ name="action_identifier",
18
+ field=models.CharField(blank=True, max_length=50, null=True, unique=True),
19
+ ),
20
+ migrations.AddField(
21
+ model_name="dmreferralfollowup",
22
+ name="action_item",
23
+ field=models.ForeignKey(
24
+ blank=True,
25
+ null=True,
26
+ on_delete=django.db.models.deletion.PROTECT,
27
+ to="edc_action_item.actionitem",
28
+ ),
29
+ ),
30
+ migrations.AddField(
31
+ model_name="dmreferralfollowup",
32
+ name="action_item_reason",
33
+ field=models.TextField(editable=False, null=True),
34
+ ),
35
+ migrations.AddField(
36
+ model_name="dmreferralfollowup",
37
+ name="parent_action_identifier",
38
+ field=models.CharField(
39
+ blank=True,
40
+ help_text="action identifier that links to parent reference model instance.",
41
+ max_length=30,
42
+ null=True,
43
+ ),
44
+ ),
45
+ migrations.AddField(
46
+ model_name="dmreferralfollowup",
47
+ name="parent_action_item",
48
+ field=models.ForeignKey(
49
+ blank=True,
50
+ null=True,
51
+ on_delete=django.db.models.deletion.PROTECT,
52
+ related_name="+",
53
+ to="edc_action_item.actionitem",
54
+ ),
55
+ ),
56
+ migrations.AddField(
57
+ model_name="dmreferralfollowup",
58
+ name="related_action_identifier",
59
+ field=models.CharField(
60
+ blank=True,
61
+ help_text="action identifier that links to related reference model instance.",
62
+ max_length=30,
63
+ null=True,
64
+ ),
65
+ ),
66
+ migrations.AddField(
67
+ model_name="dmreferralfollowup",
68
+ name="related_action_item",
69
+ field=models.ForeignKey(
70
+ blank=True,
71
+ null=True,
72
+ on_delete=django.db.models.deletion.PROTECT,
73
+ related_name="+",
74
+ to="edc_action_item.actionitem",
75
+ ),
76
+ ),
77
+ migrations.AddField(
78
+ model_name="historicaldmreferralfollowup",
79
+ name="action_identifier",
80
+ field=models.CharField(blank=True, db_index=True, max_length=50, null=True),
81
+ ),
82
+ migrations.AddField(
83
+ model_name="historicaldmreferralfollowup",
84
+ name="action_item",
85
+ field=models.ForeignKey(
86
+ blank=True,
87
+ db_constraint=False,
88
+ null=True,
89
+ on_delete=django.db.models.deletion.DO_NOTHING,
90
+ related_name="+",
91
+ to="edc_action_item.actionitem",
92
+ ),
93
+ ),
94
+ migrations.AddField(
95
+ model_name="historicaldmreferralfollowup",
96
+ name="action_item_reason",
97
+ field=models.TextField(editable=False, null=True),
98
+ ),
99
+ migrations.AddField(
100
+ model_name="historicaldmreferralfollowup",
101
+ name="parent_action_identifier",
102
+ field=models.CharField(
103
+ blank=True,
104
+ help_text="action identifier that links to parent reference model instance.",
105
+ max_length=30,
106
+ null=True,
107
+ ),
108
+ ),
109
+ migrations.AddField(
110
+ model_name="historicaldmreferralfollowup",
111
+ name="parent_action_item",
112
+ field=models.ForeignKey(
113
+ blank=True,
114
+ db_constraint=False,
115
+ null=True,
116
+ on_delete=django.db.models.deletion.DO_NOTHING,
117
+ related_name="+",
118
+ to="edc_action_item.actionitem",
119
+ ),
120
+ ),
121
+ migrations.AddField(
122
+ model_name="historicaldmreferralfollowup",
123
+ name="related_action_identifier",
124
+ field=models.CharField(
125
+ blank=True,
126
+ help_text="action identifier that links to related reference model instance.",
127
+ max_length=30,
128
+ null=True,
129
+ ),
130
+ ),
131
+ migrations.AddField(
132
+ model_name="historicaldmreferralfollowup",
133
+ name="related_action_item",
134
+ field=models.ForeignKey(
135
+ blank=True,
136
+ db_constraint=False,
137
+ null=True,
138
+ on_delete=django.db.models.deletion.DO_NOTHING,
139
+ related_name="+",
140
+ to="edc_action_item.actionitem",
141
+ ),
142
+ ),
143
+ ]
@@ -0,0 +1,54 @@
1
+ # Generated by Django 4.2.11 on 2024-04-04 14:18
2
+
3
+ from django.conf import settings
4
+ from django.db import migrations
5
+
6
+
7
+ class Migration(migrations.Migration):
8
+
9
+ dependencies = [
10
+ ("sites", "0002_alter_domain_unique"),
11
+ migrations.swappable_dependency(settings.AUTH_USER_MODEL),
12
+ ("edc_action_item", "0037_remove_actionitem_reference_model_and_more"),
13
+ ("meta_lists", "0018_missedreferralreasons"),
14
+ ("meta_subject", "0181_dmreferralfollowup_action_identifier_and_more"),
15
+ ]
16
+
17
+ operations = [
18
+ migrations.RenameModel(
19
+ old_name="DmReferralFollowup",
20
+ new_name="DmFollowup",
21
+ ),
22
+ migrations.RenameModel(
23
+ old_name="HistoricalDmReferralFollowup",
24
+ new_name="HistoricalDmFollowup",
25
+ ),
26
+ migrations.AlterModelOptions(
27
+ name="dmfollowup",
28
+ options={
29
+ "default_manager_name": "objects",
30
+ "default_permissions": ("add", "change", "delete", "view", "export", "import"),
31
+ "verbose_name": "Diabetes follow-up after referral",
32
+ "verbose_name_plural": "Diabetes follow-up after referral",
33
+ },
34
+ ),
35
+ migrations.AlterModelOptions(
36
+ name="historicaldmfollowup",
37
+ options={
38
+ "get_latest_by": ("history_date", "history_id"),
39
+ "ordering": ("-history_date", "-history_id"),
40
+ "verbose_name": "historical Diabetes follow-up after referral",
41
+ "verbose_name_plural": "historical Diabetes follow-up after referral",
42
+ },
43
+ ),
44
+ migrations.RenameIndex(
45
+ model_name="dmfollowup",
46
+ new_name="meta_subjec_subject_dd09d5_idx",
47
+ old_name="meta_subjec_subject_cfb7da_idx",
48
+ ),
49
+ migrations.RenameIndex(
50
+ model_name="dmfollowup",
51
+ new_name="meta_subjec_subject_1313a7_idx",
52
+ old_name="meta_subjec_subject_257846_idx",
53
+ ),
54
+ ]
@@ -0,0 +1,31 @@
1
+ # Generated by Django 4.2.11 on 2024-04-05 20:19
2
+
3
+ from django.db import migrations, models
4
+
5
+
6
+ class Migration(migrations.Migration):
7
+
8
+ dependencies = [
9
+ ("meta_subject", "0182_rename_dmreferralfollowup_dmfollowup_and_more"),
10
+ ]
11
+
12
+ operations = [
13
+ migrations.AlterField(
14
+ model_name="dmfollowup",
15
+ name="on_dm_medications",
16
+ field=models.CharField(
17
+ choices=[("Yes", "Yes"), ("No", "No"), ("N/A", "Not applicable")],
18
+ max_length=25,
19
+ verbose_name="Are you currently taking any drug therapy for diabetes?",
20
+ ),
21
+ ),
22
+ migrations.AlterField(
23
+ model_name="historicaldmfollowup",
24
+ name="on_dm_medications",
25
+ field=models.CharField(
26
+ choices=[("Yes", "Yes"), ("No", "No"), ("N/A", "Not applicable")],
27
+ max_length=25,
28
+ verbose_name="Are you currently taking any drug therapy for diabetes?",
29
+ ),
30
+ ),
31
+ ]