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
@@ -0,0 +1,57 @@
1
+ from django.db import models
2
+ from edc_constants.choices import YES_NO, YES_NO_NA
3
+ from edc_constants.constants import COMPLETE, DONE, NOT_APPLICABLE, NOT_AVAILABLE, YES
4
+ from edc_glucose.model_mixins import (
5
+ fasting_model_mixin_factory,
6
+ ogtt_model_mixin_factory,
7
+ )
8
+ from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
9
+ from edc_model.models import BaseUuidModel, HistoricalRecords
10
+ from edc_qareports.model_mixins import NoteModelMixin
11
+
12
+ NOTE_STATUSES = (
13
+ (COMPLETE, "Complete"),
14
+ (NOT_AVAILABLE, "Not available"),
15
+ )
16
+
17
+
18
+ class MissingOgttNote(
19
+ fasting_model_mixin_factory(
20
+ None,
21
+ fasting=models.CharField(
22
+ verbose_name="Did the participant fast?",
23
+ max_length=15,
24
+ choices=YES_NO_NA,
25
+ default=NOT_APPLICABLE,
26
+ blank=False,
27
+ ),
28
+ ),
29
+ ogtt_model_mixin_factory("ogtt"),
30
+ UniqueSubjectIdentifierFieldMixin,
31
+ NoteModelMixin,
32
+ ):
33
+ """Model class to replace default `Note` model used with
34
+ QA Report 'Screening: Missing OGTT'.
35
+ """
36
+
37
+ result_status = models.CharField(
38
+ verbose_name="Is the OGTT result available", max_length=25, default=YES, choices=YES_NO
39
+ )
40
+
41
+ status = models.CharField(max_length=25, default=DONE, choices=NOTE_STATUSES)
42
+
43
+ history = HistoricalRecords()
44
+
45
+ def __str__(self) -> str:
46
+ return f"{self._meta.verbose_name}: {self.subject_identifier}"
47
+
48
+ def save(self, *args, **kwargs):
49
+ if self.result_status == YES:
50
+ self.status = COMPLETE
51
+ else:
52
+ self.status = NOT_AVAILABLE
53
+ super().save(*args, **kwargs)
54
+
55
+ class Meta(UniqueSubjectIdentifierFieldMixin.Meta, BaseUuidModel.Meta):
56
+ verbose_name = "Screening: Missing OGTT Note"
57
+ verbose_name_plural = "Screening: Missing OGTT Notes"
@@ -0,0 +1,41 @@
1
+ from django.db import models
2
+ from django_db_views.db_view import DBView
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+ from .view_definition import get_view_definition
6
+
7
+
8
+ class MissingScreeningOgtt(QaReportModelMixin, DBView):
9
+
10
+ screening_datetime = models.DateTimeField(null=True)
11
+
12
+ fbg_datetime = models.DateTimeField(null=True)
13
+
14
+ fbg_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
15
+
16
+ ogtt_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
17
+
18
+ fbg2_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
19
+
20
+ ogtt2_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
21
+
22
+ fbg2_datetime = models.DateTimeField(null=True)
23
+
24
+ ogtt2_datetime = models.DateTimeField(null=True)
25
+
26
+ repeated = models.CharField(null=True, max_length=25, help_text="repeat_glucose_performed")
27
+
28
+ p3_ltfu = models.CharField(null=True, max_length=25)
29
+
30
+ consented = models.BooleanField(null=True)
31
+
32
+ original_id = models.UUIDField(null=True)
33
+
34
+ view_definition = get_view_definition()
35
+
36
+ class Meta:
37
+ managed = False
38
+ db_table = "missing_screening_ogtt_view"
39
+ verbose_name = "Screening: Missing OGTT"
40
+ verbose_name_plural = "Screening: Missing OGTT"
41
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,20 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+
4
+ def get_view_definition() -> dict:
5
+ subquery = """select screening_identifier, site_id, report_datetime as `screening_datetime`, fbg_datetime,
6
+ converted_fbg_value as `fbg_value`, converted_ogtt_value as `ogtt_value`, fbg2_value, ogtt2_value,
7
+ repeat_glucose_performed as `repeated`, p3_ltfu, fbg2_datetime, ogtt2_datetime, consented,
8
+ screening_identifier as `subject_identifier`, id as `original_id`
9
+ from meta_screening_subjectscreening
10
+ where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != "Yes"
11
+ """ # noqa
12
+ sql_view = SqlViewGenerator(
13
+ report_model="meta_reports.missing_screening_ogtt_view",
14
+ ordering=["subject_identifier", "site_id"],
15
+ )
16
+ return {
17
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
18
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
19
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
20
+ }
@@ -0,0 +1 @@
1
+ from .unmanged_model import OnStudyMissingLabValues
@@ -0,0 +1,53 @@
1
+ from edc_lab_panel.constants import FBC, LFT, LIPIDS, RFT
2
+ from edc_lab_panel.panels import fbc_panel, lft_panel, lipids_panel, rft_panel
3
+ from edc_qareports.sql_generator import CrfCase, RequisitionCase
4
+
5
+ qa_cases = [
6
+ RequisitionCase(
7
+ label="FBC requisitioned but not entered",
8
+ dbtable="meta_subject_bloodresultsfbc",
9
+ label_lower="meta_subject.bloodresultsfbc",
10
+ panel=FBC,
11
+ ),
12
+ RequisitionCase(
13
+ label="RFT requisitioned but not entered",
14
+ dbtable="meta_subject_bloodresultsrft",
15
+ label_lower="meta_subject.bloodresultsrft",
16
+ panel=RFT,
17
+ ),
18
+ RequisitionCase(
19
+ label="LFT requisitioned but not entered",
20
+ dbtable="meta_subject_bloodresultslft",
21
+ label_lower="meta_subject.bloodresultslft",
22
+ panel=LFT,
23
+ ),
24
+ RequisitionCase(
25
+ label="LIPIDS requisitioned but not entered",
26
+ dbtable="meta_subject_bloodresultslipids",
27
+ label_lower="meta_subject.bloodresultslipids",
28
+ panel=LIPIDS,
29
+ ),
30
+ ]
31
+
32
+ panels = {FBC: fbc_panel, RFT: rft_panel, LFT: lft_panel, LIPIDS: lipids_panel}
33
+ for abbrev, panel in panels.items():
34
+ for utest_id in panel.utest_ids:
35
+ try:
36
+ utest_id, _ = utest_id
37
+ except ValueError:
38
+ pass
39
+ qa_cases.append(
40
+ CrfCase(
41
+ label=f"{abbrev.upper()}: missing {utest_id} value/units",
42
+ dbtable=f"meta_subject_bloodresults{abbrev.lower()}",
43
+ label_lower=f"meta_subject.bloodresults{abbrev.lower()}",
44
+ where=f"crf.{utest_id}_value is null or crf.{utest_id}_units is null",
45
+ )
46
+ )
47
+
48
+ CrfCase(
49
+ label="No UREA value",
50
+ dbtable="meta_subject_bloodresultsrft",
51
+ label_lower="meta_subject.bloodresultsrft",
52
+ where="crf.urea_value is null or crf.urea_units is null",
53
+ ),
@@ -0,0 +1,20 @@
1
+ from django_db_views.db_view import DBView
2
+ from edc_qareports.model_mixins import (
3
+ OnStudyMissingValuesModelMixin,
4
+ QaReportModelMixin,
5
+ qa_reports_permissions,
6
+ )
7
+
8
+ from .view_definition import get_view_definition
9
+
10
+
11
+ class OnStudyMissingLabValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
12
+
13
+ view_definition = get_view_definition()
14
+
15
+ class Meta:
16
+ managed = False
17
+ db_table = "onstudy_missing_lab_values_view"
18
+ verbose_name = "Missing Lab values for on-study patient"
19
+ verbose_name_plural = "Missing Lab values for on-study patients"
20
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,17 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+ from .qa_cases import qa_cases
4
+
5
+
6
+ def get_view_definition() -> dict:
7
+ subquery = " UNION ".join([qa_case.sql for qa_case in qa_cases])
8
+ sql_view = SqlViewGenerator(
9
+ report_model="onstudy_missing_lab_values_view",
10
+ ordering=["subject_identifier", "site_id"],
11
+ )
12
+
13
+ return {
14
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
15
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
16
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
17
+ }
@@ -0,0 +1 @@
1
+ from .unmanged_model import OnStudyMissingValues
@@ -0,0 +1,54 @@
1
+ from edc_constants.constants import OTHER, YES
2
+ from edc_qareports.sql_generator import CrfCase
3
+
4
+ qa_cases = [
5
+ CrfCase(
6
+ label="No HIV Diagnosis date",
7
+ dbtable="meta_subject_patienthistory",
8
+ label_lower="meta_subject.patienthistory",
9
+ fld_name="hiv_diagnosis_date",
10
+ ),
11
+ CrfCase(
12
+ label="No VL value or VL date",
13
+ dbtable="meta_subject_patienthistory",
14
+ label_lower="meta_subject.patienthistory",
15
+ where="crf.viral_load is null or crf.viral_load_date is null",
16
+ ),
17
+ CrfCase(
18
+ label="No CD4 value or CD4 date",
19
+ dbtable="meta_subject_patienthistory",
20
+ label_lower="meta_subject.patienthistory",
21
+ where="crf.cd4 is null or crf.cd4_date is null",
22
+ ),
23
+ CrfCase(
24
+ label="No current ARV start date",
25
+ dbtable="meta_subject_patienthistory",
26
+ label_lower="meta_subject.patienthistory",
27
+ fld_name="current_arv_regimen_start_date",
28
+ ),
29
+ CrfCase(
30
+ label="No current ARV start date but previous ARV is YES",
31
+ dbtable="meta_subject_patienthistory",
32
+ label_lower="meta_subject.patienthistory",
33
+ where=(
34
+ f"crf.has_previous_arv_regimen ='{YES}' and "
35
+ "crf.current_arv_regimen_start_date is null"
36
+ ),
37
+ ),
38
+ CrfCase(
39
+ label="Other current ARV regimen missing",
40
+ dbtable="meta_subject_patienthistory",
41
+ label_lower="meta_subject.patienthistory",
42
+ where=f"crf.other_current_arv_regimen is null and arvregimen.name='{OTHER}'",
43
+ list_tables=[("current_arv_regimen_id", "meta_lists_arvregimens", "arvregimen")],
44
+ ),
45
+ CrfCase(
46
+ label="FBG/OGTT: missing OGTT",
47
+ dbtable="meta_subject_glucose",
48
+ label_lower="meta_subject.glucose",
49
+ where=(
50
+ "(crf.fbg_value is not null and crf.ogtt_value is null) "
51
+ f"and ogtt_performed='{YES}'"
52
+ ),
53
+ ),
54
+ ]
@@ -0,0 +1,20 @@
1
+ from django_db_views.db_view import DBView
2
+ from edc_qareports.model_mixins import (
3
+ OnStudyMissingValuesModelMixin,
4
+ QaReportModelMixin,
5
+ qa_reports_permissions,
6
+ )
7
+
8
+ from .view_definition import get_view_definition
9
+
10
+
11
+ class OnStudyMissingValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
12
+
13
+ view_definition = get_view_definition()
14
+
15
+ class Meta:
16
+ managed = False
17
+ db_table = "onstudy_missing_values_view"
18
+ verbose_name = "Missing values for on-study patient"
19
+ verbose_name_plural = "Missing values for on-study patients"
20
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,17 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+ from .qa_cases import qa_cases
4
+
5
+
6
+ def get_view_definition() -> dict:
7
+ subquery = " UNION ".join([qa_case.sql for qa_case in qa_cases])
8
+ sql_view = SqlViewGenerator(
9
+ report_model="onstudy_missing_values_view",
10
+ ordering=["subject_identifier", "site_id"],
11
+ )
12
+
13
+ return {
14
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
15
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
16
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
17
+ }
@@ -0,0 +1 @@
1
+ from .unmanaged_model import PatientHistoryMissingBaselineCd4
@@ -0,0 +1,31 @@
1
+ from django.db import models
2
+ from django_db_views.db_view import DBView
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+ from .view_definition import get_view_definition
6
+
7
+
8
+ class PatientHistoryMissingBaselineCd4(QaReportModelMixin, DBView):
9
+
10
+ visit_code = models.CharField(max_length=25)
11
+
12
+ visit_code_sequence = models.IntegerField()
13
+
14
+ cd4 = models.IntegerField(verbose_name="Last CD4")
15
+
16
+ cd4_date = models.DateField(verbose_name="Date of last CD4")
17
+
18
+ user_created = models.CharField(max_length=25)
19
+
20
+ user_modified = models.CharField(max_length=25)
21
+
22
+ modified = models.DateTimeField()
23
+
24
+ view_definition = get_view_definition()
25
+
26
+ class Meta:
27
+ managed = False
28
+ db_table = "patient_history_missing_baseline_cd4_view"
29
+ verbose_name = "Patient History: Missing Baseline Cd4"
30
+ verbose_name_plural = "Missing Baseline Cd4"
31
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,21 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+
4
+ def get_view_definition() -> dict:
5
+ subquery = """
6
+ select subject_identifier, v.visit_code, v.visit_code_sequence,cd4,
7
+ cd4_date, crf.site_id, crf.user_created, crf.user_modified,
8
+ crf.modified
9
+ from meta_subject_patienthistory as crf
10
+ left join meta_subject_subjectvisit as v on crf.subject_visit_id=v.id
11
+ where cd4 is null or cd4_date is null
12
+ """
13
+ sql_view = SqlViewGenerator(
14
+ report_model="meta_reports.patienthistorymissingbaselinecd4",
15
+ ordering=["subject_identifier", "site_id"],
16
+ )
17
+ return {
18
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
19
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
20
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
21
+ }
@@ -0,0 +1 @@
1
+ from .unmanaged_model import UnattendedThreeInRow
@@ -0,0 +1,29 @@
1
+ from django.db import models
2
+ from django_db_views.db_view import DBView
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+ from .view_definition import get_view_definition
6
+
7
+
8
+ class UnattendedThreeInRow(QaReportModelMixin, DBView):
9
+
10
+ appt_datetime = models.DateTimeField()
11
+
12
+ first_value = models.CharField(verbose_name="First", max_length=25)
13
+
14
+ second_value = models.CharField(verbose_name="Second", max_length=25)
15
+
16
+ third_value = models.CharField(verbose_name="Third", max_length=25)
17
+
18
+ interval_days = models.IntegerField()
19
+
20
+ from_now_days = models.IntegerField()
21
+
22
+ view_definition = get_view_definition()
23
+
24
+ class Meta:
25
+ managed = False
26
+ db_table = "unattended_three_in_row_view"
27
+ verbose_name = "R100: Unattended appointments: Three in a row"
28
+ verbose_name_plural = "R100: Unattended appointments: Three in a row"
29
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,31 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+
4
+ def get_view_definition() -> dict:
5
+ subquery = """
6
+ select subject_identifier, site_id, appt_datetime, `first_value`,
7
+ `second_value`, `third_value`,
8
+ datediff(`third_date`, `first_date`) as `interval_days`,
9
+ datediff(now(), `first_date`) as `from_now_days`
10
+ from (
11
+ select subject_identifier, site_id, appt_datetime,
12
+ FIRST_VALUE(visit_code) OVER w as `first_value`,
13
+ NTH_VALUE(visit_code, 2) OVER w as `second_value`,
14
+ NTH_VALUE(visit_code, 3) OVER w as `third_value`,
15
+ FIRST_VALUE(appt_datetime) OVER w as `first_date`,
16
+ NTH_VALUE(appt_datetime, 3) OVER w as `third_date`
17
+ from edc_appointment_appointment where visit_code_sequence=0 and appt_status="New"
18
+ and appt_datetime <= now()
19
+ WINDOW w as (PARTITION BY subject_identifier order by appt_datetime ROWS UNBOUNDED PRECEDING)
20
+ ) as B
21
+ where `second_value` is not null and `third_value` is not null
22
+ """ # noqa
23
+ sql_view = SqlViewGenerator(
24
+ report_model="meta_reports.unattendedthreeinrow",
25
+ ordering=["subject_identifier", "site_id"],
26
+ )
27
+ return {
28
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
29
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
30
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
31
+ }
@@ -0,0 +1 @@
1
+ from .unmanaged_model import UnattendedThreeInRow2
@@ -0,0 +1,29 @@
1
+ from django.db import models
2
+ from django_db_views.db_view import DBView
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+ from .view_definition import get_view_definition
6
+
7
+
8
+ class UnattendedThreeInRow2(QaReportModelMixin, DBView):
9
+
10
+ first_value = models.CharField(verbose_name="First", max_length=25)
11
+
12
+ second_value = models.CharField(verbose_name="Second", max_length=25)
13
+
14
+ third_value = models.CharField(verbose_name="Third", max_length=25)
15
+
16
+ interval_days = models.IntegerField()
17
+
18
+ from_now_days = models.IntegerField()
19
+
20
+ missed_count = models.IntegerField()
21
+
22
+ view_definition = get_view_definition()
23
+
24
+ class Meta:
25
+ managed = False
26
+ db_table = "unattended_three_in_row2_view"
27
+ verbose_name = "R110: Unattended appointments: Three in a row (with missed)"
28
+ verbose_name_plural = "R110: Unattended appointments: Three in a row (with missed)"
29
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,50 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+
4
+ def get_view_definition() -> dict:
5
+ subquery = """select distinct subject_identifier, site_id, `first_value`, `second_value`, `third_value`,
6
+ datediff(`third_date`, `first_date`) as interval_days,
7
+ datediff(now(), `first_date`) as from_now_days,
8
+ `first_status`, `second_status`, `third_status`, sum(missed) as missed_count
9
+ from (
10
+ select subject_identifier,site_id,appt_datetime, `missed`,
11
+ FIRST_VALUE(appt_status) OVER w as `third_status`,
12
+ NTH_VALUE(appt_status, 2) OVER w as `second_status`,
13
+ NTH_VALUE(appt_status, 3) OVER w as `first_status`,
14
+ FIRST_VALUE(visit_code) OVER w as `third_value`,
15
+ NTH_VALUE(visit_code, 2) OVER w as `second_value`,
16
+ NTH_VALUE(visit_code, 3) OVER w as `first_value`,
17
+ FIRST_VALUE(appt_datetime) OVER w as `third_date`,
18
+ NTH_VALUE(appt_datetime, 2) OVER w as `second_date`,
19
+ NTH_VALUE(appt_datetime, 3) OVER w as `first_date`
20
+ from appointments
21
+ WINDOW w as (PARTITION BY subject_identifier order by appt_datetime desc ROWS UNBOUNDED PRECEDING)
22
+ ) as B
23
+ where `second_value` is not null and `third_value` is not null
24
+ and `first_status`="New"
25
+ and `second_status`="New"
26
+ and `third_status` ="New"
27
+ group by subject_identifier, site_id, `first_value`, `second_value`, `third_value`,
28
+ datediff(`third_date`, `first_date`),
29
+ datediff(now(), `first_date`),
30
+ `first_status`, `second_status`, `third_status`
31
+ order by subject_identifier, site_id""" # noqa
32
+
33
+ with_stmt = """with appointments as (select subject_identifier, site_id, visit_code, visit_code_sequence,
34
+ appt_datetime, case when appt_timing="missed" then "New" else appt_status end as `appt_status`,
35
+ case when appt_timing="missed" then 1 else 0 end as `missed`
36
+ from edc_appointment_appointment
37
+ where visit_code_sequence=0 and appt_datetime<=now()
38
+ order by subject_identifier, appt_datetime)""" # noqa
39
+
40
+ sql_view = SqlViewGenerator(
41
+ with_stmt=with_stmt,
42
+ report_model="meta_reports.unattendedthreeinrow2",
43
+ ordering=["subject_identifier", "site_id"],
44
+ )
45
+
46
+ return {
47
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
48
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
49
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
50
+ }
@@ -0,0 +1 @@
1
+ from .unmanaged_model import UnattendedTwoInRow
@@ -0,0 +1,27 @@
1
+ from django.db import models
2
+ from django_db_views.db_view import DBView
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+ from .view_definition import get_view_definition
6
+
7
+
8
+ class UnattendedTwoInRow(QaReportModelMixin, DBView):
9
+
10
+ appt_datetime = models.DateTimeField()
11
+
12
+ first_value = models.CharField(verbose_name="First", max_length=25)
13
+
14
+ second_value = models.CharField(verbose_name="Second", max_length=25)
15
+
16
+ interval_days = models.IntegerField()
17
+
18
+ from_now_days = models.IntegerField()
19
+
20
+ view_definition = get_view_definition()
21
+
22
+ class Meta:
23
+ managed = False
24
+ db_table = "unattended_two_in_row_view"
25
+ verbose_name = "R120: Unattended appointments: Two in a row"
26
+ verbose_name_plural = "R120: Unattended appointments: Two in a row"
27
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,30 @@
1
+ from edc_qareports.sql_generator import SqlViewGenerator
2
+
3
+
4
+ def get_view_definition() -> dict:
5
+ subquery = """
6
+ select subject_identifier, site_id, appt_datetime, `first_value`, `second_value`,
7
+ datediff(`second_date`, `first_date`) as interval_days,
8
+ datediff(now(), `first_date`) as from_now_days
9
+ from (
10
+ select subject_identifier ,site_id, appt_datetime,
11
+ FIRST_VALUE(visit_code) OVER w as `first_value`,
12
+ NTH_VALUE(visit_code, 2) OVER w as `second_value`,
13
+ NTH_VALUE(visit_code, 3) OVER w as `third_value`,
14
+ FIRST_VALUE(appt_datetime) OVER w as `first_date`,
15
+ NTH_VALUE(appt_datetime, 2) OVER w as `second_date`
16
+ from edc_appointment_appointment where visit_code_sequence=0 and appt_status="New"
17
+ and appt_datetime <= now()
18
+ WINDOW w as (PARTITION BY subject_identifier order by appt_datetime ROWS UNBOUNDED PRECEDING)
19
+ ) as B
20
+ where `second_value` is not null and `third_value` is null""" # noqa
21
+
22
+ sql_view = SqlViewGenerator(
23
+ report_model="meta_reports.unattendedtwoinrow",
24
+ ordering=["site_id", "~from_now_days"],
25
+ )
26
+ return {
27
+ "django.db.backends.mysql": sql_view.as_mysql(subquery),
28
+ "django.db.backends.postgresql": sql_view.as_postgres(subquery),
29
+ "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
30
+ }
@@ -0,0 +1,31 @@
1
+ from django.db import models
2
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
3
+
4
+
5
+ class Endpoints(QaReportModelMixin, models.Model):
6
+ """A QA report model updated using an admin
7
+ action or manually.
8
+ """
9
+
10
+ visit_code = models.IntegerField(null=True)
11
+
12
+ fasting = models.CharField(max_length=10, null=True)
13
+
14
+ fbg_date = models.DateField(null=True)
15
+
16
+ fbg_value = models.FloatField(null=True)
17
+
18
+ ogtt_value = models.FloatField(null=True)
19
+
20
+ endpoint_label = models.CharField(max_length=250, null=True)
21
+
22
+ baseline_date = models.DateField(null=True)
23
+
24
+ offstudy_date = models.DateField(null=True)
25
+
26
+ offstudy_reason = models.CharField(max_length=250, null=True)
27
+
28
+ class Meta(QaReportModelMixin.Meta):
29
+ verbose_name = "Endpoints (DM)"
30
+ verbose_name_plural = "Endpoints (DM)"
31
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,11 @@
1
+ from edc_qareports.model_mixins import qa_reports_permissions
2
+
3
+ from .endpoints import Endpoints
4
+
5
+
6
+ class EndpointsProxy(Endpoints):
7
+ class Meta:
8
+ proxy = True
9
+ verbose_name = "Endpoints (DM): All"
10
+ verbose_name_plural = "Endpoints (DM): All"
11
+ default_permissions = qa_reports_permissions
@@ -0,0 +1,34 @@
1
+ from django.db import models
2
+ from django_pandas.managers import DataFrameManager
3
+ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
4
+
5
+
6
+ class LastImpRefill(QaReportModelMixin, models.Model):
7
+
8
+ reference_date = models.DateField(null=True)
9
+
10
+ imp_visit_code = models.FloatField(null=True)
11
+
12
+ imp_visit_date = models.DateField(null=True)
13
+
14
+ next_visit_code = models.FloatField(null=True)
15
+
16
+ next_appt_date = models.DateField(null=True)
17
+
18
+ visit_code = models.CharField(max_length=15, null=True)
19
+
20
+ visit_code_sequence = models.IntegerField(null=True)
21
+
22
+ days_since = models.IntegerField(null=True)
23
+
24
+ days_until = models.IntegerField(null=True)
25
+
26
+ objects = DataFrameManager()
27
+
28
+ def recreate_db_view(self, **kwargs):
29
+ raise NotImplementedError()
30
+
31
+ class Meta(QaReportModelMixin.Meta):
32
+ verbose_name = "Last IMP Refill"
33
+ verbose_name_plural = "Last IMP Refills"
34
+ default_permissions = qa_reports_permissions