meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

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  1. meta_ae/action_items.py +2 -1
  2. meta_ae/admin/__init__.py +11 -0
  3. meta_ae/admin/ae_susar_admin.py +1 -1
  4. meta_ae/admin/death_report_admin.py +1 -1
  5. meta_ae/admin/modeladmin_mixins.py +10 -12
  6. meta_ae/baker_recipes.py +3 -3
  7. meta_ae/forms/__init__.py +13 -0
  8. meta_ae/forms/modelform_mixins.py +2 -2
  9. meta_ae/migrations/0001_initial.py +27 -27
  10. meta_ae/migrations/0006_aelocalreview_aesponsorreview.py +5 -5
  11. meta_ae/migrations/0022_historicalhospitalization_hospitalization.py +5 -13
  12. meta_ae/migrations/0023_alter_aefollowup_action_identifier_and_more.py +2017 -0
  13. meta_ae/model_mixins/__init__.py +2 -0
  14. meta_ae/model_mixins/ae_review_model_mixin.py +6 -6
  15. meta_ae/model_mixins/death_report_model_mixin.py +3 -3
  16. meta_ae/models/__init__.py +13 -0
  17. meta_ae/models/hospitalization.py +3 -3
  18. meta_ae/pdf_reports/__init__.py +2 -0
  19. meta_analytics/.DS_Store +0 -0
  20. meta_analytics/dataframes/__init__.py +24 -0
  21. meta_analytics/dataframes/get_eos_df.py +1 -2
  22. meta_analytics/dataframes/get_glucose_df.py +6 -7
  23. meta_analytics/dataframes/get_glucose_fbg_df.py +2 -3
  24. meta_analytics/dataframes/get_glucose_fbg_ogtt_df.py +1 -2
  25. meta_analytics/dataframes/get_last_imp_visits_df.py +5 -6
  26. meta_analytics/dataframes/glucose_endpoints/__init__.py +2 -0
  27. meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py +13 -20
  28. meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py +9 -10
  29. meta_analytics/dataframes/screening/__init__.py +2 -0
  30. meta_analytics/dataframes/screening/get_glucose_tested_only_df.py +1 -2
  31. meta_analytics/dataframes/screening/get_screening_df.py +6 -10
  32. meta_analytics/dataframes/utils.py +3 -8
  33. meta_analytics/get_tables.py +1 -2
  34. meta_analytics/tables/__init__.py +2 -0
  35. meta_consent/action_items.py +2 -1
  36. meta_consent/admin/__init__.py +6 -0
  37. meta_consent/admin/actions/__init__.py +2 -0
  38. meta_consent/admin/actions/create_missing_prescriptions.py +1 -1
  39. meta_consent/admin/list_filters.py +2 -2
  40. meta_consent/admin/modeladmin_mixins.py +3 -4
  41. meta_consent/admin/subject_consent_v1_ext_admin.py +2 -2
  42. meta_consent/baker_recipes.py +7 -8
  43. meta_consent/form_validators/__init__.py +2 -0
  44. meta_consent/forms/__init__.py +7 -0
  45. meta_consent/forms/subject_consent_v1_ext_form.py +2 -3
  46. meta_consent/forms/subject_reconsent_form.py +4 -4
  47. meta_consent/management/commands/create_missing_prescriptions.py +4 -2
  48. meta_consent/migrations/0001_initial.py +9 -9
  49. meta_consent/migrations/0024_historicalsubjectconsentv1.py +3 -8
  50. meta_consent/migrations/0026_historicalsubjectconsentv1ext_subjectconsentv1ext.py +5 -14
  51. meta_consent/migrations/0032_alter_historicalsubjectconsent_device_created_and_more.py +678 -0
  52. meta_consent/models/__init__.py +9 -0
  53. meta_consent/models/model_mixins.py +1 -2
  54. meta_consent/models/signals.py +9 -10
  55. meta_consent/models/subject_consent.py +1 -1
  56. meta_consent/models/subject_reconsent.py +3 -3
  57. meta_dashboard/patterns.py +1 -1
  58. meta_dashboard/templatetags/meta_dashboard_extras.py +1 -1
  59. meta_dashboard/view_utils/__init__.py +7 -0
  60. meta_dashboard/view_utils/subject_screening_button.py +9 -16
  61. meta_dashboard/views/__init__.py +8 -0
  62. meta_dashboard/views/ae/__init__.py +2 -0
  63. meta_dashboard/views/ae/ae_listboard_view.py +1 -1
  64. meta_dashboard/views/ae/death_report_listboard_view.py +1 -1
  65. meta_dashboard/views/screening/__init__.py +2 -0
  66. meta_dashboard/views/subject/__init__.py +2 -0
  67. meta_dashboard/views/subject/dashboard/__init__.py +2 -0
  68. meta_dashboard/views/subject/dashboard/dashboard_view.py +1 -1
  69. meta_dashboard/views/subject/listboard/__init__.py +2 -0
  70. meta_edc/__init__.py +5 -9
  71. meta_edc/celery.py +1 -1
  72. meta_edc/celery_live.py +1 -1
  73. meta_edc/celery_uat.py +1 -1
  74. meta_edc/management/commands/update_forms_reference.py +10 -12
  75. meta_edc/settings/debug.py +5 -4
  76. meta_edc/settings/defaults.py +18 -3
  77. meta_edc/settings/live.py +3 -1
  78. meta_edc/settings/logging.py +9 -4
  79. meta_edc/settings/minimal.py +4 -5
  80. meta_edc/settings/uat.py +3 -1
  81. meta_edc/views/__init__.py +2 -0
  82. meta_edc-1.1.12.dist-info/METADATA +174 -0
  83. {meta_edc-1.1.8.dist-info → meta_edc-1.1.12.dist-info}/RECORD +413 -526
  84. meta_edc-1.1.12.dist-info/WHEEL +4 -0
  85. meta_lists/migrations/0020_alter_abnormalfootappearanceobservations_extra_value_and_more.py +404 -0
  86. meta_pharmacy/admin/__init__.py +5 -0
  87. meta_pharmacy/admin/substitutions_admin.py +2 -2
  88. meta_pharmacy/forms/__init__.py +2 -0
  89. meta_pharmacy/forms/substitutions_form.py +6 -4
  90. meta_pharmacy/labels/__init__.py +4 -2
  91. meta_pharmacy/labels/draw_label_for_subject_with_barcode.py +1 -2
  92. meta_pharmacy/labels/draw_label_with_test_data.py +2 -2
  93. meta_pharmacy/labels/label_data.py +1 -2
  94. meta_pharmacy/labels/print_sheets.py +4 -6
  95. meta_pharmacy/migrations/0002_initial.py +7 -20
  96. meta_pharmacy/migrations/0003_auto_20240909_2335.py +3 -2
  97. meta_pharmacy/migrations/0006_lotnumber_label.py +5 -14
  98. meta_pharmacy/migrations/0008_remove_lotnumber_medication_and_more.py +5 -6
  99. meta_pharmacy/migrations/0010_alter_historicallabeldata_device_created_and_more.py +382 -0
  100. meta_pharmacy/models/__init__.py +7 -0
  101. meta_pharmacy/models/label_data.py +4 -5
  102. meta_pharmacy/models/substitutions.py +3 -3
  103. meta_pharmacy/prepare_meta_pharmacy.py +1 -1
  104. meta_pharmacy/utils/__init__.py +2 -0
  105. meta_pharmacy/utils/update_initial_pharmacy_data.py +1 -1
  106. meta_prn/admin/__init__.py +16 -0
  107. meta_prn/admin/dm_referral_admin.py +2 -1
  108. meta_prn/admin/end_of_study_admin.py +6 -7
  109. meta_prn/admin/loss_to_followup_admin.py +3 -2
  110. meta_prn/admin/off_study_medication_admin.py +5 -6
  111. meta_prn/admin/offschedule_admin.py +5 -6
  112. meta_prn/admin/offschedule_dm_referral_admin.py +6 -6
  113. meta_prn/admin/offschedule_postnatal_admin.py +7 -7
  114. meta_prn/admin/offschedule_pregnancy_admin.py +8 -7
  115. meta_prn/admin/onschedule_admin.py +7 -8
  116. meta_prn/admin/onschedule_dm_referral_admin.py +6 -7
  117. meta_prn/admin/pregnancy_notification_admin.py +5 -6
  118. meta_prn/admin/protocol_incident_admin.py +1 -1
  119. meta_prn/admin/subject_transfer_admin.py +1 -1
  120. meta_prn/baker_recipes.py +4 -4
  121. meta_prn/form_validators/__init__.py +5 -0
  122. meta_prn/form_validators/end_of_study.py +2 -2
  123. meta_prn/forms/__init__.py +13 -0
  124. meta_prn/migrations/0001_initial.py +25 -25
  125. meta_prn/migrations/0017_auto_20220307_1929.py +5 -5
  126. meta_prn/migrations/0018_auto_20220309_2106.py +9 -9
  127. meta_prn/migrations/0021_auto_20220316_2147.py +13 -13
  128. meta_prn/migrations/0022_auto_20220318_0133.py +9 -9
  129. meta_prn/migrations/0032_historicalegfrnotification_egfrnotification.py +5 -13
  130. meta_prn/migrations/0038_alter_endofstudy_delivery_date_and_more.py +5 -13
  131. meta_prn/migrations/0041_endofstudy_transfer_date_and_more.py +5 -13
  132. meta_prn/migrations/0057_historicalonscheduledmreferral_and_more.py +13 -38
  133. meta_prn/migrations/0067_alter_offschedule_managers_and_more.py +2557 -0
  134. meta_prn/models/__init__.py +20 -0
  135. meta_prn/models/offschedule.py +4 -4
  136. meta_prn/models/protocol_incident.py +1 -1
  137. meta_prn/models/subject_transfer.py +8 -0
  138. meta_rando/migrations/0001_initial.py +5 -5
  139. meta_rando/migrations/0006_alter_historicalrandomizationlist_allocated_user_and_more.py +130 -0
  140. meta_reports/__init__.py +2 -0
  141. meta_reports/admin/__init__.py +16 -0
  142. meta_reports/admin/dbviews/__init__.py +13 -0
  143. meta_reports/admin/dbviews/glucose_summary_admin.py +6 -6
  144. meta_reports/admin/dbviews/imp_substitutions_admin.py +12 -11
  145. meta_reports/admin/dbviews/missing_screening_ogtt_admin/__init__.py +5 -0
  146. meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py +27 -3
  147. meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py +6 -6
  148. meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py +2 -0
  149. meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py +0 -3
  150. meta_reports/admin/dbviews/on_study_missing_values_admin/__init__.py +2 -0
  151. meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py +8 -8
  152. meta_reports/admin/dbviews/unattended_three_in_row2_admin.py +6 -6
  153. meta_reports/admin/dbviews/unattended_three_in_row_admin.py +5 -5
  154. meta_reports/admin/dbviews/unattended_two_in_row_admin.py +5 -5
  155. meta_reports/admin/endpoints_admin.py +1 -1
  156. meta_reports/admin/last_imp_refill_admin.py +9 -9
  157. meta_reports/admin/list_filters.py +2 -2
  158. meta_reports/admin/modeladmin_mixins.py +9 -16
  159. meta_reports/death_report.py +1 -1
  160. meta_reports/forms/__init__.py +2 -0
  161. meta_reports/forms/missing_ogtt_note_form.py +2 -3
  162. meta_reports/management/commands/generate_endpoints.py +5 -4
  163. meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py +5 -14
  164. meta_reports/migrations/0059_alter_endpoints_created_and_more.py +161 -0
  165. meta_reports/models/__init__.py +17 -0
  166. meta_reports/models/dbviews/__init__.py +14 -0
  167. meta_reports/models/dbviews/glucose_summary/__init__.py +2 -0
  168. meta_reports/models/dbviews/glucose_summary/unmanaged_model.py +4 -5
  169. meta_reports/models/dbviews/imp_substitutions/__init__.py +2 -0
  170. meta_reports/models/dbviews/imp_substitutions/view_definition.py +1 -1
  171. meta_reports/models/dbviews/missing_screening_ogtt/__init__.py +2 -0
  172. meta_reports/models/dbviews/missing_screening_ogtt/note_model.py +1 -1
  173. meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py +4 -3
  174. meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py +2 -0
  175. meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py +13 -11
  176. meta_reports/models/dbviews/on_study_missing_values/__init__.py +2 -0
  177. meta_reports/models/dbviews/on_study_missing_values/qa_cases.py +18 -0
  178. meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py +2 -0
  179. meta_reports/models/dbviews/unattended_three_in_row/__init__.py +2 -0
  180. meta_reports/models/dbviews/unattended_three_in_row2/__init__.py +2 -0
  181. meta_reports/models/dbviews/unattended_two_in_row/__init__.py +2 -0
  182. meta_reports/models/endpoints.py +4 -4
  183. meta_reports/models/last_imp_refill.py +2 -3
  184. meta_reports/pdf_report.py +2 -2
  185. meta_reports/tasks.py +1 -1
  186. meta_screening/admin/__init__.py +8 -0
  187. meta_screening/admin/fieldsets.py +13 -14
  188. meta_screening/admin/list_filters.py +6 -4
  189. meta_screening/admin/screening_part_one_admin.py +1 -2
  190. meta_screening/admin/screening_part_three_admin.py +2 -3
  191. meta_screening/admin/screening_part_two_admin.py +7 -10
  192. meta_screening/admin/subject_refusal_admin.py +5 -3
  193. meta_screening/admin/subject_screening_admin.py +4 -4
  194. meta_screening/baker_recipes.py +9 -9
  195. meta_screening/eligibility/__init__.py +9 -0
  196. meta_screening/eligibility/eligibility.py +7 -7
  197. meta_screening/eligibility/eligibility_part_three/__init__.py +2 -0
  198. meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py +8 -8
  199. meta_screening/eligibility/eligibility_part_three/eligibility_part_three_phase_three.py +13 -14
  200. meta_screening/form_validators/__init__.py +8 -0
  201. meta_screening/forms/__init__.py +20 -0
  202. meta_screening/forms/field_lists.py +16 -17
  203. meta_screening/forms/screening_part_one_form.py +2 -2
  204. meta_screening/forms/screening_part_three_form.py +5 -3
  205. meta_screening/forms/screening_part_two_form.py +1 -5
  206. meta_screening/forms/subject_refusal_form.py +0 -4
  207. meta_screening/forms/subject_screening_form.py +0 -4
  208. meta_screening/migrations/0001_initial.py +15 -15
  209. meta_screening/migrations/0010_auto_20191106_0828.py +5 -5
  210. meta_screening/migrations/0068_alter_historicalscreeningpartone_acute_condition_and_more.py +1579 -0
  211. meta_screening/model_mixins/__init__.py +8 -0
  212. meta_screening/model_mixins/eligibility_model_mixin.py +5 -3
  213. meta_screening/model_mixins/part_one_fields_model_mixin.py +5 -9
  214. meta_screening/model_mixins/part_three_fields_model_mixin.py +5 -6
  215. meta_screening/model_mixins/part_two_fields_model_mixin.py +18 -16
  216. meta_screening/models/__init__.py +9 -0
  217. meta_screening/models/icp_referral.py +5 -5
  218. meta_screening/models/signals.py +10 -11
  219. meta_screening/models/subject_refusal.py +1 -1
  220. meta_screening/models/subject_screening.py +1 -3
  221. meta_subject/action_items.py +13 -15
  222. meta_subject/admin/__init__.py +39 -0
  223. meta_subject/admin/birth_outcome_admin.py +4 -8
  224. meta_subject/admin/blood_results/__init__.py +9 -0
  225. meta_subject/admin/blood_results/blood_results_fbc_admin.py +1 -1
  226. meta_subject/admin/blood_results/blood_results_hba1c_admin.py +1 -1
  227. meta_subject/admin/blood_results/blood_results_ins_admin.py +1 -1
  228. meta_subject/admin/blood_results/blood_results_lft_admin.py +1 -1
  229. meta_subject/admin/blood_results/blood_results_lipids_admin.py +1 -1
  230. meta_subject/admin/blood_results/blood_results_rft_admin.py +3 -5
  231. meta_subject/admin/complications_glycemia_admin.py +1 -1
  232. meta_subject/admin/delivery_admin.py +7 -10
  233. meta_subject/admin/diabetes/__init__.py +2 -0
  234. meta_subject/admin/diabetes/dm_endpoint_admin.py +2 -2
  235. meta_subject/admin/diabetes/dm_followup_admin.py +3 -2
  236. meta_subject/admin/egfr_drop_notification_admin.py +1 -1
  237. meta_subject/admin/followup_examination_admin.py +10 -9
  238. meta_subject/admin/followup_vitals_admin.py +4 -5
  239. meta_subject/admin/glucose_admin.py +2 -4
  240. meta_subject/admin/glucose_fbg_admin.py +1 -3
  241. meta_subject/admin/health_economics/__init__.py +2 -0
  242. meta_subject/admin/health_economics/health_economics_simple_admin.py +1 -1
  243. meta_subject/admin/health_economics/health_economics_update_admin.py +1 -1
  244. meta_subject/admin/hepatitis_test_admin.py +1 -1
  245. meta_subject/admin/list_filters.py +1 -1
  246. meta_subject/admin/mnsi_admin.py +7 -5
  247. meta_subject/admin/other_arv_regimens_admin.py +3 -3
  248. meta_subject/admin/patient_history_admin.py +4 -4
  249. meta_subject/admin/physical_exam_admin.py +1 -1
  250. meta_subject/admin/pregnancy_update_admin.py +1 -1
  251. meta_subject/admin/study_medication_admin.py +8 -15
  252. meta_subject/admin/subject_requisition_admin.py +1 -1
  253. meta_subject/admin/subject_visit_admin.py +1 -1
  254. meta_subject/admin/subject_visit_missed_admin.py +1 -1
  255. meta_subject/admin/urine_dipstick_test_admin.py +1 -1
  256. meta_subject/admin/urine_pregnancy_admin.py +1 -1
  257. meta_subject/baker_recipes.py +15 -15
  258. meta_subject/form_validators/__init__.py +11 -0
  259. meta_subject/form_validators/delivery_form_validator.py +2 -3
  260. meta_subject/form_validators/dm_endpoint_form_validator.py +1 -1
  261. meta_subject/form_validators/dm_followup_form_validator.py +7 -6
  262. meta_subject/form_validators/glucose_form_validator.py +3 -5
  263. meta_subject/forms/__init__.py +41 -0
  264. meta_subject/forms/blood_results/__init__.py +9 -0
  265. meta_subject/forms/blood_results/blood_results_rft_form.py +1 -2
  266. meta_subject/forms/diabetes/__init__.py +2 -0
  267. meta_subject/forms/diabetes/dm_followup_form.py +2 -2
  268. meta_subject/forms/followup_vitals_form.py +3 -8
  269. meta_subject/forms/health_economics/__init__.py +2 -0
  270. meta_subject/forms/next_appointment_form.py +2 -3
  271. meta_subject/forms/slider_widget.py +1 -1
  272. meta_subject/forms/study_medication_form.py +11 -8
  273. meta_subject/management/commands/create_missing_refills.py +3 -3
  274. meta_subject/management/commands/create_missing_rx.py +1 -1
  275. meta_subject/management/commands/missed.py +20 -23
  276. meta_subject/metadata_rules/__init__.py +2 -0
  277. meta_subject/metadata_rules/predicates.py +25 -32
  278. meta_subject/migrations/0001_initial.py +61 -61
  279. meta_subject/migrations/0002_auto_20191021_0353.py +5 -5
  280. meta_subject/migrations/0012_auto_20200118_2334.py +5 -5
  281. meta_subject/migrations/0014_auto_20200120_1622.py +5 -5
  282. meta_subject/migrations/0018_coronakap_historicalcoronakap.py +5 -5
  283. meta_subject/migrations/0033_auto_20200516_2356.py +5 -5
  284. meta_subject/migrations/0038_auto_20200520_0020.py +5 -5
  285. meta_subject/migrations/0040_auto_20200527_2155.py +1 -1
  286. meta_subject/migrations/0045_auto_20200530_1801.py +1 -1
  287. meta_subject/migrations/0051_auto_20200617_2117.py +5 -5
  288. meta_subject/migrations/0063_auto_20210715_0337.py +5 -5
  289. meta_subject/migrations/0066_auto_20210721_0335.py +9 -9
  290. meta_subject/migrations/0067_auto_20210726_0340.py +5 -5
  291. meta_subject/migrations/0068_auto_20210728_1809.py +5 -5
  292. meta_subject/migrations/0072_auto_20210805_1545.py +7 -7
  293. meta_subject/migrations/0073_auto_20210809_0055.py +5 -5
  294. meta_subject/migrations/0077_auto_20210809_2323.py +3 -3
  295. meta_subject/migrations/0082_auto_20210823_1612.py +3 -3
  296. meta_subject/migrations/0083_auto_20210823_1620.py +3 -3
  297. meta_subject/migrations/0088_auto_20210924_0027.py +5 -5
  298. meta_subject/migrations/0090_auto_20210924_0424.py +5 -5
  299. meta_subject/migrations/0093_auto_20211117_0352.py +5 -5
  300. meta_subject/migrations/0095_auto_20220128_1719.py +5 -5
  301. meta_subject/migrations/0098_auto_20220309_2106.py +5 -5
  302. meta_subject/migrations/0101_auto_20220316_2147.py +13 -13
  303. meta_subject/migrations/0115_historicalegfrnotification_egfrnotification.py +5 -13
  304. meta_subject/migrations/0164_dmreferralfollowup_historicaldmreferralfollowup.py +5 -5
  305. meta_subject/migrations/0172_remove_historicalbloodresultsglu_action_item_and_more.py +1 -2
  306. meta_subject/migrations/0177_alter_bloodresultslft_alp_value_and_more.py +1 -2
  307. meta_subject/migrations/0178_historicalhealtheconomicsupdate_and_more.py +5 -14
  308. meta_subject/migrations/0186_healtheconomicsupdate_singleton_field_and_more.py +1 -2
  309. meta_subject/migrations/0187_dmdiagnosis_historicaldmdiagnosis_dmdxresult_and_more.py +5 -14
  310. meta_subject/migrations/0188_historicaldmdxresult_dmdxresult.py +5 -14
  311. meta_subject/migrations/0209_remove_historicaldmdxresult_dm_diagnosis_and_more.py +1 -2
  312. meta_subject/migrations/0216_historicalnextappointment_nextappointment.py +5 -6
  313. meta_subject/migrations/0220_historicalbloodresultsgludummy_bloodresultsgludummy.py +5 -14
  314. meta_subject/migrations/0227_alter_followupvitals_waist_circumference_comment_and_more.py +97 -0
  315. meta_subject/migrations/0228_bloodresultshba1c_hba1c_datetime_and_more.py +9297 -0
  316. meta_subject/model_mixins/__init__.py +8 -0
  317. meta_subject/model_mixins/search_slug_model_mixin.py +1 -2
  318. meta_subject/model_mixins/vitals_fields_model_mixin.py +1 -1
  319. meta_subject/models/__init__.py +48 -0
  320. meta_subject/models/birth_outcomes.py +3 -3
  321. meta_subject/models/blood_results/__init__.py +11 -0
  322. meta_subject/models/delivery.py +3 -3
  323. meta_subject/models/diabetes/__init__.py +2 -0
  324. meta_subject/models/diabetes/dm_endpoint.py +4 -4
  325. meta_subject/models/diabetes/dm_followup.py +3 -4
  326. meta_subject/models/diet_and_lifestyle.py +2 -2
  327. meta_subject/models/followup_examination.py +11 -11
  328. meta_subject/models/glucose.py +4 -4
  329. meta_subject/models/glucose_fbg.py +2 -3
  330. meta_subject/models/health_economics/__init__.py +2 -0
  331. meta_subject/models/health_economics/health_economics.py +7 -7
  332. meta_subject/models/health_economics/health_economics_update.py +2 -1
  333. meta_subject/models/hepatitis_test.py +2 -2
  334. meta_subject/models/other_arv_regimens_detail.py +1 -1
  335. meta_subject/models/patient_history.py +5 -6
  336. meta_subject/models/physical_exam.py +2 -2
  337. meta_subject/models/pregnancy_update.py +1 -1
  338. meta_subject/models/signals.py +14 -12
  339. meta_subject/models/subject_visit.py +1 -1
  340. meta_subject/models/urine_dipstick_test.py +1 -1
  341. meta_subject/models/urine_pregnancy.py +1 -1
  342. meta_visit_schedule/visit_schedules/__init__.py +2 -0
  343. meta_visit_schedule/visit_schedules/phase_three/__init__.py +2 -0
  344. meta_visit_schedule/visit_schedules/phase_three/schedule.py +2 -2
  345. meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py +1 -2
  346. meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py +1 -2
  347. meta_ae/tests/holidays.csv +0 -15
  348. meta_ae/tests/tests/test_actions.py +0 -126
  349. meta_ae/tests/urls.py +0 -10
  350. meta_analytics/dataframes/glucose_endpoints/utils.py +0 -0
  351. meta_analytics/notebooks/anu.ipynb +0 -95
  352. meta_analytics/notebooks/appointment_planning.ipynb +0 -329
  353. meta_analytics/notebooks/arvs.ipynb +0 -103
  354. meta_analytics/notebooks/cleaning/__init__.py +0 -0
  355. meta_analytics/notebooks/cleaning/consent_v1_ext.ipynb +0 -227
  356. meta_analytics/notebooks/cleaning/offschedule_eos.ipynb +0 -353
  357. meta_analytics/notebooks/dsmc/renal_dysfunction.ipynb +0 -435
  358. meta_analytics/notebooks/endpoints/meta_endpoints_by_date.ipynb +0 -656
  359. meta_analytics/notebooks/followup_examination.ipynb +0 -141
  360. meta_analytics/notebooks/hba1c.ipynb +0 -136
  361. meta_analytics/notebooks/hiv_regimens.ipynb +0 -429
  362. meta_analytics/notebooks/incidence.ipynb +0 -232
  363. meta_analytics/notebooks/liver.ipynb +0 -389
  364. meta_analytics/notebooks/magreth.ipynb +0 -645
  365. meta_analytics/notebooks/monitoring_report.ipynb +0 -1834
  366. meta_analytics/notebooks/pharmacy.ipynb +0 -1061
  367. meta_analytics/notebooks/pharmacy_stock_202410.ipynb +0 -306
  368. meta_analytics/notebooks/qa.ipynb +0 -273
  369. meta_analytics/notebooks/steering.ipynb +0 -61
  370. meta_analytics/notebooks/undiagnosed/meta3_screening_consort_chart.ipynb +0 -1176
  371. meta_analytics/notebooks/undiagnosed/meta3_screening_undiagnosed.ipynb +0 -519
  372. meta_analytics/notebooks/undiagnosed/meta_screening_table2.ipynb +0 -964
  373. meta_analytics/notebooks/undiagnosed/screen_undiagnosed_or.ipynb +0 -296
  374. meta_analytics/notebooks/undiagnosed/screening.ipynb +0 -273
  375. meta_analytics/notebooks/undiagnosed/screening2.ipynb +0 -958
  376. meta_analytics/notebooks/undiagnosed/screening_undiagnosed_20241002.ipynb +0 -958
  377. meta_analytics/notebooks/ven.ipynb +0 -191
  378. meta_analytics/notebooks/vitals.ipynb +0 -263
  379. meta_analytics/tests/__init__.py +0 -0
  380. meta_analytics/tests/test_endpoints_by_date.py +0 -94
  381. meta_consent/tests/__init__.py +0 -0
  382. meta_consent/tests/holidays.csv +0 -15
  383. meta_consent/tests/tests/__init__.py +0 -0
  384. meta_consent/tests/tests/test_form_validators.py +0 -110
  385. meta_consent/tests/tests/test_subject_consent.py +0 -10
  386. meta_consent/tests/urls.py +0 -17
  387. meta_dashboard/tests/__init__.py +0 -0
  388. meta_dashboard/tests/admin.py +0 -22
  389. meta_dashboard/tests/holidays.csv +0 -15
  390. meta_dashboard/tests/tests/__init__.py +0 -0
  391. meta_dashboard/tests/urls.py +0 -55
  392. meta_edc/tests/__init__.py +0 -0
  393. meta_edc/tests/tests/__init__.py +0 -0
  394. meta_edc/tests/tests/test_endpoints.py +0 -555
  395. meta_edc-1.1.8.dist-info/METADATA +0 -767
  396. meta_edc-1.1.8.dist-info/WHEEL +0 -5
  397. meta_edc-1.1.8.dist-info/licenses/AUTHORS.rst +0 -8
  398. meta_edc-1.1.8.dist-info/top_level.txt +0 -20
  399. meta_labs/tests/__init__.py +0 -0
  400. meta_labs/tests/test_labs.py +0 -27
  401. meta_labs/tests/test_reportables.py +0 -70
  402. meta_labs/tests/urls.py +0 -4
  403. meta_lists/tests/__init__.py +0 -0
  404. meta_lists/tests/test_lists.py +0 -8
  405. meta_pharmacy/notebooks/pharmacy.ipynb +0 -41
  406. meta_prn/tests/__init__.py +0 -0
  407. meta_prn/tests/tests/__init__.py +0 -0
  408. meta_prn/tests/tests/test_actions.py +0 -97
  409. meta_prn/tests/tests/test_dm_referral.py +0 -203
  410. meta_prn/tests/tests/test_eos_events.py +0 -134
  411. meta_prn/tests/tests/test_manager_order.py +0 -14
  412. meta_prn/tests/tests/test_pregnancy_notification.py +0 -93
  413. meta_prn/tests/urls.py +0 -10
  414. meta_rando/tests/__init__.py +0 -0
  415. meta_rando/tests/tests/__init__.py +0 -0
  416. meta_rando/tests/tests/test_randomizers.py +0 -57
  417. meta_reports/tests/__init__.py +0 -0
  418. meta_reports/tests/test_reports.py +0 -35
  419. meta_reports/tests/test_sql_gen.py +0 -5
  420. meta_reports/tests/urls.py +0 -4
  421. meta_screening/offline_models.py +0 -3
  422. meta_screening/tests/__init__.py +0 -0
  423. meta_screening/tests/holidays.csv +0 -15
  424. meta_screening/tests/meta_test_case_mixin.py +0 -234
  425. meta_screening/tests/options.py +0 -127
  426. meta_screening/tests/tests/__init__.py +0 -0
  427. meta_screening/tests/tests/test_forms.py +0 -404
  428. meta_screening/tests/tests/test_screening_part_one.py +0 -108
  429. meta_screening/tests/tests/test_screening_part_three.py +0 -433
  430. meta_screening/tests/tests/test_screening_part_two.py +0 -84
  431. meta_sites/tests/__init__.py +0 -0
  432. meta_sites/tests/test_sites.py +0 -12
  433. meta_sites/tests/urls.py +0 -4
  434. meta_stats/__init__.py +0 -0
  435. meta_stats/incidence.py +0 -16
  436. meta_stats/models.py +0 -0
  437. meta_stats/tests/__init__.py +0 -0
  438. meta_stats/tests/tests/__init__.py +0 -0
  439. meta_stats/tests/tests/test_incidence.py +0 -10
  440. meta_subject/tests/__init__.py +0 -0
  441. meta_subject/tests/holidays.csv +0 -15
  442. meta_subject/tests/tests/__init__.py +0 -0
  443. meta_subject/tests/tests/test_egfr.py +0 -234
  444. meta_subject/tests/tests/test_fixes.py +0 -64
  445. meta_subject/tests/tests/test_followup.py +0 -52
  446. meta_subject/tests/tests/test_manager_order.py +0 -11
  447. meta_subject/tests/tests/test_medication_adherence.py +0 -79
  448. meta_subject/tests/tests/test_metadata_rules.py +0 -135
  449. meta_subject/tests/tests/test_mnsi.py +0 -341
  450. meta_subject/tests/tests/test_next_appointment.py +0 -231
  451. meta_subject/tests/tests/test_patient_history_form.py +0 -74
  452. meta_subject/tests/tests/test_physical_exam.py +0 -84
  453. meta_subject/tests/tests/test_sf12.py +0 -161
  454. meta_subject/tests/tests/test_study_medication.py +0 -229
  455. meta_subject/tests/urls.py +0 -24
  456. meta_visit_schedule/tests/__init__.py +0 -0
  457. meta_visit_schedule/tests/tests/__init__.py +0 -0
  458. meta_visit_schedule/tests/tests/test_schedule.py +0 -181
  459. meta_visit_schedule/tests/urls.py +0 -4
  460. tests/__init__.py +0 -0
  461. tests/etc/randomization_list.csv +0 -241
  462. tests/etc/randomization_list_phase_three.csv +0 -241
  463. tests/etc/user-aes-local.key +0 -0
  464. tests/etc/user-aes-restricted.key +0 -1
  465. tests/etc/user-rsa-local-private.pem +0 -27
  466. tests/etc/user-rsa-local-public.pem +0 -9
  467. tests/etc/user-rsa-restricted-private.pem +0 -27
  468. tests/etc/user-rsa-restricted-public.pem +0 -9
  469. tests/etc/user-salt-local.key +0 -0
  470. tests/etc/user-salt-restricted.key +0 -0
  471. tests/holidays.csv +0 -15
  472. tests/test_settings.py +0 -185
  473. {meta_edc-1.1.8.dist-info → meta_edc-1.1.12.dist-info}/licenses/LICENSE +0 -0
  474. /meta_ae/tests/__init__.py → /meta_subject/management/__init__py.py +0 -0
  475. /meta_ae/tests/tests/__init__.py → /meta_subject/management/commands/__init__py.py +0 -0
@@ -1,103 +0,0 @@
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- {
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- "cells": [
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "0",
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- "metadata": {},
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- "outputs": [],
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- "source": []
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "1",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "%%capture\n",
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- "import os\n",
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- "import pandas as pd\n",
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- "import numpy as np\n",
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- "from dj_notebook import activate\n",
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- "from pathlib import Path\n",
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- "\n",
25
- "env_file = os.environ[\"META_ENV\"]\n",
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- "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
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- "reports_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
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- "plus = activate(dotenv_file=env_file)"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "2",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "from edc_pdutils.dataframes import get_crf"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "3",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_patient_history = get_crf(\"meta_subject.patienthistory\", subject_visit_model=\"meta_subject.subjectvisit\")"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "4",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_patient_history[['subject_identifier', \"current_arv_regimen\"]].groupby(by=[\"current_arv_regimen\"])[\"current_arv_regimen\"].value_counts()"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "5",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_patient_history[['subject_identifier', \"current_arv_regimen\", \"other_current_arv_regimen\"]][[ \"other_current_arv_regimen\"]].value_counts()"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "6",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_patient_history[ \"other_current_arv_regimen\"] = df_patient_history[ \"other_current_arv_regimen\"].apply(lambda x : x.split(\"-\")[0])"
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- ]
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- }
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- ],
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- "metadata": {
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- "kernelspec": {
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- "display_name": "Python 3",
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- "language": "python",
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- "name": "python3"
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- },
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- "language_info": {
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- "codemirror_mode": {
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- "name": "ipython",
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- "version": 2
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- },
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- "file_extension": ".py",
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- "mimetype": "text/x-python",
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- "name": "python",
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- "nbconvert_exporter": "python",
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- "pygments_lexer": "ipython2",
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- "version": "2.7.6"
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- }
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- },
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- "nbformat": 4,
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File without changes
@@ -1,227 +0,0 @@
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- {
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- "cells": [
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "0",
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- "metadata": {},
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- "outputs": [],
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- "source": []
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "1",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "%%capture\n",
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- "import pandas as pd\n",
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- "from django_pandas.io import read_frame\n",
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- "from pathlib import Path\n",
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- "from dj_notebook import activate\n",
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- "\n",
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- "plus = activate(dotenv_file=\"/Users/erikvw/source/edc_source/meta-edc/.env\")\n",
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- "report_folder = Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/reports/\")\n",
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- "# output is suppressed -- normally would spew out all the edc loading messages\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "2",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "from edc_registration.models import RegisteredSubject\n",
37
- "from edc_appointment.analytics import get_appointment_df\n",
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- "from meta_prn.models import OnSchedule, OffSchedule, OffSchedulePregnancy, OffSchedulePostnatal, OnScheduleDmReferral, \\\n",
39
- " EndOfStudy\n",
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- "\n",
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- "df_onschedule = read_frame(OnSchedule.objects.all(), verbose=True)\n",
42
- "df_offschedule = read_frame(OffSchedule.objects.all(), verbose=True)\n",
43
- "df_onschedule_preg = read_frame(OffSchedulePregnancy.objects.all(), verbose=True)\n",
44
- "df_onschedule_postnatal = read_frame(OffSchedulePostnatal.objects.all(), verbose=True)\n",
45
- "df_onschedule_dm = read_frame(OnScheduleDmReferral.objects.all(), verbose=True)\n",
46
- "df_eos = read_frame(EndOfStudy.objects.all(), verbose=True)\n",
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- "df_appt = get_appointment_df()\n",
48
- "df_rs = read_frame(RegisteredSubject.objects.values(\"subject_identifier\", \"registration_datetime\").all(), verbose=True)\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "3",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_appt[df_appt.visit_code > 1360][[\"visit_code\", \"schedule_name\"]].schedule_name.value_counts()"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "4",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_appt[(df_appt.visit_code > 1360) & (df_appt.schedule_name == \"schedule\")][[\"visit_code\", \"schedule_name\"]].visit_code.value_counts()"
69
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "5",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_appt[(df_appt.visit_code > 1360) & (df_appt.schedule_name == \"schedule\")][[\"subject_identifier\", \"appt_datetime\", \"visit_code\", \"appt_status\"]].sort_values(\"subject_identifier\")"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "6",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_appt = get_appointment_df()\n",
89
- "\n",
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- "df_appt = df_appt[(df_appt.visit_code >= 1360) & (df_appt.schedule_name == \"schedule\")][[\"subject_identifier\", \"appt_datetime\", \"visit_code\", \"appt_status\"]]"
91
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "7",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_magreth = pd.read_csv(Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/reports/\") / \"consented_v1_ext_magreth.csv\")\n"
101
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "8",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_magreth"
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "9",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main = pd.merge(df_appt[[\"subject_identifier\", \"appt_datetime\", \"visit_code\", \"appt_status\"]], df_magreth, on=\"subject_identifier\", how=\"right\").groupby([\"subject_identifier\", \"agreed\"]).agg({\"visit_code\": \"min\", \"date_reconsented\": \"max\"})"
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "10",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main = df_main.merge(df_appt[[\"subject_identifier\", \"visit_code\", \"appt_status\", \"appt_datetime\"]], on=[\"subject_identifier\", \"visit_code\"], how=\"left\")\n",
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- "df_main\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "11",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_rs"
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "12",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "from meta_consent.models import SubjectConsentV1Ext\n",
152
- "df_v1ext = read_frame(SubjectConsentV1Ext.objects.values(\"subject_identifier\", \"report_datetime\", \"agrees_to_extension\").all(), verbose=True)\n",
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- "df_v1ext"
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- },
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- {
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- "execution_count": null,
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- "id": "13",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main = df_main.merge(df_rs, on=\"subject_identifier\", how=\"left\")"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "14",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main = df_main.merge(df_v1ext, on=\"subject_identifier\", how=\"outer\")\n",
174
- "df_main.rename(columns={\"report_datetime\": \"v1_ext_datetime\", \"agrees_to_extension\": \"agreed\", \"visit_code\": \"last_visit_code\"}, inplace=True)\n"
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- },
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- {
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- "execution_count": null,
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- "id": "15",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main = df_main.merge(df_eos[[\"subject_identifier\", \"offstudy_datetime\"]], on=\"subject_identifier\", how=\"left\")\n"
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "16",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_main[[\"subject_identifier\",\"registration_datetime\", \"last_visit_code\", \"appt_status\", \"appt_datetime\", \"date_reconsented\", \"v1_ext_datetime\", \"agreed\"]]"
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- ]
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "source": []
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- }
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- "metadata": {
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- "kernelspec": {
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- "language": "python",
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- "codemirror_mode": {
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- "name": "ipython",
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- },
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- "file_extension": ".py",
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- "mimetype": "text/x-python",
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- "name": "python",
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- "nbconvert_exporter": "python",
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- "pygments_lexer": "ipython2",
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- "version": "2.7.6"
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- }
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- },
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- "nbformat": 4,
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- "nbformat_minor": 5
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- }
@@ -1,353 +0,0 @@
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- {
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- "cells": [
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "0",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "%%capture\n",
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- "import pandas as pd\n",
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- "from django_pandas.io import read_frame\n",
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- "from pathlib import Path\n",
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- "from dj_notebook import activate\n",
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- "\n",
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- "plus = activate(dotenv_file=\"/Users/erikvw/source/edc_source/meta-edc/.env\")\n",
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- "report_folder = Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/reports/\")\n",
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- "# output is suppressed -- normally would spew out all the edc loading messages\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "1",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "from meta_prn.models import OnSchedule, OffSchedule, EndOfStudy, OffSchedulePostnatal, OffSchedulePregnancy, \\\n",
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- " OnScheduleDmReferral, OffStudyMedication\n",
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- "from meta_lists.models import OffstudyReasons\n",
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- "from meta_analytics.dataframes import GlucoseEndpointsByDate"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "2",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_onschedule = read_frame(OnSchedule.objects.all(), verbose=True)\n",
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- "df_offschedule = read_frame(OffSchedule.objects.all(), verbose=True)\n",
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- "df_onschedule_preg = read_frame(OffSchedulePregnancy.objects.all(), verbose=True)\n",
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- "df_onschedule_postnatal = read_frame(OffSchedulePostnatal.objects.all(), verbose=True)\n",
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- "df_onschedule_dm = read_frame(OnScheduleDmReferral.objects.all(), verbose=True)\n",
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- "df_offstudy_medication = read_frame(OffStudyMedication.objects.all(), verbose=True)\n",
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- "\n",
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- "df_eos = read_frame(EndOfStudy.objects.values(\"id\", \"subject_identifier\", \"offstudy_datetime\",\"offstudy_reason\", \"other_offstudy_reason\", \"action_item__action_type__name\", \"parent_action_item__action_type__name\").all(), verbose=False)\n",
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- "df_eos.rename(columns={\"offstudy_reason\": \"offstudy_reason_id\", \"action_item__action_type__name\": \"action_item_name\", \"parent_action_item__action_type__name\": \"parent_action_item_name\"}, inplace=True)\n",
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- "\n",
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- "df_offstudy_reasons = read_frame(OffstudyReasons.objects.all(), verbose=False)\n",
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- "df_offstudy_reasons.rename(columns={\"id\": \"offstudy_reason_id\", \"name\": \"offstudy_reason\", \"display_name\": \"offstudy_reason_display\"}, inplace=True)"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "3",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "# merge df_eos with offstudyreasons\n",
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- "df_eos = df_eos.merge(df_offstudy_reasons[[\"offstudy_reason_id\", \"offstudy_reason\", \"offstudy_reason_display\"]], on=\"offstudy_reason_id\")\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "4",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "# summarize offstudy\n",
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- "df_eos_summary = df_eos[[\"offstudy_reason_id\", \"offstudy_reason\"]].value_counts().to_frame().reset_index().sort_values(\"offstudy_reason_id\", ascending=True).reset_index(drop=True)\n",
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- "df_eos_summary.rename(columns={\"count\": \"subtotal\"}, inplace=True)\n",
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- "df_eos_summary[\"cumfreq\"] = df_eos_summary.subtotal.cumsum()\n",
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- "df_eos_summary\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "5",
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- "metadata": {},
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- "outputs": [],
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- "source": []
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- },
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- {
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- "cell_type": "markdown",
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- "id": "6",
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- "metadata": {},
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- "source": [
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- "* Need to validate that all subjects off study went off study medication first.\n",
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- "* Action items are linked to this flow and block the EndOfStudy.save() if EndOfStudy was submitted before this workflow was implemented.\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "7",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "# df_eos[df_eos.offstudy_reason_id==11][[\"subject_identifier\", \"offstudy_reason_id\", \"other_offstudy_reason\"]]\n",
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- "pd.merge(df_eos, df_offstudy_medication[[\"subject_identifier\", \"stop_date\"]], on=\"subject_identifier\", how=\"left\")\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "8",
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- "metadata": {},
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- "outputs": [],
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- "source": []
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "9",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_onschedule_preg"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "10",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_dm = df_onschedule_dm[[\"subject_identifier\"]].copy()\n",
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- "df_dm.reset_index(drop=True, inplace=True)\n",
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- "df_dm[\"dm\"] =1\n",
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- "\n",
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- "df_preg = df_onschedule_preg[[\"subject_identifier\"]].copy()\n",
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- "df_preg[\"preg\"] = 1\n",
139
- "df_preg.reset_index(drop=True, inplace=True)\n",
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- "#\n",
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- "df_eos = df_eos[[\"subject_identifier\", \"offstudy_datetime\", \"offstudy_reason\", \"other_offstudy_reason\"]].copy()\n",
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- "df_eos[\"eos\"] = 1\n",
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- "df_eos.reset_index(drop=True, inplace=True)\n",
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- "\n",
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- "df = df_onschedule[[\"subject_identifier\", \"onschedule_datetime\"]].copy()\n",
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- "df[\"onschedule\"] = 1\n",
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- "df.reset_index(drop=True, inplace=True)\n",
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- "\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "11",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "# df[df.offstudy_reason.isna()]"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "12",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df = df.merge(df_dm, on=[\"subject_identifier\"], how=\"left\", suffixes=(\"\", \"_y\"))\n",
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- "df = df.merge(df_preg, on=[\"subject_identifier\"], how=\"left\", suffixes=(\"\", \"_y\"))\n"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "13",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_offschedule = df_offschedule[[\"subject_identifier\", \"offschedule_datetime\"]].copy()\n",
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- "df_offschedule[\"offschedule\"] = 1\n",
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- "df_offschedule.reset_index(drop=True, inplace=True)\n",
182
- "df = df.merge(df_offschedule, on=[\"subject_identifier\"], how=\"left\", suffixes=(\"\", \"_y\"))\n",
183
- "df = df.merge(df_eos, on=[\"subject_identifier\"], how=\"left\", suffixes=(\"\", \"_y\"))"
184
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "14",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "cls = GlucoseEndpointsByDate()\n",
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- "cls.run()"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "15",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_endpoint = cls.df\n",
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- "df_endpoint = df_endpoint[(df_endpoint.endpoint==1)][[\"subject_identifier\", \"endpoint\"]]\n",
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- "df = df.merge(df_endpoint, on=[\"subject_identifier\"], how=\"left\", suffixes=(\"\", \"_y\"))"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "16",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df.fillna({\"dm\": 0, \"preg\":0, \"offschedule\":0, \"eos\": 0, \"endpoint\": 0}, inplace=True)"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "17",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df.dm.value_counts()"
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- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "18",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df.preg.value_counts()"
237
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "19",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df_export = df[(df.offschedule_datetime.notna()) & (df.eos==0) & ((df.dm==0) & (df.preg==0))][[\"subject_identifier\", \"onschedule_datetime\", \"offschedule_datetime\", \"onschedule\", \"offschedule\", \"dm\", \"preg\", \"endpoint\", \"eos\"]].copy()\n",
247
- "df_export.reset_index(drop=True, inplace=True)\n",
248
- "df_export[\"offschedule_datetime\"] = df_export.offschedule_datetime.dt.tz_localize(None)\n",
249
- "df_export[\"offschedule_datetime\"] = df_export.offschedule_datetime.dt.normalize()\n",
250
- "df_export[\"onschedule_datetime\"] = df_export.onschedule_datetime.dt.tz_localize(None)\n",
251
- "df_export[\"onschedule_datetime\"] = df_export.onschedule_datetime.dt.normalize()\n",
252
- "df_export.sort_values(by=[\"offschedule_datetime\"], inplace=True)\n",
253
- "df_export.to_csv(report_folder / \"offschedule_eos.csv\", index=False)"
254
- ]
255
- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "20",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df"
264
- ]
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- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "21",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "df[df.endpoint==1]"
274
- ]
275
- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "22",
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- "metadata": {},
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- "outputs": [],
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- "source": [
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- "# DM Referrals onstudy/off study\n",
284
- "df.groupby(by=[\"dm\", \"eos\"]).size().reset_index(name=\"counts\")"
285
- ]
286
- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "23",
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- "metadata": {},
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- "outputs": [],
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- "source": [
294
- "df.groupby(by=[\"preg\", \"eos\"]).size().reset_index(name=\"counts\")"
295
- ]
296
- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "24",
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- "metadata": {},
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- "outputs": [],
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- "source": [
304
- "df_eos[(df_eos.other_offstudy_reason != \"\")][[\"subject_identifier\", \"offstudy_reason\", \"other_offstudy_reason\"]]"
305
- ]
306
- },
307
- {
308
- "cell_type": "code",
309
- "execution_count": null,
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- "id": "25",
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- "metadata": {},
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- "outputs": [],
313
- "source": [
314
- "df_eos.offstudy_reason.value_counts()"
315
- ]
316
- },
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- {
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- "cell_type": "code",
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- "execution_count": null,
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- "id": "26",
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- "metadata": {},
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- "outputs": [],
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- "source": [
324
- "df_eos = read_frame(EndOfStudy.objects.all(), verbose=False)\n",
325
- "df_offstudy_reasons = read_frame(OffstudyReasons.objects.all(), verbose=False)\n",
326
- "df_offstudy_reasons.rename(columns={\"id\": \"offstudy_reason_id\", \"name\": \"offstudy_reason\"}, inplace=True)\n",
327
- "df_eos = df_eos.merge(df_offstudy_reasons[\"offstudy_reason_id\", \"offstudy_reason\"], on=\"offstudy_reason_id\")\n",
328
- "df_eos.offstudy_reason.value_counts()"
329
- ]
330
- }
331
- ],
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- "metadata": {
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- "kernelspec": {
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- "display_name": "Python 3",
335
- "language": "python",
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- "name": "python3"
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- },
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- "language_info": {
339
- "codemirror_mode": {
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- "name": "ipython",
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- "version": 2
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- },
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- "file_extension": ".py",
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- "mimetype": "text/x-python",
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- "name": "python",
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- "nbconvert_exporter": "python",
347
- "pygments_lexer": "ipython2",
348
- "version": "2.7.6"
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- }
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- },
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- "nbformat": 4,
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- "nbformat_minor": 5
353
- }