meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- meta_ae/action_items.py +38 -27
- meta_ae/admin/__init__.py +11 -0
- meta_ae/admin/ae_initial_admin.py +5 -2
- meta_ae/admin/ae_susar_admin.py +1 -1
- meta_ae/admin/death_report_admin.py +1 -1
- meta_ae/admin/modeladmin_mixins.py +14 -15
- meta_ae/baker_recipes.py +4 -6
- meta_ae/choices.py +1 -1
- meta_ae/forms/__init__.py +13 -0
- meta_ae/forms/death_report_form.py +1 -1
- meta_ae/forms/modelform_mixins.py +2 -2
- meta_ae/list_data.py +1 -1
- meta_ae/migrations/0001_initial.py +27 -27
- meta_ae/migrations/0006_aelocalreview_aesponsorreview.py +5 -5
- meta_ae/migrations/0017_auto_20221130_2257.py +1 -1
- meta_ae/migrations/0022_historicalhospitalization_hospitalization.py +5 -13
- meta_ae/migrations/0023_alter_aefollowup_action_identifier_and_more.py +2017 -0
- meta_ae/model_mixins/__init__.py +2 -0
- meta_ae/model_mixins/ae_review_model_mixin.py +6 -6
- meta_ae/model_mixins/death_report_model_mixin.py +3 -3
- meta_ae/models/__init__.py +13 -0
- meta_ae/models/hospitalization.py +3 -3
- meta_ae/pdf_reports/__init__.py +2 -0
- meta_ae/templatetags/meta_ae_extras.py +4 -6
- meta_analytics/.DS_Store +0 -0
- meta_analytics/README.rst +1 -2
- meta_analytics/dataframes/__init__.py +27 -0
- meta_analytics/dataframes/constants.py +5 -2
- meta_analytics/dataframes/get_eos_df.py +16 -4
- meta_analytics/dataframes/get_glucose_df.py +166 -0
- meta_analytics/dataframes/get_glucose_fbg_df.py +26 -0
- meta_analytics/dataframes/get_glucose_fbg_ogtt_df.py +21 -0
- meta_analytics/dataframes/get_last_imp_visits_df.py +12 -10
- meta_analytics/dataframes/glucose_endpoints/__init__.py +2 -0
- meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py +125 -124
- meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py +111 -235
- meta_analytics/dataframes/screening/__init__.py +2 -0
- meta_analytics/dataframes/screening/get_glucose_tested_only_df.py +1 -2
- meta_analytics/dataframes/screening/get_screening_df.py +9 -15
- meta_analytics/dataframes/utils.py +21 -12
- meta_analytics/get_tables.py +1 -2
- meta_analytics/tables/__init__.py +2 -0
- meta_analytics/tables/enrolled/glucose.py +2 -1
- meta_analytics/utils.py +81 -0
- meta_auth/auths.py +1 -1
- meta_consent/action_items.py +22 -3
- meta_consent/admin/__init__.py +7 -0
- meta_consent/admin/actions/__init__.py +2 -0
- meta_consent/admin/actions/create_missing_prescriptions.py +2 -2
- meta_consent/admin/list_filters.py +22 -0
- meta_consent/admin/modeladmin_mixins.py +4 -5
- meta_consent/admin/subject_consent_v1_ext_admin.py +93 -0
- meta_consent/baker_recipes.py +7 -7
- meta_consent/consents.py +15 -2
- meta_consent/constants.py +1 -0
- meta_consent/form_validators/__init__.py +2 -0
- meta_consent/forms/__init__.py +8 -0
- meta_consent/forms/subject_consent_v1_ext_form.py +47 -0
- meta_consent/forms/subject_reconsent_form.py +4 -4
- meta_consent/management/commands/create_missing_prescriptions.py +5 -3
- meta_consent/migrations/0001_initial.py +9 -9
- meta_consent/migrations/0024_historicalsubjectconsentv1.py +3 -8
- meta_consent/migrations/0026_historicalsubjectconsentv1ext_subjectconsentv1ext.py +535 -0
- meta_consent/migrations/0027_auto_20250111_0344.py +30 -0
- meta_consent/migrations/0028_historicalsubjectconsentv1ext_assessment_score_and_more.py +162 -0
- meta_consent/migrations/0029_alter_historicalsubjectconsentv1ext_agrees_to_extension_and_more.py +33 -0
- meta_consent/migrations/0030_auto_20250120_2114.py +40 -0
- meta_consent/migrations/0031_alter_historicalsubjectconsent_guardian_name_and_more.py +124 -0
- meta_consent/migrations/0032_alter_historicalsubjectconsent_device_created_and_more.py +678 -0
- meta_consent/migrations/0033_historicalsubjectconsentspfq_subjectconsentspfq.py +615 -0
- meta_consent/migrations/0034_remove_subjectconsentspfq_site_and_more.py +23 -0
- meta_consent/migrations/0035_alter_historicalsubjectconsent_consent_definition_name_and_more.py +43 -0
- meta_consent/models/__init__.py +10 -0
- meta_consent/models/model_mixins.py +1 -2
- meta_consent/models/signals.py +25 -11
- meta_consent/models/subject_consent.py +2 -2
- meta_consent/models/subject_consent_v1.py +0 -1
- meta_consent/models/subject_consent_v1_ext.py +34 -0
- meta_consent/models/subject_reconsent.py +4 -4
- meta_dashboard/navbars.py +2 -6
- meta_dashboard/patterns.py +1 -1
- meta_dashboard/templates/meta_dashboard/{bootstrap3/buttons → buttons}/eligibility_button.html +1 -1
- meta_dashboard/templates/meta_dashboard/{bootstrap3/buttons → buttons}/screening_button.html +1 -1
- meta_dashboard/templates/meta_dashboard/subject/dashboard/sidebar.html +24 -0
- meta_dashboard/templates/meta_dashboard/{bootstrap3/subject → subject}/dashboard/top_bar.html +1 -1
- meta_dashboard/templates/meta_dashboard/subject/dashboard.html +14 -0
- meta_dashboard/templatetags/meta_dashboard_extras.py +9 -14
- meta_dashboard/urls.py +5 -5
- meta_dashboard/view_utils/__init__.py +13 -0
- meta_dashboard/view_utils/subject_screening_button.py +13 -20
- meta_dashboard/views/__init__.py +8 -0
- meta_dashboard/views/ae/__init__.py +2 -0
- meta_dashboard/views/ae/ae_listboard_view.py +1 -1
- meta_dashboard/views/ae/death_report_listboard_view.py +1 -1
- meta_dashboard/views/screening/__init__.py +2 -0
- meta_dashboard/views/screening/listboard_view.py +2 -3
- meta_dashboard/views/subject/__init__.py +2 -0
- meta_dashboard/views/subject/dashboard/__init__.py +2 -0
- meta_dashboard/views/subject/dashboard/dashboard_view.py +19 -8
- meta_dashboard/views/subject/listboard/__init__.py +2 -0
- meta_dashboard/views/subject/listboard/listboard_view.py +2 -3
- meta_edc/__init__.py +5 -9
- meta_edc/admin.py +3 -4
- meta_edc/celery.py +2 -2
- meta_edc/celery_live.py +19 -0
- meta_edc/celery_uat.py +25 -0
- meta_edc/management/commands/update_forms_reference.py +16 -14
- meta_edc/meta_version.py +2 -2
- meta_edc/navbars.py +7 -5
- meta_edc/settings/debug.py +13 -4
- meta_edc/settings/defaults.py +55 -18
- meta_edc/settings/live.py +4 -1
- meta_edc/settings/logging.py +9 -4
- meta_edc/settings/minimal.py +4 -5
- meta_edc/settings/uat.py +3 -1
- meta_edc/templates/meta_edc/{bootstrap3/base.html → base.html} +1 -1
- meta_edc/templates/meta_edc/{bootstrap3/home.html → home.html} +2 -2
- meta_edc/urls.py +3 -1
- meta_edc/utils.py +3 -1
- meta_edc/views/__init__.py +2 -0
- meta_edc/views/home_view.py +1 -2
- meta_edc-1.4.0.dist-info/METADATA +174 -0
- {meta_edc-0.3.39.dist-info → meta_edc-1.4.0.dist-info}/RECORD +578 -586
- meta_edc-1.4.0.dist-info/WHEEL +4 -0
- meta_labs/list_data.py +2 -2
- meta_labs/reportables.py +80 -11
- meta_lists/list_data.py +13 -4
- meta_lists/migrations/0008_auto_20200528_1517.py +2 -2
- meta_lists/migrations/0019_auto_20250128_0143.py +48 -0
- meta_lists/migrations/0020_alter_abnormalfootappearanceobservations_extra_value_and_more.py +404 -0
- meta_pharmacy/admin/__init__.py +5 -0
- meta_pharmacy/admin/rx_admin.py +1 -0
- meta_pharmacy/admin/substitutions_admin.py +3 -3
- meta_pharmacy/constants.py +1 -1
- meta_pharmacy/forms/__init__.py +2 -0
- meta_pharmacy/forms/rx_form.py +0 -1
- meta_pharmacy/forms/substitutions_form.py +6 -4
- meta_pharmacy/labels/__init__.py +5 -2
- meta_pharmacy/labels/draw_label_for_subject_with_barcode.py +4 -1
- meta_pharmacy/labels/draw_label_with_test_data.py +2 -2
- meta_pharmacy/labels/label_data.py +1 -2
- meta_pharmacy/labels/print_sheets.py +4 -6
- meta_pharmacy/management/commands/update_initial_pharmacy_data.py +4 -3
- meta_pharmacy/migrations/0002_initial.py +7 -20
- meta_pharmacy/migrations/0003_auto_20240909_2335.py +3 -2
- meta_pharmacy/migrations/0006_lotnumber_label.py +5 -14
- meta_pharmacy/migrations/0008_remove_lotnumber_medication_and_more.py +5 -6
- meta_pharmacy/migrations/0010_alter_historicallabeldata_device_created_and_more.py +382 -0
- meta_pharmacy/models/__init__.py +7 -0
- meta_pharmacy/models/label_data.py +4 -5
- meta_pharmacy/models/rx_label.py +0 -1
- meta_pharmacy/models/substitutions.py +4 -4
- meta_pharmacy/prepare_meta_pharmacy.py +1 -1
- meta_pharmacy/utils/__init__.py +2 -0
- meta_pharmacy/utils/update_initial_pharmacy_data.py +1 -1
- meta_prn/action_items.py +44 -45
- meta_prn/admin/__init__.py +16 -0
- meta_prn/admin/dm_referral_admin.py +2 -1
- meta_prn/admin/end_of_study_admin.py +26 -15
- meta_prn/admin/loss_to_followup_admin.py +3 -2
- meta_prn/admin/off_study_medication_admin.py +5 -6
- meta_prn/admin/offschedule_admin.py +12 -11
- meta_prn/admin/offschedule_dm_referral_admin.py +11 -10
- meta_prn/admin/offschedule_postnatal_admin.py +15 -7
- meta_prn/admin/offschedule_pregnancy_admin.py +18 -9
- meta_prn/admin/onschedule_admin.py +7 -8
- meta_prn/admin/onschedule_dm_referral_admin.py +11 -12
- meta_prn/admin/pregnancy_notification_admin.py +5 -6
- meta_prn/admin/protocol_incident_admin.py +1 -1
- meta_prn/admin/subject_transfer_admin.py +1 -1
- meta_prn/baker_recipes.py +10 -10
- meta_prn/choices.py +11 -7
- meta_prn/constants.py +1 -0
- meta_prn/form_validators/__init__.py +5 -0
- meta_prn/form_validators/end_of_study.py +65 -20
- meta_prn/form_validators/protocol_incident.py +1 -1
- meta_prn/forms/__init__.py +13 -0
- meta_prn/forms/dm_referral_form.py +2 -8
- meta_prn/forms/end_of_study_form.py +1 -1
- meta_prn/forms/loss_to_followup_form.py +1 -1
- meta_prn/forms/off_study_medication_form.py +2 -2
- meta_prn/forms/offschedule_form.py +25 -0
- meta_prn/forms/pregnancy_notification_form.py +15 -17
- meta_prn/list_data.py +3 -3
- meta_prn/migrations/0001_initial.py +25 -25
- meta_prn/migrations/0017_auto_20220307_1929.py +5 -5
- meta_prn/migrations/0018_auto_20220309_2106.py +9 -9
- meta_prn/migrations/0021_auto_20220316_2147.py +13 -13
- meta_prn/migrations/0022_auto_20220318_0133.py +9 -9
- meta_prn/migrations/0032_historicalegfrnotification_egfrnotification.py +5 -13
- meta_prn/migrations/0034_auto_20220630_1110.py +1 -1
- meta_prn/migrations/0035_auto_20220630_1140.py +1 -1
- meta_prn/migrations/0038_alter_endofstudy_delivery_date_and_more.py +5 -13
- meta_prn/migrations/0041_endofstudy_transfer_date_and_more.py +5 -13
- meta_prn/migrations/0057_historicalonscheduledmreferral_and_more.py +13 -38
- meta_prn/migrations/0060_alter_onschedule_managers_and_more.py +55 -0
- meta_prn/migrations/0061_auto_20250115_2025.py +56 -0
- meta_prn/migrations/0062_alter_endofstudy_offstudy_reason_and_more.py +72 -0
- meta_prn/migrations/0063_historicaloffstudymedication_singleton_field_and_more.py +37 -0
- meta_prn/migrations/0064_auto_20250602_2143.py +18 -0
- meta_prn/migrations/0065_alter_historicaloffstudymedication_subject_identifier_and_more.py +23 -0
- meta_prn/migrations/0066_alter_historicallosstofollowup_subject_identifier_and_more.py +23 -0
- meta_prn/migrations/0067_alter_offschedule_managers_and_more.py +2557 -0
- meta_prn/migrations/0068_alter_dmreferral_referral_note_and_more.py +235 -0
- meta_prn/migrations/0069_alter_historicaloffstudymedication_singleton_field_and_more.py +37 -0
- meta_prn/models/__init__.py +20 -0
- meta_prn/models/dm_referral.py +2 -2
- meta_prn/models/end_of_study.py +28 -23
- meta_prn/models/loss_to_followup.py +8 -10
- meta_prn/models/off_study_medication.py +7 -4
- meta_prn/models/offschedule.py +4 -4
- meta_prn/models/pregnancy_notification.py +3 -5
- meta_prn/models/protocol_incident.py +5 -2
- meta_prn/models/signals.py +16 -14
- meta_prn/models/subject_transfer.py +7 -0
- meta_prn/templates/meta_prn/eos/additional_instructions.html +3 -0
- meta_prn/templates/meta_prn/offschedule/additional_instructions.html +2 -0
- meta_rando/migrations/0001_initial.py +5 -5
- meta_rando/migrations/0006_alter_historicalrandomizationlist_allocated_user_and_more.py +130 -0
- meta_rando/migrations/0007_spfqlist.py +197 -0
- meta_rando/migrations/0008_delete_spfqlist.py +16 -0
- meta_rando/models/__init__.py +1 -0
- meta_rando/{models.py → models/randomization_list.py} +3 -3
- meta_rando/randomizers.py +2 -2
- meta_reports/__init__.py +2 -0
- meta_reports/admin/__init__.py +16 -0
- meta_reports/admin/dbviews/__init__.py +13 -0
- meta_reports/admin/dbviews/glucose_summary_admin.py +7 -7
- meta_reports/admin/dbviews/imp_substitutions_admin.py +14 -13
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/__init__.py +5 -0
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py +27 -3
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py +7 -7
- meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py +2 -0
- meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py +0 -3
- meta_reports/admin/dbviews/on_study_missing_values_admin/__init__.py +2 -0
- meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py +0 -1
- meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py +9 -9
- meta_reports/admin/dbviews/unattended_three_in_row2_admin.py +6 -6
- meta_reports/admin/dbviews/unattended_three_in_row_admin.py +5 -5
- meta_reports/admin/dbviews/unattended_two_in_row_admin.py +5 -5
- meta_reports/admin/endpoints_admin.py +1 -1
- meta_reports/admin/endpoints_all_admin.py +0 -1
- meta_reports/admin/last_imp_refill_admin.py +33 -36
- meta_reports/admin/list_filters.py +3 -3
- meta_reports/admin/modeladmin_mixins.py +10 -17
- meta_reports/death_report.py +2 -2
- meta_reports/forms/__init__.py +2 -0
- meta_reports/forms/missing_ogtt_note_form.py +3 -4
- meta_reports/management/commands/generate_endpoints.py +5 -4
- meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py +5 -14
- meta_reports/migrations/0054_auto_20250422_2003.py +81 -0
- meta_reports/migrations/0055_alter_glucosesummary_table.py +17 -0
- meta_reports/migrations/0056_auto_20250422_2214.py +54 -0
- meta_reports/migrations/0057_auto_20250422_2224.py +54 -0
- meta_reports/migrations/0058_auto_20250422_2232.py +54 -0
- meta_reports/migrations/0059_alter_endpoints_created_and_more.py +161 -0
- meta_reports/migrations/0060_auto_20250926_0242.py +366 -0
- meta_reports/migrations/0061_auto_20251004_0043.py +21 -0
- meta_reports/migrations/0062_auto_20251004_0106.py +21 -0
- meta_reports/models/__init__.py +17 -0
- meta_reports/models/dbviews/__init__.py +14 -0
- meta_reports/models/dbviews/glucose_summary/__init__.py +2 -0
- meta_reports/models/dbviews/glucose_summary/unmanaged_model.py +15 -3
- meta_reports/models/dbviews/glucose_summary/view_definition.py +8 -5
- meta_reports/models/dbviews/imp_substitutions/__init__.py +2 -0
- meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py +1 -2
- meta_reports/models/dbviews/imp_substitutions/view_definition.py +1 -1
- meta_reports/models/dbviews/missing_screening_ogtt/__init__.py +2 -0
- meta_reports/models/dbviews/missing_screening_ogtt/note_model.py +2 -2
- meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py +4 -3
- meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py +2 -0
- meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py +13 -11
- meta_reports/models/dbviews/on_study_missing_lab_values/unmanged_model.py +0 -1
- meta_reports/models/dbviews/on_study_missing_values/__init__.py +2 -0
- meta_reports/models/dbviews/on_study_missing_values/qa_cases.py +19 -1
- meta_reports/models/dbviews/on_study_missing_values/unmanged_model.py +0 -1
- meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py +2 -0
- meta_reports/models/dbviews/patient_history_missing_baseline_cd4/unmanaged_model.py +0 -1
- meta_reports/models/dbviews/unattended_three_in_row/__init__.py +2 -0
- meta_reports/models/dbviews/unattended_three_in_row/unmanaged_model.py +0 -1
- meta_reports/models/dbviews/unattended_three_in_row2/__init__.py +2 -0
- meta_reports/models/dbviews/unattended_three_in_row2/unmanaged_model.py +0 -1
- meta_reports/models/dbviews/unattended_two_in_row/__init__.py +2 -0
- meta_reports/models/dbviews/unattended_two_in_row/unmanaged_model.py +0 -1
- meta_reports/models/endpoints.py +8 -4
- meta_reports/models/last_imp_refill.py +2 -3
- meta_reports/pdf_report.py +2 -2
- meta_reports/tasks.py +4 -3
- meta_reports/templates/meta_reports/columns/subject_identifier_column.html +1 -1
- meta_reports/templates/meta_reports/endpoints_all_change_list_note.html +1 -1
- meta_reports/templates/meta_reports/endpoints_change_list_note.html +1 -1
- meta_reports/templates/meta_reports/last_imp_refill/changelist_note.html +13 -0
- meta_screening/admin/__init__.py +8 -0
- meta_screening/admin/fieldsets.py +13 -15
- meta_screening/admin/list_filters.py +7 -5
- meta_screening/admin/screening_part_one_admin.py +1 -3
- meta_screening/admin/screening_part_three_admin.py +2 -3
- meta_screening/admin/screening_part_two_admin.py +7 -10
- meta_screening/admin/subject_refusal_admin.py +5 -3
- meta_screening/admin/subject_screening_admin.py +21 -10
- meta_screening/baker_recipes.py +18 -10
- meta_screening/calculators.py +1 -1
- meta_screening/choices.py +1 -1
- meta_screening/constants.py +1 -1
- meta_screening/eligibility/__init__.py +9 -0
- meta_screening/eligibility/eligibility.py +21 -14
- meta_screening/eligibility/eligibility_part_one.py +1 -1
- meta_screening/eligibility/eligibility_part_three/__init__.py +2 -0
- meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py +68 -49
- meta_screening/eligibility/eligibility_part_three/eligibility_part_three_phase_three.py +14 -15
- meta_screening/eligibility/eligibility_part_two.py +1 -1
- meta_screening/form_validators/__init__.py +8 -0
- meta_screening/form_validators/screening_part_one.py +1 -1
- meta_screening/form_validators/screening_part_three.py +6 -2
- meta_screening/form_validators/screening_part_two.py +1 -1
- meta_screening/form_validators/subject_refusal.py +1 -1
- meta_screening/forms/__init__.py +20 -0
- meta_screening/forms/field_lists.py +16 -18
- meta_screening/forms/screening_part_one_form.py +2 -2
- meta_screening/forms/screening_part_three_form.py +5 -3
- meta_screening/forms/screening_part_two_form.py +1 -5
- meta_screening/forms/subject_refusal_form.py +0 -4
- meta_screening/forms/subject_screening_form.py +0 -4
- meta_screening/migrations/0001_initial.py +15 -15
- meta_screening/migrations/0010_auto_20191106_0828.py +5 -5
- meta_screening/migrations/0012_auto_20191107_0427.py +1 -1
- meta_screening/migrations/0068_alter_historicalscreeningpartone_acute_condition_and_more.py +1579 -0
- meta_screening/model_mixins/__init__.py +8 -0
- meta_screening/model_mixins/calculated_model_mixin.py +2 -2
- meta_screening/model_mixins/creatinine_fields_model_mixin.py +1 -1
- meta_screening/model_mixins/eligibility_model_mixin.py +6 -4
- meta_screening/model_mixins/part_one_fields_model_mixin.py +16 -19
- meta_screening/model_mixins/part_three_fields_model_mixin.py +6 -7
- meta_screening/model_mixins/part_two_fields_model_mixin.py +19 -17
- meta_screening/models/__init__.py +9 -0
- meta_screening/models/icp_referral.py +5 -5
- meta_screening/models/proxy_models.py +1 -1
- meta_screening/models/signals.py +10 -11
- meta_screening/models/subject_refusal.py +1 -1
- meta_screening/models/subject_screening.py +2 -4
- meta_subject/action_items.py +18 -14
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- meta_subject/migrations/0177_alter_bloodresultslft_alp_value_and_more.py +1 -2
- meta_subject/migrations/0178_historicalhealtheconomicsupdate_and_more.py +5 -14
- meta_subject/migrations/0186_healtheconomicsupdate_singleton_field_and_more.py +1 -2
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- meta_subject/migrations/0216_historicalnextappointment_nextappointment.py +553 -0
- meta_subject/migrations/0217_alter_historicalnextappointment_appt_datetime_and_more.py +42 -0
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- meta_subject/migrations/0219_remove_historicalnextappointment_allow_create_interim_and_more.py +92 -0
- meta_subject/migrations/0220_historicalbloodresultsgludummy_bloodresultsgludummy.py +825 -0
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- meta_subject/migrations/0222_alter_historicalstudymedication_stock_codes_and_more.py +46 -0
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- meta_subject/migrations/0228_bloodresultshba1c_hba1c_datetime_and_more.py +2518 -0
- meta_subject/migrations/0229_alter_glucosefbg_consent_model_and_more.py +1918 -0
- meta_subject/migrations/0230_alter_historicaldelivery_action_identifier_and_more.py +1733 -0
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- meta_subject/migrations/0232_alter_patienthistory_concomitant_conditions_and_more.py +1170 -0
- meta_subject/migrations/0233_historicalspfq_spfq.py +1066 -0
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- meta_subject/migrations/0238_historicalhivexitreview_available_and_more.py +88 -0
- meta_subject/model_mixins/__init__.py +10 -0
- meta_subject/model_mixins/arv_history_model_mixin.py +3 -44
- meta_subject/model_mixins/arv_review_model_mixin.py +53 -0
- meta_subject/model_mixins/search_slug_model_mixin.py +1 -2
- meta_subject/model_mixins/vitals_fields_model_mixin.py +33 -0
- meta_subject/models/__init__.py +52 -0
- meta_subject/models/birth_outcomes.py +3 -3
- meta_subject/models/blood_results/__init__.py +11 -0
- meta_subject/models/blood_results/blood_results_glu.py +29 -0
- meta_subject/models/blood_results/blood_results_hba1c.py +0 -1
- meta_subject/models/blood_results/blood_results_ins.py +0 -1
- meta_subject/models/blood_results/blood_results_lft.py +0 -1
- meta_subject/models/delivery.py +4 -6
- meta_subject/models/diabetes/__init__.py +2 -0
- meta_subject/models/diabetes/dm_endpoint.py +5 -5
- meta_subject/models/diabetes/dm_followup.py +7 -8
- meta_subject/models/diet_and_lifestyle.py +2 -2
- meta_subject/models/followup_examination.py +12 -14
- meta_subject/models/glucose.py +5 -5
- meta_subject/models/glucose_fbg.py +17 -4
- meta_subject/models/health_economics/__init__.py +2 -0
- meta_subject/models/health_economics/health_economics.py +8 -8
- meta_subject/models/health_economics/health_economics_simple.py +2 -2
- meta_subject/models/health_economics/health_economics_update.py +3 -2
- meta_subject/models/hepatitis_test.py +2 -2
- meta_subject/models/hiv_exit_review.py +44 -0
- meta_subject/models/next_appointment.py +15 -0
- meta_subject/models/other_arv_regimens_detail.py +1 -1
- meta_subject/models/patient_history.py +6 -7
- meta_subject/models/physical_exam.py +2 -2
- meta_subject/models/pregnancy_update.py +1 -1
- meta_subject/models/signals.py +15 -13
- meta_subject/models/subject_visit.py +2 -2
- meta_subject/models/todo.txt +1 -1
- meta_subject/models/urine_dipstick_test.py +2 -2
- meta_subject/models/urine_pregnancy.py +1 -1
- meta_subject/static/meta_subject/slider.css +1 -1
- meta_subject/templates/meta_subject/endpoint_review_instructions.html +1 -1
- meta_subject/templates/meta_subject/widgets/slider.html +0 -1
- meta_visit_schedule/visit_schedules/__init__.py +2 -0
- meta_visit_schedule/visit_schedules/phase_three/__init__.py +2 -0
- meta_visit_schedule/visit_schedules/phase_three/crfs.py +34 -1
- meta_visit_schedule/visit_schedules/phase_three/schedule.py +4 -4
- meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py +1 -2
- meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py +2 -3
- meta_ae/tests/holidays.csv +0 -15
- meta_ae/tests/tests/test_actions.py +0 -127
- meta_ae/tests/urls.py +0 -10
- meta_analytics/dataframes/enrolled/__init__.py +0 -1
- meta_analytics/dataframes/enrolled/get_glucose_df.py +0 -122
- meta_analytics/tests/__init__.py +0 -0
- meta_analytics/tests/test_endpoints_by_date.py +0 -94
- meta_consent/tests/__init__.py +0 -0
- meta_consent/tests/holidays.csv +0 -15
- meta_consent/tests/tests/__init__.py +0 -0
- meta_consent/tests/tests/test_form_validators.py +0 -110
- meta_consent/tests/tests/test_subject_consent.py +0 -10
- meta_consent/tests/urls.py +0 -17
- meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard.html +0 -11
- meta_dashboard/tests/__init__.py +0 -0
- meta_dashboard/tests/admin.py +0 -22
- meta_dashboard/tests/holidays.csv +0 -15
- meta_dashboard/tests/tests/__init__.py +0 -0
- meta_dashboard/tests/urls.py +0 -55
- meta_edc/tests/__init__.py +0 -0
- meta_edc/tests/tests/__init__.py +0 -0
- meta_edc/tests/tests/test_endpoints.py +0 -554
- meta_edc-0.3.39.dist-info/AUTHORS +0 -0
- meta_edc-0.3.39.dist-info/METADATA +0 -766
- meta_edc-0.3.39.dist-info/WHEEL +0 -5
- meta_edc-0.3.39.dist-info/top_level.txt +0 -20
- meta_labs/tests/__init__.py +0 -0
- meta_labs/tests/test_labs.py +0 -27
- meta_labs/tests/test_reportables.py +0 -16
- meta_labs/tests/urls.py +0 -4
- meta_lists/tests/__init__.py +0 -0
- meta_lists/tests/test_lists.py +0 -8
- meta_pharmacy/admin/actions.py +0 -38
- meta_prn/tests/__init__.py +0 -0
- meta_prn/tests/tests/__init__.py +0 -0
- meta_prn/tests/tests/test_actions.py +0 -97
- meta_prn/tests/tests/test_dm_referral.py +0 -206
- meta_prn/tests/tests/test_manager_order.py +0 -14
- meta_prn/tests/tests/test_pregnancy_notification.py +0 -93
- meta_prn/tests/urls.py +0 -10
- meta_rando/tests/__init__.py +0 -0
- meta_rando/tests/tests/__init__.py +0 -0
- meta_rando/tests/tests/test_randomizers.py +0 -57
- meta_reports/tests/__init__.py +0 -0
- meta_reports/tests/test_reports.py +0 -35
- meta_reports/tests/test_sql_gen.py +0 -5
- meta_reports/tests/urls.py +0 -4
- meta_screening/offline_models.py +0 -3
- meta_screening/tests/__init__.py +0 -0
- meta_screening/tests/holidays.csv +0 -15
- meta_screening/tests/meta_test_case_mixin.py +0 -216
- meta_screening/tests/options.py +0 -127
- meta_screening/tests/tests/__init__.py +0 -0
- meta_screening/tests/tests/test_forms.py +0 -397
- meta_screening/tests/tests/test_screening_part_one.py +0 -108
- meta_screening/tests/tests/test_screening_part_three.py +0 -436
- meta_screening/tests/tests/test_screening_part_two.py +0 -84
- meta_sites/tests/__init__.py +0 -0
- meta_sites/tests/test_sites.py +0 -12
- meta_sites/tests/urls.py +0 -4
- meta_stats/__init__.py +0 -0
- meta_stats/incidence.py +0 -16
- meta_stats/models.py +0 -0
- meta_stats/tests/__init__.py +0 -0
- meta_stats/tests/tests/__init__.py +0 -0
- meta_stats/tests/tests/test_incidence.py +0 -10
- meta_subject/tests/__init__.py +0 -0
- meta_subject/tests/holidays.csv +0 -15
- meta_subject/tests/tests/__init__.py +0 -0
- meta_subject/tests/tests/test_egfr.py +0 -234
- meta_subject/tests/tests/test_fixes.py +0 -64
- meta_subject/tests/tests/test_followup.py +0 -52
- meta_subject/tests/tests/test_manager_order.py +0 -11
- meta_subject/tests/tests/test_medication_adherence.py +0 -75
- meta_subject/tests/tests/test_metadata_rules.py +0 -135
- meta_subject/tests/tests/test_mnsi.py +0 -317
- meta_subject/tests/tests/test_patient_history_form.py +0 -74
- meta_subject/tests/tests/test_physical_exam.py +0 -84
- meta_subject/tests/tests/test_sf12.py +0 -173
- meta_subject/tests/tests/test_study_medication.py +0 -230
- meta_subject/tests/urls.py +0 -24
- meta_visit_schedule/tests/__init__.py +0 -0
- meta_visit_schedule/tests/tests/__init__.py +0 -0
- meta_visit_schedule/tests/tests/test_schedule.py +0 -181
- meta_visit_schedule/tests/urls.py +0 -4
- tests/__init__.py +0 -0
- tests/etc/randomization_list.csv +0 -241
- tests/etc/randomization_list_phase_three.csv +0 -241
- tests/etc/user-aes-local.key +0 -0
- tests/etc/user-aes-restricted.key +0 -1
- tests/etc/user-rsa-local-private.pem +0 -27
- tests/etc/user-rsa-local-public.pem +0 -9
- tests/etc/user-rsa-restricted-private.pem +0 -27
- tests/etc/user-rsa-restricted-public.pem +0 -9
- tests/etc/user-salt-local.key +0 -0
- tests/etc/user-salt-restricted.key +0 -0
- tests/holidays.csv +0 -15
- tests/test_settings.py +0 -186
- /meta_ae/templates/meta_ae/{bootstrap3/ae_initial_description.html → aeinitial_description.html} +0 -0
- /meta_dashboard/templates/meta_dashboard/{bootstrap3/buttons → buttons}/add_consent_button.html +0 -0
- /meta_dashboard/templates/meta_dashboard/{bootstrap3/buttons → buttons}/dashboard_button.html +0 -0
- /meta_dashboard/templates/meta_dashboard/{bootstrap3/buttons → buttons}/refusal_button.html +0 -0
- /meta_dashboard/templates/meta_dashboard/{bootstrap3/screening → screening}/listboard.html +0 -0
- /meta_dashboard/templates/meta_dashboard/{bootstrap3/subject → subject}/listboard.html +0 -0
- {meta_edc-0.3.39.dist-info → meta_edc-1.4.0.dist-info/licenses}/LICENSE +0 -0
- /meta_ae/tests/__init__.py → /meta_subject/management/__init__py.py +0 -0
- /meta_ae/tests/tests/__init__.py → /meta_subject/management/commands/__init__py.py +0 -0
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|
-
obj.save()
|
|
45
|
-
obj.refresh_from_db()
|
|
46
|
-
|
|
47
|
-
# assert eligible for part one criteria
|
|
48
|
-
self.assertEqual(obj.eligible_part_one, YES)
|
|
49
|
-
self.assertIsNone(obj.reasons_ineligible_part_one)
|
|
50
|
-
|
|
51
|
-
# assert eligible for part two criteria
|
|
52
|
-
self.assertEqual(obj.eligible_part_two, YES)
|
|
53
|
-
self.assertIsNone(obj.reasons_ineligible_part_two)
|
|
54
|
-
|
|
55
|
-
# assert eligiblility to be determined for part three
|
|
56
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
57
|
-
self.assertIsNotNone(obj.reasons_ineligible_part_three)
|
|
58
|
-
|
|
59
|
-
self.assertFalse(obj.eligible)
|
|
60
|
-
self.assertFalse(obj.consented)
|
|
61
|
-
|
|
62
|
-
def get_screening_part_three_obj(self):
|
|
63
|
-
"""Returns an SubjectScreening obj.
|
|
64
|
-
|
|
65
|
-
Remember this is just a proxy model for SubjectScreening.
|
|
66
|
-
"""
|
|
67
|
-
return ScreeningPartThree.objects.get(
|
|
68
|
-
screening_identifier=self.screening_identifier,
|
|
69
|
-
)
|
|
70
|
-
|
|
71
|
-
def test_eligible_part_three_defaults_phase_three(self):
|
|
72
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
73
|
-
part_three_eligible_options["fbg_value"] = 6.9
|
|
74
|
-
part_three_eligible_options["ogtt_value"] = 7.8
|
|
75
|
-
self._test_eligible(part_three_eligible_options)
|
|
76
|
-
|
|
77
|
-
def _test_eligible(self, part_three_eligible_options):
|
|
78
|
-
obj = self.get_screening_part_three_obj()
|
|
79
|
-
for k, v in part_three_eligible_options.items():
|
|
80
|
-
setattr(obj, k, v)
|
|
81
|
-
obj.save()
|
|
82
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
83
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
84
|
-
|
|
85
|
-
def test_eligible_datetime_does_not_change_on_resave(self):
|
|
86
|
-
obj = self.get_screening_part_three_obj()
|
|
87
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
88
|
-
for k, v in part_three_eligible_options.items():
|
|
89
|
-
setattr(obj, k, v)
|
|
90
|
-
obj.save()
|
|
91
|
-
obj.refresh_from_db()
|
|
92
|
-
eligibility_datetime = obj.eligibility_datetime
|
|
93
|
-
obj.save()
|
|
94
|
-
obj.refresh_from_db()
|
|
95
|
-
self.assertEqual(eligibility_datetime, obj.eligibility_datetime)
|
|
96
|
-
|
|
97
|
-
def test_eligible2_phase_three(self):
|
|
98
|
-
obj = self.get_screening_part_three_obj()
|
|
99
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
100
|
-
for k, v in part_three_eligible_options.items():
|
|
101
|
-
setattr(obj, k, v)
|
|
102
|
-
obj.save()
|
|
103
|
-
obj.refresh_from_db()
|
|
104
|
-
|
|
105
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
106
|
-
|
|
107
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
108
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
109
|
-
obj.severe_htn = YES
|
|
110
|
-
obj.save()
|
|
111
|
-
obj.refresh_from_db()
|
|
112
|
-
self.assertIn("Severe HTN", obj.reasons_ineligible_part_three)
|
|
113
|
-
self.assertEqual(obj.eligible_part_three, NO)
|
|
114
|
-
obj.severe_htn = NO
|
|
115
|
-
obj.save()
|
|
116
|
-
obj.refresh_from_db()
|
|
117
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
118
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
119
|
-
|
|
120
|
-
def test_eligible2_phase_three_missing_ogtt(self):
|
|
121
|
-
obj = self.get_screening_part_three_obj()
|
|
122
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
123
|
-
for k, v in part_three_eligible_options.items():
|
|
124
|
-
setattr(obj, k, v)
|
|
125
|
-
obj.ogtt_base_datetime = None
|
|
126
|
-
obj.ogtt_datetime = None
|
|
127
|
-
obj.ogtt_units = None
|
|
128
|
-
obj.ogtt_value = None
|
|
129
|
-
obj.save()
|
|
130
|
-
obj.refresh_from_db()
|
|
131
|
-
self._test_eligible2(obj, FBG_OGTT_INCOMPLETE, FBG_OGTT)
|
|
132
|
-
|
|
133
|
-
def test_eligible2_phase_three_ogtt2_not_performed_is_ok(self):
|
|
134
|
-
obj = self.get_screening_part_three_obj()
|
|
135
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
136
|
-
for k, v in part_three_eligible_options.items():
|
|
137
|
-
setattr(obj, k, v)
|
|
138
|
-
obj.save()
|
|
139
|
-
obj.refresh_from_db()
|
|
140
|
-
obj.save()
|
|
141
|
-
obj.refresh_from_db()
|
|
142
|
-
|
|
143
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
144
|
-
|
|
145
|
-
def test_eligible2_phase_three_repeat_ogtt2_updates_converted(self):
|
|
146
|
-
obj = self.get_screening_part_three_obj()
|
|
147
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
148
|
-
for k, v in part_three_eligible_options.items():
|
|
149
|
-
setattr(obj, k, v)
|
|
150
|
-
obj.save()
|
|
151
|
-
obj.refresh_from_db()
|
|
152
|
-
|
|
153
|
-
obj.repeat_glucose_opinion = YES
|
|
154
|
-
obj.ogtt2_base_datetime = obj.ogtt_base_datetime + relativedelta(days=3)
|
|
155
|
-
obj.ogtt2_datetime = obj.ogtt_datetime + relativedelta(days=3)
|
|
156
|
-
obj.ogtt2_units = obj.ogtt_units
|
|
157
|
-
obj.ogtt2_value = 6.9
|
|
158
|
-
obj.save()
|
|
159
|
-
obj.refresh_from_db()
|
|
160
|
-
|
|
161
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
162
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
163
|
-
|
|
164
|
-
def test_eligible2_phase_three_by_repeat_ogtt(self):
|
|
165
|
-
obj = self.get_screening_part_three_obj()
|
|
166
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
167
|
-
|
|
168
|
-
for k, v in part_three_eligible_options.items():
|
|
169
|
-
setattr(obj, k, v)
|
|
170
|
-
obj.save()
|
|
171
|
-
obj.refresh_from_db()
|
|
172
|
-
|
|
173
|
-
# eligible by single OGTT
|
|
174
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
175
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
176
|
-
|
|
177
|
-
# repeat OGTT, result in range
|
|
178
|
-
# cannot just repeat OGTT2
|
|
179
|
-
obj.repeat_glucose_opinion = YES
|
|
180
|
-
obj.ogtt2_base_datetime = obj.ogtt_base_datetime + relativedelta(days=3)
|
|
181
|
-
obj.ogtt2_datetime = obj.ogtt_datetime + relativedelta(days=3)
|
|
182
|
-
obj.ogtt2_units = obj.ogtt_units
|
|
183
|
-
obj.ogtt2_value = Decimal("8.1000")
|
|
184
|
-
obj.save()
|
|
185
|
-
obj.refresh_from_db()
|
|
186
|
-
|
|
187
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
188
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
189
|
-
self.assertIsNotNone(obj.reasons_ineligible_part_three)
|
|
190
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
191
|
-
|
|
192
|
-
# also repeat the FBG
|
|
193
|
-
obj.fbg2_datetime = obj.ogtt_datetime + relativedelta(days=3)
|
|
194
|
-
obj.fbg2_units = obj.fbg_units
|
|
195
|
-
obj.fbg2_value = Decimal("6.1000")
|
|
196
|
-
obj.save()
|
|
197
|
-
obj.refresh_from_db()
|
|
198
|
-
|
|
199
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
200
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
201
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
202
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
203
|
-
|
|
204
|
-
# repeat OGTT, result too low
|
|
205
|
-
obj.ogtt2_value = Decimal("5.5000")
|
|
206
|
-
obj.save()
|
|
207
|
-
obj.refresh_from_db()
|
|
208
|
-
|
|
209
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
210
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
211
|
-
# still eligible because the FBG qualifies
|
|
212
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
213
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
214
|
-
|
|
215
|
-
# repeat FBG, result too low
|
|
216
|
-
obj.fbg2_value = Decimal("5.5000")
|
|
217
|
-
obj.save()
|
|
218
|
-
obj.refresh_from_db()
|
|
219
|
-
|
|
220
|
-
self.assertEqual(obj.converted_fbg_value, obj.fbg_value)
|
|
221
|
-
self.assertEqual(obj.converted_fbg2_value, obj.fbg2_value)
|
|
222
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
223
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
224
|
-
# not eligible because the FBG2 and OGTT2 do not qualify
|
|
225
|
-
self.assertEqual(obj.eligible_part_three, NO)
|
|
226
|
-
self.assertIsNotNone(obj.reasons_ineligible_part_three)
|
|
227
|
-
self.assertIn(NORMAL_FBG_OGTT, obj.reasons_ineligible_part_three)
|
|
228
|
-
|
|
229
|
-
obj.ogtt2_value = Decimal("7.9000")
|
|
230
|
-
obj.save()
|
|
231
|
-
obj.refresh_from_db()
|
|
232
|
-
|
|
233
|
-
self.assertEqual(obj.converted_fbg_value, obj.fbg_value)
|
|
234
|
-
self.assertEqual(obj.converted_fbg2_value, obj.fbg2_value)
|
|
235
|
-
self.assertEqual(obj.converted_ogtt_value, obj.ogtt_value)
|
|
236
|
-
self.assertEqual(obj.converted_ogtt2_value, obj.ogtt2_value)
|
|
237
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
238
|
-
self.assertIsNone(obj.reasons_ineligible_part_three)
|
|
239
|
-
|
|
240
|
-
def _test_eligible2(self, obj, incomplete_reason: str, ineligible_reason: str):
|
|
241
|
-
self.assertIsNone(obj.reasons_ineligible_part_one)
|
|
242
|
-
self.assertEqual(obj.eligible_part_one, YES)
|
|
243
|
-
self.assertIsNone(obj.reasons_ineligible_part_two)
|
|
244
|
-
self.assertEqual(obj.eligible_part_two, YES)
|
|
245
|
-
|
|
246
|
-
self.assertEqual(obj.reasons_ineligible_part_three, incomplete_reason)
|
|
247
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
248
|
-
self.assertFalse(obj.eligible)
|
|
249
|
-
self.assertFalse(obj.consented)
|
|
250
|
-
|
|
251
|
-
obj.hba1c_performed = YES
|
|
252
|
-
obj.hba1c_value = 7.0
|
|
253
|
-
obj.creatinine_performed = NO
|
|
254
|
-
obj.save()
|
|
255
|
-
|
|
256
|
-
self.assertEqual(obj.reasons_ineligible_part_three, incomplete_reason)
|
|
257
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
258
|
-
self.assertFalse(obj.eligible)
|
|
259
|
-
self.assertFalse(obj.consented)
|
|
260
|
-
|
|
261
|
-
obj.creatinine_performed = YES
|
|
262
|
-
obj.creatinine_value = 50
|
|
263
|
-
obj.creatinine_units = MICROMOLES_PER_LITER
|
|
264
|
-
obj.save()
|
|
265
|
-
|
|
266
|
-
self.assertEqual(obj.reasons_ineligible_part_three, incomplete_reason)
|
|
267
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
268
|
-
self.assertFalse(obj.eligible)
|
|
269
|
-
self.assertFalse(obj.consented)
|
|
270
|
-
|
|
271
|
-
obj.fasting = NO
|
|
272
|
-
obj.save()
|
|
273
|
-
|
|
274
|
-
self.assertEqual(obj.reasons_ineligible_part_three, incomplete_reason)
|
|
275
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
276
|
-
self.assertFalse(obj.eligible)
|
|
277
|
-
self.assertFalse(obj.consented)
|
|
278
|
-
|
|
279
|
-
obj.fasting = YES
|
|
280
|
-
obj.fasting_duration_str = "8h"
|
|
281
|
-
obj.fbg_value = 6.9
|
|
282
|
-
obj.fbg_units = MILLIMOLES_PER_LITER
|
|
283
|
-
obj.fbg_datetime = get_utcnow()
|
|
284
|
-
obj.save()
|
|
285
|
-
|
|
286
|
-
self.assertEqual(obj.reasons_ineligible_part_three, incomplete_reason)
|
|
287
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
288
|
-
self.assertFalse(obj.eligible)
|
|
289
|
-
self.assertFalse(obj.consented)
|
|
290
|
-
|
|
291
|
-
obj.ogtt_base_datetime = get_utcnow()
|
|
292
|
-
obj.ogtt_value = 3.0
|
|
293
|
-
obj.ogtt_units = MICROMOLES_PER_LITER
|
|
294
|
-
obj.ogtt_datetime = get_utcnow()
|
|
295
|
-
try:
|
|
296
|
-
obj.save()
|
|
297
|
-
except ConversionNotHandled:
|
|
298
|
-
pass
|
|
299
|
-
else:
|
|
300
|
-
self.fail("ConversionNotHandled unexpectedly not raised.")
|
|
301
|
-
|
|
302
|
-
obj.refresh_from_db()
|
|
303
|
-
obj.ogtt_units = MILLIMOLES_PER_LITER
|
|
304
|
-
obj.save()
|
|
305
|
-
|
|
306
|
-
self.assertIn(ineligible_reason, obj.reasons_ineligible_part_three)
|
|
307
|
-
self.assertEqual(obj.eligible_part_three, TBD)
|
|
308
|
-
self.assertFalse(obj.eligible)
|
|
309
|
-
self.assertFalse(obj.consented)
|
|
310
|
-
|
|
311
|
-
obj.ogtt_base_datetime = get_utcnow()
|
|
312
|
-
obj.ogtt_value = 7.8
|
|
313
|
-
obj.ogtt_units = MILLIMOLES_PER_LITER
|
|
314
|
-
obj.ogtt_datetime = get_utcnow()
|
|
315
|
-
obj.save()
|
|
316
|
-
|
|
317
|
-
self.assertFalse(obj.reasons_ineligible_part_three)
|
|
318
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
319
|
-
self.assertTrue(obj.eligible)
|
|
320
|
-
self.assertFalse(obj.consented)
|
|
321
|
-
|
|
322
|
-
def test_yes_eligible_egfr_not_calculated_phase_three(self):
|
|
323
|
-
"""Is eligible, since phase three will allow for EGFR to be considered
|
|
324
|
-
late exclusion.
|
|
325
|
-
"""
|
|
326
|
-
fbg_value = 6.9
|
|
327
|
-
ogtt_value = 7.8
|
|
328
|
-
obj = self._test_egfr_not_calculated(fbg_value, ogtt_value)
|
|
329
|
-
self.assertNotIn(EGFR_NOT_CALCULATED, obj.reasons_ineligible_part_three or "")
|
|
330
|
-
self.assertEqual(obj.eligible_part_three, YES)
|
|
331
|
-
self.assertTrue(obj.eligible)
|
|
332
|
-
self.assertFalse(obj.consented)
|
|
333
|
-
|
|
334
|
-
def _test_egfr_not_calculated(self, fbg_value, ogtt_value):
|
|
335
|
-
obj = self.get_screening_part_three_obj()
|
|
336
|
-
self.assertEqual(obj.eligible_part_one, YES)
|
|
337
|
-
self.assertFalse(obj.reasons_ineligible_part_one)
|
|
338
|
-
self.assertEqual(obj.eligible_part_two, YES)
|
|
339
|
-
self.assertFalse(obj.reasons_ineligible_part_two)
|
|
340
|
-
|
|
341
|
-
obj.fbg_value = fbg_value
|
|
342
|
-
obj.ogtt_value = ogtt_value
|
|
343
|
-
|
|
344
|
-
obj.part_three_report_datetime = get_utcnow()
|
|
345
|
-
obj.weight = 65
|
|
346
|
-
obj.height = 110
|
|
347
|
-
obj.hba1c_performed = YES
|
|
348
|
-
obj.hba1c_value = 7.0
|
|
349
|
-
obj.creatinine_performed = NO
|
|
350
|
-
obj.fasting = YES
|
|
351
|
-
obj.fasting_duration_str = "8h"
|
|
352
|
-
obj.fbg_units = MILLIMOLES_PER_LITER
|
|
353
|
-
obj.fbg_datetime = get_utcnow()
|
|
354
|
-
obj.ogtt_base_datetime = get_utcnow()
|
|
355
|
-
obj.ogtt_units = MILLIMOLES_PER_LITER
|
|
356
|
-
obj.ogtt_datetime = get_utcnow()
|
|
357
|
-
obj.severe_htn = NO
|
|
358
|
-
obj.save()
|
|
359
|
-
return obj
|
|
360
|
-
|
|
361
|
-
def test_not_eligible_egfr_less_than_45_phase_three(self):
|
|
362
|
-
fbg_value = 6.9
|
|
363
|
-
ogtt_value = 7.8
|
|
364
|
-
self._test_not_eligible_egfr_less_than_45(fbg_value, ogtt_value)
|
|
365
|
-
|
|
366
|
-
def _test_not_eligible_egfr_less_than_45(self, fbg_value, ogtt_value):
|
|
367
|
-
obj = self.get_screening_part_three_obj()
|
|
368
|
-
self.assertEqual(obj.eligible_part_one, YES)
|
|
369
|
-
self.assertFalse(obj.reasons_ineligible_part_one)
|
|
370
|
-
self.assertEqual(obj.eligible_part_two, YES)
|
|
371
|
-
self.assertFalse(obj.reasons_ineligible_part_two)
|
|
372
|
-
|
|
373
|
-
obj.fbg_value = fbg_value
|
|
374
|
-
obj.ogtt_value = ogtt_value
|
|
375
|
-
|
|
376
|
-
# defaults
|
|
377
|
-
obj.creatinine_performed = NO
|
|
378
|
-
obj.creatinine_units = MICROMOLES_PER_LITER
|
|
379
|
-
obj.creatinine_value = 200
|
|
380
|
-
obj.fasting = YES
|
|
381
|
-
obj.fasting_duration_str = "8h"
|
|
382
|
-
obj.hba1c_performed = YES
|
|
383
|
-
obj.hba1c_value = 7.0
|
|
384
|
-
obj.height = 110
|
|
385
|
-
obj.fbg_datetime = get_utcnow()
|
|
386
|
-
obj.fbg_units = MILLIMOLES_PER_LITER
|
|
387
|
-
obj.ogtt_base_datetime = get_utcnow()
|
|
388
|
-
obj.ogtt_datetime = get_utcnow()
|
|
389
|
-
obj.ogtt_units = MILLIMOLES_PER_LITER
|
|
390
|
-
obj.part_three_report_datetime = get_utcnow()
|
|
391
|
-
obj.severe_htn = NO
|
|
392
|
-
obj.weight = 65
|
|
393
|
-
obj.save()
|
|
394
|
-
|
|
395
|
-
self.assertIn(EGFR_LT_45, obj.reasons_ineligible_part_three)
|
|
396
|
-
self.assertEqual(obj.eligible_part_three, NO)
|
|
397
|
-
self.assertFalse(obj.eligible)
|
|
398
|
-
self.assertFalse(obj.consented)
|
|
399
|
-
|
|
400
|
-
def test_pregnancy_detected_in_p3(self):
|
|
401
|
-
"""P1 pregnant==NO, p3"""
|
|
402
|
-
# pregnant==NO
|
|
403
|
-
# urine_bhcg_performed == YES
|
|
404
|
-
# urine_bhcg_value == POS
|
|
405
|
-
|
|
406
|
-
part_one_eligible_options = deepcopy(get_part_one_eligible_options())
|
|
407
|
-
part_one_eligible_options.update(gender=FEMALE, pregnant=NO)
|
|
408
|
-
model_obj = ScreeningPartOne(**part_one_eligible_options)
|
|
409
|
-
model_obj.save()
|
|
410
|
-
part_two_eligible_options = deepcopy(get_part_two_eligible_options())
|
|
411
|
-
|
|
412
|
-
for k, v in part_two_eligible_options.items():
|
|
413
|
-
setattr(model_obj, k, v)
|
|
414
|
-
model_obj.save()
|
|
415
|
-
self.assertEqual(YES, model_obj.eligible_part_one)
|
|
416
|
-
self.assertEqual(YES, model_obj.eligible_part_two)
|
|
417
|
-
self.assertEqual(TBD, model_obj.eligible_part_three)
|
|
418
|
-
|
|
419
|
-
part_three_eligible_options = deepcopy(get_part_three_eligible_options())
|
|
420
|
-
model_obj = self.get_screening_part_three_obj()
|
|
421
|
-
for k, v in part_three_eligible_options.items():
|
|
422
|
-
setattr(model_obj, k, v)
|
|
423
|
-
|
|
424
|
-
model_obj.urine_bhcg_performed = NO
|
|
425
|
-
model_obj.urine_bhcg_value = NOT_APPLICABLE
|
|
426
|
-
model_obj.urine_bhcg_date = None
|
|
427
|
-
model_obj.save()
|
|
428
|
-
self.assertIsNone(model_obj.reasons_ineligible_part_three)
|
|
429
|
-
self.assertEqual(model_obj.eligible_part_three, YES)
|
|
430
|
-
|
|
431
|
-
model_obj.urine_bhcg_performed = YES
|
|
432
|
-
model_obj.urine_bhcg_value = POS
|
|
433
|
-
model_obj.urine_bhcg_date = model_obj.part_three_report_datetime
|
|
434
|
-
model_obj.save()
|
|
435
|
-
self.assertIn("UPT positive", model_obj.reasons_ineligible_part_three)
|
|
436
|
-
self.assertEqual(model_obj.eligible_part_three, NO)
|
|
@@ -1,84 +0,0 @@
|
|
|
1
|
-
from copy import deepcopy
|
|
2
|
-
|
|
3
|
-
from dateutil.relativedelta import relativedelta
|
|
4
|
-
from django.test import TestCase
|
|
5
|
-
from edc_constants.constants import NO, NOT_APPLICABLE, TBD, YES
|
|
6
|
-
from edc_utils.date import get_utcnow
|
|
7
|
-
|
|
8
|
-
from meta_pharmacy.constants import METFORMIN
|
|
9
|
-
from meta_screening.models import ScreeningPartOne, ScreeningPartTwo
|
|
10
|
-
|
|
11
|
-
from ...eligibility import EligibilityPartOne
|
|
12
|
-
from ..options import get_part_one_eligible_options, get_part_two_eligible_options
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
class TestScreeningPartTwo(TestCase):
|
|
16
|
-
def setUp(self):
|
|
17
|
-
part_one_eligible_options = deepcopy(get_part_one_eligible_options())
|
|
18
|
-
model_obj = ScreeningPartOne(**part_one_eligible_options)
|
|
19
|
-
model_obj.save()
|
|
20
|
-
self.assertIsNone(getattr(model_obj, EligibilityPartOne.reasons_ineligible_fld_name))
|
|
21
|
-
self.assertEqual(
|
|
22
|
-
getattr(model_obj, EligibilityPartOne.eligible_fld_name),
|
|
23
|
-
EligibilityPartOne.is_eligible_value,
|
|
24
|
-
)
|
|
25
|
-
|
|
26
|
-
self.screening_identifier = model_obj.screening_identifier
|
|
27
|
-
|
|
28
|
-
def test_defaults_phase_three(self):
|
|
29
|
-
self._test_defaults()
|
|
30
|
-
|
|
31
|
-
def test_eligible_phase_three(self):
|
|
32
|
-
self._test_eligible()
|
|
33
|
-
|
|
34
|
-
def _test_defaults(self):
|
|
35
|
-
obj = ScreeningPartTwo.objects.get(screening_identifier=self.screening_identifier)
|
|
36
|
-
self.assertEqual(obj.eligible_part_two, TBD)
|
|
37
|
-
self.assertIn("not answered", obj.reasons_ineligible_part_two)
|
|
38
|
-
|
|
39
|
-
self.assertFalse(obj.eligible)
|
|
40
|
-
self.assertFalse(obj.consented)
|
|
41
|
-
|
|
42
|
-
def _test_eligible(self):
|
|
43
|
-
obj = ScreeningPartTwo.objects.get(screening_identifier=self.screening_identifier)
|
|
44
|
-
self.assertEqual(obj.eligible_part_one, YES)
|
|
45
|
-
self.assertIsNone(obj.reasons_ineligible_part_one)
|
|
46
|
-
|
|
47
|
-
part_two_eligible_options = deepcopy(get_part_two_eligible_options())
|
|
48
|
-
|
|
49
|
-
for k, v in part_two_eligible_options.items():
|
|
50
|
-
setattr(obj, k, v)
|
|
51
|
-
|
|
52
|
-
obj.advised_to_fast = NOT_APPLICABLE
|
|
53
|
-
obj.appt_datetime = None
|
|
54
|
-
obj.acute_condition = None
|
|
55
|
-
obj.metformin_sensitivity = None
|
|
56
|
-
obj.save()
|
|
57
|
-
obj.refresh_from_db()
|
|
58
|
-
|
|
59
|
-
self.assertIn("not answered", obj.reasons_ineligible_part_two)
|
|
60
|
-
self.assertNotIn("Appt Datetime", obj.reasons_ineligible_part_two)
|
|
61
|
-
self.assertNotIn("Advised To Fast", obj.reasons_ineligible_part_two)
|
|
62
|
-
self.assertEqual(obj.eligible_part_two, TBD)
|
|
63
|
-
self.assertFalse(obj.eligible)
|
|
64
|
-
self.assertFalse(obj.consented)
|
|
65
|
-
|
|
66
|
-
obj.acute_condition = NO
|
|
67
|
-
obj.metformin_sensitivity = YES
|
|
68
|
-
obj.save()
|
|
69
|
-
|
|
70
|
-
self.assertIn(METFORMIN, (obj.reasons_ineligible_part_two or "").lower())
|
|
71
|
-
self.assertEqual(obj.eligible_part_two, NO)
|
|
72
|
-
self.assertFalse(obj.eligible)
|
|
73
|
-
self.assertFalse(obj.consented)
|
|
74
|
-
|
|
75
|
-
obj.acute_condition = NO
|
|
76
|
-
obj.metformin_sensitivity = NO
|
|
77
|
-
obj.advised_to_fast = YES
|
|
78
|
-
obj.appt_datetime = get_utcnow() + relativedelta(days=1)
|
|
79
|
-
obj.save()
|
|
80
|
-
|
|
81
|
-
self.assertIsNone(obj.reasons_ineligible_part_two)
|
|
82
|
-
self.assertEqual(obj.eligible_part_two, YES)
|
|
83
|
-
self.assertFalse(obj.eligible)
|
|
84
|
-
self.assertFalse(obj.consented)
|
meta_sites/tests/__init__.py
DELETED
|
File without changes
|
meta_sites/tests/test_sites.py
DELETED
|
@@ -1,12 +0,0 @@
|
|
|
1
|
-
from django.test import TestCase
|
|
2
|
-
from edc_sites.exceptions import InvalidSiteError
|
|
3
|
-
from edc_sites.site import sites
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
class SiteTests(TestCase):
|
|
7
|
-
def test_all(self):
|
|
8
|
-
self.assertEqual(sites.get_by_attr("name", "hindu_mandal").site_id, 10)
|
|
9
|
-
self.assertEqual(sites.get_by_attr("name", "amana").site_id, 20)
|
|
10
|
-
|
|
11
|
-
def test_bad(self):
|
|
12
|
-
self.assertRaises(InvalidSiteError, sites.get_by_attr, "name", "erik")
|
meta_sites/tests/urls.py
DELETED
meta_stats/__init__.py
DELETED
|
File without changes
|
meta_stats/incidence.py
DELETED
|
@@ -1,16 +0,0 @@
|
|
|
1
|
-
from edc_registration.models import RegisteredSubject
|
|
2
|
-
|
|
3
|
-
from meta_subject.models import Glucose
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
def get_sequential_fgb():
|
|
7
|
-
"""look for anyone with two or more sequential FBG measurements"""
|
|
8
|
-
|
|
9
|
-
for rs in RegisteredSubject.objects.all().order_by("subject_identifier"):
|
|
10
|
-
values = []
|
|
11
|
-
for index, glucose in enumerate(
|
|
12
|
-
Glucose.objects.filter(
|
|
13
|
-
subject_visit__subject_identifier=rs.subject_identifier
|
|
14
|
-
).order_by("report_datetime")
|
|
15
|
-
):
|
|
16
|
-
values.append(glucose.fbg_value)
|
meta_stats/models.py
DELETED
|
File without changes
|
meta_stats/tests/__init__.py
DELETED
|
File without changes
|
|
File without changes
|
|
@@ -1,10 +0,0 @@
|
|
|
1
|
-
from django.test import TestCase
|
|
2
|
-
from edc_constants.constants import FEMALE
|
|
3
|
-
|
|
4
|
-
from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
class TestIncidence(MetaTestCaseMixin, TestCase):
|
|
8
|
-
def setUp(self):
|
|
9
|
-
super().setUp()
|
|
10
|
-
self.subject_visit = self.get_subject_visit(gender=FEMALE)
|
meta_subject/tests/__init__.py
DELETED
|
File without changes
|
meta_subject/tests/holidays.csv
DELETED
|
@@ -1,15 +0,0 @@
|
|
|
1
|
-
2019-01-01,New Year's Day,tanzania
|
|
2
|
-
2019-01-12,Zanzibar Revolution Day,tanzania
|
|
3
|
-
2019-04-07,The Sheikh Abeid Amani Karume Day,tanzania
|
|
4
|
-
2019-04-17,Easter Monday,tanzania
|
|
5
|
-
2019-04-26,Union Day,tanzania
|
|
6
|
-
2019-05-01,Labour Day,tanzania
|
|
7
|
-
2019-06-26,Eid al-Fitr,tanzania
|
|
8
|
-
2019-07-07,Saba Saba Day,tanzania
|
|
9
|
-
2019-07-14,Good Friday,tanzania
|
|
10
|
-
2019-08-08,Nane Nane Day,tanzania
|
|
11
|
-
2019-10-14,Nyerere Day,tanzania
|
|
12
|
-
2019-12-01,Mawlid Day,tanzania
|
|
13
|
-
2019-12-09,Independence Day,tanzania
|
|
14
|
-
2019-12-25,Christmas Day,tanzania
|
|
15
|
-
2019-12-26,Boxing Day,tanzania
|
|
File without changes
|