meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl
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- meta_ae/action_items.py +2 -2
- meta_ae/migrations/0017_auto_20221130_2257.py +12 -7
- meta_ae/tests/holidays.csv +1 -1
- meta_analytics/README.rst +17 -0
- meta_analytics/dataframes/__init__.py +19 -0
- meta_analytics/dataframes/constants.py +33 -0
- meta_analytics/dataframes/enrolled/__init__.py +1 -0
- meta_analytics/dataframes/enrolled/get_glucose_df.py +122 -0
- meta_analytics/dataframes/get_eos_df.py +26 -0
- meta_analytics/dataframes/get_last_imp_visits_df.py +101 -0
- meta_analytics/dataframes/glucose_endpoints/__init__.py +2 -0
- meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py +183 -0
- meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py +531 -0
- meta_analytics/dataframes/screening/__init__.py +2 -0
- meta_analytics/dataframes/screening/get_glucose_tested_only_df.py +20 -0
- meta_analytics/dataframes/screening/get_screening_df.py +163 -0
- meta_analytics/dataframes/utils.py +65 -0
- meta_analytics/get_tables.py +81 -0
- meta_analytics/tables/__init__.py +2 -0
- meta_analytics/tables/eligible.py +106 -0
- meta_analytics/tables/enrolled/__init__.py +0 -0
- meta_analytics/tables/enrolled/glucose.py +28 -0
- meta_analytics/tables/has_dm.py +61 -0
- meta_analytics/tests/__init__.py +0 -0
- meta_analytics/tests/test_endpoints_by_date.py +94 -0
- meta_auth/auth_objects.py +32 -3
- meta_auth/auths.py +18 -3
- meta_consent/action_items.py +18 -1
- meta_consent/admin/__init__.py +1 -0
- meta_consent/admin/subject_consent_v1_ext_admin.py +45 -0
- meta_consent/baker_recipes.py +5 -4
- meta_consent/consents.py +21 -2
- meta_consent/constants.py +1 -0
- meta_consent/forms/__init__.py +1 -0
- meta_consent/forms/subject_consent_v1_ext_form.py +16 -0
- meta_consent/locale/lg/LC_MESSAGES/django.po +69 -0
- meta_consent/locale/sw/LC_MESSAGES/django.po +12 -12
- meta_consent/migrations/0025_alter_historicalsubjectconsent_first_name_and_more.py +151 -0
- meta_consent/migrations/0026_historicalsubjectconsentv1ext_subjectconsentv1ext.py +544 -0
- meta_consent/migrations/0027_auto_20250111_0344.py +30 -0
- meta_consent/models/__init__.py +1 -0
- meta_consent/models/signals.py +34 -13
- meta_consent/models/subject_consent_v1.py +1 -3
- meta_consent/models/subject_consent_v1_ext.py +29 -0
- meta_consent/tests/holidays.csv +1 -1
- meta_consent/tests/tests/test_form_validators.py +1 -1
- meta_dashboard/locale/lg/LC_MESSAGES/django.po +30 -0
- meta_dashboard/locale/sw/LC_MESSAGES/django.po +11 -2
- meta_dashboard/navbars.py +3 -1
- meta_dashboard/templates/meta_dashboard/bootstrap3/buttons/eligibility_button.html +1 -1
- meta_dashboard/templates/meta_dashboard/bootstrap3/buttons/screening_button.html +1 -1
- meta_dashboard/templates/meta_dashboard/bootstrap3/screening/listboard.html +4 -4
- meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard/sidebar.html +24 -0
- meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard.html +3 -0
- meta_dashboard/templates/meta_dashboard/bootstrap3/subject/listboard.html +1 -2
- meta_dashboard/templatetags/meta_dashboard_extras.py +1 -1
- meta_dashboard/tests/holidays.csv +1 -1
- meta_dashboard/tests/urls.py +0 -1
- meta_dashboard/view_utils/__init__.py +6 -0
- meta_dashboard/view_utils/subject_screening_button.py +2 -2
- meta_dashboard/views/subject/dashboard/dashboard_view.py +38 -0
- meta_edc/__init__.py +7 -0
- meta_edc/celery.py +4 -13
- meta_edc/celery_live.py +18 -0
- meta_edc/celery_uat.py +24 -0
- meta_edc/management/commands/update_forms_reference.py +6 -2
- meta_edc/migrations/__init__.py +0 -0
- meta_edc/navbars.py +2 -1
- meta_edc/settings/debug.py +17 -9
- meta_edc/settings/defaults.py +82 -60
- meta_edc/settings/live.py +1 -9
- meta_edc/settings/uat.py +1 -14
- meta_edc/templates/meta_edc/bootstrap3/home.html +13 -7
- meta_edc/tests/tests/test_endpoints.py +22 -19
- meta_edc/urls.py +5 -2
- meta_edc/wsgi.py +1 -1
- meta_edc/wsgi_live.py +1 -1
- meta_edc/wsgi_uat.py +1 -1
- meta_edc-0.3.50.dist-info/AUTHORS +0 -0
- meta_edc-0.3.50.dist-info/METADATA +766 -0
- {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/RECORD +400 -157
- {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/WHEEL +1 -1
- {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/top_level.txt +1 -0
- meta_pharmacy/admin/__init__.py +2 -0
- meta_pharmacy/admin/rx_admin.py +75 -0
- meta_pharmacy/admin/substitutions_admin.py +67 -0
- meta_pharmacy/admin_site.py +9 -0
- meta_pharmacy/apps.py +5 -0
- meta_pharmacy/constants.py +10 -0
- meta_pharmacy/forms/__init__.py +2 -0
- meta_pharmacy/forms/rx_form.py +16 -0
- meta_pharmacy/forms/substitutions_form.py +54 -0
- meta_pharmacy/label_configs.py +30 -0
- meta_pharmacy/labels/__init__.py +5 -0
- meta_pharmacy/labels/draw_label_for_subject_with_barcode.py +62 -0
- meta_pharmacy/labels/draw_label_for_subject_with_code128.py +14 -0
- meta_pharmacy/labels/draw_label_with_test_data.py +26 -0
- meta_pharmacy/labels/label_data.py +14 -0
- meta_pharmacy/labels/print_sheets.py +97 -0
- meta_pharmacy/list_data.py +8 -0
- meta_pharmacy/management/__init__.py +0 -0
- meta_pharmacy/management/commands/__init__.py +0 -0
- meta_pharmacy/management/commands/update_initial_pharmacy_data.py +10 -0
- meta_pharmacy/migrations/0002_initial.py +695 -0
- meta_pharmacy/migrations/0003_auto_20240909_2335.py +64 -0
- meta_pharmacy/migrations/0004_alter_historicalsubstitutions_report_datetime_and_more.py +23 -0
- meta_pharmacy/migrations/0005_auto_20240911_0352.py +17 -0
- meta_pharmacy/migrations/0006_lotnumber_label.py +289 -0
- meta_pharmacy/migrations/0007_lotnumber_medication.py +24 -0
- meta_pharmacy/migrations/0008_remove_lotnumber_medication_and_more.py +390 -0
- meta_pharmacy/migrations/0009_remove_historicalrx_slug.py +17 -0
- meta_pharmacy/models/__init__.py +3 -0
- meta_pharmacy/models/label_data.py +38 -0
- meta_pharmacy/models/rx.py +18 -0
- meta_pharmacy/models/rx_label.py +39 -0
- meta_pharmacy/models/substitutions.py +88 -0
- meta_pharmacy/urls.py +8 -0
- meta_pharmacy/utils/__init__.py +1 -0
- meta_pharmacy/utils/update_initial_pharmacy_data.py +146 -0
- meta_prn/action_items.py +52 -2
- meta_prn/admin/__init__.py +3 -0
- meta_prn/admin/dm_referral_admin.py +49 -0
- meta_prn/admin/offschedule_dm_referral_admin.py +47 -0
- meta_prn/admin/onschedule_dm_referral_admin.py +39 -0
- meta_prn/admin/pregnancy_notification_admin.py +6 -2
- meta_prn/baker_recipes.py +8 -1
- meta_prn/choices.py +2 -1
- meta_prn/constants.py +4 -1
- meta_prn/forms/__init__.py +2 -0
- meta_prn/forms/dm_referral_form.py +40 -0
- meta_prn/forms/offschedule_dm_referral_form.py +35 -0
- meta_prn/forms/offschedule_form.py +6 -0
- meta_prn/migrations/0034_auto_20220630_1110.py +3 -3
- meta_prn/migrations/0035_auto_20220630_1140.py +59 -56
- meta_prn/migrations/0057_historicalonscheduledmreferral_and_more.py +1156 -0
- meta_prn/migrations/0058_dmreferral_referral_note_and_more.py +29 -0
- meta_prn/migrations/0059_alter_historicaloffstudymedication_reason_and_more.py +53 -0
- meta_prn/models/__init__.py +13 -2
- meta_prn/models/dm_referral.py +39 -0
- meta_prn/models/offschedule.py +15 -1
- meta_prn/models/onschedule.py +6 -0
- meta_prn/models/signals.py +41 -1
- meta_prn/tests/tests/test_dm_referral.py +203 -0
- meta_reports/__init__.py +1 -0
- meta_reports/admin/__init__.py +15 -0
- meta_reports/admin/dbviews/__init__.py +14 -0
- meta_reports/admin/dbviews/glucose_summary_admin.py +116 -0
- meta_reports/admin/dbviews/imp_substitutions_admin.py +101 -0
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/__init__.py +2 -0
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py +53 -0
- meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py +84 -0
- meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py +1 -0
- meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py +13 -0
- meta_reports/admin/dbviews/on_study_missing_values_admin/__init__.py +1 -0
- meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py +13 -0
- meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py +58 -0
- meta_reports/admin/dbviews/unattended_three_in_row2_admin.py +47 -0
- meta_reports/admin/dbviews/unattended_three_in_row_admin.py +35 -0
- meta_reports/admin/dbviews/unattended_two_in_row_admin.py +34 -0
- meta_reports/admin/endpoints_admin.py +14 -0
- meta_reports/admin/endpoints_all_admin.py +13 -0
- meta_reports/admin/last_imp_refill_admin.py +181 -0
- meta_reports/admin/list_filters.py +30 -0
- meta_reports/admin/modeladmin_mixins.py +112 -0
- meta_reports/admin_site.py +5 -0
- meta_reports/apps.py +1 -16
- meta_reports/forms/__init__.py +1 -0
- meta_reports/forms/missing_ogtt_note_form.py +33 -0
- meta_reports/management/__init__.py +0 -0
- meta_reports/management/commands/__init__.py +0 -0
- meta_reports/management/commands/generate_endpoints.py +13 -0
- meta_reports/migrations/0001_initial.py +87 -0
- meta_reports/migrations/0002_patienthistorymissingbaselinecd4_and_more.py +64 -0
- meta_reports/migrations/0003_auto_20240618_0505.py +12 -0
- meta_reports/migrations/0004_alter_patienthistorymissingbaselinecd4_table.py +17 -0
- meta_reports/migrations/0005_endpoints.py +47 -0
- meta_reports/migrations/0006_endpoints_baseline_datetime.py +18 -0
- meta_reports/migrations/0007_alter_endpoints_endpoint_label_and_more.py +43 -0
- meta_reports/migrations/0008_alter_endpoints_endpoint_label.py +18 -0
- meta_reports/migrations/0009_alter_endpoints_options.py +21 -0
- meta_reports/migrations/0010_alter_patienthistorymissingbaselinecd4_options_and_more.py +49 -0
- meta_reports/migrations/0011_auto_20240813_0156.py +54 -0
- meta_reports/migrations/0012_auto_20240813_1516.py +48 -0
- meta_reports/migrations/0013_auto_20240813_1516.py +48 -0
- meta_reports/migrations/0014_auto_20240813_1517.py +48 -0
- meta_reports/migrations/0015_alter_endpoints_site.py +22 -0
- meta_reports/migrations/0016_missingscreeningogtt.py +47 -0
- meta_reports/migrations/0017_auto_20240819_1711.py +166 -0
- meta_reports/migrations/0018_auto_20240819_1713.py +54 -0
- meta_reports/migrations/0019_auto_20240819_1721.py +54 -0
- meta_reports/migrations/0020_auto_20240819_1811.py +54 -0
- meta_reports/migrations/0021_auto_20240819_1817.py +54 -0
- meta_reports/migrations/0022_auto_20240819_1832.py +54 -0
- meta_reports/migrations/0023_endpoints_meta_report_subject_a56b22_idx.py +20 -0
- meta_reports/migrations/0024_glucosesummary.py +38 -0
- meta_reports/migrations/0025_auto_20240822_0115.py +87 -0
- meta_reports/migrations/0026_auto_20240822_0120.py +54 -0
- meta_reports/migrations/0027_auto_20240822_0140.py +54 -0
- meta_reports/migrations/0028_alter_glucosesummary_options.py +22 -0
- meta_reports/migrations/0029_auto_20240822_0149.py +54 -0
- meta_reports/migrations/0030_auto_20240822_1637.py +54 -0
- meta_reports/migrations/0031_endpointsproxy.py +25 -0
- meta_reports/migrations/0032_alter_endpointsproxy_options.py +21 -0
- meta_reports/migrations/0033_auto_20240823_0012.py +54 -0
- meta_reports/migrations/0034_auto_20240823_1642.py +54 -0
- meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py +457 -0
- meta_reports/migrations/0036_historicalmissingogttnote_fasting_and_more.py +86 -0
- meta_reports/migrations/0037_historicalmissingogttnote_result_status_and_more.py +51 -0
- meta_reports/migrations/0038_alter_historicalmissingogttnote_fasting_and_more.py +33 -0
- meta_reports/migrations/0039_onstudymissingvalues.py +44 -0
- meta_reports/migrations/0040_auto_20240824_0412.py +282 -0
- meta_reports/migrations/0041_auto_20240828_2229.py +14 -0
- meta_reports/migrations/0042_onstudymissinglabvalues.py +43 -0
- meta_reports/migrations/0043_auto_20240828_2309.py +88 -0
- meta_reports/migrations/0044_auto_20240828_2323.py +93 -0
- meta_reports/migrations/0045_auto_20240829_0248.py +54 -0
- meta_reports/migrations/0046_auto_20240829_0250.py +54 -0
- meta_reports/migrations/0047_impsubstitutions.py +56 -0
- meta_reports/migrations/0048_auto_20240909_2338.py +48 -0
- meta_reports/migrations/0049_auto_20240911_0327.py +54 -0
- meta_reports/migrations/0050_alter_endpoints_created.py +19 -0
- meta_reports/migrations/0051_remove_endpoints_baseline_datetime_and_more.py +40 -0
- meta_reports/migrations/0052_lastimpvisit.py +57 -0
- meta_reports/migrations/0053_rename_lastimpvisit_lastimprefill_and_more.py +31 -0
- meta_reports/models/__init__.py +16 -0
- meta_reports/models/dbviews/README +14 -0
- meta_reports/models/dbviews/__init__.py +9 -0
- meta_reports/models/dbviews/glucose_summary/__init__.py +2 -0
- meta_reports/models/dbviews/glucose_summary/unmanaged_model.py +35 -0
- meta_reports/models/dbviews/glucose_summary/view_definition.py +28 -0
- meta_reports/models/dbviews/imp_substitutions/__init__.py +1 -0
- meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py +41 -0
- meta_reports/models/dbviews/imp_substitutions/view_definition.py +21 -0
- meta_reports/models/dbviews/missing_screening_ogtt/__init__.py +2 -0
- meta_reports/models/dbviews/missing_screening_ogtt/note_model.py +57 -0
- meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py +41 -0
- meta_reports/models/dbviews/missing_screening_ogtt/view_definition.py +20 -0
- meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py +1 -0
- meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py +53 -0
- meta_reports/models/dbviews/on_study_missing_lab_values/unmanged_model.py +20 -0
- meta_reports/models/dbviews/on_study_missing_lab_values/view_definition.py +17 -0
- meta_reports/models/dbviews/on_study_missing_values/__init__.py +1 -0
- meta_reports/models/dbviews/on_study_missing_values/qa_cases.py +54 -0
- meta_reports/models/dbviews/on_study_missing_values/unmanged_model.py +20 -0
- meta_reports/models/dbviews/on_study_missing_values/view_definition.py +17 -0
- meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py +1 -0
- meta_reports/models/dbviews/patient_history_missing_baseline_cd4/unmanaged_model.py +31 -0
- meta_reports/models/dbviews/patient_history_missing_baseline_cd4/view_definition.py +21 -0
- meta_reports/models/dbviews/unattended_three_in_row/__init__.py +1 -0
- meta_reports/models/dbviews/unattended_three_in_row/unmanaged_model.py +29 -0
- meta_reports/models/dbviews/unattended_three_in_row/view_definition.py +31 -0
- meta_reports/models/dbviews/unattended_three_in_row2/__init__.py +1 -0
- meta_reports/models/dbviews/unattended_three_in_row2/unmanaged_model.py +29 -0
- meta_reports/models/dbviews/unattended_three_in_row2/view_definition.py +50 -0
- meta_reports/models/dbviews/unattended_two_in_row/__init__.py +1 -0
- meta_reports/models/dbviews/unattended_two_in_row/unmanaged_model.py +27 -0
- meta_reports/models/dbviews/unattended_two_in_row/view_definition.py +30 -0
- meta_reports/models/endpoints.py +31 -0
- meta_reports/models/endpoints_proxy.py +11 -0
- meta_reports/models/last_imp_refill.py +34 -0
- meta_reports/tasks.py +12 -0
- meta_reports/templates/meta_reports/columns/subject_identifier_column.html +1 -0
- meta_reports/templates/meta_reports/endpoints_all_change_list_note.html +12 -0
- meta_reports/templates/meta_reports/endpoints_change_list_note.html +12 -0
- meta_reports/tests/test_sql_gen.py +5 -0
- meta_reports/urls.py +8 -0
- meta_reports/utils.py +0 -0
- meta_screening/admin/subject_screening_admin.py +1 -0
- meta_screening/form_validators/screening_part_two.py +1 -1
- meta_screening/migrations/0062_remove_icpreferral_site_and_more.py +27 -0
- meta_screening/migrations/0063_alter_historicalscreeningpartone_fasting_duration_str_and_more.py +184 -0
- meta_screening/migrations/0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more.py +126 -0
- meta_screening/migrations/0065_auto_20240516_0352.py +31 -0
- meta_screening/migrations/0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more.py +103 -0
- meta_screening/migrations/0067_alter_historicalscreeningpartone_report_datetime_and_more.py +84 -0
- meta_screening/models/__init__.py +1 -1
- meta_screening/tests/holidays.csv +1 -1
- meta_screening/tests/meta_test_case_mixin.py +17 -2
- meta_screening/tests/options.py +3 -3
- meta_sites/__init__.py +0 -1
- meta_sites/sites.py +8 -7
- meta_sites/tests/test_sites.py +1 -1
- meta_subject/action_items.py +25 -2
- meta_subject/admin/__init__.py +2 -1
- meta_subject/admin/birth_outcome_admin.py +4 -3
- meta_subject/admin/blood_results/__init__.py +1 -1
- meta_subject/admin/blood_results/{blood_results_lipid_admin.py → blood_results_lipids_admin.py} +7 -7
- meta_subject/admin/delivery_admin.py +0 -1
- meta_subject/admin/diabetes/__init__.py +2 -0
- meta_subject/admin/diabetes/dm_endpoint_admin.py +35 -0
- meta_subject/admin/{dm_referral_followup_admin.py → diabetes/dm_followup_admin.py} +15 -8
- meta_subject/admin/glucose_admin.py +1 -1
- meta_subject/admin/glucose_fbg_admin.py +38 -8
- meta_subject/admin/other_arv_regimens_admin.py +2 -0
- meta_subject/admin/study_medication_admin.py +10 -0
- meta_subject/admin/subject_visit_admin.py +4 -1
- meta_subject/baker_recipes.py +6 -0
- meta_subject/choices.py +8 -0
- meta_subject/constants.py +2 -1
- meta_subject/form_validators/__init__.py +2 -1
- meta_subject/form_validators/dm_endpoint_form_validator.py +35 -0
- meta_subject/form_validators/{dm_referral_followup_form_validator.py → dm_followup_form_validator.py} +41 -2
- meta_subject/forms/__init__.py +2 -1
- meta_subject/forms/blood_results/__init__.py +1 -1
- meta_subject/forms/blood_results/{blood_results_lipid_form.py → blood_results_lipids_form.py} +5 -5
- meta_subject/forms/diabetes/__init__.py +2 -0
- meta_subject/forms/diabetes/dm_endpoint_form.py +13 -0
- meta_subject/forms/diabetes/dm_followup_form.py +25 -0
- meta_subject/forms/glucose_fbg_form.py +38 -16
- meta_subject/forms/study_medication_form.py +35 -0
- meta_subject/forms/subject_visit_form.py +16 -0
- meta_subject/locale/lg/LC_MESSAGES/django.po +470 -0
- meta_subject/locale/sw/LC_MESSAGES/django.po +191 -89
- meta_subject/metadata_rules/metadata_rules.py +21 -0
- meta_subject/metadata_rules/predicates.py +67 -8
- meta_subject/migrations/0107_auto_20220415_0043.py +28 -22
- meta_subject/migrations/0126_auto_20220719_2142.py +4 -4
- meta_subject/migrations/0131_auto_20220722_0411.py +28 -23
- meta_subject/migrations/0132_auto_20220722_1825.py +10 -6
- meta_subject/migrations/0135_auto_20220722_2212.py +39 -35
- meta_subject/migrations/0150_auto_20220914_0039.py +15 -11
- meta_subject/migrations/0181_dmreferralfollowup_action_identifier_and_more.py +143 -0
- meta_subject/migrations/0182_rename_dmreferralfollowup_dmfollowup_and_more.py +54 -0
- meta_subject/migrations/0183_alter_dmfollowup_on_dm_medications_and_more.py +31 -0
- meta_subject/migrations/0184_alter_glucose_options_and_more.py +31 -0
- meta_subject/migrations/0185_alter_bloodresultsins_fasting_duration_str_and_more.py +82 -0
- meta_subject/migrations/0186_healtheconomicsupdate_singleton_field_and_more.py +55 -0
- meta_subject/migrations/0187_dmdiagnosis_historicaldmdiagnosis_dmdxresult_and_more.py +451 -0
- meta_subject/migrations/0188_historicaldmdxresult_dmdxresult.py +403 -0
- meta_subject/migrations/0189_alter_dmdxresult_options_and_more.py +116 -0
- meta_subject/migrations/0190_dmdiagnosis_dx_no_tmg_reason_and_more.py +65 -0
- meta_subject/migrations/0191_alter_dmdiagnosis_dx_no_tmg_reason_and_more.py +70 -0
- meta_subject/migrations/0192_rename_glucose_quantifier_glucosefbg_fbg_quantifier_and_more.py +44 -0
- meta_subject/migrations/0193_alter_glucosefbg_fbg_value_and_more.py +44 -0
- meta_subject/migrations/0194_remove_glucosefbg_assay_datetime_and_more.py +166 -0
- meta_subject/migrations/0195_alter_glucosefbg_fbg_datetime_and_more.py +27 -0
- meta_subject/migrations/0196_glucosefbg_fbg_not_performed_reason_and_more.py +49 -0
- meta_subject/migrations/0197_glucosefbg_fasting_duration_estimated_and_more.py +33 -0
- meta_subject/migrations/0198_alter_glucosefbg_fasting_duration_estimated_and_more.py +33 -0
- meta_subject/migrations/0199_auto_20240516_0247.py +18 -0
- meta_subject/migrations/0200_rename_fasting_duration_minutes_bloodresultsins_fasting_duration_delta_and_more.py +43 -0
- meta_subject/migrations/0201_alter_bloodresultsins_fasting_duration_delta_and_more.py +58 -0
- meta_subject/migrations/0202_auto_20240516_0315.py +32 -0
- meta_subject/migrations/0203_alter_bloodresultsins_fasting_duration_delta_and_more.py +67 -0
- meta_subject/migrations/0204_glucosefbg_repeat_fbg_date_and_more.py +27 -0
- meta_subject/migrations/0205_historicalsubjectrequisition_crf_status_and_more.py +80 -0
- meta_subject/migrations/0206_bloodresultsfbc_crf_status_and_more.py +62 -0
- meta_subject/migrations/0207_alter_historicalphysicalexam_waist_circumference_and_more.py +46 -0
- meta_subject/migrations/0208_birthoutcomes_crf_status_and_more.py +62 -0
- meta_subject/migrations/0209_remove_historicaldmdxresult_dm_diagnosis_and_more.py +37 -0
- meta_subject/migrations/0210_remove_dmdxresult_dm_diagnosis_and_more.py +123 -0
- meta_subject/migrations/0211_dmendpoint_endpoint_reached_and_more.py +45 -0
- meta_subject/migrations/0212_auto_20240827_2222.py +23 -0
- meta_subject/migrations/0213_rename_bloodresultslipid_bloodresultslipids_and_more.py +35 -0
- meta_subject/migrations/0214_historicalstudymedication_stock_codes_and_more.py +44 -0
- meta_subject/migrations/0215_alter_historicalstudymedication_stock_codes_and_more.py +46 -0
- meta_subject/model_mixins/arv_history_model_mixin.py +3 -3
- meta_subject/models/__init__.py +3 -2
- meta_subject/models/birth_outcomes.py +6 -1
- meta_subject/models/blood_results/__init__.py +1 -1
- meta_subject/models/blood_results/blood_results_fbc.py +3 -2
- meta_subject/models/blood_results/blood_results_hba1c.py +2 -0
- meta_subject/models/blood_results/blood_results_ins.py +2 -0
- meta_subject/models/blood_results/blood_results_lft.py +2 -0
- meta_subject/models/blood_results/{blood_results_lipid.py → blood_results_lipids.py} +5 -3
- meta_subject/models/blood_results/blood_results_rft.py +2 -0
- meta_subject/models/diabetes/__init__.py +2 -0
- meta_subject/models/diabetes/dm_endpoint.py +61 -0
- meta_subject/models/{dm_referral_followup.py → diabetes/dm_followup.py} +18 -6
- meta_subject/models/glucose.py +7 -14
- meta_subject/models/glucose_fbg.py +40 -51
- meta_subject/models/health_economics/health_economics_update.py +2 -0
- meta_subject/models/physical_exam.py +1 -0
- meta_subject/models/signals.py +19 -0
- meta_subject/models/subject_requisition.py +3 -4
- meta_subject/models/todo.txt +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_subject/tests/holidays.csv +1 -1
- meta_subject/tests/tests/test_egfr.py +6 -5
- meta_subject/tests/tests/test_medication_adherence.py +5 -1
- meta_subject/tests/tests/test_metadata_rules.py +34 -4
- meta_subject/tests/tests/test_mnsi.py +212 -121
- meta_subject/tests/tests/test_sf12.py +0 -12
- meta_visit_schedule/constants.py +7 -1
- meta_visit_schedule/tests/tests/test_schedule.py +4 -0
- meta_visit_schedule/visit_schedules/phase_three/crfs.py +87 -14
- meta_visit_schedule/visit_schedules/phase_three/requisitions.py +12 -0
- meta_visit_schedule/visit_schedules/phase_three/schedule.py +65 -2
- meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py +60 -0
- meta_visit_schedule/visit_schedules/phase_three/visit_schedule.py +2 -0
- tests/etc/randomization_list.csv +1 -1
- {meta_edc/tests → tests}/etc/randomization_list_phase_three.csv +4 -4
- tests/holidays.csv +1 -1
- tests/test_settings.py +186 -0
- meta_edc/tests/etc/user-aes-local.key +0 -1
- meta_edc/tests/etc/user-aes-restricted.key +0 -0
- meta_edc/tests/etc/user-rsa-local-private.pem +0 -27
- meta_edc/tests/etc/user-rsa-local-public.pem +0 -9
- meta_edc/tests/etc/user-rsa-restricted-private.pem +0 -27
- meta_edc/tests/etc/user-rsa-restricted-public.pem +0 -9
- meta_edc/tests/etc/user-salt-local.key +0 -0
- meta_edc/tests/etc/user-salt-restricted.key +0 -0
- meta_edc-0.3.7.dist-info/METADATA +0 -87
- meta_reports/tests/holidays.csv +0 -15
- meta_subject/forms/dm_referral_followup.py +0 -18
- /meta_edc-0.3.7.dist-info/AUTHORS → /meta_analytics/__init__.py +0 -0
- /meta_pharmacy/models.py → /meta_analytics/constants.py +0 -0
- /meta_reports/models.py → /meta_analytics/notebooks/cleaning/__init__.py +0 -0
- {meta_edc-0.3.7.dist-info → meta_edc-0.3.50.dist-info}/LICENSE +0 -0
meta_edc/settings/defaults.py
CHANGED
@@ -2,6 +2,7 @@ import os
|
|
2
2
|
import sys
|
3
3
|
from importlib.metadata import version
|
4
4
|
from pathlib import Path
|
5
|
+
from urllib.parse import quote
|
5
6
|
|
6
7
|
import django
|
7
8
|
import environ
|
@@ -16,7 +17,6 @@ env = environ.Env(
|
|
16
17
|
CELERY_ENABLED=(bool, False),
|
17
18
|
DATABASE_SQLITE_ENABLED=(bool, False),
|
18
19
|
DJANGO_AUTO_CREATE_KEYS=(bool, False),
|
19
|
-
DJANGO_CRYPTO_FIELDS_TEMP_PATH=(bool, False),
|
20
20
|
DJANGO_CSRF_COOKIE_SECURE=(bool, True),
|
21
21
|
DJANGO_DEBUG=(bool, False),
|
22
22
|
DJANGO_EDC_BOOTSTRAP=(int, 3),
|
@@ -31,29 +31,30 @@ env = environ.Env(
|
|
31
31
|
EDC_RANDOMIZATION_REGISTER_DEFAULT_RANDOMIZER=(bool, True),
|
32
32
|
EDC_LABEL_BROWSER_PRINT_PAGE_AUTO_BACK=(bool, True),
|
33
33
|
TWILIO_ENABLED=(bool, False),
|
34
|
+
EDC_SITES_DOMAIN_SUFFIX="meta4.clinicedc.org",
|
34
35
|
)
|
35
36
|
|
36
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-
|
37
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-
|
38
|
-
if LOGGING_ENABLED := env("DJANGO_LOGGING_ENABLED"):
|
39
|
-
from .logging import * # noqa
|
40
|
-
|
41
|
-
BASE_DIR = str(Path(os.path.dirname(os.path.abspath(__file__))).parent.parent)
|
42
|
-
ENV_DIR = str(Path(os.path.dirname(os.path.abspath(__file__))).parent.parent)
|
37
|
+
BASE_DIR = Path(__file__).resolve().parent.parent.parent
|
38
|
+
ENV_DIR = Path(__file__).resolve().parent.parent.parent
|
43
39
|
|
44
40
|
# copy your .env file from .envs/ to BASE_DIR
|
45
41
|
if "test" in sys.argv:
|
46
|
-
env.read_env(
|
47
|
-
print(f"Reading env from {
|
42
|
+
env.read_env(ENV_DIR / ".env-tests")
|
43
|
+
print(f"Reading env from {(BASE_DIR /'.env-tests')}") # noqa
|
48
44
|
else:
|
49
|
-
if not
|
50
|
-
raise FileExistsError(
|
51
|
-
|
52
|
-
|
53
|
-
|
45
|
+
if not (ENV_DIR / ".env").exists():
|
46
|
+
raise FileExistsError(f"Environment file does not exist. Got `{(ENV_DIR / '.env')}`")
|
47
|
+
env.read_env(ENV_DIR / ".env")
|
48
|
+
|
49
|
+
|
50
|
+
LOGGING_ENABLED = env("DJANGO_LOGGING_ENABLED")
|
51
|
+
if LOGGING_ENABLED:
|
52
|
+
from .logging import * # noqa
|
54
53
|
|
55
54
|
META_PHASE = 3
|
56
55
|
|
56
|
+
EDC_SITES_DOMAIN_SUFFIX = env.str("EDC_SITES_DOMAIN_SUFFIX") # "meta4.clinicedc.org"
|
57
|
+
|
57
58
|
DEBUG = env("DJANGO_DEBUG")
|
58
59
|
|
59
60
|
SECRET_KEY = env.str("DJANGO_SECRET_KEY")
|
@@ -64,10 +65,11 @@ LIVE_SYSTEM = env.str("DJANGO_LIVE_SYSTEM")
|
|
64
65
|
|
65
66
|
ETC_DIR = env.str("DJANGO_ETC_FOLDER")
|
66
67
|
|
67
|
-
TEST_DIR =
|
68
|
+
TEST_DIR = BASE_DIR / APP_NAME / "tests"
|
68
69
|
|
69
|
-
|
70
|
-
|
70
|
+
ALLOWED_HOSTS = env.list("DJANGO_ALLOWED_HOSTS")
|
71
|
+
|
72
|
+
META3_DOMAIN_SUFFIX = "meta4.clinicedc.org"
|
71
73
|
|
72
74
|
ENFORCE_RELATED_ACTION_ITEM_EXISTS = False
|
73
75
|
|
@@ -86,8 +88,12 @@ INSTALLED_APPS = [
|
|
86
88
|
"django.contrib.messages",
|
87
89
|
"django.contrib.staticfiles",
|
88
90
|
"django.contrib.sites",
|
91
|
+
"multisite.apps.AppConfig",
|
89
92
|
"defender",
|
90
|
-
"
|
93
|
+
"sequences.apps.SequencesConfig",
|
94
|
+
# "django_celery_beat",
|
95
|
+
# "django_celery_results",
|
96
|
+
"django_db_views",
|
91
97
|
"fontawesomefree",
|
92
98
|
"django_crypto_fields.apps.AppConfig",
|
93
99
|
"django_revision.apps.AppConfig",
|
@@ -95,10 +101,13 @@ INSTALLED_APPS = [
|
|
95
101
|
"logentry_admin",
|
96
102
|
"simple_history",
|
97
103
|
"storages",
|
104
|
+
"django_pylabels.apps.AppConfig",
|
105
|
+
"edc_pylabels.apps.AppConfig",
|
98
106
|
"edc_sites.apps.AppConfig",
|
99
107
|
"edc_action_item.apps.AppConfig",
|
100
108
|
"edc_appointment.apps.AppConfig",
|
101
109
|
"edc_auth.apps.AppConfig",
|
110
|
+
"edc_adherence.apps.AppConfig",
|
102
111
|
"edc_adverse_event.apps.AppConfig",
|
103
112
|
"edc_consent.apps.AppConfig",
|
104
113
|
"edc_crf.apps.AppConfig",
|
@@ -135,6 +144,7 @@ INSTALLED_APPS = [
|
|
135
144
|
"edc_protocol.apps.AppConfig",
|
136
145
|
"edc_protocol_incident.apps.AppConfig",
|
137
146
|
"edc_prn.apps.AppConfig",
|
147
|
+
"edc_qareports.apps.AppConfig",
|
138
148
|
"edc_qol.apps.AppConfig",
|
139
149
|
"edc_randomization.apps.AppConfig",
|
140
150
|
"edc_refusal.apps.AppConfig",
|
@@ -146,7 +156,6 @@ INSTALLED_APPS = [
|
|
146
156
|
"edc_timepoint.apps.AppConfig",
|
147
157
|
"edc_unblinding.apps.AppConfig",
|
148
158
|
"edc_form_describer.apps.AppConfig",
|
149
|
-
"edc_adherence.apps.AppConfig",
|
150
159
|
"edc_dx.apps.AppConfig",
|
151
160
|
"meta_consent.apps.AppConfig",
|
152
161
|
"meta_data_manager.apps.AppConfig",
|
@@ -154,6 +163,7 @@ INSTALLED_APPS = [
|
|
154
163
|
"meta_dashboard.apps.AppConfig",
|
155
164
|
"meta_labs.apps.AppConfig",
|
156
165
|
"meta_subject.apps.AppConfig",
|
166
|
+
"meta_reports.apps.AppConfig",
|
157
167
|
"meta_visit_schedule.apps.AppConfig",
|
158
168
|
"meta_ae.apps.AppConfig",
|
159
169
|
"meta_auth.apps.AppConfig",
|
@@ -173,11 +183,13 @@ if not DEFENDER_ENABLED:
|
|
173
183
|
MIDDLEWARE = [
|
174
184
|
"django.middleware.security.SecurityMiddleware",
|
175
185
|
"django.contrib.sessions.middleware.SessionMiddleware",
|
186
|
+
"django.middleware.locale.LocaleMiddleware",
|
176
187
|
"django.middleware.common.CommonMiddleware",
|
177
188
|
"multisite.middleware.DynamicSiteMiddleware",
|
178
189
|
"django.contrib.sites.middleware.CurrentSiteMiddleware",
|
179
190
|
"django.middleware.csrf.CsrfViewMiddleware",
|
180
191
|
"django.contrib.auth.middleware.AuthenticationMiddleware",
|
192
|
+
"django.contrib.auth.middleware.LoginRequiredMiddleware",
|
181
193
|
"defender.middleware.FailedLoginMiddleware",
|
182
194
|
"django.contrib.messages.middleware.MessageMiddleware",
|
183
195
|
"django.middleware.clickjacking.XFrameOptionsMiddleware",
|
@@ -224,7 +236,7 @@ if env("DATABASE_SQLITE_ENABLED"):
|
|
224
236
|
DATABASES = {
|
225
237
|
"default": {
|
226
238
|
"ENGINE": "django.db.backends.sqlite3",
|
227
|
-
"NAME":
|
239
|
+
"NAME": BASE_DIR / "db.sqlite3",
|
228
240
|
}
|
229
241
|
}
|
230
242
|
|
@@ -238,12 +250,11 @@ if env.str("DJANGO_CACHE") == "redis":
|
|
238
250
|
"default": {
|
239
251
|
"BACKEND": "django_redis.cache.RedisCache",
|
240
252
|
"LOCATION": "redis://127.0.0.1:6379/1",
|
241
|
-
# "LOCATION": "unix://[:{DJANGO_REDIS_PASSWORD}]@/path/to/socket.sock?db=0",
|
242
253
|
"OPTIONS": {
|
243
254
|
"CLIENT_CLASS": "django_redis.client.DefaultClient",
|
244
255
|
"PASSWORD": env.str("DJANGO_REDIS_PASSWORD"),
|
245
256
|
},
|
246
|
-
"KEY_PREFIX":
|
257
|
+
"KEY_PREFIX": env.str("DJANGO_REDIS_KEY_PREFIX", default=APP_NAME),
|
247
258
|
}
|
248
259
|
}
|
249
260
|
SESSION_ENGINE = "django.contrib.sessions.backends.cache"
|
@@ -292,13 +303,16 @@ USE_TZ = True
|
|
292
303
|
|
293
304
|
LANG_INFO = dict(django.conf.locale.LANG_INFO, **EXTRA_LANG_INFO)
|
294
305
|
django.conf.locale.LANG_INFO = LANG_INFO
|
295
|
-
|
306
|
+
|
307
|
+
LANGUAGE_CODE = "en-gb"
|
296
308
|
LANGUAGE_LIST = ["sw", "en-gb", "en", "mas"]
|
297
309
|
LANGUAGES = [(code, LANG_INFO[code]["name"]) for code in LANGUAGE_LIST]
|
298
310
|
|
311
|
+
# LOCALE_PATHS = [
|
312
|
+
# base_dir / "locale",
|
313
|
+
# base_dir.parent / "edc-pharmacy" / "edc_pharmacy" / "locale",
|
314
|
+
# ]
|
299
315
|
|
300
|
-
# LANGUAGE_CODE = env.str("DJANGO_LANGUAGE_CODE") # ignored if USE_L10N = False
|
301
|
-
# LANGUAGES = [x.split(":") for x in env.list("DJANGO_LANGUAGES")] or (("en", "English"),)
|
302
316
|
TIME_ZONE = env.str("DJANGO_TIME_ZONE")
|
303
317
|
DATE_INPUT_FORMATS = ["%Y-%m-%d", "%d/%m/%Y"]
|
304
318
|
DATETIME_INPUT_FORMATS = [
|
@@ -341,8 +355,8 @@ if not DEBUG:
|
|
341
355
|
SECURE_BROWSER_XSS_FILTER = True
|
342
356
|
|
343
357
|
# edc_lab and label
|
344
|
-
LABEL_TEMPLATE_FOLDER = env.str("DJANGO_LABEL_TEMPLATE_FOLDER") or
|
345
|
-
BASE_DIR
|
358
|
+
LABEL_TEMPLATE_FOLDER = env.str("DJANGO_LABEL_TEMPLATE_FOLDER") or (
|
359
|
+
BASE_DIR / "label_templates" / "2.25x1.25in"
|
346
360
|
)
|
347
361
|
CUPS_SERVERS = env.dict("DJANGO_CUPS_SERVERS")
|
348
362
|
|
@@ -355,8 +369,9 @@ SUBJECT_VISIT_MODEL = env.str("EDC_SUBJECT_VISIT_MODEL")
|
|
355
369
|
SUBJECT_VISIT_MISSED_MODEL = env.str("EDC_SUBJECT_VISIT_MISSED_MODEL")
|
356
370
|
SUBJECT_VISIT_MISSED_REASONS_MODEL = env.str("EDC_SUBJECT_VISIT_MISSED_REASONS_MODEL")
|
357
371
|
SUBJECT_REFUSAL_MODEL = env.str("EDC_SUBJECT_REFUSAL_MODEL")
|
358
|
-
EDC_BLOOD_RESULTS_MODEL_APP_LABEL = "meta_subject"
|
359
372
|
|
373
|
+
EDC_BLOOD_RESULTS_MODEL_APP_LABEL = "meta_subject"
|
374
|
+
EDC_DASHBOARD_APP_LABEL = "meta_dashboard"
|
360
375
|
EDC_NAVBAR_DEFAULT = env("EDC_NAVBAR_DEFAULT")
|
361
376
|
|
362
377
|
# dashboards
|
@@ -388,6 +403,18 @@ EDC_MNSI_MODEL = "meta_subject.mnsi"
|
|
388
403
|
|
389
404
|
EDC_OFFSTUDY_OFFSTUDY_MODEL = "meta_prn.endofstudy"
|
390
405
|
|
406
|
+
# edc-pharmacy
|
407
|
+
EDC_PDF_REPORTS_WATERMARK_WORD = env.str("EDC_PDF_REPORTS_WATERMARK_WORD")
|
408
|
+
EDC_PDF_REPORTS_WATERMARK_FONT = env.str("EDC_PDF_REPORTS_WATERMARK_FONT")
|
409
|
+
EDC_PDF_REPORTS_WATERMARK_FONTSIZE = env.int("EDC_PDF_REPORTS_WATERMARK_FONTSIZE")
|
410
|
+
EDC_PHARMACY_LABEL_WATERMARK_WORD = env.str("EDC_PHARMACY_LABEL_WATERMARK_WORD")
|
411
|
+
if EDC_PDF_REPORTS_WATERMARK_FONT:
|
412
|
+
EDC_PDF_REPORTS_WATERMARK_FONT = (
|
413
|
+
EDC_PDF_REPORTS_WATERMARK_FONT,
|
414
|
+
EDC_PDF_REPORTS_WATERMARK_FONTSIZE,
|
415
|
+
)
|
416
|
+
else:
|
417
|
+
EDC_PDF_REPORTS_WATERMARK_FONT = ()
|
391
418
|
# edc-protocol-incident
|
392
419
|
EDC_PROTOCOL_VIOLATION_TYPE = PROTOCOL_INCIDENT
|
393
420
|
|
@@ -405,9 +432,14 @@ EDC_RANDOMIZATION_SKIP_VERIFY_CHECKS = True
|
|
405
432
|
# edc-sites
|
406
433
|
EDC_SITES_MODULE_NAME = env.str("EDC_SITES_MODULE_NAME")
|
407
434
|
|
435
|
+
# meta_pharmacy
|
436
|
+
META_PHARMACY_RX_SUBSTITUTION_FILE = env.str("META_PHARMACY_RX_SUBSTITUTION_FILE")
|
437
|
+
|
408
438
|
# django-multisite
|
409
|
-
CACHE_MULTISITE_KEY_PREFIX =
|
439
|
+
CACHE_MULTISITE_KEY_PREFIX = "meta4"
|
410
440
|
SILENCED_SYSTEM_CHECKS = ["sites.E101"]
|
441
|
+
MULTISITE_SYNC_ALIAS_MANUALLY = True
|
442
|
+
MULTISITE_REGISTER_POST_MIGRATE_SYNC_ALIAS = False
|
411
443
|
|
412
444
|
# django-defender
|
413
445
|
# see if env.str("DJANGO_CACHE") == "redis" above
|
@@ -444,7 +476,7 @@ GIT_DIR = BASE_DIR
|
|
444
476
|
KEY_PATH = env.str("DJANGO_KEY_FOLDER")
|
445
477
|
AUTO_CREATE_KEYS = env("DJANGO_AUTO_CREATE_KEYS")
|
446
478
|
|
447
|
-
EXPORT_FOLDER = env.str("DJANGO_EXPORT_FOLDER") or
|
479
|
+
EXPORT_FOLDER = env.str("DJANGO_EXPORT_FOLDER") or Path("~/").expanduser()
|
448
480
|
|
449
481
|
# django_simple_history
|
450
482
|
SIMPLE_HISTORY_ENFORCE_HISTORY_MODEL_PERMISSIONS = True
|
@@ -469,6 +501,9 @@ DATA_DICTIONARY_APP_LABELS = [
|
|
469
501
|
"edc_offstudy",
|
470
502
|
]
|
471
503
|
|
504
|
+
# edc_form_runners
|
505
|
+
EDC_FORM_RUNNERS_ENABLED = False
|
506
|
+
|
472
507
|
# edc_protocol
|
473
508
|
EDC_PROTOCOL = env.str("EDC_PROTOCOL")
|
474
509
|
EDC_PROTOCOL_INSTITUTION_NAME = env.str("EDC_PROTOCOL_INSTITUTION_NAME")
|
@@ -498,49 +533,36 @@ if env("AWS_ENABLED"):
|
|
498
533
|
AWS_S3_OBJECT_PARAMETERS = {"CacheControl": "max-age=86400"}
|
499
534
|
AWS_LOCATION = env.str("AWS_LOCATION")
|
500
535
|
AWS_IS_GZIPPED = True
|
501
|
-
|
536
|
+
STORAGES = {"staticfiles": {"BACKEND": "storages.backends.s3boto3.S3Boto3Storage"}}
|
502
537
|
STATIC_URL = f"{os.path.join(AWS_S3_CUSTOM_DOMAIN, AWS_LOCATION)}/"
|
503
538
|
STATIC_ROOT = ""
|
504
539
|
elif DEBUG:
|
505
540
|
STATIC_URL = env.str("DJANGO_STATIC_URL")
|
506
|
-
STATIC_ROOT =
|
541
|
+
STATIC_ROOT = Path("~/source/edc_source/meta-edc/static/").expanduser()
|
507
542
|
else:
|
508
543
|
# run collectstatic, check nginx LOCATION
|
509
544
|
STATIC_URL = env.str("DJANGO_STATIC_URL")
|
510
545
|
STATIC_ROOT = env.str("DJANGO_STATIC_ROOT")
|
511
546
|
|
512
547
|
# CELERY
|
513
|
-
# see docs on setting up the broker
|
514
548
|
CELERY_ENABLED = env("CELERY_ENABLED")
|
515
549
|
if CELERY_ENABLED:
|
516
|
-
|
517
|
-
|
518
|
-
CELERY_BROKER_HOST = env.str("CELERY_BROKER_HOST")
|
519
|
-
CELERY_BROKER_PORT = env.str("CELERY_BROKER_PORT")
|
520
|
-
if DEBUG:
|
521
|
-
CELERY_BROKER_VHOST = f"{APP_NAME}_debug"
|
522
|
-
elif LIVE_SYSTEM:
|
523
|
-
CELERY_BROKER_VHOST = f"{APP_NAME}_production"
|
524
|
-
else:
|
525
|
-
CELERY_BROKER_VHOST = f"{APP_NAME}_uat"
|
550
|
+
CELERY_CACHE_BACKEND = "default"
|
551
|
+
if env.str("DJANGO_REDIS_PASSWORD"):
|
526
552
|
CELERY_BROKER_URL = (
|
527
|
-
f"
|
528
|
-
f"{CELERY_BROKER_HOST}:{CELERY_BROKER_PORT}/{CELERY_BROKER_VHOST}"
|
553
|
+
f"redis://:{quote(env.str('DJANGO_REDIS_PASSWORD'), safe='')}@127.0.0.1:6379/0"
|
529
554
|
)
|
530
|
-
|
531
|
-
|
532
|
-
|
533
|
-
|
534
|
-
|
535
|
-
|
536
|
-
|
537
|
-
|
538
|
-
|
539
|
-
|
540
|
-
|
541
|
-
# 'edc_data_manager.tasks.*': {'queue': 'normal'},
|
542
|
-
# }
|
543
|
-
|
555
|
+
CELERY_RESULT_BACKEND = (
|
556
|
+
f"redis://:{quote(env.str('DJANGO_REDIS_PASSWORD'), safe='')}@127.0.0.1:6379/0"
|
557
|
+
)
|
558
|
+
else:
|
559
|
+
CELERY_BROKER_URL = "redis://127.0.0.1:6379/0"
|
560
|
+
CELERY_RESULT_BACKEND = "redis://localhost:6379/0"
|
561
|
+
# CELERY_BEAT_SCHEDULER = "django_celery_beat.schedulers.DatabaseScheduler"
|
562
|
+
CELERY_ACCEPT_CONTENT = ["json"]
|
563
|
+
CELERY_TASK_SERIALIZER = "json"
|
564
|
+
CELERY_RESULT_SERIALIZER = "json"
|
565
|
+
CELERY_TIMEZONE = "UTC"
|
544
566
|
|
545
567
|
if "test" in sys.argv:
|
546
568
|
|
meta_edc/settings/live.py
CHANGED
@@ -4,16 +4,8 @@ from .defaults import * # noqa
|
|
4
4
|
|
5
5
|
print(f"Settings file {__file__}")
|
6
6
|
|
7
|
-
|
8
7
|
SITE_ID = SiteID(default=1)
|
9
8
|
EDC_SITES_UAT_DOMAIN = False
|
10
|
-
ALLOWED_HOSTS = [
|
11
|
-
"amana.tz.meta3.clinicedc.org",
|
12
|
-
"hindu-mandal.tz.meta3.clinicedc.org",
|
13
|
-
"mbagala.tz.meta3.clinicedc.org",
|
14
|
-
"mnazi-moja.tz.meta3.clinicedc.org",
|
15
|
-
"mwananyamala.tz.meta3.clinicedc.org",
|
16
|
-
"temeke.tz.meta3.clinicedc.org",
|
17
|
-
]
|
18
9
|
EDC_MODEL_ADMIN_CSS_THEME = "edc_indigo"
|
19
10
|
LIVE_SYSTEM = True
|
11
|
+
EDC_SITES_DOMAIN_SUFFIX = "meta4.clinicedc.org"
|
meta_edc/settings/uat.py
CHANGED
@@ -1,24 +1,11 @@
|
|
1
|
-
from importlib.metadata import version
|
2
|
-
|
3
1
|
from multisite import SiteID
|
4
2
|
|
5
3
|
from .defaults import * # noqa
|
6
4
|
|
7
5
|
print(f"Settings file {__file__}")
|
8
|
-
print(f"Version: {version('meta_edc')}")
|
9
6
|
|
10
7
|
SITE_ID = SiteID(default=1)
|
11
8
|
EDC_SITES_UAT_DOMAIN = True
|
12
|
-
EDC_CONSENT_BYPASS_CONSENT_DATETIME_VALIDATION = True
|
13
|
-
ALLOWED_HOSTS = [
|
14
|
-
"amana.uat.tz.meta4.clinicedc.org",
|
15
|
-
"hindu-mandal.uat.tz.meta4.clinicedc.org",
|
16
|
-
"mbagala.uat.tz.meta4.clinicedc.org",
|
17
|
-
"mnazi-moja.uat.tz.meta4.clinicedc.org",
|
18
|
-
"mwananyamala.uat.tz.meta4.clinicedc.org",
|
19
|
-
"temeke.uat.tz.meta4.clinicedc.org",
|
20
|
-
]
|
21
|
-
|
22
|
-
# edc_model_admin
|
23
9
|
EDC_MODEL_ADMIN_CSS_THEME = "edc_purple"
|
24
10
|
LIVE_SYSTEM = False
|
11
|
+
EDC_CONSENT_BYPASS_CONSENT_DATETIME_VALIDATION = True
|
@@ -4,7 +4,7 @@
|
|
4
4
|
{% block main %}
|
5
5
|
|
6
6
|
<style>
|
7
|
-
|
7
|
+
a { cursor: pointer; }
|
8
8
|
.bg-1 {
|
9
9
|
background-color: #428bca; /* dark blue */
|
10
10
|
color: #ffffff;
|
@@ -21,8 +21,8 @@
|
|
21
21
|
</style>
|
22
22
|
|
23
23
|
{{ block.super }}
|
24
|
-
|
25
|
-
|
24
|
+
<form id="switch_sites_form" method="post" action="{% url 'switch_sites_url' %}">{% csrf_token %}</form>
|
25
|
+
<form id="logout_form" method="post" action="{% url 'edc_auth_admin:logout' %}">{% csrf_token %}</form>
|
26
26
|
|
27
27
|
<div class="row">
|
28
28
|
|
@@ -56,14 +56,20 @@
|
|
56
56
|
{% if perms.edc_data_manager.nav_data_manager_section %}
|
57
57
|
<a href="{% url 'edc_data_manager:home_url' %}" class="list-group-item"><i class="fas fa-database fa-lg fa-fw"></i> Data Management</a>
|
58
58
|
{% endif %}
|
59
|
-
{% if perms.
|
60
|
-
<a href="{% url
|
59
|
+
{% if perms.meta_reports %}
|
60
|
+
<a href="{% url 'meta_reports:home_url' %}" class="list-group-item"><i class="fa-solid fa-stroopwafel fa-lg fa-fw"></i></i> QA Reports</a>
|
61
|
+
{% endif %}
|
62
|
+
{% if perms.edc_pharmacy.nav_pharmacy_section %}
|
63
|
+
<a href="{% url 'edc_pharmacy:home_url' %}" class="list-group-item"><i class="fas fa-prescription fa-lg fa-fw"></i> Pharmacy</a>
|
61
64
|
{% endif %}
|
62
65
|
{% if perms.edc_export %}
|
63
66
|
<a href="{% url 'edc_export:home_url' %}" class="list-group-item"><i class="fas fa-file-export fa-lg fa-fw"></i> Export data</a>
|
64
67
|
{% endif %}
|
65
|
-
|
66
|
-
<a href="{% url '
|
68
|
+
{% if perms.edc_auth.change_userprofile %}
|
69
|
+
<a href="{% url 'edc_auth:home_url' %}" class="list-group-item"><i class="fas fa-users fa-lg fa-fw"></i> Account Management</a>
|
70
|
+
{% endif %}
|
71
|
+
<a onclick="document.getElementById('switch_sites_form').submit();" class="list-group-item" title="{% url 'switch_sites_url' %}"><i class="fas fa-arrows-alt fa-lg fa-fw"></i> Switch sites</a>
|
72
|
+
<a onclick="document.getElementById('logout_form').submit();" class="list-group-item" title="{% url 'edc_auth_admin:logout' %}"><i class="fas fa-sign-out-alt fa-lg fa-fw"></i> Log out</a>
|
67
73
|
</div>
|
68
74
|
</div>
|
69
75
|
</div>
|
@@ -12,8 +12,7 @@ from django.apps import apps as django_apps
|
|
12
12
|
from django.conf import settings
|
13
13
|
from django.contrib.auth import get_user_model
|
14
14
|
from django.contrib.sites.models import Site
|
15
|
-
from django.test import tag
|
16
|
-
from django.test.utils import override_settings
|
15
|
+
from django.test.utils import override_settings, tag
|
17
16
|
from django.urls.base import reverse
|
18
17
|
from django.urls.exceptions import NoReverseMatch
|
19
18
|
from django_extensions.management.color import color_style
|
@@ -25,7 +24,7 @@ from edc_auth.auth_updater import AuthUpdater
|
|
25
24
|
from edc_auth.constants import AUDITOR_ROLE, CLINICIAN_ROLE, STAFF_ROLE
|
26
25
|
from edc_auth.site_auths import site_auths
|
27
26
|
from edc_consent.site_consents import site_consents
|
28
|
-
from edc_constants.constants import
|
27
|
+
from edc_constants.constants import YES
|
29
28
|
from edc_dashboard.url_names import url_names
|
30
29
|
from edc_export.constants import DATA_EXPORTER_ROLE
|
31
30
|
from edc_lab.auth_objects import LAB_TECHNICIAN_ROLE
|
@@ -86,8 +85,10 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
86
85
|
import_module("edc_adverse_event.auths")
|
87
86
|
import_module("edc_appointment.auths")
|
88
87
|
import_module("edc_consent.auths")
|
88
|
+
import_module("edc_pylabels.auths")
|
89
89
|
import_module("edc_dashboard.auths")
|
90
90
|
import_module("edc_data_manager.auths")
|
91
|
+
import_module("edc_qareports.auths")
|
91
92
|
import_module("edc_export.auths")
|
92
93
|
import_module("edc_lab.auths")
|
93
94
|
import_module("edc_lab_dashboard.auths")
|
@@ -217,7 +218,7 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
217
218
|
else:
|
218
219
|
self.assertNotIn(label, response)
|
219
220
|
|
220
|
-
@
|
221
|
+
@skip
|
221
222
|
@time_machine.travel(datetime(2019, 6, 11, 8, 00, tzinfo=ZoneInfo("UTC")))
|
222
223
|
def test_screening_form_phase3(self):
|
223
224
|
self.login(superuser=False, roles=[STAFF_ROLE, CLINICIAN_ROLE])
|
@@ -241,18 +242,18 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
241
242
|
add_screening_part_two,
|
242
243
|
screening_identifier,
|
243
244
|
) = self.webtest_for_screening_form_part_one(part_one_data)
|
244
|
-
|
245
|
-
|
246
|
-
|
247
|
-
"
|
248
|
-
|
249
|
-
if part_two_data["appt_datetime"] < get_utcnow():
|
250
|
-
part_two_data.update(p3_ltfu=PENDING)
|
251
|
-
# part_two_data.update(p3_ltfu_date=get_utcnow().date())
|
252
|
-
# part_two_data.update()
|
253
|
-
|
254
|
-
traveller = time_machine.travel(part_two_data["part_two_report_datetime"])
|
245
|
+
|
246
|
+
# travel 10 min into the future
|
247
|
+
traveller = time_machine.travel(
|
248
|
+
part_one_data["report_datetime"] + relativedelta(minutes=10)
|
249
|
+
)
|
255
250
|
traveller.start()
|
251
|
+
part_two_data = deepcopy(
|
252
|
+
get_part_two_eligible_options(
|
253
|
+
report_datetime=get_utcnow() + relativedelta(minutes=1)
|
254
|
+
)
|
255
|
+
)
|
256
|
+
part_two_data["appt_datetime"] = get_utcnow() + relativedelta(days=10)
|
256
257
|
part_two_data.update(
|
257
258
|
dict(
|
258
259
|
part_two_report_datetime_0=part_two_data["part_two_report_datetime"].strftime(
|
@@ -272,11 +273,14 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
272
273
|
) = self.webtest_for_screening_form_part_two(
|
273
274
|
home_page, add_screening_part_two, screening_identifier, part_two_data
|
274
275
|
)
|
276
|
+
traveller.stop()
|
275
277
|
|
278
|
+
# travel 10 days into the future
|
276
279
|
traveller = time_machine.travel(part_two_data["appt_datetime"])
|
277
280
|
traveller.start()
|
278
|
-
part_three_data = deepcopy(
|
279
|
-
|
281
|
+
part_three_data = deepcopy(
|
282
|
+
get_part_three_eligible_options(report_datetime=get_utcnow())
|
283
|
+
)
|
280
284
|
|
281
285
|
traveller = time_machine.travel(part_two_data.get("part_three_report_datetime"))
|
282
286
|
traveller.start()
|
@@ -311,7 +315,6 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
311
315
|
self.assertIn(screening_identifier, screening_listboard_page)
|
312
316
|
self.assertIn("Consent", screening_listboard_page)
|
313
317
|
|
314
|
-
@tag("1")
|
315
318
|
def webtest_for_screening_form_part_one(self, part_one_data):
|
316
319
|
home_page = self.app.get(reverse("home_url"), user=self.user, status=200)
|
317
320
|
screening_listboard_page = home_page.click(description="Screening", index=1)
|
@@ -367,7 +370,7 @@ class AdminSiteTest(MetaTestCaseMixin, WebTest):
|
|
367
370
|
errorlist = soup.find_all("ul", "errorlist")
|
368
371
|
self.assertEqual([], errorlist)
|
369
372
|
# redirects back to listboard
|
370
|
-
obj = SubjectScreening.objects.
|
373
|
+
obj = SubjectScreening.objects.get(screening_identifier=screening_identifier)
|
371
374
|
url = reverse(screening_listboard_url, args=(obj.screening_identifier,))
|
372
375
|
self.assertRedirects(page, url)
|
373
376
|
# shows P1 | P2 | P3 | PENDING
|
meta_edc/urls.py
CHANGED
@@ -1,8 +1,8 @@
|
|
1
1
|
from django.conf import settings
|
2
|
+
from django.contrib.auth.views import LogoutView
|
2
3
|
from django.urls.conf import include, path, re_path
|
3
4
|
from django.views.defaults import page_not_found, server_error # noqa
|
4
5
|
from django.views.generic import RedirectView
|
5
|
-
from edc_auth.views import LogoutView
|
6
6
|
from edc_dashboard.utils import get_index_page
|
7
7
|
from edc_dashboard.views import AdministrationView
|
8
8
|
from edc_utils.paths_for_urlpatterns import paths_for_urlpatterns
|
@@ -22,6 +22,7 @@ urlpatterns = [
|
|
22
22
|
path("accounts/", include("edc_auth.urls_for_accounts", namespace="auth")),
|
23
23
|
path("administration/", AdministrationView.as_view(), name="administration_url"),
|
24
24
|
path("subject/", include("meta_dashboard.urls")),
|
25
|
+
*paths_for_urlpatterns("edc_pylabels"),
|
25
26
|
*paths_for_urlpatterns("edc_auth"),
|
26
27
|
*paths_for_urlpatterns("edc_action_item"),
|
27
28
|
*paths_for_urlpatterns("edc_adverse_event"),
|
@@ -56,15 +57,17 @@ urlpatterns = [
|
|
56
57
|
*paths_for_urlpatterns("edc_sites"),
|
57
58
|
*paths_for_urlpatterns("edc_subject_dashboard"),
|
58
59
|
*paths_for_urlpatterns("edc_unblinding"),
|
60
|
+
*paths_for_urlpatterns("edc_qareports"),
|
59
61
|
*paths_for_urlpatterns("edc_visit_schedule"),
|
60
|
-
# *paths_for_urlpatterns("canned_views"),
|
61
62
|
*paths_for_urlpatterns("meta_ae"),
|
62
63
|
*paths_for_urlpatterns("meta_consent"),
|
63
64
|
*paths_for_urlpatterns("meta_export"),
|
64
65
|
*paths_for_urlpatterns("meta_lists"),
|
66
|
+
*paths_for_urlpatterns("meta_pharmacy"),
|
65
67
|
*paths_for_urlpatterns("meta_prn"),
|
66
68
|
*paths_for_urlpatterns("meta_screening"),
|
67
69
|
*paths_for_urlpatterns("meta_subject"),
|
70
|
+
*paths_for_urlpatterns("meta_reports"),
|
68
71
|
]
|
69
72
|
|
70
73
|
if settings.DEFENDER_ENABLED:
|
meta_edc/wsgi.py
CHANGED
meta_edc/wsgi_live.py
CHANGED
meta_edc/wsgi_uat.py
CHANGED
File without changes
|