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