endoreg-db 0.6.4__py3-none-any.whl → 0.8.2__py3-none-any.whl
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- endoreg_db/admin.py +26 -26
- endoreg_db/api_urls.py +4 -0
- endoreg_db/apps.py +12 -0
- endoreg_db/assets/dummy_model.ckpt +1 -0
- endoreg_db/codemods/readme.md +88 -0
- endoreg_db/codemods/rename_datetime_fields.py +92 -0
- endoreg_db/config/env.py +101 -0
- endoreg_db/data/__init__.py +12 -0
- endoreg_db/data/ai_model/data.yaml +1 -1
- endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
- endoreg_db/data/ai_model_label/label-set/data.yaml +20 -1
- endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
- endoreg_db/data/center/data.yaml +13 -12
- endoreg_db/data/center_shift/ukw.yaml +9 -0
- endoreg_db/data/db_summary.csv +58 -0
- endoreg_db/data/db_summary.xlsx +0 -0
- endoreg_db/data/disease/misc.yaml +1 -2
- endoreg_db/data/endoscopy_processor/data.yaml +3 -0
- endoreg_db/data/event/cardiology.yaml +0 -13
- endoreg_db/data/examination/examinations/data.yaml +14 -9
- endoreg_db/data/examination_indication/endoscopy.yaml +30 -30
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +11 -11
- endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
- endoreg_db/data/finding/anatomy_colon.yaml +128 -0
- endoreg_db/data/finding/colonoscopy.yaml +40 -0
- endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
- endoreg_db/data/finding/complication.yaml +16 -0
- endoreg_db/data/finding/data.yaml +3 -46
- endoreg_db/data/finding/examination_setting.yaml +16 -0
- endoreg_db/data/finding/medication_related.yaml +18 -0
- endoreg_db/data/finding/outcome.yaml +12 -0
- endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
- endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
- endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
- endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
- endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
- endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
- endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
- endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
- endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
- endoreg_db/data/finding_classification/medication_related.yaml +23 -0
- endoreg_db/data/finding_classification/visualized.yaml +33 -0
- endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_circularity_default.yaml +0 -2
- endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_nice.yaml +4 -7
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_paris.yaml +0 -8
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_planarity_default.yaml +6 -13
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_surface_intact_default.yaml +3 -6
- endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} +11 -22
- endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
- endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
- endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
- endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
- endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
- endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
- endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +8 -3
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +6 -6
- endoreg_db/data/finding_type/data.yaml +23 -10
- endoreg_db/data/gender/data.yaml +8 -1
- endoreg_db/data/information_source/annotation.yaml +6 -0
- endoreg_db/data/information_source/prediction.yaml +7 -0
- endoreg_db/data/information_source_type/data.yaml +8 -0
- endoreg_db/data/lab_value/misc.yaml +43 -0
- endoreg_db/data/medication/anticoagulation.yaml +5 -5
- endoreg_db/data/medication/tah.yaml +5 -5
- endoreg_db/data/medication_intake_time/base.yaml +4 -4
- endoreg_db/data/names_first/first_names.yaml +3 -0
- endoreg_db/data/pdf_type/data.yaml +26 -2
- endoreg_db/data/qualification/endoscopy.yaml +36 -0
- endoreg_db/data/qualification/m2.yaml +39 -0
- endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
- endoreg_db/data/qualification/sonography.yaml +36 -0
- endoreg_db/data/qualification_type/base.yaml +29 -0
- endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
- endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +5 -0
- endoreg_db/data/requirement/age.yaml +26 -0
- endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/requirement/disease_cardiovascular.yaml +6 -6
- endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +9 -6
- endoreg_db/data/requirement/disease_hepatology.yaml +1 -1
- endoreg_db/data/requirement/disease_misc.yaml +3 -3
- endoreg_db/data/requirement/disease_renal.yaml +18 -2
- endoreg_db/data/requirement/{colonoscopy_indications.yaml → endoscopy_bleeding_risk.yaml} +6 -3
- endoreg_db/data/requirement/event_cardiology.yaml +17 -17
- endoreg_db/data/requirement/event_requirements.yaml +145 -0
- endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/requirement/gender.yaml +25 -0
- endoreg_db/data/requirement/lab_value.yaml +352 -31
- endoreg_db/data/requirement/medication.yaml +93 -0
- endoreg_db/data/requirement_operator/age.yaml +13 -0
- endoreg_db/data/requirement_operator/lab_operators.yaml +36 -35
- endoreg_db/data/requirement_operator/model_operators.yaml +13 -7
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
- endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +42 -2
- endoreg_db/data/requirement_type/requirement_types.yaml +82 -0
- endoreg_db/data/shift/endoscopy.yaml +21 -0
- endoreg_db/data/shift_type/base.yaml +35 -0
- endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
- endoreg_db/data/unit/concentration.yaml +23 -0
- endoreg_db/exceptions.py +19 -0
- endoreg_db/forms/patient_finding_intervention_form.py +4 -5
- endoreg_db/forms/patient_form.py +7 -6
- endoreg_db/forms/questionnaires/__init__.py +1 -1
- endoreg_db/forms/questionnaires/tto_questionnaire.py +19 -19
- endoreg_db/helpers/count_db.py +45 -0
- endoreg_db/helpers/data_loader.py +208 -0
- endoreg_db/helpers/default_objects.py +359 -0
- endoreg_db/helpers/download_segmentation_model.py +31 -0
- endoreg_db/helpers/interact.py +6 -0
- endoreg_db/helpers/test_video_helper.py +119 -0
- endoreg_db/logger_conf.py +140 -0
- endoreg_db/management/__init__.py +1 -0
- endoreg_db/management/commands/__init__.py +1 -0
- endoreg_db/management/commands/anonymize_video.py +0 -0
- endoreg_db/management/commands/check_auth.py +125 -0
- endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
- endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
- endoreg_db/management/commands/fix_video_paths.py +165 -0
- endoreg_db/management/commands/import_fallback_video.py +203 -0
- endoreg_db/management/commands/import_report.py +298 -0
- endoreg_db/management/commands/import_video.py +422 -0
- endoreg_db/management/commands/import_video_with_classification.py +367 -0
- endoreg_db/management/commands/init_default_ai_model.py +112 -0
- endoreg_db/management/commands/load_ai_model_data.py +2 -7
- endoreg_db/management/commands/load_base_db_data.py +1 -0
- endoreg_db/management/commands/load_endoscope_data.py +2 -2
- endoreg_db/management/commands/load_examination_indication_data.py +2 -3
- endoreg_db/management/commands/load_finding_data.py +49 -92
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +0 -1
- endoreg_db/management/commands/load_information_source.py +13 -7
- endoreg_db/management/commands/load_name_data.py +37 -0
- endoreg_db/management/commands/load_qualification_data.py +59 -0
- endoreg_db/management/commands/load_requirement_data.py +30 -6
- endoreg_db/management/commands/load_shift_data.py +60 -0
- endoreg_db/management/commands/load_tag_data.py +57 -0
- endoreg_db/management/commands/register_ai_model.py +1 -1
- endoreg_db/management/commands/start_filewatcher.py +106 -0
- endoreg_db/management/commands/storage_management.py +548 -0
- endoreg_db/management/commands/summarize_db_content.py +189 -0
- endoreg_db/management/commands/validate_video.py +204 -0
- endoreg_db/management/commands/validate_video_files.py +161 -0
- endoreg_db/management/commands/video_validation.py +22 -0
- endoreg_db/migrations/0001_initial.py +625 -813
- endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
- endoreg_db/models/__init__.py +270 -307
- endoreg_db/models/administration/__init__.py +116 -0
- endoreg_db/models/{ai_model → administration/ai}/__init__.py +6 -1
- endoreg_db/models/administration/ai/active_model.py +35 -0
- endoreg_db/models/administration/ai/ai_model.py +156 -0
- endoreg_db/models/{ai_model → administration/ai}/model_type.py +6 -1
- endoreg_db/models/administration/case/__init__.py +19 -0
- endoreg_db/models/administration/case/case.py +114 -0
- endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +3 -3
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +3 -10
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +2 -4
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +1 -3
- endoreg_db/models/{center → administration/center}/__init__.py +3 -1
- endoreg_db/models/administration/center/center.py +61 -0
- endoreg_db/models/administration/center/center_product.py +64 -0
- endoreg_db/models/{center → administration/center}/center_resource.py +19 -3
- endoreg_db/models/administration/center/center_shift.py +88 -0
- endoreg_db/models/administration/center/center_waste.py +30 -0
- endoreg_db/models/administration/permissions/__init__.py +44 -0
- endoreg_db/models/administration/person/__init__.py +24 -0
- endoreg_db/models/administration/person/employee/__init__.py +3 -0
- endoreg_db/models/administration/person/employee/employee.py +35 -0
- endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
- endoreg_db/models/administration/person/employee/employee_type.py +42 -0
- endoreg_db/models/administration/person/examiner/__init__.py +4 -0
- endoreg_db/models/administration/person/examiner/examiner.py +54 -0
- endoreg_db/models/administration/person/names/__init__.py +0 -0
- endoreg_db/models/{persons → administration/person/names}/first_name.py +1 -1
- endoreg_db/models/{persons → administration/person/names}/last_name.py +2 -3
- endoreg_db/models/administration/person/patient/__init__.py +5 -0
- endoreg_db/models/administration/person/patient/patient.py +460 -0
- endoreg_db/models/administration/person/profession/__init__.py +24 -0
- endoreg_db/models/administration/person/user/__init__.py +5 -0
- endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
- endoreg_db/models/administration/product/product.py +97 -0
- endoreg_db/models/administration/product/product_group.py +39 -0
- endoreg_db/models/administration/product/product_material.py +54 -0
- endoreg_db/models/{product → administration/product}/product_weight.py +9 -0
- endoreg_db/models/{product → administration/product}/reference_product.py +26 -11
- endoreg_db/models/administration/qualification/__init__.py +7 -0
- endoreg_db/models/administration/qualification/qualification.py +37 -0
- endoreg_db/models/administration/qualification/qualification_type.py +35 -0
- endoreg_db/models/administration/shift/__init__.py +9 -0
- endoreg_db/models/administration/shift/scheduled_days.py +69 -0
- endoreg_db/models/administration/shift/shift.py +51 -0
- endoreg_db/models/administration/shift/shift_type.py +108 -0
- endoreg_db/models/label/__init__.py +24 -1
- endoreg_db/models/label/annotation/__init__.py +12 -0
- endoreg_db/models/label/annotation/image_classification.py +84 -0
- endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
- endoreg_db/models/label/label.py +45 -74
- endoreg_db/models/label/label_set.py +53 -0
- endoreg_db/models/label/label_type.py +29 -0
- endoreg_db/models/label/label_video_segment/__init__.py +3 -0
- endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
- endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
- endoreg_db/models/label/video_segmentation_label.py +31 -0
- endoreg_db/models/{annotation → label}/video_segmentation_labelset.py +7 -0
- endoreg_db/models/media/__init__.py +14 -0
- endoreg_db/models/media/frame/__init__.py +3 -0
- endoreg_db/models/media/frame/frame.py +111 -0
- endoreg_db/models/media/pdf/__init__.py +11 -0
- endoreg_db/models/media/pdf/raw_pdf.py +608 -0
- endoreg_db/models/media/pdf/report_file.py +162 -0
- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
- endoreg_db/models/media/video/__init__.py +4 -0
- endoreg_db/models/media/video/create_from_file.py +336 -0
- endoreg_db/models/media/video/pipe_1.py +207 -0
- endoreg_db/models/media/video/pipe_2.py +105 -0
- endoreg_db/models/media/video/refactor_plan.md +0 -0
- endoreg_db/models/media/video/video_file.py +680 -0
- endoreg_db/models/media/video/video_file_ai.py +443 -0
- endoreg_db/models/media/video/video_file_anonymize.py +348 -0
- endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
- endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
- endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
- endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
- endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
- endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
- endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +129 -0
- endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
- endoreg_db/models/media/video/video_file_frames.py +0 -0
- endoreg_db/models/media/video/video_file_io.py +166 -0
- endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
- endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
- endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
- endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
- endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
- endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
- endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
- endoreg_db/models/media/video/video_file_meta.py +11 -0
- endoreg_db/models/media/video/video_file_segments.py +209 -0
- endoreg_db/models/medical/__init__.py +146 -0
- endoreg_db/models/{contraindication → medical/contraindication}/__init__.py +1 -5
- endoreg_db/models/{disease.py → medical/disease.py} +60 -52
- endoreg_db/models/{event.py → medical/event.py} +31 -54
- endoreg_db/models/{examination → medical/examination}/__init__.py +1 -1
- endoreg_db/models/medical/examination/examination.py +148 -0
- endoreg_db/models/{examination → medical/examination}/examination_indication.py +64 -35
- endoreg_db/models/{examination → medical/examination}/examination_time.py +0 -4
- endoreg_db/models/{examination → medical/examination}/examination_time_type.py +1 -8
- endoreg_db/models/{examination → medical/examination}/examination_type.py +1 -7
- endoreg_db/models/medical/finding/__init__.py +18 -0
- endoreg_db/models/medical/finding/finding.py +96 -0
- endoreg_db/models/medical/finding/finding_classification.py +142 -0
- endoreg_db/models/{finding → medical/finding}/finding_intervention.py +2 -10
- endoreg_db/models/medical/finding/finding_type.py +35 -0
- endoreg_db/models/medical/hardware/__init__.py +8 -0
- endoreg_db/models/{hardware → medical/hardware}/endoscope.py +28 -23
- endoreg_db/models/medical/laboratory/__init__.py +5 -0
- endoreg_db/models/medical/laboratory/lab_value.py +419 -0
- endoreg_db/models/{medication → medical/medication}/medication.py +1 -3
- endoreg_db/models/{medication → medical/medication}/medication_indication_type.py +8 -3
- endoreg_db/models/{medication → medical/medication}/medication_intake_time.py +21 -3
- endoreg_db/models/{medication → medical/medication}/medication_schedule.py +13 -5
- endoreg_db/models/{organ → medical/organ}/__init__.py +3 -6
- endoreg_db/models/medical/patient/__init__.py +56 -0
- endoreg_db/models/medical/patient/medication_examples.py +38 -0
- endoreg_db/models/medical/patient/patient_disease.py +63 -0
- endoreg_db/models/medical/patient/patient_event.py +75 -0
- endoreg_db/models/medical/patient/patient_examination.py +249 -0
- endoreg_db/models/{persons → medical}/patient/patient_examination_indication.py +21 -9
- endoreg_db/models/medical/patient/patient_finding.py +357 -0
- endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
- endoreg_db/models/{patient → medical/patient}/patient_finding_intervention.py +15 -1
- endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
- endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +40 -15
- endoreg_db/models/medical/patient/patient_medication.py +104 -0
- endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
- endoreg_db/models/{risk → medical/risk}/risk_type.py +0 -4
- endoreg_db/models/{data_file/metadata → metadata}/__init__.py +6 -0
- endoreg_db/models/metadata/frame_ocr_result.py +0 -0
- endoreg_db/models/metadata/model_meta.py +193 -0
- endoreg_db/models/metadata/model_meta_logic.py +236 -0
- endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +28 -13
- endoreg_db/models/metadata/sensitive_meta.py +288 -0
- endoreg_db/models/metadata/sensitive_meta_logic.py +643 -0
- endoreg_db/models/metadata/video_meta.py +332 -0
- endoreg_db/models/metadata/video_prediction_logic.py +190 -0
- endoreg_db/models/metadata/video_prediction_meta.py +270 -0
- endoreg_db/models/other/__init__.py +17 -0
- endoreg_db/models/other/distribution/date_value_distribution.py +0 -2
- endoreg_db/models/other/distribution/numeric_value_distribution.py +30 -2
- endoreg_db/models/{emission → other/emission}/emission_factor.py +15 -6
- endoreg_db/models/{persons → other}/gender.py +8 -3
- endoreg_db/models/other/information_source.py +159 -0
- endoreg_db/models/other/material.py +10 -2
- endoreg_db/models/other/resource.py +6 -2
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- endoreg_db/models/{rules → rule}/ruleset.py +0 -2
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- endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +0 -19
- endoreg_db/models/data_file/base_classes/utils.py +0 -58
- endoreg_db/models/data_file/frame.py +0 -29
- endoreg_db/models/data_file/import_classes/__init__.py +0 -18
- endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
- endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
- endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
- endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -254
- endoreg_db/models/data_file/import_classes/raw_video.py +0 -290
- endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -290
- endoreg_db/models/data_file/metadata/video_meta.py +0 -199
- endoreg_db/models/data_file/report_file.py +0 -56
- endoreg_db/models/data_file/video/__init__.py +0 -11
- endoreg_db/models/data_file/video/import_meta.py +0 -25
- endoreg_db/models/data_file/video/video.py +0 -196
- endoreg_db/models/data_file/video_segment.py +0 -214
- endoreg_db/models/examination/examination.py +0 -67
- endoreg_db/models/finding/__init__.py +0 -11
- endoreg_db/models/finding/finding.py +0 -75
- endoreg_db/models/finding/finding_location_classification.py +0 -94
- endoreg_db/models/finding/finding_morphology_classification.py +0 -89
- endoreg_db/models/finding/finding_type.py +0 -22
- endoreg_db/models/hardware/__init__.py +0 -2
- endoreg_db/models/information_source.py +0 -65
- endoreg_db/models/laboratory/__init__.py +0 -1
- endoreg_db/models/laboratory/lab_value.py +0 -162
- endoreg_db/models/logging/__init__.py +0 -11
- endoreg_db/models/logging/agl_service.py +0 -19
- endoreg_db/models/logging/base.py +0 -22
- endoreg_db/models/logging/log_type.py +0 -23
- endoreg_db/models/logging/network_device.py +0 -27
- endoreg_db/models/lx/__init__.py +0 -4
- endoreg_db/models/lx/client.py +0 -57
- endoreg_db/models/lx/identity.py +0 -34
- endoreg_db/models/lx/permission.py +0 -18
- endoreg_db/models/lx/user.py +0 -16
- endoreg_db/models/network/__init__.py +0 -9
- endoreg_db/models/network/agl_service.py +0 -38
- endoreg_db/models/network/network_device.py +0 -58
- endoreg_db/models/network/network_device_type.py +0 -23
- endoreg_db/models/other/distribution.py +0 -5
- endoreg_db/models/patient/__init__.py +0 -24
- endoreg_db/models/patient/patient_examination.py +0 -182
- endoreg_db/models/patient/patient_finding.py +0 -143
- endoreg_db/models/patient/patient_finding_location.py +0 -120
- endoreg_db/models/patient/patient_finding_morphology.py +0 -166
- endoreg_db/models/permissions/__init__.py +0 -44
- endoreg_db/models/persons/__init__.py +0 -34
- endoreg_db/models/persons/examiner/__init__.py +0 -2
- endoreg_db/models/persons/examiner/examiner.py +0 -60
- endoreg_db/models/persons/examiner/examiner_type.py +0 -2
- endoreg_db/models/persons/patient/__init__.py +0 -8
- endoreg_db/models/persons/patient/patient.py +0 -389
- endoreg_db/models/persons/patient/patient_disease.py +0 -22
- endoreg_db/models/persons/patient/patient_event.py +0 -52
- endoreg_db/models/persons/patient/patient_lab_sample.py +0 -108
- endoreg_db/models/persons/patient/patient_medication.py +0 -59
- endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -88
- endoreg_db/models/persons/portal_user_information.py +0 -27
- endoreg_db/models/prediction/__init__.py +0 -8
- endoreg_db/models/prediction/image_classification.py +0 -51
- endoreg_db/models/prediction/video_prediction_meta.py +0 -306
- endoreg_db/models/product/product.py +0 -110
- endoreg_db/models/product/product_group.py +0 -27
- endoreg_db/models/product/product_material.py +0 -28
- endoreg_db/models/questionnaires/__init__.py +0 -114
- endoreg_db/models/quiz/__init__.py +0 -9
- endoreg_db/models/quiz/quiz_answer.py +0 -41
- endoreg_db/models/quiz/quiz_question.py +0 -54
- endoreg_db/models/report_reader/report_reader_config.py +0 -53
- endoreg_db/models/rules/__init__.py +0 -5
- endoreg_db/queries/get/__init__.py +0 -6
- endoreg_db/queries/get/center.py +0 -42
- endoreg_db/queries/get/model.py +0 -13
- endoreg_db/queries/get/patient.py +0 -14
- endoreg_db/queries/get/patient_examination.py +0 -20
- endoreg_db/queries/get/report_file.py +0 -33
- endoreg_db/queries/get/video.py +0 -31
- endoreg_db/serializers/ai_model.py +0 -19
- endoreg_db/serializers/annotation.py +0 -14
- endoreg_db/serializers/center.py +0 -11
- endoreg_db/serializers/examination.py +0 -33
- endoreg_db/serializers/frame.py +0 -9
- endoreg_db/serializers/hardware.py +0 -21
- endoreg_db/serializers/label.py +0 -22
- endoreg_db/serializers/patient.py +0 -33
- endoreg_db/serializers/prediction.py +0 -10
- endoreg_db/serializers/raw_pdf_anony_text_validation.py +0 -137
- endoreg_db/serializers/report_file.py +0 -7
- endoreg_db/serializers/video.py +0 -20
- endoreg_db/serializers/video_segmentation.py +0 -574
- endoreg_db/tests.py +0 -3
- endoreg_db/utils/legacy_ocr.py +0 -201
- endoreg_db/utils/video/transcode_videofile.py +0 -111
- endoreg_db/views/patient_views.py +0 -90
- endoreg_db/views/raw_pdf_anony_text_validation_views.py +0 -95
- endoreg_db/views/raw_pdf_meta_validation_views.py +0 -111
- endoreg_db/views/raw_video_meta_validation_views.py +0 -148
- endoreg_db/views/report_views.py +0 -96
- endoreg_db/views/video_segmentation_views.py +0 -166
- endoreg_db-0.6.4.dist-info/METADATA +0 -161
- endoreg_db-0.6.4.dist-info/RECORD +0 -470
- /endoreg_db/{case_generator/__init__.py → api/serializers/finding_descriptions.py} +0 -0
- /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
- /endoreg_db/{queries/get/prediction.py → data/shift/m2.yaml} +0 -0
- /endoreg_db/{queries/get/video_import_meta.py → factories/__init__.py} +0 -0
- /endoreg_db/{queries/get/video_prediction_meta.py → helpers/__init__.py} +0 -0
- /endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +0 -0
- /endoreg_db/models/{persons → administration/person}/person.py +0 -0
- /endoreg_db/models/{product → administration/product}/__init__.py +0 -0
- /endoreg_db/models/{report_reader → media/pdf/report_reader}/__init__.py +0 -0
- /endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +0 -0
- /endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +0 -0
- /endoreg_db/models/{medication → medical/medication}/__init__.py +0 -0
- /endoreg_db/models/{medication → medical/medication}/medication_indication.py +0 -0
- /endoreg_db/models/{risk → medical/risk}/__init__.py +0 -0
- /endoreg_db/models/{risk → medical/risk}/risk.py +0 -0
- /endoreg_db/models/{emission → other/emission}/__init__.py +0 -0
- /endoreg_db/models/{rules → rule}/rule_applicator.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/case_generator.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/lab_sample_factory.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/utils.py +0 -0
- /endoreg_db/views/{csrf.py → misc/csrf.py} +0 -0
- {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.2.dist-info}/WHEEL +0 -0
- {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.2.dist-info}/licenses/LICENSE +0 -0
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from endoreg_db.models import VideoFile
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from django.shortcuts import get_object_or_404
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from rest_framework import status
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from rest_framework.response import Response
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from rest_framework.views import APIView
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class VideoReprocessView(APIView):
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"""
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POST /api/video-reprocess/{id}/ - Reprocess video with updated settings
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"""
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permission_classes = [EnvironmentAwarePermission]
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video = get_object_or_404(VideoFile, pk=pk)
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return Response(
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)
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return Response(
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"""
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Video Streaming Views (Phase 3.2)
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Separate view for streaming raw and processed video files.
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Created: October 9, 2025
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import os
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import re
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import logging
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from ...models import VideoFile
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"""
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Parse HTTP Range header and return (start, end) byte positions.
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Args:
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def stream_file_chunk(file_path: Path, start: int, end: int, chunk_size: int = 8192):
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Generator that yields chunks of a file within the specified byte range.
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def _stream_video_file(vf: VideoFile, frontend_origin: str, file_type: str = 'raw', range_header: Optional[str] = None) -> FileResponse | StreamingHttpResponse:
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# FIX: Handle both relative and absolute paths
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# Django FileField.path returns .name if MEDIA_ROOT is not set
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# Import services store relative paths like "videos/UUID.mp4"
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# We need to resolve to absolute path: STORAGE_DIR / "videos/UUID.mp4"
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file_name = file_ref.name
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else:
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# Relative path - make absolute by prepending STORAGE_DIR
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path = STORAGE_DIR / file_name
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# Validate file exists on disk
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# Validate file size before streaming
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try:
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file_size = path.stat().st_size
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if file_size == 0:
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raise Http404("Video file is empty")
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except OSError as e:
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# Determine MIME type
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mime, _ = mimetypes.guess_type(str(path))
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content_type = mime or 'video/mp4' # Default to mp4 if detection fails
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# ✅ NEW: HTTP Range Request support for video seeking
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if range_header:
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try:
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# Parse Range header
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start, end = parse_range_header(range_header, file_size)
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logger.debug("Range request: bytes=%d-%d (total: %d)", start, end, file_size)
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# Stream partial content (HTTP 206)
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response = StreamingHttpResponse(
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|
+
stream_file_chunk(path, start, end),
|
|
168
|
+
status=206, # Partial Content
|
|
169
|
+
content_type=content_type
|
|
170
|
+
)
|
|
171
|
+
|
|
172
|
+
# Set Range-specific headers
|
|
173
|
+
response['Content-Range'] = f'bytes {start}-{end}/{file_size}'
|
|
174
|
+
response['Content-Length'] = str(end - start + 1)
|
|
175
|
+
response['Accept-Ranges'] = 'bytes'
|
|
176
|
+
response['Content-Disposition'] = f'inline; filename="{path.name}"'
|
|
177
|
+
|
|
178
|
+
except ValueError as e:
|
|
179
|
+
# Invalid range header - return 416 Range Not Satisfiable
|
|
180
|
+
logger.warning("Invalid Range header: %s", str(e))
|
|
181
|
+
response = StreamingHttpResponse(
|
|
182
|
+
status=416, # Range Not Satisfiable
|
|
183
|
+
content_type=content_type
|
|
184
|
+
)
|
|
185
|
+
response['Content-Range'] = f'bytes */{file_size}'
|
|
186
|
+
|
|
187
|
+
else:
|
|
188
|
+
# No Range header - stream entire file (HTTP 200)
|
|
189
|
+
try:
|
|
190
|
+
# Open file in binary mode - FileResponse will handle closing
|
|
191
|
+
file_handle = open(path, 'rb')
|
|
192
|
+
response = FileResponse(file_handle, content_type=content_type)
|
|
193
|
+
|
|
194
|
+
# Set HTTP headers for video streaming
|
|
195
|
+
response['Content-Length'] = str(file_size)
|
|
196
|
+
response['Accept-Ranges'] = 'bytes' # Enable HTTP range requests for seeking
|
|
197
|
+
response['Content-Disposition'] = f'inline; filename="{path.name}"'
|
|
198
|
+
|
|
199
|
+
except IOError as e:
|
|
200
|
+
raise Http404(f"Cannot open video file: {str(e)}")
|
|
201
|
+
|
|
202
|
+
# CORS headers for frontend access (both HTTP 200 and 206)
|
|
203
|
+
response["Access-Control-Allow-Origin"] = frontend_origin
|
|
204
|
+
response["Access-Control-Allow-Credentials"] = "true"
|
|
205
|
+
|
|
206
|
+
return response
|
|
207
|
+
|
|
208
|
+
except Exception as e:
|
|
209
|
+
# Log unexpected errors but don't expose internal details
|
|
210
|
+
logger.error("Unexpected error in _stream_video_file: %s", str(e))
|
|
211
|
+
raise Http404("Video file cannot be streamed")
|
|
212
|
+
|
|
213
|
+
|
|
214
|
+
class VideoStreamView(APIView):
|
|
215
|
+
"""
|
|
216
|
+
Separate view for video streaming to avoid DRF content negotiation issues.
|
|
217
|
+
|
|
218
|
+
Supports streaming both raw (original) and processed (anonymized) videos.
|
|
219
|
+
|
|
220
|
+
Query Parameters:
|
|
221
|
+
type: 'raw' (default) or 'processed' - Selects which video file to stream
|
|
222
|
+
file_type: (deprecated, use 'type') - Legacy parameter for backwards compatibility
|
|
223
|
+
|
|
224
|
+
Examples:
|
|
225
|
+
GET /api/media/videos/1/?type=raw - Stream original raw video
|
|
226
|
+
GET /api/media/videos/1/?type=processed - Stream anonymized/masked video
|
|
227
|
+
GET /api/videostream/1/ - Default to raw video (legacy endpoint)
|
|
228
|
+
|
|
229
|
+
Phase 3.2 Implementation:
|
|
230
|
+
- Supports dual video comparison (raw vs processed)
|
|
231
|
+
- Backward compatible with legacy ?file_type= parameter
|
|
232
|
+
- Proper error handling with Http404
|
|
233
|
+
- CORS support for frontend access
|
|
234
|
+
- HTTP range support for video seeking
|
|
235
|
+
"""
|
|
236
|
+
permission_classes = [EnvironmentAwarePermission]
|
|
237
|
+
|
|
238
|
+
def get(self, request, pk=None):
|
|
239
|
+
"""
|
|
240
|
+
Stream raw or anonymized video file with HTTP Range Request and CORS support.
|
|
241
|
+
|
|
242
|
+
Supports HTTP 206 Partial Content for video seeking functionality.
|
|
243
|
+
|
|
244
|
+
Args:
|
|
245
|
+
request: HTTP request object
|
|
246
|
+
pk: Video ID (primary key)
|
|
247
|
+
|
|
248
|
+
Returns:
|
|
249
|
+
FileResponse: HTTP 200 streaming entire video file (no range header)
|
|
250
|
+
StreamingHttpResponse: HTTP 206 streaming partial content (with range header)
|
|
251
|
+
|
|
252
|
+
Raises:
|
|
253
|
+
Http404: If video not found or file cannot be accessed
|
|
254
|
+
"""
|
|
255
|
+
if pk is None:
|
|
256
|
+
raise Http404("Video ID is required")
|
|
257
|
+
|
|
258
|
+
# Initialize variables in outer scope
|
|
259
|
+
video_id_int = None
|
|
260
|
+
|
|
261
|
+
try:
|
|
262
|
+
# Validate video_id is numeric
|
|
263
|
+
try:
|
|
264
|
+
video_id_int = int(pk)
|
|
265
|
+
except (ValueError, TypeError):
|
|
266
|
+
raise Http404("Invalid video ID format")
|
|
267
|
+
|
|
268
|
+
# Support both 'type' (frontend standard) and 'file_type' (legacy)
|
|
269
|
+
# Priority: type > file_type > default 'raw'
|
|
270
|
+
file_type = 'raw' # Default value
|
|
271
|
+
try:
|
|
272
|
+
file_type_param = request.query_params.get('type') or request.query_params.get('file_type')
|
|
273
|
+
if file_type_param:
|
|
274
|
+
file_type = file_type_param.lower()
|
|
275
|
+
|
|
276
|
+
if file_type not in ['raw', 'processed']:
|
|
277
|
+
logger.warning("Invalid file_type '%s', defaulting to 'raw'", file_type)
|
|
278
|
+
file_type = 'raw'
|
|
279
|
+
|
|
280
|
+
except Exception as e:
|
|
281
|
+
logger.warning("Error parsing file_type parameter: %s, defaulting to 'raw'", e)
|
|
282
|
+
file_type = 'raw'
|
|
283
|
+
|
|
284
|
+
# Fetch video from database
|
|
285
|
+
vf = VideoFile.objects.get(pk=video_id_int)
|
|
286
|
+
|
|
287
|
+
# Get frontend origin for CORS
|
|
288
|
+
frontend_origin = os.environ.get('FRONTEND_ORIGIN', 'http://localhost:8000')
|
|
289
|
+
|
|
290
|
+
# ✅ NEW: Extract Range header for HTTP 206 support
|
|
291
|
+
range_header = request.META.get('HTTP_RANGE')
|
|
292
|
+
|
|
293
|
+
# Stream the video file with optional range support
|
|
294
|
+
return _stream_video_file(vf, frontend_origin, file_type, range_header)
|
|
295
|
+
|
|
296
|
+
except VideoFile.DoesNotExist:
|
|
297
|
+
raise Http404(f"Video with ID {pk} not found")
|
|
298
|
+
|
|
299
|
+
except Http404:
|
|
300
|
+
# Re-raise Http404 exceptions as they should bubble up
|
|
301
|
+
raise
|
|
302
|
+
|
|
303
|
+
except Exception as e:
|
|
304
|
+
# Log unexpected errors and convert to Http404
|
|
305
|
+
logger.error("Unexpected error in VideoStreamView for video_id=%s: %s", pk, str(e))
|
|
306
|
+
raise Http404("Video streaming failed")
|