endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.9.2__py3-none-any.whl
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- endoreg_db/data/__init__.py +22 -8
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +0 -1
- endoreg_db/data/examination/examinations/data.yaml +114 -14
- endoreg_db/data/examination/time-type/data.yaml +0 -3
- endoreg_db/data/examination_indication/endoscopy.yaml +108 -173
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +0 -70
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +33 -37
- endoreg_db/data/finding/00_generic.yaml +35 -0
- endoreg_db/data/finding/00_generic_complication.yaml +9 -0
- endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
- endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
- endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
- endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
- endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
- endoreg_db/data/finding_classification/00_generic.yaml +44 -0
- endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
- endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
- endoreg_db/data/finding_classification/{colonoscopy_bowel_preparation.yaml → 02_colonoscopy_baseline.yaml} +35 -20
- endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
- endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
- endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
- endoreg_db/data/finding_classification_choice/{yes_no_na.yaml → 00_generic.yaml} +5 -1
- endoreg_db/data/finding_classification_choice/{examination_setting_generic_types.yaml → 00_generic_baseline.yaml} +10 -2
- endoreg_db/data/finding_classification_choice/{complication_generic_types.yaml → 00_generic_complication.yaml} +1 -1
- endoreg_db/data/finding_classification_choice/{histology.yaml → 00_generic_histology.yaml} +1 -4
- endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
- endoreg_db/data/finding_classification_choice/{bowel_preparation.yaml → 02_colonoscopy_bowel_preparation.yaml} +1 -30
- endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_not_complete_reason.yaml → finding_classification_choice/02_colonoscopy_generic.yaml} +1 -1
- endoreg_db/data/finding_classification_choice/{histology_polyp.yaml → 02_colonoscopy_histology.yaml} +1 -1
- endoreg_db/data/{_examples/finding_classification_choice/colonoscopy_location.yaml → finding_classification_choice/02_colonoscopy_location.yaml} +23 -4
- endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
- endoreg_db/data/{_examples/finding_classification_choice/colon_lesion_paris.yaml → finding_classification_choice/02_colonoscopy_polyp_morphology.yaml} +26 -8
- endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
- endoreg_db/data/finding_classification_type/{colonoscopy_basic.yaml → 00_generic.yaml} +18 -13
- endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
- endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
- endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
- endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
- endoreg_db/data/finding_type/data.yaml +8 -12
- endoreg_db/data/requirement/01_patient_data.yaml +93 -0
- endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +0 -2
- endoreg_db/data/requirement_set/90_coloreg.yaml +20 -8
- endoreg_db/exceptions.py +0 -1
- endoreg_db/forms/examination_form.py +1 -1
- endoreg_db/helpers/data_loader.py +124 -52
- endoreg_db/helpers/default_objects.py +116 -81
- endoreg_db/import_files/__init__.py +27 -0
- endoreg_db/import_files/context/__init__.py +7 -0
- endoreg_db/import_files/context/default_sensitive_meta.py +81 -0
- endoreg_db/import_files/context/ensure_center.py +17 -0
- endoreg_db/import_files/context/file_lock.py +66 -0
- endoreg_db/import_files/context/import_context.py +43 -0
- endoreg_db/import_files/context/validate_directories.py +56 -0
- endoreg_db/import_files/file_storage/__init__.py +15 -0
- endoreg_db/import_files/file_storage/create_report_file.py +76 -0
- endoreg_db/import_files/file_storage/create_video_file.py +75 -0
- endoreg_db/import_files/file_storage/sensitive_meta_storage.py +39 -0
- endoreg_db/import_files/file_storage/state_management.py +496 -0
- endoreg_db/import_files/file_storage/storage.py +36 -0
- endoreg_db/import_files/import_service.md +26 -0
- endoreg_db/import_files/processing/__init__.py +11 -0
- endoreg_db/import_files/processing/report_processing/report_anonymization.py +94 -0
- endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
- endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
- endoreg_db/import_files/pseudonymization/fake.py +52 -0
- endoreg_db/import_files/pseudonymization/k_anonymity.py +182 -0
- endoreg_db/import_files/pseudonymization/k_pseudonymity.py +128 -0
- endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
- endoreg_db/import_files/report_import_service.py +141 -0
- endoreg_db/import_files/video_import_service.py +150 -0
- endoreg_db/management/commands/import_report.py +130 -65
- endoreg_db/management/commands/import_video_with_classification.py +1 -1
- endoreg_db/management/commands/load_ai_model_data.py +5 -5
- endoreg_db/management/commands/load_ai_model_label_data.py +9 -7
- endoreg_db/management/commands/load_base_db_data.py +5 -134
- endoreg_db/management/commands/load_contraindication_data.py +14 -16
- endoreg_db/management/commands/load_disease_classification_choices_data.py +15 -18
- endoreg_db/management/commands/load_disease_classification_data.py +15 -18
- endoreg_db/management/commands/load_disease_data.py +25 -28
- endoreg_db/management/commands/load_endoscope_data.py +20 -27
- endoreg_db/management/commands/load_event_data.py +14 -16
- endoreg_db/management/commands/load_examination_data.py +31 -44
- endoreg_db/management/commands/load_examination_indication_data.py +20 -21
- endoreg_db/management/commands/load_finding_data.py +52 -80
- endoreg_db/management/commands/load_information_source.py +21 -23
- endoreg_db/management/commands/load_lab_value_data.py +17 -26
- endoreg_db/management/commands/load_medication_data.py +13 -12
- endoreg_db/management/commands/load_organ_data.py +15 -19
- endoreg_db/management/commands/load_pdf_type_data.py +19 -18
- endoreg_db/management/commands/load_profession_data.py +14 -17
- endoreg_db/management/commands/load_qualification_data.py +20 -23
- endoreg_db/management/commands/load_report_reader_flag_data.py +17 -19
- endoreg_db/management/commands/load_requirement_data.py +14 -20
- endoreg_db/management/commands/load_risk_data.py +7 -6
- endoreg_db/management/commands/load_shift_data.py +20 -23
- endoreg_db/management/commands/load_tag_data.py +8 -11
- endoreg_db/management/commands/load_unit_data.py +17 -19
- endoreg_db/management/commands/start_filewatcher.py +46 -37
- endoreg_db/management/commands/validate_video_files.py +1 -5
- endoreg_db/migrations/0001_initial.py +1360 -1812
- endoreg_db/models/administration/person/patient/patient.py +72 -46
- endoreg_db/models/label/__init__.py +2 -2
- endoreg_db/models/label/annotation/video_segmentation_annotation.py +18 -26
- endoreg_db/models/label/label_video_segment/label_video_segment.py +23 -1
- endoreg_db/models/media/pdf/raw_pdf.py +136 -64
- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +34 -10
- endoreg_db/models/media/processing_history/__init__.py +5 -0
- endoreg_db/models/media/processing_history/processing_history.py +96 -0
- endoreg_db/models/media/video/create_from_file.py +101 -31
- endoreg_db/models/media/video/video_file.py +125 -105
- endoreg_db/models/media/video/video_file_io.py +31 -26
- endoreg_db/models/medical/contraindication/README.md +1 -0
- endoreg_db/models/medical/examination/examination.py +28 -8
- endoreg_db/models/medical/examination/examination_indication.py +13 -79
- endoreg_db/models/medical/examination/examination_time.py +8 -3
- endoreg_db/models/medical/finding/finding.py +5 -12
- endoreg_db/models/medical/finding/finding_classification.py +18 -37
- endoreg_db/models/medical/finding/finding_intervention.py +7 -9
- endoreg_db/models/medical/hardware/endoscope.py +6 -0
- endoreg_db/models/medical/patient/medication_examples.py +5 -1
- endoreg_db/models/medical/patient/patient_finding.py +1 -1
- endoreg_db/models/metadata/pdf_meta.py +22 -10
- endoreg_db/models/metadata/sensitive_meta.py +3 -0
- endoreg_db/models/metadata/sensitive_meta_logic.py +200 -124
- endoreg_db/models/other/information_source.py +27 -6
- endoreg_db/models/report/__init__.py +0 -0
- endoreg_db/models/report/images.py +0 -0
- endoreg_db/models/report/report.py +6 -0
- endoreg_db/models/requirement/requirement.py +59 -399
- endoreg_db/models/requirement/requirement_operator.py +86 -98
- endoreg_db/models/state/audit_ledger.py +4 -5
- endoreg_db/models/state/raw_pdf.py +69 -30
- endoreg_db/models/state/video.py +65 -49
- endoreg_db/models/upload_job.py +33 -9
- endoreg_db/models/utils.py +27 -23
- endoreg_db/queries/__init__.py +3 -1
- endoreg_db/schemas/examination_evaluation.py +1 -1
- endoreg_db/serializers/__init__.py +2 -8
- endoreg_db/serializers/label_video_segment/label_video_segment.py +2 -29
- endoreg_db/serializers/meta/__init__.py +1 -6
- endoreg_db/serializers/misc/sensitive_patient_data.py +50 -26
- endoreg_db/serializers/patient_examination/patient_examination.py +3 -3
- endoreg_db/serializers/pdf/anony_text_validation.py +39 -23
- endoreg_db/serializers/video/video_file_list.py +65 -34
- endoreg_db/services/__old/pdf_import.py +1487 -0
- endoreg_db/services/__old/video_import.py +1306 -0
- endoreg_db/services/anonymization.py +63 -26
- endoreg_db/services/lookup_service.py +28 -28
- endoreg_db/services/lookup_store.py +2 -2
- endoreg_db/services/pdf_import.py +0 -1480
- endoreg_db/services/report_import.py +10 -0
- endoreg_db/services/video_import.py +6 -1165
- endoreg_db/tasks/upload_tasks.py +79 -70
- endoreg_db/tasks/video_ingest.py +8 -4
- endoreg_db/urls/__init__.py +0 -14
- endoreg_db/urls/ai.py +32 -0
- endoreg_db/urls/media.py +21 -24
- endoreg_db/utils/dataloader.py +87 -57
- endoreg_db/utils/paths.py +110 -46
- endoreg_db/utils/pipelines/Readme.md +1 -1
- endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +97 -0
- endoreg_db/utils/video/ffmpeg_wrapper.py +217 -52
- endoreg_db/views/__init__.py +85 -173
- endoreg_db/views/ai/__init__.py +8 -0
- endoreg_db/views/ai/label.py +155 -0
- endoreg_db/views/anonymization/media_management.py +8 -7
- endoreg_db/views/anonymization/overview.py +97 -68
- endoreg_db/views/anonymization/validate.py +25 -21
- endoreg_db/views/media/__init__.py +5 -20
- endoreg_db/views/media/pdf_media.py +109 -65
- endoreg_db/views/media/sensitive_metadata.py +163 -148
- endoreg_db/views/meta/__init__.py +0 -8
- endoreg_db/views/misc/__init__.py +1 -7
- endoreg_db/views/misc/upload_views.py +94 -93
- endoreg_db/views/report/__init__.py +7 -0
- endoreg_db/views/{pdf → report}/reimport.py +45 -24
- endoreg_db/views/{pdf/pdf_stream.py → report/report_stream.py} +40 -32
- endoreg_db/views/requirement/lookup_store.py +22 -90
- endoreg_db/views/video/__init__.py +23 -22
- endoreg_db/views/video/correction.py +201 -172
- endoreg_db/views/video/reimport.py +1 -1
- endoreg_db/views/{media/video_segments.py → video/segments_crud.py} +75 -37
- endoreg_db/views/video/{video_meta.py → video_meta_stats.py} +2 -2
- endoreg_db/views/video/video_stream.py +7 -8
- {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/METADATA +2 -2
- {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/RECORD +217 -335
- {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/WHEEL +1 -1
- endoreg_db/data/_examples/disease.yaml +0 -55
- endoreg_db/data/_examples/disease_classification.yaml +0 -13
- endoreg_db/data/_examples/disease_classification_choice.yaml +0 -62
- endoreg_db/data/_examples/event.yaml +0 -64
- endoreg_db/data/_examples/examination.yaml +0 -72
- endoreg_db/data/_examples/finding/anatomy_colon.yaml +0 -128
- endoreg_db/data/_examples/finding/colonoscopy.yaml +0 -40
- endoreg_db/data/_examples/finding/colonoscopy_bowel_prep.yaml +0 -56
- endoreg_db/data/_examples/finding/complication.yaml +0 -16
- endoreg_db/data/_examples/finding/data.yaml +0 -105
- endoreg_db/data/_examples/finding/examination_setting.yaml +0 -16
- endoreg_db/data/_examples/finding/medication_related.yaml +0 -18
- endoreg_db/data/_examples/finding/outcome.yaml +0 -12
- endoreg_db/data/_examples/finding_classification/colonoscopy_bowel_preparation.yaml +0 -68
- endoreg_db/data/_examples/finding_classification/colonoscopy_jnet.yaml +0 -22
- endoreg_db/data/_examples/finding_classification/colonoscopy_kudo.yaml +0 -25
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_size.yaml +0 -68
- endoreg_db/data/_examples/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
- endoreg_db/data/_examples/finding_classification/colonoscopy_location.yaml +0 -80
- endoreg_db/data/_examples/finding_classification/colonoscopy_lst.yaml +0 -21
- endoreg_db/data/_examples/finding_classification/colonoscopy_nice.yaml +0 -20
- endoreg_db/data/_examples/finding_classification/colonoscopy_paris.yaml +0 -26
- endoreg_db/data/_examples/finding_classification/colonoscopy_sano.yaml +0 -22
- endoreg_db/data/_examples/finding_classification/colonoscopy_summary.yaml +0 -53
- endoreg_db/data/_examples/finding_classification/complication_generic.yaml +0 -25
- endoreg_db/data/_examples/finding_classification/examination_setting_generic.yaml +0 -40
- endoreg_db/data/_examples/finding_classification/histology_colo.yaml +0 -51
- endoreg_db/data/_examples/finding_classification/intervention_required.yaml +0 -26
- endoreg_db/data/_examples/finding_classification/medication_related.yaml +0 -23
- endoreg_db/data/_examples/finding_classification/visualized.yaml +0 -33
- endoreg_db/data/_examples/finding_classification_choice/bowel_preparation.yaml +0 -78
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_lst.yaml +0 -15
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_nice.yaml +0 -17
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_sano.yaml +0 -14
- endoreg_db/data/_examples/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_size.yaml +0 -82
- endoreg_db/data/_examples/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
- endoreg_db/data/_examples/finding_classification_choice/complication_generic_types.yaml +0 -15
- endoreg_db/data/_examples/finding_classification_choice/examination_setting_generic_types.yaml +0 -15
- endoreg_db/data/_examples/finding_classification_choice/histology.yaml +0 -24
- endoreg_db/data/_examples/finding_classification_choice/histology_polyp.yaml +0 -20
- endoreg_db/data/_examples/finding_classification_choice/outcome.yaml +0 -19
- endoreg_db/data/_examples/finding_classification_choice/yes_no_na.yaml +0 -11
- endoreg_db/data/_examples/finding_classification_type/colonoscopy_basic.yaml +0 -48
- endoreg_db/data/_examples/finding_intervention/endoscopy.yaml +0 -43
- endoreg_db/data/_examples/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
- endoreg_db/data/_examples/finding_intervention/endoscopy_egd.yaml +0 -128
- endoreg_db/data/_examples/finding_intervention/endoscopy_ercp.yaml +0 -32
- endoreg_db/data/_examples/finding_intervention/endoscopy_eus_lower.yaml +0 -9
- endoreg_db/data/_examples/finding_intervention/endoscopy_eus_upper.yaml +0 -36
- endoreg_db/data/_examples/finding_intervention_type/endoscopy.yaml +0 -15
- endoreg_db/data/_examples/finding_type/data.yaml +0 -43
- endoreg_db/data/_examples/requirement/age.yaml +0 -26
- endoreg_db/data/_examples/requirement/gender.yaml +0 -25
- endoreg_db/data/_examples/requirement_set/01_endoscopy_generic.yaml +0 -48
- endoreg_db/data/_examples/requirement_set/colonoscopy_austria_screening.yaml +0 -57
- endoreg_db/data/_examples/requirement_set/endoscopy_bleeding_risk.yaml +0 -52
- endoreg_db/data/_examples/yaml_examples.xlsx +0 -0
- endoreg_db/data/finding/anatomy_colon.yaml +0 -128
- endoreg_db/data/finding/colonoscopy.yaml +0 -40
- endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +0 -56
- endoreg_db/data/finding/complication.yaml +0 -16
- endoreg_db/data/finding/data.yaml +0 -105
- endoreg_db/data/finding/examination_setting.yaml +0 -16
- endoreg_db/data/finding/medication_related.yaml +0 -18
- endoreg_db/data/finding/outcome.yaml +0 -12
- endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +0 -22
- endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +0 -25
- endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +0 -38
- endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +0 -49
- endoreg_db/data/finding_classification/colonoscopy_lst.yaml +0 -21
- endoreg_db/data/finding_classification/colonoscopy_nice.yaml +0 -20
- endoreg_db/data/finding_classification/colonoscopy_paris.yaml +0 -26
- endoreg_db/data/finding_classification/colonoscopy_sano.yaml +0 -22
- endoreg_db/data/finding_classification/colonoscopy_summary.yaml +0 -53
- endoreg_db/data/finding_classification/complication_generic.yaml +0 -25
- endoreg_db/data/finding_classification/examination_setting_generic.yaml +0 -40
- endoreg_db/data/finding_classification/histology_colo.yaml +0 -43
- endoreg_db/data/finding_classification/intervention_required.yaml +0 -26
- endoreg_db/data/finding_classification/medication_related.yaml +0 -23
- endoreg_db/data/finding_classification/visualized.yaml +0 -33
- endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
- endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
- endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
- endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +0 -15
- endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +0 -17
- endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +0 -57
- endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +0 -14
- endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
- endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +0 -229
- endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +0 -19
- endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +0 -82
- endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
- endoreg_db/data/finding_classification_choice/outcome.yaml +0 -19
- endoreg_db/data/finding_intervention/endoscopy.yaml +0 -43
- endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
- endoreg_db/data/finding_intervention/endoscopy_egd.yaml +0 -128
- endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +0 -32
- endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +0 -9
- endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +0 -36
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +0 -79
- endoreg_db/data/requirement/age.yaml +0 -26
- endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +0 -45
- endoreg_db/data/requirement/disease_cardiovascular.yaml +0 -79
- endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +0 -41
- endoreg_db/data/requirement/disease_hepatology.yaml +0 -12
- endoreg_db/data/requirement/disease_misc.yaml +0 -12
- endoreg_db/data/requirement/disease_renal.yaml +0 -96
- endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +0 -59
- endoreg_db/data/requirement/event_cardiology.yaml +0 -251
- endoreg_db/data/requirement/event_requirements.yaml +0 -145
- endoreg_db/data/requirement/finding_colon_polyp.yaml +0 -50
- endoreg_db/data/requirement/gender.yaml +0 -25
- endoreg_db/data/requirement/lab_value.yaml +0 -441
- endoreg_db/data/requirement/medication.yaml +0 -93
- endoreg_db/data/requirement_operator/age.yaml +0 -13
- endoreg_db/data/requirement_operator/lab_operators.yaml +0 -129
- endoreg_db/data/requirement_operator/model_operators.yaml +0 -96
- endoreg_db/management/commands/init_default_ai_model.py +0 -112
- endoreg_db/management/commands/reset_celery_schedule.py +0 -9
- endoreg_db/management/commands/validate_video.py +0 -204
- endoreg_db/migrations/0002_requirementset_depends_on.py +0 -18
- endoreg_db/migrations/_old/0001_initial.py +0 -1857
- endoreg_db/migrations/_old/0002_add_video_correction_models.py +0 -52
- endoreg_db/migrations/_old/0003_add_center_display_name.py +0 -30
- endoreg_db/migrations/_old/0004_employee_city_employee_post_code_employee_street_and_more.py +0 -68
- endoreg_db/migrations/_old/0004_remove_casetemplate_rules_and_more.py +0 -77
- endoreg_db/migrations/_old/0005_merge_20251111_1003.py +0 -14
- endoreg_db/migrations/_old/0006_sensitivemeta_anonymized_text_and_more.py +0 -68
- endoreg_db/migrations/_old/0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more.py +0 -89
- endoreg_db/migrations/_old/0008_remove_event_event_classification_and_more.py +0 -27
- endoreg_db/migrations/_old/0009_alter_modelmeta_options_and_more.py +0 -21
- endoreg_db/renames.yml +0 -8
- endoreg_db/serializers/_old/raw_pdf_meta_validation.py +0 -223
- endoreg_db/serializers/_old/raw_video_meta_validation.py +0 -179
- endoreg_db/serializers/_old/video.py +0 -71
- endoreg_db/serializers/meta/pdf_file_meta_extraction.py +0 -115
- endoreg_db/serializers/meta/report_meta.py +0 -53
- endoreg_db/serializers/report/__init__.py +0 -9
- endoreg_db/serializers/report/mixins.py +0 -45
- endoreg_db/serializers/report/report.py +0 -105
- endoreg_db/serializers/report/report_list.py +0 -22
- endoreg_db/serializers/report/secure_file_url.py +0 -26
- endoreg_db/services/requirements_object.py +0 -147
- endoreg_db/services/storage_aware_video_processor.py +0 -370
- endoreg_db/urls/files.py +0 -6
- endoreg_db/urls/label_video_segment_validate.py +0 -33
- endoreg_db/urls/label_video_segments.py +0 -46
- endoreg_db/views/label/__init__.py +0 -5
- endoreg_db/views/label/label.py +0 -15
- endoreg_db/views/label_video_segment/__init__.py +0 -16
- endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +0 -44
- endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +0 -50
- endoreg_db/views/label_video_segment/label_video_segment.py +0 -77
- endoreg_db/views/label_video_segment/label_video_segment_by_label.py +0 -174
- endoreg_db/views/label_video_segment/label_video_segment_detail.py +0 -73
- endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +0 -46
- endoreg_db/views/label_video_segment/validate.py +0 -226
- endoreg_db/views/media/segments.py +0 -71
- endoreg_db/views/meta/available_files_list.py +0 -146
- endoreg_db/views/meta/report_meta.py +0 -53
- endoreg_db/views/meta/sensitive_meta_detail.py +0 -85
- endoreg_db/views/misc/secure_file_serving_view.py +0 -80
- endoreg_db/views/misc/secure_file_url_view.py +0 -84
- endoreg_db/views/misc/secure_url_validate.py +0 -79
- endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +0 -164
- endoreg_db/views/patient_finding_location/__init__.py +0 -5
- endoreg_db/views/patient_finding_location/pfl_create.py +0 -70
- endoreg_db/views/patient_finding_morphology/__init__.py +0 -5
- endoreg_db/views/patient_finding_morphology/pfm_create.py +0 -70
- endoreg_db/views/pdf/__init__.py +0 -8
- endoreg_db/views/video/segmentation.py +0 -274
- endoreg_db/views/video/task_status.py +0 -49
- endoreg_db/views/video/timeline.py +0 -46
- endoreg_db/views/video/video_analyze.py +0 -52
- /endoreg_db/data/requirement/{colon_polyp_intervention.yaml → old/colon_polyp_intervention.yaml} +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/colonoscopy_baseline_austria.yaml +0 -0
- /endoreg_db/data/requirement/{coloreg_colon_polyp.yaml → old/coloreg_colon_polyp.yaml} +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/disease_cardiovascular.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/disease_classification_choice_cardiovascular.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/disease_hepatology.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/disease_misc.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/disease_renal.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/endoscopy_bleeding_risk.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/event_cardiology.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/event_requirements.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/finding_colon_polyp.yaml +0 -0
- /endoreg_db/{urls/sensitive_meta.py → data/requirement/old/gender.yaml} +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/lab_value.yaml +0 -0
- /endoreg_db/data/{_examples/requirement → requirement/old}/medication.yaml +0 -0
- /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/age.yaml +0 -0
- /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/lab_operators.yaml +0 -0
- /endoreg_db/data/{_examples/requirement_operator → requirement_operator/_old}/model_operators.yaml +0 -0
- /endoreg_db/{views/pdf/pdf_stream_views.py → import_files/pseudonymization/__init__.py} +0 -0
- /endoreg_db/utils/requirement_operator_logic/{lab_value_operators.py → _old/lab_value_operators.py} +0 -0
- /endoreg_db/utils/requirement_operator_logic/{model_evaluators.py → _old/model_evaluators.py} +0 -0
- {endoreg_db-0.8.8.0.dist-info → endoreg_db-0.8.9.2.dist-info}/licenses/LICENSE +0 -0
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# Generated by Django 5.2.5 on 2025-10-09 10:12
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class Migration(migrations.Migration):
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('endoreg_db', '0001_initial'),
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operations = [
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migrations.CreateModel(
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name='VideoMetadata',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('sensitive_frame_count', models.IntegerField(blank=True, help_text='Number of frames detected as containing sensitive information', null=True)),
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('sensitive_ratio', models.FloatField(blank=True, help_text='Ratio of sensitive frames to total frames (0.0-1.0)', null=True)),
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('sensitive_frame_ids', models.TextField(blank=True, help_text='JSON array of sensitive frame indices (0-based)', null=True)),
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('analyzed_at', models.DateTimeField(auto_now=True, help_text='Timestamp of last analysis')),
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('video', models.OneToOneField(help_text='Video file this metadata belongs to', on_delete=django.db.models.deletion.CASCADE, related_name='metadata', to='endoreg_db.videofile')),
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],
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options={
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'verbose_name': 'Video Metadata',
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'db_table': 'video_metadata',
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},
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('operation', models.CharField(choices=[('mask_overlay', 'Mask Overlay'), ('frame_removal', 'Frame Removal'), ('analysis', 'Sensitivity Analysis'), ('reprocessing', 'Full Reprocessing')], help_text='Type of processing operation', max_length=50)),
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('status', models.CharField(choices=[('pending', 'Pending'), ('running', 'Running'), ('success', 'Success'), ('failure', 'Failure'), ('cancelled', 'Cancelled')], default='pending', help_text='Current status of the operation', max_length=20)),
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('config', models.JSONField(default=dict, help_text='Operation configuration (mask settings, frame list, etc.)')),
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('output_file', models.CharField(blank=True, help_text='Path to output file (relative to MEDIA_ROOT)', max_length=500)),
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('details', models.TextField(blank=True, help_text='Additional details or error messages')),
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('task_id', models.CharField(blank=True, help_text='Celery task ID for progress tracking', max_length=100)),
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('created_at', models.DateTimeField(auto_now_add=True, help_text='When the operation was started')),
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('completed_at', models.DateTimeField(blank=True, help_text='When the operation completed (success or failure)', null=True)),
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('video', models.ForeignKey(help_text='Video file this operation was performed on', on_delete=django.db.models.deletion.CASCADE, related_name='processing_history', to='endoreg_db.videofile')),
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],
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options={
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'db_table': 'video_processing_history',
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'ordering': ['-created_at'],
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'indexes': [models.Index(fields=['video', '-created_at'], name='video_proce_video_i_98ffe0_idx'), models.Index(fields=['task_id'], name='video_proce_task_id_ec8b15_idx'), models.Index(fields=['status'], name='video_proce_status_6f71fd_idx')],
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endoreg_db/migrations/_old/0004_employee_city_employee_post_code_employee_street_and_more.py
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# Generated by Django 5.2.7 on 2025-11-05 08:39
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('endoreg_db', '0003_add_center_display_name'),
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operations = [
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name='city',
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migrations.AddField(
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name='post_code',
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migrations.AddField(
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name='street',
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migrations.AddField(
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name='city',
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migrations.AddField(
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name='post_code',
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migrations.AddField(
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name='street',
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('external_id', models.CharField(max_length=255, unique=True)),
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('origin', models.CharField(max_length=255)),
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# Generated by Django 5.2.7 on 2025-11-10 16:54
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import django.core.validators
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name='rules',
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name='secondary_rules',
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migrations.RemoveField(
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name='template_type',
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migrations.RemoveField(
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name='chained_rules',
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migrations.RemoveField(
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name='date_value_distribution',
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migrations.RemoveField(
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migrations.RemoveField(
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name='numerical_value_distribution',
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migrations.RemoveField(
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migrations.RemoveField(
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),
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50
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-
migrations.RemoveField(
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51
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model_name='casetemplaterule',
|
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52
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name='value_type',
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53
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-
),
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54
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-
migrations.DeleteModel(
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55
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-
name='CaseTemplateRuleValue',
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56
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-
),
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57
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-
migrations.AlterField(
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58
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model_name='modelmeta',
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59
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-
name='weights',
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60
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field=models.FileField(blank=True, help_text='Path to the model weights file (.safetensors), relative to MEDIA_ROOT.', null=True, upload_to='model_weights', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['safetensors', 'pth', 'pt'])]),
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-
),
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62
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-
migrations.DeleteModel(
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name='CaseTemplate',
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64
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-
),
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65
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migrations.DeleteModel(
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66
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name='CaseTemplateType',
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67
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-
),
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68
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migrations.DeleteModel(
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69
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-
name='CaseTemplateRuleType',
|
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70
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),
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-
migrations.DeleteModel(
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name='CaseTemplateRule',
|
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73
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-
),
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74
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-
migrations.DeleteModel(
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75
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-
name='CaseTemplateRuleValueType',
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76
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-
),
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77
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-
]
|
|
@@ -1,14 +0,0 @@
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1
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-
# Generated by Django 5.2.7 on 2025-11-11 09:03
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2
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-
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3
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-
from django.db import migrations
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4
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-
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5
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-
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6
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class Migration(migrations.Migration):
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7
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-
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8
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-
dependencies = [
|
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9
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-
('endoreg_db', '0004_employee_city_employee_post_code_employee_street_and_more'),
|
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10
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-
('endoreg_db', '0004_remove_casetemplate_rules_and_more'),
|
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11
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-
]
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12
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-
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13
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-
operations = [
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14
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-
]
|
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@@ -1,68 +0,0 @@
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1
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-
# Generated by Django 5.2.7 on 2025-11-11 15:54
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2
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-
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3
|
-
import django.db.models.deletion
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4
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from django.db import migrations, models
|
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5
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-
|
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6
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-
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7
|
-
class Migration(migrations.Migration):
|
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8
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-
|
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9
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-
dependencies = [
|
|
10
|
-
('endoreg_db', '0005_merge_20251111_1003'),
|
|
11
|
-
]
|
|
12
|
-
|
|
13
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-
operations = [
|
|
14
|
-
migrations.AddField(
|
|
15
|
-
model_name='sensitivemeta',
|
|
16
|
-
name='anonymized_text',
|
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17
|
-
field=models.TextField(blank=True, null=True),
|
|
18
|
-
),
|
|
19
|
-
migrations.AddField(
|
|
20
|
-
model_name='sensitivemeta',
|
|
21
|
-
name='casenumber',
|
|
22
|
-
field=models.CharField(blank=True, max_length=255, null=True),
|
|
23
|
-
),
|
|
24
|
-
migrations.AddField(
|
|
25
|
-
model_name='sensitivemeta',
|
|
26
|
-
name='examination_time',
|
|
27
|
-
field=models.TimeField(blank=True, null=True),
|
|
28
|
-
),
|
|
29
|
-
migrations.AddField(
|
|
30
|
-
model_name='sensitivemeta',
|
|
31
|
-
name='external_id',
|
|
32
|
-
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.patientexternalid'),
|
|
33
|
-
),
|
|
34
|
-
migrations.AddField(
|
|
35
|
-
model_name='sensitivemeta',
|
|
36
|
-
name='file_path',
|
|
37
|
-
field=models.CharField(blank=True, max_length=1024, null=True),
|
|
38
|
-
),
|
|
39
|
-
migrations.AddField(
|
|
40
|
-
model_name='sensitivemeta',
|
|
41
|
-
name='text',
|
|
42
|
-
field=models.TextField(blank=True, null=True),
|
|
43
|
-
),
|
|
44
|
-
migrations.AlterField(
|
|
45
|
-
model_name='patientexternalid',
|
|
46
|
-
name='external_id',
|
|
47
|
-
field=models.CharField(max_length=255),
|
|
48
|
-
),
|
|
49
|
-
migrations.AlterField(
|
|
50
|
-
model_name='sensitivemeta',
|
|
51
|
-
name='center',
|
|
52
|
-
field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.center'),
|
|
53
|
-
),
|
|
54
|
-
migrations.AlterField(
|
|
55
|
-
model_name='sensitivemeta',
|
|
56
|
-
name='examiners',
|
|
57
|
-
field=models.ManyToManyField(blank=True, help_text='Pseudo-anonymized examiner(s)', to='endoreg_db.examiner'),
|
|
58
|
-
),
|
|
59
|
-
migrations.AlterField(
|
|
60
|
-
model_name='sensitivemeta',
|
|
61
|
-
name='patient_dob',
|
|
62
|
-
field=models.DateTimeField(blank=True, help_text='Date of birth (can be auto-generated).', null=True),
|
|
63
|
-
),
|
|
64
|
-
migrations.AddConstraint(
|
|
65
|
-
model_name='patientexternalid',
|
|
66
|
-
constraint=models.UniqueConstraint(fields=('origin', 'external_id'), name='uniq_patient_external_id_per_origin'),
|
|
67
|
-
),
|
|
68
|
-
]
|
endoreg_db/migrations/_old/0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more.py
DELETED
|
@@ -1,89 +0,0 @@
|
|
|
1
|
-
# Generated by Django 5.2.7 on 2025-11-12 15:57
|
|
2
|
-
|
|
3
|
-
import django.core.validators
|
|
4
|
-
import django.db.models.deletion
|
|
5
|
-
from django.db import migrations, models
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
class Migration(migrations.Migration):
|
|
9
|
-
|
|
10
|
-
dependencies = [
|
|
11
|
-
('endoreg_db', '0006_sensitivemeta_anonymized_text_and_more'),
|
|
12
|
-
]
|
|
13
|
-
|
|
14
|
-
operations = [
|
|
15
|
-
migrations.RemoveField(
|
|
16
|
-
model_name='rule',
|
|
17
|
-
name='attribute_dtype',
|
|
18
|
-
),
|
|
19
|
-
migrations.RemoveField(
|
|
20
|
-
model_name='rule',
|
|
21
|
-
name='rule_type',
|
|
22
|
-
),
|
|
23
|
-
migrations.RemoveField(
|
|
24
|
-
model_name='ruleset',
|
|
25
|
-
name='rules',
|
|
26
|
-
),
|
|
27
|
-
migrations.AddField(
|
|
28
|
-
model_name='numericvaluedistribution',
|
|
29
|
-
name='max_value',
|
|
30
|
-
field=models.FloatField(blank=True, help_text='Upper hard limit for generated values', null=True),
|
|
31
|
-
),
|
|
32
|
-
migrations.AddField(
|
|
33
|
-
model_name='numericvaluedistribution',
|
|
34
|
-
name='mean',
|
|
35
|
-
field=models.FloatField(blank=True, help_text='Mean used for normal or skewed normal distributions', null=True),
|
|
36
|
-
),
|
|
37
|
-
migrations.AddField(
|
|
38
|
-
model_name='numericvaluedistribution',
|
|
39
|
-
name='min_value',
|
|
40
|
-
field=models.FloatField(blank=True, help_text='Lower hard limit for generated values', null=True),
|
|
41
|
-
),
|
|
42
|
-
migrations.AddField(
|
|
43
|
-
model_name='numericvaluedistribution',
|
|
44
|
-
name='skewness',
|
|
45
|
-
field=models.FloatField(blank=True, help_text='Shape parameter for skewed normal distributions', null=True),
|
|
46
|
-
),
|
|
47
|
-
migrations.AddField(
|
|
48
|
-
model_name='numericvaluedistribution',
|
|
49
|
-
name='std_dev',
|
|
50
|
-
field=models.FloatField(blank=True, help_text='Standard deviation for bell-shaped distributions', null=True),
|
|
51
|
-
),
|
|
52
|
-
migrations.AlterField(
|
|
53
|
-
model_name='anonymexaminationreport',
|
|
54
|
-
name='file',
|
|
55
|
-
field=models.FileField(blank=True, null=True, upload_to='pdfs'),
|
|
56
|
-
),
|
|
57
|
-
migrations.AlterField(
|
|
58
|
-
model_name='anonymhistologyreport',
|
|
59
|
-
name='file',
|
|
60
|
-
field=models.FileField(blank=True, null=True, upload_to='pdfs'),
|
|
61
|
-
),
|
|
62
|
-
migrations.AlterField(
|
|
63
|
-
model_name='rawpdffile',
|
|
64
|
-
name='anonymized_file',
|
|
65
|
-
field=models.FileField(blank=True, null=True, upload_to='pdfs', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
|
|
66
|
-
),
|
|
67
|
-
migrations.AlterField(
|
|
68
|
-
model_name='rawpdffile',
|
|
69
|
-
name='file',
|
|
70
|
-
field=models.FileField(upload_to='pdfs', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
|
|
71
|
-
),
|
|
72
|
-
migrations.AlterField(
|
|
73
|
-
model_name='sensitivemeta',
|
|
74
|
-
name='center',
|
|
75
|
-
field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.center'),
|
|
76
|
-
),
|
|
77
|
-
migrations.DeleteModel(
|
|
78
|
-
name='RuleAttributeDType',
|
|
79
|
-
),
|
|
80
|
-
migrations.DeleteModel(
|
|
81
|
-
name='RuleType',
|
|
82
|
-
),
|
|
83
|
-
migrations.DeleteModel(
|
|
84
|
-
name='Rule',
|
|
85
|
-
),
|
|
86
|
-
migrations.DeleteModel(
|
|
87
|
-
name='Ruleset',
|
|
88
|
-
),
|
|
89
|
-
]
|
|
@@ -1,27 +0,0 @@
|
|
|
1
|
-
# Generated by Django 5.2.7 on 2025-11-13 09:13
|
|
2
|
-
|
|
3
|
-
import django.db.models.deletion
|
|
4
|
-
from django.db import migrations, models
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
class Migration(migrations.Migration):
|
|
8
|
-
dependencies = [
|
|
9
|
-
("endoreg_db", "0007_remove_rule_attribute_dtype_remove_rule_rule_type_and_more"),
|
|
10
|
-
]
|
|
11
|
-
|
|
12
|
-
operations = [
|
|
13
|
-
migrations.RemoveField(
|
|
14
|
-
model_name="event",
|
|
15
|
-
name="event_classification",
|
|
16
|
-
),
|
|
17
|
-
migrations.RemoveField(
|
|
18
|
-
model_name="organ",
|
|
19
|
-
name="location_choices",
|
|
20
|
-
),
|
|
21
|
-
migrations.AddField(
|
|
22
|
-
model_name="eventclassification",
|
|
23
|
-
name="event",
|
|
24
|
-
field=models.ForeignKey(default=1, on_delete=django.db.models.deletion.CASCADE, related_name="event_classifications", to="endoreg_db.event"),
|
|
25
|
-
preserve_default=False,
|
|
26
|
-
),
|
|
27
|
-
]
|
|
@@ -1,21 +0,0 @@
|
|
|
1
|
-
# Generated by Django 5.2.7 on 2025-11-16 16:47
|
|
2
|
-
|
|
3
|
-
from django.db import migrations
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
class Migration(migrations.Migration):
|
|
7
|
-
|
|
8
|
-
dependencies = [
|
|
9
|
-
('endoreg_db', '0008_remove_event_event_classification_and_more'),
|
|
10
|
-
]
|
|
11
|
-
|
|
12
|
-
operations = [
|
|
13
|
-
migrations.AlterModelOptions(
|
|
14
|
-
name='modelmeta',
|
|
15
|
-
options={'ordering': ['-date_created'], 'verbose_name': 'Model Metadata', 'verbose_name_plural': 'Model Metadata'},
|
|
16
|
-
),
|
|
17
|
-
migrations.AlterUniqueTogether(
|
|
18
|
-
name='modelmeta',
|
|
19
|
-
unique_together={('name', 'version', 'model')},
|
|
20
|
-
),
|
|
21
|
-
]
|