endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.0__py3-none-any.whl

endoreg_db/data/_examples/requirement/disease_renal.yaml

@@ -0,0 +1,96 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_is_chronic_kidney_disease"
+    name_de: "Erkrankung chronische Nierenerkrankung"
+    name_en: "Disease Chronic Kidney Disease"
+    description: "Disease Chronic Kidney Disease"
+    requirement_types:
+      - "patient"
+    operators:
+      - models_match_all
+    diseases:
+      - "chronic_kidney_disease"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_1"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 1)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 1)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 1)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_1"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_2"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 2)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 2)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 2)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_2"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_3a"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 3a)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3a)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3a)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_3a"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_3b"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 3b)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3b)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3b)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_3b"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_4"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 4)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 4)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 4)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_4"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "disease_classification_choice_is_ckd_kdigo_5"
+    name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 5)"
+    name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 5)"
+    description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 5)"
+    requirement_types:
+      - "patient_disease"
+      - "patient"
+    operators:
+      - models_match_all
+    disease_classification_choices:
+      - "ckd_kdigo_5"

endoreg_db/data/_examples/requirement/endoscopy_bleeding_risk.yaml

@@ -0,0 +1,59 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "endoscopy_intervention_bleeding_risk_high"
+    name_de: "Endoskopische Intervention - Blutungsrisiko: hoch"
+    name_en: "Endoscopy Intervention - Bleeding Risk: High"
+    description: "Endoskopische Intervention - Blutungsrisiko: hoch"
+    requirement_types:
+      - "examination_indication"
+    operators:
+      - "models_match_any"
+    finding_interventions:
+      - "egd_lesion_polypectomy_cold_snare"
+      - "egd_lesion_polypectomy_hot_snare"
+      - "colon_lesion_polypectomy_cold_snare"
+      - "colon_lesion_polypectomy_hot_snare"
+      - "colon_lesion_emr"
+      - "colon_lesion_esd"
+      - "colon_lesion_eftr"
+      - "egd_lesion_emr"
+      - "egd_lesion_esd"
+      - "egd_poem"
+      - "ercp_sphincterotomy"
+      - "egd_varice_band_ligation"
+      - "egd_varice_sclerotherapy"
+      - "egd_percutaneous_gastroenterostomy"
+      - "percutaneous_transhepatic_cholangiography"
+      - "percutaneous_transhepatic_biliary_drainage"
+      - "ercp_radiofrequency_ablation"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "endoscopy_intervention_bleeding_risk_low"
+    name_de: "Endoskopische Intervention - Blutungsrisiko: niedrig"
+    name_en: "Endoscopy Intervention - Bleeding Risk: Low"
+    description: "Endoskopische Intervention - Blutungsrisiko: niedrig"
+    requirement_types:
+      - "examination_indication"
+    operators:
+      - "models_match_any"
+    finding_interventions:
+      - "egd_lesion_biopsy"
+      - "colon_lesion_biopsy"
+      - "ercp"
+      - "egd_argon_plasma_coagulation"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "indication_is_colon_emr"
+    name_de: "Indikation Kolon EMR"
+    name_en: "Indication colon EMR"
+    description: "This functions evaluates whether the input ()"
+    requirement_types:
+      - "examination_indication"
+    operators:
+      - "models_match_any"
+    # when creating a requirement involving other models,
+    # we need to create the relationship here:
+    examination_indications:
+      - "colonoscopy_lesion_removal_emr"

endoreg_db/data/_examples/requirement/event_cardiology.yaml

@@ -0,0 +1,251 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_implantation"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt"
+    name_en: "Event: Coronary Stent Implantation (DES) performed"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt"
+    operators:
+      - "models_match_any"
+    events:
+      - "coro_des_implantation"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_implantation_count_between_1_and_3 (exclusive)"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt zwischen 1 und 3 (exklusive)"
+    name_en: "Event: Coronary Stent Implantation (DES) performed between 1 and 3 (exclusive)"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt zwischen 1 und 3 (exklusive)"
+    operators:
+      - "models_match_count_in_range"
+    events:
+      - "coro_des_implantation"
+    numeric_value_min: 1
+    numeric_value_max: 3
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_implantation_count_greater_than_3"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt mehr als 3"
+    name_en: "Event: Coronary Stent Implantation (DES) performed more than 3"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt mehr als 3"
+    operators:
+      - "models_match_n_or_more"
+    events:
+      - "coro_des_implantation"
+    numeric_value: 3
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_bms_implantation"
+    name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt"
+    name_en: "Event: Coronary Stent Implantation (BMS) performed"
+    description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt"
+    operators:
+      - "models_match_any"
+    events:
+      - "coro_bms_implantation"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_complication_coro_stent_thrombosis"
+    name_de: "Ereignis: Komplikation Koronar Stent Thrombose"
+    name_en: "Event: Complication Coronary Stent Thrombosis"
+    description: "Ereignis: Komplikation Koronar Stent Thrombose"
+    operators:
+      - "models_match_any"
+    events:
+      - "complication_coro_stent_thrombosis"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_pulmonary_embolism"
+    name_de: "Ereignis: Lungenembolie"
+    name_en: "Event: Pulmonary Embolism"
+    description: "Ereignis: Lungenembolie"
+    operators:
+      - "models_match_any"
+    events:
+      - "pulmonary_embolism"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_deep_vein_thrombosis"
+    name_de: "Ereignis: Tiefe Beinvenenthrombose"
+    name_en: "Event: Deep Vein Thrombosis"
+    description: "Ereignis: Tiefe Beinvenenthrombose"
+    operators:
+      - "models_match_any"
+    events:
+      - "deep_vein_thrombosis"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_deep_vein_thrombosis_10_d"
+    name_de: "Ereignis: Tiefe Beinvenenthrombose innerhalb 10 Tage"
+    name_en: "Event: Deep Vein Thrombosis within 10 days"
+    description: "Ereignis: Tiefe Beinvenenthrombose innerhalb 10 Tage"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "deep_vein_thrombosis"
+    numeric_value_min: -10
+    numeric_value_max: 0
+    unit: "days"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_more_than_1_deep_vein_thrombosis"
+    name_de: "Ereignis: Mehr als 1 Tiefe Beinvenenthrombose"
+    name_en: "Event: More than 1 Deep Vein Thrombosis"
+    description: "Ereignis: Mehr als 1 Tiefe Beinvenenthrombose"
+    operators:
+      - "models_match_n_or_more"
+    events:
+      - "deep_vein_thrombosis"
+    numeric_value: 1
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_stent_implantation_30_d"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 30 Tage"
+    name_en: "Event: Coronary Stent Implantation (DES) performed within 30 days"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 30 Tage"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_des_implantation"
+    numeric_value_min: -30
+    numeric_value_max: 0
+    unit: "days"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_stent_implantation_6_w"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Wochen"
+    name_en: "Event: Coronary Stent Implantation (DES) performed within 6 weeks"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Wochen"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_des_implantation"
+    numeric_value_min: -6
+    numeric_value_max: 0
+    unit: "weeks"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_stent_implantation_6_m"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Monate"
+    name_en: "Event: Coronary Stent Implantation (DES) performed within 6 months"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Monate"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_des_implantation"
+    numeric_value_min: -6
+    numeric_value_max: 0
+    unit: "months"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_des_stent_implantation_1_y"
+    name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 1 Jahr"
+    name_en: "Event: Coronary Stent Implantation (DES) performed within 1 year"
+    description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 1 Jahr"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_des_implantation"
+    numeric_value_min: -1
+    numeric_value_max: 0
+    unit: "years"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_bms_stent_implantation_30_d"
+    name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 30 Tage"
+    name_en: "Event: Coronary Stent Implantation (BMS) performed within 30 days"
+    description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 30 Tage"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_bms_implantation"
+    numeric_value_min: -30
+    numeric_value_max: 0
+    unit: "days"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_bms_stent_implantation_6_w"
+    name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Wochen"
+    name_en: "Event: Coronary Stent Implantation (BMS) performed within 6 weeks"
+    description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Wochen"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_bms_implantation"
+    numeric_value_min: -6
+    numeric_value_max: 0
+    unit: "weeks"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_bms_stent_implantation_6_m"
+    name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Monate"
+    name_en: "Event: Coronary Stent Implantation (BMS) performed within 6 months"
+    description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Monate"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_bms_implantation"
+    numeric_value_min: -6
+    numeric_value_max: 0
+    unit: "months"
+    requirement_types:
+      - "patient"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_had_coro_bms_stent_implantation_1_y"
+    name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 1 Jahr"
+    name_en: "Event: Coronary Stent Implantation (BMS) performed within 1 year"
+    description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 1 Jahr"
+    operators:
+      - "models_match_any_in_timeframe"
+    events:
+      - "coro_bms_implantation"
+    numeric_value_min: -1
+    numeric_value_max: 0
+    unit: "years"
+    requirement_types:
+      - "patient"

endoreg_db/data/_examples/requirement/event_requirements.yaml

@@ -0,0 +1,145 @@
+# /home/admin/dev/endo-ai/endoreg-db/endoreg_db/data/requirement/event_requirements.yaml
+- model: endoreg_db.requirement
+  fields:
+    name: "event_coro_des_implantation_exists"
+    name_de: "Ereignis Koronarstent-Implantation (DES) vorhanden"
+    name_en: "Event Coronary Stent Implantation (DES) exists"
+    description: "Checks if a 'coro_des_implantation' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "coro_des_implantation"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_coro_bms_implantation_exists"
+    name_de: "Ereignis Koronarstent-Implantation (BMS) vorhanden"
+    name_en: "Event Coronary Stent Implantation (BMS) exists"
+    description: "Checks if a 'coro_bms_implantation' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "coro_bms_implantation"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_pulmonary_embolism_exists"
+    name_de: "Ereignis Lungenembolie vorhanden"
+    name_en: "Event Pulmonary Embolism exists"
+    description: "Checks if a 'pulmonary_embolism' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "pulmonary_embolism"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_deep_vein_thrombosis_exists"
+    name_de: "Ereignis Tiefe Beinvenenthrombose vorhanden"
+    name_en: "Event Deep Vein Thrombosis exists"
+    description: "Checks if a 'deep_vein_thrombosis' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "deep_vein_thrombosis"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_stroke_exists"
+    name_de: "Ereignis Schlaganfall vorhanden"
+    name_en: "Event Stroke exists"
+    description: "Checks if a 'stroke' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "stroke"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_transient_ischemic_attack_exists"
+    name_de: "Ereignis Transitorische ischämische Attacke vorhanden"
+    name_en: "Event Transient Ischemic Attack exists"
+    description: "Checks if a 'transient_ischemic_attack' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "transient_ischemic_attack"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_hip_replacement_surgery_exists"
+    name_de: "Ereignis Hüft-TEP Operation vorhanden"
+    name_en: "Event Hip replacement surgery exists"
+    description: "Checks if a 'hip_replacement_surgery' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "hip_replacement_surgery"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_knee_replacement_surgery_exists"
+    name_de: "Ereignis Knie-TEP Operation vorhanden"
+    name_en: "Event Knee replacement surgery exists"
+    description: "Checks if a 'knee_replacement_surgery' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "knee_replacement_surgery"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "event_recurrent_thrombembolism_exists"
+    name_de: "Ereignis Rezidivierende Thrombembolien vorhanden"
+    name_en: "Event Recurrent Thrombembolism exists"
+    description: "Checks if a 'recurrent_thrombembolism' event exists for the patient."
+    requirement_types:
+      - "patient"
+      - "patient_event" # Added patient_event
+    operators:
+      - models_match_any
+    events:
+      - "recurrent_thrombembolism"
+
+# Example for models_match_any_in_timeframe
+- model: endoreg_db.requirement
+  fields:
+    name: "event_stroke_in_last_30_days"
+    name_de: "Ereignis Schlaganfall in den letzten 30 Tagen"
+    name_en: "Event Stroke in the last 30 days"
+    description: "Checks if a 'stroke' event occurred for the patient in the last 30 days."
+    requirement_types: # Defines which input models are expected by Requirement.evaluate()
+      - "patient"
+      - "patient_event" # This tells the system to look for PatientEvent models in the input
+    operators:
+      - models_match_any_in_timeframe
+    events: # This links the Requirement to specific Event models (e.g. "stroke")
+      - "stroke"
+    # Timeframe definition for the operator:
+    numeric_value_min: -30 # Start of timeframe (days ago)
+    numeric_value_max: 0   # End of timeframe (days ago, i.e., today)
+    unit: "days"           # Unit for the timeframe

endoreg_db/data/_examples/requirement/finding_colon_polyp.yaml

@@ -0,0 +1,50 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "colon_austria_screening_polyp_size"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    operators:
+      - "models_match_any"
+    finding_classifications:
+      - "colon_lesion_size_mm"
+      - "colon_lesion_size_austria_categorical"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_location"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    operators:
+      - "models_match_any"
+    finding_classifications:
+      - "colonoscopy_austria_screening_location"
+      - "colonoscopy_location_default"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_morphology"
+    operators:
+      - "models_match_any"
+    requirement_types:
+      - "patient_examination"
+      - "patient_finding"
+    finding_classifications:
+      - "colon_lesion_paris"
+      - "colon_lesion_lst"
+      - "colon_lesion_planarity_default"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "colonoscopy_austria_screening_polyp_histology"
+    requirement_types:
+      - "patient_finding" 
+      - "patient_examination"
+    operators:
+      - "models_match_all"
+    finding_classifications:
+      - "colonoscopy_polyp_histology"
+      - "colonoscopy_polyp_histology_dysplasia"
+      - "colonoscopy_histology_dignity"
+    

endoreg_db/data/_examples/requirement/gender.yaml

@@ -0,0 +1,25 @@
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_gender_is_male"
+    name_de: "Patient ist männlich"
+    name_en: "Patient is male"
+    description: "Checks if the patient is male."
+    requirement_types:
+      - "patient"
+    operators:
+      - models_match_all
+    genders:
+      - "male"
+
+- model: endoreg_db.requirement
+  fields:
+    name: "patient_gender_is_female"
+    name_de: "Patient ist weiblich"
+    name_en: "Patient is female"
+    description: "Checks if the patient is female."
+    requirement_types:
+      - "patient"
+    operators:
+      - models_match_all
+    genders:
+      - "female"