endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml

@@ -0,0 +1,20 @@
+- model: endoreg_db.video_segmentation_label_set
+  fields:
+    name: "colonoscopy_video_segmentation_raw"
+    labels:
+      [
+        "appendix",
+        "blood",
+        "diverticule",
+        "grasper",
+        "ileocaecalvalve",
+        "ileum",
+        "low_quality",
+        "nbi",
+        "needle",
+        "outside",
+        "polyp",
+        "snare",
+        "water_jet",
+        "wound",
+      ]

endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml

@@ -0,0 +1,167 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-sodium-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "sodium",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+# potassium
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-potassium-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "potassium",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-hemoglobin-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "hemoglobin",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+# hematocrit
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-hematocrit-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "hematocrit",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+# platelet count
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-platelets-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "platelets",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+# white cell count
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-white_blood_cells-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "white_blood_cells",
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+# estimated glomerular filtration rate
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_lab_sample-add_value-egfr-default"
+    rule_type: "create-object"
+    parent_model: "PatientLabSample"
+    parent_field: "sample"
+    target_model: "PatientLabValue"
+    extra_parameters: {
+      "create_method": {
+          "name": "create_lab_value_by_sample",
+          "kwargs": {
+            "lab_value_name": "estimated_glomerular_filtration_rate", 
+          }
+        },
+        "actions": [
+          {
+            "name": "set_value_by_distribution",
+            "kwargs": {} 
+          }
+        ]
+  
+      }
+
+

endoreg_db/data/case_template/rule/01_patient-set-age.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient-set-age-screening_colo_population"
+    rule_type: "set-field-by_distribution"
+    parent_model: "Patient"
+    target_field: "dob"
+    value_type: "date"
+    date_value_distribution: "age-screening_colo_population"

endoreg_db/data/case_template/rule/01_patient-set-gender.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient-set-gender-random"
+    rule_type: "set-field-by_distribution"
+    parent_model: "Patient"
+    target_field: "gender"
+    target_model: "Gender"
+    value_type: "foreign_key"
+    single_categorical_value_distribution: "gender-random"

endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml

@@ -0,0 +1,23 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient_lab_sample-default"
+    rule_type: "create-object"
+    target_model: "PatientLabSample"
+    parent_field: "patient"
+    chained_rules: [
+      "patient_lab_sample-add_value-sodium-default",
+      "patient_lab_sample-add_value-potassium-default",
+      "patient_lab_sample-add_value-egfr-default",
+      "patient_lab_sample-add_value-hemoglobin-default",
+      "patient_lab_sample-add_value-hematocrit-default",
+      "patient_lab_sample-add_value-platelets-default",
+      "patient_lab_sample-add_value-white_blood_cells-default"
+    ]
+    extra_parameters: {
+      "create_method": {
+        "name": "create_by_patient",
+        "kwargs": {
+          "sample_type": "generic"
+        }
+      }
+    }

endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml

@@ -0,0 +1,19 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient_medication_schedule-anticoagulation-non_valvular_af"
+    rule_type: "create-object"
+    target_model: "PatientMedication"
+    parent_field: "patient"
+
+    chained_rules: [
+
+    ]
+    
+    extra_parameters: {
+      "create_method": {
+        "name": "create_by_patient_and_indication_type",
+        "kwargs": {
+          "indication_type": "thromboembolism-prevention-non_valvular_af"
+        }
+      }
+    }

endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml

@@ -0,0 +1,19 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient_medication_schedule-anticoagulation-non_valvular_af"
+    rule_type: "create-object"
+    target_model: "PatientMedicationSchedule"
+    parent_field: "patient"
+
+    chained_rules: [
+
+    ]
+    
+    extra_parameters: {
+      "create_method": {
+        "name": "create_by_patient_and_indication_type",
+        "kwargs": {
+          "indication_type": "thromboembolism-prevention-non_valvular_af"
+        }
+      }
+    }

endoreg_db/data/case_template/rule/19_create_patient.yaml

@@ -0,0 +1,17 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient-default"
+    rule_type: "create-object"
+    target_model: "Patient"
+    chained_rules: [
+      "patient-set-age-screening_colo_population",
+      "create-patient_lab_sample-default"
+    ]
+    extra_parameters: {
+      "create_method": {
+        "name": "create_generic",
+        "kwargs": {
+          "center": "gplay_case_generator",
+         }
+        }
+    }

endoreg_db/data/case_template/rule_type/base_types.yaml

@@ -0,0 +1,35 @@
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "set-field-default"
+    name_de: "Default Wert eines Feldes setzen"
+    name_en: "Set value of field"
+
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "set-field-by_distribution"
+    name_de: "Wert eines Feldes anhand einer Verteilung setzen"
+    name_en: "Set value of field by distribution"
+
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "set-field-by_value"
+    name_de: "Wert eines Feldes auf einen bestimmten Wert setzen"
+    name_en: "Set value of field to a specific value"
+
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "set-field-single_choice"
+    name_de: "Wert eines Feldes auf einen bestimmten Wert anhand einer Auswahl setzen"
+    name_en: "Set value of field to a specific value based on a choice"
+
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "set-field-multiple_choice"
+    name_de: "Wert eines Feldes auf einen bestimmten Wert anhand einer Mehrfachauswahl setzen"
+    name_en: "Set value of field to a specific value based on a multiple choice"
+
+- model: endoreg_db.case_template_rule_type
+  fields:
+    name: "create-object"
+    name_de: "Datenbank Objekt erstellen"
+    name_en: "Create Db Object"

endoreg_db/data/case_template/rule_value_type/base_types.yaml

@@ -0,0 +1,59 @@
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "foreign_key"
+    distribution_type: "single_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "many_to_many"
+    distribution_type: "multiple_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "object"
+    distribution_type: "single_categorical"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "date"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "integer"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "string"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "boolean"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "float"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "text"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "integer_range"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type 
+  fields:
+    name: "float_range"
+    distribution_type: "numeric"
+
+- model: endoreg_db.case_template_rule_value_type
+  fields:
+    name: "date_range"
+    distribution_type: "numeric"

endoreg_db/data/case_template/template/base.yaml

@@ -0,0 +1,8 @@
+- model: endoreg_db.case_template
+  fields:
+    name: "pre_default_screening_colonoscopy"
+    rules: [
+      "create-patient-default",
+      "create-patient_medication_schedule-anticoagulation-non_valvular_af",
+    ]
+    template_type: "pre_endoscopy"

endoreg_db/data/case_template/template_type/pre_endoscopy.yaml

@@ -0,0 +1,3 @@
+- model: endoreg_db.case_template_type
+  fields:
+    name: "pre_endoscopy"

endoreg_db/data/case_template/tmp/_rule_value

@@ -0,0 +1,13 @@
+- model: endoreg_db.case_template_rule_value
+  fields:
+    name: "diagnosis_value-non_valvular_atrial-fibrillation"
+    target_field: "disease"
+    value_type: "foreign_key"
+    fk_value: "non_valvular_atrial_fibrillation"
+    
+- model: endoreg_db.case_template_rule_value
+  fields:
+    name: "medication_schedule-apixaban-5mg-twice_daily"
+    target_field: "medication_indication"
+    value_type: "foreign_key"
+    fk_value: "te_prevention-recurrent-te-apixaban"

endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml

@@ -0,0 +1,21 @@
+
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient-add_medication_indication-anticoagulation-non_valvular_af"
+    rule_type: "add_one_value"
+    target_model: "endoreg_db.patient_medication_indication"
+    rule_values: [
+      "medication_schedule-apixaban-5mg-twice_daily"
+    ]
+
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "patient_add_diagnosis_atrial-fibrillation"
+    rule_type: "add_one_value"
+    target_model: "endoreg_db.patient_disease"
+    rule_values: [
+      "diagnosis_value-non_valvular_atrial-fibrillation"
+    ]
+    chained_rules: [
+      "patient-add_medication_indication-anticoagulation-non_valvular_af"
+    ]

endoreg_db/data/case_template/tmp/rule/02_create_object.yaml

@@ -0,0 +1,10 @@
+- model: endoreg_db.case_template_rule
+  fields:
+    name: "create-patient-screening_colo"
+    rule_type: "create_object"
+    target_model: "Patient"
+    rule_value_type: "object"
+    target_field: null
+    chained_rules: [
+      "patient-set-gender-random"
+    ]

endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.case_template_type
+  fields:
+    name: "pre_endo-anticoagulation-af-low_risk"
+    template_type: "pre_endoscopy"
+    rules: [
+      "patient_add_diagnosis_atrial-fibrillation"
+    ]

endoreg_db/data/center/data.yaml

@@ -0,0 +1,90 @@
+# center/data.yaml
+
+- model: endoreg_db.center
+  fields:
+    name: "university_hospital_wuerzburg"
+    name_de: "Universitätsklinikum Würzburg"
+    name_en: "University Hospital Würzburg"
+
+    first_names: [
+      "Markus",
+      "Linhel",
+      "Rainer",
+      "Hans",
+      "Anja",
+      "Dorothea",
+      "Doro",
+      "Angelika",
+      "Sven",
+      "Theodor",
+      "Alexander",
+      "Mandy",
+      "Kathrin",
+      "Florian",
+      "Philip",
+      "Laura",
+      "Tanja",
+    ]
+    
+    last_names: [
+      "Kozielski",
+      "Reiter",
+      "Purrer",
+      "Hossner",
+      "Kudlich",
+      "Brand",
+      "Weich",
+      "Lux",
+      "Meining",
+      "Hann",
+      "Retzbach",
+      "Hose",
+      "Henniger",
+      "Weich",
+      "Dela Cruz",
+      "Wiesemann",
+      "Wiese",
+      "Sodmann"
+    ]
+- model: endoreg_db.center
+  fields:
+    name: "rbk_stuttgart"
+    name_de: "Robert-Bosch-Krankenhaus Stuttgart"
+    name_en: "Robert Bosch Hospital Stuttgart"
+    first_names: [] # many to many; if foreign key, we would just have a string; strings represent "name" attribute
+    last_names: []
+
+# bbk_regensburg
+- model: endoreg_db.center
+  fields:
+    name: "bbk_regensburg"
+    name_de: "Barmherzige  Brüder Krankenhaus Regensburg"
+    name_en: "Barmherzige Brüder Hospital Regensburg"
+    first_names: []
+    last_names: []
+
+# uke_hamburg
+- model: endoreg_db.center
+  fields:
+    name: "uke_hamburg"
+    name_de: "Universitätsklinikum Hamburg-Eppendorf"
+    name_en: "University Hospital Hamburg-Eppendorf"
+    first_names: []
+    last_names: []
+
+# rkh_ludwigsburg
+- model: endoreg_db.center
+  fields:
+    name: "rkh_ludwigsburg"
+    name_de: "RKH Krankenhaus Ludwigsburg"
+    name_en: "RKH Hospital Ludwigsburg"
+    first_names: []
+    last_names: []
+
+- model: endoreg_db.center
+  fields:
+    name: "endoreg_db_demo"
+    name_de: "Demo Center"
+    name_en: "Demo Center"
+    first_names: []
+    last_names: []