endoreg-db 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

endoreg_db/admin.py

@@ -1,3 +1,3 @@
-from django.contrib import admin
-
-# Register your models here.
+from django.contrib import admin
+
+# Register your models here.

endoreg_db/apps.py

@@ -1,6 +1,6 @@
-from django.apps import AppConfig
-
-
-class EndoregDbConfig(AppConfig):
-    default_auto_field = 'django.db.models.BigAutoField'
-    name = 'endoreg_db'
+from django.apps import AppConfig
+
+
+class EndoregDbConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'endoreg_db'

endoreg_db/data/__init__.py

@@ -1,16 +1,65 @@
-from pathlib import Path
-
-DATA_DIR = Path(__file__).parent
-
-INFORMATION_DATA_DIR = DATA_DIR / "information_source"
-UNIT_DATA_DIR = DATA_DIR / "unit"
-CENTER_DATA_DIR = DATA_DIR / "center"
-EXAMINATION_DATA_DIR = DATA_DIR / "examination"
-LABEL_DATA_DIR = DATA_DIR / "label"
-MODEL_TYPE_DATA_DIR = DATA_DIR / "model_type"
-ENDOSCOPY_PROCESSOR_DATA_DIR = DATA_DIR / "endoscopy_processor"
-ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
-ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
-PROFESSION_DATA_DIR = DATA_DIR / "profession"
-PDF_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
-REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
+from pathlib import Path
+
+DATA_DIR = Path(__file__).parent
+
+INFORMATION_DATA_DIR = DATA_DIR / "information_source"
+UNIT_DATA_DIR = DATA_DIR / "unit"
+CENTER_DATA_DIR = DATA_DIR / "center"
+EXAMINATION_DATA_DIR = DATA_DIR / "examination"
+LABEL_DATA_DIR = DATA_DIR / "label"
+MODEL_TYPE_DATA_DIR = DATA_DIR / "model_type"
+ENDOSCOPY_PROCESSOR_DATA_DIR = DATA_DIR / "endoscopy_processor"
+ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
+ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
+PROFESSION_DATA_DIR = DATA_DIR / "profession"
+PDF_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
+REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
+EVENT_DATA_DIR = DATA_DIR / "event"
+GENDER_DATA_DIR = DATA_DIR / "gender"
+
+# Green Endoscopy Dashboard Stuffs
+CENTER_RESOURCE_DATA_DIR = DATA_DIR / "center_resource"
+CENTER_WASTE_DATA_DIR = DATA_DIR / "center_waste"
+EMISSION_FACTOR_DATA_DIR = DATA_DIR / "emission_factor"
+MATERIAL_DATA_DIR = DATA_DIR / "material"
+PRODUCT_DATA_DIR = DATA_DIR / "product"
+PRODUCT_GROUP_DATA_DIR = DATA_DIR / "product_group"
+PRODUCT_MATERIAL_DATA_DIR = DATA_DIR / "product_material"
+PRODUCT_WEIGHT_DATA_DIR = DATA_DIR / "product_weight"
+REFERENCE_PRODUCT_DATA_DIR = DATA_DIR / "reference_product"
+RESOURCE_DATA_DIR = DATA_DIR / "resource"
+WASTE_DATA_DIR = DATA_DIR / "waste"
+TRANSPORT_ROUTE_DATA_DIR = DATA_DIR / "transport_route"
+DISEASE_CLASSIFICATION_DATA_DIR = DATA_DIR / "disease_classification"
+DISEASE_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "disease_classification_choice"
+DISEASE_DATA_DIR = DATA_DIR / "disease"
+MEDICATION_DATA_DIR = DATA_DIR / "medication"
+MEDICATION_INDICATION_DATA_DIR = DATA_DIR / "medication_indication"
+MEDICATION_INDICATION_TYPE_DATA_DIR = DATA_DIR / "medication_indication_type"
+
+DISTRIBUTION_BASE_DIR = DATA_DIR / "distribution"
+DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "single_categorical"
+DISTRIBUTION_NUMERIC_DATA_DIR = DISTRIBUTION_BASE_DIR / "numeric"
+DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "multiple_categorical"
+DISTRIBUTION_DATE_DATA_DIR = DISTRIBUTION_BASE_DIR / "date"
+
+# G-Play Stuffs
+CASE_TEMPLATE_BASE_DIR = DATA_DIR / "case_template"
+CASE_TEMPLATE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template"
+CASE_TEMPLATE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template_type"
+CASE_TEMPLATE_RULE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule"
+CASE_TEMPLATE_RULE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_type"
+CASE_TEMPLATE_RULE_VALUE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value"
+CASE_TEMPLATE_RULE_VALUE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value_type"
+
+
+# To Do
+LAB_VALUE_DATA_DIR = DATA_DIR / "lab_value"
+PATIENT_LAB_SAMPLE_TYPE_DATA_DIR = DATA_DIR / "patient_lab_sample_type"
+MEDICATION_SCHEDULE_DATA_DIR = DATA_DIR / "medication_schedule"
+MEDICATION_INTAKE_TIME_DATA_DIR = DATA_DIR / "medication_intake_time"
+
+
+RULE_TYPE_DATA_DIR = DATA_DIR / "rule_type"
+RULE_ATTRIBUTE_DTYPE_DATA_DIR = DATA_DIR / "rule_attribute_dtype"
+RULESET_DATA_DIR = DATA_DIR / "ruleset"

endoreg_db/data/active_model/data.yaml

@@ -1,3 +1,3 @@
-- model: endoreg_db.active_model
-  data:
+- model: endoreg_db.active_model
+  data:
     - name: "multilabel_image_classification"

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

@@ -1,52 +1,60 @@
-# 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"
-    ]
-    last_names: [
-      "Kozielski",
-      "Reiter",
-      "Purrer",
-      "Kudlich",
-      "Brand",
-      "Weich",
-      "Lux",
-      "Meining",
-      "Hann",
-      "Retzbach",
-      "Hose",
-      "Henniger",
-      "Weich",
-      "Dela Cruz",
-      "Wiesemann",
-      "Weise",
-      "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: []
+# 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"
+    ]
+    last_names: [
+      "Kozielski",
+      "Reiter",
+      "Purrer",
+      "Kudlich",
+      "Brand",
+      "Weich",
+      "Lux",
+      "Meining",
+      "Hann",
+      "Retzbach",
+      "Hose",
+      "Henniger",
+      "Weich",
+      "Dela Cruz",
+      "Wiesemann",
+      "Weise",
+      "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: []
+
+- model: endoreg_db.center
+  fields:
+    name: "gplay_case_generator"
+    name_de: "GPlay Case Generator"
+    name_en: "GPlay Case Generator"
+    first_names: []
+    last_names: []