endoreg-db 0.8.6.4__py3-none-any.whl

endoreg_db/management/commands/load_examination_data.py

@@ -0,0 +1,75 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from ...models import (
+    Examination,
+    ExaminationType,  # Replace 'your_app_name' with the actual app name
+    ExaminationTime,
+    ExaminationTimeType,
+)
+import os
+from ...utils import load_model_data_from_yaml
+from ...data import EXAMINATION_DATA_DIR
+
+SOURCE_DIR = EXAMINATION_DATA_DIR 
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    "ExaminationType",
+    "Examination",
+    "ExaminationTimeType",
+    "ExaminationTime"
+]
+
+IMPORT_METADATA = {
+    # "": { # same as model name in "import models", e.g. "Intervention"
+    #     "subdir": os.path.join(SOURCE_DIR,""), # e.g. "interventions"
+    #     "model": None, # e.g. Intervention
+    #     "foreign_keys": [], # e.g. ["intervention_types"]
+    #     "foreign_key_models": [] # e.g. [InterventionType]
+    # },
+    "ExaminationType": {
+        "dir": os.path.join(SOURCE_DIR,"type"), # e.g. "interventions"
+        "model": ExaminationType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    "Examination": {
+        "dir": os.path.join(SOURCE_DIR,"examinations"), # e.g. "interventions"
+        "model": Examination, # e.g. Intervention
+        "foreign_keys": ["examination_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [ExaminationType] # e.g. [InterventionType]
+    },
+    "ExaminationTimeType": {
+        "dir": os.path.join(SOURCE_DIR,"time-type"), # e.g. "interventions"
+        "model": ExaminationTimeType, # e.g. Intervention
+        "foreign_keys": ["examinations"], # e.g. ["intervention_types"]
+        "foreign_key_models": [Examination] # e.g. [InterventionType]
+    },
+    "ExaminationTime": {
+        "dir": os.path.join(SOURCE_DIR,"time"), # e.g. "interventions"
+        "model": ExaminationTime, # e.g. Intervention
+        "foreign_keys": ["time_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [ExaminationTimeType] # e.g. [InterventionType]
+    },
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_examination_indication_data.py

@@ -0,0 +1,86 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from ...models import (
+    ExaminationIndicationClassification,
+    ExaminationIndication,
+    ExaminationIndicationClassificationChoice,
+    Examination,
+    FindingIntervention,
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR,
+    EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR,
+    EXAMINATION_INDICATION_DATA_DIR,
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    ExaminationIndication.__name__,
+    ExaminationIndicationClassification.__name__,
+    ExaminationIndicationClassificationChoice.__name__,
+]
+
+IMPORT_METADATA = {
+    ExaminationIndication.__name__: {
+        "dir": EXAMINATION_INDICATION_DATA_DIR,
+        "model": ExaminationIndication,
+        "foreign_keys": [
+            "examinations",
+            "expected_interventions",
+        ],
+        "foreign_key_models": [
+            Examination,
+            FindingIntervention,
+        ],
+    },
+    ExaminationIndicationClassification.__name__: {
+        "dir": EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR,
+        "model": ExaminationIndicationClassification,
+        "foreign_keys": [
+            "examinations",
+            "indications",  # This is a many-to-many field
+        ],
+        "foreign_key_models": [
+            Examination,
+            ExaminationIndication,
+        ],
+    },
+    ExaminationIndicationClassificationChoice.__name__: {
+        "dir": EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR,
+        "model": ExaminationIndicationClassificationChoice,
+        "foreign_keys": ["classification"],
+        "foreign_key_models": [ExaminationIndicationClassification],
+    },
+}
+
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        """
+        Add the --verbose flag to the command-line argument parser.
+        
+        This method augments the parser with a '--verbose' option to enable detailed output
+        during command execution.
+        """
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        """
+        Executes YAML data import for configured models.
+        
+        Retrieves the verbosity flag from the options and iterates through each model
+        in IMPORT_MODELS. For every model, it obtains the associated metadata from
+        IMPORT_METADATA and invokes load_model_data_from_yaml to load data from its YAML files.
+        """
+        verbose = options["verbose"]
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)

endoreg_db/management/commands/load_finding_data.py

@@ -0,0 +1,128 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Finding, FindingType, Examination,
+    FindingClassification, FindingClassificationType, FindingClassificationChoice,
+    Organ,
+    FindingIntervention, FindingInterventionType, LabValue, Contraindication
+
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    FINDING_DATA_DIR, FINDING_TYPE_DATA_DIR,
+    FINDING_INTERVETION_DATA_DIR,
+    FINIDNG_INTERVENTION_TYPE_DATA_DIR,
+    FINDING_CLASSIFICATION_TYPE_DATA_DIR,
+    FINDING_CLASSIFICATION_DATA_DIR,
+    FINDING_CLASSIFICATION_CHOICE_DATA_DIR
+)
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    FindingInterventionType.__name__,
+    FindingIntervention.__name__,
+    FindingType.__name__,
+    Finding.__name__,
+    FindingClassificationType.__name__,
+    FindingClassificationChoice.__name__,
+    FindingClassification.__name__,
+]
+
+IMPORT_METADATA = {
+    FindingType.__name__: {
+        "dir": FINDING_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": FindingType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    Finding.__name__: {
+        "dir": FINDING_DATA_DIR, # e.g. "interventions"
+        "model": Finding, # e.g. Intervention
+        "foreign_keys": [
+            "finding_types",
+            "examinations",
+            "finding_interventions",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            FindingType,
+            Examination,
+            FindingIntervention,
+            FindingIntervention,
+            FindingIntervention,
+        ] # e.g. [InterventionType]
+    },
+    FindingInterventionType.__name__: {
+        "dir": FINIDNG_INTERVENTION_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": FindingInterventionType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    FindingIntervention.__name__: {
+        "dir": FINDING_INTERVETION_DATA_DIR, # e.g. "interventions"
+        "model": FindingIntervention, # e.g. Intervention
+        "foreign_keys": [
+            "intervention_types",
+            "required_lab_values",
+            "contraindications"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            FindingInterventionType,
+            LabValue,
+            Contraindication
+        ] # e.g. [InterventionType]
+    },
+    FindingClassificationType.__name__: {
+        "dir": FINDING_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassificationType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    FindingClassification.__name__: {
+        "dir": FINDING_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassification, # e.g. Intervention
+        "foreign_keys": [
+            "classification_types",
+            "findings",
+            "examinations",
+            "finding_types",
+            "choices"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            FindingClassificationType,
+            Finding,
+            Examination,
+            FindingType,
+            FindingClassificationChoice,
+        ] # e.g. [InterventionType]
+    },
+    FindingClassificationChoice.__name__: {
+        "dir": FINDING_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
+        "model": FindingClassificationChoice, # e.g. Intervention
+        "foreign_keys": [
+            # "classifications",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            # FindingClassification
+        ] # e.g. [InterventionType]
+    },
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_gender_data.py

@@ -0,0 +1,44 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Gender,
+
+    # Other models for ForeignKeys
+    Unit, Center
+)
+from collections import OrderedDict
+
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    GENDER_DATA_DIR,
+)
+
+IMPORT_METADATA = OrderedDict({
+    Gender.__name__: {
+        "dir": GENDER_DATA_DIR,
+        "model": Gender, 
+        "foreign_keys": [], 
+        "foreign_key_models": [] 
+    },    
+})
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_METADATA.keys():
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py

@@ -0,0 +1,132 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    EmissionFactor,
+    Resource,
+    Waste,
+    Material,
+    Product,
+    ProductGroup,
+    ReferenceProduct,
+    TransportRoute,
+    CenterWaste,
+    CenterResource,
+    ProductMaterial,
+    ProductWeight,
+
+    # Other models for ForeignKeys
+    Unit, Center
+)
+from collections import OrderedDict
+
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    EMISSION_FACTOR_DATA_DIR,
+    RESOURCE_DATA_DIR,
+    WASTE_DATA_DIR,
+    MATERIAL_DATA_DIR,
+    PRODUCT_DATA_DIR,
+    PRODUCT_GROUP_DATA_DIR,
+    REFERENCE_PRODUCT_DATA_DIR,
+    TRANSPORT_ROUTE_DATA_DIR,
+    CENTER_WASTE_DATA_DIR,
+    CENTER_RESOURCE_DATA_DIR,
+    PRODUCT_MATERIAL_DATA_DIR,
+    PRODUCT_WEIGHT_DATA_DIR,
+)
+
+IMPORT_METADATA = OrderedDict({
+    EmissionFactor.__name__: {
+        "dir": EMISSION_FACTOR_DATA_DIR,
+        "model": EmissionFactor, 
+        "foreign_keys": ["unit"], 
+        "foreign_key_models": [Unit] 
+    },
+    Resource.__name__: {
+        "dir": RESOURCE_DATA_DIR,
+        "model": Resource,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    },
+    Waste.__name__: {
+        "dir": WASTE_DATA_DIR,
+        "model": Waste,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    },
+    Material.__name__: {
+        "dir": MATERIAL_DATA_DIR,
+        "model": Material,
+        "foreign_keys": ["emission_factor"],
+        "foreign_key_models": [EmissionFactor]
+    },
+    ProductGroup.__name__: {
+        "dir": PRODUCT_GROUP_DATA_DIR,
+        "model": ProductGroup,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    },
+    TransportRoute.__name__: {
+        "dir": TRANSPORT_ROUTE_DATA_DIR,
+        "model": TransportRoute,
+        "foreign_keys": ["emission_factor", "unit"],
+        "foreign_key_models": [EmissionFactor, Unit]
+    },
+    Product.__name__: {
+        "dir": PRODUCT_DATA_DIR,
+        "model": Product,
+        "foreign_keys": ["product_group", "transport_route"],
+        "foreign_key_models": [ProductGroup, TransportRoute]
+    },
+    ReferenceProduct.__name__: {
+        "dir": REFERENCE_PRODUCT_DATA_DIR,
+        "model": ReferenceProduct,
+        "foreign_keys": ["product","product_group"],
+        "foreign_key_models": [Product,ProductGroup]
+    },
+    CenterWaste.__name__: {
+        "dir": CENTER_WASTE_DATA_DIR,
+        "model": CenterWaste,
+        "foreign_keys": ["waste", "center", "unit", "emission_factor"],
+        "foreign_key_models": [Waste, Center, Unit, EmissionFactor]
+    },
+    CenterResource.__name__: {
+        "dir": CENTER_RESOURCE_DATA_DIR,
+        "model": CenterResource,
+        "foreign_keys": ["center","resource", "unit", "transport_emission_factor", "use_emission_factor"],
+        "foreign_key_models": [Center,Resource, Unit, EmissionFactor, EmissionFactor]
+    },
+    ProductMaterial.__name__: {
+        "dir": PRODUCT_MATERIAL_DATA_DIR,
+        "model": ProductMaterial,
+        "foreign_keys": ["product", "material", "unit"],
+        "foreign_key_models": [Product, Material, Unit]
+    },
+    ProductWeight.__name__: {
+        "dir": PRODUCT_WEIGHT_DATA_DIR,
+        "model": ProductWeight,
+        "foreign_keys": ["product", "unit"],
+        "foreign_key_models": [Product, Unit]
+    }
+})
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_METADATA.keys():
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_information_source.py

@@ -0,0 +1,51 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import InformationSource, InformationSourceType
+from ...utils import load_model_data_from_yaml
+from ...data import INFORMATION_DATA_DIR, INFORMATION_SOURCE_TYPE_DATA_DIR
+
+SOURCE_DIR = INFORMATION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    InformationSourceType.__name__,
+    InformationSource.__name__,
+]
+
+IMPORT_METADATA = {
+    InformationSourceType.__name__: {
+        "dir": INFORMATION_SOURCE_TYPE_DATA_DIR, # e.g. "intervention_type"
+        "model": InformationSourceType, # e.g. InterventionType
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    InformationSource.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": InformationSource, # e.g. Intervention
+        "foreign_keys": ["information_source_types"], # e.g. ["intervention_types"]
+        "foreign_key_models": [InformationSourceType] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_lab_value_data.py

@@ -0,0 +1,50 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import LabValue as MODEL_0
+from endoreg_db.models import PatientLabSampleType, NumericValueDistribution
+from ...utils import load_model_data_from_yaml
+from ...data import LAB_VALUE_DATA_DIR as SOURCE_DIR
+from ...data import PATIENT_LAB_SAMPLE_TYPE_DATA_DIR
+
+from endoreg_db.models import Unit
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+    PatientLabSampleType.__name__
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": ["default_unit","default_numerical_value_distribution"], # e.g. ["intervention_types"]
+        "foreign_key_models": [Unit, NumericValueDistribution] # e.g. [InterventionType]
+    },
+    PatientLabSampleType.__name__: {
+        "dir": PATIENT_LAB_SAMPLE_TYPE_DATA_DIR,
+        "model": PatientLabSampleType,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    }
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/load_medication_data.py

@@ -0,0 +1,103 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Medication,
+    MedicationIndication,
+    MedicationIndicationType,
+    MedicationIntakeTime,
+    MedicationSchedule,
+    Unit,
+    Disease,
+    Event,
+    InformationSource,
+    DiseaseClassificationChoice,
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    MEDICATION_DATA_DIR,
+    MEDICATION_INDICATION_TYPE_DATA_DIR,
+    MEDICATION_INTAKE_TIME_DATA_DIR,
+    MEDICATION_SCHEDULE_DATA_DIR,
+    MEDICATION_INDICATION_DATA_DIR,
+)
+
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    Medication.__name__,
+    MedicationIndicationType.__name__,
+    MedicationIntakeTime.__name__,
+    MedicationSchedule.__name__,
+    MedicationIndication.__name__,
+]
+
+IMPORT_METADATA = {
+    Medication.__name__: {
+        "dir": MEDICATION_DATA_DIR,  # e.g. "interventions"
+        "model": Medication,  # e.g. Intervention
+        "foreign_keys": ["default_unit"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [Unit],  # e.g. [InterventionType]
+    },
+    MedicationIndicationType.__name__: {
+        "dir": MEDICATION_INDICATION_TYPE_DATA_DIR,  # e.g. "interventions"
+        "model": MedicationIndicationType,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    MedicationIntakeTime.__name__: {
+        "dir": MEDICATION_INTAKE_TIME_DATA_DIR,  # e.g. "interventions"
+        "model": MedicationIntakeTime,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    MedicationSchedule.__name__: {
+        "dir": MEDICATION_SCHEDULE_DATA_DIR,  # e.g. "interventions"
+        "model": MedicationSchedule,  # e.g. Intervention
+        "foreign_keys": [
+            "medication",
+            "intake_times",
+            "unit",
+        ],  # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Medication,
+            MedicationIntakeTime,
+            Unit,
+        ],  # e.g. [InterventionType]
+    },
+    MedicationIndication.__name__: {
+        "dir": MEDICATION_INDICATION_DATA_DIR,  # e.g. "interventions"
+        "model": MedicationIndication,  # e.g. Intervention
+        "foreign_keys": [
+            "indication_type",
+            "medication_schedules",
+            "diseases",
+            "events",
+            "disease_classification_choices",
+            "sources",
+        ],  # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            MedicationIndicationType,
+            MedicationSchedule,
+            Disease,
+            Event,
+            DiseaseClassificationChoice,
+            InformationSource,
+        ],  # e.g. [InterventionType]
+    },
+}
+
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        verbose = options["verbose"]
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)