endoreg-db 0.5.3__py3-none-any.whl → 0.6.1__py3-none-any.whl

endoreg_db/management/commands/load_finding_data.py

@@ -0,0 +1,171 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Finding, FindingType, Examination,
+    FindingLocationClassification, FindingLocationClassificationChoice,
+    Organ,
+    FindingMorphologyClassificationType, FindingMorphologyClassification,
+    FindingMorphologyClassificationChoice,
+    FindingIntervention, FindingInterventionType, LabValue, Contraindication
+
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    FINDING_DATA_DIR, FINDING_TYPE_DATA_DIR,
+    FINDING_LOCATION_CLASSIFICATION_DATA_DIR, 
+    FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR,
+    FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR, 
+    FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR,
+    FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR,
+    FINDING_INTERVETION_DATA_DIR,
+    FINIDNG_INTERVENTION_TYPE_DATA_DIR
+)
+
+MODEL_0 = FindingType
+MODEL_1 = Finding
+MODEL_2 = FindingLocationClassificationChoice
+MODEL_3 = FindingLocationClassification
+MODEL_4 = FindingMorphologyClassificationType
+MODEL_5 = FindingMorphologyClassification
+MODEL_6 = FindingMorphologyClassificationChoice
+MODEL_7 = FindingInterventionType
+MODEL_8 = FindingIntervention
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_7.__name__,
+    MODEL_8.__name__,
+    MODEL_0.__name__,
+    MODEL_1.__name__,
+    MODEL_2.__name__,
+    MODEL_3.__name__,
+    MODEL_4.__name__,
+    MODEL_5.__name__,
+    MODEL_6.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": FINDING_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_0, # 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": MODEL_1, # e.g. Intervention
+        "foreign_keys": [
+            "finding_types",
+            "examinations",
+            "finding_interventions",
+            "causing_finding_interventions",
+            "opt_causing_finding_interventions",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            FindingType,
+            Examination,
+            FindingIntervention,
+            FindingIntervention,
+            FindingIntervention,
+        ] # e.g. [InterventionType]
+    },
+    MODEL_2.__name__: {
+        "dir": FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_2, # e.g. Intervention
+        "foreign_keys": [
+            "organs"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Organ
+        ] # e.g. [InterventionType]
+    },
+    MODEL_3.__name__: {
+        "dir": FINDING_LOCATION_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_3, # e.g. Intervention
+        "foreign_keys": [
+            "examinations",
+            "finding_types",
+            "findings",
+            "choices"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Examination,
+            FindingType,
+            Finding,
+            FindingLocationClassificationChoice
+        ] # e.g. [InterventionType]
+    },
+    MODEL_4.__name__: {
+        "dir": FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_4, # e.g. Intervention
+        "foreign_keys": [
+            "required_by_findings",
+            "optional_for_findings"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Finding,
+            Finding
+        ] # e.g. [InterventionType]
+    },
+
+    MODEL_5.__name__: {
+        "dir": FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_5, # e.g. Intervention
+        "foreign_keys": [
+            "classification_type",
+        ],
+        "foreign_key_models": [
+            FindingMorphologyClassificationType,
+        ] 
+    },
+    MODEL_6.__name__: {
+        "dir": FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_6, # e.g. Intervention
+        "foreign_keys": [
+            "classification",
+        ],
+        "foreign_key_models": [
+            FindingMorphologyClassification,
+        ] 
+    },
+    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]
+    },
+}
+
+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

@@ -1,6 +1,6 @@
 from django.core.management.base import BaseCommand
 from endoreg_db.models import LabValue as MODEL_0
-from endoreg_db.models import PatientLabSampleType
+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
@@ -16,8 +16,8 @@ IMPORT_METADATA = {
     MODEL_0.__name__: {
         "dir": SOURCE_DIR, # e.g. "interventions"
         "model": MODEL_0, # e.g. Intervention
-        "foreign_keys": ["default_unit"], # e.g. ["intervention_types"]
-        "foreign_key_models": [Unit] # e.g. [InterventionType]
+        "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,

endoreg_db/management/commands/load_lx_data.py

@@ -0,0 +1,64 @@
+# Management command to load LuxNix Model Data
+
+from django.core.management.base import BaseCommand
+
+from endoreg_db.models import (
+    LxClientType, LxClientTag, LxPermission
+)
+
+from ...utils import load_model_data_from_yaml
+
+from ...data import (
+    LX_CLIENT_TYPE_DATA_DIR,
+    LX_CLIENT_TAG_DATA_DIR,
+    LX_PERMISSION_DATA_DIR
+)
+
+IMPORT_MODELS = [
+    LxPermission.__name__,
+    LxClientType.__name__,
+    LxClientTag.__name__, # M2M relationship with LxPermission ("permissions")
+]
+
+IMPORT_METADATA = {
+    LxPermission.__name__: {
+        "dir": LX_PERMISSION_DATA_DIR,
+        "model": LxPermission,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    },
+    LxClientType.__name__: {
+        "dir": LX_CLIENT_TYPE_DATA_DIR,
+        "model": LxClientType,
+        "foreign_keys": [],
+        "foreign_key_models": []
+    },
+    LxClientTag.__name__: {
+        "dir": LX_CLIENT_TAG_DATA_DIR,
+        "model": LxClientTag,
+        "foreign_keys": ["permissions"],
+        "foreign_key_models": [LxPermission]
+    },
+}
+
+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

@@ -1,41 +1,103 @@
 from django.core.management.base import BaseCommand
-from endoreg_db.models import Medication, Unit
+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 as SOURCE_DIR
+from ...data import (
+    MEDICATION_DATA_DIR,
+    MEDICATION_INDICATION_TYPE_DATA_DIR,
+    MEDICATION_INTAKE_TIME_DATA_DIR,
+    MEDICATION_SCHEDULE_DATA_DIR,
+    MEDICATION_INDICATION_DATA_DIR,
+)
 
-MODEL_0 = Medication
 
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    Medication.__name__,
+    MedicationIndicationType.__name__,
+    MedicationIntakeTime.__name__,
+    MedicationSchedule.__name__,
+    MedicationIndication.__name__,
 ]
 
 IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # e.g. Intervention
-        "foreign_keys": ["default_unit"], # e.g. ["intervention_types"]
-        "foreign_key_models": [Unit] # e.g. [InterventionType]
-    }
+    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',
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
         )
 
     def handle(self, *args, **options):
-        verbose = options['verbose']
+        verbose = options["verbose"]
         for model_name in IMPORT_MODELS:
             _metadata = IMPORT_METADATA[model_name]
-            load_model_data_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )
+            load_model_data_from_yaml(self, model_name, _metadata, verbose)

endoreg_db/management/commands/load_name_data.py

@@ -0,0 +1,37 @@
+# endoreg_db/management/commands/generate_names.py
+
+import os
+from django.core.management.base import BaseCommand
+from endoreg_db.utils import collect_center_names  # Import your function here
+from pathlib import Path
+
+class Command(BaseCommand):
+    help = "Generate first_names.yaml and last_names.yaml from center data"
+
+    def add_arguments(self, parser):
+        # Adding an argument for the input file path
+        # parser.add_argument(
+        #     '--input_file_path',
+        #     type=str,
+        #     required=False,
+        #     help="Path to the input YAML file containing center data",
+        #     default="data/center/data.yaml",
+        # )
+        # parser.add_argument(
+        #     '--output-dir',
+        #     type=str,
+        #     default=os.getcwd(),
+        #     help="Directory where the output files will be saved (default: current directory)",
+        # )
+        pass
+
+    def handle(self, *args, **options):
+
+        # Run the function with the provided arguments
+        try:
+            collect_center_names()
+            self.stdout.write(self.style.SUCCESS("Successfully generated YAML files."))
+        except Exception as e:
+            self.stderr.write(self.style.ERROR(f"An error occurred: {e}"))
+
+            self.stderr.write(self.style.ERROR(f"PWD: {os.getcwd()}"))

endoreg_db/management/commands/{load_endoscopy_processor_data.py → load_organ_data.py}

@@ -1,21 +1,19 @@
-from django.conf import settings
-import os
 from django.core.management.base import BaseCommand
-from ...models import EndoscopyProcessor
+from endoreg_db.models import Organ
 from ...utils import load_model_data_from_yaml
-from ...data import ENDOSCOPY_PROCESSOR_DATA_DIR
+from ...data import (
+    ORGAN_DATA_DIR
+)
 
-SOURCE_DIR = ENDOSCOPY_PROCESSOR_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = EndoscopyProcessor
+MODEL_0 = Organ
 
 IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
+    MODEL_0.__name__,#
 ]
 
 IMPORT_METADATA = {
     MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
+        "dir": ORGAN_DATA_DIR, # e.g. "interventions"
         "model": MODEL_0, # e.g. Intervention
         "foreign_keys": [], # e.g. ["intervention_types"]
         "foreign_key_models": [] # e.g. [InterventionType]