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

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_logging_data.py

@@ -0,0 +1,39 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import LogType as MODEL_0
+from ...utils import load_model_data_from_yaml
+from ...data import LOG_TYPE_DATA_DIR as SOURCE_DIR
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # 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_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

@@ -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)

endoreg_db/management/commands/load_medication_indication_data.py

@@ -0,0 +1,63 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    MedicationIndication,
+    MedicationIndicationType,
+    MedicationSchedule,
+    Disease,
+    Event,
+    DiseaseClassificationChoice,
+    InformationSource
+)
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INDICATION_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIndication
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [
+            "indication_type",
+            "medication_schedules",
+            "diseases",
+            "events",
+            "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
+            )

endoreg_db/management/commands/load_medication_indication_type_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import MedicationIndicationType
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INDICATION_TYPE_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIndicationType
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # 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_medication_intake_time_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import MedicationIntakeTime
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_INTAKE_TIME_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationIntakeTime
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # 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_medication_schedule_data.py

@@ -0,0 +1,55 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    MedicationSchedule,
+    Medication,
+    MedicationIntakeTime,
+    Unit,
+    InformationSource
+)
+from ...utils import load_model_data_from_yaml
+from ...data import MEDICATION_SCHEDULE_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = MedicationSchedule
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [
+            "medication",
+            "intake_times",
+            "unit",
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            Medication,
+            MedicationIntakeTime,
+            Unit,
+        ] # 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_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_network_data.py

@@ -0,0 +1,57 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import NetworkDevice, NetworkDeviceType, AglService
+from ...utils import load_model_data_from_yaml
+from ...data import NETWORK_DEVICE_DATA_DIR, NETWORK_DEVICE_TYPE_DATA_DIR, AGL_SERVICE_DATA_DIR
+
+MODEL_0 = NetworkDeviceType
+MODEL_1 = NetworkDevice
+MODEL_2 = AglService
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+    MODEL_1.__name__,
+    MODEL_2.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": NETWORK_DEVICE_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    MODEL_1.__name__: {
+        "dir": NETWORK_DEVICE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_1, # e.g. Intervention
+        "foreign_keys": ["device_type"], # e.g. ["intervention_types"]
+        "foreign_key_models": [NetworkDeviceType] # e.g. [InterventionType]
+    },
+    MODEL_2.__name__: {
+        "dir": AGL_SERVICE_DATA_DIR, # e.g. "interventions"
+        "model": MODEL_2, # e.g. Intervention
+        "foreign_keys": ["devices"], # e.g. ["intervention_types"]
+        "foreign_key_models": [NetworkDevice] # 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_organ_data.py

@@ -0,0 +1,43 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Organ
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    ORGAN_DATA_DIR
+)
+
+MODEL_0 = Organ
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,#
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "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]
+    }
+}
+
+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_pdf_type_data.py

@@ -0,0 +1,61 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+
+import yaml
+from ...utils import load_model_data_from_yaml
+
+
+#### CUSTOMIZE
+from ...models import PdfType, ReportReaderFlag
+from ...data import PDF_TYPE_DATA_DIR
+
+SOURCE_DIR = PDF_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = PdfType
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    MODEL_0.__name__,
+]
+
+IMPORT_METADATA = {
+    MODEL_0.__name__: {
+        "dir": SOURCE_DIR, # e.g. "interventions"
+        "model": MODEL_0, # e.g. Intervention
+        "foreign_keys": [
+            "patient_info_line",
+            "endoscope_info_line",
+            "examiner_info_line",
+            "cut_off_below_lines",
+            "cut_off_above_lines"
+        ], # e.g. ["intervention_types"]
+        "foreign_key_models": [
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag,
+            ReportReaderFlag
+        ] # e.g. [InterventionType]
+    }
+}
+
+class Command(BaseCommand):
+    help = f"""Load all .yaml files in the {SOURCE_DIR} directory"""
+
+    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
+            )