endoreg-db 0.8.6.4__py3-none-any.whl

endoreg_db/management/commands/load_base_db_data.py

@@ -0,0 +1,192 @@
+from django.core.management import BaseCommand, call_command
+from io import StringIO
+
+
+class Command(BaseCommand):
+    help = "Run all data loading commands in the correct order"
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output for all commands",
+        )
+
+    def handle(self, *args, **options):
+        # verbose = options['verbose']
+        """
+        Orchestrates the sequential execution of data loading commands to populate base database models.
+        
+        This management command displays an initial message and then runs a series of data loading routines 
+        (via call_command) in a specified order. It ignores any verbose setting from the command-line options 
+        and forces verbose output. A final success message is printed after all commands complete.
+        """
+        verbose = True
+
+        self.stdout.write(self.style.SUCCESS("Populating base db models with data..."))
+
+        out = self.stdout
+
+        call_command("load_tag_data", stdout=out, verbose=verbose)
+        call_command("load_information_source", stdout=out, verbose=verbose)
+
+        call_command("load_risk_data", stdout=out, verbose=verbose)
+
+        # Load Center Data
+        call_command("load_center_data", stdout=out, verbose=verbose)
+        call_command("load_endoscope_data", stdout=out, verbose=verbose)
+        call_command("load_distribution_data", stdout=out, verbose=verbose)
+
+        call_command("load_gender_data", stdout=out, verbose=verbose)
+        call_command("load_report_reader_flag_data", stdout=out, verbose=verbose)
+        call_command("load_pdf_type_data", stdout=out, verbose=verbose)
+        call_command("load_unit_data", stdout=out, verbose=verbose)
+        call_command("load_disease_data", stdout=out, verbose=verbose)
+        call_command("load_event_data", stdout=out, verbose=verbose)
+        call_command("load_organ_data", stdout=out, verbose=verbose)
+        call_command("load_contraindication_data", stdout=out, verbose=verbose)
+        call_command("load_examination_data", stdout=out, verbose=verbose)
+        call_command("load_lab_value_data", stdout=out, verbose=verbose)
+        call_command("load_finding_data", stdout=out, verbose=verbose)
+        call_command("load_examination_indication_data", stdout=out, verbose=verbose)
+        call_command("load_medication_data", stdout=out, verbose=verbose)
+
+        call_command("load_requirement_data", stdout=out, verbose=verbose)
+
+        # Load AI Model Data
+        call_command("load_ai_model_label_data", stdout=out, verbose=verbose)
+        call_command("load_ai_model_data", stdout=out, verbose=verbose)
+
+        self.stdout.write(
+            self.style.SUCCESS(  # pylint: disable=no-member
+                "All data loading commands executed successfully."
+            )
+        )
+
+        # # Run the load_network_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
+        # call_command('load_network_data', verbose=verbose)
+        # Run the load_network_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_network_data..."))
+        # call_command("load_network_data", verbose=verbose)
+
+        # # Run the load_logging_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_logging_data..."))
+        # call_command("load_logging_data", verbose=verbose)
+
+        # # Run the load_profession_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_profession_data..."))
+        # call_command("load_profession_data", verbose=verbose)
+
+        # # run the load_gender_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_gender_data..."))
+        # call_command("load_gender_data", verbose=verbose)
+
+        # # Run the load_examination_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_examination_data..."))
+        # call_command("load_examination_data", verbose=verbose)
+
+        # # run the load_finding_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_finding_data..."))
+        # call_command("load_finding_data", verbose=verbose)
+
+        # # Run the load_disease data command
+        # self.stdout.write(self.style.SUCCESS("Running load_disease_data..."))
+        # call_command("load_disease_data", verbose=verbose)
+
+        # # # Run the load_disease_classification data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_data..."))
+        # # call_command('load_disease_classification_data', verbose=verbose)
+
+        # # # Run the load_disease_classification_choices data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_disease_classification_choices_data..."))
+        # # call_command('load_disease_classification_choices_data', verbose=verbose)
+
+        # # rund the load_user_groups command
+        # self.stdout.write(self.style.SUCCESS("Running load_user_groups..."))
+        # call_command("load_user_groups", verbose=verbose)
+
+        # # run the load_report_reader_flag command
+        # self.stdout.write(self.style.SUCCESS("Running load_report_reader_flag..."))
+        # call_command("load_report_reader_flag", verbose=verbose)
+
+        # # Run the load_pdf_type_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_pdf_type_data..."))
+        # call_command("load_pdf_type_data", verbose=verbose)
+
+        # # Run the load_endoscopy_processor_data command
+        # self.stdout.write(
+        #     self.style.SUCCESS("Running load_endoscopy_processor_data...")
+        # )
+        # call_command("load_endoscopy_processor_data", verbose=verbose)
+
+        # # Run the load_endoscope_type_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_endoscope_type_data..."))
+        # call_command("load_endoscope_type_data", verbose=verbose)
+
+        # # Run the load_unit_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_unit_data..."))
+        # call_command("load_unit_data", verbose=verbose)
+
+        # # Run the load_lab_value_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_lab_value_data..."))
+        # call_command("load_lab_value_data", verbose=verbose)
+
+        # # Run the load_information_source command
+        # self.stdout.write(self.style.SUCCESS("Running load_information_source..."))
+        # call_command("load_information_source", verbose=verbose)
+
+        # # Run the load_center_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_center_data..."))
+        # call_command("load_center_data", verbose=verbose)
+
+        # # Run the load_label_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_label_data..."))
+        # call_command("load_label_data", verbose=verbose)
+
+        # # Run the load_ai_model_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_ai_model_data..."))
+        # call_command("load_ai_model_data", verbose=verbose)
+
+        # # Run the load_event_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_event_data..."))
+        # call_command("load_event_data", verbose=verbose)
+
+        # # run the load_medication_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_medication_data..."))
+        # call_command("load_medication_data", verbose=verbose)
+
+        # # # Run the load_medication_indication_type_data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_type_data..."))
+        # # call_command('load_medication_indication_type_data', verbose=verbose)
+
+        # # # Run the load_medication_intake_time_data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_medication_intake_time_data..."))
+        # # call_command('load_medication_intake_time_data', verbose=verbose)
+
+        # # # Run the load_medication_schedule_data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_medication_schedule_data..."))
+        # # call_command('load_medication_schedule_data', verbose=verbose)
+
+        # # # Run the load_medication_indication_data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_medication_indication_data..."))
+        # # call_command('load_medication_indication_data', verbose=verbose)
+
+        # # Run the load_green_endoscopy_wuerzburg_data command
+        # self.stdout.write(
+        #     self.style.SUCCESS("Running load_green_endoscopy_wuerzburg_data...")
+        # )
+        # call_command("load_green_endoscopy_wuerzburg_data", verbose=verbose)
+
+        # # Load G-Play Data
+        # # run the load_distribution_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_distribution_data..."))
+        # call_command("load_distribution_data", verbose=verbose)
+        # # Run the load_g_play_data command
+        # self.stdout.write(self.style.SUCCESS("Running load_g_play_data..."))
+        # call_command("load_g_play_data", verbose=verbose)
+
+        # # Necessary? Migrate? FIXME
+        # # # Run the load_active_model_data command
+        # # self.stdout.write(self.style.SUCCESS("Running load_active_model_data..."))
+        # # call_command('load_active_model_data', verbose=verbose)

endoreg_db/management/commands/load_center_data.py

@@ -0,0 +1,68 @@
+from django.core.management.base import BaseCommand
+from ...utils import load_model_data_from_yaml
+from ...models import Center, FirstName, LastName
+from ...data import CENTER_DATA_DIR, NAMES_FIRST_DATA_DIR, NAMES_LAST_DATA_DIR
+
+
+SOURCE_DIR = CENTER_DATA_DIR  # e.g. settings.DATA_DIR_INTERVENTION
+
+IMPORT_MODELS = [  # string as model key, serves as key in IMPORT_METADATA
+    FirstName.__name__,
+    LastName.__name__,
+    Center.__name__,
+]
+
+IMPORT_METADATA = {
+    FirstName.__name__: {
+        "dir": NAMES_FIRST_DATA_DIR,  # e.g. "interventions"
+        "model": FirstName,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    LastName.__name__: {
+        "dir": NAMES_LAST_DATA_DIR,  # e.g. "interventions"
+        "model": LastName,  # e.g. Intervention
+        "foreign_keys": [],  # e.g. ["intervention_types"]
+        "foreign_key_models": [],  # e.g. [InterventionType]
+    },
+    Center.__name__: {
+        "dir": SOURCE_DIR,  # e.g. "interventions"
+        "model": Center,  # e.g. Intervention
+        "foreign_keys": ["first_names", "last_names"],  # e.g. ["intervention_types"]
+        "foreign_key_models": [FirstName, LastName],  # 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):
+        """
+        Adds the '--verbose' flag to the argument parser.
+        
+        When specified, this flag enables verbose output for the management command.
+        """
+        parser.add_argument(
+            "--verbose",
+            action="store_true",
+            help="Display verbose output",
+        )
+
+    def handle(self, *args, **options):
+        """
+        Load YAML data for each predefined model.
+        
+        Iterates over the models specified in IMPORT_MODELS, retrieving each model's metadata from
+        IMPORT_METADATA and invoking load_model_data_from_yaml to load YAML data. The verbosity of
+        the output is determined by the 'verbose' flag in the command options.
+        
+        Args:
+            *args: Additional positional arguments.
+            **options: Command options; must include a 'verbose' key to control output detail.
+        """
+        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_contraindication_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Contraindication
+from ...utils import load_model_data_from_yaml
+from ...data import CONTRAINDICATION_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = Contraindication
+
+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_disease_classification_choices_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import DiseaseClassificationChoice as MODEL_0
+from ...utils import load_model_data_from_yaml
+from ...data import DISEASE_CLASSIFICATION_CHOICE_DATA_DIR as SOURCE_DIR
+
+from endoreg_db.models import DiseaseClassification
+
+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": ["disease_classification"], # e.g. ["intervention_types"]
+        "foreign_key_models": [DiseaseClassification] # 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_disease_classification_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import DiseaseClassification as MODEL_0
+from ...utils import load_model_data_from_yaml
+from ...data import DISEASE_CLASSIFICATION_DATA_DIR as SOURCE_DIR
+
+from endoreg_db.models import Disease
+
+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": ["disease"], # e.g. ["intervention_types"]
+        "foreign_key_models": [Disease] # 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_disease_data.py

@@ -0,0 +1,62 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    Disease, 
+    DiseaseClassification,
+    DiseaseClassificationChoice,
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    DISEASE_DATA_DIR, 
+    DISEASE_CLASSIFICATION_DATA_DIR,
+    DISEASE_CLASSIFICATION_CHOICE_DATA_DIR,
+)
+
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    Disease.__name__,
+    DiseaseClassification.__name__,
+    DiseaseClassificationChoice.__name__,
+]
+
+IMPORT_METADATA = {
+    Disease.__name__: {
+        "dir": DISEASE_DATA_DIR, # e.g. "interventions"
+        "model": Disease, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    DiseaseClassification.__name__: {
+        "dir": DISEASE_CLASSIFICATION_DATA_DIR, # e.g. "interventions"
+        "model": DiseaseClassification, # e.g. Intervention
+        "foreign_keys": ["disease"], # e.g. ["intervention_types"]
+        "foreign_key_models": [Disease] # e.g. [InterventionType]
+    },
+    DiseaseClassificationChoice.__name__: {
+        "dir": DISEASE_CLASSIFICATION_CHOICE_DATA_DIR, # e.g. "interventions"
+        "model": DiseaseClassificationChoice, # e.g. Intervention
+        "foreign_keys": ["disease_classification"], # e.g. ["intervention_types"]
+        "foreign_key_models": [DiseaseClassification] # 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_distribution_data.py

@@ -0,0 +1,66 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import (
+    NumericValueDistribution,
+    SingleCategoricalValueDistribution,
+    MultipleCategoricalValueDistribution,
+    DateValueDistribution
+
+)
+from collections import OrderedDict
+
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    DISTRIBUTION_NUMERIC_DATA_DIR,
+    DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
+    DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
+    DISTRIBUTION_DATE_DATA_DIR,
+)
+
+IMPORT_METADATA = OrderedDict({
+    NumericValueDistribution.__name__: {
+        "dir": DISTRIBUTION_NUMERIC_DATA_DIR,
+        "model": NumericValueDistribution, 
+        "foreign_keys": [], 
+        "foreign_key_models": [] 
+    },
+    SingleCategoricalValueDistribution.__name__: {
+        "dir": DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR,
+        "model": SingleCategoricalValueDistribution, 
+        "foreign_keys": [], 
+        "foreign_key_models": [] 
+    },
+    MultipleCategoricalValueDistribution.__name__: {
+        "dir": DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR,
+        "model": MultipleCategoricalValueDistribution, 
+        "foreign_keys": [], 
+        "foreign_key_models": [] 
+    },
+    DateValueDistribution.__name__: {
+        "dir": DISTRIBUTION_DATE_DATA_DIR,
+        "model": DateValueDistribution, 
+        "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_endoscope_data.py

@@ -0,0 +1,68 @@
+from django.conf import settings
+import os
+from django.core.management.base import BaseCommand
+from ...models import (
+    EndoscopeType,
+    Endoscope,
+    EndoscopyProcessor,
+    Center
+)
+from ...utils import load_model_data_from_yaml
+from ...data import (
+    ENDOSCOPE_TYPE_DATA_DIR,
+    ENDOSCOPY_PROCESSOR_DATA_DIR,
+    ENDOSCOPE_DATA_DIR,
+)
+
+SOURCE_DIR = ENDOSCOPE_TYPE_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
+
+MODEL_0 = EndoscopeType
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+    EndoscopeType.__name__,
+    EndoscopyProcessor.__name__,
+    Endoscope.__name__,
+]
+
+IMPORT_METADATA = {
+    EndoscopeType.__name__: {
+        "dir": ENDOSCOPE_TYPE_DATA_DIR, # e.g. "interventions"
+        "model": EndoscopeType, # e.g. Intervention
+        "foreign_keys": [], # e.g. ["intervention_types"]
+        "foreign_key_models": [] # e.g. [InterventionType]
+    },
+    EndoscopyProcessor.__name__: {
+        "dir": ENDOSCOPY_PROCESSOR_DATA_DIR,
+        "model": EndoscopyProcessor,
+        "foreign_keys": ["centers"],
+        "foreign_key_models": [Center]
+    },
+    Endoscope.__name__: {
+        "dir": ENDOSCOPE_DATA_DIR,
+        "model": Endoscope,
+        "foreign_keys": ["center", "endoscope_type"],
+        "foreign_key_models": [Center, EndoscopeType]
+    },
+}
+
+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_event_data.py

@@ -0,0 +1,41 @@
+from django.core.management.base import BaseCommand
+from endoreg_db.models import Event
+from ...utils import load_model_data_from_yaml
+from ...data import EVENT_DATA_DIR as SOURCE_DIR
+
+MODEL_0 = Event
+
+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
+            )