endoreg-db 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

endoreg_db/management/commands/load_medication_data.py

@@ -1,41 +0,0 @@
-from django.core.management.base import BaseCommand
-from endoreg_db.models import Medication, Unit
-from ...utils import load_model_data_from_yaml
-from ...data import MEDICATION_DATA_DIR as SOURCE_DIR
-
-MODEL_0 = Medication
-
-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": ["default_unit"], # e.g. ["intervention_types"]
-        "foreign_key_models": [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_medication_indication_data.py

@@ -1,63 +0,0 @@
-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

@@ -1,41 +0,0 @@
-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

@@ -1,41 +0,0 @@
-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

@@ -1,55 +0,0 @@
-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_network_data.py

@@ -1,57 +0,0 @@
-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_pdf_type_data.py

@@ -1,61 +0,0 @@
-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
-            )

endoreg_db/management/commands/load_profession_data.py

@@ -1,44 +0,0 @@
-from django.conf import settings
-from django.core.management.base import BaseCommand
-from ...models import Profession
-from ...utils import load_model_data_from_yaml
-from ...data import PROFESSION_DATA_DIR
-
-SOURCE_DIR = PROFESSION_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = Profession
-
-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_report_reader_flag.py

@@ -1,46 +0,0 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import ReportReaderFlag
-import yaml
-from ...utils import load_model_data_from_yaml
-from ...data import REPORT_READER_FLAG_DATA_DIR
-
-SOURCE_DIR = REPORT_READER_FLAG_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = ReportReaderFlag
-
-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_unit_data.py

@@ -1,46 +0,0 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import Unit
-import yaml
-from ...utils import load_model_data_from_yaml
-from ...data import UNIT_DATA_DIR
-
-SOURCE_DIR = UNIT_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = Unit
-
-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_user_groups.py

@@ -1,28 +0,0 @@
-from django.core.management.base import BaseCommand
-from django.contrib.auth.models import Group, Permission
-from django.contrib.contenttypes.models import ContentType
-from django.apps import apps
-
-
-class Command(BaseCommand):
-    help = "Create additional user groups and permissions for all models in 'endoreg_db' app."
-
-    def add_arguments(self, parser):
-        parser.add_argument(
-            '--verbose',
-            action='store_true',
-            help='Display verbose output',
-        )
-
-    def handle(self, *args, **options):
-        verbose = options['verbose']
-
-        # Create groups
-        groups = ["demo", "verified", "agl", "endo_reg_user", "g_play_user", "ukw_user"]
-        for group_name in groups:
-            _group, created = Group.objects.get_or_create(name=group_name)
-            if verbose and created:
-                self.stdout.write(self.style.SUCCESS(f"Created group {group_name}"))
-
-        if verbose:
-            self.stdout.write(self.style.SUCCESS("All groups processed successfully."))

endoreg_db/management/commands/register_ai_model.py

@@ -1,64 +0,0 @@
-# django command to register a new AI model
-# expects path to model_meta.json file
-# example model_meta: {
-# "name": "multilabel_classification",
-# "version": 0,
-# "model_type": "multilabel_classification", # name of modeltype, is unique
-# "labelset": "multilabel_classification", #labelset name, combination of name and version is unique
-# "labelset_version": 0,
-# "weights_path": "weights/multilabel_classification_0.pth", # path to weights file
-#}
-
-from django.core.management.base import BaseCommand
-from django.core.files import File
-from endoreg_db.models import ModelMeta, ModelType, LabelSet
-import json
-from pathlib import Path
-
-class Command(BaseCommand):
-    """
-    Registers a new AI model in the database.
-    """
-    help = 'Registers a new AI model in the database.'
-
-    def add_arguments(self, parser):
-        parser.add_argument('model_meta_path', type=str)
-
-    def handle(self, *args, **options):
-        model_meta_path = Path(options['model_meta_path']).resolve()
-
-        with open(model_meta_path, 'r') as f:
-            model_meta = json.load(f)
-
-        # get or create model type
-        model_type = ModelType.objects.get(name=model_meta['model_type'])
-
-        # get or create labelset
-        labelset = LabelSet.objects.get(name=model_meta['labelset'], version=model_meta['labelset_version'])
-
-        # Handle weights file
-        weights_path = model_meta['weights_path']
-        # weights path is realative to model_meta_path
-        weights_path = model_meta_path.parent / weights_path
-
-        assert weights_path.exists(), f"weights file at {weights_path} does not exist"
-
-        # Make sure the path is correct and the file exists
-        try:
-            with open(weights_path, 'rb') as file:
-                model_name_string = f"{model_meta['name']}_{model_meta['version']}"
-                weights = File(file, name = model_name_string)
-                # Create ModelMeta instance
-                model_meta_instance = ModelMeta.objects.create(
-                    name=model_meta['name'],
-                    version=model_meta['version'],
-                    type=model_type,
-                    labelset=labelset,
-                    weights=weights,
-                    description=model_meta.get('description', '')  # Assuming description is optional
-                )
-                print(f"Successfully registered model {model_meta_instance}")
-        except IOError:
-            print(f"Failed to open weights file at {weights_path}. Make sure the file exists.")
-
-

endoreg_db/management/commands/reset_celery_schedule.py

@@ -1,9 +0,0 @@
-from django.core.management.base import BaseCommand
-from django_celery_beat.models import PeriodicTask
-
-class Command(BaseCommand):
-    help = 'Deletes all periodic tasks from the database to reset the schedule'
-
-    def handle(self, *args, **kwargs):
-        PeriodicTask.objects.all().delete()
-        self.stdout.write(self.style.SUCCESS('Successfully deleted all periodic tasks.'))