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

endoreg_db/management/commands/load_profession_data.py

@@ -0,0 +1,44 @@
+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_data.py

@@ -0,0 +1,46 @@
+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

@@ -0,0 +1,46 @@
+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

@@ -0,0 +1,28 @@
+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

@@ -0,0 +1,64 @@
+# 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

@@ -0,0 +1,9 @@
+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.'))