endoreg-db 0.8.8.9__py3-none-any.whl → 0.8.9.10__py3-none-any.whl

endoreg_db/models/administration/ai/ai_model.py

@@ -1,19 +1,25 @@
 """
 Django model for AI models.
 """
+
 from django.db import models
 from icecream import ic
 from typing import TYPE_CHECKING
+from logging import getLogger
+
+logger = getLogger(__name__)
 
 if TYPE_CHECKING:
     from .model_type import ModelType
-    from ...metadata import ModelMeta 
+    from ...metadata import ModelMeta
     from ...label import VideoSegmentationLabelSet
+
     # Forward reference AiModel for use in type hints within the class itself
     from typing import ForwardRef
+
     AiModelRef = ForwardRef("'AiModel'")
 
-     
+
 class AiModelManager(models.Manager):
     """
     Manager for AI models with custom query methods.
@@ -22,13 +28,13 @@ class AiModelManager(models.Manager):
     def get_by_natural_key(self, name: str):
         """
         Retrieves the AiModel instance with the specified unique name.
-        
+
         Args:
             name: The unique identifier of the AiModel to retrieve.
-        
+
         Returns:
             The AiModel instance matching the given name.
-        
+
         Raises:
             AiModel.DoesNotExist: If no AiModel with the specified name exists.
         """
@@ -48,6 +54,7 @@ class AiModel(models.Model):
         video_segmentation_labelset (VideoSegmentationLabelSet): Optional associated label set for video segmentation tasks.
         active_meta (ModelMeta): Optional reference to the currently active ModelMeta instance associated with the model.
     """
+
     objects = AiModelManager()
 
     name = models.CharField(max_length=255, unique=True)
@@ -71,29 +78,29 @@ class AiModel(models.Model):
     active_meta = models.ForeignKey(
         "ModelMeta",
         on_delete=models.SET_NULL,
-        related_name="active_model", 
+        related_name="active_model",
         blank=True,
         null=True,
     )
 
     if TYPE_CHECKING:
         metadata_versions: models.QuerySet["ModelMeta"]
-        model_type:models.ForeignKey["ModelType|None"]
-        active_meta:models.ForeignKey["ModelMeta|None"]
-        video_segmentation_labelset:models.ForeignKey["VideoSegmentationLabelSet|None"]
+        model_type: models.ForeignKey["ModelType|None"]
+        active_meta: models.ForeignKey["ModelMeta|None"]
+        video_segmentation_labelset: models.ForeignKey["VideoSegmentationLabelSet|None"]
 
     def get_version(self, version: int) -> "ModelMeta":
         """
         Retrieves the ModelMeta instance for the specified version.
-        
+
         If the active_meta matches the requested version, it is returned. Otherwise, searches related metadata_versions for a matching version. Raises ValueError if no matching metadata is found.
-        
+
         Args:
             version: The version number of the desired ModelMeta.
-        
+
         Returns:
             The ModelMeta instance corresponding to the specified version.
-        
+
         Raises:
             ValueError: If no ModelMeta with the given version exists.
         """
@@ -108,24 +115,40 @@ class AiModel(models.Model):
         raise ValueError(f"No model metadata found for version {version}.")
 
     def get_latest_version(self) -> "ModelMeta":
-        """
-        Get the model_metadata object from metadata_versions with the highest version number.
-        """
         if self.active_meta is not None:
             return self.active_meta
 
-        # Get the latest version of the model metadata
         latest_version = self.metadata_versions.order_by("-version").first()
         if latest_version is not None:
             return latest_version
 
+        # Only in environments where auto-download is acceptable:
+        try:
+            logger.info(
+                "Locally, no segmentation model was available. We are using colo_segmentation_RegNetX800MF_base."
+            )
+            from endoreg_db.services.model_meta_from_hf import ensure_model_meta_from_hf
+
+            model_meta = ensure_model_meta_from_hf(
+                model_id="wg-lux/colo_segmentation_RegNetX800MF_base",
+                model_name="image_multilabel_classification_colonoscopy_default",
+                labelset_name="multilabel_classification_colonoscopy_default",
+                meta_version="1",
+            )
+            return model_meta
+        except Exception:
+            logger.exception(
+                "Failed to ensure ModelMeta from Hugging Face for AiModel '%s'",
+                self.name,
+            )
+
         raise ValueError("No model metadata found for this model.")
 
     @classmethod
     def set_active_model_meta(cls, model_name: str, meta_name: str, meta_version: int):
         """
         Sets the active metadata version for the specified AI model.
-        
+
         Updates the `active_meta` field of the AiModel identified by `model_name` to the ModelMeta instance matching `meta_name` and `meta_version`.
         """
         from ...metadata import ModelMeta

endoreg_db/models/administration/ai/model_type.py

@@ -4,6 +4,7 @@ from typing import TYPE_CHECKING
 if TYPE_CHECKING:
     from .ai_model import AiModel
 
+
 class ModelTypeManager(models.Manager):
     """
     Custom manager for ModelType with additional query methods.

endoreg_db/models/administration/case/case.py

@@ -1,11 +1,13 @@
 from django.db import models
 
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     from ..person import Patient
     from ...medical.patient.patient_examination import PatientExamination
 from django.utils import timezone
 
+
 class Case(models.Model):
     """
     Represents a clinical case, linking a patient to one or more examinations over a specific period.
@@ -22,64 +24,62 @@ class Case(models.Model):
         created_at (datetime): Timestamp of case creation.
         updated_at (datetime): Timestamp of last case update.
     """
+
     patient = models.ForeignKey(
-        'Patient',
+        "Patient",
         on_delete=models.CASCADE,
-        related_name='cases',
+        related_name="cases",
         help_text="The patient associated with this case.",
-        db_index=True
+        db_index=True,
     )
     patient_examinations = models.ManyToManyField(
-        'PatientExamination',
-        related_name='cases',
-        help_text="The examinations included in this case."
+        "PatientExamination",
+        related_name="cases",
+        help_text="The examinations included in this case.",
     )
     hash = models.CharField(
         max_length=255,
         blank=True,
         null=True,
-        help_text="An optional hash value associated with the case."
+        help_text="An optional hash value associated with the case.",
     )
 
     start_date = models.DateTimeField(
-        help_text="The start date and time of the case.",
-        db_index=True
+        help_text="The start date and time of the case.", db_index=True
     )
     end_date = models.DateTimeField(
-        null=True,
-        blank=True,
-        help_text="The end date and time of the case (optional)."
+        null=True, blank=True, help_text="The end date and time of the case (optional)."
     )
     is_active = models.BooleanField(
         default=True,
         help_text="Flag indicating if the case is currently active.",
-        db_index=True
+        db_index=True,
     )
     is_closed = models.BooleanField(
         default=False,
         help_text="Flag indicating if the case has been closed.",
-        db_index=True
+        db_index=True,
     )
     is_deleted = models.BooleanField(
         default=False,
         help_text="Flag indicating if the case is marked as deleted.",
-        db_index=True
+        db_index=True,
     )
     created_at = models.DateTimeField(
-        auto_now_add=True,
-        help_text="The date and time the case was created."
+        auto_now_add=True, help_text="The date and time the case was created."
     )
     updated_at = models.DateTimeField(
-        auto_now=True,
-        help_text="The date and time the case was last updated."
+        auto_now=True, help_text="The date and time the case was last updated."
     )
 
     if TYPE_CHECKING:
         patient: models.ForeignKey["Patient"]
-        patient_examinations: models.ManyToManyField["PatientExamination", "PatientExamination"]
-        
+        patient_examinations: models.ManyToManyField[
+            "PatientExamination", "PatientExamination"
+        ]
+
     class Meta:
-        ordering = ['-start_date', 'patient']
+        ordering = ["-start_date", "patient"]
         verbose_name = "Case"
         verbose_name_plural = "Cases"
 

endoreg_db/models/administration/center/__init__.py

@@ -5,9 +5,9 @@ from .center_waste import CenterWaste
 from .center_shift import CenterShift
 
 __all__ = [
-    'Center',
-    'CenterProduct',
-    'CenterResource',
-    'CenterWaste',
-    'CenterShift',
+    "Center",
+    "CenterProduct",
+    "CenterResource",
+    "CenterWaste",
+    "CenterShift",
 ]

endoreg_db/models/administration/center/center.py

@@ -48,10 +48,14 @@ class Center(models.Model):
         def endoscopes(self) -> RelatedManager[Endoscope]: ...
 
         @property
-        def anonymexaminationreport_set(self) -> RelatedManager[AnonymExaminationReport]: ...
+        def anonymexaminationreport_set(
+            self,
+        ) -> RelatedManager[AnonymExaminationReport]: ...
 
         @property
-        def anonymhistologyreport_set(self) -> RelatedManager[AnonymHistologyReport]: ...
+        def anonymhistologyreport_set(
+            self,
+        ) -> RelatedManager[AnonymHistologyReport]: ...
 
     @classmethod
     def get_by_name(cls, name):

endoreg_db/models/administration/center/center_resource.py

@@ -19,9 +19,17 @@ class CenterResource(models.Model):
     quantity = models.FloatField()
     resource = models.ForeignKey("Resource", on_delete=models.CASCADE)
     transport_emission_factor = models.ForeignKey(
-        "EmissionFactor", on_delete=models.SET_NULL, null=True, related_name="center_resource_transport_emission_factor"
+        "EmissionFactor",
+        on_delete=models.SET_NULL,
+        null=True,
+        related_name="center_resource_transport_emission_factor",
+    )
+    use_emission_factor = models.ForeignKey(
+        "EmissionFactor",
+        on_delete=models.SET_NULL,
+        null=True,
+        related_name="center_resource_use_emission_factor",
     )
-    use_emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True, related_name="center_resource_use_emission_factor")
     year = models.IntegerField()
     unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
 
@@ -46,9 +54,15 @@ class CenterResource(models.Model):
         result_string += "\tUnit\t-\t" + str(self.unit) + "\n"
 
         if self.transport_emission_factor is not None:
-            result_string += "\tTransport Emission Factor\t-\t" + str(self.transport_emission_factor) + "\n"
+            result_string += (
+                "\tTransport Emission Factor\t-\t"
+                + str(self.transport_emission_factor)
+                + "\n"
+            )
 
-        result_string += "\tUse Emission Factor\t-\t" + str(self.use_emission_factor) + "\n"
+        result_string += (
+            "\tUse Emission Factor\t-\t" + str(self.use_emission_factor) + "\n"
+        )
 
         result_string += "\n"
 

endoreg_db/models/administration/center/center_shift.py

@@ -61,7 +61,9 @@ class CenterShift(models.Model):
     if TYPE_CHECKING:
         center: models.ForeignKey["Center"]
         shift: models.ForeignKey["Shift"]
-        scheduled_days = cast(models.manager.RelatedManager["ScheduledDays"], scheduled_days)
+        scheduled_days = cast(
+            models.manager.RelatedManager["ScheduledDays"], scheduled_days
+        )
 
     def __str__(self):
         """

endoreg_db/models/administration/center/center_waste.py

@@ -16,10 +16,14 @@ class CenterWaste(models.Model):
         related_name="center_wastes",
     )
     year = models.IntegerField()
-    waste: models.ForeignKey["Waste"] = models.ForeignKey("Waste", on_delete=models.CASCADE)
+    waste: models.ForeignKey["Waste"] = models.ForeignKey(
+        "Waste", on_delete=models.CASCADE
+    )
     quantity = models.FloatField()
     unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True)
+    emission_factor = models.ForeignKey(
+        "EmissionFactor", on_delete=models.SET_NULL, null=True
+    )
 
     if TYPE_CHECKING:
         center: models.ForeignKey["Center"]

endoreg_db/models/administration/person/__init__.py

@@ -23,4 +23,4 @@ __all__ = [
     "Employee",
     "EmployeeType",
     "EmployeeQualification",
-]
+]

endoreg_db/models/administration/person/employee/__init__.py

@@ -1,3 +1,3 @@
 from .employee import Employee
 from .employee_type import EmployeeType
-from .employee_qualification import EmployeeQualification
+from .employee_qualification import EmployeeQualification

endoreg_db/models/administration/person/employee/employee_type.py

@@ -34,7 +34,9 @@ class EmployeeType(models.Model):
     )
 
     if TYPE_CHECKING:
-        qualifications = cast(models.manager.RelatedManager["Qualification"], qualifications)
+        qualifications = cast(
+            models.manager.RelatedManager["Qualification"], qualifications
+        )
 
         @property
         def employees(self) -> models.QuerySet["Employee"]: ...

endoreg_db/models/administration/person/examiner/__init__.py

@@ -1,4 +1,4 @@
 from .examiner import Examiner
 
 
-__all__ = ["Examiner"]
+__all__ = ["Examiner"]

endoreg_db/models/administration/person/examiner/examiner.py

@@ -12,7 +12,9 @@ if TYPE_CHECKING:
 
 
 class Examiner(Person):
-    center = models.ForeignKey("Center", on_delete=models.CASCADE, blank=True, null=True)
+    center = models.ForeignKey(
+        "Center", on_delete=models.CASCADE, blank=True, null=True
+    )
     hash = models.CharField(max_length=255, unique=True)
 
     if TYPE_CHECKING:
@@ -23,7 +25,13 @@ class Examiner(Person):
         return self.first_name + " " + self.last_name
 
     @classmethod
-    def custom_get_or_create(cls, first_name: str, last_name: str, center: "administration.Center", substitute_names: bool = True):
+    def custom_get_or_create(
+        cls,
+        first_name: str,
+        last_name: str,
+        center: "administration.Center",
+        substitute_names: bool = True,
+    ):
         from endoreg_db.models import (
             FirstName,
             LastName,

endoreg_db/models/administration/person/names/first_name.py

@@ -3,16 +3,18 @@
 
 from django.db import models
 
+
 class FirstNameManager(models.Manager):
     def get_by_natural_key(self, name):
         return self.get(name=name)
-    
+
+
 class FirstName(models.Model):
     objects = FirstNameManager()
     name = models.CharField(max_length=255, unique=True)
-    
+
     def natural_key(self):
         return (self.name,)
-    
+
     def __str__(self):
-        return str(self.name)
+        return str(self.name)

endoreg_db/models/administration/person/names/last_name.py

@@ -1,10 +1,11 @@
-
 from django.db import models
 
+
 class LastNameManager(models.Manager):
     def get_by_natural_key(self, name):
         return self.get(name=name)
 
+
 class LastName(models.Model):
     objects = LastNameManager()
     name = models.CharField(max_length=255, unique=True)
@@ -14,6 +15,6 @@ class LastName(models.Model):
 
     def __str__(self):
         return str(self.name)
-    
+
+
 # Path: endoreg_db/models/persons/first_name.py
-        

endoreg_db/models/administration/person/patient/__init__.py

@@ -4,4 +4,4 @@ from .patient_external_id import PatientExternalID
 __all__ = [
     "Patient",
     "PatientExternalID",
-]
+]

endoreg_db/models/administration/person/patient/patient.py

@@ -18,7 +18,6 @@ if TYPE_CHECKING:
         AnonymExaminationReport,
         AnonymHistologyReport,
         Center,
-        ExaminationIndication,
         Gender,
         PatientDisease,
         PatientEvent,

endoreg_db/models/administration/person/patient/patient_external_id.py

@@ -34,4 +34,3 @@ class PatientExternalID(models.Model):
     if TYPE_CHECKING:
         patient: models.ForeignKey["Patient"]
         origin: models.CharField[str]
-        

endoreg_db/models/administration/person/person.py

@@ -1,6 +1,7 @@
 from abc import abstractmethod
 from django.db import models
 
+
 class Person(models.Model):
     """
     Abstract base class for a person.
@@ -32,4 +33,3 @@ class Person(models.Model):
 
     class Meta:
         abstract = True
-

endoreg_db/models/administration/product/__init__.py

@@ -1,4 +1,5 @@
-'''Module for product models'''
+"""Module for product models"""
+
 from .product import Product
 from .product_material import ProductMaterial
 from .product_group import ProductGroup
@@ -6,9 +7,9 @@ from .reference_product import ReferenceProduct
 from .product_weight import ProductWeight
 
 __all__ = [
-    'Product',
-    'ProductMaterial',
-    'ProductGroup',
-    'ReferenceProduct',
-    'ProductWeight',
+    "Product",
+    "ProductMaterial",
+    "ProductGroup",
+    "ReferenceProduct",
+    "ProductWeight",
 ]

endoreg_db/models/administration/product/product.py

@@ -23,7 +23,9 @@ class Product(models.Model):
 
     name = models.CharField(max_length=255)
 
-    transport_route = models.ForeignKey("TransportRoute", on_delete=models.SET_NULL, null=True)
+    transport_route = models.ForeignKey(
+        "TransportRoute", on_delete=models.SET_NULL, null=True
+    )
     product_group = models.ForeignKey(
         "ProductGroup",
         on_delete=models.SET_NULL,
@@ -56,7 +58,9 @@ class Product(models.Model):
 
     def _calculate_material_metric(self, component: str, calculation_func):
         """Helper method to calculate weight or emission for materials of a specific component."""
-        from .product_material import ProductMaterial  # Import locally to avoid circular dependency issues at module level
+        from .product_material import (
+            ProductMaterial,
+        )  # Import locally to avoid circular dependency issues at module level
 
         materials = ProductMaterial.objects.filter(product=self, component=component)
         return calculation_func(materials)

endoreg_db/models/administration/product/product_group.py

@@ -7,33 +7,35 @@ if TYPE_CHECKING:
         ReferenceProduct,
     )
 
+
 class ProductGroupManager(models.Manager):
     def get_by_natural_key(self, name):
         return self.get(name=name)
-    
+
+
 class ProductGroup(models.Model):
     objects = ProductGroupManager()
 
     name = models.CharField(max_length=255)
-    
+
     if TYPE_CHECKING:
         reference_product: "ReferenceProduct"
         products: models.QuerySet["Product"]
 
     def natural_key(self):
         return (self.name,)
-    
+
     def __str__(self):
         return str(self.name)
-    
+
     def get_products(self) -> models.QuerySet["Product"]:
         from .product import Product
+
         products = self.products.all()
         if products:
             return products
         else:
             return Product.objects.none()
-        
-    def get_reference_product(self) -> "None | ReferenceProduct":
-        return self.reference_product 
 
+    def get_reference_product(self) -> "None | ReferenceProduct":
+        return self.reference_product

endoreg_db/models/administration/product/product_material.py

@@ -37,12 +37,19 @@ class ProductMaterial(models.Model):
     def get_emission(self) -> tuple[float, Unit]:
         emission_factor = self.material.emission_factor
         if emission_factor is None:
-            raise Exception("No emission factor for material " + self.material.name + " found.")
+            raise Exception(
+                "No emission factor for material " + self.material.name + " found."
+            )
 
         # make sure product_material.unit is the same as emission_factor.unit
         if self.unit is not None and emission_factor.unit is not None:
             if self.unit != emission_factor.unit:
-                raise Exception("Unit mismatch: " + self.unit.name + " != " + emission_factor.unit.name)
+                raise Exception(
+                    "Unit mismatch: "
+                    + self.unit.name
+                    + " != "
+                    + emission_factor.unit.name
+                )
 
         emmision_value = emission_factor.value * self.quantity
         assert isinstance(emission_factor.unit, Unit)