endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.9.2__py3-none-any.whl

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

@@ -48,8 +48,12 @@ class Patient(Person):
     first_name = models.CharField(max_length=100)
     last_name = models.CharField(max_length=100)
     dob = models.DateField(null=True, blank=True)
-    gender = models.ForeignKey("Gender", on_delete=models.SET_NULL, null=True, blank=True)
-    center = models.ForeignKey("Center", on_delete=models.SET_NULL, null=True, blank=True)
+    gender = models.ForeignKey(
+        "Gender", on_delete=models.SET_NULL, null=True, blank=True
+    )
+    center = models.ForeignKey(
+        "Center", on_delete=models.SET_NULL, null=True, blank=True
+    )
     patient_hash = models.CharField(max_length=255, blank=True, null=True)
 
     objects = models.Manager()  # Default manager
@@ -73,10 +77,14 @@ class Patient(Person):
         def patient_examinations(self) -> RelatedManager[PatientExamination]: ...
 
         @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]: ...
 
         @property
         def external_ids(self) -> RelatedManager[PatientExternalID]: ...
@@ -114,7 +122,9 @@ class Patient(Person):
         # If no patient with the given hash exists, create a new pseudo patient
         assert center, "Center must be provided to create a new pseudo patient"
         assert gender, "Gender must be provided to create a new pseudo patient"
-        assert birth_month, "Birth month must be provided to create a new pseudo patient"
+        assert birth_month, (
+            "Birth month must be provided to create a new pseudo patient"
+        )
         assert birth_year, "Birth year must be provided to create a new pseudo patient"
 
         # Ensure gender is a Gender object
@@ -173,35 +183,15 @@ class Patient(Person):
             )
 
         else:
-            patient_examination = PatientExamination(patient=self, date_start=date_start, date_end=date_end)
+            patient_examination = PatientExamination(
+                patient=self, date_start=date_start, date_end=date_end
+            )
 
         if save:
             patient_examination.save()
 
         return patient_examination
 
-    def create_examination_by_indication(self, indication: "ExaminationIndication", date_start: Optional[datetime] = None, date_end: Optional[datetime] = None):
-        from ....medical import (
-            PatientExamination,
-            PatientExaminationIndication,
-        )
-
-        examination = indication.get_examination()
-
-        patient_examination = PatientExamination.objects.create(
-            patient=self,
-            examination=examination,
-            date_start=date_start,
-            date_end=date_end,
-        )
-
-        patient_examination.save()
-
-        patient_examination_indication = PatientExaminationIndication.objects.create(patient_examination=patient_examination, examination_indication=indication)
-        patient_examination_indication.save()
-
-        return patient_examination, patient_examination_indication
-
     def create_event(
         self,
         event_name_str: str,
@@ -231,9 +221,9 @@ class Patient(Person):
 
     def create_examination_by_pdf(self, pdf: "RawPdfFile"):
         """
-        Creates a patient examination and associates it with the provided PDF report file.
+        Creates a patient examination and associates it with the provided report report file.
 
-        The examination is created for this patient, saved, and linked to the given RawPdfFile instance. The PDF's examination field is updated and saved. Returns the created examination instance.
+        The examination is created for this patient, saved, and linked to the given RawPdfFile instance. The report's examination field is updated and saved. Returns the created examination instance.
 
         Args:
             pdf: The RawPdfFile to associate with the new examination.
@@ -273,7 +263,9 @@ class Patient(Person):
         return gender_obj
 
     @classmethod
-    def get_random_age(cls, min_age=55, max_age=90, mean_age=65, std_age=10, distribution="normal"):
+    def get_random_age(
+        cls, min_age=55, max_age=90, mean_age=65, std_age=10, distribution="normal"
+    ):
         """
         Get a random age based on the given distribution.
 
@@ -371,11 +363,17 @@ class Patient(Person):
         :return: The age of the patient.
         """
         # calculate correct age based on current date including day and month
-        current_date = timezone.now().date()  # Use timezone.now() here too for consistency
+        current_date = (
+            timezone.now().date()
+        )  # Use timezone.now() here too for consistency
         dob = self.dob
         # Ensure dob is not None before calculation
         if dob:
-            age = current_date.year - dob.year - ((current_date.month, current_date.day) < (dob.month, dob.day))
+            age = (
+                current_date.year
+                - dob.year
+                - ((current_date.month, current_date.day) < (dob.month, dob.day))
+            )
             return age
         return None  # Or handle the case where dob is None appropriately
 
@@ -394,16 +392,24 @@ class Patient(Person):
             date = timezone.now()  # Use timezone.now() instead of datetime.now()
         # Ensure the provided date is timezone-aware if it's not None
         elif timezone.is_naive(date):
-            logger.warning(f"Received naive datetime {date} for PatientLabSample. Making it timezone-aware using current timezone.")
+            logger.warning(
+                f"Received naive datetime {date} for PatientLabSample. Making it timezone-aware using current timezone."
+            )
             date = timezone.make_aware(date, timezone.get_current_timezone())
 
         if isinstance(sample_type, str):
             sample_type = PatientLabSampleType.objects.get(name=sample_type)
-            assert sample_type is not None, f"Sample type with name '{sample_type}' not found."
+            assert sample_type is not None, (
+                f"Sample type with name '{sample_type}' not found."
+            )
         elif not isinstance(sample_type, PatientLabSampleType):
-            raise ValueError("Sample type must be either a string or a PatientLabSampleType object.")
+            raise ValueError(
+                "Sample type must be either a string or a PatientLabSampleType object."
+            )
 
-        patient_lab_sample = PatientLabSample.objects.create(patient=self, sample_type=sample_type, date=date)
+        patient_lab_sample = PatientLabSample.objects.create(
+            patient=self, sample_type=sample_type, date=date
+        )
 
         return patient_lab_sample
 
@@ -414,27 +420,41 @@ class Patient(Person):
         as a RequirementLinks object. For a Patient, this includes their diseases, associated classification choices,
         all their lab values, and medication information.
         """
-        from endoreg_db.models.medical.disease import Disease, DiseaseClassificationChoice
+        from endoreg_db.models.medical.disease import (
+            Disease,
+            DiseaseClassificationChoice,
+        )
 
         # Imports for medication related models
         from endoreg_db.models.medical.medication.medication import Medication
-        from endoreg_db.models.medical.medication.medication_indication import MedicationIndication
-        from endoreg_db.models.medical.medication.medication_intake_time import MedicationIntakeTime
+        from endoreg_db.models.medical.medication.medication_indication import (
+            MedicationIndication,
+        )
+        from endoreg_db.models.medical.medication.medication_intake_time import (
+            MedicationIntakeTime,
+        )
         from endoreg_db.utils.links.requirement_link import RequirementLinks
+
         # PatientMedication objects are retrieved via self.patientmedication_set
         # PatientLabValue objects are retrieved via self.lab_values
 
-        patient_disease_instances = list(self.diseases.all())  # These are PatientDisease model instances
+        patient_disease_instances = list(
+            self.diseases.all()
+        )  # These are PatientDisease model instances
         actual_diseases: List[Disease] = []
         all_classification_choices: List[DiseaseClassificationChoice] = []
 
         for pd_instance in patient_disease_instances:
             if pd_instance.disease:  # pd_instance.disease is a Disease instance
                 actual_diseases.append(pd_instance.disease)
-            all_classification_choices.extend(list(pd_instance.classification_choices.all()))
+            all_classification_choices.extend(
+                list(pd_instance.classification_choices.all())
+            )
 
         # Assuming self.lab_values is a related manager for PatientLabValue instances
-        patient_lab_value_instances = list(self.lab_values.all())  # These are PatientLabValue model instances
+        patient_lab_value_instances = list(
+            self.lab_values.all()
+        )  # These are PatientLabValue model instances
 
         # Medication information
         # self.patientmedication_set gives a QuerySet of PatientMedication
@@ -445,11 +465,17 @@ class Patient(Person):
         med_intake_times: List[MedicationIntakeTime] = []
 
         for pm_instance in patient_medication_instances:
-            if pm_instance.medication:  # pm_instance.medication is a Medication instance
+            if (
+                pm_instance.medication
+            ):  # pm_instance.medication is a Medication instance
                 actual_medications.append(pm_instance.medication)
-            if pm_instance.medication_indication:  # pm_instance.medication_indication is a MedicationIndication instance
+            if (
+                pm_instance.medication_indication
+            ):  # pm_instance.medication_indication is a MedicationIndication instance
                 med_indications.append(pm_instance.medication_indication)
-            med_intake_times.extend(list(pm_instance.intake_times.all()))  # pm_instance.intake_times is a ManyRelatedManager for MedicationIntakeTime
+            med_intake_times.extend(
+                list(pm_instance.intake_times.all())
+            )  # pm_instance.intake_times is a ManyRelatedManager for MedicationIntakeTime
 
         return RequirementLinks(
             diseases=list(set(actual_diseases)),

endoreg_db/models/label/__init__.py

@@ -1,6 +1,5 @@
 from .annotation import (
     ImageClassificationAnnotation,
-    VideoSegmentationAnnotation,
 )
 from .label import Label
 from .label_set import LabelSet
@@ -10,6 +9,7 @@ from .label_video_segment import (
 )
 from .video_segmentation_label import VideoSegmentationLabel
 from .video_segmentation_labelset import VideoSegmentationLabelSet
+from .annotation import VideoSegmentationAnnotation
 
 __all__ = [
     "Label",
@@ -19,5 +19,5 @@ __all__ = [
     "VideoSegmentationLabelSet",
     "LabelVideoSegment",
     "ImageClassificationAnnotation",
-    "VideoSegmentationAnnotation",
+    "VideoSegmentationAnnotation"
 ]

endoreg_db/models/label/annotation/video_segmentation_annotation.py

@@ -3,6 +3,7 @@ from typing import TYPE_CHECKING
 from django.db import models
 from django.db.models import CheckConstraint, F, Q
 
+
 if TYPE_CHECKING:
     from ...media.video.video_file import VideoFile
     from ..video_segmentation_label import VideoSegmentationLabel
@@ -14,27 +15,23 @@ class VideoSegmentationAnnotation(models.Model):
     within a specific video file.
 
     An annotation must be associated with exactly one `VideoFile`.
-
-    Attributes:
-        video_file (ForeignKey): The video file associated with the annotation.
-        label (ForeignKey): The label for the annotation.
-        start_time (float): The start time of the annotation in seconds.
-        stop_time (float): The stop time of the annotation in seconds.
-        is_true (bool): Indicates if the annotation is valid (defaults to True).
     """
 
-    # Foreign key to the unified VideoFile model.
     video_file = models.ForeignKey(
         "VideoFile",
         on_delete=models.CASCADE,
         related_name="video_segmentation_annotations",
-        null=False,
-        blank=False,
     )
 
-    label = models.ForeignKey("VideoSegmentationLabel", on_delete=models.CASCADE)
-    start_time = models.FloatField()  # in seconds
-    stop_time = models.FloatField()  # in seconds
+    label = models.ForeignKey(
+        "VideoSegmentationLabel",
+        on_delete=models.CASCADE,
+    )
+
+    # times in seconds
+    start_time = models.FloatField()
+    stop_time = models.FloatField()
+
     is_true = models.BooleanField(default=True)
 
     if TYPE_CHECKING:
@@ -42,28 +39,23 @@ class VideoSegmentationAnnotation(models.Model):
         label: models.ForeignKey["VideoSegmentationLabel"]
 
     def __str__(self) -> str:
-        """
-        String representation of the annotation.
-        """
-        video_repr = self.get_video()  # Get the actual video object for representation
-        return f"{video_repr} - {self.label.name} - {self.start_time} to {self.stop_time}"
+        return f"{self.video_file.pk} - {self.label.name} - {self.start_time} to {self.stop_time}"
 
     def get_video(self) -> "VideoFile":
         """
-        Get the video file associated with this annotation.
-
-        Returns the `VideoFile` instance.
+        Convenience accessor for the associated VideoFile instance.
         """
-        if self.video_file:
-            return self.video_file
-        else:
-            # This state should ideally not be reachable due to null=False, blank=False
+        if self.video_file.pk is None:
+            # Should not happen due to null=False
             raise ValueError("Annotation is not linked to a VideoFile.")
+        return self.video_file
 
     class Meta:
         constraints = [
             CheckConstraint(
-                check=Q(start_time__lt=F("stop_time")),
+                condition=Q(start_time__lt=F("stop_time")),
                 name="start_time_less_than_stop_time",
             ),
         ]
+        # optional but usually helpful:
+        # ordering = ("video_file_id", "start_time")

endoreg_db/models/label/label_video_segment/label_video_segment.py

@@ -74,7 +74,7 @@ class LabelVideoSegment(models.Model):
 
     class Meta:
         constraints = [
-            CheckConstraint(check=Q(start_frame_number__lt=F("end_frame_number")), name="segment_start_lt_end"),
+            CheckConstraint(condition=Q(start_frame_number__lt=F("end_frame_number")), name="segment_start_lt_end"),
         ]
         indexes = [
             models.Index(fields=["video_file", "label", "start_frame_number"]),
@@ -131,6 +131,28 @@ class LabelVideoSegment(models.Model):
             # Should not happen if self.state exists and has the is_validated attribute.
             logger.error("AttributeError accessing 'state.is_validated' for LabelVideoSegment %s.", self.pk)
             return False
+    
+    def mark_validated(
+        self,
+        is_validated: bool = True,
+        information_source_name: str = "frontend",
+    ) -> None:
+        """
+        Domain helper: update validation state (and optionally information source).
+        """
+        from endoreg_db.models import InformationSource  # avoid import cycle
+
+        # ensure state exists
+        state, _ = self.get_or_create_state()
+        state.is_validated = is_validated
+        state.save()
+
+        # update information source
+        info_source, _ = InformationSource.objects.get_or_create(
+            name=information_source_name
+        )
+        self.source = info_source
+        self.save(update_fields=["source"])
 
     def extract_segment_frame_files(self, overwrite: bool = False, **kwargs) -> bool:
         """