endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/models/media/video/video_processing.py

@@ -4,148 +4,149 @@ Video Processing History Model
 Tracks all video correction operations (masking, frame removal, reprocessing).
 Created as part of Phase 1.1: Video Correction API Endpoints.
 """
+
+import logging
+from pathlib import Path
+
+from django.conf import settings
 from django.db import models
 from django.utils import timezone
+
 from .video_file import VideoFile
 
+logger = logging.getLogger(__name__)
+
+
 class VideoProcessingHistory(models.Model):
     """
     History of all video processing operations.
-    
+
     Stores configuration and results of masking, frame removal, and reprocessing
     operations for audit trail and download access.
     """
-    
+
     # Operation Types
-    OPERATION_MASKING = 'mask_overlay'
-    OPERATION_FRAME_REMOVAL = 'frame_removal'
-    OPERATION_ANALYSIS = 'analysis'
-    OPERATION_REPROCESSING = 'reprocessing'
-    
+    OPERATION_MASKING = "mask_overlay"
+    OPERATION_FRAME_REMOVAL = "frame_removal"
+    OPERATION_ANALYSIS = "analysis"
+    OPERATION_REPROCESSING = "reprocessing"
+
     OPERATION_CHOICES = [
-        (OPERATION_MASKING, 'Mask Overlay'),
-        (OPERATION_FRAME_REMOVAL, 'Frame Removal'),
-        (OPERATION_ANALYSIS, 'Sensitivity Analysis'),
-        (OPERATION_REPROCESSING, 'Full Reprocessing'),
+        (OPERATION_MASKING, "Mask Overlay"),
+        (OPERATION_FRAME_REMOVAL, "Frame Removal"),
+        (OPERATION_ANALYSIS, "Sensitivity Analysis"),
+        (OPERATION_REPROCESSING, "Full Reprocessing"),
     ]
-    
+
     # Status Types
-    STATUS_PENDING = 'pending'
-    STATUS_RUNNING = 'running'
-    STATUS_SUCCESS = 'success'
-    STATUS_FAILURE = 'failure'
-    STATUS_CANCELLED = 'cancelled'
-    
+    STATUS_PENDING = "pending"
+    STATUS_RUNNING = "running"
+    STATUS_SUCCESS = "success"
+    STATUS_FAILURE = "failure"
+    STATUS_CANCELLED = "cancelled"
+
     STATUS_CHOICES = [
-        (STATUS_PENDING, 'Pending'),
-        (STATUS_RUNNING, 'Running'),
-        (STATUS_SUCCESS, 'Success'),
-        (STATUS_FAILURE, 'Failure'),
-        (STATUS_CANCELLED, 'Cancelled'),
+        (STATUS_PENDING, "Pending"),
+        (STATUS_RUNNING, "Running"),
+        (STATUS_SUCCESS, "Success"),
+        (STATUS_FAILURE, "Failure"),
+        (STATUS_CANCELLED, "Cancelled"),
     ]
-    
-    video = models.ForeignKey(
-        VideoFile, 
-        on_delete=models.CASCADE, 
-        related_name='processing_history',
-        help_text="Video file this operation was performed on"
-    )
-    
-    operation = models.CharField(
-        max_length=50,
-        choices=OPERATION_CHOICES,
-        help_text="Type of processing operation"
-    )
-    
-    status = models.CharField(
-        max_length=20,
-        choices=STATUS_CHOICES,
-        default=STATUS_PENDING,
-        help_text="Current status of the operation"
-    )
-    
+
+    video = models.ForeignKey(VideoFile, on_delete=models.CASCADE, related_name="processing_history", help_text="Video file this operation was performed on")
+
+    operation = models.CharField(max_length=50, choices=OPERATION_CHOICES, help_text="Type of processing operation")
+
+    status = models.CharField(max_length=20, choices=STATUS_CHOICES, default=STATUS_PENDING, help_text="Current status of the operation")
+
     # Configuration & Results
-    config = models.JSONField(
-        default=dict,
-        help_text="Operation configuration (mask settings, frame list, etc.)"
-    )
-    
-    output_file = models.CharField(
-        max_length=500,
-        blank=True,
-        help_text="Path to output file (relative to MEDIA_ROOT)"
-    )
-    
-    details = models.TextField(
-        blank=True,
-        help_text="Additional details or error messages"
-    )
-    
+    config = models.JSONField(default=dict, help_text="Operation configuration (mask settings, frame list, etc.)")
+
+    output_file = models.CharField(max_length=500, blank=True, help_text="Path to output file (relative to MEDIA_ROOT)")
+
+    details = models.TextField(blank=True, help_text="Additional details or error messages")
+
     # Celery Integration
-    task_id = models.CharField(
-        max_length=100,
-        blank=True,
-        help_text="Celery task ID for progress tracking"
-    )
-    
+    task_id = models.CharField(max_length=100, blank=True, help_text="Celery task ID for progress tracking")
+
     # Timestamps
-    created_at = models.DateTimeField(
-        auto_now_add=True,
-        help_text="When the operation was started"
-    )
-    
-    completed_at = models.DateTimeField(
-        null=True,
-        blank=True,
-        help_text="When the operation completed (success or failure)"
-    )
-    
+    created_at = models.DateTimeField(auto_now_add=True, help_text="When the operation was started")
+
+    completed_at = models.DateTimeField(null=True, blank=True, help_text="When the operation completed (success or failure)")
+
     class Meta:
-        db_table = 'video_processing_history'
-        verbose_name = 'Video Processing History'
-        verbose_name_plural = 'Video Processing Histories'
-        ordering = ['-created_at']
+        db_table = "video_processing_history"
+        verbose_name = "Video Processing History"
+        verbose_name_plural = "Video Processing Histories"
+        ordering = ["-created_at"]
         indexes = [
-            models.Index(fields=['video', '-created_at']),
-            models.Index(fields=['task_id']),
-            models.Index(fields=['status']),
+            models.Index(fields=["video", "-created_at"]),
+            models.Index(fields=["task_id"]),
+            models.Index(fields=["status"]),
         ]
-    
+
     def __str__(self):
-        return f"{self.get_operation_display()} on {self.video.uuid} - {self.get_status_display()}"
-    
+        operation_display = getattr(self, "get_operation_display", None)
+        status_display = getattr(self, "get_status_display", None)
+
+        operation = operation_display() if callable(operation_display) else self.operation
+        status = status_display() if callable(status_display) else self.status
+        return f"{operation} on {self.video.uuid} - {status}"
+
     def mark_running(self, save=True):
         """Mark operation as running."""
         self.status = self.STATUS_RUNNING
         if save:
-            self.save(update_fields=['status'])
-    
+            self.save(update_fields=["status"])
+
+    @staticmethod
+    def _normalize_output_path(path: str | Path | None) -> str:
+        """Return a path relative to MEDIA_ROOT when possible."""
+        if not path:
+            return ""
+
+        raw_path = Path(path)
+        if not raw_path.is_absolute():
+            return raw_path.as_posix()
+        media_root = Path(settings.MEDIA_ROOT)
+
+        try:
+            relative = raw_path.resolve().relative_to(media_root.resolve())
+            return relative.as_posix()
+        except (ValueError, RuntimeError):
+            logger.warning(
+                "Storing absolute output path '%s' because it is outside MEDIA_ROOT (%s).",
+                raw_path,
+                media_root,
+            )
+            return raw_path.as_posix()
+
     def mark_success(self, output_file=None, details=None, save=True):
         """Mark operation as successful."""
         self.status = self.STATUS_SUCCESS
         self.completed_at = timezone.now()
         if output_file:
-            self.output_file = output_file
+            self.output_file = self._normalize_output_path(output_file)
         if details:
             self.details = details
         if save:
-            self.save(update_fields=['status', 'completed_at', 'output_file', 'details'])
-    
+            self.save(update_fields=["status", "completed_at", "output_file", "details"])
+
     def mark_failure(self, error_message, save=True):
         """Mark operation as failed."""
         self.status = self.STATUS_FAILURE
         self.completed_at = timezone.now()
         self.details = error_message
         if save:
-            self.save(update_fields=['status', 'completed_at', 'details'])
-    
+            self.save(update_fields=["status", "completed_at", "details"])
+
     @property
     def duration(self):
         """Calculate operation duration if completed."""
         if self.completed_at and self.created_at:
             return (self.completed_at - self.created_at).total_seconds()
         return None
-    
+
     @property
     def is_complete(self) -> bool:
         """Check if operation is in a terminal state."""

endoreg_db/models/medical/contraindication/README.md

@@ -0,0 +1 @@
+not yet properly implemented

endoreg_db/models/medical/contraindication/__init__.py

@@ -1,17 +1,27 @@
+from typing import TYPE_CHECKING
+
 from django.db import models
 
+
 class ContraindicationManager(models.Manager):
     def get_by_natural_key(self, name):
         return self.get(name=name)
-    
+
+
 class Contraindication(models.Model):
     name = models.CharField(max_length=100, unique=True)
     description = models.TextField(blank=True, null=True)
 
     objects = ContraindicationManager()
-    
+
+    if TYPE_CHECKING:
+        from endoreg_db.models import FindingIntervention
+
+        @property
+        def contraindicating_finding_interventions(self) -> "models.manager.RelatedManager[FindingIntervention]": ...
+
     def natural_key(self):
         return (self.name,)
-    
+
     def __str__(self):
         return str(self.name)

endoreg_db/models/medical/disease.py

@@ -1,5 +1,6 @@
+from typing import TYPE_CHECKING, List
+
 from django.db import models
-from typing import List, TYPE_CHECKING
 
 if TYPE_CHECKING:
     from .patient import PatientDisease
@@ -27,6 +28,7 @@ class Disease(models.Model):
 
     Can define associated subcategories and numerical descriptors applicable to the disease itself.
     """
+
     name = models.CharField(max_length=255, unique=True)
     subcategories = models.JSONField(default=dict)
     numerical_descriptors = models.JSONField(default=dict)
@@ -34,8 +36,12 @@ class Disease(models.Model):
     objects = DiseaseManager()
 
     if TYPE_CHECKING:
-        disease_classifications: models.QuerySet["DiseaseClassification"]
-        patient_diseases: models.QuerySet["PatientDisease"]
+
+        @property
+        def disease_classifications(self) -> models.QuerySet["DiseaseClassification"]: ...
+
+        @property
+        def patient_diseases(self) -> models.QuerySet["PatientDisease"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
@@ -52,9 +58,7 @@ class Disease(models.Model):
         Returns:
             List[DiseaseClassification]: A list of related disease classification objects.
         """
-        classifications: List[DiseaseClassification] = [
-            _ for _ in self.disease_classifications.all()
-        ]
+        classifications: List[DiseaseClassification] = [_ for _ in self.disease_classifications.all()]
         return classifications
 
 
@@ -78,17 +82,18 @@ class DiseaseClassification(models.Model):
     """
     Represents a classification system applicable to a specific disease (e.g., Forrest classification for ulcers).
     """
+
     name = models.CharField(max_length=255, unique=True)
 
-    disease = models.ForeignKey(
-        Disease, on_delete=models.CASCADE, related_name="disease_classifications"
-    )
+    disease = models.ForeignKey(Disease, on_delete=models.CASCADE, related_name="disease_classifications")
 
     objects = DiseaseClassificationManager()
 
     if TYPE_CHECKING:
-        disease: "Disease"
-        disease_classification_choices: models.QuerySet["DiseaseClassificationChoice"]
+        disease: models.ForeignKey["Disease"]
+
+        @property
+        def disease_classification_choices(self) -> models.manager.RelatedManager["DiseaseClassificationChoice"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
@@ -105,9 +110,7 @@ class DiseaseClassification(models.Model):
         Returns:
             List[DiseaseClassificationChoice]: A list of related disease classification choices.
         """
-        choices: List[DiseaseClassificationChoice] = [
-            _ for _ in self.disease_classification_choices.all()
-        ]
+        choices: List[DiseaseClassificationChoice] = [_ for _ in self.disease_classification_choices.all()]
         return choices
 
 
@@ -133,6 +136,7 @@ class DiseaseClassificationChoice(models.Model):
     """
     Represents a specific choice within a disease classification system (e.g., Forrest IIa).
     """
+
     name = models.CharField(max_length=255, unique=True)
 
     disease_classification = models.ForeignKey(
@@ -144,8 +148,10 @@ class DiseaseClassificationChoice(models.Model):
     objects = DiseaseClassificationChoiceManager()
 
     if TYPE_CHECKING:
-        disease_classification: "DiseaseClassification"
-        patient_diseases: models.QuerySet["PatientDisease"]
+        disease_classification: models.ForeignKey["DiseaseClassification"]
+
+        @property
+        def patient_diseases(self) -> models.manager.RelatedManager["PatientDisease"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""

endoreg_db/models/medical/event.py

@@ -1,5 +1,6 @@
+from typing import TYPE_CHECKING, List
+
 from django.db import models
-from typing import List, TYPE_CHECKING
 
 if TYPE_CHECKING:
     from endoreg_db.models import PatientEvent
@@ -13,14 +14,14 @@ class EventManager(models.Manager):
     def get_by_natural_key(self, name: str) -> "Event":
         """
         Retrieves an Event instance using its natural key.
-        
+
         This method returns the event whose name matches the provided natural key.
-        It is primarily used to support Django's natural key serialization during 
+        It is primarily used to support Django's natural key serialization during
         data import/export and deserialization processes.
-        
+
         Args:
             name: The unique event name serving as the natural key.
-        
+
         Returns:
             The Event object corresponding to the given name.
         """
@@ -38,22 +39,19 @@ class Event(models.Model):
 
     name = models.CharField(max_length=100, unique=True)
     description = models.TextField(blank=True, null=True)
-    event_classification: models.ForeignKey["EventClassification"] = models.ForeignKey(
-        "EventClassification",
-        on_delete=models.CASCADE,
-        related_name="events",
-        null=True,
-        blank=True,
-    )
+
     objects = EventManager()
 
     if TYPE_CHECKING:
-        patient_events: models.QuerySet["PatientEvent"]
+        patient_events: models.ForeignKey["PatientEvent"]
+
+        @property
+        def event_classifications(self) -> models.QuerySet["EventClassification"]: ...
 
     def natural_key(self):
         """
         Returns a tuple representing the natural key for this instance.
-        
+
         The natural key consists of the instance's unique name.
         """
         return (self.name,)
@@ -61,7 +59,7 @@ class Event(models.Model):
     def __str__(self):
         """
         Return a string representation of the instance's name.
-        
+
         This method converts the 'name' attribute to a string, providing a human-readable
         representation of the model instance.
         """
@@ -85,6 +83,18 @@ class EventClassification(models.Model):
 
     objects = EventClassificationManager()
 
+    event = models.ForeignKey(
+        Event,
+        on_delete=models.CASCADE,
+        related_name="event_classifications",
+    )
+
+    if TYPE_CHECKING:
+        event: models.ForeignKey["Event"]
+
+        @property
+        def event_classification_choices(self) -> models.QuerySet["EventClassificationChoice"]: ...
+
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
         return (self.name,)
@@ -95,9 +105,7 @@ class EventClassification(models.Model):
 
     def get_choices(self) -> List["EventClassificationChoice"]:
         """Retrieves all choices associated with this classification."""
-        choices: List[EventClassificationChoice] = [
-            _ for _ in self.event_classification_choices.all()
-        ]
+        choices: List[EventClassificationChoice] = [_ for _ in self.event_classification_choices.all()]
         return choices
 
 
@@ -128,6 +136,11 @@ class EventClassificationChoice(models.Model):
 
     objects = EventClassificationChoiceManager()
 
+    @property
+    def event(self):
+        """Returns the associated Event instance."""
+        return self.event_classification.event
+
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
         return (self.name,)

endoreg_db/models/medical/examination/__init__.py

@@ -1,9 +1,16 @@
 from .examination import Examination, ExaminationRequirementSet
-from .examination_type import ExaminationType
+from .examination_indication import ExaminationIndication, ExaminationIndicationClassification, ExaminationIndicationClassificationChoice
 from .examination_time import ExaminationTime
 from .examination_time_type import ExaminationTimeType
-from .examination_indication import(
-    ExaminationIndication,
-    ExaminationIndicationClassification,
-    ExaminationIndicationClassificationChoice
-)
+from .examination_type import ExaminationType
+
+__all__ = [
+    "Examination",
+    "ExaminationRequirementSet",
+    "ExaminationType",
+    "ExaminationTime",
+    "ExaminationTimeType",
+    "ExaminationIndication",
+    "ExaminationIndicationClassification",
+    "ExaminationIndicationClassificationChoice",
+]

endoreg_db/models/medical/examination/examination.py

@@ -1,6 +1,6 @@
+from typing import TYPE_CHECKING, List, cast
+
 from django.db import models
-from typing import List
-from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from endoreg_db.models import Finding
@@ -28,24 +28,43 @@ class Examination(models.Model):
     name = models.CharField(max_length=100, unique=True)
     examination_types = models.ManyToManyField("ExaminationType", blank=True)
     description = models.TextField(blank=True, null=True)
+    indications = models.ManyToManyField(
+        "ExaminationIndication",
+        related_name="examinations",
+        blank=True,
+    )
+    examination_times = models.ManyToManyField(
+        "ExaminationTime",
+        related_name="examinations",
+        blank=True,
+    )
+
+    findings = models.ManyToManyField(
+        "Finding",
+        blank=True,
+        related_name="examinations",
+    )
+    information_sources = models.ManyToManyField(
+        "InformationSource",
+        related_name="examinations",
+        blank=True,
+    )
 
     objects = ExaminationManager()
 
     if TYPE_CHECKING:
-        from endoreg_db.models import ExaminationIndication, Finding, FindingClassification
-        finding_classifications: models.QuerySet['FindingClassification']
-        indications: models.QuerySet[ExaminationIndication]
-        findings: models.QuerySet["Finding"]
-        exam_reqset_links: models.QuerySet["ExaminationRequirementSet"]
-
-    # # Requirement sets associated with the examination.
-    # requirement_sets = models.ManyToManyField(
-    #     "RequirementSet",
-    #     through="ExaminationRequirementSet",
-    #     related_name="examinations",
-    #     blank=True,
-    # )
+        from endoreg_db.models import ExaminationIndication, ExaminationTime, Finding, FindingClassification, InformationSource
+
+        indications = cast("models.manager.RelatedManager[ExaminationIndication]", indications)
+        examination_times = cast("models.manager.RelatedManager[ExaminationTime]", examination_times)
+        findings = cast("models.manager.RelatedManager[Finding]", findings)
+        information_sources = cast("models.manager.RelatedManager[InformationSource]", information_sources)
 
+        @property
+        def finding_classifications(self) -> "models.manager.RelatedManager[FindingClassification]": ...
+
+        @property
+        def exam_reqset_links(self) -> "models.manager.RelatedManager[ExaminationRequirementSet]": ...
 
     @property
     def links(self) -> "RequirementLinks":
@@ -61,7 +80,7 @@ class Examination(models.Model):
             examinations=[self],
             findings=list(self.findings.all()),
             finding_classifications=list(self.finding_classifications.all()),
-            examination_indications=list(self.indications.all())
+            examination_indications=list(self.indications.all()),
         )
 
     def __str__(self) -> str:
@@ -108,12 +127,13 @@ class ExaminationRequirementSetManager(models.Manager):
     def get_by_natural_key(self, name: str) -> "ExaminationRequirementSet":
         return self.get(name=name)
 
-        
+
 class ExaminationRequirementSet(models.Model):
     """
     Through table for Examination ↔ RequirementSet link.
     Lets you store per-link metadata (order, default, etc.)
     """
+
     examinations = models.ManyToManyField(
         "Examination",
         related_name="exam_reqset_links",
@@ -126,7 +146,7 @@ class ExaminationRequirementSet(models.Model):
     # )
     # Optional metadata
     enabled_by_default = models.BooleanField(default=False)
-    
+
     name = models.CharField(max_length=100, unique=True)
 
     objects = ExaminationRequirementSetManager()
@@ -136,7 +156,7 @@ class ExaminationRequirementSet(models.Model):
 
     # def __str__(self) -> str:
     #     return f"{self.examination} ↔ {self.requirement_set} (prio={self.priority})"
-    
+
     def natural_key(self) -> tuple:
         """
         Returns the natural key for the ExaminationRequirementSet.
@@ -145,4 +165,3 @@ class ExaminationRequirementSet(models.Model):
             tuple: The natural key consisting of the name.
         """
         return (self.name,)
-