endoreg-db 0.6.1__py3-none-any.whl → 0.6.3__py3-none-any.whl

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Files changed (28) hide show
  1. endoreg_db/data/distribution/numeric/data.yaml +1 -1
  2. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  3. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  4. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
  5. endoreg_db/mermaid/classification.md +8 -0
  6. endoreg_db/mermaid/examination.md +8 -0
  7. endoreg_db/mermaid/findings.md +7 -0
  8. endoreg_db/mermaid/image_classification.md +28 -0
  9. endoreg_db/mermaid/interventions.md +8 -0
  10. endoreg_db/mermaid/morphology.md +8 -0
  11. endoreg_db/mermaid/patient_creation.md +14 -0
  12. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  13. endoreg_db/models/ai_model/ai_model.py +1 -1
  14. endoreg_db/models/ai_model/model_meta.py +1 -1
  15. endoreg_db/models/data_file/base_classes/utils.py +1 -1
  16. endoreg_db/serializers/raw_pdf_anony_text_validation.py +137 -0
  17. endoreg_db/serializers/raw_pdf_meta_validation.py +223 -0
  18. endoreg_db/serializers/raw_video_meta_validation.py +163 -1
  19. endoreg_db/serializers/video_segmentation.py +207 -112
  20. endoreg_db/urls.py +110 -11
  21. endoreg_db/views/raw_pdf_anony_text_validation_views.py +95 -0
  22. endoreg_db/views/raw_pdf_meta_validation_views.py +111 -0
  23. endoreg_db/views/raw_video_meta_validation_views.py +128 -18
  24. endoreg_db/views/video_segmentation_views.py +28 -11
  25. {endoreg_db-0.6.1.dist-info → endoreg_db-0.6.3.dist-info}/METADATA +11 -1
  26. {endoreg_db-0.6.1.dist-info → endoreg_db-0.6.3.dist-info}/RECORD +28 -13
  27. {endoreg_db-0.6.1.dist-info → endoreg_db-0.6.3.dist-info}/WHEEL +0 -0
  28. {endoreg_db-0.6.1.dist-info → endoreg_db-0.6.3.dist-info}/licenses/LICENSE +0 -0
@@ -1,13 +1,175 @@
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+ from pathlib import Path
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  from rest_framework import serializers
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+ from django.conf import settings
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  from ..models import RawVideoFile, SensitiveMeta
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+ import cv2
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+ from datetime import datetime
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+
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  class VideoFileForMetaSerializer(serializers.ModelSerializer):
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  """
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  Serializer to fetch video metadata along with linked `SensitiveMeta` details.
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+ Ensures that Vue.js can properly access and play videos.
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  """
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+ # Fetch patient name and DOB from `SensitiveMeta` table
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  patient_first_name = serializers.CharField(source="sensitive_meta.patient_first_name", read_only=True)
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+ patient_last_name = serializers.CharField(source="sensitive_meta.patient_last_name", read_only=True)
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+ patient_dob = serializers.CharField(source="sensitive_meta.patient_dob", read_only=True)
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+ examination_date = serializers.CharField(source="sensitive_meta.examination_date", read_only=True)
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+
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+ duration = serializers.SerializerMethodField()
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+
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+
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+ # `video_url` generates the full URL where Vue.js can fetch & play the video
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+ video_url = serializers.SerializerMethodField()
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+
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+ # `full_video_path` dynamically constructs the absolute path using MEDIA_ROOT
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+ full_video_path = serializers.SerializerMethodField()
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+
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+ file = serializers.SerializerMethodField()
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  class Meta:
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  model = RawVideoFile
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- fields = ['id', 'original_file_name', 'file', 'sensitive_meta_id', 'patient_first_name']
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+ fields = ['id', 'original_file_name', 'file', 'video_url', 'full_video_path',
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+ 'sensitive_meta_id', 'patient_first_name', 'patient_last_name', 'patient_dob', 'examination_date','duration']
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+
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+ @staticmethod
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+ def get_next_video(last_id=None):
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+ """
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+ Fetches the first or next available video.
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+ Returns a model instance if found, else returns None.
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+ """
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+ query_filter = {} if last_id is None else {"id__gt": int(last_id)}
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+
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+ # Get next available video
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+ video_entry = RawVideoFile.objects.select_related("sensitive_meta").filter(**query_filter).order_by('id').first()
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+
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+ return video_entry # Always return model instance or None
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+
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+ def get_video_url(self, obj):
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+ """
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+ Generates the full URL where Vue.js can fetch and stream the video.
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+ """
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+ request = self.context.get('request')
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+ if request and obj.file:
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+ print("---------------------------:",obj.file)
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+ return request.build_absolute_uri(f"/api/video/{obj.id}/") # Generates full URL
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+ return None # Return None instead of an error dictionary
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+
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+ def get_file(self, obj):
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+ """
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+ Returns only the relative file path, without `/media/`.
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+ """
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+ if not obj.file:
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+ return None # No file associated
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+
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+ video_relative_path = str(obj.file.name).strip()
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+ return video_relative_path if video_relative_path else None # Avoids errors if the file path is empty
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+
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+ def get_full_video_path(self, obj):
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+ """
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+ Constructs the full absolute file path using `settings.MEDIA_ROOT`
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+ and the `file` field from the database.
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+ """
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+ if not obj.file:
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+ return None # No file associated
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+
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+ video_relative_path = str(obj.file.name).strip()
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+ full_path = Path(settings.MEDIA_ROOT) / video_relative_path
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+
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+ return str(full_path) if full_path.exists() else None # Return path or None if not found
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+
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+ def get_duration(self, obj):
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+ """
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+ Returns the total duration of the video in seconds.
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+ - If stored in the database, use it.
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+ - Otherwise, calculate dynamically using OpenCV.
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+ """
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+
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+ # Step 1: Check if the `duration` field is already stored in the database.
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+ if hasattr(obj, "duration") and obj.duration:
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+ return obj.duration # If duration exists in the database, return it immediately.
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+
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+ # Step 2: Get the actual video file path
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+ video_path = obj.file.path if obj.file else None # Extracts the file path if it exists
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+
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+ # Step 3: Validate if the file exists
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+ if not video_path or not Path(video_path).exists():
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+ return None # Return None if the file path is invalid or missing
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+
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+ # Step 4: Open the video file using OpenCV
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+ cap = cv2.VideoCapture(video_path) # Load the video file
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+
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+ if not cap.isOpened():
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+ return None # If OpenCV fails to open the video, return None (invalid or corrupted file)
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+
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+ # Step 5: Extract FPS (Frames Per Second)
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+ fps = cap.get(cv2.CAP_PROP_FPS) # Get the number of frames per second
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+ print("here is the fps------------", fps) # Debugging print to check FPS value
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+
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+ # Step 6: Get Total Number of Frames
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+ total_frames = cap.get(cv2.CAP_PROP_FRAME_COUNT) # Get the total number of frames in the video
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+
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+ # Step 7: Release the video file from OpenCV memory
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+ cap.release() # Free up system memory
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+
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+ # Step 8: Calculate and Return Video Duration
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+ return round(total_frames / fps, 2) if fps > 0 else None # Divide frames by FPS to get duration (seconds)
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+
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+
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+
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+
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+ class SensitiveMetaUpdateSerializer(serializers.ModelSerializer):
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+ """
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+ Serializer to update patient information in the `SensitiveMeta` table.
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+ Handles validation and saves the data directly in the serializer.
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+ """
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+
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+ sensitive_meta_id = serializers.IntegerField(write_only=True) # Needed for lookup but not included in response
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+
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+ class Meta:
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+ model = SensitiveMeta
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+ fields = ['sensitive_meta_id', 'patient_first_name', 'patient_last_name', 'patient_dob', 'examination_date']
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+
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+ def validate(self, data):
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+ """
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+ Validate input data before updating.
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+ """
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+ errors = {}
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+
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+ # Ensure the SensitiveMeta ID exists
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+ sensitive_meta_id = data.get("sensitive_meta_id")
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+ if not SensitiveMeta.objects.filter(id=sensitive_meta_id).exists():
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+ raise serializers.ValidationError({"sensitive_meta_id": "SensitiveMeta entry not found."})
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+
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+ # Validate each field separately
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+ if 'patient_first_name' in data and (data['patient_first_name'] is None or data['patient_first_name'].strip() == ""):
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+ errors['patient_first_name'] = "First name cannot be empty."
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+
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+ if 'patient_last_name' in data and (data['patient_last_name'] is None or data['patient_last_name'].strip() == ""):
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+ errors['patient_last_name'] = "Last name cannot be empty."
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+
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+ if 'patient_dob' in data and not data['patient_dob']:
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+ errors['patient_dob'] = "Date of birth is required."
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+
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+ if 'examination_date' in data and not data['examination_date']:
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+ errors['examination_date'] = "Examination date is required."
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+
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+ if errors:
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+ raise serializers.ValidationError(errors) # Raise errors before saving
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+
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+ return data
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+
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+ def update(self, instance, validated_data):
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+ """
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+ Update the SensitiveMeta entry directly inside the serializer.
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+ """
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+ # Remove `sensitive_meta_id` before updating
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+ validated_data.pop("sensitive_meta_id", None)
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+
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+ for attr, value in validated_data.items():
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+ setattr(instance, attr, value) # Set attributes dynamically
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+
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+ instance.save() # Save changes
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+ return instance # Return updated instance