endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/services/__old/pdf_import.py

@@ -0,0 +1,1487 @@
+"""
+report import service module.
+
+Provides high-level functions for importing and anonymizing report files,
+combining RawPdfFile creation with text extraction and anonymization using lx anonymizer.
+
+All Fields should be overwritten from anonymizer defaults except for the center which is given.
+"""
+
+import errno
+import hashlib
+import logging
+import os
+import shutil
+import subprocess
+import sys
+import time
+from contextlib import contextmanager
+from datetime import date, datetime
+from pathlib import Path
+from typing import TYPE_CHECKING, Union
+
+import lx_anonymizer
+from django.core.exceptions import ObjectDoesNotExist
+from django.db import transaction
+
+from endoreg_db.models import SensitiveMeta
+from endoreg_db.models.media.pdf.raw_pdf import RawPdfFile
+from endoreg_db.models.state.raw_pdf import RawPdfState
+from endoreg_db.utils import paths as path_utils
+
+logger = logging.getLogger(__name__)
+
+# Treat lock files older than this as stale and reclaim them (in seconds)
+STALE_LOCK_SECONDS = 600
+
+if TYPE_CHECKING:
+    pass  # RawPdfFile already imported above
+
+
+class PdfImportService:
+    """
+    Service class for importing and processing report files with text extraction and anonymization.
+    Uses a central report instance pattern for cleaner state management.
+
+    Supports two processing modes:
+    - 'blackening': Simple report masking with black rectangles over sensitive areas
+    - 'cropping': Advanced mode that crops sensitive regions to separate images
+    """
+
+    def __init__(
+        self, allow_meta_overwrite: bool = True, processing_mode: str = "blackening"
+    ):
+        """
+        Initialize the report import service.
+
+        Args:
+            allow_meta_overwrite: Whether to allow overwriting existing SensitiveMeta fields
+            processing_mode: Processing mode - 'blackening' for simple masking, 'cropping' for advanced cropping
+        """
+        self.processed_files = set()
+        self._report_reader_available = None
+        self._report_reader_class = None
+        self.allow_meta_overwrite = allow_meta_overwrite
+
+        # Validate and set processing mode
+        valid_modes = ["blackening", "cropping"]
+        if processing_mode not in valid_modes:
+            raise ValueError(
+                f"Invalid processing_mode '{processing_mode}'. Must be one of: {valid_modes}"
+            )
+        self.processing_mode = processing_mode
+
+        # Central report instance management
+        self.current_pdf = None
+        self.current_pdf_state = None
+        self.processing_context = {}
+        self.original_path = None
+
+        self.DEFAULT_PATIENT_FIRST_NAME = "Patient"
+        self.DEFAULT_PATIENT_LAST_NAME = "Unknown"
+        self.DEFAULT_PATIENT_DOB = date(1990, 1, 1)
+        self.DEFAULT_CENTER_NAME = "university_hospital_wuerzburg"
+
+    def import_and_anonymize(
+        self,
+        file_path: Union[Path, str],
+        center_name: str,
+        delete_source: bool = False,
+        retry: bool = False,
+    ) -> "RawPdfFile | None":
+        """
+        Import a report file and anonymize it using ReportReader.
+        Uses centralized report instance management pattern.
+
+        The processing mode is determined by the service initialization:
+        - 'blackening': Creates an anonymized report with black rectangles over sensitive regions
+        - 'cropping': Advanced mode that crops sensitive regions to separate images
+
+        Args:
+            file_path: Path to the report file to import
+            center_name: Name of the center to associate with report
+            delete_source: Whether to delete the source file after import
+            retry: Whether this is a retry attempt
+
+        Returns:
+            RawPdfFile instance after import and processing
+
+        Raises:
+            Exception: On any failure during import or processing
+        """
+        try:
+            # Initialize processing context
+            self._initialize_processing_context(
+                file_path, center_name, delete_source, retry
+            )
+
+            # Step 1: Validate and prepare file
+            self._validate_and_prepare_file()
+
+            # Step 2: Create or retrieve report instance
+            self._create_or_retrieve_pdf_instance()
+
+            # Early return check - if no report instance was created, return None
+            if not self.current_pdf:
+                logger.warning(
+                    f"No report instance created for {file_path}, returning None"
+                )
+                raise ObjectDoesNotExist
+            # Step 3: Setup processing environment
+            self._setup_processing_environment()
+
+            # Step 4: Process text and metadata
+            self._process_text_and_metadata()
+
+            # Step 5: Finalize processing
+            self._finalize_processing()
+
+            return self.current_pdf
+
+        except ValueError as e:
+            # Handle "File already being processed" case specifically
+            if "already being processed" in str(e):
+                logger.info(f"Skipping file {file_path}: {e}")
+                return
+            else:
+                logger.error(f"report import failed for {file_path}: {e}")
+                self._cleanup_on_error()
+                raise
+        except Exception as e:
+            logger.error(f"report import failed for {file_path}: {e}")
+            # Cleanup on error
+            self._cleanup_on_error()
+            raise
+        finally:
+            # Always cleanup context
+            self._cleanup_processing_context()
+
+    def _initialize_processing_context(
+        self,
+        file_path: Union[Path, str],
+        center_name: str,
+        delete_source: bool,
+        retry: bool,
+    ):
+        """Initialize the processing context for the current report."""
+        self.processing_context = {
+            "file_path": Path(file_path),
+            "original_file_path": Path(file_path),
+            "center_name": center_name,
+            "delete_source": delete_source,
+            "retry": retry,
+            "file_hash": None,
+            "processing_started": False,
+            "text_extracted": False,
+            "metadata_processed": False,
+            "anonymization_completed": False,
+        }
+        self.original_path = Path(file_path)
+
+        # Check if already processed (only during current session to prevent race conditions)
+        if str(file_path) in self.processed_files:
+            logger.info(
+                f"File {file_path} already being processed in current session, skipping"
+            )
+            raise ValueError("File already being processed")
+
+        logger.info(f"Starting import and processing for: {file_path}")
+
+    @classmethod
+    def with_blackening(cls, allow_meta_overwrite: bool = False) -> "PdfImportService":
+        """
+        Create a PdfImportService configured for simple report blackening mode.
+
+        Args:
+            allow_meta_overwrite: Whether to allow overwriting existing SensitiveMeta fields
+
+        Returns:
+            PdfImportService instance configured for blackening mode
+        """
+        return cls(
+            allow_meta_overwrite=allow_meta_overwrite, processing_mode="blackening"
+        )
+
+    @classmethod
+    def with_cropping(cls, allow_meta_overwrite: bool = False) -> "PdfImportService":
+        """
+        Create a PdfImportService configured for advanced cropping mode.
+
+        Args:
+            allow_meta_overwrite: Whether to allow overwriting existing SensitiveMeta fields
+
+        Returns:
+            PdfImportService instance configured for cropping mode
+        """
+        return cls(
+            allow_meta_overwrite=allow_meta_overwrite, processing_mode="cropping"
+        )
+
+    @contextmanager
+    def _file_lock(self, path: Path):
+        """Create a file lock to prevent duplicate processing.
+        Handles stale lock files by reclaiming after STALE_LOCK_SECONDS.
+        """
+        lock_path = Path(str(path) + ".lock")
+        fd = None
+        try:
+            try:
+                # atomic create; fail if exists
+                fd = os.open(lock_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0o644)
+            except FileExistsError:
+                # Check for stale lock
+                age = None
+                try:
+                    st = os.stat(lock_path)
+                    age = time.time() - st.st_mtime
+                except FileNotFoundError:
+                    # race: lock removed between exists and stat; just retry acquiring below
+                    pass
+
+                if age is not None and age > STALE_LOCK_SECONDS:
+                    try:
+                        logger.warning(
+                            "Stale lock detected for %s (age %.0fs). Reclaiming lock...",
+                            path,
+                            age,
+                        )
+                        lock_path.unlink()
+                    except Exception as e:
+                        logger.warning(
+                            "Failed to remove stale lock %s: %s", lock_path, e
+                        )
+                    # retry acquire
+                    fd = os.open(lock_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0o644)
+                else:
+                    # Another worker is processing this file
+
+                    raise ValueError(f"File already being processed: {path}")
+
+            os.write(fd, b"lock")
+            os.close(fd)
+            fd = None
+            yield
+        finally:
+            try:
+                if fd is not None:
+                    os.close(fd)
+                if lock_path.exists():
+                    lock_path.unlink()
+            except OSError:
+                pass
+
+    def _get_pdf_dir(self) -> Path | None:
+        """Resolve the configured report directory to a concrete Path."""
+        candidate = getattr(path_utils, "REPORT_DIR", None)
+        if isinstance(candidate, Path):
+            return candidate
+        if candidate is None:
+            return None
+        try:
+            derived = candidate / "."
+        except Exception:
+            derived = None
+
+        if derived is not None:
+            try:
+                return Path(derived)
+            except Exception:
+                return None
+
+        try:
+            return Path(str(candidate))
+        except Exception:
+            return None
+
+    def _quarantine(self, source: Path) -> Path:
+        """Move file to quarantine directory to prevent re-processing."""
+        qdir = path_utils.REPORT_DIR / "_processing"
+        qdir.mkdir(parents=True, exist_ok=True)
+        target = qdir / source.name
+        try:
+            # Try atomic rename first (fastest when on same filesystem)
+            source.rename(target)
+        except OSError as exc:
+            if exc.errno == errno.EXDEV:
+                # Cross-device move, fall back to shutil.move which copies+removes
+                shutil.move(str(source), str(target))
+            else:
+                raise
+        lock_path = Path(str(source) + ".lock")
+        if lock_path.exists():
+            lock_path.unlink()
+
+        return target
+
+    def _ensure_state(self, pdf_file: "RawPdfFile"):
+        """Ensure report file has a state object."""
+        if getattr(pdf_file, "state", None):
+            return pdf_file.state
+        if hasattr(pdf_file, "get_or_create_state"):
+            state = pdf_file.get_or_create_state()
+            pdf_file.state = state
+            self.current_pdf_state = state
+            assert isinstance(self.current_pdf_state, RawPdfState)
+            return state
+
+    def _ensure_report_reading_available(self):
+        """
+        Ensure report reading modules are available by adding lx-anonymizer to path.
+
+        Returns:
+            Tuple of (availability_flag, ReportReader_class)
+        """
+        if self._report_reader_available is not None:
+            return self._report_reader_available, self._report_reader_class
+
+        try:
+            # Try direct import first
+            from lx_anonymizer import ReportReader
+
+            logger.info("Successfully imported lx_anonymizer ReportReader module")
+            self._report_reader_available = True
+            self._report_reader_class = ReportReader
+            return True, ReportReader
+
+        except ImportError:
+            # Optional: honor LX_ANONYMIZER_PATH=/abs/path/to/src
+            import importlib
+
+            extra = os.getenv("LX_ANONYMIZER_PATH")
+            if extra and extra not in sys.path and Path(extra).exists():
+                sys.path.insert(0, extra)
+                try:
+                    mod = importlib.import_module("lx_anonymizer")
+                    ReportReader = getattr(mod, "ReportReader")
+                    logger.info(
+                        "Imported lx_anonymizer.ReportReader via LX_ANONYMIZER_PATH"
+                    )
+                    self._report_reader_available = True
+                    self._report_reader_class = ReportReader
+                    return True, ReportReader
+                except Exception as e:
+                    logger.warning(
+                        "Failed importing lx_anonymizer via LX_ANONYMIZER_PATH: %s", e
+                    )
+                finally:
+                    # Keep path for future imports if it worked; otherwise remove.
+                    if "ReportReader" not in locals() and extra in sys.path:
+                        sys.path.remove(extra)
+
+        self._report_reader_available = False
+        self._report_reader_class = None
+        return False, None
+
+    def _ensure_default_patient_data(self, pdf_instance: "RawPdfFile") -> None:
+        """
+        Ensure report has minimum required patient data in SensitiveMeta.
+        Creates default values if data is missing after text processing.
+        Uses the central report instance if no specific instance provided.
+
+        Args:
+            pdf_instance: Optional specific report instance, defaults to self.current_pdf
+        """
+        pdf_file = pdf_instance or self.current_pdf
+        if not pdf_file:
+            logger.warning(
+                "No report instance available for ensuring default patient data"
+            )
+            return
+
+        if not pdf_file.sensitive_meta:
+            logger.info(
+                f"No SensitiveMeta found for report {pdf_file.pdf_hash}, creating default"
+            )
+
+            # Create default SensitiveMeta with placeholder data
+            default_data = {
+                "patient_first_name": self.DEFAULT_PATIENT_FIRST_NAME,
+                "patient_last_name": self.DEFAULT_PATIENT_LAST_NAME,
+                "patient_dob": self.DEFAULT_PATIENT_DOB,
+                "examination_date": date.today(),  # today is intentionally *not* a constant
+                "center_name": (
+                    pdf_file.center.name
+                    if pdf_file.center
+                    else self.DEFAULT_CENTER_NAME
+                ),
+            }
+
+            try:
+                sensitive_meta = SensitiveMeta.create_from_dict(default_data)
+                pdf_file.sensitive_meta = sensitive_meta
+                pdf_file.save(update_fields=["sensitive_meta"])
+                logger.info(
+                    f"Created default SensitiveMeta for report {pdf_file.pdf_hash}"
+                )
+            except Exception as e:
+                logger.error(
+                    f"Failed to create default SensitiveMeta for report {pdf_file.pdf_hash}: {e}"
+                )
+
+    def _validate_and_prepare_file(self):
+        """Validate file existence and calculate hash."""
+        file_path = self.processing_context["file_path"]
+
+        if not file_path.exists():
+            raise FileNotFoundError(f"report file not found: {file_path}")
+
+    def _create_or_retrieve_pdf_instance(self):
+        """Create new or retrieve existing report instance."""
+        file_path = self.processing_context["file_path"]
+        center_name = self.processing_context["center_name"]
+        delete_source = self.processing_context["delete_source"]
+        retry = self.processing_context["retry"]
+        file_hash = self.processing_context["file_hash"]
+
+        if not retry:
+            # Check for existing report and handle duplicates
+            with self._file_lock(file_path):
+                existing = None
+                if file_hash and RawPdfFile.objects.filter(pdf_hash=file_hash).exists():
+                    existing = RawPdfFile.objects.get(pdf_hash=file_hash)
+
+                if existing:
+                    logger.info(f"Found existing RawPdfFile {existing.pdf_hash}")
+                    if existing.text:
+                        logger.info(
+                            f"Existing report {existing.pdf_hash} already processed - returning"
+                        )
+                        self.current_pdf = existing
+                        return
+                    else:
+                        # Retry processing
+                        logger.info(f"Reprocessing existing report {existing.pdf_hash}")
+                        return self._retry_existing_pdf(existing)
+
+        # Create new report instance
+        logger.info("Creating new RawPdfFile instance...")
+        from django.db import IntegrityError
+
+        try:
+            if not retry:
+                self.current_pdf = RawPdfFile.create_from_file_initialized(
+                    file_path=file_path,
+                    center_name=center_name,
+                    delete_source=delete_source,
+                )
+            else:
+                # Retrieve existing for retry
+                self.current_pdf = RawPdfFile.objects.get(pdf_hash=file_hash)
+                logger.info(
+                    f"Retrying import for existing RawPdfFile {self.current_pdf.pdf_hash}"
+                )
+
+                # Check if retry is actually needed
+                if self.current_pdf.text:
+                    logger.info(
+                        f"Existing report {self.current_pdf.pdf_hash} already processed during retry - returning"
+                    )
+                    return
+
+            if not self.current_pdf:
+                raise RuntimeError("Failed to create RawPdfFile instance")
+
+            logger.info(f"report instance ready: {self.current_pdf.pdf_hash}")
+
+        except IntegrityError:
+            # Race condition - another worker created it
+            if file_hash:
+                self.current_pdf = RawPdfFile.objects.get(pdf_hash=file_hash)
+                logger.info("Race condition detected, using existing RawPdfFile")
+            else:
+                raise
+
+    def _setup_processing_environment(self):
+        """Setup processing environment and state."""
+        original_path = self.processing_context.get("file_path")
+        if not original_path or not self.current_pdf:
+            try:
+                self.current_pdf = RawPdfFile.objects.get(
+                    pdf_hash=self.processing_context["file_hash"]
+                )
+                self.original_path = Path(str(self.current_pdf.file.path))
+
+            except RawPdfFile.DoesNotExist:
+                raise RuntimeError("Processing environment setup failed")
+        # Create sensitive file copy
+        if original_path is None or not isinstance(original_path, (str, Path)):
+            logger.error(f"No original path: {original_path!r}")
+            return
+        self.create_sensitive_file(self.current_pdf, original_path)
+
+        # Update file path to point to sensitive copy
+        self.processing_context["file_path"] = self.current_pdf.file.path
+        self.processing_context["sensitive_copy_created"] = True
+        try:
+            self.processing_context["sensitive_file_path"] = Path(
+                self.current_pdf.file.path
+            )
+        except Exception:
+            self.processing_context["sensitive_file_path"] = None
+
+        # Ensure state exists
+        state = self.current_pdf.get_or_create_state()
+        state.mark_processing_started()
+        self.processing_context["processing_started"] = True
+
+        # Mark as processed to prevent duplicates
+        self.processed_files.add(str(self.processing_context["file_path"]))
+
+        # Ensure default patient data
+        logger.info("Ensuring default patient data...")
+        self._ensure_default_patient_data(self.current_pdf)
+
+    def _process_text_and_metadata(self):
+        """Process text extraction and metadata using ReportReader."""
+        report_reading_available, ReportReaderCls = (
+            self._ensure_report_reading_available()
+        )
+        try:
+            assert ReportReaderCls is not None and report_reading_available
+            assert self.current_pdf is not None
+        except AssertionError as e:
+            logger.error(
+                f"report Import failed on Error:{e} Ensure the pdf was passed correctly and report reading is available in function _process_text_and_metadata() "
+            )
+        if not report_reading_available:
+            logger.warning("Report reading not available (lx_anonymizer not found)")
+            self._mark_processing_incomplete("no_report_reader")
+            return
+        assert self.current_pdf is not None
+        if not self.current_pdf.file:
+            logger.warning("No file available for text processing")
+            self._mark_processing_incomplete("no_file")
+            return
+
+        try:
+            logger.info(
+                f"Starting text extraction and metadata processing with ReportReader (mode: {self.processing_mode})..."
+            )
+            ReportReaderCls = lx_anonymizer.ReportReader
+
+            # Initialize ReportReader
+            report_reader = ReportReaderCls(
+                report_root_path=str(path_utils.STORAGE_DIR),
+                locale="de_DE",
+                text_date_format="%d.%m.%Y",
+            )
+
+            if self.processing_mode == "cropping":
+                # Use advanced cropping method (existing implementation)
+                self._process_with_cropping(report_reader)
+            else:  # blackening mode
+                # Use enhanced process_report with report masking
+                self._process_with_blackening(report_reader)
+
+        except Exception as e:
+            logger.warning(f"Text processing failed: {e}")
+            self._mark_processing_incomplete("text_processing_failed")
+
+    def _process_with_blackening(self, report_reader):
+        """Process report using simple blackening/masking mode."""
+        logger.info("Using simple report blackening mode...")
+
+        # Setup anonymized directory
+        anonymized_dir = path_utils.REPORT_DIR / "anonymized"
+        anonymized_dir.mkdir(parents=True, exist_ok=True)
+        assert self.current_pdf is not None
+        # Generate output path for anonymized report
+        pdf_hash = self.current_pdf.pdf_hash
+        anonymized_output_path = anonymized_dir / f"{pdf_hash}_anonymized.pdf"
+
+        # Process with enhanced process_report method (returns 4-tuple now)
+        original_text, anonymized_text, extracted_metadata, anonymized_pdf_path = (
+            report_reader.process_report(
+                pdf_path=self.processing_context["file_path"],
+                create_anonymized_pdf=True,
+                anonymized_pdf_output_path=str(anonymized_output_path),
+            )
+        )
+
+        # Store results in context
+        self.processing_context.update(
+            {
+                "original_text": original_text,
+                "anonymized_text": anonymized_text,
+                "extracted_metadata": extracted_metadata,
+                "cropped_regions": None,  # Not available in blackening mode
+                "anonymized_pdf_path": anonymized_pdf_path,
+            }
+        )
+
+        # Apply results
+        if original_text:
+            self._apply_text_results()
+            self.processing_context["text_extracted"] = True
+
+        if extracted_metadata:
+            self._apply_metadata_results()
+            self.processing_context["metadata_processed"] = True
+
+        if anonymized_pdf_path:
+            self._apply_anonymized_pdf()
+            self.processing_context["anonymization_completed"] = True
+
+        logger.info("report blackening processing completed")
+
+    def _process_with_cropping(self, report_reader):
+        """Process report using advanced cropping mode (existing implementation)."""
+        logger.info("Using advanced cropping mode...")
+
+        # Setup output directories
+        crops_dir = path_utils.REPORT_DIR / "cropped_regions"
+        anonymized_dir = path_utils.REPORT_DIR / "anonymized"
+        crops_dir.mkdir(parents=True, exist_ok=True)
+        anonymized_dir.mkdir(parents=True, exist_ok=True)
+
+        # Process with cropping (returns 5-tuple)
+        (
+            original_text,
+            anonymized_text,
+            extracted_metadata,
+            cropped_regions,
+            anonymized_pdf_path,
+        ) = report_reader.process_report_with_cropping(
+            pdf_path=self.processing_context["file_path"],
+            crop_sensitive_regions=True,
+            crop_output_dir=str(crops_dir),
+            anonymization_output_dir=str(anonymized_dir),
+        )
+
+        # Store results in context
+        self.processing_context.update(
+            {
+                "original_text": original_text,
+                "anonymized_text": anonymized_text,
+                "extracted_metadata": extracted_metadata,
+                "cropped_regions": cropped_regions,
+                "anonymized_pdf_path": anonymized_pdf_path,
+            }
+        )
+
+        # Apply results
+        if original_text:
+            self._apply_text_results()
+            self.processing_context["text_extracted"] = True
+
+        if extracted_metadata:
+            self._apply_metadata_results()
+            self.processing_context["metadata_processed"] = True
+
+        if anonymized_pdf_path:
+            self._apply_anonymized_pdf()
+            self.processing_context["anonymization_completed"] = True
+
+        logger.info("report cropping processing completed")
+
+    def _apply_text_results(self):
+        """Apply text extraction results to the report instance."""
+        if not self.current_pdf:
+            logger.warning("Cannot apply text results - no report instance available")
+            return
+
+        original_text = self.processing_context.get("original_text")
+        anonymized_text = self.processing_context.get("anonymized_text")
+
+        if not original_text:
+            logger.warning("No original text available to apply")
+            return
+
+        # Store extracted text
+        self.current_pdf.text = original_text
+        logger.info(f"Extracted {len(original_text)} characters of text from report")
+
+        # Handle anonymized text
+        if anonymized_text and anonymized_text != original_text:
+            self.current_pdf.state.anonymization_status.mark_anonymized()
+            logger.info("report text anonymization completed")
+
+    def _apply_metadata_results(self):
+        """Apply metadata extraction results to SensitiveMeta."""
+        if not self.current_pdf:
+            logger.warning(
+                "Cannot apply metadata results - no report instance available"
+            )
+            return
+
+        extracted_metadata = self.processing_context.get("extracted_metadata")
+
+        if not self.current_pdf.sensitive_meta or not extracted_metadata:
+            logger.debug("No sensitive meta or extracted metadata available")
+            return
+
+        sm = self.current_pdf.sensitive_meta
+
+        # Map ReportReader metadata to SensitiveMeta fields
+        metadata_mapping = {
+            "patient_first_name": "patient_first_name",
+            "patient_last_name": "patient_last_name",
+            "patient_dob": "patient_dob",
+            "examination_date": "examination_date",
+            "examiner_first_name": "examiner_first_name",
+            "examiner_last_name": "examiner_last_name",
+            "endoscope_type": "endoscope_type",
+            "casenumber": "casenumber",
+            "center_name": "center_name",
+        }
+
+        # Update fields with extracted information
+        updated_fields = []
+        for meta_key, sm_field in metadata_mapping.items():
+            if extracted_metadata.get(meta_key) and hasattr(sm, sm_field):
+                old_value = getattr(sm, sm_field)
+                raw_value = extracted_metadata[meta_key]
+
+                # Skip if we just got the field name as a string (indicates no actual data)
+                if isinstance(raw_value, str) and raw_value == meta_key:
+                    continue
+
+                # Handle date fields specially
+                if sm_field in ["patient_dob", "examination_date"]:
+                    new_value = self._parse_date_field(raw_value, meta_key, sm_field)
+                    if new_value is None:
+                        continue
+                else:
+                    new_value = raw_value
+
+                # Configurable overwrite policy
+                should_overwrite = (
+                    self.allow_meta_overwrite
+                    or self._is_placeholder_value(sm_field, old_value)
+                )
+
+                if new_value and should_overwrite:
+                    setattr(sm, sm_field, new_value)
+                    updated_fields.append(sm_field)
+
+        if updated_fields:
+            sm.save()
+            logger.info(f"Updated SensitiveMeta fields: {updated_fields}")
+
+    def _parse_date_field(self, raw_value, meta_key, sm_field):
+        """Parse date field with error handling."""
+        try:
+            if isinstance(raw_value, str):
+                # Skip if the value is just the field name itself
+                if raw_value == meta_key:
+                    logger.warning(
+                        "Skipping date field %s - got field name '%s' instead of actual date",
+                        sm_field,
+                        raw_value,
+                    )
+                    return None
+
+                # Try common date formats
+                date_formats = ["%Y-%m-%d", "%d.%m.%Y", "%d/%m/%Y", "%m/%d/%Y"]
+                for fmt in date_formats:
+                    try:
+                        return datetime.strptime(raw_value, fmt).date()
+                    except ValueError:
+                        continue
+
+                logger.warning(
+                    "Could not parse date '%s' for field %s", raw_value, sm_field
+                )
+                return None
+
+            elif hasattr(raw_value, "date"):
+                return raw_value.date()
+            else:
+                return raw_value
+
+        except (ValueError, AttributeError) as e:
+            logger.warning("Date parsing failed for %s: %s", sm_field, e)
+            return None
+
+    # from gc-08
+    def _apply_anonymized_pdf(self):
+        """
+        Attach the already-generated anonymized report without copying bytes.
+
+        We do NOT re-upload or re-save file bytes via Django storage (which would
+        place a new file under upload_to='raw_pdfs' and retrigger the watcher).
+        Instead, we point the FileField to the path that the anonymizer already
+        wrote (ideally relative to STORAGE_DIR). Additionally, we make sure the
+        model/state reflect that anonymization is done even if text didn't change.
+        """
+        if not self.current_pdf:
+            logger.warning(
+                "Cannot apply anonymized report - no report instance available"
+            )
+            return
+
+        anonymized_pdf_path = self.processing_context.get("anonymized_pdf_path")
+        if not anonymized_pdf_path:
+            logger.debug("No anonymized_pdf_path present in processing context")
+            return
+
+        anonymized_path = Path(anonymized_pdf_path)
+        if not anonymized_path.exists():
+            logger.warning(
+                "Anonymized report path returned but file does not exist: %s",
+                anonymized_path,
+            )
+            return
+
+        logger.info("Anonymized report created by ReportReader at: %s", anonymized_path)
+
+        try:
+            # Prefer storing a path relative to STORAGE_DIR so Django serves it correctly
+            try:
+                relative_name = str(anonymized_path.relative_to(path_utils.STORAGE_DIR))
+            except ValueError:
+                # Fallback to absolute path if the file lives outside STORAGE_DIR
+                relative_name = str(anonymized_path)
+
+            # Only update if something actually changed
+            if getattr(self.current_pdf.processed_file, "name", None) != relative_name:
+                self.current_pdf.processed_file.name = relative_name
+
+            # Ensure model/state reflect anonymization even if text didn't differ
+            if not getattr(self.current_pdf, "anonymized", False):
+                self.current_pdf.state.anonymization_status.mark_anonymized()
+
+            # Persist cropped regions info somewhere useful (optional & non-breaking)
+            # If your model has a field for this, persist there; otherwise we just log.
+            cropped_regions = self.processing_context.get("cropped_regions")
+            if cropped_regions:
+                logger.debug(
+                    "Cropped regions recorded (%d regions).", len(cropped_regions)
+                )
+
+            # Save model changes
+            update_fields = ["processed_file"]
+            if "anonymized" in self.current_pdf.__dict__:
+                update_fields.append("anonymized")
+            self.current_pdf.save(update_fields=update_fields)
+
+            # Mark state as anonymized immediately; this keeps downstream flows working
+            state = self._ensure_state(self.current_pdf)
+
+            if state and not state.processing_started:
+                state.mark_processing_started()
+
+            logger.info(
+                "Updated processed_file reference to: %s",
+                self.current_pdf.processed_file.name,
+            )
+
+        except Exception as e:
+            logger.warning("Could not set anonymized file reference: %s", e)
+
+    def _finalize_processing(self):
+        """Finalize processing and update state."""
+        if not self.current_pdf:
+            logger.warning("Cannot finalize processing - no report instance available")
+            return
+
+        try:
+            # Update state based on processing results
+            state = self._ensure_state(self.current_pdf)
+
+            if self.processing_context.get("text_extracted") and state:
+                state.mark_anonymized()
+
+            # Mark as ready for validation after successful anonymization
+            if self.processing_context.get("anonymization_completed") and state:
+                state.mark_sensitive_meta_processed()
+                logger.info(
+                    f"report {self.current_pdf.pdf_hash} processing completed - "
+                    f"ready for validation (status: {state.anonymization_status})"
+                )
+
+            # Save all changes
+            with transaction.atomic():
+                self.current_pdf.save()
+                if state:
+                    state.save()
+
+            logger.info("report processing completed successfully")
+        except Exception as e:
+            logger.warning(f"Failed to finalize processing: {e}")
+
+    def _mark_processing_incomplete(self, reason: str):
+        """Mark processing as incomplete with reason."""
+        if not self.current_pdf:
+            logger.warning(
+                f"Cannot mark processing incomplete - no report instance available. Reason: {reason}"
+            )
+            return
+
+        try:
+            state = self._ensure_state(self.current_pdf)
+            if state:
+                state.text_meta_extracted = False
+                state.pdf_meta_extracted = False
+                state.sensitive_meta_processed = False
+                state.save()
+                logger.info(f"Set report state: processed=False due to {reason}")
+
+            # Save changes
+            with transaction.atomic():
+                self.current_pdf.save()
+        except Exception as e:
+            logger.warning(f"Failed to mark processing incomplete: {e}")
+
+    def _retry_existing_pdf(self, existing_pdf):
+        """
+        Retry processing for existing report.
+
+        Uses get_raw_file_path() to find the original raw file instead of
+        relying on the file field which may point to a deleted sensitive file.
+        """
+        try:
+            # ✅ FIX: Use get_raw_file_path() to find original file
+            raw_file_path = existing_pdf.get_raw_file_path()
+
+            if not raw_file_path or not raw_file_path.exists():
+                logger.error(
+                    f"Cannot retry report {existing_pdf.pdf_hash}: Raw file not found. "
+                    f"Please re-upload the original report file."
+                )
+                self.current_pdf = existing_pdf
+                return existing_pdf
+
+            logger.info(f"Found raw file for retry at: {raw_file_path}")
+
+            # Remove from processed files to allow retry
+            file_path_str = str(raw_file_path)
+            if file_path_str in self.processed_files:
+                self.processed_files.remove(file_path_str)
+                logger.debug(f"Removed {file_path_str} from processed files for retry")
+
+            return self.import_and_anonymize(
+                file_path=raw_file_path,  # ✅ Use raw file path, not sensitive path
+                center_name=existing_pdf.center.name
+                if existing_pdf.center
+                else "unknown_center",
+                delete_source=False,  # Never delete during retry
+                retry=True,
+            )
+        except Exception as e:
+            logger.error(
+                f"Failed to re-import existing report {existing_pdf.pdf_hash}: {e}"
+            )
+            self.current_pdf = existing_pdf
+            return existing_pdf
+
+    def _cleanup_on_error(self):
+        """Cleanup processing context on error."""
+        original_path = self.original_path
+        try:
+            if self.current_pdf and hasattr(self.current_pdf, "state"):
+                state = self._ensure_state(self.current_pdf)
+                raw_file_path = self.current_pdf.get_raw_file_path()
+                if raw_file_path is not None and original_path is not None:
+                    # Ensure reprocessing for next attempt by restoring original file
+                    shutil.copy2(str(raw_file_path), str(original_path))
+
+                # Ensure no two files can remain
+                if (
+                    raw_file_path == original_path
+                    and raw_file_path is not None
+                    and original_path is not None
+                ):
+                    os.remove(str(raw_file_path))
+
+                # Remove Lock file also
+                lock_path = Path(str(path_utils.REPORT_DIR) + ".lock")
+                try:
+                    if lock_path.exists():
+                        lock_path.unlink()
+                        logger.info(
+                            "Removed lock file during quarantine: %s", lock_path
+                        )
+                except Exception as e:
+                    logger.warning(
+                        "Could not remove lock file during quarantine: %s", e
+                    )
+
+                if state and self.processing_context.get("processing_started"):
+                    state.text_meta_extracted = False
+                    state.pdf_meta_extracted = False
+                    state.sensitive_meta_processed = False
+                    state.anonymized = False
+                    state.save()
+                    logger.debug("Updated report state to indicate processing failure")
+            else:
+                # 🔧 Early failure: no current_pdf (or no state).
+                # In this case we want to make sure we don't leave stray files
+                # under REPORT_DIR or REPORT_DIR/sensitive.
+
+                pdf_dir = self._get_pdf_dir()
+                if pdf_dir and pdf_dir.exists():
+                    for candidate_dir in (pdf_dir, pdf_dir / "sensitive"):
+                        if candidate_dir.exists():
+                            for candidate in candidate_dir.glob("*.pdf"):
+                                # Don't delete the original ingress file
+                                if (
+                                    original_path is not None
+                                    and candidate.resolve()
+                                    == Path(original_path).resolve()
+                                ):
+                                    continue
+                                try:
+                                    candidate.unlink()
+                                    logger.debug(
+                                        "Removed stray report during early error cleanup: %s",
+                                        candidate,
+                                    )
+                                except Exception as e:
+                                    logger.warning(
+                                        "Failed to remove stray report %s: %s",
+                                        candidate,
+                                        e,
+                                    )
+
+        except Exception as e:
+            logger.warning(f"Error during cleanup: {e}")
+        finally:
+            # Remove any sensitive copy created during this processing run
+            sensitive_created = self.processing_context.get("sensitive_copy_created")
+            if sensitive_created:
+                pdf_obj = self.current_pdf
+                try:
+                    if pdf_obj:
+                        file_field = getattr(pdf_obj, "file", None)
+                        if file_field and getattr(file_field, "name", None):
+                            storage_name = file_field.name
+                            file_field.delete(save=False)
+                            logger.debug(
+                                "Deleted sensitive copy %s during error cleanup",
+                                storage_name,
+                            )
+                except Exception as cleanup_exc:
+                    logger.warning(
+                        "Failed to remove sensitive copy during error cleanup: %s",
+                        cleanup_exc,
+                    )
+                pdf_dir = self._get_pdf_dir()
+                if original_path and pdf_dir:
+                    # Try to remove any extra file that was created during import
+                    # Simplest heuristic: same basename as original, but in pdf dir or pdf/sensitive dir
+                    for candidate_dir in (pdf_dir, pdf_dir / "sensitive"):
+                        candidate = candidate_dir / original_path.name
+                        if candidate.exists() and candidate != original_path:
+                            try:
+                                candidate.unlink()
+                                logger.debug(
+                                    "Removed stray report copy during early error cleanup: %s",
+                                    candidate,
+                                )
+                            except Exception as e:
+                                logger.warning(
+                                    "Failed to remove stray report copy %s: %s",
+                                    candidate,
+                                    e,
+                                )
+
+            # Always clean up processed files set to prevent blocks
+            file_path = self.processing_context.get("file_path")
+            if file_path and str(file_path) in self.processed_files:
+                self.processed_files.remove(str(file_path))
+                logger.debug(
+                    f"Removed {file_path} from processed files during error cleanup"
+                )
+
+            try:
+                raw_dir = (
+                    original_path.parent if isinstance(original_path, Path) else None
+                )
+
+                pdf_dir = self._get_pdf_dir()
+                if not pdf_dir and raw_dir:
+                    base_dir = raw_dir.parent
+                    dir_name = getattr(path_utils, "REPORT_DIR_NAME", "pdfs")
+                    fallback_pdf_dir = base_dir / dir_name
+                    logger.debug(
+                        "report cleanup fallback resolution - base: %s, dir_name: %s, exists: %s",
+                        base_dir,
+                        dir_name,
+                        fallback_pdf_dir.exists(),
+                    )
+                    if fallback_pdf_dir.exists():
+                        pdf_dir = fallback_pdf_dir
+
+                # Remove empty report subdirectories that might have been created during setup
+                if pdf_dir and pdf_dir.exists():
+                    for subdir_name in (
+                        "sensitive",
+                        "cropped_regions",
+                        "anonymized",
+                        "_processing",
+                    ):
+                        subdir_path = pdf_dir / subdir_name
+                        if subdir_path.exists() and subdir_path.is_dir():
+                            try:
+                                next(subdir_path.iterdir())
+                            except StopIteration:
+                                try:
+                                    subdir_path.rmdir()
+                                    logger.debug(
+                                        "Removed empty directory %s during error cleanup",
+                                        subdir_path,
+                                    )
+                                except OSError as rm_err:
+                                    logger.debug(
+                                        "Could not remove directory %s: %s",
+                                        subdir_path,
+                                        rm_err,
+                                    )
+                            except Exception as iter_err:
+                                logger.debug(
+                                    "Could not inspect directory %s: %s",
+                                    subdir_path,
+                                    iter_err,
+                                )
+
+                raw_count = (
+                    len(list(raw_dir.glob("*")))
+                    if raw_dir and raw_dir.exists()
+                    else None
+                )
+                pdf_count = (
+                    len(list(pdf_dir.glob("*")))
+                    if pdf_dir and pdf_dir.exists()
+                    else None
+                )
+
+                sensitive_path = self.processing_context.get("sensitive_file_path")
+                if sensitive_path:
+                    sensitive_parent = Path(sensitive_path).parent
+                    sensitive_count = (
+                        len(list(sensitive_parent.glob("*")))
+                        if sensitive_parent.exists()
+                        else None
+                    )
+                else:
+                    sensitive_dir = pdf_dir / "sensitive" if pdf_dir else None
+                    sensitive_count = (
+                        len(list(sensitive_dir.glob("*")))
+                        if sensitive_dir and sensitive_dir.exists()
+                        else None
+                    )
+
+                logger.info(
+                    "report import error cleanup counts - raw: %s, pdf: %s, sensitive: %s",
+                    raw_count,
+                    pdf_count,
+                    sensitive_count,
+                )
+            except Exception:
+                pass
+
+    def _cleanup_processing_context(self):
+        """Cleanup processing context."""
+        try:
+            # Clean up temporary directories
+            if self.processing_context.get("text_extracted"):
+                crops_dir = path_utils.REPORT_DIR / "cropped_regions"
+                if crops_dir.exists() and not any(crops_dir.iterdir()):
+                    crops_dir.rmdir()
+
+            # Always remove from processed files set after processing attempt
+            file_path = self.processing_context.get("file_path")
+            if file_path and str(file_path) in self.processed_files:
+                self.processed_files.remove(str(file_path))
+                logger.debug(f"Removed {file_path} from processed files set")
+
+        except Exception as e:
+            logger.warning(f"Error during context cleanup: {e}")
+        finally:
+            # Reset context
+            self.current_pdf = None
+            self.processing_context = {}
+
+    def import_simple(
+        self, file_path: Union[Path, str], center_name: str, delete_source: bool = False
+    ) -> "RawPdfFile":
+        """
+        Simple report import without text processing or anonymization.
+        Uses centralized report instance management pattern.
+
+        Args:
+            file_path: Path to the report file to import
+            center_name: Name of the center to associate with report
+            delete_source: Whether to delete the source file after import
+
+        Returns:
+            RawPdfFile instance after basic import
+        """
+        try:
+            # Initialize simple processing context
+            self._initialize_processing_context(
+                file_path, center_name, delete_source, False
+            )
+
+            # Validate file
+            self._validate_and_prepare_file()
+
+            # Create report instance
+            logger.info("Starting simple import - creating RawPdfFile instance...")
+            self.current_pdf = RawPdfFile.create_from_file_initialized(
+                file_path=self.processing_context["file_path"],
+                center_name=center_name,
+                delete_source=delete_source,
+            )
+
+            if not self.current_pdf:
+                raise RuntimeError("Failed to create RawPdfFile instance")
+
+            # Mark as processed
+            self.processed_files.add(str(self.processing_context["file_path"]))
+
+            # Set basic state for simple import
+            state = self._ensure_state(self.current_pdf)
+            if state:
+                state.text_meta_extracted = False
+                state.pdf_meta_extracted = False
+                state.sensitive_meta_processed = False
+                state.save()
+                logger.info("Set report state: processed=False for simple import")
+
+            # Save changes
+            with transaction.atomic():
+                self.current_pdf.save()
+
+            logger.info(
+                "Simple import completed for RawPdfFile hash: %s",
+                self.current_pdf.pdf_hash,
+            )
+            return self.current_pdf
+
+        except Exception as e:
+            logger.error(f"Simple report import failed for {file_path}: {e}")
+            self._cleanup_on_error()
+            raise
+        finally:
+            self._cleanup_processing_context()
+
+    def check_storage_capacity(
+        self, file_path: Union[Path, str], storage_root, min_required_space
+    ) -> bool:
+        """
+        Check if there is sufficient storage capacity for the report file.
+
+        Args:
+            file_path: Path to the report file to check
+
+        Raises:
+            InsufficientStorageError: If there is not enough space
+        """
+        import shutil
+
+        from endoreg_db.exceptions import InsufficientStorageError
+
+        file_path = Path(file_path)
+        if not file_path.exists():
+            raise FileNotFoundError(f"File not found for storage check: {file_path}")
+
+        # Get the size of the file
+        file_size = file_path.stat().st_size
+
+        # Get available space in the storage directory
+
+        total, used, free = shutil.disk_usage(storage_root)
+
+        if file_size:
+            min_required_space = file_size if isinstance(min_required_space, int) else 0
+
+        # Check if there is enough space
+        if file_size > free:
+            raise InsufficientStorageError(
+                f"Not enough space to store report file: {file_path}"
+            )
+        logger.info(
+            f"Storage check passed for {file_path}: {file_size} bytes, {free} bytes available"
+        )
+
+        return True
+
+    def create_sensitive_file(
+        self, pdf_instance: "RawPdfFile", file_path: Union[Path, str]
+    ) -> None:
+        """
+        Create a copy of the report file in the sensitive directory and update the file reference.
+        Delete the source path to avoid duplicates.
+        Uses the central report instance and processing context if parameters not provided.
+
+        Ensures the FileField points to the file under STORAGE_DIR/pdfs/sensitive and never back to raw_pdfs.
+        """
+        pdf_file = pdf_instance or self.current_pdf
+        source_path = (
+            Path(file_path) if file_path else self.processing_context.get("file_path")
+        )
+
+        if not pdf_file:
+            raise ValueError("No report instance available for creating sensitive file")
+        if not source_path:
+            raise ValueError("No file path available for creating sensitive file")
+
+        SENSITIVE_DIR = path_utils.REPORT_DIR / "sensitive"
+        target = SENSITIVE_DIR / f"{pdf_file.pdf_hash}.pdf"
+
+        try:
+            os.makedirs(SENSITIVE_DIR, exist_ok=True)
+
+            # If source already is the target, just ensure FileField points correctly
+            if source_path.resolve() == target.resolve():
+                pass
+            else:
+                # Move the file from ingress to sensitive storage
+                # Using replace semantics when target exists (re-import)
+                if target.exists():
+                    try:
+                        target.unlink()
+                    except Exception as e:
+                        logger.warning(
+                            "Could not remove existing sensitive target %s: %s",
+                            target,
+                            e,
+                        )
+                shutil.move(str(source_path), str(target))
+                logger.info(f"Moved report to sensitive directory: {target}")
+
+            # Update FileField to reference the file under STORAGE_DIR
+            # We avoid re-saving file content (the file is already at target); set .name relative to STORAGE_DIR
+            try:
+                relative_name = str(
+                    target.relative_to(path_utils.STORAGE_DIR)
+                )  # Point Django FileField to sensitive storage
+            except ValueError:
+                # Fallback: if target is not under STORAGE_DIR, store absolute path (not ideal)
+                relative_name = str(target)
+
+            # Only update when changed
+            if getattr(pdf_file.file, "name", None) != relative_name:
+                pdf_file.file.name = relative_name
+                pdf_file.save(update_fields=["file"])
+                logger.info(
+                    "Updated report FileField reference to sensitive path: %s",
+                    pdf_file.file.path,
+                )
+            else:
+                logger.debug(
+                    "report FileField already points to sensitive path: %s",
+                    pdf_file.file.path,
+                )
+
+            # Best-effort: if original source still exists (e.g., copy), remove it to avoid re-triggers
+            try:
+                if source_path.exists() and source_path != target:
+                    os.remove(source_path)
+                    logger.info(
+                        f"Removed original report file at ingress: {source_path}"
+                    )
+            except OSError as e:
+                logger.warning(
+                    f"Could not delete original report file {source_path}: {e}"
+                )
+
+        except Exception as e:
+            logger.warning(
+                f"Could not create sensitive file copy for {pdf_file.pdf_hash}: {e}",
+                exc_info=True,
+            )
+
+    def archive_or_quarantine_file(
+        self,
+        pdf_instance: "RawPdfFile",
+        source_file_path: Union[Path, str],
+        quarantine_reason: str,
+        is_pdf_problematic: bool,
+    ) -> bool:
+        """
+        Archive or quarantine file based on the state of the report processing.
+        Uses the central report instance and processing context if parameters not provided.
+
+        Args:
+            pdf_instance: Optional report instance, defaults to self.current_pdf
+            source_file_path: Optional source file path, defaults to processing_context['file_path']
+            quarantine_reason: Optional quarantine reason, defaults to processing_context['error_reason']
+            is_pdf_problematic: Optional override for problematic state
+
+        Returns:
+            bool: True if file was quarantined, False if archived successfully
+        """
+        pdf_file = pdf_instance or self.current_pdf
+        file_path = (
+            Path(source_file_path)
+            if source_file_path
+            else self.processing_context.get("file_path")
+        )
+        quarantine_reason = str(
+            quarantine_reason or self.processing_context.get("error_reason")
+        )
+
+        if not pdf_file:
+            raise ValueError("No report instance available for archiving/quarantine")
+        if not file_path:
+            raise ValueError("No file path available for archiving/quarantine")
+
+        # Determine if the report is problematic
+        pdf_problematic = (
+            is_pdf_problematic
+            if is_pdf_problematic is not None
+            else pdf_file.is_problematic
+        )
+
+        if pdf_problematic:
+            # Quarantine the file
+            logger.warning(
+                f"Quarantining problematic report: {pdf_file.pdf_hash}, reason: {quarantine_reason}"
+            )
+            quarantine_dir = path_utils.REPORT_DIR / "quarantine"
+            os.makedirs(quarantine_dir, exist_ok=True)
+
+            quarantine_path = quarantine_dir / f"{pdf_file.pdf_hash}.pdf"
+            try:
+                shutil.move(file_path, quarantine_path)
+                pdf_file.save(update_fields=["quarantine_reason"])
+                logger.info(
+                    f"Moved problematic report to quarantine: {quarantine_path}"
+                )
+                return True
+            except Exception as e:
+                logger.error(f"Failed to quarantine report {pdf_file.pdf_hash}: {e}")
+                return (
+                    True  # Still consider as quarantined to prevent further processing
+                )
+        else:
+            # Archive the file normally
+            logger.info(f"Archiving successfully processed report: {pdf_file.pdf_hash}")
+            archive_dir = path_utils.REPORT_DIR / "processed"
+            os.makedirs(archive_dir, exist_ok=True)
+
+            archive_path = archive_dir / f"{pdf_file.pdf_hash}.pdf"
+            try:
+                shutil.move(file_path, archive_path)
+                logger.info(f"Moved processed report to archive: {archive_path}")
+                return False
+            except Exception as e:
+                logger.error(f"Failed to archive report {pdf_file.pdf_hash}: {e}")
+                return False
+
+    def _is_placeholder_value(self, field_name: str, value) -> bool:
+        """Return True if a SensitiveMeta field still has a dummy/default value."""
+        if value is None:
+            return True
+
+        # String placeholders
+        if isinstance(value, str):
+            if value in {
+                self.DEFAULT_PATIENT_FIRST_NAME,
+                self.DEFAULT_PATIENT_LAST_NAME,
+            }:
+                return True
+
+        # Date placeholders
+        if isinstance(value, date):
+            # Default DOB
+            if field_name == "patient_dob" and value == self.DEFAULT_PATIENT_DOB:
+                return True
+            # "Today" exam date created as fallback – allow anonymizer to override
+            if field_name == "examination_date" and value == date.today():
+                return True
+
+        return False