Expected duration: 1 day or less The objective is to build a structured blood test database that allows pathology results to be viewed, edited, filtered, and exported to Excel via a web-based HTML interface. The system stores results in a clean, standardised format so trends can be analysed accurately over time.
Using AI-assisted OCR, I have built a local Python extraction pipeline that converts PDF pathology reports into machine-readable text and inserts structured data into a SQLite database. The majority of blood tests extract correctly, including canonical test name, result value, unit, and reference range.
However, I have reached a specific technical issue with three markers:
• CRP (C-reactive protein) • ESR • GLU (Glucose)
The OCR output clearly contains the correct lines, and debug logs confirm they are processed. Yet no rows are inserted for these markers.
The failure appears to occur between canonical matching, numeric extraction, or validation logic.
Current System Architecture
The system runs locally and consists of:
• extraction_core_2.py (main engine) • Supporting modules for OCR preprocessing, lab dictionary building, regex matching, and validation • SQLite backend • Schema-driven canonical lab dictionary • Controlled fuzzy fallback logic • HTML viewer for results display and Excel export
Pipeline flow:
Convert PDF to image (pdf2image)
Preprocess
Run Tesseract OCR
Clean and normalise text
Match against canonical lab dictionary
Extract:
canonical test name
numeric result
unit
reference range
Validate
Insert into SQLite
The engine is deterministic and rule-based.
The Specific Problem
Example OCR line:
CRP H 5.2 mg/L 0-5
OCR text is correct. NUMBER_PATTERN matches. The canonical dictionary contains the test.
Yet:
Inserted 0 rows from 0126251OrderReport_23B00006604_CRP.pdf
Likely failure points include:
• Canonical containment match failing due to normalisation • Flag tokens (“H”, “L”) interfering with numeric capture • Numeric extraction anchored incorrectly • Validation rejecting due to strict range formatting • Unit pattern mismatch (e.g. mmol/L) • Dictionary indexing issue • Match overridden by another lab name • Guard conditions too strict
If validation fails, the row is rejected silently.
All other panels extract correctly. The issue appears isolated.
This is a focused debugging and refinement request. I have spent many hours attempting to isolate the issue and now require an experienced developer to identify the blocking condition and implement a practical fix.
I have been advised this should take 1–2 hours for a senior developer.
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