europemedqa / source /processed_csv /build_edn_csvs.py
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#!/usr/bin/env python3
"""Parse EDN France exam PDFs (CNG annales 2023-2025) into question/answer CSVs.
Reads pdftotext -layout text dumps, splits stems/questions, extracts choices,
links embedded figures, writes one CSV per year.
No answer key exists (official CNG PDFs are questions-only; community
corrections are platform-locked) -> correct_answer left empty.
"""
import csv, os, re, sys
try:
import fitz
HAVE_FITZ = True
except ImportError:
HAVE_FITZ = False
SRC = os.path.expanduser('~/workspace/medical-ai-leaderboard-staging/repo/data/updates_raw/edn_france')
TXTDIR = '/tmp/edn_txt'
OUTDIR = os.path.expanduser('~/workspace/medical-ai-leaderboard-staging/repo/data/processed_csv')
IMGDIR = os.path.join(OUTDIR, 'images')
import subprocess as _sp
# (year, paper_label, pdf_rel, txt_name)
PAPERS_TXT = [
('2023', 'P1', '2023/EDN_P1.pdf', '2023_EDN_P1.txt'),
('2023', 'P2', '2023/EDN_P2.pdf', '2023_EDN_P2.txt'),
('2023', 'P3', '2023/EDN_P3.pdf', '2023_EDN_P3.txt'),
('2023', 'LCA', '2023/lca/EDN_LCA_P.pdf', '2023_LCA.txt'),
('2024', 'P1', '2024/EDN_P1.pdf', '2024_EDN_P1.txt'),
('2024', 'P2', '2024/EDN_P2.pdf', '2024_EDN_P2.txt'),
('2024', 'P3', '2024/EDN_P3.pdf', '2024_EDN_P3.txt'),
('2024', 'LCA', '2024/lca/EDN_LCA_P.pdf', '2024_LCA.txt'),
('2025', 'R1', '2025/EDN_P1_reserve.pdf', '2025_EDN_P1.txt'),
('2025', 'P2', '2025/EDN_P2.pdf', '2025_EDN_P2.txt'),
('2025', 'P3', '2025/EDN_P3.pdf', '2025_EDN_P3.txt'),
('2025', 'LCA', '2025/lca/EDN_LCA_P.pdf', '2025_LCA.txt'),
]
def ensure_text():
os.makedirs(TXTDIR, exist_ok=True)
for year, paper, pdf_rel, txt_name in PAPERS_TXT:
dest = os.path.join(TXTDIR, txt_name)
if not os.path.exists(dest):
_sp.run(['pdftotext', '-layout', os.path.join(SRC, pdf_rel), dest], check=True)
# (year, paper_label, pdf_name)
PAPERS = [
('2023', 'P1', 'EDN_P1.pdf'), ('2023', 'P2', 'EDN_P2.pdf'), ('2023', 'P3', 'EDN_P3.pdf'),
('2023', 'LCA', 'lca/EDN_LCA_P.pdf'),
('2024', 'P1', 'EDN_P1.pdf'), ('2024', 'P2', 'EDN_P2.pdf'), ('2024', 'P3', 'EDN_P3.pdf'),
('2024', 'LCA', 'lca/EDN_LCA_P.pdf'),
('2025', 'R1', 'EDN_P1_reserve.pdf'), ('2025', 'P2', 'EDN_P2.pdf'), ('2025', 'P3', 'EDN_P3.pdf'),
('2025', 'LCA', 'lca/EDN_LCA_P.pdf'),
]
PDFMAP = {(y, p): f'{y}/{pdf}' for y, p, pdf in PAPERS}
MIN_DIM = 100 # min(w,h) for a figure worth extracting (<100 = UI decoration)
RE_STEM = re.compile(r'^(KFP|DP|QI|TCS|LCA) (\d+)\s*$')
RE_Q = re.compile(r'^Question (\d+) - (.+?)\s*$')
RE_FOOTER = re.compile(r'^Epreuve .*?\b(\d+)/(\d+)\s*$')
RE_TITLE = re.compile(r'^\s*Epreuve de .*$')
RE_PROP = re.compile(r'^ {1,12}Proposition ([A-P])\s*$')
RE_REPONSE = re.compile(r'^\s*Réponse\s*:\s*$')
RE_FIN = re.compile(r'--- Fin de copie ---')
RE_ZONELABEL = re.compile(r'^\s*(\d+)\s*-\s*(.*?)\s*$')
LIKERT = ['Très peu probable', 'Peu probable', 'Ni plus ni moins', 'Probable', 'Très probable']
IMG_KW = re.compile(
r'ci-dessous|ci-dessus|'
r'\b(figures?|images?|clichés?|photos?|schémas?|tracés?|courbes?)\b|'
r'\b(ECG|électrocardiogrammes?)\b|'
r'\b(radiographies?|scanners?|scanographies?|coupes?)\b|'
r'\bradio\b',
re.I)
issues = [] # (year, paper, qid, message)
def clean(s):
s = re.sub(r'\s+', ' ', s).strip()
return s
def join_lines(lines):
"""Join wrapped layout lines; trailing '-' = hyphenation -> concat directly."""
out = ''
for ln in lines:
ln = ln.strip()
if not ln:
continue
if out.endswith('-'):
out += ln
else:
out = (out + ' ' + ln).strip() if out else ln
return clean(out)
def parse_paper(year, paper, txt_path):
raw = open(txt_path, encoding='utf-8').read().replace('\f', '\n')
lines = raw.split('\n')
questions = []
page = 1
stem = None # (type, num)
stem_text_lines = [] # vignette text between stem header and its first question
cur = None # current question dict
q_pages = []
def flush():
nonlocal cur
if cur is not None:
finalize(cur)
questions.append(cur)
cur = None
def finalize(q):
# split body into question text vs choices
body = q['body'] # list of (line, page)
text_lines, choices, zone_labels = [], [], []
mode = 'text'
cur_letter, cur_clines = None, []
likert_done = False
in_legend = False # QZP: inside figure zone-label legend
for ln, pg in body:
if RE_FIN.search(ln):
break
# QZP figure legend: "N - label" lines (label may wrap onto following lines)
if q['is_qzp'] and mode == 'text':
mz = RE_ZONELABEL.match(ln)
if mz:
zone_labels.append([mz.group(1), clean(mz.group(2))])
in_legend = True
continue
if in_legend and ln.strip():
zone_labels[-1][1] = (zone_labels[-1][1] + ' ' + clean(ln)).strip()
continue
mp = RE_PROP.match(ln)
if mp and mode == 'text':
# start of choices
if cur_letter:
choices.append((cur_letter, join_lines(cur_clines)))
cur_letter, cur_clines = mp.group(1), []
mode = 'choices'
continue
if mode == 'text' and RE_REPONSE.match(ln):
mode = 'reponse' # QROC answer area: ignore rest
continue
if mode == 'text' and 'Très peu probable' in ln and 'Très probable' in ln:
parts = [p.strip() for p in re.split(r'\s{2,}', ln.strip()) if p.strip()]
if len(parts) >= 5:
choices.extend([(chr(65 + i), parts[i]) for i in range(5)])
else: # fallback: fixed labels
choices.extend([(chr(65 + i), LIKERT[i]) for i in range(5)])
likert_done = True
mode = 'likert'
continue
if mode == 'choices':
if mp: # next proposition
choices.append((cur_letter, join_lines(cur_clines)))
cur_letter, cur_clines = mp.group(1), []
else:
cur_clines.append(ln)
continue
if mode == 'reponse':
continue
if mode == 'likert':
continue
text_lines.append(ln)
if cur_letter:
choices.append((cur_letter, join_lines(cur_clines)))
q['choices'] = choices
q['text'] = join_lines(text_lines)
if zone_labels:
zl = '; '.join(f'{n} - {t}' for n, t in zone_labels)
q['text'] = (q['text'] + f' [Zones de la figure : {zl}]').strip()
q['pages'] = sorted(set(q_pages))
for ln in lines:
if RE_FIN.search(ln):
flush()
break
mf = RE_FOOTER.match(ln)
if mf:
page = int(mf.group(1))
continue
if RE_TITLE.match(ln):
continue
ms = RE_STEM.match(ln)
if ms:
flush()
stem = (ms.group(1), ms.group(2))
stem_text_lines = []
continue
mq = RE_Q.match(ln)
if mq:
flush()
fmt = mq.group(2)
cur = {'sub': int(mq.group(1)), 'format': fmt, 'body': [],
'stem': stem, 'start_page': page,
'stem_text': join_lines(stem_text_lines),
'is_qzp': 'zone à pointer' in fmt}
q_pages = [page]
continue
if cur is not None:
if ln.strip() == '':
cur['body'].append(('', page))
else:
cur['body'].append((ln, page))
q_pages.append(page)
elif stem is not None and ln.strip():
stem_text_lines.append(ln)
flush()
# assign ids
for q in questions:
st, sn = q['stem'] if q['stem'] else ('NA', '0')
q['qid'] = f"edn{year}_{paper}_{st}{sn}_q{q['sub']}"
return questions
def extract_images(year, paper, pdf_rel):
"""Save embedded figures (min dim >= MIN_DIM, skip title page). Returns {1-idx page: [fnames]}."""
page_map, saved = {}, {}
if not HAVE_FITZ:
return page_map, 0
d = fitz.open(os.path.join(SRC, pdf_rel))
outdir = os.path.join(IMGDIR, f'edn_france_{year}')
os.makedirs(outdir, exist_ok=True)
for pno, page in enumerate(d):
if pno == 0:
continue # title page: EDN banner
for img in page.get_images(full=True):
xref, w, h = img[0], img[2], img[3]
if min(w, h) < MIN_DIM:
continue
if xref not in saved:
fname = f'edn_france_{year}_{paper}_p{pno + 1:03d}_xref{xref}.png'
try:
pix = fitz.Pixmap(d, xref)
if pix.n > 4:
pix = fitz.Pixmap(fitz.csRGB, pix)
# skip blank/uniform images (masks, empty placeholders)
s = pix.samples
step = max(1, len(s) // 4000)
vals = s[::step]
if max(vals) - min(vals) < 12:
continue
pix.save(os.path.join(outdir, fname))
except Exception as e:
issues.append((year, paper, f'image save failed {fname}: {e}'))
continue
saved[xref] = fname
page_map.setdefault(pno + 1, [])
if saved[xref] not in page_map[pno + 1]:
page_map[pno + 1].append(saved[xref])
d.close()
return page_map, len(saved)
def link_images(year, paper, pdf_rel, qs):
page_map, n_saved = extract_images(year, paper, pdf_rel)
linked = 0
claimed = {} # image fname -> stem key of question that claimed it
for q in qs:
cands = []
for pg in q['pages'] + [max(q['pages']) + 1]:
cands.extend(page_map.get(pg, []))
cands = list(dict.fromkeys(cands))
needs = q['is_qzp'] or IMG_KW.search(q['text'] or '') or IMG_KW.search(q.get('stem_text') or '')
if needs:
stemkey = q['stem']
# prefer a figure not already claimed by a *different* stem
# (sub-questions of one stem legitimately share a figure)
pick = None
for c in cands:
if claimed.get(c, stemkey) == stemkey:
pick = c
break
if pick is None and cands:
pick = cands[0]
if pick:
q['image_file'] = pick
claimed.setdefault(pick, stemkey)
linked += 1
else:
issues.append((year, q['qid'],
'QZP but no figure found' if q['is_qzp'] else 'image keyword but no figure found'))
else:
q['image_file'] = ''
return n_saved, linked
def main():
ensure_text()
all_q = {}
img_stats = {}
for year, paper, pdf_rel, txt_name in PAPERS_TXT:
txt = os.path.join(TXTDIR, txt_name)
qs = parse_paper(year, paper, txt)
n_saved, linked = link_images(year, paper, pdf_rel, qs)
img_stats[(year, paper)] = (n_saved, linked)
all_q.setdefault(year, []).extend(qs)
print(f'{year} {paper}: {len(qs)} questions, {n_saved} images, {linked} linked')
# write CSVs
cols = ['exam_id', 'question_number', 'question_id', 'question_text',
'choice_a', 'choice_b', 'choice_c', 'choice_d', 'choice_e',
'correct_answer', 'image_file', 'language', 'country', 'year']
for year in ('2023', '2024', '2025'):
qs = all_q[year]
path = os.path.join(OUTDIR, f'edn_france_{year}.csv')
with open(path, 'w', encoding='utf-8', newline='') as fh:
w = csv.writer(fh)
w.writerow(cols)
for i, q in enumerate(qs, 1):
ch = {letter: text for letter, text in q['choices']}
if len(q['choices']) > 5:
issues.append((year, q['qid'], f"{len(q['choices'])} proposals; kept A-E, dropped {len(q['choices'])-5}"))
if not q['choices'] and not q['is_qzp'] and 'ouverte' not in q['format'] and 'concordance' not in q['format']:
issues.append((year, q['qid'], f"no choices parsed (format: {q['format']})"))
if not q['text']:
issues.append((year, q['qid'], 'empty question text'))
w.writerow([
f'edn_france_{year}', i, q['qid'], q['text'],
ch.get('A', ''), ch.get('B', ''), ch.get('C', ''),
ch.get('D', ''), ch.get('E', ''),
'', # correct_answer: no key exists
q.get('image_file', ''),
'fr', 'France', year,
])
print(f'wrote {path}: {len(qs)} rows')
print('\nISSUES:', len(issues))
for it in issues[:60]:
print(it)
with open(os.path.join(OUTDIR, 'edn_france_build_issues.log'), 'w', encoding='utf-8') as fh:
fh.write(f'total issues: {len(issues)}\n')
for it in issues:
fh.write(repr(it) + '\n')
print('full issue list -> edn_france_build_issues.log')
if __name__ == '__main__':
main()