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"""Extract IE-CoR (Indo-European Cognate Relationships) cognate pairs.
Reads sources/iecor/cldf/cognates.csv + forms.csv + languages.csv.
Standard CLDF CognateTable format.
Output: staging/cognate_pairs/iecor_cognate_pairs.tsv (14-column schema)
"""
from __future__ import annotations
import csv
import io
import sys
from collections import defaultdict
from itertools import combinations
from pathlib import Path
sys.stdout = io.TextIOWrapper(sys.stdout.buffer, encoding="utf-8")
sys.stderr = io.TextIOWrapper(sys.stderr.buffer, encoding="utf-8")
ROOT = Path(__file__).resolve().parent.parent
sys.path.insert(0, str(ROOT / "cognate_pipeline" / "src"))
sys.path.insert(0, str(ROOT / "scripts"))
from cognate_pipeline.normalise.sound_class import ipa_to_sound_class # noqa: E402
SOURCES_DIR = ROOT / "sources" / "iecor" / "cldf"
STAGING_DIR = ROOT / "staging" / "cognate_pairs"
STAGING_DIR.mkdir(parents=True, exist_ok=True)
HEADER = (
"Lang_A\tWord_A\tIPA_A\tLang_B\tWord_B\tIPA_B\tConcept_ID\t"
"Relationship\tScore\tSource\tRelation_Detail\tDonor_Language\t"
"Confidence\tSource_Record_ID\n"
)
def sca_similarity(ipa_a: str, ipa_b: str) -> float:
"""Compute normalised Levenshtein similarity on SCA strings."""
try:
sca_a = ipa_to_sound_class(ipa_a)
sca_b = ipa_to_sound_class(ipa_b)
except Exception:
return 0.0
if not sca_a or not sca_b:
return 0.0
m, n = len(sca_a), len(sca_b)
if m == 0 or n == 0:
return 0.0
dp = list(range(n + 1))
for i in range(1, m + 1):
prev = dp[0]
dp[0] = i
for j in range(1, n + 1):
temp = dp[j]
if sca_a[i - 1] == sca_b[j - 1]:
dp[j] = prev
else:
dp[j] = 1 + min(prev, dp[j], dp[j - 1])
prev = temp
dist = dp[n]
return round(1.0 - dist / max(m, n), 4)
def main():
print("=" * 60)
print("IE-CoR Cognate Extraction")
print("=" * 60)
# Step 1: Read languages.csv → Language_ID → ISO code
lang_path = SOURCES_DIR / "languages.csv"
lang_iso = {}
with open(lang_path, "r", encoding="utf-8") as f:
reader = csv.DictReader(f)
for row in reader:
lid = row["ID"]
iso = row.get("ISO639P3code", "").strip()
if iso:
lang_iso[lid] = iso
print(f" Languages with ISO codes: {len(lang_iso)}")
# Step 2: Read parameters.csv for concept glosses
params_path = SOURCES_DIR / "parameters.csv"
param_concept = {}
if params_path.exists():
with open(params_path, "r", encoding="utf-8") as f:
reader = csv.DictReader(f)
for row in reader:
pid = row["ID"]
concept = row.get("Concepticon_Gloss", row.get("Name", pid)).strip()
if concept:
param_concept[pid] = concept
# Step 3: Read forms.csv → Form_ID → {iso, word, ipa, concept}
forms_path = SOURCES_DIR / "forms.csv"
forms = {}
with open(forms_path, "r", encoding="utf-8") as f:
reader = csv.DictReader(f)
for row in reader:
fid = row["ID"]
lid = str(row["Language_ID"])
iso = lang_iso.get(lid, "")
if not iso:
continue
form = row.get("Form", row.get("Value", "")).strip()
if not form:
continue
# IE-CoR has phon_form and Phonemic columns for IPA
ipa = row.get("phon_form", "").strip()
if not ipa:
ipa = row.get("Phonemic", "").strip()
if not ipa:
ipa = form.lower() # fallback to orthographic
param_id = row.get("Parameter_ID", "").strip()
concept = param_concept.get(param_id, param_id)
forms[fid] = {
"iso": iso,
"word": form,
"ipa": ipa,
"concept": concept,
}
print(f" Forms loaded: {len(forms)}")
# Step 4a: Read loans.csv → collect Cognateset_IDs involved in loans
loans_path = SOURCES_DIR / "loans.csv"
loan_cogset_ids: set[str] = set()
if loans_path.exists():
with open(loans_path, "r", encoding="utf-8") as f:
reader = csv.DictReader(f)
for row in reader:
cid = row.get("Cognateset_ID", "").strip()
if cid:
loan_cogset_ids.add(cid)
print(f" Loan-involved cognate sets: {len(loan_cogset_ids)}")
# Step 4b: Read cognates.csv → group by Cognateset_ID
cognates_path = SOURCES_DIR / "cognates.csv"
cogsets: dict[str, list[dict]] = defaultdict(list)
doubt_count = 0
total_rows = 0
with open(cognates_path, "r", encoding="utf-8") as f:
reader = csv.DictReader(f)
for row in reader:
total_rows += 1
form_id = row["Form_ID"]
cogset_id = row["Cognateset_ID"]
doubt = row.get("Doubt", "false").strip().lower() == "true"
if doubt:
doubt_count += 1
form_data = forms.get(form_id)
if form_data is None:
continue
cogsets[cogset_id].append({
**form_data,
"doubt": doubt,
"cogset_id": cogset_id,
})
print(f" Cognate rows: {total_rows}")
print(f" Doubtful: {doubt_count}")
print(f" Cognate sets: {len(cogsets)}")
# Step 5: Generate cross-language pairs
output_path = STAGING_DIR / "iecor_cognate_pairs.tsv"
pair_count = 0
loan_pair_count = 0
inherited_pair_count = 0
with open(output_path, "w", encoding="utf-8") as out:
out.write(HEADER)
for cogset_id, members in cogsets.items():
is_loan = cogset_id in loan_cogset_ids
relation_detail = "loan_involved" if is_loan else "inherited"
for a, b in combinations(members, 2):
if a["iso"] == b["iso"]:
continue
score = sca_similarity(a["ipa"], b["ipa"])
confidence = "doubtful" if (a["doubt"] or b["doubt"]) else "certain"
out.write(
f"{a['iso']}\t{a['word']}\t{a['ipa']}\t"
f"{b['iso']}\t{b['word']}\t{b['ipa']}\t"
f"{a['concept']}\texpert_cognate\t{score}\tiecor\t"
f"{relation_detail}\t-\t{confidence}\t{cogset_id}\n"
)
pair_count += 1
if is_loan:
loan_pair_count += 1
else:
inherited_pair_count += 1
if pair_count % 100000 == 0:
print(f" ... {pair_count:,} pairs written")
print(f"\n Total pairs: {pair_count:,}")
print(f" Loan-involved pairs: {loan_pair_count:,}")
print(f" Purely inherited pairs: {inherited_pair_count:,}")
print(f" Output: {output_path}")
print("=" * 60)
if __name__ == "__main__":
main()
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