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#!/usr/bin/python3
import sys, re
import csv, sqlite3
usageInfo = f"usage: {sys.argv[0]}\n"
usageInfo += "Reads vernacular-names CSV data (from the Encyclopedia of Life site),\n"
usageInfo += "makes associations with node data in a sqlite database, and writes\n"
usageInfo += "name data to that database.\n"
usageInfo += "\n"
usageInfo += "Expects a CSV header describing lines with format:\n"
usageInfo += " page_id, canonical_form, vernacular_string, language_code,\n"
usageInfo += " resource_name, is_preferred_by_resource, is_preferred_by_eol\n"
if len(sys.argv) > 1:
print(usageInfo, file=sys.stderr)
sys.exit(1)
vnamesFile = "eol/vernacularNames.csv"
dbFile = "data.db"
# Read in vernacular-names data
# Note: Canonical-names may have multiple pids
# Note: A canonical-name's associated pids might all have other associated names
nameToPids = {}
pidToNames = {}
canonicalNameToPids = {}
pidToPreferred = {}
def updateMaps(name, pid, canonical, preferredAlt):
if name not in nameToPids:
nameToPids[name] = {pid}
else:
nameToPids[name].add(pid)
if canonical:
if name not in canonicalNameToPids:
canonicalNameToPids[name] = {pid}
else:
canonicalNameToPids[name].add(pid)
if pid not in pidToNames:
pidToNames[pid] = {name}
else:
pidToNames[pid].add(name)
if preferredAlt:
pidToPreferred[pid] = name
with open(vnamesFile, newline="") as csvfile:
reader = csv.reader(csvfile)
lineNum = 0
for row in reader:
lineNum += 1
if lineNum == 1:
continue
# Parse line
pid = int(row[0])
name1 = re.sub(r"<[^>]+>", "", row[1].lower()) # Remove tags
name2 = row[2].lower()
lang = row[3]
preferred = row[6] == "preferred"
# Add to maps
updateMaps(name1, pid, True, False)
if lang == "eng":
updateMaps(name2, pid, False, preferred)
# Open db connection
dbCon = sqlite3.connect(dbFile)
dbCur = dbCon.cursor()
# Create tables
dbCur.execute("CREATE TABLE names(name TEXT, alt_name TEXT, pref_alt INT, PRIMARY KEY(name, alt_name))")
dbCur.execute("CREATE TABLE eol_ids(id INT PRIMARY KEY, name TEXT)")
# Iterate through 'nodes' table, resolving to canonical-names
usedPids = set()
unresolvedNodeNames = set()
dbCur2 = dbCon.cursor()
iterationNum = 0
for row in dbCur2.execute("SELECT name FROM nodes"):
name = row[0]
iterationNum += 1
if iterationNum % 10000 == 0:
print("Loop 1 iteration {}".format(iterationNum))
# If name matches a canonical-name, add alt-name entries to 'names' table
if name in canonicalNameToPids:
pidToUse = 0
for pid in canonicalNameToPids[name]:
if pid not in usedPids:
pidToUse = pid
break
if pidToUse > 0:
usedPids.add(pidToUse)
altNames = {name}
preferredName = pidToPreferred[pidToUse] if (pidToUse in pidToPreferred) else None
dbCur.execute("INSERT INTO eol_ids VALUES (?, ?)", (pidToUse, name))
for n in pidToNames[pidToUse]:
altNames.add(n)
for n in altNames:
isPreferred = 1 if (n == preferredName) else 0
dbCur.execute("INSERT INTO names VALUES (?, ?, ?)", (name, n, isPreferred))
elif name in nameToPids:
unresolvedNodeNames.add(name)
# Iterate through unresolved nodes, resolving to vernacular-names
iterationNum = 0
for name in unresolvedNodeNames:
iterationNum += 1
if iterationNum % 10000 == 0:
print("Loop 2 iteration {}".format(iterationNum))
# Add alt-name entries to 'names' table for first corresponding pid
pidToUse = 0
for pid in nameToPids[name]:
if pid not in usedPids:
pidToUse = pid
break
if pidToUse > 0:
usedPids.add(pidToUse)
altNames = {name}
preferredName = pidToPreferred[pidToUse] if (pidToUse in pidToPreferred) else None
dbCur.execute("INSERT INTO eol_ids VALUES (?, ?)", (pidToUse, name))
for n in pidToNames[pidToUse]:
altNames.add(n)
for n in altNames:
isPreferred = 1 if (n == preferredName) else 0
dbCur.execute("INSERT INTO names VALUES (?, ?, ?)", (name, n, isPreferred))
# Close db
dbCon.commit()
dbCon.close()
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