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#!/usr/bin/python3
import sys, re, os
import sqlite3
usageInfo = f"""
Usage: {sys.argv[0]}
Reads a database containing data from Wikipedia, and tries to associate
wiki pages with nodes in the tree-of-life database, and add descriptions for
nodes that don't have them.
"""
if len(sys.argv) > 1:
print(usageInfo, file=sys.stderr)
sys.exit(1)
enwikiDb = "enwiki/descData.db"
dbFile = "data.db"
namesToSkipFile = "pickedEnwikiNamesToSkip.txt"
pickedLabelsFile = "pickedEnwikiLabels.txt"
# Got about 25k descriptions when testing
print("Opening databases")
enwikiCon = sqlite3.connect(enwikiDb)
enwikiCur = enwikiCon.cursor()
dbCon = sqlite3.connect(dbFile)
dbCur = dbCon.cursor()
print("Checking for names to skip")
namesToSkip = set()
if os.path.exists(namesToSkipFile):
with open(namesToSkipFile) as file:
for line in file:
namesToSkip.add(line.rstrip())
print(f"Found {len(namesToSkip)}")
print("Checking for picked-titles")
nameToPickedTitle = {}
if os.path.exists(pickedLabelsFile):
with open(pickedLabelsFile) as file:
for line in file:
(name, _, title) = line.rstrip().partition("|")
nameToPickedTitle[name.lower()] = title
print(f"Found {len(nameToPickedTitle)}")
print("Getting names of nodes without descriptions")
nodeNames = set()
query = "SELECT nodes.name FROM nodes LEFT JOIN wiki_ids ON nodes.name = wiki_ids.name WHERE wiki_ids.id IS NULL"
for (name,) in dbCur.execute(query):
nodeNames.add(name)
print(f"Found {len(nodeNames)}")
nodeNames.difference_update(namesToSkip)
print("Associating nodes with page IDs")
nodeToPageId = {}
iterNum = 0
for name in nodeNames:
iterNum += 1
if iterNum % 1e4 == 0:
print(f"At iteration {iterNum}")
#
if name not in nameToPickedTitle:
row = enwikiCur.execute("SELECT id FROM pages WHERE pages.title = ? COLLATE NOCASE", (name,)).fetchone()
if row != None:
nodeToPageId[name] = row[0]
else:
title = nameToPickedTitle[name]
row = enwikiCur.execute("SELECT id FROM pages WHERE pages.title = ?", (title,)).fetchone()
if row != None:
nodeToPageId[name] = row[0]
else:
print("WARNING: Picked title {title} not found", file=sys.stderr)
print("Resolving redirects")
redirectingNames = set()
iterNum = 0
for (name, pageId) in nodeToPageId.items():
iterNum += 1
if iterNum % 1e3 == 0:
print(f"At iteration {iterNum}")
#
query = "SELECT pages.id FROM redirects INNER JOIN pages ON redirects.target = pages.title WHERE redirects.id = ?"
row = enwikiCur.execute(query, (pageId,)).fetchone()
if row != None:
nodeToPageId[name] = row[0]
redirectingNames.add(name)
print("Adding description data")
iterNum = 0
for (name, pageId) in nodeToPageId.items():
iterNum += 1
if iterNum % 1e3 == 0:
print(f"At iteration {iterNum}")
#
row = enwikiCur.execute("SELECT desc FROM descs where descs.id = ?", (pageId,)).fetchone()
if row != None:
dbCur.execute("INSERT INTO wiki_ids VALUES (?, ?, ?)", (name, pageId, 1 if name in redirectingNames else 0))
dbCur.execute("INSERT OR IGNORE INTO descs VALUES (?, ?, ?)", (pageId, row[0], 0))
print("Closing databases")
dbCon.commit()
dbCon.close()
enwikiCon.close()
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