#!/usr/bin/python3 """ Maps nodes to vernacular names, using data from EOL, enwiki, and a picked-names file, and stores results in the database. """ import argparse import re import os import html import csv import sqlite3 EOL_NAMES_FILE = os.path.join('eol', 'vernacularNames.csv') ENWIKI_DB = os.path.join('enwiki', 'desc_data.db') PICKED_NAMES_FILE = 'picked_names.txt' DB_FILE = 'data.db' def genData(eolNamesFile: str, enwikiDb: str, pickedNamesFile: str, dbFile: str) -> None: """ Reads the files and adds to db """ dbCon = sqlite3.connect(dbFile) dbCur = dbCon.cursor() print('Creating table') dbCur.execute('CREATE TABLE names(name TEXT, alt_name TEXT, pref_alt INT, src TEXT, PRIMARY KEY(name, alt_name))') dbCur.execute('CREATE INDEX names_idx ON names(name)') dbCur.execute('CREATE INDEX names_alt_idx ON names(alt_name)') dbCur.execute('CREATE INDEX names_alt_idx_nc ON names(alt_name COLLATE NOCASE)') print('Getting node mappings') nodeToTips: dict[str, int] = {} for name, tips in dbCur.execute('SELECT name, tips from nodes'): nodeToTips[name] = tips addEolNames(eolNamesFile, nodeToTips, dbCur) addEnwikiNames(enwikiDb, nodeToTips, dbCur) addPickedNames(pickedNamesFile, nodeToTips, dbCur) print('Closing database') dbCon.commit() dbCon.close() def addEolNames(eolNamesFile: str, nodeToTips: dict[str, int], dbCur: sqlite3.Cursor) -> None: """ Reads EOL names, associates them with otol nodes, and writes to db """ # The CSV file has a header line, then lines with these fields: # page_id, canonical_form (canonical name, not always unique to page ID), # vernacular_string (vernacular name), language_code, # resource_name, is_preferred_by_resource, is_preferred_by_eol print('Getting EOL mappings') eolIdToNode: dict[int, str] = {} # Maps eol ID to node name (if there are multiple, choose one with most tips) for name, eolId in dbCur.execute('SELECT name, id from eol_ids'): if eolId not in eolIdToNode or nodeToTips[eolIdToNode[eolId]] < nodeToTips[name]: eolIdToNode[eolId] = name print('Adding names from EOL') namesToSkip = {'unknown', 'unknown species', 'unidentified species'} with open(eolNamesFile, newline='') as file: for lineNum, fields in enumerate(csv.reader(file), 1): if lineNum % 1e5 == 0: print(f'At line {lineNum}') # Reached about 2.8e6 # Skip header line if lineNum == 1: continue # Parse line eolId = int(fields[0]) name = html.unescape(fields[2]).lower() lang = fields[3] isPreferred = 1 if fields[6] == 'preferred' else 0 # Add to db if eolId in eolIdToNode and name not in namesToSkip and name not in nodeToTips \ and lang == 'eng' and len(name.split(' ')) <= 3: # Ignore names with >3 words cmd = 'INSERT OR IGNORE INTO names VALUES (?, ?, ?, \'eol\')' # The 'OR IGNORE' accounts for duplicate lines dbCur.execute(cmd, (eolIdToNode[eolId], name, isPreferred)) def addEnwikiNames(enwikiDb: str, nodeToTips: dict[str, int], dbCur: sqlite3.Cursor) -> None: """ Reads enwiki names, associates them with otol nodes, and writes to db """ print('Getting enwiki mappings') wikiIdToNode: dict[int, str] = {} for name, wikiId in dbCur.execute('SELECT name, id from wiki_ids'): if wikiId not in wikiIdToNode or nodeToTips[wikiIdToNode[wikiId]] < nodeToTips[name]: wikiIdToNode[wikiId] = name print('Adding names from enwiki') altNameRegex = re.compile(r'[a-z]+') # Avoids names like 'evolution of elephants', 'banana fiber', 'fish (zoology)', enwikiCon = sqlite3.connect(enwikiDb) enwikiCur = enwikiCon.cursor() iterNum = 0 for wikiId, nodeName in wikiIdToNode.items(): iterNum += 1 if iterNum % 1e4 == 0: print(f'At iteration {iterNum}') # Reached about 3.6e5 query = 'SELECT p1.title FROM pages p1' \ ' INNER JOIN redirects r1 ON p1.id = r1.id' \ ' INNER JOIN pages p2 ON r1.target = p2.title WHERE p2.id = ?' for (name,) in enwikiCur.execute(query, (wikiId,)): name = name.lower() if altNameRegex.fullmatch(name) is not None and name != nodeName and name not in nodeToTips: dbCur.execute('INSERT OR IGNORE INTO names VALUES (?, ?, ?, \'enwiki\')', (nodeName, name, 0)) def addPickedNames(pickedNamesFile: str, nodeToTips: dict[str, int], dbCur: sqlite3.Cursor) -> None: # File format: # nodename1|altName1|isPreferred1 -> Add an alt-name # nodename1|altName1| -> Remove an alt-name # nodename1|nodeName1| -> Remove any preferred-alt status if os.path.exists(pickedNamesFile): print('Getting picked names') with open(pickedNamesFile) as file: for line in file: nodeName, altName, isPreferredStr = line.lower().rstrip().split('|') if nodeName not in nodeToTips: print(f'Skipping "{nodeName}", as no such node exists') continue if isPreferredStr: isPreferred = 1 if isPreferredStr == '1' else 0 if isPreferred == 1: # Remove any existing preferred-alt status cmd = 'UPDATE names SET pref_alt = 0 WHERE name = ? AND alt_name = ? AND pref_alt = 1' dbCur.execute(cmd, (nodeName, altName)) # Remove any existing record dbCur.execute('DELETE FROM names WHERE name = ? AND alt_name = ?', (nodeName, altName)) # Add record dbCur.execute('INSERT INTO names VALUES (?, ?, ?, "picked")', (nodeName, altName, isPreferred)) elif nodeName != altName: # Remove any matching record dbCur.execute('DELETE FROM names WHERE name = ? AND alt_name = ?', (nodeName, altName)) else: # Remove any preferred-alt status cmd = 'UPDATE names SET pref_alt = 0 WHERE name = ? AND pref_alt = 1' dbCur.execute(cmd, (nodeName,)) if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) args = parser.parse_args() genData(EOL_NAMES_FILE, ENWIKI_DB, PICKED_NAMES_FILE, DB_FILE)