#!/usr/bin/python3 import sys, re, os import html, csv, sqlite3 import argparse parser = argparse.ArgumentParser(description=''' Maps nodes to vernacular names, using data from EOL, enwiki, and a picked-names file, and stores results in the database. ''', formatter_class=argparse.RawDescriptionHelpFormatter) args = parser.parse_args() eolNamesFile = 'eol/vernacularNames.csv' enwikiDb = 'enwiki/descData.db' pickedNamesFile = 'pickedNames.txt' dbFile = 'data.db' dbCon = sqlite3.connect(dbFile) dbCur = dbCon.cursor() print('Getting node mappings') nodeToTips = {} eolIdToNode = {} # Maps eol ID to node name (if there are multiple, choose one with most tips) wikiIdToNode = {} for name, tips in dbCur.execute('SELECT name, tips from nodes'): nodeToTips[name] = 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 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('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 names from EOL') # 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 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)) print('Getting names from Wikipedia') 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) != None and name != nodeName and name not in nodeToTips: dbCur.execute('INSERT OR IGNORE INTO names VALUES (?, ?, ?, \'enwiki\')', (nodeName, name, 0)) print('Getting picked names') # File format: # nodename1|altName1|isPreferred1 -> Add an alt-name # nodename1|altName1| -> Remove an alt-name # nodename1|nodeName1| -> Remove any preferred-alt status altNamesToSkip = {} # Maps node names to alt-names to exclude if os.path.exists(pickedNamesFile): with open(pickedNamesFile) as file: for line in file: nodeName, altName, isPreferred = line.lower().rstrip().split('|') if nodeName not in nodeToTips: print(f"Skipping \"{nodeName}\", as no such node exists") continue if isPreferred: isPreferred = 1 if isPreferred == '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 alt_name = ? AND pref_alt = 1' dbCur.execute(cmd, (nodeName, altName)) print('Closing database') dbCon.commit() dbCon.close()