1 files changed, 0 insertions, 240 deletions
diff --git a/backend/tolData/wikidata/genTaxonSrcData.py b/backend/tolData/wikidata/genTaxonSrcData.py
deleted file mode 100755
index 5d10c71..0000000
--- a/backend/tolData/wikidata/genTaxonSrcData.py
+++ /dev/null
@@ -1,240 +0,0 @@
-#!/usr/bin/python3
-
-import sys, os, re, math, io
-from collections import defaultdict
-import bz2, json, sqlite3
-import multiprocessing, indexed_bzip2, pickle, tempfile
-
-import argparse
-parser = argparse.ArgumentParser(description="""
-Reads a wikidata JSON dump, looking for enwiki taxon items, and associated
-IDs from sources like GBIF/etc, and IUCN conservation status. Writes results
-into a database.
-
-The JSON dump contains an array of objects, each of which describes a
-Wikidata item item1, and takes up it's own line.
-- Getting item1's Wikidata ID: item1['id'] (eg: "Q144")
-- Checking if item1 is a taxon: item1['claims']['P31'][idx1]['mainsnak']['datavalue']['value']['numeric-id'] == id1
-	'idx1' indexes an array of statements
-	'id1' is a Wikidata ID denoting a taxon item type (eg: 310890 means 'monotypic taxon')
-- Checking if item1 is a taxon-alt: item1['claims']['P31'][idx1]['mainsnak']['datavalue']['value']['numeric-id'] == id1
-	'id1' denotes a common-name-alternative item type (eg: 55983715 means 'organisms known by a particular common name')
-	Getting the ID of the item that item1 is an alternative for:
-		item1['claims']['P31'][idx1]['qualifiers']['P642'][idx2]['datavalue']['value']['numeric-id']
-- Checking for an EOL/NCBI/etc ID: item['claims'][prop1][idx1]['mainsnak']['datavalue']['value'] (eg: "328672")
-	'prop1' denotes a 'has ID from source *' property (eg: 'P830' means 'has EOL ID')
-- Checking for an IUCN status: item['claims']['P141'][idx1]['mainsnak']['datavalue']['value']['id'] (eg: "Q219127")
-
-Based on code from https://github.com/OneZoom/OZtree, located in
-OZprivate/ServerScripts/TaxonMappingAndPopularity/ (22 Aug 2022).
-""", formatter_class=argparse.RawDescriptionHelpFormatter)
-args = parser.parse_args()
-
-# On Linux, running on the full dataset caused the processes to hang after processing. This was resolved by:
-# - Storing subprocess results in temp files. Apparently passing large objects through pipes can cause deadlock.
-# - Using set_start_method('spawn'). Apparently 'fork' can cause unexpected copying of lock/semaphore/etc state.
-#   Related: https://bugs.python.org/issue6721
-# - Using pool.map() instead of pool.imap_unordered(), which seems to hang in some cases (was using python 3.8).
-#   Possibly related: https://github.com/python/cpython/issues/72882
-
-WD_FILE = 'latest-all.json.bz2'
-OFFSETS_FILE = 'offsets.dat'
-DB_FILE = 'taxonSrcs.db'
-N_PROCS = 6 # Took about 3 hours (probably would've taken 6-12 with N_PROCS=1)
-
-# Wikidata entity IDs
-TAXON_IDS = ['Q16521', 'Q310890', 'Q23038290', 'Q713623'] # 'taxon', 'monotypic taxon', 'fossil taxon', 'clade'
-TAXON_ALT_IDS = ['Q55983715', 'Q502895'] # 'organisms known by a particular common name', 'common name'
-SRC_PROP_IDS = {'P830': 'eol', 'P685': 'ncbi', 'P1391': 'if', 'P850': 'worms', 'P5055': 'irmng', 'P846': 'gbif'}
-IUCN_STATUS_IDS = {
-	'Q211005': 'least concern', 'Q719675': 'near threatened', 'Q278113': 'vulnerable',
-	'Q11394': 'endangered', 'Q219127': 'critically endangered', 'Q239509': 'extinct in the wild',
-	'Q237350': 'extinct species', 'Q3245245': 'data deficient'
-}
-# For filtering lines before parsing JSON
-LINE_REGEX = re.compile(('"numeric-id":(?:' + '|'.join([s[1:] for s in TAXON_IDS + TAXON_ALT_IDS]) + ')\D').encode())
-
-def main() -> None:
-	# Maps to populate
-	srcIdToId: dict[str, dict[int, int]] = defaultdict(dict) # Maps 'eol'/etc to {srcId1: wikidataId1, ...}
-	idToTitle: dict[int, str] = {} # Maps wikidata ID to enwiki title
-	idToAltId: dict[int, int] = {} # Maps taxon-item wikidata ID to taxon-alt ID (eg: 'canis lupus familiaris' -> 'dog')
-	idToIucnStatus: dict[int, str] = {} # Maps wikidata ID to iucn-status string ('least concern', etc)
-	# Check db
-	if os.path.exists(DB_FILE):
-		print('ERROR: Database already exists')
-		sys.exit(1)
-	# Read dump
-	if N_PROCS == 1:
-		with bz2.open(WD_FILE, mode='rb') as file:
-			for lineNum, line in enumerate(file, 1):
-				if lineNum % 1e4 == 0:
-					print(f'At line {lineNum}')
-				readDumpLine(line, srcIdToId, idToTitle, idToAltId, idToIucnStatus)
-	else:
-		if not os.path.exists(OFFSETS_FILE):
-			print('Creating offsets file') # For indexed access for multiprocessing (creation took about 6.7 hours)
-			with indexed_bzip2.open(WD_FILE) as file:
-				with open(OFFSETS_FILE, 'wb') as file2:
-					pickle.dump(file.block_offsets(), file2)
-		print('Allocating file into chunks')
-		fileSz: int # About 1.4 TB
-		with indexed_bzip2.open(WD_FILE) as file:
-			with open(OFFSETS_FILE, 'rb') as file2:
-				file.set_block_offsets(pickle.load(file2))
-				fileSz = file.seek(0, io.SEEK_END)
-		chunkSz = math.floor(fileSz / N_PROCS)
-		chunkIdxs = [-1] + [chunkSz * i for i in range(1, N_PROCS)] + [fileSz-1]
-			# Each adjacent pair specifies a start+end byte index for readDumpChunk()
-		print(f'- Chunk size: {chunkSz:,}')
-		print('Starting processes to read dump')
-		with tempfile.TemporaryDirectory() as tempDirName:
-			# Using maxtasksperchild=1 to free resources on task completion
-			with multiprocessing.Pool(processes=N_PROCS, maxtasksperchild=1) as pool:
-				for outFilename in pool.map(readDumpChunkOneParam,
-					((i, chunkIdxs[i], chunkIdxs[i+1], f'{tempDirName}/{i}.pickle') for i in range(N_PROCS))):
-					# Get map data from subprocess output file
-					with open(outFilename, 'rb') as file:
-						maps = pickle.load(file)
-					# Add to maps
-					for src, idMap in maps[0].items():
-						srcIdToId[src].update(idMap)
-					idToTitle.update(maps[1])
-					idToAltId.update(maps[2])
-					idToIucnStatus.update(maps[3])
-	#
-	print('Writing to db')
-	dbCon = sqlite3.connect(DB_FILE)
-	dbCur = dbCon.cursor()
-	dbCur.execute('CREATE TABLE src_id_to_title (src TEXT, id INT, title TEXT, PRIMARY KEY(src, id))')
-	for src, submap in srcIdToId.items():
-		for srcId, wId in submap.items():
-			if wId not in idToTitle: # Check for a title, possibly via an alt-taxon
-				if wId in idToAltId:
-					wId = idToAltId[wId]
-				else:
-					continue
-			dbCur.execute('INSERT INTO src_id_to_title VALUES (?, ?, ?)', (src, srcId, idToTitle[wId]))
-	dbCur.execute('CREATE TABLE title_iucn (title TEXT PRIMARY KEY, status TEXT)')
-	for wId, status in idToIucnStatus.items():
-		if wId not in idToTitle: # Check for a title, possibly via an alt-taxon
-			if wId in idToAltId and idToAltId[wId] not in idToIucnStatus:
-				wId = idToAltId[wId]
-			else:
-				continue
-		dbCur.execute('INSERT OR IGNORE INTO title_iucn VALUES (?, ?)', (idToTitle[wId], status))
-			# The 'OR IGNORE' allows for multiple taxons using the same alt
-	#dbCur.execute('CREATE TABLE id_to_alt_title (id TEXT PRIMARY KEY, title TEXT, alt TEXT)')
-	#for wId, altId in idToAltId.items():
-	#	dbCur.execute('INSERT INTO id_to_alt_title VALUES (?, ?, ?)',
-	#		(wId, idToTitle[wId] if wId in idToTitle else None, idToTitle[altId]))
-	dbCon.commit()
-	dbCon.close()
-
-def readDumpLine(
-		lineBytes: bytes,
-		srcIdToId: dict[str, dict[int, int]],
-		idToTitle: dict[int, str],
-		idToAltId: dict[int, int],
-		idToIucnStatus: dict[int, str]) -> None:
-	# Check if taxon item
-	if LINE_REGEX.search(lineBytes) is None:
-		return
-	try:
-		line = lineBytes.decode('utf-8').rstrip().rstrip(',')
-		jsonItem = json.loads(line)
-	except json.JSONDecodeError:
-		print(f'Unable to parse line {line} as JSON')
-		return
-	isTaxon = False
-	altTaxa: list[int] = [] # For a taxon-alt item, holds associated taxon-item IDs
-	claims = None
-	try:
-		claims = jsonItem['claims']
-		for statement in claims['P31']: # Check for 'instance of' statements
-			typeId: str = statement['mainsnak']['datavalue']['value']['id']
-			if typeId in TAXON_IDS:
-				isTaxon = True
-				break
-			elif typeId in TAXON_ALT_IDS:
-				snaks = statement['qualifiers']['P642'] # Check for 'of' qualifiers
-				altTaxa.extend([int(s['datavalue']['value']['numeric-id']) for s in snaks])
-				break
-	except (KeyError, ValueError):
-		return
-	if not isTaxon and not altTaxa:
-		return
-	# Get wikidata ID and enwiki title
-	itemId: int | None = None
-	itemTitle: str | None = None
-	try:
-		itemId = int(jsonItem['id'][1:]) # Skips initial 'Q'
-		itemTitle = jsonItem['sitelinks']['enwiki']['title']
-	except KeyError:
-		# Allow taxon-items without titles (they might get one via a taxon-alt)
-		if itemId is not None and isTaxon:
-			itemTitle = None
-		else:
-			return
-	# Update maps
-	if itemTitle is not None:
-		idToTitle[itemId] = itemTitle
-	for altId in altTaxa:
-		idToAltId[altId] = itemId
-	# Check for source IDs
-	for srcPropId, src in SRC_PROP_IDS.items():
-		if srcPropId in claims:
-			try:
-				srcId = int(claims[srcPropId][0]['mainsnak']['datavalue']['value'])
-				srcIdToId[src][srcId] = itemId
-			except (KeyError, ValueError):
-				continue
-	# Check for IUCN status
-	if 'P141' in claims: # Check for 'iucn conservation status' statement
-		try:
-			iucnStatusId: str = claims['P141'][0]['mainsnak']['datavalue']['value']['id']
-			idToIucnStatus[itemId] = IUCN_STATUS_IDS[iucnStatusId]
-		except KeyError:
-			pass
-
-def readDumpChunkOneParam(params: tuple[int, int, int, str]) -> str:
-	""" Forwards to readDumpChunk(), for use with pool.map() """
-	return readDumpChunk(*params)
-
-# Reads lines in the dump that begin after a start-byte, and not after an end byte
-	# If startByte is -1, start at the first line
-def readDumpChunk(procId: int, startByte: int, endByte: int, outFilename: str) -> str:
-	# Maps to populate
-	maps: tuple[
-		dict[str, dict[int, int]],
-		dict[int, str],
-		dict[int, int],
-		dict[int, str]] = (defaultdict(dict), {}, {}, {})
-	# Read dump
-	with indexed_bzip2.open(WD_FILE) as file:
-		# Load offsets file
-		with open(OFFSETS_FILE, 'rb') as file2:
-			offsets = pickle.load(file2)
-			file.set_block_offsets(offsets)
-		# Seek to chunk
-		if startByte != -1:
-			file.seek(startByte)
-			file.readline()
-		else:
-			startByte = 0 # Used for progress calculation
-		# Read lines
-		count = 0
-		while file.tell() <= endByte:
-			count += 1
-			if count % 1e4 == 0:
-				perc = (file.tell() - startByte) / (endByte - startByte) * 100
-				print(f'Thread {procId}: {perc:.2f}%')
-			readDumpLine(file.readline(), *maps)
-	# Output results into file
-	with open(outFilename, 'wb') as file:
-		pickle.dump(maps, file)
-	return outFilename
-
-if __name__ == '__main__': # Guard needed for multiprocessing
-	multiprocessing.set_start_method('spawn')
-	main()