Add python type annotations

Also use consistent quote symbols
Also use 'is None' instead of '== None'
Also use 'if list1' instead of 'if len(list1) > 0'

1 files changed, 66 insertions, 67 deletions

diff --git a/backend/tolData/genOtolData.py b/backend/tolData/genOtolData.py
index 6310cc9..d4d6ee8 100755
--- a/backend/tolData/genOtolData.py
+++ b/backend/tolData/genOtolData.py
@@ -1,6 +1,6 @@
 #!/usr/bin/python3
 
-import sys, re, os
+import re, os
 import json, sqlite3
 
 import argparse
@@ -26,16 +26,8 @@ Reads from a picked-names file, if present, which specifies name and node ID pai
 """, formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.parse_args()
 
-treeFile = "otol/labelled_supertree_ottnames.tre" # Had about 2.5e9 nodes
-annFile = "otol/annotations.json"
-dbFile = "data.db"
-nodeMap = {} # Maps node IDs to node objects
-nameToFirstId = {} # Maps node names to first found ID (names might have multiple IDs)
-dupNameToIds = {} # Maps names of nodes with multiple IDs to those IDs
-pickedNamesFile = "pickedOtolNames.txt"
-
 class Node:
-	" Represents a tree-of-life node "
+	' Represents a tree-of-life node '
 	def __init__(self, name, childIds, parentId, tips, pSupport):
 		self.name = name
 		self.childIds = childIds
@@ -43,35 +35,43 @@ class Node:
 		self.tips = tips
 		self.pSupport = pSupport
 
-print("Parsing tree file")
+treeFile = 'otol/labelled_supertree_ottnames.tre' # Had about 2.5e9 nodes
+annFile = 'otol/annotations.json'
+dbFile = 'data.db'
+nodeMap: dict[str, Node] = {} # Maps node IDs to node objects
+nameToFirstId: dict[str, str] = {} # Maps node names to first found ID (names might have multiple IDs)
+dupNameToIds: dict[str, list[str]] = {} # Maps names of nodes with multiple IDs to those IDs
+pickedNamesFile = 'pickedOtolNames.txt'
+
+print('Parsing tree file')
 # Read file
-data = None
+data: str
 with open(treeFile) as file:
 	data = file.read()
 dataIdx = 0
 # Parse content
 iterNum = 0
-def parseNewick():
-	" Parses a node using 'data' and 'dataIdx', updates nodeMap accordingly, and returns the node's ID "
+def parseNewick() -> str:
+	""" Parses a node using 'data' and 'dataIdx', updates nodeMap accordingly, and returns the node's ID """
 	global data, dataIdx, iterNum
 	iterNum += 1
 	if iterNum % 1e5 == 0:
-		print(f"At iteration {iterNum}")
+		print(f'At iteration {iterNum}')
 	# Check for EOF
 	if dataIdx == len(data):
-		raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+		raise Exception(f'ERROR: Unexpected EOF at index {dataIdx}')
 	# Check for node
-	if data[dataIdx] == "(": # parse inner node
+	if data[dataIdx] == '(': # parse inner node
 		dataIdx += 1
-		childIds = []
+		childIds: list[str] = []
 		while True:
 			# Read child
 			childId = parseNewick()
 			childIds.append(childId)
 			if (dataIdx == len(data)):
-				raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+				raise Exception(f'ERROR: Unexpected EOF at index {dataIdx}')
 			# Check for next child
-			if (data[dataIdx] == ","):
+			if (data[dataIdx] == ','):
 				dataIdx += 1
 				continue
 			else:
@@ -94,10 +94,10 @@ def parseNewick():
 		updateNameMaps(name, id)
 		nodeMap[id] = Node(name, [], None, 1, False)
 		return id
-def parseNewickName():
-	" Parses a node name using 'data' and 'dataIdx', and returns a (name, id) pair "
+def parseNewickName() -> tuple[str, str]:
+	""" Parses a node name using 'data' and 'dataIdx', and returns a (name, id) pair """
 	global data, dataIdx
-	name = None
+	name: str
 	end = dataIdx
 	# Get name
 	if (end < len(data) and data[end] == "'"): # Check for quoted name
@@ -114,33 +114,33 @@ def parseNewickName():
 					break
 			end += 1
 		if inQuote:
-			raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+			raise Exception(f'ERROR: Unexpected EOF at index {dataIdx}')
 		name = data[dataIdx:end]
 		dataIdx = end
 	else:
-		while end < len(data) and not re.match(r"[(),]", data[end]):
+		while end < len(data) and not re.match(r'[(),]', data[end]):
 			end += 1
 		if (end == dataIdx):
-			raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+			raise Exception(f'ERROR: Unexpected EOF at index {dataIdx}')
 		name = data[dataIdx:end].rstrip()
 		if end == len(data): # Ignore trailing input semicolon
 			name = name[:-1]
 		dataIdx = end
 	# Convert to (name, id)
 	name = name.lower()
-	if name.startswith("mrca"):
+	if name.startswith('mrca'):
 		return (name, name)
 	elif name[0] == "'":
-		match = re.fullmatch(r"'([^\\\"]+) (ott\d+)'", name)
-		if match == None:
-			raise Exception(f"ERROR: invalid name \"{name}\"")
+		match = re.fullmatch(r"'([^\\\']+) (ott\d+)'", name)
+		if match is None:
+			raise Exception(f'ERROR: invalid name \'{name}\'')
 		name = match.group(1).replace("''", "'")
 		return (name, match.group(2))
 	else:
-		match = re.fullmatch(r"([^\\\"]+)_(ott\d+)", name)
-		if match == None:
-			raise Exception(f"ERROR: invalid name \"{name}\"")
-		return (match.group(1).replace("_", " "), match.group(2))
+		match = re.fullmatch(r"([^\\\']+)_(ott\d+)", name)
+		if match is None:
+			raise Exception(f'ERROR: invalid name \'{name}\'')
+		return (match.group(1).replace('_', ' '), match.group(2))
 def updateNameMaps(name, id):
 	global nameToFirstId, dupNameToIds
 	if name not in nameToFirstId:
@@ -150,18 +150,18 @@ def updateNameMaps(name, id):
 			dupNameToIds[name] = [nameToFirstId[name], id]
 		else:
 			dupNameToIds[name].append(id)
-rootId = parseNewick()
+rootId: str = parseNewick()
 
-print("Resolving duplicate names")
+print('Resolving duplicate names')
 # Read picked-names file
-nameToPickedId = {}
+nameToPickedId: dict[str, str] = {}
 if os.path.exists(pickedNamesFile):
 	with open(pickedNamesFile) as file:
 		for line in file:
-			(name, _, otolId) = line.rstrip().partition("|")
+			name, _, otolId = line.rstrip().partition('|')
 			nameToPickedId[name] = otolId
 # Resolve duplicates
-for (dupName, ids) in dupNameToIds.items():
+for dupName, ids in dupNameToIds.items():
 	# Check for picked id
 	if dupName in nameToPickedId:
 		idToUse = nameToPickedId[dupName]
@@ -174,16 +174,16 @@ for (dupName, ids) in dupNameToIds.items():
 	counter = 2
 	for id in ids:
 		if id != idToUse:
-			nodeMap[id].name += f" [{counter}]"
+			nodeMap[id].name += f' [{counter}]'
 			counter += 1
 
-print("Changing mrca* names")
-def convertMrcaName(id):
+print('Changing mrca* names')
+def convertMrcaName(id: str):
 	node = nodeMap[id]
 	name = node.name
 	childIds = node.childIds
 	if len(childIds) < 2:
-		print(f"WARNING: MRCA node \"{name}\" has less than 2 children")
+		print(f'WARNING: MRCA node \'{name}\' has less than 2 children')
 		return
 	# Get 2 children with most tips
 	childTips = [nodeMap[id].tips for id in childIds]
@@ -195,53 +195,52 @@ def convertMrcaName(id):
 	childName1 = nodeMap[childId1].name
 	childName2 = nodeMap[childId2].name
 	# Check for mrca* child names
-	if childName1.startswith("mrca"):
+	if childName1.startswith('mrca'):
 		childName1 = convertMrcaName(childId1)
-	if childName2.startswith("mrca"):
+	if childName2.startswith('mrca'):
 		childName2 = convertMrcaName(childId2)
 	# Check for composite names
-	match = re.fullmatch(r"\[(.+) \+ (.+)]", childName1)
-	if match != None:
+	match = re.fullmatch(r'\[(.+) \+ (.+)]', childName1)
+	if match is not None:
 		childName1 = match.group(1)
-	match = re.fullmatch(r"\[(.+) \+ (.+)]", childName2)
-	if match != None:
+	match = re.fullmatch(r'\[(.+) \+ (.+)]', childName2)
+	if match is not None:
 		childName2 = match.group(1)
 	# Create composite name
-	node.name = f"[{childName1} + {childName2}]"
+	node.name = f'[{childName1} + {childName2}]'
 	return childName1
-for (id, node) in nodeMap.items():
-	if node.name.startswith("mrca"):
+for id, node in nodeMap.items():
+	if node.name.startswith('mrca'):
 		convertMrcaName(id)
 
-print("Parsing annotations file")
+print('Parsing annotations file')
 # Read file
-data = None
 with open(annFile) as file:
 	data = file.read()
 obj = json.loads(data)
-nodeAnnsMap = obj["nodes"]
+nodeAnnsMap = obj['nodes']
 # Find relevant annotations
-for (id, node) in nodeMap.items():
+for id, node in nodeMap.items():
 	# Set has-support value using annotations
 	if id in nodeAnnsMap:
 		nodeAnns = nodeAnnsMap[id]
-		supportQty = len(nodeAnns["supported_by"]) if "supported_by" in nodeAnns else 0
-		conflictQty = len(nodeAnns["conflicts_with"]) if "conflicts_with" in nodeAnns else 0
+		supportQty = len(nodeAnns['supported_by']) if 'supported_by' in nodeAnns else 0
+		conflictQty = len(nodeAnns['conflicts_with']) if 'conflicts_with' in nodeAnns else 0
 		node.pSupport = supportQty > 0 and conflictQty == 0
 
-print("Creating nodes and edges tables")
+print('Creating nodes and edges tables')
 dbCon = sqlite3.connect(dbFile)
 dbCur = dbCon.cursor()
-dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)")
-dbCur.execute("CREATE INDEX nodes_idx_nc ON nodes(name COLLATE NOCASE)")
-dbCur.execute("CREATE TABLE edges (parent TEXT, child TEXT, p_support INT, PRIMARY KEY (parent, child))")
-dbCur.execute("CREATE INDEX edges_child_idx ON edges(child)")
-for (otolId, node) in nodeMap.items():
-	dbCur.execute("INSERT INTO nodes VALUES (?, ?, ?)", (node.name, otolId, node.tips))
+dbCur.execute('CREATE TABLE nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)')
+dbCur.execute('CREATE INDEX nodes_idx_nc ON nodes(name COLLATE NOCASE)')
+dbCur.execute('CREATE TABLE edges (parent TEXT, child TEXT, p_support INT, PRIMARY KEY (parent, child))')
+dbCur.execute('CREATE INDEX edges_child_idx ON edges(child)')
+for otolId, node in nodeMap.items():
+	dbCur.execute('INSERT INTO nodes VALUES (?, ?, ?)', (node.name, otolId, node.tips))
 	for childId in node.childIds:
 		childNode = nodeMap[childId]
-		dbCur.execute("INSERT INTO edges VALUES (?, ?, ?)",
+		dbCur.execute('INSERT INTO edges VALUES (?, ?, ?)',
 			(node.name, childNode.name, 1 if childNode.pSupport else 0))
-print("Closing database")
+print('Closing database')
 dbCon.commit()
 dbCon.close()