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, 52 insertions, 50 deletions

diff --git a/backend/tolData/genLinkedImgs.py b/backend/tolData/genLinkedImgs.py
index eb991b9..6d2feff 100755
--- a/backend/tolData/genLinkedImgs.py
+++ b/backend/tolData/genLinkedImgs.py
@@ -1,6 +1,6 @@
 #!/usr/bin/python3
 
-import sys, re
+import re
 import sqlite3
 
 import argparse
@@ -10,113 +10,115 @@ associate them with images from their children
 """, formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.parse_args()
 
-dbFile = "data.db"
-compoundNameRegex = re.compile(r"\[(.+) \+ (.+)]")
+dbFile = 'data.db'
+compoundNameRegex = re.compile(r'\[(.+) \+ (.+)]')
 upPropagateCompoundImgs = False
 
-print("Opening databases")
+print('Opening databases')
 dbCon = sqlite3.connect(dbFile)
 dbCur = dbCon.cursor()
-dbCur.execute("CREATE TABLE linked_imgs (name TEXT PRIMARY KEY, otol_ids TEXT)")
+dbCur.execute('CREATE TABLE linked_imgs (name TEXT PRIMARY KEY, otol_ids TEXT)')
 
-print("Getting nodes with images")
-resolvedNodes = {} # Will map node names to otol IDs with a usable image
-query = "SELECT nodes.name, nodes.id FROM nodes INNER JOIN node_imgs ON nodes.name = node_imgs.name"
-for (name, otolId) in dbCur.execute(query):
+print('Getting nodes with images')
+resolvedNodes: dict[str, str] = {} # Will map node names to otol IDs with a usable image
+query = 'SELECT nodes.name, nodes.id FROM nodes INNER JOIN node_imgs ON nodes.name = node_imgs.name'
+for name, otolId in dbCur.execute(query):
 	resolvedNodes[name] = otolId
-print(f"Found {len(resolvedNodes)}")
+print(f'Found {len(resolvedNodes)}')
 
-print("Iterating through nodes, trying to resolve images for ancestors")
-nodesToResolve = {} # Maps a node name to a list of objects that represent possible child images
-processedNodes = {} # Map a node name to an OTOL ID, representing a child node whose image is to be used
-parentToChosenTips = {} # Used to prefer images from children with more tips
+print('Iterating through nodes, trying to resolve images for ancestors')
+nodesToResolve: dict[str, list[dict[str, str | int | None]]] = {}
+	# Maps a node name to a list of objects that represent possible child images
+processedNodes: dict[str, str] = {} # Map a node name to an OTOL ID, representing a child node whose image is to be used
+parentToChosenTips: dict[str, int] = {} # Used to prefer images from children with more tips
 iterNum = 0
-while len(resolvedNodes) > 0:
+while resolvedNodes:
 	iterNum += 1
 	if iterNum % 1e3 == 0:
-		print(f"At iteration {iterNum}")
+		print(f'At iteration {iterNum}')
 	# Get next node
-	(nodeName, otolId) = resolvedNodes.popitem()
+	nodeName, otolId = resolvedNodes.popitem()
 	processedNodes[nodeName] = otolId
 	# Traverse upwards, resolving ancestors if able
 	while True:
 		# Get parent
-		row = dbCur.execute("SELECT parent FROM edges WHERE child = ?", (nodeName,)).fetchone()
-		if row == None or row[0] in processedNodes or row[0] in resolvedNodes:
+		row = dbCur.execute('SELECT parent FROM edges WHERE child = ?', (nodeName,)).fetchone()
+		if row is None or row[0] in processedNodes or row[0] in resolvedNodes:
 			break
-		parent = row[0]
+		parent: str = row[0]
 		# Get parent data
 		if parent not in nodesToResolve:
-			childNames = [row[0] for row in dbCur.execute("SELECT child FROM edges WHERE parent = ?", (parent,))]
-			query = "SELECT name, tips FROM nodes WHERE name IN ({})".format(",".join(["?"] * len(childNames)))
-			childObjs = [{"name": row[0], "tips": row[1], "otolId": None} for row in dbCur.execute(query, childNames)]
-			childObjs.sort(key=lambda x: x["tips"], reverse=True)
+			childNames: list[str] = [
+				row[0] for row in dbCur.execute('SELECT child FROM edges WHERE parent = ?', (parent,))]
+			query = 'SELECT name, tips FROM nodes WHERE name IN ({})'.format(','.join(['?'] * len(childNames)))
+			childObjs = [{'name': row[0], 'tips': row[1], 'otolId': None} for row in dbCur.execute(query, childNames)]
+			childObjs.sort(key=lambda x: x['tips'], reverse=True)
 			nodesToResolve[parent] = childObjs
 		else:
 			childObjs = nodesToResolve[parent]
 		# Check if highest-tips child
-		if (childObjs[0]["name"] == nodeName):
+		if childObjs[0]['name'] == nodeName:
 			# Resolve parent, and continue from it
-			dbCur.execute("INSERT INTO linked_imgs VALUES (?, ?)", (parent, otolId))
+			dbCur.execute('INSERT INTO linked_imgs VALUES (?, ?)', (parent, otolId))
 			del nodesToResolve[parent]
 			processedNodes[parent] = otolId
-			parentToChosenTips[parent] = childObjs[0]["tips"]
+			parentToChosenTips[parent] = childObjs[0]['tips']
 			nodeName = parent
 			continue
 		else:
 			# Mark child as a potential choice
-			childObj = next(c for c in childObjs if c["name"] == nodeName)
-			childObj["otolId"] = otolId
+			childObj = next(c for c in childObjs if c['name'] == nodeName)
+			childObj['otolId'] = otolId
 			break
 	# When out of resolved nodes, resolve nodesToResolve nodes, possibly adding more nodes to resolve
-	if len(resolvedNodes) == 0:
-		for (name, childObjs) in nodesToResolve.items():
-			childObj = next(c for c in childObjs if c["otolId"] != None)
-			resolvedNodes[name] = childObj["otolId"]
-			parentToChosenTips[name] = childObj["tips"]
-			dbCur.execute("INSERT INTO linked_imgs VALUES (?, ?)", (name, childObj["otolId"]))
+	if not resolvedNodes:
+		for name, childObjs in nodesToResolve.items():
+			childObj = next(c for c in childObjs if c['otolId'] is not None)
+			resolvedNodes[name] = childObj['otolId']
+			parentToChosenTips[name] = childObj['tips']
+			dbCur.execute('INSERT INTO linked_imgs VALUES (?, ?)', (name, childObj['otolId']))
 		nodesToResolve.clear()
 
-print("Replacing linked-images for compound nodes")
+print('Replacing linked-images for compound nodes')
 iterNum = 0
 for nodeName in processedNodes.keys():
 	iterNum += 1
 	if iterNum % 1e4 == 0:
-		print(f"At iteration {iterNum}")
+		print(f'At iteration {iterNum}')
 	#
 	match = compoundNameRegex.fullmatch(nodeName)
-	if match != None:
+	if match is not None:
 		# Replace associated image with subname images
-		(subName1, subName2) = match.group(1,2)
-		otolIdPair = ["", ""]
+		subName1, subName2 = match.group(1,2)
+		otolIdPair = ['', '']
 		if subName1 in processedNodes:
 			otolIdPair[0] = processedNodes[subName1]
 		if subName2 in processedNodes:
 			otolIdPair[1] = processedNodes[subName2]
 		# Use no image if both subimages not found
-		if otolIdPair[0] == "" and otolIdPair[1] == "":
-			dbCur.execute("DELETE FROM linked_imgs WHERE name = ?", (nodeName,))
+		if otolIdPair[0] == '' and otolIdPair[1] == '':
+			dbCur.execute('DELETE FROM linked_imgs WHERE name = ?', (nodeName,))
 			continue
 		# Add to db
-		dbCur.execute("UPDATE linked_imgs SET otol_ids = ? WHERE name = ?",
-			(otolIdPair[0] + "," + otolIdPair[1], nodeName))
+		dbCur.execute('UPDATE linked_imgs SET otol_ids = ? WHERE name = ?',
+			(otolIdPair[0] + ',' + otolIdPair[1], nodeName))
 		# Possibly repeat operation upon parent/ancestors
 		if upPropagateCompoundImgs:
 			while True:
 				# Get parent
-				row = dbCur.execute("SELECT parent FROM edges WHERE child = ?", (nodeName,)).fetchone()
-				if row != None:
+				row = dbCur.execute('SELECT parent FROM edges WHERE child = ?', (nodeName,)).fetchone()
+				if row is not None:
 					parent = row[0]
 					# Check num tips
-					(numTips,) = dbCur.execute("SELECT tips from nodes WHERE name = ?", (nodeName,)).fetchone()
+					(numTips,) = dbCur.execute('SELECT tips from nodes WHERE name = ?', (nodeName,)).fetchone()
 					if parent in parentToChosenTips and parentToChosenTips[parent] <= numTips:
 						# Replace associated image
-						dbCur.execute("UPDATE linked_imgs SET otol_ids = ? WHERE name = ?",
-							(otolIdPair[0] + "," + otolIdPair[1], parent))
+						dbCur.execute('UPDATE linked_imgs SET otol_ids = ? WHERE name = ?',
+							(otolIdPair[0] + ',' + otolIdPair[1], parent))
 						nodeName = parent
 						continue
 				break
 
-print("Closing databases")
+print('Closing databases')
 dbCon.commit()
 dbCon.close()