Make backend dev server script serve the image files

Previously, image files in backend/data/img were moved to, or
symlinked from, public/. This needed to be changed before each
build, otherwise vite would end up copying gigabytes of images.

1 files changed, 250 insertions, 0 deletions

diff --git a/backend/tolData/genOtolData.py b/backend/tolData/genOtolData.py
new file mode 100755
index 0000000..b5e0055
--- /dev/null
+++ b/backend/tolData/genOtolData.py
@@ -0,0 +1,250 @@
+#!/usr/bin/python3
+
+import sys, re, os
+import json, sqlite3
+
+usageInfo = f"""
+Usage: {sys.argv[0]}
+
+Reads files describing a tree-of-life from an 'Open Tree of Life' release,
+and stores tree information in a database.
+
+Reads a labelled_supertree_ottnames.tre file, which is assumed to have this format:
+    The tree-of-life is represented in Newick format, which looks like: (n1,n2,(n3,n4)n5)n6
+		The root node is named n6, and has children n1, n2, and n5.
+    Name examples include: Homo_sapiens_ott770315, mrcaott6ott22687, 'Oxalis san-miguelii ott5748753', 
+		'ott770315' and 'mrcaott6ott22687' are node IDs. The latter is for a 'compound node'.
+		The node with ID 'ott770315' will get the name 'homo sapiens'.
+		A compound node will get a name composed from it's sub-nodes (eg: [name1 + name2]).
+	It is possible for multiple nodes to have the same name.
+		In these cases, extra nodes will be named sequentially, as 'name1 [2]', 'name1 [3]', etc.
+Reads an annotations.json file, which is assumed to have this format:
+    Holds a JSON object, whose 'nodes' property maps node IDs to objects holding information about that node,
+    such as the properties 'supported_by' and 'conflicts_with', which list phylogenetic trees that
+	support/conflict with the node's placement.
+Reads from a picked-names file, if present, which specifies name and node ID pairs.
+	These help resolve cases where multiple nodes share the same name.
+"""
+if len(sys.argv) > 1:
+	print(usageInfo, file=sys.stderr)
+	sys.exit(1)
+
+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 "
+	def __init__(self, name, childIds, parentId, tips, pSupport):
+		self.name = name
+		self.childIds = childIds
+		self.parentId = parentId
+		self.tips = tips
+		self.pSupport = pSupport
+
+print("Parsing tree file")
+# Read file
+data = None
+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 "
+	global data, dataIdx, iterNum
+	iterNum += 1
+	if iterNum % 1e5 == 0:
+		print(f"At iteration {iterNum}")
+	# Check for EOF
+	if dataIdx == len(data):
+		raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+	# Check for node
+	if data[dataIdx] == "(": # parse inner node
+		dataIdx += 1
+		childIds = []
+		while True:
+			# Read child
+			childId = parseNewick()
+			childIds.append(childId)
+			if (dataIdx == len(data)):
+				raise Exception(f"ERROR: Unexpected EOF at index {dataIdx}")
+			# Check for next child
+			if (data[dataIdx] == ","):
+				dataIdx += 1
+				continue
+			else:
+				# Get node name and id
+				dataIdx += 1 # Consume an expected ')'
+				name, id = parseNewickName()
+				updateNameMaps(name, id)
+				# Get child num-tips total
+				tips = 0
+				for childId in childIds:
+					tips += nodeMap[childId].tips
+				# Add node to nodeMap
+				nodeMap[id] = Node(name, childIds, None, tips, False)
+				# Update childrens' parent reference
+				for childId in childIds:
+					nodeMap[childId].parentId = id
+				return id
+	else: # Parse node name
+		name, id = parseNewickName()
+		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 "
+	global data, dataIdx
+	name = None
+	end = dataIdx
+	# Get name
+	if (end < len(data) and data[end] == "'"): # Check for quoted name
+		end += 1
+		inQuote = True
+		while end < len(data):
+			if (data[end] == "'"):
+				if end + 1 < len(data) and data[end + 1] == "'": # Account for '' as escaped-quote
+					end += 2
+					continue
+				else:
+					end += 1
+					inQuote = False
+					break
+			end += 1
+		if inQuote:
+			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]):
+			end += 1
+		if (end == 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"):
+		return (name, name)
+	elif name[0] == "'":
+		match = re.fullmatch(r"'([^\\\"]+) (ott\d+)'", name)
+		if match == 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))
+def updateNameMaps(name, id):
+	global nameToFirstId, dupNameToIds
+	if name not in nameToFirstId:
+		nameToFirstId[name] = id
+	else:
+		if name not in dupNameToIds:
+			dupNameToIds[name] = [nameToFirstId[name], id]
+		else:
+			dupNameToIds[name].append(id)
+rootId = parseNewick()
+
+print("Resolving duplicate names")
+# Read picked-names file
+nameToPickedId = {}
+if os.path.exists(pickedNamesFile):
+	with open(pickedNamesFile) as file:
+		for line in file:
+			(name, _, otolId) = line.rstrip().partition("|")
+			nameToPickedId[name] = otolId
+# Resolve duplicates
+for (dupName, ids) in dupNameToIds.items():
+	# Check for picked id
+	if dupName in nameToPickedId:
+		idToUse = nameToPickedId[dupName]
+	else:
+		# Get conflicting node with most tips
+		tipNums = [nodeMap[id].tips for id in ids]
+		maxIdx = tipNums.index(max(tipNums))
+		idToUse = ids[maxIdx]
+	# Adjust name of other conflicting nodes
+	counter = 2
+	for id in ids:
+		if id != idToUse:
+			nodeMap[id].name += f" [{counter}]"
+			counter += 1
+
+print("Changing mrca* names")
+def convertMrcaName(id):
+	node = nodeMap[id]
+	name = node.name
+	childIds = node.childIds
+	if len(childIds) < 2:
+		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]
+	maxIdx1 = childTips.index(max(childTips))
+	childTips[maxIdx1] = 0
+	maxIdx2 = childTips.index(max(childTips))
+	childId1 = childIds[maxIdx1]
+	childId2 = childIds[maxIdx2]
+	childName1 = nodeMap[childId1].name
+	childName2 = nodeMap[childId2].name
+	# Check for mrca* child names
+	if childName1.startswith("mrca"):
+		childName1 = convertMrcaName(childId1)
+	if childName2.startswith("mrca"):
+		childName2 = convertMrcaName(childId2)
+	# Check for composite names
+	match = re.fullmatch(r"\[(.+) \+ (.+)]", childName1)
+	if match != None:
+		childName1 = match.group(1)
+	match = re.fullmatch(r"\[(.+) \+ (.+)]", childName2)
+	if match != None:
+		childName2 = match.group(1)
+	# Create composite name
+	node.name = f"[{childName1} + {childName2}]"
+	return childName1
+for (id, node) in nodeMap.items():
+	if node.name.startswith("mrca"):
+		convertMrcaName(id)
+
+print("Parsing annotations file")
+# Read file
+data = None
+with open(annFile) as file:
+	data = file.read()
+obj = json.loads(data)
+nodeAnnsMap = obj["nodes"]
+# Find relevant annotations
+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
+		node.pSupport = supportQty > 0 and conflictQty == 0
+
+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))
+	for childId in node.childIds:
+		childNode = nodeMap[childId]
+		dbCur.execute("INSERT INTO edges VALUES (?, ?, ?)",
+			(node.name, childNode.name, 1 if childNode.pSupport else 0))
+print("Closing database")
+dbCon.commit()
+dbCon.close()