Adapt to handle open-tree-of-life data

Added data_otol/ with script that converts data from 'Open Tree of Life' release 13.4 into a JSON form.
Moved old tree-of-life data and images into data_tol_old/.
Added TolMap type to tol.ts, changed TolNode, and adapted other code to handle it.
Temporarily disabling tile images until image data is added.

1 files changed, 76 insertions, 0 deletions

diff --git a/data_tol_old/txtTreeToJSON.py b/data_tol_old/txtTreeToJSON.py
new file mode 100755
index 0000000..3b77622
--- /dev/null
+++ b/data_tol_old/txtTreeToJSON.py
@@ -0,0 +1,76 @@
+#!/usr/bin/python3
+
+import sys, re
+
+usageInfo =  f"usage: {sys.argv[0]}\n"
+usageInfo += "Reads, from stdin, tab-indented lines representing trees, and outputs corresponding JSON.\n"
+
+if len(sys.argv) > 1:
+	print(usageInfo, file=sys.stderr)
+	sys.exit(1)
+
+lineNum = 0
+trees = [] #each node is a pair holding a name and an array of child nodes
+nodeList = []
+while True: 
+	#read line
+	line = sys.stdin.readline()
+	if line == "": break
+	line = line.rstrip()
+	lineNum += 1
+	#create node
+	match = re.match(r"^\t*", line)
+	indent = len(match.group())
+	newNode = [line[indent:], []]
+	#add node
+	if indent == len(nodeList): #sibling or new tree
+		if len(nodeList) == 0:
+			nodeList.append(newNode)
+			trees.append(newNode)
+		else:
+			nodeList[-1] = newNode
+			if len(nodeList) == 1:
+				trees[-1][1].append(newNode)
+			else:
+				nodeList[-2][1].append(newNode)
+	elif indent == len(nodeList) + 1: #direct child
+		if len(nodeList) == 0:
+			print(f"ERROR: Child without preceding root (line {lineNum})")
+			sys.exit(1)
+		nodeList.append(newNode)
+		nodeList[-2][1].append(newNode)
+	elif indent < len(nodeList): #ancestor sibling or new tree
+		nodeList = nodeList[:indent]
+		if len(nodeList) == 0:
+			nodeList.append(newNode)
+			trees.append(newNode)
+		else:
+			nodeList[-1] = newNode
+			if len(nodeList) == 1:
+				trees[-1][1].append(newNode)
+			else:
+				nodeList[-2][1].append(newNode)
+	else:
+		print(f"ERROR: Child with invalid relative indent (line {lineNum})")
+		sys.exit(1)
+#print as JSON
+if len(trees) > 1:
+	print("[")
+def printNode(node, indent):
+	if len(node[1]) == 0:
+		print(indent + "{\"name\": \"" + node[0] + "\"}", end="")
+	else:
+		print(indent + "{\"name\": \"" + node[0] + "\", \"children\": [")
+		for i in range(len(node[1])):
+			printNode(node[1][i], indent + "\t")
+			if i < len(node[1])-1:
+				print(",", end="")
+			print()
+		print(indent + "]}", end="")
+for i in range(len(trees)):
+	printNode(trees[i], "")
+	if i < len(trees)-1:
+		print(",", end="")
+	print()
+if len(trees) > 1:
+	print("]")