Convert server code to CGI scriptdeployable

Also adjust server-client API, for clarity/consistency

2 files changed, 132 insertions, 145 deletions

diff --git a/backend/README.md b/backend/README.md
index 20263fd..3efa585 100644
--- a/backend/README.md
+++ b/backend/README.md
@@ -1,3 +1,8 @@
 # Files
--   server.py: Runs the server
--   data/: For generating the server's tree-of-life database
+-   cgi-bin/data.py: CGI script for providing tree-of-life data to client
+-   data: Contains scripts for generating the tree-of-life database
+
+# During development
+Having generated the database as data/data.db, and with this as the current
+directory, running `python3 -m http.server --cgi 8000` allows the client to access
+the CGI script, and hence the database, via `localhost:8000/cgi-bin/data.py`.
diff --git a/backend/server.py b/backend/cgi-bin/data.py
index a1f1585..05ed81b 100755
--- a/backend/server.py
+++ b/backend/cgi-bin/data.py
@@ -1,15 +1,12 @@
 #!/usr/bin/python3
 
-import sys, re, sqlite3, time
-import os.path
-from http.server import HTTPServer, BaseHTTPRequestHandler
+import sys, os.path, re, time
 import urllib.parse
+import sqlite3
 import gzip, jsonpickle
 
-hostname = "localhost"
-port = 8000
 dbFile = "data/data.db"
-imgDir = "../public/img/"
+imgDir = "data/img/"
 DEFAULT_SUGG_LIM = 5
 MAX_SUGG_LIM = 50
 CORS_ANY_ORIGIN = True # Used during development to avoid Cross-Origin Resource Sharing restrictions
@@ -17,16 +14,19 @@ CORS_ANY_ORIGIN = True # Used during development to avoid Cross-Origin Resource
 usageInfo = f"""
 Usage: {sys.argv[0]}
 
-Starts a server that listens for GET requests to http://" + hostname + ":" + str(port) + ".
-Responds to path+query /data/type1?name=name1 with JSON data.
-The 'name' parameter can be omitted, which specifies the root node.
-An additional query parameter tree=reduced is usable to get reduced-tree data.
+CGI script that provides tree-of-life data, in JSON form.
 
-If type1 is 'node': Responds with a name-to-TolNode map, describing the node and it's children.
-If type1 is 'chain': Like 'node', but also gets nodes upward to the root, and their direct children.
-If type1 is 'search': Responds with a SearchSuggResponse.
-    A query parameter 'limit=n1' specifies the max number of suggestions (default 5).
-If type1 is 'info': Responds with an InfoResponse.
+Query parameters:
+- name: Provides a name, or partial name, of a tree-of-life node. If absent, the root node is used.
+- type: Specifies what data to reply with.
+    If 'node', reply with a name-to-TolNode map, describing the named node and it's children.
+    If 'sugg', reply with a SearchSuggResponse, describing search suggestions for the possibly-partial name.
+    If 'info', reply with an InfoResponse, describing the named node.
+- toroot: Used with type=node, and causes inclusion of nodes upward to the root, and their children.
+    If specified, the value should be 'true'.
+- limit: Used with type=sugg to specify the max number of suggestions.
+- rtree: Specifies whether the reduced tree should be used.
+    If specified, the value should be 'true'.
 """
 if len(sys.argv) > 1:
 	print(usageInfo, file=sys.stderr)
@@ -49,7 +49,7 @@ class SearchSugg:
 		self.name = name                   # string
 		self.canonicalName = canonicalName # string | null
 class SearchSuggResponse:
-	" Sent as responses to 'search' requests "
+	" Sent as responses to 'sugg' requests "
 	def __init__(self, searchSuggs, hasMore):
 		self.suggs = searchSuggs # SearchSugg[]
 		self.hasMore = hasMore   # boolean
@@ -81,54 +81,45 @@ class InfoResponse:
 		self.nodeInfo = nodeInfo         # NodeInfo
 		self.subNodesInfo = subNodesInfo # [] | [NodeInfo, NodeInfo]
 
-# Connect to db
-dbCon = sqlite3.connect(dbFile)
-# Get root node
-dbCur = dbCon.cursor()
-query = "SELECT name FROM nodes LEFT JOIN edges ON nodes.name = edges.child WHERE edges.parent IS NULL LIMIT 1"
-(rootName,) = dbCur.execute(query).fetchone()
-
-# Some helper functions
-def lookupNodes(names, useReducedTree):
+# For data lookup
+def lookupNodes(names, useReducedTree, dbCur):
 	" For a set of node names, returns a name-to-TolNode map that describes those nodes "
-	global dbCon
-	cur = dbCon.cursor()
 	# Get node info
 	nameToNodes = {}
 	nodesTable = "nodes" if not useReducedTree else "r_nodes"
 	edgesTable = "edges" if not useReducedTree else "r_edges"
 	queryParamStr = ",".join(["?"] * len(names))
 	query = f"SELECT name, id, tips FROM {nodesTable} WHERE name IN ({queryParamStr})"
-	for (nodeName, otolId, tips) in cur.execute(query, names):
+	for (nodeName, otolId, tips) in dbCur.execute(query, names):
 		nameToNodes[nodeName] = TolNode(otolId, [], tips=tips)
 	# Get child info
 	query = f"SELECT parent, child FROM {edgesTable} WHERE parent IN ({queryParamStr})"
-	for (nodeName, childName) in cur.execute(query, names):
+	for (nodeName, childName) in dbCur.execute(query, names):
 		nameToNodes[nodeName].children.append(childName)
 	# Order children by tips
 	for (nodeName, node) in nameToNodes.items():
 		childToTips = {}
 		query = "SELECT name, tips FROM {} WHERE name IN ({})"
 		query = query.format(nodesTable, ",".join(["?"] * len(node.children)))
-		for (n, tips) in cur.execute(query, node.children):
+		for (n, tips) in dbCur.execute(query, node.children):
 			childToTips[n] = tips
 		node.children.sort(key=lambda n: childToTips[n], reverse=True)
 	# Get parent info
 	query = f"SELECT parent, child, p_support FROM {edgesTable} WHERE child IN ({queryParamStr})"
-	for (nodeName, childName, pSupport) in cur.execute(query, names):
+	for (nodeName, childName, pSupport) in dbCur.execute(query, names):
 		nameToNodes[childName].parent = nodeName
 		nameToNodes[childName].pSupport = (pSupport == 1)
 	# Get image names
 	idsToNames = {nameToNodes[n].otolId: n for n in nameToNodes.keys()}
 	query = "SELECT nodes.id from nodes INNER JOIN node_imgs ON nodes.name = node_imgs.name" \
 		" WHERE nodes.id IN ({})".format(",".join(["?"] * len(idsToNames)))
-	for (otolId,) in cur.execute(query, list(idsToNames.keys())):
+	for (otolId,) in dbCur.execute(query, list(idsToNames.keys())):
 		nameToNodes[idsToNames[otolId]].imgName = otolId + ".jpg"
 	# Get 'linked' images for unresolved names
 	unresolvedNames = [n for n in nameToNodes if nameToNodes[n].imgName == None]
 	query = "SELECT name, otol_ids from linked_imgs WHERE name IN ({})"
 	query = query.format(",".join(["?"] * len(unresolvedNames)))
-	for (name, otolIds) in cur.execute(query, unresolvedNames):
+	for (name, otolIds) in dbCur.execute(query, unresolvedNames):
 		if "," not in otolIds:
 			nameToNodes[name].imgName = otolIds + ".jpg"
 		else:
@@ -139,14 +130,12 @@ def lookupNodes(names, useReducedTree):
 			]
 	# Get preferred-name info
 	query = f"SELECT name, alt_name FROM names WHERE pref_alt = 1 AND name IN ({queryParamStr})"
-	for (name, altName) in cur.execute(query, names):
+	for (name, altName) in dbCur.execute(query, names):
 		nameToNodes[name].commonName = altName
 	#
 	return nameToNodes
-def lookupName(searchStr, suggLimit, useReducedTree):
+def lookupSuggs(searchStr, suggLimit, useReducedTree, dbCur):
 	" For a search string, returns a SearchSuggResponse describing search suggestions "
-	global dbCon
-	cur = dbCon.cursor()
 	results = []
 	hasMore = False
 	# Get node names and alt-names
@@ -164,21 +153,21 @@ def lookupName(searchStr, suggLimit, useReducedTree):
 			" WHERE alt_name LIKE ? ORDER BY length(alt_name) LIMIT ?"
 	# Join results, and get shortest
 	suggs = []
-	for (nodeName,) in cur.execute(query1, (searchStr + "%", suggLimit + 1)):
+	for (nodeName,) in dbCur.execute(query1, (searchStr + "%", suggLimit + 1)):
 		suggs.append(SearchSugg(nodeName))
-	for (altName, nodeName) in cur.execute(query2, (searchStr + "%", suggLimit + 1)):
+	for (altName, nodeName) in dbCur.execute(query2, (searchStr + "%", suggLimit + 1)):
 		suggs.append(SearchSugg(altName, nodeName))
 	# If insufficient results, try substring-search
 	foundNames = {n.name for n in suggs}
 	if len(suggs) < suggLimit:
 		newLim = suggLimit + 1 - len(suggs)
-		for (nodeName,) in cur.execute(query1, ("%" + searchStr + "%", newLim)):
+		for (nodeName,) in dbCur.execute(query1, ("%" + searchStr + "%", newLim)):
 			if nodeName not in foundNames:
 				suggs.append(SearchSugg(nodeName))
 				foundNames.add(nodeName)
 	if len(suggs) < suggLimit:
 		newLim = suggLimit + 1 - len(suggs)
-		for (altName, nodeName) in cur.execute(query2, ("%" + searchStr + "%", suggLimit + 1)):
+		for (altName, nodeName) in dbCur.execute(query2, ("%" + searchStr + "%", suggLimit + 1)):
 			if altName not in foundNames:
 				suggs.append(SearchSugg(altName, nodeName))
 				foundNames.add(altName)
@@ -191,12 +180,10 @@ def lookupName(searchStr, suggLimit, useReducedTree):
 		hasMore = True
 	#
 	return SearchSuggResponse(results, hasMore)
-def lookupNodeInfo(name, useReducedTree):
+def lookupInfo(name, useReducedTree, dbCur):
 	" For a node name, returns an InfoResponse, or None "
-	global dbCon
-	cur = dbCon.cursor()
 	# Get node info
-	nameToNodes = lookupNodes([name], useReducedTree)
+	nameToNodes = lookupNodes([name], useReducedTree, dbCur)
 	tolNode = nameToNodes[name] if name in nameToNodes else None
 	if tolNode == None:
 		return None
@@ -204,7 +191,7 @@ def lookupNodeInfo(name, useReducedTree):
 	match = re.fullmatch(r"\[(.+) \+ (.+)]", name)
 	subNames = [match.group(1), match.group(2)] if match != None else []
 	if len(subNames) > 0:
-		nameToSubNodes = lookupNodes(subNames, useReducedTree)
+		nameToSubNodes = lookupNodes(subNames, useReducedTree, dbCur)
 		if len(nameToSubNodes) < 2:
 			print(f"ERROR: Unable to find sub-names entries for {name}", file=sys.stderr)
 			return None
@@ -215,7 +202,7 @@ def lookupNodeInfo(name, useReducedTree):
 	query = "SELECT name, desc, wiki_id, redirected, from_dbp FROM" \
 		" wiki_ids INNER JOIN descs ON wiki_ids.id = descs.wiki_id" \
 		" WHERE wiki_ids.name IN ({})".format(",".join(["?"] * len(namesToLookup)))
-	for (nodeName, desc, wikiId, redirected, fromDbp) in cur.execute(query, namesToLookup):
+	for (nodeName, desc, wikiId, redirected, fromDbp) in dbCur.execute(query, namesToLookup):
 		nameToDescInfo[nodeName] = DescInfo(desc, wikiId, redirected == 1, fromDbp == 1)
 	# Get image info
 	nameToImgInfo = {}
@@ -225,7 +212,7 @@ def lookupNodeInfo(name, useReducedTree):
 		" nodes INNER JOIN node_imgs ON nodes.name = node_imgs.name" \
 		" INNER JOIN images ON node_imgs.img_id = images.id AND node_imgs.src = images.src" \
 		" WHERE nodes.id IN ({})".format(",".join(["?"] * len(idsToLookup)))
-	for (id, imgId, imgSrc, url, license, artist, credit) in cur.execute(query, idsToLookup):
+	for (id, imgId, imgSrc, url, license, artist, credit) in dbCur.execute(query, idsToLookup):
 		nameToImgInfo[idsToNames[id]] = ImgInfo(imgId, imgSrc, url, license, artist, credit)
 	# Construct response
 	nodeInfoObjs = [
@@ -237,102 +224,97 @@ def lookupNodeInfo(name, useReducedTree):
 	]
 	return InfoResponse(nodeInfoObjs[0], nodeInfoObjs[1:])
 
-class DbServer(BaseHTTPRequestHandler):
-	" Provides handlers for requests to the server "
-	def do_GET(self):
-		global rootName
-		# Parse URL
-		urlParts = urllib.parse.urlparse(self.path)
-		path = urllib.parse.unquote(urlParts.path)
-		queryDict = urllib.parse.parse_qs(urlParts.query)
-		# Check first element of path
-		match = re.match(r"/([^/]+)/(.+)", path)
-		if match != None and match.group(1) == "data" and \
-			("tree" not in queryDict or queryDict["tree"][0] == "reduced"):
-			reqType = match.group(2)
-			name = queryDict["name"][0] if "name" in queryDict else rootName
-			useReducedTree = "tree" in queryDict
-			# Check query string
-			if reqType == "node":
-				tolNodes = lookupNodes([name], useReducedTree)
-				if len(tolNodes) > 0:
-					tolNode = tolNodes[name]
-					childNodeObjs = lookupNodes(tolNode.children, useReducedTree)
-					childNodeObjs[name] = tolNode
-					self.respondJson(childNodeObjs)
-					return
-			elif reqType == "chain":
-				results = {}
-				ranOnce = False
-				while True:
-					# Get node
-					tolNodes = lookupNodes([name], useReducedTree)
-					if len(tolNodes) == 0:
-						if not ranOnce:
-							self.respondJson(results)
-							return
-						print(f"ERROR: Parent-chain node {name} not found", file=sys.stderr)
-						break
-					tolNode = tolNodes[name]
-					results[name] = tolNode
-					# Potentially add children
+# For handling request
+def respondJson(val):
+	content = jsonpickle.encode(val, unpicklable=False).encode("utf-8")
+	print("Content-type: application/json")
+	if "HTTP_ACCEPT_ENCODING" in os.environ and "gzip" in os.environ["HTTP_ACCEPT_ENCODING"]:
+		if len(content) > 100:
+			content = gzip.compress(content, compresslevel=5)
+			print(f"Content-length: {len(content)}")
+			print(f"Content-encoding: gzip")
+	if CORS_ANY_ORIGIN:
+		print("Access-Control-Allow-Origin: *")
+	print()
+	sys.stdout.flush()
+	sys.stdout.buffer.write(content)
+def handleReq(dbCur):
+	# Get query params
+	queryStr = os.environ["QUERY_STRING"] if "QUERY_STRING" in os.environ else ""
+	queryDict = urllib.parse.parse_qs(queryStr)
+	# Set vars from params
+	name = queryDict["name"][0] if "name" in queryDict else None
+	if name == None: # Get root node
+		query = "SELECT name FROM nodes LEFT JOIN edges ON nodes.name = edges.child WHERE edges.parent IS NULL LIMIT 1"
+		(name,) = dbCur.execute(query).fetchone()
+	reqType = queryDict["type"][0] if "type" in queryDict else None
+	useReducedTree = "rtree" in queryDict and queryDict["rtree"][0] == "true"
+	# Get data of requested type
+	if reqType == "node":
+		toroot = "toroot" in queryDict and queryDict["toroot"][0] == "true"
+		if not toroot:
+			tolNodes = lookupNodes([name], useReducedTree, dbCur)
+			if len(tolNodes) > 0:
+				tolNode = tolNodes[name]
+				childNodeObjs = lookupNodes(tolNode.children, useReducedTree, dbCur)
+				childNodeObjs[name] = tolNode
+				respondJson(childNodeObjs)
+				return
+		else:
+			results = {}
+			ranOnce = False
+			while True:
+				# Get node
+				tolNodes = lookupNodes([name], useReducedTree, dbCur)
+				if len(tolNodes) == 0:
 					if not ranOnce:
-						ranOnce = True
-					else:
-						childNamesToAdd = []
-						for childName in tolNode.children:
-							if childName not in results:
-								childNamesToAdd.append(childName)
-						childNodeObjs = lookupNodes(childNamesToAdd, useReducedTree)
-						results.update(childNodeObjs)
-					# Check if root
-					if tolNode.parent == None:
-						self.respondJson(results)
+						respondJson(results)
 						return
-					else:
-						name = tolNode.parent
-			elif reqType == "search":
-				# Check for suggestion-limit
-				suggLimit = None
-				invalidLimit = False
-				try:
-					suggLimit = int(queryDict["limit"][0]) if "limit" in queryDict else DEFAULT_SUGG_LIM
-					if suggLimit <= 0 or suggLimit > MAX_SUGG_LIM:
-						invalidLimit = True
-				except ValueError:
-					invalidLimit = True
-					print(f"Invalid limit {suggLimit}")
-				# Get search suggestions
-				if not invalidLimit:
-					self.respondJson(lookupName(name, suggLimit, useReducedTree))
-					return
-			elif reqType == "info":
-				infoResponse = lookupNodeInfo(name, useReducedTree)
-				if infoResponse != None:
-					self.respondJson(infoResponse)
+					print(f"ERROR: Parent-chain node {name} not found", file=sys.stderr)
+					break
+				tolNode = tolNodes[name]
+				results[name] = tolNode
+				# Potentially add children
+				if not ranOnce:
+					ranOnce = True
+				else:
+					childNamesToAdd = []
+					for childName in tolNode.children:
+						if childName not in results:
+							childNamesToAdd.append(childName)
+					childNodeObjs = lookupNodes(childNamesToAdd, useReducedTree, dbCur)
+					results.update(childNodeObjs)
+				# Check if root
+				if tolNode.parent == None:
+					respondJson(results)
 					return
-		self.send_response(404)
-	def respondJson(self, val):
-		global CORS_ANY_ORIGIN
-		content = jsonpickle.encode(val, unpicklable=False).encode("utf-8")
-		self.send_response(200)
-		self.send_header("Content-type", "application/json")
-		if CORS_ANY_ORIGIN:
-			self.send_header("Access-Control-Allow-Origin", "*")
-		if "accept-encoding" in self.headers and "gzip" in self.headers["accept-encoding"]:
-			if len(content) > 100:
-				content = gzip.compress(content, compresslevel=5)
-				self.send_header("Content-length", str(len(content)))
-				self.send_header("Content-encoding", "gzip")
-		self.end_headers()
-		self.wfile.write(content)
+				else:
+					name = tolNode.parent
+	elif reqType == "sugg":
+		# Check for suggestion-limit
+		suggLimit = None
+		invalidLimit = False
+		try:
+			suggLimit = int(queryDict["limit"][0]) if "limit" in queryDict else DEFAULT_SUGG_LIM
+			if suggLimit <= 0 or suggLimit > MAX_SUGG_LIM:
+				invalidLimit = True
+		except ValueError:
+			invalidLimit = True
+			print(f"INFO: Invalid limit {suggLimit}", file=sys.stderr)
+		# Get search suggestions
+		if not invalidLimit:
+			respondJson(lookupSuggs(name, suggLimit, useReducedTree, dbCur))
+			return
+	elif reqType == "info":
+		infoResponse = lookupInfo(name, useReducedTree, dbCur)
+		if infoResponse != None:
+			respondJson(infoResponse)
+			return
+	# On failure, provide empty response
+	respondJson(None)
 
-server = HTTPServer((hostname, port), DbServer)
-print(f"Server started at http://{hostname}:{port}")
-try:
-	server.serve_forever()
-except KeyboardInterrupt:
-	pass
-server.server_close()
-dbCon.close()
-print("Server stopped")
+# Open db
+dbCon = sqlite3.connect(dbFile)
+dbCur = dbCon.cursor()
+# Handle request
+handleReq(dbCur)