Mercurial > repos > fubar > jbrowse2
view jb2_webserver.py @ 113:878c27dfea9d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
author | bgruening |
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date | Sun, 28 Jul 2024 02:42:43 +0000 |
parents | f350467f9433 |
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#!/usr/bin/env python3 # spec: simplest python web server with range support and multithreading that takes root path, # port and bind address as command line arguments; by default uses the current dir as webroot, # port 8000 and bind address of 0.0.0.0 # borrowed from https://github.com/danvk/RangeHTTPServer # and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068 # # The Apache 2.0 license copy in this repository is distributed with this code in accordance with that licence. # https://www.apache.org/licenses/LICENSE-2.0.txt # This part is not MIT licenced like the other components. # APPENDIX: How to apply the Apache License to your work. # To apply the Apache License to your work, attach the following # boilerplate notice, with the fields enclosed by brackets "[]" # replaced with your own identifying information. (Don't include # the brackets!) The text should be enclosed in the appropriate # comment syntax for the file format. We also recommend that a # file or class name and description of purpose be included on the # same "printed page" as the copyright notice for easier # identification within third-party archives. # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # http://www.apache.org/licenses/LICENSE-2.0 # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import argparse import functools import os import re import socketserver import webbrowser from http.server import SimpleHTTPRequestHandler DEFAULT_PORT = 8081 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024): """Like shutil.copyfileobj, but only copy a range of the streams. Both start and stop are inclusive. """ if start is not None: infile.seek(start) while 1: to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize) buf = infile.read(to_read) if not buf: break outfile.write(buf) BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$") def parse_byte_range(byte_range): """Returns the two numbers in 'bytes=123-456' or throws ValueError. The last number or both numbers may be None. """ if byte_range.strip() == "": return None, None m = BYTE_RANGE_RE.match(byte_range) if not m: raise ValueError("Invalid byte range %s" % byte_range) first, last = [x and int(x) for x in m.groups()] if last and last < first: raise ValueError("Invalid byte range %s" % byte_range) return first, last class RangeRequestHandler(SimpleHTTPRequestHandler): """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler The approach is to: - Override send_head to look for 'Range' and respond appropriately. - Override copyfile to only transmit a range when requested. """ def handle(self): try: SimpleHTTPRequestHandler.handle(self) except Exception: # ignored, thrown whenever the client aborts streaming (broken pipe) pass def send_head(self): if "Range" not in self.headers: self.range = None return SimpleHTTPRequestHandler.send_head(self) try: self.range = parse_byte_range(self.headers["Range"]) except ValueError: self.send_error(400, "Invalid byte range") return None first, last = self.range # Mirroring SimpleHTTPServer.py here path = self.translate_path(self.path) f = None ctype = self.guess_type(path) try: f = open(path, "rb") except IOError: self.send_error(404, "File not found") return None fs = os.fstat(f.fileno()) file_len = fs[6] if first >= file_len: self.send_error(416, "Requested Range Not Satisfiable") return None self.send_response(206) self.send_header("Content-type", ctype) if last is None or last >= file_len: last = file_len - 1 response_length = last - first + 1 self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len)) self.send_header("Content-Length", str(response_length)) self.send_header("Last-Modified", self.date_time_string(fs.st_mtime)) self.end_headers() return f def end_headers(self): self.send_header("Accept-Ranges", "bytes") return SimpleHTTPRequestHandler.end_headers(self) def copyfile(self, source, outputfile): if not self.range: return SimpleHTTPRequestHandler.copyfile(self, source, outputfile) # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let # you stop the copying before the end of the file. start, stop = self.range # set in send_head() copy_byte_range(source, outputfile, start, stop) class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer): allow_reuse_address = True if __name__ == "__main__": parser = argparse.ArgumentParser( description="Tiny Python Web Server supporting range requests, for local viewing of unzipped Galaxy JBrowse2 configurations" ) parser.add_argument( "--root", default=os.getcwd(), help="Root path to serve files from (default: current working directory)", ) parser.add_argument( "--port", type=int, default=DEFAULT_PORT, help=f"Port to listen on (default: {DEFAULT_PORT})", ) parser.add_argument( "--bind", default="127.0.0.1", help="IP address to bind to (default: 127.0.0.1 - use 0.0.0.0 to allow access on your network)", ) args = parser.parse_args() handler = functools.partial(RangeRequestHandler, directory=args.root) webbrowser.open(f"http://{args.bind}:{args.port}") with ThreadedTCPServer((args.bind, args.port), handler) as httpd: print( f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)" ) httpd.serve_forever()