Mercurial > repos > fubar > jbrowse2

annotate jb2_webserver.py @ 49:7e867ff86e44 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
author fubar
date Thu, 07 Mar 2024 00:27:48 +0000
parents 460d5b6c5d98
children f350467f9433
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1 #!/usr/bin/env python3
f728cf0df71d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
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2 # spec: simplest python web server with range support and multithreading that takes root path,
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3 # port and bind address as command line arguments; by default uses the current dir as webroot,
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4 # port 8000 and bind address of 0.0.0.0
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5 # borrowed from https://github.com/danvk/RangeHTTPServer
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6 # and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068
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7 #
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8 # The Apache 2.0 license copy in this repository is distributed with this code in accordance with that licence.
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9 # https://www.apache.org/licenses/LICENSE-2.0.txt
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10 # This part is not MIT licenced like the other components.
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12 # APPENDIX: How to apply the Apache License to your work.
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14 # To apply the Apache License to your work, attach the following
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15 # boilerplate notice, with the fields enclosed by brackets "[]"
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16 # replaced with your own identifying information. (Don't include
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17 # the brackets!) The text should be enclosed in the appropriate
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18 # comment syntax for the file format. We also recommend that a
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19 # file or class name and description of purpose be included on the
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20 # same "printed page" as the copyright notice for easier
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21 # identification within third-party archives.
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23 # Licensed under the Apache License, Version 2.0 (the "License");
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24 # you may not use this file except in compliance with the License.
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25 # You may obtain a copy of the License at
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27 # http://www.apache.org/licenses/LICENSE-2.0
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29 # Unless required by applicable law or agreed to in writing, software
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30 # distributed under the License is distributed on an "AS IS" BASIS,
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31 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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32 # See the License for the specific language governing permissions and
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33 # limitations under the License.
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36 import argparse
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37 import functools
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38 import os
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39 import re
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40 import socketserver
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41 import ssl
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42 import webbrowser
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43 from http.server import SimpleHTTPRequestHandler
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45
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46 DEFAULT_PORT = 8443
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49 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
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50 """Like shutil.copyfileobj, but only copy a range of the streams.
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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51
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52 Both start and stop are inclusive.
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53 """
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54 if start is not None:
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55 infile.seek(start)
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56 while 1:
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57 to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize)
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58 buf = infile.read(to_read)
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59 if not buf:
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60 break
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61 outfile.write(buf)
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64 BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$")
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65
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66
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67 def parse_byte_range(byte_range):
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68 """Returns the two numbers in 'bytes=123-456' or throws ValueError.
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69
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70 The last number or both numbers may be None.
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71 """
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72 if byte_range.strip() == "":
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73 return None, None
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74
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75 m = BYTE_RANGE_RE.match(byte_range)
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76 if not m:
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77 raise ValueError("Invalid byte range %s" % byte_range)
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78
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79 first, last = [x and int(x) for x in m.groups()]
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80 if last and last < first:
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81 raise ValueError("Invalid byte range %s" % byte_range)
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82 return first, last
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83
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84
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85 class RangeRequestHandler(SimpleHTTPRequestHandler):
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86 """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler
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87
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88 The approach is to:
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89 - Override send_head to look for 'Range' and respond appropriately.
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90 - Override copyfile to only transmit a range when requested.
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91 """
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92
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93 def handle(self):
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94 try:
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95 SimpleHTTPRequestHandler.handle(self)
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96 except Exception:
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97 # ignored, thrown whenever the client aborts streaming (broken pipe)
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98 pass
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99
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100 def send_head(self):
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101 if "Range" not in self.headers:
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102 self.range = None
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103 return SimpleHTTPRequestHandler.send_head(self)
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104 try:
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105 self.range = parse_byte_range(self.headers["Range"])
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106 except ValueError:
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107 self.send_error(400, "Invalid byte range")
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108 return None
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109 first, last = self.range
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110
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111 # Mirroring SimpleHTTPServer.py here
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112 path = self.translate_path(self.path)
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113 f = None
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114 ctype = self.guess_type(path)
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115 try:
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116 f = open(path, "rb")
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117 except IOError:
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118 self.send_error(404, "File not found")
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119 return None
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120
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121 fs = os.fstat(f.fileno())
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122 file_len = fs[6]
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123 if first >= file_len:
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124 self.send_error(416, "Requested Range Not Satisfiable")
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125 return None
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126
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127 self.send_response(206)
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128 self.send_header("Content-type", ctype)
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129
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130 if last is None or last >= file_len:
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131 last = file_len - 1
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132 response_length = last - first + 1
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133
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134 self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len))
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135 self.send_header("Content-Length", str(response_length))
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136 self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
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137 self.end_headers()
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138 return f
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139
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140 def end_headers(self):
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141 self.send_header("Accept-Ranges", "bytes")
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142 return SimpleHTTPRequestHandler.end_headers(self)
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143
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144 def copyfile(self, source, outputfile):
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145 if not self.range:
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146 return SimpleHTTPRequestHandler.copyfile(self, source, outputfile)
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147
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148 # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let
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149 # you stop the copying before the end of the file.
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150 start, stop = self.range # set in send_head()
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151 copy_byte_range(source, outputfile, start, stop)
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152
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153
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154 class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
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155 allow_reuse_address = True
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156
48
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157 def server_bind(self):
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158 ctx = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
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159 ctx.load_cert_chain('cert.pem', 'key.pem')
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160 socketserver.TCPServer.server_bind(self)
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161 self.socket = ctx.wrap_socket( self.socket, server_hostname = "127.0.0.1", server_side=False,)
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162
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163
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164 def get_request(self):
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165 (socket, addr) = socketserver.TCPServer.get_request(self)
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166 socket.do_handshake()
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167 return (socket, addr)
7
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168
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169 if __name__ == "__main__":
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170 parser = argparse.ArgumentParser(
46
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171 description="Tiny Python Web Server supporting range requests, for local viewing of unzipped Galaxy JBrowse2 configurations"
7
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172 )
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173 parser.add_argument(
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174 "--root",
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175 default=os.getcwd(),
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176 help="Root path to serve files from (default: current working directory)",
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177 )
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178 parser.add_argument(
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179 "--port",
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180 type=int,
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181 default=DEFAULT_PORT,
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182 help=f"Port to listen on (default: {DEFAULT_PORT})",
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183 )
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184 parser.add_argument(
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185 "--bind",
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186 default="127.0.0.1",
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187 help="IP address to bind to (default: 127.0.0.1)",
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188 )
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189 args = parser.parse_args()
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190
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191 handler = functools.partial(RangeRequestHandler, directory=args.root)
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192
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193 webbrowser.open(f"https://{args.bind}:{args.port}")
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194
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195 with ThreadedTCPServer((args.bind, args.port), handler) as httpd:
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196 print(
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197 f"Serving HTTPS on {args.bind} port {args.port} (https://{args.bind}:{args.port}/)"
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198 )
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199 httpd.serve_forever()