Mercurial > repos > fubar > jbrowse2

annotate jb2_webserver.py @ 17:4c201a3d4755 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
author fubar
date Sun, 28 Jan 2024 06:48:52 +0000
parents b04fd993b31e
children f728cf0df71d
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b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1 #!/usr/bin/env python3# spec: simplest python web server with range support and multithreading that takes root path,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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2 # port and bind address as command line arguments; by default uses the current dir as webroot,
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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3 # port 8000 and bind address of 0.0.0.0
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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4 # borrowed from https://github.com/danvk/RangeHTTPServer
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5 # and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068
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6 #
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7 # The Apache 2.0 license copy in this repository is distributed with this code in accordance with that licence.
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8 # https://www.apache.org/licenses/LICENSE-2.0.txt
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9 # This part is not MIT licenced like the other components.
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11 # APPENDIX: How to apply the Apache License to your work.
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13 # To apply the Apache License to your work, attach the following
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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14 # boilerplate notice, with the fields enclosed by brackets "[]"
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15 # replaced with your own identifying information. (Don't include
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16 # the brackets!) The text should be enclosed in the appropriate
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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17 # comment syntax for the file format. We also recommend that a
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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18 # file or class name and description of purpose be included on the
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19 # same "printed page" as the copyright notice for easier
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20 # identification within third-party archives.
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22 # Licensed under the Apache License, Version 2.0 (the "License");
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23 # you may not use this file except in compliance with the License.
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24 # You may obtain a copy of the License at
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26 # http://www.apache.org/licenses/LICENSE-2.0
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28 # Unless required by applicable law or agreed to in writing, software
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29 # distributed under the License is distributed on an "AS IS" BASIS,
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30 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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31 # See the License for the specific language governing permissions and
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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32 # limitations under the License.
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35 import argparse
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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36 import functools
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37 import os
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38 import re
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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39 import socketserver
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40 import webbrowser
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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41 from http.server import SimpleHTTPRequestHandler
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44 DEFAULT_PORT = 8080
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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47 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
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48 """Like shutil.copyfileobj, but only copy a range of the streams.
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49
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50 Both start and stop are inclusive.
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51 """
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52 if start is not None:
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53 infile.seek(start)
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54 while 1:
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55 to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize)
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56 buf = infile.read(to_read)
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57 if not buf:
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58 break
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59 outfile.write(buf)
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61
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62 BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$")
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63
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64
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65 def parse_byte_range(byte_range):
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66 """Returns the two numbers in 'bytes=123-456' or throws ValueError.
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67
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68 The last number or both numbers may be None.
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69 """
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70 if byte_range.strip() == "":
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71 return None, None
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72
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73 m = BYTE_RANGE_RE.match(byte_range)
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74 if not m:
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75 raise ValueError("Invalid byte range %s" % byte_range)
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76
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77 first, last = [x and int(x) for x in m.groups()]
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78 if last and last < first:
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79 raise ValueError("Invalid byte range %s" % byte_range)
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80 return first, last
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81
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82
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83 class RangeRequestHandler(SimpleHTTPRequestHandler):
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84 """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler
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85
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86 The approach is to:
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87 - Override send_head to look for 'Range' and respond appropriately.
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88 - Override copyfile to only transmit a range when requested.
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89 """
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90
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91 def handle(self):
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92 try:
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93 SimpleHTTPRequestHandler.handle(self)
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94 except Exception:
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95 # ignored, thrown whenever the client aborts streaming (broken pipe)
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96 pass
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97
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98 def send_head(self):
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99 if "Range" not in self.headers:
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100 self.range = None
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101 return SimpleHTTPRequestHandler.send_head(self)
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102 try:
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103 self.range = parse_byte_range(self.headers["Range"])
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104 except ValueError:
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105 self.send_error(400, "Invalid byte range")
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106 return None
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107 first, last = self.range
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108
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109 # Mirroring SimpleHTTPServer.py here
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110 path = self.translate_path(self.path)
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111 f = None
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112 ctype = self.guess_type(path)
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113 try:
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114 f = open(path, "rb")
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115 except IOError:
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116 self.send_error(404, "File not found")
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117 return None
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118
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119 fs = os.fstat(f.fileno())
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120 file_len = fs[6]
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121 if first >= file_len:
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122 self.send_error(416, "Requested Range Not Satisfiable")
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123 return None
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124
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125 self.send_response(206)
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126 self.send_header("Content-type", ctype)
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127
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128 if last is None or last >= file_len:
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129 last = file_len - 1
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130 response_length = last - first + 1
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131
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132 self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len))
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133 self.send_header("Content-Length", str(response_length))
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134 self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
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135 self.end_headers()
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136 return f
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137
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138 def end_headers(self):
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139 self.send_header("Accept-Ranges", "bytes")
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140 return SimpleHTTPRequestHandler.end_headers(self)
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141
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142 def copyfile(self, source, outputfile):
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143 if not self.range:
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144 return SimpleHTTPRequestHandler.copyfile(self, source, outputfile)
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145
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146 # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let
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147 # you stop the copying before the end of the file.
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148 start, stop = self.range # set in send_head()
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149 copy_byte_range(source, outputfile, start, stop)
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150
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151
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152 class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
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153 allow_reuse_address = True
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154
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155
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156 if __name__ == "__main__":
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157 parser = argparse.ArgumentParser(
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158 description="Simple Python Web Server with Range Support"
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159 )
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160 parser.add_argument(
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161 "--root",
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162 default=os.getcwd(),
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163 help="Root path to serve files from (default: current working directory)",
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164 )
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165 parser.add_argument(
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166 "--port",
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167 type=int,
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168 default=DEFAULT_PORT,
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169 help=f"Port to listen on (default: {DEFAULT_PORT})",
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170 )
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171 parser.add_argument(
17
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172 "--bind",
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173 default="0.0.0.0",
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174 help="IP address to bind to (default: 0.0.0.0)",
7
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175 )
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176 args = parser.parse_args()
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177
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178 handler = functools.partial(RangeRequestHandler, directory=args.root)
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179
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180 webbrowser.open(f"http://{args.bind}:{args.port}")
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181
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182 with ThreadedTCPServer((args.bind, args.port), handler) as httpd:
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183 print(
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184 f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)"
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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185 )
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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186 httpd.serve_forever()