Mercurial > repos > fubar > jbrowse2

annotate jb2_webserver.py @ 124:137e08517410 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec-dirty
author fubar
date Fri, 04 Oct 2024 23:32:20 +0000
parents f350467f9433
children
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f728cf0df71d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
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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
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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18 # 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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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
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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.
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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32 # 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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33 # limitations under the License.
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36 import argparse
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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37 import functools
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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38 import os
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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39 import re
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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40 import socketserver
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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41 import webbrowser
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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42 from http.server import SimpleHTTPRequestHandler
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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45 DEFAULT_PORT = 8081
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48 def copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16 * 1024):
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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49 """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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50
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51 Both start and stop are inclusive.
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52 """
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53 if start is not None:
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54 infile.seek(start)
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55 while 1:
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56 to_read = min(bufsize, stop + 1 - infile.tell() if stop else bufsize)
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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57 buf = infile.read(to_read)
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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58 if not buf:
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59 break
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60 outfile.write(buf)
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63 BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$")
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64
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66 def parse_byte_range(byte_range):
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67 """Returns the two numbers in 'bytes=123-456' or throws ValueError.
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68
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69 The last number or both numbers may be None.
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70 """
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71 if byte_range.strip() == "":
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72 return None, None
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74 m = BYTE_RANGE_RE.match(byte_range)
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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75 if not m:
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76 raise ValueError("Invalid byte range %s" % byte_range)
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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77
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78 first, last = [x and int(x) for x in m.groups()]
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79 if last and last < first:
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80 raise ValueError("Invalid byte range %s" % byte_range)
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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81 return first, last
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82
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83
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84 class RangeRequestHandler(SimpleHTTPRequestHandler):
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85 """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler
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86
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87 The approach is to:
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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88 - Override send_head to look for 'Range' and respond appropriately.
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89 - Override copyfile to only transmit a range when requested.
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90 """
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91
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92 def handle(self):
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93 try:
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94 SimpleHTTPRequestHandler.handle(self)
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95 except Exception:
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96 # ignored, thrown whenever the client aborts streaming (broken pipe)
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97 pass
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98
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99 def send_head(self):
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100 if "Range" not in self.headers:
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101 self.range = None
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102 return SimpleHTTPRequestHandler.send_head(self)
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103 try:
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104 self.range = parse_byte_range(self.headers["Range"])
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105 except ValueError:
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106 self.send_error(400, "Invalid byte range")
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107 return None
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108 first, last = self.range
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109
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110 # Mirroring SimpleHTTPServer.py here
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111 path = self.translate_path(self.path)
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112 f = None
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113 ctype = self.guess_type(path)
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114 try:
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115 f = open(path, "rb")
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116 except IOError:
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117 self.send_error(404, "File not found")
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118 return None
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119
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120 fs = os.fstat(f.fileno())
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121 file_len = fs[6]
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122 if first >= file_len:
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123 self.send_error(416, "Requested Range Not Satisfiable")
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124 return None
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125
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126 self.send_response(206)
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127 self.send_header("Content-type", ctype)
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128
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129 if last is None or last >= file_len:
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130 last = file_len - 1
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131 response_length = last - first + 1
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132
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133 self.send_header("Content-Range", "bytes %s-%s/%s" % (first, last, file_len))
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134 self.send_header("Content-Length", str(response_length))
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135 self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
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136 self.end_headers()
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137 return f
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138
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139 def end_headers(self):
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140 self.send_header("Accept-Ranges", "bytes")
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141 return SimpleHTTPRequestHandler.end_headers(self)
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142
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143 def copyfile(self, source, outputfile):
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144 if not self.range:
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145 return SimpleHTTPRequestHandler.copyfile(self, source, outputfile)
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146
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147 # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let
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148 # you stop the copying before the end of the file.
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149 start, stop = self.range # set in send_head()
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150 copy_byte_range(source, outputfile, start, stop)
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151
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152
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153 class ThreadedTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
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154 allow_reuse_address = True
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155
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156
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157 if __name__ == "__main__":
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158 parser = argparse.ArgumentParser(
46
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159 description="Tiny Python Web Server supporting range requests, for local viewing of unzipped Galaxy JBrowse2 configurations"
7
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160 )
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161 parser.add_argument(
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162 "--root",
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163 default=os.getcwd(),
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164 help="Root path to serve files from (default: current working directory)",
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165 )
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166 parser.add_argument(
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167 "--port",
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168 type=int,
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169 default=DEFAULT_PORT,
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170 help=f"Port to listen on (default: {DEFAULT_PORT})",
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171 )
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172 parser.add_argument(
17
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173 "--bind",
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174 default="127.0.0.1",
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175 help="IP address to bind to (default: 127.0.0.1 - use 0.0.0.0 to allow access on your network)",
7
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176 )
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177 args = parser.parse_args()
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178
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179 handler = functools.partial(RangeRequestHandler, directory=args.root)
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180
50
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181 webbrowser.open(f"http://{args.bind}:{args.port}")
7
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182
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183 with ThreadedTCPServer((args.bind, args.port), handler) as httpd:
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184 print(
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f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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185 f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)"
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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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186 )
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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187 httpd.serve_forever()