Mercurial > repos > fubar > jbrowse2
annotate jb2_webserver.py @ 47:3e53204c2419 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
author | fubar |
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date | Wed, 06 Mar 2024 00:23:02 +0000 |
parents | 4181e97c70a7 |
children | 460d5b6c5d98 |
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29
f728cf0df71d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
fubar
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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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b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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3 # 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
fubar
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4 # 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
fubar
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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
fubar
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6 # and reborrowed from https://gist.github.com/glowinthedark/b99900abe935e4ab4857314d647a9068 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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7 # |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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8 # The Apache 2.0 license copy in this repository is distributed with this code in accordance with that licence. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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9 # https://www.apache.org/licenses/LICENSE-2.0.txt |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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10 # This part is not MIT licenced like the other components. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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11 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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12 # APPENDIX: How to apply the Apache License to your work. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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13 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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14 # 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
fubar
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15 # boilerplate notice, with the fields enclosed by brackets "[]" |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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16 # replaced with your own identifying information. (Don't include |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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
fubar
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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
fubar
parents:
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19 # file or class name and description of purpose be included on the |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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20 # same "printed page" as the copyright notice for easier |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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21 # identification within third-party archives. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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22 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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23 # Licensed under the Apache License, Version 2.0 (the "License"); |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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24 # you may not use this file except in compliance with the License. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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25 # You may obtain a copy of the License at |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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26 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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27 # http://www.apache.org/licenses/LICENSE-2.0 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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28 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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
fubar
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30 # distributed under the License is distributed on an "AS IS" BASIS, |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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
fubar
parents:
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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
fubar
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33 # limitations under the License. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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34 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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35 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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36 import argparse |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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
fubar
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41 import webbrowser |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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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43 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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44 |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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45 DEFAULT_PORT = 8081 |
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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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46 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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47 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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51 Both start and stop are inclusive. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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52 """ |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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53 if start is not None: |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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54 infile.seek(start) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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55 while 1: |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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: |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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59 break |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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60 outfile.write(buf) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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61 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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62 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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63 BYTE_RANGE_RE = re.compile(r"bytes=(\d+)-(\d+)?$") |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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64 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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65 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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66 def parse_byte_range(byte_range): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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67 """Returns the two numbers in 'bytes=123-456' or throws ValueError. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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68 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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69 The last number or both numbers may be None. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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70 """ |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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71 if byte_range.strip() == "": |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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72 return None, None |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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73 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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
fubar
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75 if not m: |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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78 first, last = [x and int(x) for x in m.groups()] |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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79 if last and last < first: |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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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 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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82 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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83 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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84 class RangeRequestHandler(SimpleHTTPRequestHandler): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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85 """Adds support for HTTP 'Range' requests to SimpleHTTPRequestHandler |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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86 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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87 The approach is to: |
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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. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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89 - Override copyfile to only transmit a range when requested. |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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90 """ |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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91 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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92 def handle(self): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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93 try: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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94 SimpleHTTPRequestHandler.handle(self) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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95 except Exception: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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96 # ignored, thrown whenever the client aborts streaming (broken pipe) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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97 pass |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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101 self.range = None |
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102 return SimpleHTTPRequestHandler.send_head(self) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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103 try: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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104 self.range = parse_byte_range(self.headers["Range"]) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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105 except ValueError: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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106 self.send_error(400, "Invalid byte range") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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107 return None |
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108 first, last = self.range |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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109 |
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110 # Mirroring SimpleHTTPServer.py here |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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111 path = self.translate_path(self.path) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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112 f = None |
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113 ctype = self.guess_type(path) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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114 try: |
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115 f = open(path, "rb") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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123 self.send_error(416, "Requested Range Not Satisfiable") |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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144 if not self.range: |
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145 return SimpleHTTPRequestHandler.copyfile(self, source, outputfile) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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146 |
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147 # SimpleHTTPRequestHandler uses shutil.copyfileobj, which doesn't let |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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171 ) |
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172 parser.add_argument( |
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173 "--bind", |
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174 default="0.0.0.0", |
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175 help="IP address to bind to (default: 0.0.0.0)", |
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176 ) |
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177 args = parser.parse_args() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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178 |
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179 handler = functools.partial(RangeRequestHandler, directory=args.root) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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180 |
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181 webbrowser.open(f"http://{args.bind}:{args.port}") |
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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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185 f"Serving HTTP on {args.bind} port {args.port} (http://{args.bind}:{args.port}/)" |
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186 ) |
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187 httpd.serve_forever() |