Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/streamball.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 """
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2 A simple wrapper for writing tarballs as a stream.
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3 """
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4 from __future__ import absolute_import
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5
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6 import logging
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7 import os
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8 import tarfile
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9
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10 from galaxy.exceptions import ObjectNotFound
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11 from .path import safe_walk
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12
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13 log = logging.getLogger(__name__)
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14
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15
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16 class StreamBall(object):
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17 def __init__(self, mode, members=None):
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18 self.members = members
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19 if members is None:
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20 self.members = []
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21 self.mode = mode
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22 self.wsgi_status = None
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23 self.wsgi_headeritems = None
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24
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25 def add(self, file, relpath, check_file=False):
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26 if check_file and len(file) > 0:
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27 if not os.path.isfile(file):
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28 raise ObjectNotFound
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29 else:
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30 self.members.append((file, relpath))
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31 else:
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32 self.members.append((file, relpath))
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33
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34 def stream(self, environ, start_response):
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35 response_write = start_response(self.wsgi_status, self.wsgi_headeritems)
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36
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37 class tarfileobj(object):
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38 def write(self, *args, **kwargs):
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39 response_write(*args, **kwargs)
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40 tf = tarfile.open(mode=self.mode, fileobj=tarfileobj())
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41 for (file, rel) in self.members:
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42 tf.add(file, arcname=rel)
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43 tf.close()
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44 return []
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45
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46
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47 class ZipBall(object):
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48 def __init__(self, tmpf, tmpd):
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49 self._tmpf = tmpf
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50 self._tmpd = tmpd
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51
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52 def stream(self, environ, start_response):
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53 response_write = start_response(self.wsgi_status, self.wsgi_headeritems)
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54 tmpfh = open(self._tmpf)
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55 response_write(tmpfh.read())
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56 tmpfh.close()
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57 try:
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58 os.unlink(self._tmpf)
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59 os.rmdir(self._tmpd)
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60 except OSError:
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61 log.exception("Unable to remove temporary library download archive and directory")
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62 return []
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63
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64
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65 def stream_archive(trans, path, upstream_gzip=False):
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66 archive_type_string = 'w|gz'
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67 archive_ext = 'tgz'
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68 if upstream_gzip:
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69 archive_type_string = 'w|'
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70 archive_ext = 'tar'
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71 archive = StreamBall(mode=archive_type_string)
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72 for root, directories, files in safe_walk(path):
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73 for filename in files:
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74 p = os.path.join(root, filename)
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75 relpath = os.path.relpath(p, os.path.join(path, os.pardir))
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76 archive.add(file=os.path.join(path, p), relpath=relpath)
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77 archive_name = "%s.%s" % (os.path.basename(path), archive_ext)
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78 trans.response.set_content_type("application/x-tar")
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79 trans.response.headers["Content-Disposition"] = 'attachment; filename="{}"'.format(archive_name)
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80 archive.wsgi_status = trans.response.wsgi_status()
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81 archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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82 return archive.stream