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Merge pull request #10330 from mvdbeek/fix_download_of_composite_data_from_collections
[20.09] Fix composite data download from collection
This commit is contained in:
Marius van den Beek
@@ -261,84 +261,78 @@ class Data(metaclass=DataMeta):
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messagetype = "error"
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return error, msg, messagetype
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def _archive_composite_dataset(self, trans, data=None, **kwd):
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def _archive_composite_dataset(self, trans, data, do_action='zip'):
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# save a composite object into a compressed archive for downloading
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params = util.Params(kwd)
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outfname = data.name[0:150]
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outfname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in outfname)
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if params.do_action is None:
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params.do_action = 'zip' # default
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msg = util.restore_text(params.get('msg', ''))
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if not data:
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msg = "You must select at least one dataset"
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else:
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error = False
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try:
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if params.do_action == 'zip':
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# Can't use mkstemp - the file must not exist first
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tmpd = tempfile.mkdtemp(dir=trans.app.config.new_file_path, prefix='gx_composite_archive_')
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util.umask_fix_perms(tmpd, trans.app.config.umask, 0o777, trans.app.config.gid)
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tmpf = os.path.join(tmpd, 'library_download.' + params.do_action)
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archive = zipfile.ZipFile(tmpf, 'w', zipfile.ZIP_DEFLATED, True)
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error = False
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msg = ''
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try:
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if do_action == 'zip':
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# Can't use mkstemp - the file must not exist first
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tmpd = tempfile.mkdtemp(dir=trans.app.config.new_file_path, prefix='gx_composite_archive_')
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util.umask_fix_perms(tmpd, trans.app.config.umask, 0o777, trans.app.config.gid)
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tmpf = os.path.join(tmpd, 'library_download.' + do_action)
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archive = zipfile.ZipFile(tmpf, 'w', zipfile.ZIP_DEFLATED, True)
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def zipfile_add(fpath, arcname):
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encoded_arcname = arcname.encode('CP437')
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try:
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archive.write(fpath, encoded_arcname)
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except TypeError:
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# Despite documenting the need for CP437 encoded arcname,
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# python 3 actually needs this to be a unicode string ...
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# https://bugs.python.org/issue24110
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archive.write(fpath, arcname)
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def zipfile_add(fpath, arcname):
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encoded_arcname = arcname.encode('CP437')
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try:
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archive.write(fpath, encoded_arcname)
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except TypeError:
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# Despite documenting the need for CP437 encoded arcname,
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# python 3 actually needs this to be a unicode string ...
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# https://bugs.python.org/issue24110
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archive.write(fpath, arcname)
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archive.add = zipfile_add
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archive.add = zipfile_add
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elif params.do_action == 'tgz':
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archive = util.streamball.StreamBall('w|gz')
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elif params.do_action == 'tbz':
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archive = util.streamball.StreamBall('w|bz2')
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except (OSError, zipfile.BadZipFile):
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error = True
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log.exception("Unable to create archive for download")
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msg = "Unable to create archive for %s for download, please report this error" % outfname
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elif do_action == 'tgz':
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archive = util.streamball.StreamBall('w|gz')
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elif do_action == 'tbz':
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archive = util.streamball.StreamBall('w|bz2')
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except (OSError, zipfile.BadZipFile):
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error = True
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log.exception("Unable to create archive for download")
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msg = "Unable to create archive for %s for download, please report this error" % outfname
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if not error:
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ext = data.extension
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path = data.file_name
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efp = data.extra_files_path
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# Add any central file to the archive,
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display_name = os.path.splitext(outfname)[0]
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if not display_name.endswith(ext):
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display_name = '{}_{}'.format(display_name, ext)
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error, msg = self._archive_main_file(archive, display_name, path)[:2]
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if not error:
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ext = data.extension
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path = data.file_name
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efp = data.extra_files_path
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# Add any central file to the archive,
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display_name = os.path.splitext(outfname)[0]
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if not display_name.endswith(ext):
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display_name = '{}_{}'.format(display_name, ext)
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error, msg = self._archive_main_file(archive, display_name, path)[:2]
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if not error:
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# Add any child files to the archive,
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for fpath, rpath in self.__archive_extra_files_path(extra_files_path=efp):
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try:
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archive.add(fpath, rpath)
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except OSError:
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error = True
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log.exception("Unable to add %s to temporary library download archive", rpath)
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msg = "Unable to create archive for download, please report this error"
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continue
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if not error:
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if params.do_action == 'zip':
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archive.close()
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tmpfh = open(tmpf, 'rb')
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# CANNOT clean up - unlink/rmdir was always failing because file handle retained to return - must rely on a cron job to clean up tmp
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trans.response.set_content_type("application/x-zip-compressed")
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trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.zip"' % outfname
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return tmpfh
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else:
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trans.response.set_content_type("application/x-tar")
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outext = 'tgz'
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if params.do_action == 'tbz':
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outext = 'tbz'
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trans.response.headers["Content-Disposition"] = 'attachment; filename="{}.{}"'.format(outfname, outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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return archive.stream
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# Add any child files to the archive,
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for fpath, rpath in self.__archive_extra_files_path(extra_files_path=efp):
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try:
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archive.add(fpath, rpath)
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except OSError:
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error = True
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log.exception("Unable to add %s to temporary library download archive", rpath)
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msg = "Unable to create archive for download, please report this error"
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continue
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if not error:
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if do_action == 'zip':
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archive.close()
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tmpfh = open(tmpf, 'rb')
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# CANNOT clean up - unlink/rmdir was always failing because file handle retained to return - must rely on a cron job to clean up tmp
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trans.response.set_content_type("application/x-zip-compressed")
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trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.zip"' % outfname
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return tmpfh
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else:
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trans.response.set_content_type("application/x-tar")
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outext = 'tgz'
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if do_action == 'tbz':
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outext = 'tbz'
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trans.response.headers["Content-Disposition"] = 'attachment; filename="{}.{}"'.format(outfname, outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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return archive.stream
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return trans.show_error_message(msg)
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def __archive_extra_files_path(self, extra_files_path):
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@@ -441,7 +435,7 @@ class Data(metaclass=DataMeta):
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from galaxy import datatypes # DBTODO REMOVE THIS AT REFACTOR
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if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file
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if data.extension in composite_extensions:
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return self._archive_composite_dataset(trans, data, **kwd)
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return self._archive_composite_dataset(trans, data, do_action=kwd.get('do_action'))
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else:
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trans.response.headers['Content-Length'] = int(os.stat(data.file_name).st_size)
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filename = self._download_filename(data, to_ext, hdca=kwd.get("hdca", None), element_identifier=kwd.get("element_identifier", None))
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