Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/boto/services/submit.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
---|---|
date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
children |
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/boto/services/submit.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -# Copyright (c) 2006,2007 Mitch Garnaat http://garnaat.org/ -# -# Permission is hereby granted, free of charge, to any person obtaining a -# copy of this software and associated documentation files (the -# "Software"), to deal in the Software without restriction, including -# without limitation the rights to use, copy, modify, merge, publish, dis- -# tribute, sublicense, and/or sell copies of the Software, and to permit -# persons to whom the Software is furnished to do so, subject to the fol- -# lowing conditions: -# -# The above copyright notice and this permission notice shall be included -# in all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- -# ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT -# SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS -# IN THE SOFTWARE. -import time -import os - - -class Submitter(object): - - def __init__(self, sd): - self.sd = sd - self.input_bucket = self.sd.get_obj('input_bucket') - self.output_bucket = self.sd.get_obj('output_bucket') - self.output_domain = self.sd.get_obj('output_domain') - self.queue = self.sd.get_obj('input_queue') - - def get_key_name(self, fullpath, prefix): - key_name = fullpath[len(prefix):] - l = key_name.split(os.sep) - return '/'.join(l) - - def write_message(self, key, metadata): - if self.queue: - m = self.queue.new_message() - m.for_key(key, metadata) - if self.output_bucket: - m['OutputBucket'] = self.output_bucket.name - self.queue.write(m) - - def submit_file(self, path, metadata=None, cb=None, num_cb=0, prefix='/'): - if not metadata: - metadata = {} - key_name = self.get_key_name(path, prefix) - k = self.input_bucket.new_key(key_name) - k.update_metadata(metadata) - k.set_contents_from_filename(path, replace=False, cb=cb, num_cb=num_cb) - self.write_message(k, metadata) - - def submit_path(self, path, tags=None, ignore_dirs=None, cb=None, num_cb=0, status=False, prefix='/'): - path = os.path.expanduser(path) - path = os.path.expandvars(path) - path = os.path.abspath(path) - total = 0 - metadata = {} - if tags: - metadata['Tags'] = tags - l = [] - for t in time.gmtime(): - l.append(str(t)) - metadata['Batch'] = '_'.join(l) - if self.output_domain: - self.output_domain.put_attributes(metadata['Batch'], {'type' : 'Batch'}) - if os.path.isdir(path): - for root, dirs, files in os.walk(path): - if ignore_dirs: - for ignore in ignore_dirs: - if ignore in dirs: - dirs.remove(ignore) - for file in files: - fullpath = os.path.join(root, file) - if status: - print('Submitting %s' % fullpath) - self.submit_file(fullpath, metadata, cb, num_cb, prefix) - total += 1 - elif os.path.isfile(path): - self.submit_file(path, metadata, cb, num_cb) - total += 1 - else: - print('problem with %s' % path) - return (metadata['Batch'], total)