Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/boto/services/result.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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#!/usr/bin/env python # 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 os from datetime import datetime, timedelta from boto.utils import parse_ts import boto class ResultProcessor(object): LogFileName = 'log.csv' def __init__(self, batch_name, sd, mimetype_files=None): self.sd = sd self.batch = batch_name self.log_fp = None self.num_files = 0 self.total_time = 0 self.min_time = timedelta.max self.max_time = timedelta.min self.earliest_time = datetime.max self.latest_time = datetime.min self.queue = self.sd.get_obj('output_queue') self.domain = self.sd.get_obj('output_domain') def calculate_stats(self, msg): start_time = parse_ts(msg['Service-Read']) end_time = parse_ts(msg['Service-Write']) elapsed_time = end_time - start_time if elapsed_time > self.max_time: self.max_time = elapsed_time if elapsed_time < self.min_time: self.min_time = elapsed_time self.total_time += elapsed_time.seconds if start_time < self.earliest_time: self.earliest_time = start_time if end_time > self.latest_time: self.latest_time = end_time def log_message(self, msg, path): keys = sorted(msg.keys()) if not self.log_fp: self.log_fp = open(os.path.join(path, self.LogFileName), 'a') line = ','.join(keys) self.log_fp.write(line+'\n') values = [] for key in keys: value = msg[key] if value.find(',') > 0: value = '"%s"' % value values.append(value) line = ','.join(values) self.log_fp.write(line+'\n') def process_record(self, record, path, get_file=True): self.log_message(record, path) self.calculate_stats(record) outputs = record['OutputKey'].split(',') if 'OutputBucket' in record: bucket = boto.lookup('s3', record['OutputBucket']) else: bucket = boto.lookup('s3', record['Bucket']) for output in outputs: if get_file: key_name = output.split(';')[0] key = bucket.lookup(key_name) file_name = os.path.join(path, key_name) print('retrieving file: %s to %s' % (key_name, file_name)) key.get_contents_to_filename(file_name) self.num_files += 1 def get_results_from_queue(self, path, get_file=True, delete_msg=True): m = self.queue.read() while m: if 'Batch' in m and m['Batch'] == self.batch: self.process_record(m, path, get_file) if delete_msg: self.queue.delete_message(m) m = self.queue.read() def get_results_from_domain(self, path, get_file=True): rs = self.domain.query("['Batch'='%s']" % self.batch) for item in rs: self.process_record(item, path, get_file) def get_results_from_bucket(self, path): bucket = self.sd.get_obj('output_bucket') if bucket: print('No output queue or domain, just retrieving files from output_bucket') for key in bucket: file_name = os.path.join(path, key) print('retrieving file: %s to %s' % (key, file_name)) key.get_contents_to_filename(file_name) self.num_files + 1 def get_results(self, path, get_file=True, delete_msg=True): if not os.path.isdir(path): os.mkdir(path) if self.queue: self.get_results_from_queue(path, get_file) elif self.domain: self.get_results_from_domain(path, get_file) else: self.get_results_from_bucket(path) if self.log_fp: self.log_fp.close() print('%d results successfully retrieved.' % self.num_files) if self.num_files > 0: self.avg_time = float(self.total_time)/self.num_files print('Minimum Processing Time: %d' % self.min_time.seconds) print('Maximum Processing Time: %d' % self.max_time.seconds) print('Average Processing Time: %f' % self.avg_time) self.elapsed_time = self.latest_time-self.earliest_time print('Elapsed Time: %d' % self.elapsed_time.seconds) tput = 1.0 / ((self.elapsed_time.seconds/60.0) / self.num_files) print('Throughput: %f transactions / minute' % tput)