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Merge pull request #151 from natefoo/runtime_stats
A command line script for collecting stats on job runtimes
This commit is contained in:
John Chilton
Executable
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#!/usr/bin/env python
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"""
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Collect and report statistics on job run times
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To use metrics (which provide more accurate information), see:
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https://github.com/galaxyproject/galaxy/blob/dev/config/job_metrics_conf.xml.sample
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If you do not have metrics enabled, use the `--source history` option to use
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the less accurate job_state_history table.
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Examples
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--------
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# Stats for Nate's runs of the Bowtie 2 tool installed from the Tool Shed (all
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# versions):
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% ./runtime_stats.py -c galaxy.ini -u nate@bx.psu.edu 'toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/'
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# Stats for all runs of the Bowtie 2 tool installed from the Tool Shed (version
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# 0.4 only):
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% ./runtime_stats.py -c galaxy.ini 'toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4'
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# Stats for all runs of the Bowtie 2 tool installed from the Tool Shed but we
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# don't feel like figuring out or typing the long ID (matches any tool with
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# '/tophat2/' in its full ID):
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% ./runtime_stats.py -c galaxy.ini --like 'bowtie2'
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# Stats for all runs of Tophat 2 that took longer than 2 minutes but less than
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# 2 days:
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% ./runtime_stats.py -c galaxy.ini --like -m $((2 * 60)) -M $((2 * 24 * 60 * 60)) 'tophat2'
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"""
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from __future__ import print_function
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import re
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import sys
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import argparse
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try:
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import configparser
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except:
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import ConfigParser as configparser
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import numpy
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import psycopg2
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from sqlalchemy.engine import url
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DATA_SOURCES = ('metrics', 'history')
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METRICS_SQL = """
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SELECT metric_value
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FROM job_metric_numeric jmn
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JOIN job j ON jmn.job_id = j.id
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WHERE j.state = 'ok'
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AND jmn.plugin = 'core'
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AND jmn.metric_name = 'runtime_seconds'
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{tool_clause}
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{user_clause}
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{time_clause}
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"""
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HISTORY_SQL = """
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SELECT ctimes[1] - ctimes[2] AS delta
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FROM (SELECT jsh.job_id,
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array_agg(jsh.create_time ORDER BY jsh.create_time DESC) AS ctimes
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FROM job_state_history jsh
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JOIN job j ON jsh.job_id = j.id
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WHERE jsh.state IN ('running','ok')
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AND j.state = 'ok'
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{tool_clause}
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{user_clause}
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GROUP BY jsh.job_id) AS t_arrs
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{time_clause}
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"""
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def parse_arguments():
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parser = argparse.ArgumentParser(
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description='Generate walltime statistics')
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parser.add_argument('tool_id', help='Tool (by ID) to collect stats about')
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parser.add_argument('--like',
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action='store_true',
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default=False,
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help='Use SQL `LIKE` operator to find '
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'a shed-installed tool using the tool\'s '
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'"short" id')
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parser.add_argument('-c', '--config', help='Galaxy config file')
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parser.add_argument('-d', '--debug',
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action='store_true',
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default=False,
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help='Print extra info')
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parser.add_argument('-m', '--min',
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type=int,
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default=-1,
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help='Ignore runtimes less than MIN seconds')
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parser.add_argument('-M', '--max',
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type=int,
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default=-1,
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help='Ignore runtimes greater than MAX seconds')
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parser.add_argument('-u', '--user',
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help='Return stats for only this user (id, email, '
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'or username)')
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parser.add_argument('-s', '--source',
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default='metrics',
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help='Runtime data source (SOURCES: %s)'
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% ', '.join(DATA_SOURCES))
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args = parser.parse_args()
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if args.like and '/' in args.tool_id:
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print('ERROR: Do not use --like with a tool shed tool id (the tool '
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'id should not contain `/` characters)')
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sys.exit(2)
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args.source = args.source.lower()
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if args.source not in ('metrics', 'history'):
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print('ERROR: Data source `%s` unknown, valid source are: %s'
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% (args.source, ', '.join(DATA_SOURCES)))
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if args.config:
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cp = configparser.ConfigParser()
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cp.readfp(open(args.config))
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uri = cp.get('app:main', 'database_connection')
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names = { 'database' : 'dbname', 'username' : 'user' }
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args.connect_args = url.make_url(uri).translate_connect_args(**names)
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else:
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args.connect_args = {}
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if args.debug:
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print('Got options:')
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for i in vars(args).items():
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print('%s: %s' % i)
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return args
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def query(tool_id=None, user=None, like=None, source='metrics',
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connect_args=None, debug=False, min=-1, max=-1, **kwargs):
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connect_arg_str = ''
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for k, v in connect_args.items():
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connect_arg_str += '%s=%s' % (k, v)
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pc = psycopg2.connect(connect_arg_str)
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cur = pc.cursor()
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if user:
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try:
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user_id = int(user)
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except:
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if '@' not in user:
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field = 'username'
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else:
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field = 'email'
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sql = 'SELECT id FROM galaxy_user WHERE %s = %s' % (field, '%s')
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cur.execute(sql, (user,))
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if debug:
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print('Executed:')
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print(cur.query)
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row = cur.fetchone()
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if row:
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user_id = row[0]
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else:
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print('Invalid user: %s' % user)
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sys.exit(1)
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if like:
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query_tool_id = '%%/%s/%%' % tool_id
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elif '/' in tool_id and not re.match('\d+\.\d+', tool_id.split('/')[-1]):
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query_tool_id = '%s%%' % tool_id
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like = True
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else:
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query_tool_id = tool_id
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sql_args = [query_tool_id]
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if like:
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tool_clause = "AND j.tool_id LIKE %s"
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else:
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tool_clause = "AND j.tool_id = %s"
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if user:
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user_clause = "AND j.user_id = %s"
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sql_args.append(user_id)
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else:
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user_clause = ""
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if source == 'metrics':
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if min > 0 and max > 0:
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time_clause = """AND metric_value > %s
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AND metric_value < %s"""
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sql_args.append(min)
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sql_args.append(max)
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elif min > 0:
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time_clause = "AND metric_value > %s"
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sql_args.append(min)
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elif max > 0:
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time_clause = "AND metric_value < %s"
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sql_args.append(max)
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else:
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time_clause = ""
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sql = METRICS_SQL
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elif source == 'history':
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if min > 0 and max > 0:
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time_clause = """WHERE ctimes[1] - ctimes[2] > interval %s
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AND ctimes[1] - ctimes[2] < interval %s"""
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sql_args.append('%s seconds' % min)
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sql_args.append('%s seconds' % max)
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elif min > 0:
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time_clause = "WHERE ctimes[1] - ctimes[2] > interval %s"
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sql_args.append('%s seconds' % min)
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elif max > 0:
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time_clause = "WHERE ctimes[1] - ctimes[2] < interval %s"
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sql_args.append('%s seconds' % max)
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else:
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time_clause = ""
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sql = HISTORY_SQL
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sql = sql.format(tool_clause=tool_clause, user_clause=user_clause,
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time_clause=time_clause)
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cur.execute(sql, sql_args)
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if debug:
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print('Executed:')
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print(cur.query)
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print('Query returned %d rows' % cur.rowcount)
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if source == 'metrics':
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times = numpy.array([ r[0] for r in cur if r[0] ])
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elif source == 'history':
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times = numpy.array([ r[0].total_seconds() for r in cur if r[0] ])
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print('Collected %d times' % times.size)
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if times.size == 0:
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return
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if user:
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print('Displaying statistics for user %s' % user)
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stats = (('Mean runtime', numpy.mean(times)),
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('Standard deviation', numpy.std(times)),
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('Minimum runtime', times.min()),
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('Maximum runtime', times.max()))
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for name, seconds in stats:
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hours, minutes = nice_times(seconds)
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msg = name + ' is %0.0f seconds' % seconds
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if minutes:
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msg += ' (=%0.2f minutes)' % minutes
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if hours:
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msg += ' (=%0.2f hours)' % hours
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print(msg)
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def nice_times(seconds):
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if seconds < 60*60:
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hours = None
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if seconds < 60:
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minutes = None
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else:
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minutes = seconds / 60
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else:
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minutes = seconds / 60
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hours = seconds / 60 / 60
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return hours, minutes
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def main():
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args = parse_arguments()
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query(**vars(args))
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if __name__ == '__main__':
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main()
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