def _read_model_arguments(argv, use_argparse=False):
if use_argparse:
parser = argparse.ArgumentParser()
parser.add_argument('database', metavar='DATABASE', type=str,
default="galaxy",
nargs='?',
help='database to target (galaxy, tool_shed, install)')
populate_config_args(parser)
args = parser.parse_args(argv[1:] if argv else [])
return args.config_file, args.config_section, args.database
else:
config_file = None
for arg in ["-c", "--config", "--config-file"]:
if arg in argv:
pos = argv.index(arg)
argv.pop(pos)
config_file = argv.pop(pos)
config_section = None
if "--config-section" in argv:
pos = argv.index("--config-section")
argv.pop(pos)
config_section = argv.pop(pos)
if argv and (argv[-1] in DATABASE):
database = argv.pop() # database name tool_shed, galaxy, or install.
else:
database = 'galaxy'
return config_file, config_section, database
def main(argv):
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='')
parser.add_argument('-d', '--dry-run', help='No changes, just test it.', action='store_true')
populate_config_args(parser)
args = parser.parse_args()
properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**properties)
secret = args.secret_key or config.id_secret
security_helper = SecurityHelper(id_secret=secret)
object_store = build_object_store_from_config(config)
if not config.database_connection:
print("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
model = galaxy.config.init_models_from_config(config, object_store=object_store)
session = model.context.current
pagerevs = session.query(model.PageRevision).all()
mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session)
for p in pagerevs:
try:
processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave)
processor.feed(p.content)
newcontent = unicodify(processor.output(), 'utf-8')
if p.content != newcontent:
if not args.dry_run:
p.content = unicodify(processor.output(), 'utf-8')
session.add(p)
session.flush()
else:
print("Modifying revision %s." % p.id)
print(difflib.unified_diff(p.content, newcontent))
except Exception:
logging.exception("Error parsing page, rolling changes back and skipping revision %s. Please report this error." % p.id)
session.rollback()
def parse_arguments():
parser = argparse.ArgumentParser(
description='Generate walltime statistics')
parser.add_argument('tool_id', help='Tool (by ID) to collect stats about')
parser.add_argument('--like',
action='store_true',
default=False,
help='Use SQL `LIKE` operator to find '
'a shed-installed tool using the tool\'s '
'"short" id')
populate_config_args(parser)
parser.add_argument('-d',
'--debug',
action='store_true',
default=False,
help='Print extra info')
parser.add_argument('-m',
'--min',
type=int,
default=-1,
help='Ignore runtimes less than MIN seconds')
parser.add_argument('-M',
'--max',
type=int,
default=-1,
help='Ignore runtimes greater than MAX seconds')
parser.add_argument('-u',
'--user',
help='Return stats for only this user (id, email, '
'or username)')
parser.add_argument('-s',
'--source',
default='metrics',
help='Runtime data source (SOURCES: %s)' %
', '.join(DATA_SOURCES))
args = parser.parse_args()
if args.like and '/' in args.tool_id:
print('ERROR: Do not use --like with a tool shed tool id (the tool '
'id should not contain `/` characters)')
sys.exit(2)
args.source = args.source.lower()
if args.source not in ('metrics', 'history'):
print('ERROR: Data source `%s` unknown, valid source are: %s' %
(args.source, ', '.join(DATA_SOURCES)))
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
uri = args.config.get_database_url(config)
names = {'database': 'dbname', 'username': '******'}
args.connect_args = url.make_url(uri).translate_connect_args(**names)
if args.debug:
print('Got options:')
for i in vars(args).items():
print('%s: %s' % i)
return args
def main(argv):
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-k', '--secret-key', help='Key to convert pages with', default='')
parser.add_argument('-d', '--dry-run', help='No changes, just test it.', action='store_true')
populate_config_args(parser)
args = parser.parse_args()
properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**properties)
secret = args.secret_key or config.id_secret
security_helper = IdEncodingHelper(id_secret=secret)
object_store = build_object_store_from_config(config)
if not config.database_connection:
print("The database connection is empty. If you are using the default value, please uncomment that in your galaxy.yml")
model = galaxy.config.init_models_from_config(config, object_store=object_store)
session = model.context.current
pagerevs = session.query(model.PageRevision).all()
mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session)
for p in pagerevs:
try:
processor = _PageContentProcessor(mock_trans, _placeholderRenderForSave)
processor.feed(p.content)
newcontent = unicodify(processor.output(), 'utf-8')
if p.content != newcontent:
if not args.dry_run:
p.content = unicodify(processor.output(), 'utf-8')
session.add(p)
session.flush()
else:
print("Modifying revision %s." % p.id)
print(difflib.unified_diff(p.content, newcontent))
except Exception:
logging.exception("Error parsing page, rolling changes back and skipping revision %s. Please report this error." % p.id)
session.rollback()
def __parse_args(self):
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-d',
'--debug',
action='store_true',
default=False,
help='Enable debug logging (SQL queries)')
parser.add_argument('--dry-run',
action='store_true',
default=False,
help="Dry run (rollback all transactions)")
parser.add_argument('--force-retry',
action='store_true',
default=False,
help="Retry file removals (on applicable actions)")
parser.add_argument(
'-o',
'--older-than',
dest='days',
type=int,
default=14,
help=
'Only perform action(s) on objects that have not been updated since the specified number of days'
)
parser.add_argument('-U',
'--no-update-time',
action='store_false',
dest='update_time',
default=True,
help="Don't set update_time on updated objects")
parser.add_argument(
'-s',
'--sequence',
dest='sequence',
default='',
help='DEPRECATED: Comma-separated sequence of actions')
parser.add_argument('-w',
'--work-mem',
dest='work_mem',
default=None,
help='Set PostgreSQL work_mem for this connection')
parser.add_argument('-l',
'--log-dir',
default=DEFAULT_LOG_DIR,
help='Log file directory')
parser.add_argument('actions',
nargs='*',
metavar='ACTION',
default=[],
help='Action(s) to perform, chosen from: %s' %
', '.join(sorted(self.actions.keys())))
self.args = parser.parse_args()
# add deprecated sequence arg to actions
self.args.sequence = [x.strip() for x in self.args.sequence.split(',')]
if self.args.sequence != ['']:
self.args.actions.extend(self.args.sequence)
if not self.args.actions:
parser.error("Please specify one or more actions")
def _read_model_arguments(argv, use_argparse=False):
if use_argparse:
parser = argparse.ArgumentParser()
parser.add_argument('database', metavar='DATABASE', type=str,
default="galaxy",
nargs='?',
help='database to target (galaxy, tool_shed, install)')
populate_config_args(parser)
args = parser.parse_args(argv[1:] if argv else [])
return args.config_file, args.config_section, args.database
else:
config_file = None
for arg in ["-c", "--config", "--config-file"]:
if arg in argv:
pos = argv.index(arg)
argv.pop(pos)
config_file = argv.pop(pos)
config_section = None
if "--config-section" in argv:
pos = argv.index("--config-section")
argv.pop(pos)
config_section = argv.pop(pos)
if argv and (argv[-1] in DATABASE):
database = argv.pop() # database name tool_shed, galaxy, or install.
else:
database = 'galaxy'
return config_file, config_section, database
def parse_arguments():
parser = argparse.ArgumentParser(
description='Generate walltime statistics')
parser.add_argument('tool_id', help='Tool (by ID) to collect stats about')
parser.add_argument('--like',
action='store_true',
default=False,
help='Use SQL `LIKE` operator to find '
'a shed-installed tool using the tool\'s '
'"short" id')
populate_config_args(parser)
parser.add_argument('-d', '--debug',
action='store_true',
default=False,
help='Print extra info')
parser.add_argument('-m', '--min',
type=int,
default=-1,
help='Ignore runtimes less than MIN seconds')
parser.add_argument('-M', '--max',
type=int,
default=-1,
help='Ignore runtimes greater than MAX seconds')
parser.add_argument('-u', '--user',
help='Return stats for only this user (id, email, '
'or username)')
parser.add_argument('-s', '--source',
default='metrics',
help='Runtime data source (SOURCES: %s)'
% ', '.join(DATA_SOURCES))
args = parser.parse_args()
if args.like and '/' in args.tool_id:
print('ERROR: Do not use --like with a tool shed tool id (the tool '
'id should not contain `/` characters)')
sys.exit(2)
args.source = args.source.lower()
if args.source not in ('metrics', 'history'):
print('ERROR: Data source `%s` unknown, valid source are: %s'
% (args.source, ', '.join(DATA_SOURCES)))
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
uri = args.config.get_database_url(config)
names = {'database': 'dbname', 'username': '******'}
args.connect_args = url.make_url(uri).translate_connect_args(**names)
if args.debug:
print('Got options:')
for i in vars(args).items():
print('%s: %s' % i)
return args
def __parse_args(self):
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-d', '--debug', action='store_true', dest='debug', help='Enable debug logging', default=False)
parser.add_argument('--dry-run', action='store_true', dest='dry_run', help="Dry run (rollback all transactions)", default=False)
parser.add_argument('--force-retry', action='store_true', dest='force_retry', help="Retry file removals (on applicable actions)", default=False)
parser.add_argument('-o', '--older-than', type=int, dest='days', help='Only perform action(s) on objects that have not been updated since the specified number of days', default=14)
parser.add_argument('-U', '--no-update-time', action='store_false', dest='update_time', help="Don't set update_time on updated objects", default=True)
parser.add_argument('-s', '--sequence', dest='sequence', help='Comma-separated sequence of actions, chosen from: %s' % self.action_names, default='')
parser.add_argument('-w', '--work-mem', dest='work_mem', help='Set PostgreSQL work_mem for this connection', default=None)
parser.add_argument('-l', '--log-dir', dest='log_dir', help='Log file directory', default=os.path.join(galaxy_root, 'scripts', 'cleanup_datasets'))
self.args = parser.parse_args()
self.args.sequence = [x.strip() for x in self.args.sequence.split(',')]
if self.args.sequence == ['']:
print("Error: At least one action must be specified in the action sequence\n")
parser.print_help()
sys.exit(0)
def main():
parser = argparse.ArgumentParser(DESCRIPTION)
populate_config_args(parser)
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
model = galaxy.config.init_models_from_config(config)
for row in model.context.query(model.Dataset):
if row.uuid is None:
row.uuid = uuid.uuid4()
print("Setting dataset:", row.id, " UUID to ", row.uuid)
model.context.flush()
for row in model.context.query(model.Workflow):
if row.uuid is None:
row.uuid = uuid.uuid4()
print("Setting Workflow:", row.id, " UUID to ", row.uuid)
model.context.flush()
print("Complete")
def parse_arguments():
parser = argparse.ArgumentParser(
description=
'Build a disk-backed Toolshed repository index and tool index for searching.'
)
populate_config_args(parser)
parser.add_argument('-d',
'--debug',
action='store_true',
default=False,
help='Print extra info')
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = ts_config.ToolShedAppConfiguration(**app_properties)
args.dburi = config.database_connection
args.hgweb_config_dir = config.hgweb_config_dir
args.whoosh_index_dir = config.whoosh_index_dir
args.file_path = config.file_path
if args.debug:
log.setLevel(logging.DEBUG)
log.debug('Full options:')
for i in vars(args).items():
log.debug('%s: %s' % i)
return args
def main():
"""
Datasets that are older than the specified cutoff and for which the tool_id
contains the specified text will be marked as deleted in user's history and
the user will be notified by email using the specified template file.
"""
parser = argparse.ArgumentParser()
parser.add_argument('legacy_config', metavar='CONFIG', type=str,
default=None,
nargs='?',
help='config file (legacy, use --config instead)')
parser.add_argument("-d", "--days", dest="days", action="store",
type=int, help="number of days (60)", default=60)
parser.add_argument("--tool_id", default=None,
help="Text to match against tool_id"
"Default: match all")
parser.add_argument("--template", default=None,
help="Mako Template file to use as email "
"Variables are 'cutoff' for the cutoff in days, "
"'email' for users email and "
"'datasets' which is a list of tuples "
"containing 'dataset' and 'history' names. "
"Default: admin_cleanup_deletion_template.txt")
parser.add_argument("-i", "--info_only", action="store_true",
dest="info_only", help="info about the requested action",
default=False)
parser.add_argument("-e", "--email_only", action="store_true",
dest="email_only", help="Send emails only, don't delete",
default=False)
parser.add_argument("--smtp", default=None,
help="SMTP Server to use to send email. "
"Default: [read from galaxy ini file]")
parser.add_argument("--fromaddr", default=None,
help="From address to use to send email. "
"Default: [read from galaxy ini file]")
populate_config_args(parser)
args = parser.parse_args()
config_override = None
if args.legacy_config:
config_override = args.legacy_config
app_properties = app_properties_from_args(args, legacy_config_override=config_override)
if args.smtp is not None:
app_properties['smtp_server'] = args.smtp
if app_properties.get('smtp_server') is None:
parser.error("SMTP Server must be specified as an option (--smtp) "
"or in the config file (smtp_server)")
if args.fromaddr is not None:
app_properties['email_from'] = args.fromaddr
if app_properties.get('email_from') is None:
parser.error("From address must be specified as an option "
"(--fromaddr) or in the config file "
"(email_from)")
scriptdir = os.path.dirname(os.path.abspath(__file__))
template_file = args.template
if template_file is None:
default_template = os.path.join(scriptdir,
'admin_cleanup_deletion_template.txt')
sample_template_file = "%s.sample" % default_template
if os.path.exists(default_template):
template_file = default_template
elif os.path.exists(sample_template_file):
print("Copying %s to %s" % (sample_template_file, default_template))
shutil.copyfile(sample_template_file, default_template)
template_file = default_template
else:
parser.error("Default template (%s) or sample template (%s) not "
"found, please specify template as an option "
"(--template)." % default_template,
sample_template_file)
elif not os.path.exists(template_file):
parser.error("Specified template file (%s) not found." % template_file)
config = galaxy.config.Configuration(**app_properties)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=args.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print("##########################################")
print("\n# %s - Handling stuff older than %i days" % (now, args.days))
if args.info_only:
print("# Displaying info only ( --info_only )\n")
elif args.email_only:
print("# Sending emails only, not deleting ( --email_only )\n")
administrative_delete_datasets(
app, cutoff_time, args.days, tool_id=args.tool_id,
template_file=template_file, config=config,
email_only=args.email_only, info_only=args.info_only)
app.shutdown()
sys.exit(0)
def main(argv):
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-r',
'--report-directory',
help='Directory to store reports in',
default=os.path.abspath(os.path.join('.', 'reports')))
parser.add_argument('-g',
'--grt-config',
help='Path to GRT config file',
default=default_config)
parser.add_argument(
"-l",
"--loglevel",
choices=['debug', 'info', 'warning', 'error', 'critical'],
help="Set the logging level",
default='warning')
parser.add_argument("-b",
"--batch-size",
type=int,
default=1000,
help="Batch size for sql queries")
parser.add_argument(
"-m",
"--max-records",
type=int,
default=0,
help=
"Maximum number of records to include in a single report. This option should ONLY be used when reporting historical data. Setting this may require running GRT multiple times to capture all historical logs."
)
populate_config_args(parser)
args = parser.parse_args()
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
_times = []
_start_time = time.time()
def annotate(label, human_label=None):
if human_label:
logging.info(human_label)
_times.append((label, time.time() - _start_time))
annotate('init_start', 'Loading GRT configuration...')
try:
with open(args.grt_config) as handle:
config = yaml.safe_load(handle)
except Exception:
logging.info('Using default GRT configuration')
with open(sample_config) as handle:
config = yaml.safe_load(handle)
annotate('init_end')
REPORT_DIR = args.report_directory
CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
REPORT_IDENTIFIER = str(time.time())
REPORT_BASE = os.path.join(REPORT_DIR, REPORT_IDENTIFIER)
if os.path.exists(CHECK_POINT_FILE):
with open(CHECK_POINT_FILE, 'r') as handle:
last_job_sent = int(handle.read())
else:
last_job_sent = -1
annotate('galaxy_init', 'Loading Galaxy...')
model, object_store, gxconfig, app = _init(
args, need_app=config['grt']['share_toolbox'])
# Galaxy overrides our logging level.
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
sa_session = model.context.current
annotate('galaxy_end')
# Fetch jobs COMPLETED with status OK that have not yet been sent.
# Set up our arrays
active_users = defaultdict(int)
job_state_data = defaultdict(int)
annotate('san_init', 'Building Sanitizer')
san = Sanitization(config['sanitization'], model, sa_session)
annotate('san_end')
if not os.path.exists(REPORT_DIR):
os.makedirs(REPORT_DIR)
# Pick an end point so our queries can return uniform data.
annotate('endpoint_start', 'Identifying a safe endpoint for SQL queries')
end_job_id = sa_session.query(model.Job.id) \
.order_by(model.Job.id.desc()) \
.first()[0]
# Allow users to only report N records at once.
if args.max_records > 0:
if end_job_id - last_job_sent > args.max_records:
end_job_id = last_job_sent + args.max_records
annotate('endpoint_end',
'Processing jobs (%s, %s]' % (last_job_sent, end_job_id))
# Remember the last job sent.
if end_job_id == last_job_sent:
logging.info("No new jobs to report")
# So we can just quit now.
sys.exit(0)
# Unfortunately we have to keep this mapping for the sanitizer to work properly.
job_tool_map = {}
blacklisted_tools = config['sanitization']['tools']
annotate('export_jobs_start', 'Exporting Jobs')
handle_job = open(REPORT_BASE + '.jobs.tsv', 'w')
handle_job.write('\t'.join(('id', 'tool_id', 'tool_version', 'state',
'create_time')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
.filter(model.Job.id > offset_start) \
.filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# If the tool is blacklisted, exclude everywhere
if job[2] in blacklisted_tools:
continue
handle_job.write(str(job[0])) # id
handle_job.write('\t')
handle_job.write(job[2]) # tool_id
handle_job.write('\t')
handle_job.write(job[3]) # tool_version
handle_job.write('\t')
handle_job.write(job[4]) # state
handle_job.write('\t')
handle_job.write(str(job[5])) # create_time
handle_job.write('\n')
# meta counts
job_state_data[job[4]] += 1
active_users[job[1]] += 1
job_tool_map[job[0]] = job[2]
handle_job.close()
annotate('export_jobs_end')
annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
handle_metric_num = open(REPORT_BASE + '.metric_num.tsv', 'w')
handle_metric_num.write('\t'.join(('job_id', 'plugin', 'name', 'value')) +
'\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
.filter(model.JobMetricNumeric.job_id > offset_start) \
.filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# No associated job
if metric[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[metric[0]] in blacklisted_tools:
continue
handle_metric_num.write(str(metric[0]))
handle_metric_num.write('\t')
handle_metric_num.write(metric[1])
handle_metric_num.write('\t')
handle_metric_num.write(metric[2])
handle_metric_num.write('\t')
handle_metric_num.write(str(metric[3]))
handle_metric_num.write('\n')
handle_metric_num.close()
annotate('export_metric_num_end')
annotate('export_params_start', 'Export Job Parameters')
handle_params = open(REPORT_BASE + '.params.tsv', 'w')
handle_params.write('\t'.join(('job_id', 'name', 'value')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
for param in sa_session.query(model.JobParameter.job_id, model.JobParameter.name, model.JobParameter.value) \
.filter(model.JobParameter.job_id > offset_start) \
.filter(model.JobParameter.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# No associated job
if param[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[param[0]] in blacklisted_tools:
continue
sanitized = san.sanitize_data(job_tool_map[param[0]], param[1],
param[2])
handle_params.write(str(param[0]))
handle_params.write('\t')
handle_params.write(param[1])
handle_params.write('\t')
handle_params.write(json.dumps(sanitized))
handle_params.write('\n')
handle_params.close()
annotate('export_params_end')
# Now on to outputs.
with tarfile.open(REPORT_BASE + '.tar.gz', 'w:gz') as handle:
for name in ('jobs', 'metric_num', 'params'):
handle.add(REPORT_BASE + '.' + name + '.tsv')
for name in ('jobs', 'metric_num', 'params'):
os.unlink(REPORT_BASE + '.' + name + '.tsv')
_times.append(('job_finish', time.time() - _start_time))
sha = hash_util.memory_bound_hexdigest(hash_util.sha256,
REPORT_BASE + ".tar.gz")
_times.append(('hash_finish', time.time() - _start_time))
# Now serialize the individual report data.
with open(REPORT_BASE + '.json', 'w') as handle:
if config['grt']['share_toolbox']:
toolbox = [(tool.id, tool.name, tool.version, tool.tool_shed,
tool.repository_id, tool.repository_name)
for tool_id, tool in app.toolbox._tools_by_id.items()]
else:
toolbox = None
json.dump(
{
"version": 1,
"galaxy_version": gxconfig.version_major,
"generated": REPORT_IDENTIFIER,
"report_hash": "sha256:" + sha,
"metrics": {
"_times": _times,
},
"users": {
"active": len(active_users.keys()),
"total": sa_session.query(model.User.id).count(),
},
"jobs": job_state_data,
"tools": toolbox
}, handle)
# Write our checkpoint file so we know where to start next time.
with open(CHECK_POINT_FILE, 'w') as handle:
handle.write(str(end_job_id))
Encodes and decodes IDs, returns Dataset IDs if provided an HDA or LDDA id,
returns the disk path of a dataset.
"""
import argparse
import os
import sys
sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
import galaxy.config
from galaxy.security import idencoding
from galaxy.util.script import app_properties_from_args, populate_config_args
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-e', '--encode-id', dest='encode_id', help='Encode an ID')
parser.add_argument('-d', '--decode-id', dest='decode_id', help='Decode an ID')
parser.add_argument('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
parser.add_argument('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
model = galaxy.config.init_models_from_config(config)
if args.encode_id:
print('Encoded "{}": {}'.format(args.encode_id, helper.encode_id(args.encode_id)))
if args.decode_id:
def __parse_args(self):
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-d',
'--debug',
action='store_true',
dest='debug',
help='Enable debug logging',
default=False)
parser.add_argument('--dry-run',
action='store_true',
dest='dry_run',
help="Dry run (rollback all transactions)",
default=False)
parser.add_argument('--force-retry',
action='store_true',
dest='force_retry',
help="Retry file removals (on applicable actions)",
default=False)
parser.add_argument(
'-o',
'--older-than',
type=int,
dest='days',
help=
'Only perform action(s) on objects that have not been updated since the specified number of days',
default=14)
parser.add_argument('-U',
'--no-update-time',
action='store_false',
dest='update_time',
help="Don't set update_time on updated objects",
default=True)
parser.add_argument(
'-s',
'--sequence',
dest='sequence',
help='Comma-separated sequence of actions, chosen from: %s' %
self.action_names,
default='')
parser.add_argument('-w',
'--work-mem',
dest='work_mem',
help='Set PostgreSQL work_mem for this connection',
default=None)
parser.add_argument('-l',
'--log-dir',
dest='log_dir',
help='Log file directory',
default=os.path.join(galaxy_root, 'scripts',
'cleanup_datasets'))
self.args = parser.parse_args()
self.args.sequence = [x.strip() for x in self.args.sequence.split(',')]
if self.args.sequence == ['']:
print(
"Error: At least one action must be specified in the action sequence\n"
)
parser.print_help()
sys.exit(0)
def main():
"""
Datasets that are older than the specified cutoff and for which the tool_id
contains the specified text will be marked as deleted in user's history and
the user will be notified by email using the specified template file.
"""
parser = argparse.ArgumentParser()
parser.add_argument('legacy_config',
metavar='CONFIG',
type=str,
default=None,
nargs='?',
help='config file (legacy, use --config instead)')
parser.add_argument("-d",
"--days",
dest="days",
action="store",
type=int,
help="number of days (60)",
default=60)
parser.add_argument("--tool_id",
default=None,
help="Text to match against tool_id"
"Default: match all")
parser.add_argument("--template",
default=None,
help="Mako Template file to use as email "
"Variables are 'cutoff' for the cutoff in days, "
"'email' for users email and "
"'datasets' which is a list of tuples "
"containing 'dataset' and 'history' names. "
"Default: admin_cleanup_deletion_template.txt")
parser.add_argument("-i",
"--info_only",
action="store_true",
dest="info_only",
help="info about the requested action",
default=False)
parser.add_argument("-e",
"--email_only",
action="store_true",
dest="email_only",
help="Send emails only, don't delete",
default=False)
parser.add_argument("--smtp",
default=None,
help="SMTP Server to use to send email. "
"Default: [read from galaxy ini file]")
parser.add_argument("--fromaddr",
default=None,
help="From address to use to send email. "
"Default: [read from galaxy ini file]")
populate_config_args(parser)
args = parser.parse_args()
config_override = None
if args.legacy_config:
config_override = args.legacy_config
app_properties = app_properties_from_args(
args, legacy_config_override=config_override)
if args.smtp is not None:
app_properties['smtp_server'] = args.smtp
if app_properties.get('smtp_server') is None:
parser.error("SMTP Server must be specified as an option (--smtp) "
"or in the config file (smtp_server)")
if args.fromaddr is not None:
app_properties['email_from'] = args.fromaddr
if app_properties.get('email_from') is None:
parser.error("From address must be specified as an option "
"(--fromaddr) or in the config file "
"(email_from)")
scriptdir = os.path.dirname(os.path.abspath(__file__))
template_file = args.template
if template_file is None:
default_template = os.path.join(scriptdir,
'admin_cleanup_deletion_template.txt')
sample_template_file = "%s.sample" % default_template
if os.path.exists(default_template):
template_file = default_template
elif os.path.exists(sample_template_file):
print("Copying %s to %s" %
(sample_template_file, default_template))
shutil.copyfile(sample_template_file, default_template)
template_file = default_template
else:
parser.error(
"Default template (%s) or sample template (%s) not "
"found, please specify template as an option "
"(--template)." % default_template, sample_template_file)
elif not os.path.exists(template_file):
parser.error("Specified template file (%s) not found." % template_file)
config = galaxy.config.Configuration(**app_properties)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=args.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print("##########################################")
print("\n# %s - Handling stuff older than %i days" % (now, args.days))
if args.info_only:
print("# Displaying info only ( --info_only )\n")
elif args.email_only:
print("# Sending emails only, not deleting ( --email_only )\n")
administrative_delete_datasets(app,
cutoff_time,
args.days,
tool_id=args.tool_id,
template_file=template_file,
config=config,
email_only=args.email_only,
info_only=args.info_only)
app.shutdown()
sys.exit(0)
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
from galaxy.util.script import app_properties_from_args, populate_config_args
from galaxy.web.security import SecurityHelper
logging.basicConfig()
log = logging.getLogger(__name__)
parser = argparse.ArgumentParser()
parser.add_argument('action', metavar='ACTION', type=str,
default=None,
help='decode|encode')
parser.add_argument('value', metavar='VALUE', type=str,
default=None,
help='value to encode or decode')
populate_config_args(parser)
args = parser.parse_args()
app_properties = app_properties_from_args(args)
helper = SecurityHelper(id_secret=app_properties.get('id_secret'))
# We need the ID secret for configuring the security helper to decrypt
# galaxysession cookies.
if "id_secret" not in app_properties:
log.warning('No ID_SECRET specified. Please set the "id_secret" in your galaxy.yml.')
id_secret = app_properties.get('id_secret', 'dangerous_default')
security_helper = SecurityHelper(id_secret=id_secret)
# And get access to the models
# Login manager to manage current_user functionality
def main(argv):
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-r',
'--report-directory',
help='Directory to store reports in',
default=os.path.abspath(os.path.join('.', 'reports')))
parser.add_argument('-g',
'--grt-config',
help='Path to GRT config file',
default=default_config)
parser.add_argument(
"-l",
"--loglevel",
choices=['debug', 'info', 'warning', 'error', 'critical'],
help="Set the logging level",
default='warning')
parser.add_argument("-b",
"--batch-size",
type=int,
default=1000,
help="Batch size for sql queries")
parser.add_argument(
"-m",
"--max-records",
type=int,
default=5000000,
help=
"Maximum number of records to include in a single report. This option should ONLY be used when reporting historical data. Setting this may require running GRT multiple times to capture all historical logs."
)
populate_config_args(parser)
args = parser.parse_args()
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
_times = []
_start_time = time.time()
def annotate(label, human_label=None):
if human_label:
logging.info(human_label)
_times.append((label, time.time() - _start_time))
annotate('init_start', 'Loading GRT configuration...')
try:
with open(args.grt_config) as handle:
config = yaml.safe_load(handle)
except Exception:
logging.info('Using default GRT configuration')
with open(sample_config) as handle:
config = yaml.safe_load(handle)
annotate('init_end')
REPORT_DIR = args.report_directory
CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
REPORT_IDENTIFIER = str(time.time())
REPORT_BASE = os.path.join(REPORT_DIR, REPORT_IDENTIFIER)
if os.path.exists(CHECK_POINT_FILE):
with open(CHECK_POINT_FILE, 'r') as handle:
last_job_sent = int(handle.read())
else:
last_job_sent = -1
annotate('galaxy_init', 'Loading Galaxy...')
model, object_store, gxconfig = _init(args)
# Galaxy overrides our logging level.
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
sa_session = model.context.current
annotate('galaxy_end')
# Fetch jobs COMPLETED with status OK that have not yet been sent.
# Set up our arrays
active_users = defaultdict(int)
job_state_data = defaultdict(int)
if not os.path.exists(REPORT_DIR):
os.makedirs(REPORT_DIR)
# Pick an end point so our queries can return uniform data.
annotate('endpoint_start', 'Identifying a safe endpoint for SQL queries')
end_job_id = sa_session.query(model.Job.id) \
.order_by(model.Job.id.desc()) \
.first()[0]
# Allow users to only report N records at once.
if args.max_records > 0:
if end_job_id - last_job_sent > args.max_records:
end_job_id = last_job_sent + args.max_records
annotate('endpoint_end',
'Processing jobs (%s, %s]' % (last_job_sent, end_job_id))
# Remember the last job sent.
if end_job_id == last_job_sent:
logging.info("No new jobs to report")
# So we can just quit now.
sys.exit(0)
# Unfortunately we have to keep this mapping for the sanitizer to work properly.
job_tool_map = {}
blacklisted_tools = config['sanitization']['tools']
annotate('export_jobs_start', 'Exporting Jobs')
with io.open(REPORT_BASE + '.jobs.tsv', 'w',
encoding='utf-8') as handle_job:
handle_job.write(u'\t'.join(('id', 'tool_id', 'tool_version', 'state',
'create_time')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
.filter(model.Job.id > offset_start) \
.filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# If the tool is blacklisted, exclude everywhere
if job[2] in blacklisted_tools:
continue
try:
line = [
str(job[0]), # id
job[2], # tool_id
job[3], # tool_version
job[4], # state
str(job[5]) # create_time
]
cline = unicodify('\t'.join(line) + '\n')
handle_job.write(cline)
except Exception:
logging.warning(
"Unable to write out a 'handle_job' row. Ignoring the row.",
exc_info=True)
continue
# meta counts
job_state_data[job[4]] += 1
active_users[job[1]] += 1
job_tool_map[job[0]] = job[2]
annotate('export_jobs_end')
annotate('export_datasets_start', 'Exporting Datasets')
with io.open(REPORT_BASE + '.datasets.tsv', 'w',
encoding='utf-8') as handle_datasets:
handle_datasets.write(u'\t'.join(('job_id', 'dataset_id', 'extension',
'file_size', 'param_name', 'type')) +
'\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
# four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
job_to_input_hda_ids = sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
model.JobToInputDatasetAssociation.name) \
.filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
job_to_output_hda_ids = sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
model.JobToOutputDatasetAssociation.name) \
.filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
# add type and concat
job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids
] + [[list(i), "output"]
for i in job_to_output_hda_ids]
# put all of the hda_ids into a list
hda_ids = [i[0][1] for i in job_to_hda_ids]
hdas = sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
model.HistoryDatasetAssociation.extension) \
.filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
.all()
# put all the dataset ids into a list
dataset_ids = [i[1] for i in hdas]
# get the sizes of the datasets
datasets = sa_session.query(model.Dataset.id, model.Dataset.total_size) \
.filter(model.Dataset.id.in_(dataset_ids)) \
.all()
# datasets to dictionay for easy search
hdas = {i[0]: i[1:] for i in hdas}
datasets = {i[0]: i[1:] for i in datasets}
for job_to_hda in job_to_hda_ids:
job = job_to_hda[0] # job_id, hda_id, name
filetype = job_to_hda[1] # input|output
# No associated job
if job[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[job[0]] in blacklisted_tools:
continue
hda_id = job[1]
if hda_id is None:
continue
dataset_id = hdas[hda_id][0]
if dataset_id is None:
continue
try:
line = [
str(job[0]), # Job ID
str(hda_id), # HDA ID
str(hdas[hda_id][1]), # Extension
round_to_2sd(datasets[dataset_id][0]), # File size
job[2], # Parameter name
str(filetype) # input/output
]
cline = unicodify('\t'.join(line) + '\n')
handle_datasets.write(cline)
except Exception:
logging.warning(
"Unable to write out a 'handle_datasets' row. Ignoring the row.",
exc_info=True)
continue
annotate('export_datasets_end')
annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
with io.open(REPORT_BASE + '.metric_num.tsv', 'w',
encoding='utf-8') as handle_metric_num:
handle_metric_num.write(u'\t'.join(('job_id', 'plugin', 'name',
'value')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start,
min(end_job_id, offset_start + args.batch_size))
for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
.filter(model.JobMetricNumeric.job_id > offset_start) \
.filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# No associated job
if metric[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[metric[0]] in blacklisted_tools:
continue
try:
line = [
str(metric[0]), # job id
metric[1], # plugin
metric[2], # name
str(metric[3]) # value
]
cline = unicodify('\t'.join(line) + '\n')
handle_metric_num.write(cline)
except Exception:
logging.warning(
"Unable to write out a 'handle_metric_num' row. Ignoring the row.",
exc_info=True)
continue
annotate('export_metric_num_end')
# Now on to outputs.
with tarfile.open(REPORT_BASE + '.tar.gz', 'w:gz') as handle:
for name in ('jobs', 'metric_num', 'datasets'):
path = REPORT_BASE + '.' + name + '.tsv'
if os.path.exists(path):
handle.add(path)
for name in ('jobs', 'metric_num', 'datasets'):
path = REPORT_BASE + '.' + name + '.tsv'
if os.path.exists(path):
os.unlink(REPORT_BASE + '.' + name + '.tsv')
_times.append(('job_finish', time.time() - _start_time))
sha = hash_util.memory_bound_hexdigest(hash_func=hash_util.sha256,
path=REPORT_BASE + ".tar.gz")
_times.append(('hash_finish', time.time() - _start_time))
# Now serialize the individual report data.
with open(REPORT_BASE + '.json', 'w') as handle:
json.dump(
{
"version": 3,
"galaxy_version": gxconfig.version_major,
"generated": REPORT_IDENTIFIER,
"report_hash": "sha256:" + sha,
"metrics": {
"_times": _times,
},
"users": {
"active": len(active_users.keys()),
"total": sa_session.query(model.User.id).count(),
},
"jobs": job_state_data,
}, handle)
# Write our checkpoint file so we know where to start next time.
with open(CHECK_POINT_FILE, 'w') as handle:
handle.write(str(end_job_id))
def main():
"""
Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities
of handling library datasets is mostly contained in the delete_datasets() method in this script.
Assume we have 1 library dataset with: LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset
At this point, we have the following database column values:
LibraryDatasetDatasetAssociation deleted: False
LibraryDataset deleted: False, purged: False
Dataset deleted: False purged: False
1. A user deletes the assumed dataset above from a data library via a UI menu option.
This action results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: False
LibraryDataset deleted: True*, purged: False
Dataset deleted: False, purged: False
2. After the number of days configured for the delete_datasets() method (option -6 below) have passed, execution
of the delete_datasets() method results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: True*
LibraryDataset deleted: True, purged: True*
Dataset deleted: True*, purged: False
3. After the number of days configured for the purge_datasets() method (option -3 below) have passed, execution
of the purge_datasets() method results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: True
LibraryDataset deleted: True, purged: True
Dataset deleted: True, purged: True* (dataset file removed from disk if -r flag is used)
This scenario is about as simple as it gets. Keep in mind that a Dataset object can have many HistoryDatasetAssociations
and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations.
Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects,
and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.
"""
parser = argparse.ArgumentParser()
parser.add_argument('legacy_config',
metavar='CONFIG',
type=str,
default=None,
nargs='?',
help='config file (legacy, use --config instead)')
parser.add_argument("-d",
"--days",
dest="days",
action="store",
type=int,
help="number of days (60)",
default=60)
parser.add_argument("-r",
"--remove_from_disk",
action="store_true",
dest="remove_from_disk",
help="remove datasets from disk when purged",
default=False)
parser.add_argument("-i",
"--info_only",
action="store_true",
dest="info_only",
help="info about the requested action",
default=False)
parser.add_argument(
"-f",
"--force_retry",
action="store_true",
dest="force_retry",
help=
"performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been",
default=False)
parser.add_argument("-1",
"--delete_userless_histories",
action="store_true",
dest="delete_userless_histories",
default=False,
help="delete userless histories and datasets")
parser.add_argument("-2",
"--purge_histories",
action="store_true",
dest="purge_histories",
default=False,
help="purge deleted histories")
parser.add_argument("-3",
"--purge_datasets",
action="store_true",
dest="purge_datasets",
default=False,
help="purge deleted datasets")
parser.add_argument("-4",
"--purge_libraries",
action="store_true",
dest="purge_libraries",
default=False,
help="purge deleted libraries")
parser.add_argument("-5",
"--purge_folders",
action="store_true",
dest="purge_folders",
default=False,
help="purge deleted library folders")
parser.add_argument(
"-6",
"--delete_datasets",
action="store_true",
dest="delete_datasets",
default=False,
help=
"mark deletable datasets as deleted and purge associated dataset instances"
)
populate_config_args(parser)
args = parser.parse_args()
config_override = None
if args.legacy_config:
config_override = args.legacy_config
if not (args.purge_folders ^ args.delete_userless_histories
^ args.purge_libraries ^ args.purge_histories ^ args.purge_datasets
^ args.delete_datasets):
parser.print_help()
sys.exit(0)
if args.remove_from_disk and args.info_only:
parser.error("remove_from_disk and info_only are mutually exclusive")
app_properties = app_properties_from_args(
args, legacy_config_override=config_override)
config = galaxy.config.Configuration(**app_properties)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=args.days)
now = strftime("%Y-%m-%d %H:%M:%S")
log.info("##########################################")
log.info("\n# %s - Handling stuff older than %i days" % (now, args.days))
if args.info_only:
log.info("# Displaying info only ( --info_only )\n")
elif args.remove_from_disk:
log.info("Datasets will be removed from disk.\n")
else:
log.info("Datasets will NOT be removed from disk.\n")
if args.delete_userless_histories:
delete_userless_histories(app,
cutoff_time,
info_only=args.info_only,
force_retry=args.force_retry)
elif args.purge_histories:
purge_histories(app,
cutoff_time,
args.remove_from_disk,
info_only=args.info_only,
force_retry=args.force_retry)
elif args.purge_datasets:
purge_datasets(app,
cutoff_time,
args.remove_from_disk,
info_only=args.info_only,
force_retry=args.force_retry)
elif args.purge_libraries:
purge_libraries(app,
cutoff_time,
args.remove_from_disk,
info_only=args.info_only,
force_retry=args.force_retry)
elif args.purge_folders:
purge_folders(app,
cutoff_time,
args.remove_from_disk,
info_only=args.info_only,
force_retry=args.force_retry)
elif args.delete_datasets:
delete_datasets(app,
cutoff_time,
args.remove_from_disk,
info_only=args.info_only,
force_retry=args.force_retry)
app.shutdown()
sys.exit(0)
def main(argv):
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-r', '--report-directory', help='Directory to store reports in',
default=os.path.abspath(os.path.join('.', 'reports')))
parser.add_argument('-g', '--grt-config', help='Path to GRT config file',
default=default_config)
parser.add_argument("-l", "--loglevel", choices=['debug', 'info', 'warning', 'error', 'critical'],
help="Set the logging level", default='warning')
parser.add_argument("-b", "--batch-size", type=int, default=1000,
help="Batch size for sql queries")
parser.add_argument("-m", "--max-records", type=int, default=0,
help="Maximum number of records to include in a single report. This option should ONLY be used when reporting historical data. Setting this may require running GRT multiple times to capture all historical logs.")
populate_config_args(parser)
args = parser.parse_args()
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
_times = []
_start_time = time.time()
def annotate(label, human_label=None):
if human_label:
logging.info(human_label)
_times.append((label, time.time() - _start_time))
annotate('init_start', 'Loading GRT configuration...')
try:
with open(args.grt_config) as handle:
config = yaml.safe_load(handle)
except Exception:
logging.info('Using default GRT configuration')
with open(sample_config) as handle:
config = yaml.safe_load(handle)
annotate('init_end')
REPORT_DIR = args.report_directory
CHECK_POINT_FILE = os.path.join(REPORT_DIR, '.checkpoint')
REPORT_IDENTIFIER = str(time.time())
REPORT_BASE = os.path.join(REPORT_DIR, REPORT_IDENTIFIER)
if os.path.exists(CHECK_POINT_FILE):
with open(CHECK_POINT_FILE, 'r') as handle:
last_job_sent = int(handle.read())
else:
last_job_sent = -1
annotate('galaxy_init', 'Loading Galaxy...')
model, object_store, gxconfig, app = _init(args, need_app=config['grt']['share_toolbox'])
# Galaxy overrides our logging level.
logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
sa_session = model.context.current
annotate('galaxy_end')
# Fetch jobs COMPLETED with status OK that have not yet been sent.
# Set up our arrays
active_users = defaultdict(int)
job_state_data = defaultdict(int)
annotate('san_init', 'Building Sanitizer')
san = Sanitization(config['sanitization'], model, sa_session)
annotate('san_end')
if not os.path.exists(REPORT_DIR):
os.makedirs(REPORT_DIR)
# Pick an end point so our queries can return uniform data.
annotate('endpoint_start', 'Identifying a safe endpoint for SQL queries')
end_job_id = sa_session.query(model.Job.id) \
.order_by(model.Job.id.desc()) \
.first()[0]
# Allow users to only report N records at once.
if args.max_records > 0:
if end_job_id - last_job_sent > args.max_records:
end_job_id = last_job_sent + args.max_records
annotate('endpoint_end', 'Processing jobs (%s, %s]' % (last_job_sent, end_job_id))
# Remember the last job sent.
if end_job_id == last_job_sent:
logging.info("No new jobs to report")
# So we can just quit now.
sys.exit(0)
# Unfortunately we have to keep this mapping for the sanitizer to work properly.
job_tool_map = {}
blacklisted_tools = config['sanitization']['tools']
annotate('export_jobs_start', 'Exporting Jobs')
handle_job = open(REPORT_BASE + '.jobs.tsv', 'w')
handle_job.write('\t'.join(('id', 'tool_id', 'tool_version', 'state', 'create_time')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
for job in sa_session.query(model.Job.id, model.Job.user_id, model.Job.tool_id, model.Job.tool_version, model.Job.state, model.Job.create_time) \
.filter(model.Job.id > offset_start) \
.filter(model.Job.id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# If the tool is blacklisted, exclude everywhere
if job[2] in blacklisted_tools:
continue
try:
handle_job.write(str(job[0])) # id
handle_job.write('\t')
handle_job.write(job[2]) # tool_id
handle_job.write('\t')
handle_job.write(job[3]) # tool_version
handle_job.write('\t')
handle_job.write(job[4]) # state
handle_job.write('\t')
handle_job.write(str(job[5])) # create_time
handle_job.write('\n')
except Exception:
logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True)
continue
# meta counts
job_state_data[job[4]] += 1
active_users[job[1]] += 1
job_tool_map[job[0]] = job[2]
handle_job.close()
annotate('export_jobs_end')
annotate('export_datasets_start', 'Exporting Datasets')
handle_datasets = open(REPORT_BASE + '.datasets.tsv', 'w')
handle_datasets.write('\t'.join(('job_id', 'dataset_id', 'extension', 'file_size', 'param_name', 'type')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
# four queries: JobToInputDatasetAssociation, JobToOutputDatasetAssociation, HistoryDatasetAssociation, Dataset
job_to_input_hda_ids = sa_session.query(model.JobToInputDatasetAssociation.job_id, model.JobToInputDatasetAssociation.dataset_id,
model.JobToInputDatasetAssociation.name) \
.filter(model.JobToInputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToInputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
job_to_output_hda_ids = sa_session.query(model.JobToOutputDatasetAssociation.job_id, model.JobToOutputDatasetAssociation.dataset_id,
model.JobToOutputDatasetAssociation.name) \
.filter(model.JobToOutputDatasetAssociation.job_id > offset_start) \
.filter(model.JobToOutputDatasetAssociation.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all()
# add type and concat
job_to_hda_ids = [[list(i), "input"] for i in job_to_input_hda_ids] + [[list(i), "output"] for i in job_to_output_hda_ids]
# put all of the hda_ids into a list
hda_ids = [i[0][1] for i in job_to_hda_ids]
hdas = sa_session.query(model.HistoryDatasetAssociation.id, model.HistoryDatasetAssociation.dataset_id,
model.HistoryDatasetAssociation.extension) \
.filter(model.HistoryDatasetAssociation.id.in_(hda_ids)) \
.all()
# put all the dataset ids into a list
dataset_ids = [i[1] for i in hdas]
# get the sizes of the datasets
datasets = sa_session.query(model.Dataset.id, model.Dataset.total_size) \
.filter(model.Dataset.id.in_(dataset_ids)) \
.all()
# datasets to dictionay for easy search
hdas = {i[0]: i[1:] for i in hdas}
datasets = {i[0]: i[1:] for i in datasets}
for job_to_hda in job_to_hda_ids:
job = job_to_hda[0] # job_id, hda_id, name
filetype = job_to_hda[1] # input|output
# No associated job
if job[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[job[0]] in blacklisted_tools:
continue
hda_id = job[1]
if hda_id is None:
continue
dataset_id = hdas[hda_id][0]
if dataset_id is None:
continue
try:
handle_datasets.write(str(job[0]))
handle_datasets.write('\t')
handle_datasets.write(str(hda_id))
handle_datasets.write('\t')
handle_datasets.write(str(hdas[hda_id][1]))
handle_datasets.write('\t')
handle_datasets.write(str(datasets[dataset_id][0]))
handle_datasets.write('\t')
handle_datasets.write(str(job[2]))
handle_datasets.write('\t')
handle_datasets.write(str(filetype))
handle_datasets.write('\n')
except Exception:
logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True)
continue
handle_datasets.close()
annotate('export_datasets_end')
annotate('export_metric_num_start', 'Exporting Metrics (Numeric)')
handle_metric_num = open(REPORT_BASE + '.metric_num.tsv', 'w')
handle_metric_num.write('\t'.join(('job_id', 'plugin', 'name', 'value')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
for metric in sa_session.query(model.JobMetricNumeric.job_id, model.JobMetricNumeric.plugin, model.JobMetricNumeric.metric_name, model.JobMetricNumeric.metric_value) \
.filter(model.JobMetricNumeric.job_id > offset_start) \
.filter(model.JobMetricNumeric.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# No associated job
if metric[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[metric[0]] in blacklisted_tools:
continue
try:
handle_metric_num.write(str(metric[0]))
handle_metric_num.write('\t')
handle_metric_num.write(metric[1])
handle_metric_num.write('\t')
handle_metric_num.write(metric[2])
handle_metric_num.write('\t')
handle_metric_num.write(str(metric[3]))
handle_metric_num.write('\n')
except Exception:
logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True)
continue
handle_metric_num.close()
annotate('export_metric_num_end')
annotate('export_params_start', 'Export Job Parameters')
handle_params = open(REPORT_BASE + '.params.tsv', 'w')
handle_params.write('\t'.join(('job_id', 'name', 'value')) + '\n')
for offset_start in range(last_job_sent, end_job_id, args.batch_size):
logging.debug("Processing %s:%s", offset_start, min(end_job_id, offset_start + args.batch_size))
for param in sa_session.query(model.JobParameter.job_id, model.JobParameter.name, model.JobParameter.value) \
.filter(model.JobParameter.job_id > offset_start) \
.filter(model.JobParameter.job_id <= min(end_job_id, offset_start + args.batch_size)) \
.all():
# No associated job
if param[0] not in job_tool_map:
continue
# If the tool is blacklisted, exclude everywhere
if job_tool_map[param[0]] in blacklisted_tools:
continue
try:
sanitized = san.sanitize_data(job_tool_map[param[0]], param[1], param[2])
handle_params.write(str(param[0]))
handle_params.write('\t')
handle_params.write(param[1])
handle_params.write('\t')
handle_params.write(json.dumps(sanitized))
handle_params.write('\n')
except Exception:
logging.warning("Unable to write out a 'handle_params' row. Ignoring the row.", exc_info=True)
continue
handle_params.close()
annotate('export_params_end')
# Now on to outputs.
with tarfile.open(REPORT_BASE + '.tar.gz', 'w:gz') as handle:
for name in ('jobs', 'metric_num', 'params', 'datasets'):
handle.add(REPORT_BASE + '.' + name + '.tsv')
for name in ('jobs', 'metric_num', 'params', 'datasets'):
os.unlink(REPORT_BASE + '.' + name + '.tsv')
_times.append(('job_finish', time.time() - _start_time))
sha = hash_util.memory_bound_hexdigest(hash_util.sha256, REPORT_BASE + ".tar.gz")
_times.append(('hash_finish', time.time() - _start_time))
# Now serialize the individual report data.
with open(REPORT_BASE + '.json', 'w') as handle:
if config['grt']['share_toolbox']:
toolbox = [
(tool.id, tool.name, tool.version, tool.tool_shed, tool.repository_id, tool.repository_name)
for tool_id, tool in app.toolbox._tools_by_id.items()
]
else:
toolbox = None
json.dump({
"version": 1,
"galaxy_version": gxconfig.version_major,
"generated": REPORT_IDENTIFIER,
"report_hash": "sha256:" + sha,
"metrics": {
"_times": _times,
},
"users": {
"active": len(active_users.keys()),
"total": sa_session.query(model.User.id).count(),
},
"jobs": job_state_data,
"tools": toolbox
}, handle)
# Write our checkpoint file so we know where to start next time.
with open(CHECK_POINT_FILE, 'w') as handle:
handle.write(str(end_job_id))
def main():
"""
Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities
of handling library datasets is mostly contained in the delete_datasets() method in this script.
Assume we have 1 library dataset with: LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset
At this point, we have the following database column values:
LibraryDatasetDatasetAssociation deleted: False
LibraryDataset deleted: False, purged: False
Dataset deleted: False purged: False
1. A user deletes the assumed dataset above from a data library via a UI menu option.
This action results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: False
LibraryDataset deleted: True*, purged: False
Dataset deleted: False, purged: False
2. After the number of days configured for the delete_datasets() method (option -6 below) have passed, execution
of the delete_datasets() method results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: True*
LibraryDataset deleted: True, purged: True*
Dataset deleted: True*, purged: False
3. After the number of days configured for the purge_datasets() method (option -3 below) have passed, execution
of the purge_datasets() method results in the following database column values (changes from previous step marked with *):
LibraryDatasetDatasetAssociation deleted: True
LibraryDataset deleted: True, purged: True
Dataset deleted: True, purged: True* (dataset file removed from disk if -r flag is used)
This scenario is about as simple as it gets. Keep in mind that a Dataset object can have many HistoryDatasetAssociations
and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations.
Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects,
and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.
"""
parser = argparse.ArgumentParser()
parser.add_argument('legacy_config', metavar='CONFIG', type=str,
default=None,
nargs='?',
help='config file (legacy, use --config instead)')
parser.add_argument("-d", "--days", dest="days", action="store", type=int, help="number of days (60)", default=60)
parser.add_argument("-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False)
parser.add_argument("-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False)
parser.add_argument("-f", "--force_retry", action="store_true", dest="force_retry", help="performs the requested actions, but ignores whether it might have been done before. Useful when -r wasn't used, but should have been", default=False)
parser.add_argument("-1", "--delete_userless_histories", action="store_true", dest="delete_userless_histories", default=False, help="delete userless histories and datasets")
parser.add_argument("-2", "--purge_histories", action="store_true", dest="purge_histories", default=False, help="purge deleted histories")
parser.add_argument("-3", "--purge_datasets", action="store_true", dest="purge_datasets", default=False, help="purge deleted datasets")
parser.add_argument("-4", "--purge_libraries", action="store_true", dest="purge_libraries", default=False, help="purge deleted libraries")
parser.add_argument("-5", "--purge_folders", action="store_true", dest="purge_folders", default=False, help="purge deleted library folders")
parser.add_argument("-6", "--delete_datasets", action="store_true", dest="delete_datasets", default=False, help="mark deletable datasets as deleted and purge associated dataset instances")
populate_config_args(parser)
args = parser.parse_args()
config_override = None
if args.legacy_config:
config_override = args.legacy_config
if not (args.purge_folders ^ args.delete_userless_histories ^
args.purge_libraries ^ args.purge_histories ^
args.purge_datasets ^ args.delete_datasets):
parser.print_help()
sys.exit(0)
if args.remove_from_disk and args.info_only:
parser.error("remove_from_disk and info_only are mutually exclusive")
app_properties = app_properties_from_args(args, legacy_config_override=config_override)
config = galaxy.config.Configuration(**app_properties)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=args.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print("##########################################")
print("\n# %s - Handling stuff older than %i days" % (now, args.days))
if args.info_only:
print("# Displaying info only ( --info_only )\n")
elif args.remove_from_disk:
print("Datasets will be removed from disk.\n")
else:
print("Datasets will NOT be removed from disk.\n")
if args.delete_userless_histories:
delete_userless_histories(app, cutoff_time, info_only=args.info_only, force_retry=args.force_retry)
elif args.purge_histories:
purge_histories(app, cutoff_time, args.remove_from_disk, info_only=args.info_only, force_retry=args.force_retry)
elif args.purge_datasets:
purge_datasets(app, cutoff_time, args.remove_from_disk, info_only=args.info_only, force_retry=args.force_retry)
elif args.purge_libraries:
purge_libraries(app, cutoff_time, args.remove_from_disk, info_only=args.info_only, force_retry=args.force_retry)
elif args.purge_folders:
purge_folders(app, cutoff_time, args.remove_from_disk, info_only=args.info_only, force_retry=args.force_retry)
elif args.delete_datasets:
delete_datasets(app, cutoff_time, args.remove_from_disk, info_only=args.info_only, force_retry=args.force_retry)
app.shutdown()
sys.exit(0)
