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 = OptionParser()
parser.add_option("-d",
"--days",
dest="days",
action="store",
type="int",
help="number of days (60)",
default=60)
parser.add_option("--tool_id",
default=None,
help="Text to match against tool_id"
"Default: match all")
parser.add_option("--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_option("-i",
"--info_only",
action="store_true",
dest="info_only",
help="info about the requested action",
default=False)
parser.add_option("-e",
"--email_only",
action="store_true",
dest="email_only",
help="Send emails only, don't delete",
default=False)
parser.add_option("--smtp",
default=None,
help="SMTP Server to use to send email. "
"Default: [read from galaxy ini file]")
parser.add_option("--fromaddr",
default=None,
help="From address to use to send email. "
"Default: [read from galaxy ini file]")
(options, args) = parser.parse_args()
ini_file = args[0]
config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
config_parser.read(ini_file)
config_dict = {}
for key, value in config_parser.items("app:main"):
config_dict[key] = value
if options.smtp is not None:
config_dict['smtp_server'] = options.smtp
if config_dict.get('smtp_server') is None:
parser.error("SMTP Server must be specified as an option (--smtp) "
"or in the config file (smtp_server)")
if options.fromaddr is not None:
config_dict['error_email_to'] = options.fromaddr
if config_dict.get('error_email_to') is None:
parser.error("From address must be specified as an option "
"(--fromaddr) or in the config file "
"(error_email_to)")
scriptdir = os.path.dirname(os.path.abspath(__file__))
template_file = options.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(**config_dict)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=options.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print "##########################################"
print "\n# %s - Handling stuff older than %i days" % (now, options.days)
if options.info_only:
print "# Displaying info only ( --info_only )\n"
elif options.email_only:
print "# Sending emails only, not deleting ( --email_only )\n"
administrative_delete_datasets(app,
cutoff_time,
options.days,
tool_id=options.tool_id,
template_file=template_file,
config=config,
email_only=options.email_only,
info_only=options.info_only)
app.shutdown()
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.
"""
usage = "usage: %prog [options] galaxy.ini"
parser = OptionParser(usage=usage)
parser.add_option("-d", "--days", dest="days", action="store",
type="int", help="number of days (60)", default=60)
parser.add_option("--tool_id", default=None,
help="Text to match against tool_id"
"Default: match all")
parser.add_option("--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_option("-i", "--info_only", action="store_true",
dest="info_only", help="info about the requested action",
default=False)
parser.add_option("-e", "--email_only", action="store_true",
dest="email_only", help="Send emails only, don't delete",
default=False)
parser.add_option("--smtp", default=None,
help="SMTP Server to use to send email. "
"Default: [read from galaxy ini file]")
parser.add_option("--fromaddr", default=None,
help="From address to use to send email. "
"Default: [read from galaxy ini file]")
(options, args) = parser.parse_args()
if len(args) != 1 :
parser.print_help()
sys.exit()
ini_file = args[0]
config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
config_parser.read(ini_file)
config_dict = {}
for key, value in config_parser.items("app:main"):
config_dict[key] = value
if options.smtp is not None:
config_dict['smtp_server'] = options.smtp
if config_dict.get('smtp_server') is None:
parser.error("SMTP Server must be specified as an option (--smtp) "
"or in the config file (smtp_server)")
if options.fromaddr is not None:
config_dict['email_from'] = options.fromaddr
if config_dict.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 = options.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(**config_dict)
app = CleanupDatasetsApplication(config)
cutoff_time = datetime.utcnow() - timedelta(days=options.days)
now = strftime("%Y-%m-%d %H:%M:%S")
print "##########################################"
print "\n# %s - Handling stuff older than %i days" % (now, options.days)
if options.info_only:
print "# Displaying info only ( --info_only )\n"
elif options.email_only:
print "# Sending emails only, not deleting ( --email_only )\n"
administrative_delete_datasets(
app, cutoff_time, options.days, tool_id=options.tool_id,
template_file=template_file, config=config,
email_only=options.email_only, info_only=options.info_only)
app.shutdown()
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)
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)