def biomaj_owner(options):
'''
Bank ownership management
'''
if not options.bank:
return (False, "Bank option is missing")
bank = Bank(options.bank, options=options, no_log=True)
bank.set_owner(options.owner)
return (True, None)
def test_owner(self):
'''
test ACL with owner
'''
b = Bank('local')
res = b.update()
self.assertTrue(res)
b.set_owner('sample')
b2 = Bank('local')
try:
res = b2.update()
self.fail('not owner, should not be allowed')
except Exception as e:
pass
def test_owner(self):
'''
test ACL with owner
'''
b = Bank('local')
res = b.update()
self.assertTrue(res)
b.set_owner('sample')
b2 = Bank('local')
try:
res = b2.update()
self.fail('not owner, should not be allowed')
except Exception as e:
pass
def test_owner(self):
"""
test ACL with owner
"""
b = Bank("local")
res = b.update()
self.assertTrue(res)
b.set_owner("sample")
b2 = Bank("local")
try:
res = b2.update()
self.fail("not owner, should not be allowed")
except Exception as e:
pass
def main():
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument('-c', '--config', dest="config",help="Configuration file")
parser.add_argument('--check', dest="check", help="Check bank property file", action="store_true", default=False)
parser.add_argument('-u', '--update', dest="update", help="Update action", action="store_true", default=False)
parser.add_argument('--fromscratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False)
parser.add_argument('-z', '--from-scratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False)
parser.add_argument('-p', '--publish', dest="publish", help="Publish", action="store_true", default=False)
parser.add_argument('--unpublish', dest="unpublish", help="Unpublish", action="store_true", default=False)
parser.add_argument('--release', dest="release", help="release of the bank")
parser.add_argument('--from-task', dest="from_task", help="Start cycle at a specific task (init always executed)")
parser.add_argument('--process', dest="process", help="Linked to from-task, optionally specify a block, meta or process name to start from")
parser.add_argument('-l', '--log', dest="log", help="log level")
parser.add_argument('-r', '--remove', dest="remove", help="Remove a bank release", action="store_true", default=False)
parser.add_argument('--remove-all', dest="removeall", help="Remove all bank releases and database records", action="store_true", default=False)
parser.add_argument('--remove-pending', dest="removepending", help="Remove pending release", action="store_true", default=False)
parser.add_argument('-s', '--status', dest="status", help="Get status", action="store_true", default=False)
parser.add_argument('-b', '--bank', dest="bank", help="bank name")
parser.add_argument('--owner', dest="owner", help="change owner of the bank")
parser.add_argument('--stop-before', dest="stop_before", help="Store workflow before task")
parser.add_argument('--stop-after', dest="stop_after", help="Store workflow after task")
parser.add_argument('--freeze', dest="freeze", help="Freeze a bank release", action="store_true", default=False)
parser.add_argument('--unfreeze', dest="unfreeze", help="Unfreeze a bank release", action="store_true", default=False)
parser.add_argument('-f', '--force', dest="force", help="Force action", action="store_true", default=False)
parser.add_argument('-h', '--help', dest="help", help="Show usage", action="store_true", default=False)
parser.add_argument('--search', dest="search", help="Search by format and types", action="store_true", default=False)
parser.add_argument('--formats', dest="formats", help="List of formats to search, comma separated")
parser.add_argument('--types', dest="types", help="List of types to search, comma separated")
parser.add_argument('--query', dest="query", help="Lucene query syntax to search in index")
parser.add_argument('--show', dest="show", help="Show format files for selected bank", action="store_true", default=False)
parser.add_argument('-n', '--change-dbname', dest="newbank", help="Change old bank name to this new bank name")
parser.add_argument('-e', '--move-production-directories', dest="newdir",help="Change bank production directories location to this new path, path must exists")
parser.add_argument('--visibility', dest="visibility", help="visibility status of the bank")
parser.add_argument('--maintenance', dest="maintenance", help="Maintenance mode (on/off/status)")
parser.add_argument('--version', dest="version", help="Show version", action="store_true", default=False)
parser.add_argument('--status-ko', dest="statusko", help="Get bank in KO status", action="store_true", default=False)
options = Options()
parser.parse_args(namespace=options)
options.no_log = False
if options.help:
print('''
--config: global.properties file path
--status: list of banks with published release
[OPTIONAL]
--bank xx / bank: Get status details of bank
--status-ko: list of banks in error status (last run)
--log DEBUG|INFO|WARN|ERR [OPTIONAL]: set log level in logs for this run, default is set in global.properties file
--check: Check bank property file
[MANDATORY]
--bank xx: name of the bank to check (will check xx.properties)
--owner yy: Change owner of the bank (user id)
[MANDATORY]
--bank xx: name of the bank
--visibility public|private: change visibility public/private of a bank
[MANDATORY]
--bank xx: name of the bank
--change-dbname yy: Change name of the bank to this new name
[MANDATORY]
--bank xx: current name of the bank
--move-production-directories yy: Change bank production directories location to this new path, path must exists
[MANDATORY]
--bank xx: current name of the bank
--update: Update bank
[MANDATORY]
--bank xx: name of the bank(s) to update, comma separated
[OPTIONAL]
--publish: after update set as *current* version
--from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1)
--stop-before xx: stop update cycle before the start of step xx
--stop-after xx: stop update cycle after step xx has completed
--from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx*
--process xx: linked to from-task, optionally specify a block, meta or process name to start from
--release xx: release to update
--publish: Publish bank as current release to use
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to publish
--unpublish: Unpublish bank (remove current)
[MANDATORY]
--bank xx: name of the bank to update
--remove-all: Remove all bank releases and database records
[MANDATORY]
--bank xx: name of the bank to update
[OPTIONAL]
--force: remove freezed releases
--remove-pending: Remove pending releases
[MANDATORY]
--bank xx: name of the bank to update
--remove: Remove bank release (files and database release)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
Release must not be the *current* version. If this is the case, publish a new release before.
--freeze: Freeze bank release (cannot be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--unfreeze: Unfreeze bank release (can be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--search: basic search in bank production releases, return list of banks
--formats xx,yy : list of comma separated format
AND/OR
--types xx,yy : list of comma separated type
--query "LUCENE query syntax": search in index (if activated)
--show: Show bank files per format
[MANDATORY]
--bank xx: name of the bank to show
[OPTIONAL]
--release xx: release of the bank to show
--maintenance on/off/status: (un)set biomaj in maintenance mode to prevent updates/removal
''')
return
if options.version:
version = pkg_resources.require('biomaj')[0].version
print('Version: '+str(version))
return
if options.stop_after or options.stop_before or options.from_task:
available_steps = []
for flow in UpdateWorkflow.FLOW:
available_steps.append(flow['name'])
for flow in RemoveWorkflow.FLOW:
available_steps.append(flow['name'])
if options.stop_after:
if options.stop_after not in available_steps:
print('Invalid step: '+options.stop_after)
sys.exit(1)
if options.stop_before:
if options.stop_before not in available_steps:
print('Invalid step: '+options.stop_before)
sys.exit(1)
if options.from_task:
if options.from_task not in available_steps:
print('Invalid step: '+options.from_task)
sys.exit(1)
bmaj = None
try:
if options.config is not None:
BiomajConfig.load_config(options.config)
else:
BiomajConfig.load_config()
except Exception as e:
print(str(e))
sys.exit(1)
try:
if options.maintenance:
if options.maintenance not in ['on', 'off', 'status']:
print("Wrong maintenance value [on,off,status]")
sys.exit(1)
data_dir = BiomajConfig.global_config.get('GENERAL', 'data.dir')
if BiomajConfig.global_config.has_option('GENERAL', 'lock.dir'):
lock_dir = BiomajConfig.global_config.get('GENERAL', 'lock.dir')
else:
lock_dir = data_dir
maintenance_lock_file = os.path.join(lock_dir,'biomaj.lock')
if options.maintenance == 'status':
if os.path.exists(maintenance_lock_file):
print("Maintenance: On")
else:
print("Maintenance: Off")
sys.exit(0)
if options.maintenance == 'on':
f = open(maintenance_lock_file, 'w')
f.write('1')
f.close()
print("Maintenance set to On")
sys.exit(0)
if options.maintenance == 'off':
if os.path.exists(maintenance_lock_file):
os.remove(maintenance_lock_file)
print("Maintenance set to Off")
sys.exit(0)
if options.owner:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
bank.set_owner(options.owner)
sys.exit(0)
if options.visibility:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
if options.visibility not in ['public', 'private']:
print("Valid values are public|private")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
bank.set_visibility(options.visibility)
print("Do not forget to update accordingly the visibility.default parameter in the configuration file")
sys.exit(0)
if options.newdir:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
if not os.path.exists(options.newdir):
print("Destination directory does not exists")
bank = Bank(options.bank, options=options, no_log=True)
if not bank.bank['production']:
print("Nothing to move, no production directory")
sys.exit(0)
bank.load_session(Workflow.FLOW, None)
w = Workflow(bank)
res = w.wf_init()
if not res:
sys.exit(1)
for prod in bank.bank['production']:
session = bank.get_session_from_release(prod['release'])
bank.load_session(Workflow.FLOW, session)
prod_path = bank.session.get_full_release_directory()
if os.path.exists(prod_path):
shutil.move(prod_path, options.newdir)
prod['data_dir'] = options.newdir
bank.banks.update({'name': options.bank}, {'$set' : { 'production': bank.bank['production'] }})
print("Bank production directories moved to " + options.newdir)
print("WARNING: do not forget to update accordingly the data.dir and dir.version properties")
w.wf_over()
sys.exit(0)
if options.newbank:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir')
bank_prop_file = os.path.join(conf_dir,options.bank+'.properties')
config_bank = configparser.SafeConfigParser()
config_bank.read([os.path.join(conf_dir,options.bank+'.properties')])
config_bank.set('GENERAL', 'db.name', options.newbank)
newbank_prop_file = open(os.path.join(conf_dir,options.newbank+'.properties'),'w')
config_bank.write(newbank_prop_file)
newbank_prop_file.close()
bank.banks.update({'name': options.bank}, {'$set' : { 'name': options.newbank }})
os.remove(bank_prop_file)
print("Bank "+options.bank+" renamed to "+options.newbank)
sys.exit(0)
if options.search:
if options.query:
res = Bank.searchindex(options.query)
print("Query matches for :"+options.query)
results = [["Release", "Format(s)", "Type(s)", "Files"]]
for match in res:
results.append([match['_source']['release'],
str(match['_source']['format']),
str(match['_source']['types']),
','.join(match['_source']['files'])])
print(tabulate(results, headers="firstrow", tablefmt="grid"))
else:
formats = []
if options.formats:
formats = options.formats.split(',')
types = []
if options.types:
types = options.types.split(',')
print("Search by formats="+str(formats)+", types="+str(types))
res = Bank.search(formats, types, False)
results = [["Name", "Release", "Format(s)", "Type(s)", 'Current']]
for bank in sorted(res, key=lambda bank: (bank['name'])):
b = bank['name']
bank['production'].sort(key=lambda n: n['release'], reverse=True)
for prod in bank['production']:
iscurrent = ""
if prod['session'] == bank['current']:
iscurrent = "yes"
results.append([b if b else '', prod['release'], ','.join(prod['formats']),
','.join(prod['types']), iscurrent])
b = None
print(tabulate(results, headers="firstrow", tablefmt="grid"))
sys.exit(0)
if options.show:
if not options.bank:
print("Bank option is required")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
results = [["Name", "Release", "Format(s)", "Type(s)", "Tag(s)", "File(s)"]]
current = None
fformat = None
if 'current' in bank.bank and bank.bank['current']:
current = bank.bank['current']
for prod in bank.bank['production']:
include = True
release = prod['release']
if current == prod['session']:
release += ' (current)'
if options.release and (prod['release'] != options.release and prod['prod_dir'] != options.release):
include =False
if include:
session = bank.get_session_from_release(prod['release'])
formats = session['formats']
afiles = []
atags = []
atypes = []
for fformat in list(formats.keys()):
for elt in formats[fformat]:
atypes.append(','.join(elt['types']))
for tag in list(elt['tags'].keys()):
atags.append(elt['tags'][tag])
for eltfile in elt['files']:
afiles.append(eltfile)
results.append([bank.bank['name'], release, fformat, ','.join(atypes),
','.join(atags), ','.join(afiles)])
print(tabulate(results, headers="firstrow", tablefmt="grid"))
sys.exit(0)
if options.check:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
print(options.bank+" check: "+str(bank.check())+"\n")
sys.exit(0)
if options.status:
if options.bank:
bank = Bank(options.bank, no_log=True)
info = bank.get_bank_release_info(full=True)
print(tabulate(info['info'], headers='firstrow', tablefmt='psql'))
print(tabulate(info['prod'], headers='firstrow', tablefmt='psql'))
# do we have some pending release(s)
if 'pend' in info and len(info['pend']) > 1:
print(tabulate(info['pend'], headers='firstrow', tablefmt='psql'))
else:
banks = Bank.list()
# Headers of output table
banks_list = [["Name", "Type(s)", "Release", "Visibility"]]
for bank in sorted(banks, key=lambda k: k['name']):
bank = Bank(bank['name'], no_log=True)
banks_list.append(bank.get_bank_release_info()['info'])
print(tabulate(banks_list, headers="firstrow", tablefmt="psql"))
sys.exit(0)
if options.statusko:
banks = Bank.list()
banks_list = [["Name", "Type(s)", "Release", "Visibility"]]
for bank in sorted(banks, key=lambda k: k['name']):
try:
bank = Bank(bank['name'], no_log=True)
bank.load_session(UpdateWorkflow.FLOW)
if bank.session is not None:
if bank.use_last_session and not bank.session.get_status(Workflow.FLOW_OVER):
wf_status = bank.session.get('workflow_status')
if wf_status is None or not wf_status:
banks_list.append(bank.get_bank_release_info()['info'])
except Exception as e:
print(str(e))
print(tabulate(banks_list, headers="firstrow", tablefmt="psql"))
if options.update:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
banks = options.bank.split(',')
gres = True
for bank in banks:
options.bank = bank
bmaj = Bank(bank, options)
print('Log file: '+bmaj.config.log_file)
check_status = bmaj.check()
if not check_status:
print('Skip bank ' + options.bank + ': wrong config')
gres = False
continue
res = bmaj.update(depends=True)
if not res:
gres = False
Notify.notifyBankAction(bmaj)
if not gres:
sys.exit(1)
if options.freeze:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if not options.release:
print("Bank release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options)
res = bmaj.freeze(options.release)
if not res:
sys.exit(1)
if options.unfreeze:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if not options.release:
print("Bank release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options)
res = bmaj.unfreeze(options.release)
if not res:
sys.exit(1)
if options.remove or options.removeall:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if options.remove and not options.release:
print("Bank release is missing")
sys.exit(1)
if options.removeall:
bmaj = Bank(options.bank, options, no_log=True)
print('Log file: '+bmaj.config.log_file)
res = bmaj.removeAll(options.force)
else:
bmaj = Bank(options.bank, options)
print('Log file: '+bmaj.config.log_file)
res = bmaj.remove(options.release)
Notify.notifyBankAction(bmaj)
if not res:
sys.exit(1)
if options.removepending:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
print('Log file: '+bmaj.config.log_file)
res = bmaj.remove_pending(options.release)
if not res:
sys.exit(1)
if options.unpublish:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
bmaj.load_session()
bmaj.unpublish()
sys.exit(0)
if options.publish:
if not options.bank:
print("Bank name or release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
print('Log file: '+bmaj.config.log_file)
bmaj.load_session()
bank = bmaj.bank
session = None
if options.get_option('release') is None:
# Get latest prod release
if len(bank['production'])>0:
prod = bank['production'][len(bank['production'])-1]
for s in bank['sessions']:
if s['id'] == prod['session']:
session = s
break
else:
# Search production release matching release
for prod in bank['production']:
if prod['release'] == options.release or prod['prod_dir'] == options.release:
# Search session related to this production release
for s in bank['sessions']:
if s['id'] == prod['session']:
session = s
break
break
if session is None:
print("No production session could be found for this release")
sys.exit(1)
bmaj.session._session = session
bmaj.publish()
except Exception as e:
print(str(e))
def update_bank_config(request):
settings = request.registry.settings
user = is_authenticated(request)
if user is None:
return HTTPForbidden('Not authenticated')
name = request.matchdict['id']
body = request.body
if sys.version_info >= (3,):
body = request.body.decode()
props = json.loads(body)
newprops = copy.deepcopy(props)
if 'db.post.process' in newprops:
del newprops['db.post.process']
for key,value in props.iteritems():
if key == 'no.extract':
if props['no.extract']:
newprops['no.extract'] = 'true'
else:
newprops['no.extract'] = 'false'
elif 'depends' in props and props['depends']:
depnames = []
for dep in props['depends']:
depnames.append(dep['name'])
newprops[dep['name']+'.files.move'] = dep['files.move']
newprops['depends'] = ','.join(depnames)
elif 'multi' in props and props['multi']:
count = 0
for m in props['multi']:
newprops['remote.file.'+str(count)+'name'] = m['name']
newprops['remote.file.'+str(count)+'method'] = m['method']
newprops['remote.file.'+str(count)+'protocol'] = m['protocol']
newprops['remote.file.'+str(count)+'server'] = m['server']
newprops['remote.file.'+str(count)+'path'] = m['path']
newprops['remote.file.'+str(count)+'credentials'] = m['credentials']
count += 1
del newprops['multi']
elif 'db.pre.process' in props and props['db.pre.process']:
metas = set_metas(newprops, props['db.pre.process'])
newprops['db.pre.process'] = ','.join(metas)
elif 'db.remove.process' in props and props['db.remove.process']:
metas = set_metas(newprops, props['db.remove.process'])
newprops['db.remove.process'] = ','.join(metas)
elif 'blocks' in props and props['blocks']:
blocks = set_blocks(newprops, props['blocks'])
newprops['blocks'] = ','.join(blocks)
bank = None
try:
config = BiomajConfig(name, options)
except Exception:
# config does not exists, create it
conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir')
config_bank = ConfigParser.SafeConfigParser()
config_bank.add_section('GENERAL')
for key,value in newprops.iteritems():
if value is None:
value = ""
config_bank.set('GENERAL',key,value)
config_bank_file = open(os.path.join(conf_dir,name+".properties"),'w')
config_bank.write(config_bank_file)
config_bank_file.close()
finally:
bank = Bank(name, no_log=True)
# Force owner to user logged in
bank.set_owner(user['id'])
test = bank.config.check()
if not test:
return {'msg': 'invalid configuration'}
if bank is None or not can_edit_bank(request, bank.bank):
return HTTPForbidden('Not authorized to access this resource')
return {'msg': 'bank created/updated'}
def main():
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument('-c',
'--config',
dest="config",
help="Configuration file")
parser.add_argument('--check',
dest="check",
help="Check bank property file",
action="store_true",
default=False)
parser.add_argument('-u',
'--update',
dest="update",
help="Update action",
action="store_true",
default=False)
parser.add_argument('--fromscratch',
dest="fromscratch",
help="Force a new cycle update",
action="store_true",
default=False)
parser.add_argument('-z',
'--from-scratch',
dest="fromscratch",
help="Force a new cycle update",
action="store_true",
default=False)
parser.add_argument('-p',
'--publish',
dest="publish",
help="Publish",
action="store_true",
default=False)
parser.add_argument('--unpublish',
dest="unpublish",
help="Unpublish",
action="store_true",
default=False)
parser.add_argument('--release',
dest="release",
help="release of the bank")
parser.add_argument(
'--from-task',
dest="from_task",
help="Start cycle at a specific task (init always executed)")
parser.add_argument(
'--process',
dest="process",
help=
"Linked to from-task, optionally specify a block, meta or process name to start from"
)
parser.add_argument('-l', '--log', dest="log", help="log level")
parser.add_argument('-r',
'--remove',
dest="remove",
help="Remove a bank release",
action="store_true",
default=False)
parser.add_argument('--remove-all',
dest="removeall",
help="Remove all bank releases and database records",
action="store_true",
default=False)
parser.add_argument('--remove-pending',
dest="removepending",
help="Remove pending release",
action="store_true",
default=False)
parser.add_argument('-s',
'--status',
dest="status",
help="Get status",
action="store_true",
default=False)
parser.add_argument('-b', '--bank', dest="bank", help="bank name")
parser.add_argument('--owner',
dest="owner",
help="change owner of the bank")
parser.add_argument('--stop-before',
dest="stop_before",
help="Store workflow before task")
parser.add_argument('--stop-after',
dest="stop_after",
help="Store workflow after task")
parser.add_argument('--freeze',
dest="freeze",
help="Freeze a bank release",
action="store_true",
default=False)
parser.add_argument('--unfreeze',
dest="unfreeze",
help="Unfreeze a bank release",
action="store_true",
default=False)
parser.add_argument('-f',
'--force',
dest="force",
help="Force action",
action="store_true",
default=False)
parser.add_argument('-h',
'--help',
dest="help",
help="Show usage",
action="store_true",
default=False)
parser.add_argument('--search',
dest="search",
help="Search by format and types",
action="store_true",
default=False)
parser.add_argument('--formats',
dest="formats",
help="List of formats to search, comma separated")
parser.add_argument('--types',
dest="types",
help="List of types to search, comma separated")
parser.add_argument('--query',
dest="query",
help="Lucene query syntax to search in index")
parser.add_argument('--show',
dest="show",
help="Show format files for selected bank",
action="store_true",
default=False)
parser.add_argument('-n',
'--change-dbname',
dest="newbank",
help="Change old bank name to this new bank name")
parser.add_argument(
'-e',
'--move-production-directories',
dest="newdir",
help=
"Change bank production directories location to this new path, path must exists"
)
parser.add_argument('--visibility',
dest="visibility",
help="visibility status of the bank")
parser.add_argument('--maintenance',
dest="maintenance",
help="Maintenance mode (on/off/status)")
parser.add_argument('--version',
dest="version",
help="Show version",
action="store_true",
default=False)
parser.add_argument('--status-ko',
dest="statusko",
help="Get bank in KO status",
action="store_true",
default=False)
options = Options()
parser.parse_args(namespace=options)
options.no_log = False
if options.help:
print('''
--config: global.properties file path
--status: list of banks with published release
[OPTIONAL]
--bank xx / bank: Get status details of bank
--status-ko: list of banks in error status (last run)
--log DEBUG|INFO|WARN|ERR [OPTIONAL]: set log level in logs for this run, default is set in global.properties file
--check: Check bank property file
[MANDATORY]
--bank xx: name of the bank to check (will check xx.properties)
--owner yy: Change owner of the bank (user id)
[MANDATORY]
--bank xx: name of the bank
--visibility public|private: change visibility public/private of a bank
[MANDATORY]
--bank xx: name of the bank
--change-dbname yy: Change name of the bank to this new name
[MANDATORY]
--bank xx: current name of the bank
--move-production-directories yy: Change bank production directories location to this new path, path must exists
[MANDATORY]
--bank xx: current name of the bank
--update: Update bank
[MANDATORY]
--bank xx: name of the bank(s) to update, comma separated
[OPTIONAL]
--publish: after update set as *current* version
--from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1)
--stop-before xx: stop update cycle before the start of step xx
--stop-after xx: stop update cycle after step xx has completed
--from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx*
--process xx: linked to from-task, optionally specify a block, meta or process name to start from
--release xx: release to update
--publish: Publish bank as current release to use
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to publish
--unpublish: Unpublish bank (remove current)
[MANDATORY]
--bank xx: name of the bank to update
--remove-all: Remove all bank releases and database records
[MANDATORY]
--bank xx: name of the bank to update
[OPTIONAL]
--force: remove freezed releases
--remove-pending: Remove pending releases
[MANDATORY]
--bank xx: name of the bank to update
--remove: Remove bank release (files and database release)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
Release must not be the *current* version. If this is the case, publish a new release before.
--freeze: Freeze bank release (cannot be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--unfreeze: Unfreeze bank release (can be removed)
[MANDATORY]
--bank xx: name of the bank to update
--release xx: release of the bank to remove
--search: basic search in bank production releases, return list of banks
--formats xx,yy : list of comma separated format
AND/OR
--types xx,yy : list of comma separated type
--query "LUCENE query syntax": search in index (if activated)
--show: Show bank files per format
[MANDATORY]
--bank xx: name of the bank to show
[OPTIONAL]
--release xx: release of the bank to show
--maintenance on/off/status: (un)set biomaj in maintenance mode to prevent updates/removal
''')
return
if options.version:
version = pkg_resources.require('biomaj')[0].version
print('Version: ' + str(version))
return
if options.stop_after or options.stop_before or options.from_task:
available_steps = []
for flow in UpdateWorkflow.FLOW:
available_steps.append(flow['name'])
for flow in RemoveWorkflow.FLOW:
available_steps.append(flow['name'])
if options.stop_after:
if options.stop_after not in available_steps:
print('Invalid step: ' + options.stop_after)
sys.exit(1)
if options.stop_before:
if options.stop_before not in available_steps:
print('Invalid step: ' + options.stop_before)
sys.exit(1)
if options.from_task:
if options.from_task not in available_steps:
print('Invalid step: ' + options.from_task)
sys.exit(1)
bmaj = None
try:
if options.config is not None:
BiomajConfig.load_config(options.config)
else:
BiomajConfig.load_config()
except Exception as e:
print(str(e))
sys.exit(1)
try:
if options.maintenance:
if options.maintenance not in ['on', 'off', 'status']:
print("Wrong maintenance value [on,off,status]")
sys.exit(1)
data_dir = BiomajConfig.global_config.get('GENERAL', 'data.dir')
if BiomajConfig.global_config.has_option('GENERAL', 'lock.dir'):
lock_dir = BiomajConfig.global_config.get(
'GENERAL', 'lock.dir')
else:
lock_dir = data_dir
maintenance_lock_file = os.path.join(lock_dir, 'biomaj.lock')
if options.maintenance == 'status':
if os.path.exists(maintenance_lock_file):
print("Maintenance: On")
else:
print("Maintenance: Off")
sys.exit(0)
if options.maintenance == 'on':
f = open(maintenance_lock_file, 'w')
f.write('1')
f.close()
print("Maintenance set to On")
sys.exit(0)
if options.maintenance == 'off':
if os.path.exists(maintenance_lock_file):
os.remove(maintenance_lock_file)
print("Maintenance set to Off")
sys.exit(0)
if options.owner:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
bank.set_owner(options.owner)
sys.exit(0)
if options.visibility:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
if options.visibility not in ['public', 'private']:
print("Valid values are public|private")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
bank.set_visibility(options.visibility)
print(
"Do not forget to update accordingly the visibility.default parameter in the configuration file"
)
sys.exit(0)
if options.newdir:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
if not os.path.exists(options.newdir):
print("Destination directory does not exists")
bank = Bank(options.bank, options=options, no_log=True)
if not bank.bank['production']:
print("Nothing to move, no production directory")
sys.exit(0)
bank.load_session(Workflow.FLOW, None)
w = Workflow(bank)
res = w.wf_init()
if not res:
sys.exit(1)
for prod in bank.bank['production']:
session = bank.get_session_from_release(prod['release'])
bank.load_session(Workflow.FLOW, session)
prod_path = bank.session.get_full_release_directory()
if os.path.exists(prod_path):
shutil.move(prod_path, options.newdir)
prod['data_dir'] = options.newdir
bank.banks.update(
{'name': options.bank},
{'$set': {
'production': bank.bank['production']
}})
print("Bank production directories moved to " + options.newdir)
print(
"WARNING: do not forget to update accordingly the data.dir and dir.version properties"
)
w.wf_over()
sys.exit(0)
if options.newbank:
if not options.bank:
print("Bank option is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir')
bank_prop_file = os.path.join(conf_dir,
options.bank + '.properties')
config_bank = configparser.SafeConfigParser()
config_bank.read(
[os.path.join(conf_dir, options.bank + '.properties')])
config_bank.set('GENERAL', 'db.name', options.newbank)
newbank_prop_file = open(
os.path.join(conf_dir, options.newbank + '.properties'), 'w')
config_bank.write(newbank_prop_file)
newbank_prop_file.close()
bank.banks.update({'name': options.bank},
{'$set': {
'name': options.newbank
}})
os.remove(bank_prop_file)
print("Bank " + options.bank + " renamed to " + options.newbank)
sys.exit(0)
if options.search:
if options.query:
res = Bank.searchindex(options.query)
print("Query matches for :" + options.query)
results = [["Release", "Format(s)", "Type(s)", "Files"]]
for match in res:
results.append([
match['_source']['release'],
str(match['_source']['format']),
str(match['_source']['types']),
','.join(match['_source']['files'])
])
print(tabulate(results, headers="firstrow", tablefmt="grid"))
else:
formats = []
if options.formats:
formats = options.formats.split(',')
types = []
if options.types:
types = options.types.split(',')
print("Search by formats=" + str(formats) + ", types=" +
str(types))
res = Bank.search(formats, types, False)
results = [[
"Name", "Release", "Format(s)", "Type(s)", 'Published'
]]
for bank in sorted(res, key=lambda bank: (bank['name'])):
b = bank['name']
bank['production'].sort(key=lambda n: n['release'],
reverse=True)
for prod in bank['production']:
iscurrent = ""
if prod['session'] == bank['current']:
iscurrent = "yes"
results.append([
b if b else '', prod['release'],
','.join(prod['formats']), ','.join(prod['types']),
iscurrent
])
print(tabulate(results, headers="firstrow", tablefmt="grid"))
sys.exit(0)
if options.show:
if not options.bank:
print("Bank option is required")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
results = [[
"Name", "Release", "Format(s)", "Type(s)", "Tag(s)", "File(s)"
]]
current = None
fformat = None
if 'current' in bank.bank and bank.bank['current']:
current = bank.bank['current']
for prod in bank.bank['production']:
include = True
release = prod['release']
if current == prod['session']:
release += ' (current)'
if options.release and (prod['release'] != options.release and
prod['prod_dir'] != options.release):
include = False
if include:
session = bank.get_session_from_release(prod['release'])
formats = session['formats']
afiles = []
atags = []
atypes = []
for fformat in list(formats.keys()):
for elt in formats[fformat]:
atypes.append(','.join(elt['types']))
for tag in list(elt['tags'].keys()):
atags.append(elt['tags'][tag])
for eltfile in elt['files']:
afiles.append(eltfile)
results.append([
bank.bank['name'], release, fformat, ','.join(atypes),
','.join(atags), ','.join(afiles)
])
print(tabulate(results, headers="firstrow", tablefmt="grid"))
sys.exit(0)
if options.check:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bank = Bank(options.bank, no_log=True)
print(options.bank + " check: " + str(bank.check()) + "\n")
sys.exit(0)
if options.status:
if options.bank:
bank = Bank(options.bank, no_log=True)
info = bank.get_bank_release_info(full=True)
print(
tabulate(info['info'], headers='firstrow',
tablefmt='psql'))
print(
tabulate(info['prod'], headers='firstrow',
tablefmt='psql'))
# do we have some pending release(s)
if 'pend' in info and len(info['pend']) > 1:
print(
tabulate(info['pend'],
headers='firstrow',
tablefmt='psql'))
else:
banks = Bank.list()
# Headers of output table
banks_list = [["Name", "Type(s)", "Release", "Visibility"]]
for bank in sorted(banks, key=lambda k: k['name']):
bank = Bank(bank['name'], no_log=True)
banks_list.append(bank.get_bank_release_info()['info'])
print(tabulate(banks_list, headers="firstrow",
tablefmt="psql"))
sys.exit(0)
if options.statusko:
banks = Bank.list()
banks_list = [[
"Name", "Type(s)", "Release", "Visibility", "Last run"
]]
for bank in sorted(banks, key=lambda k: k['name']):
try:
bank = Bank(bank['name'], no_log=True)
bank.load_session(UpdateWorkflow.FLOW)
if bank.session is not None:
if bank.use_last_session and not bank.session.get_status(
Workflow.FLOW_OVER):
wf_status = bank.session.get('workflow_status')
if wf_status is None or not wf_status:
banks_list.append(
bank.get_bank_release_info()['info'])
except Exception as e:
print(str(e))
print(tabulate(banks_list, headers="firstrow", tablefmt="psql"))
if options.update:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
banks = options.bank.split(',')
gres = True
for bank in banks:
options.bank = bank
bmaj = Bank(bank, options)
print('Log file: ' + bmaj.config.log_file)
check_status = bmaj.check()
if not check_status:
print('Skip bank ' + options.bank + ': wrong config')
gres = False
continue
res = bmaj.update(depends=True)
if not res:
gres = False
Notify.notifyBankAction(bmaj)
if not gres:
sys.exit(1)
if options.freeze:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if not options.release:
print("Bank release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options)
res = bmaj.freeze(options.release)
if not res:
sys.exit(1)
if options.unfreeze:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if not options.release:
print("Bank release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options)
res = bmaj.unfreeze(options.release)
if not res:
sys.exit(1)
if options.remove or options.removeall:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
if options.remove and not options.release:
print("Bank release is missing")
sys.exit(1)
if options.removeall:
bmaj = Bank(options.bank, options, no_log=True)
print('Log file: ' + bmaj.config.log_file)
res = bmaj.removeAll(options.force)
else:
bmaj = Bank(options.bank, options)
print('Log file: ' + bmaj.config.log_file)
res = bmaj.remove(options.release)
Notify.notifyBankAction(bmaj)
if not res:
sys.exit(1)
if options.removepending:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
res = bmaj.remove_pending(options.release)
if not res:
sys.exit(1)
if options.unpublish:
if not options.bank:
print("Bank name is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
bmaj.load_session()
bmaj.unpublish()
sys.exit(0)
if options.publish:
if not options.bank:
print("Bank name or release is missing")
sys.exit(1)
bmaj = Bank(options.bank, options, no_log=True)
bmaj.load_session()
bank = bmaj.bank
session = None
if options.get_option('release') is None:
# Get latest prod release
if len(bank['production']) > 0:
prod = bank['production'][len(bank['production']) - 1]
for s in bank['sessions']:
if s['id'] == prod['session']:
session = s
break
else:
# Search production release matching release
for prod in bank['production']:
if prod['release'] == options.release or prod[
'prod_dir'] == options.release:
# Search session related to this production release
for s in bank['sessions']:
if s['id'] == prod['session']:
session = s
break
break
if session is None:
print("No production session could be found for this release")
sys.exit(1)
bmaj.session._session = session
bmaj.publish()
except Exception as e:
print(str(e))