def main(argv=None):
"""Search a Cheshire3 database based on query in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(session, "database identifier not specified, discovered: {0}".format(dbid))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(
dbid
)
server.log_critical(session, msg)
return 2
else:
qFac = db.get_object(session, "defaultQueryFactory")
query = qFac.get_query(session, args.query, format=args.format)
resultSet = db.search(session, query)
return _format_resultSet(resultSet, maximumRecords=args.maxRecs, startRecord=args.startRec)
def main(argv=None):
global argparser, lockfilepath, lgr
global session, server, db, lgr
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
return 2
else:
lgr = db.get_path(session, 'defaultLogger')
pass
return args.func(args)
def main(argv=None):
"""Load data into a Cheshire3 database based on parameters in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
return 2
else:
docFac = db.get_object(session, 'defaultDocumentFactory')
docFac.load(session, args.data,
args.cache, args.format, args.tagname, args.codec)
wf = db.get_object(session, 'buildIndexWorkflow')
wf.process(session, docFac)
def main(argv=None):
"""Load data into a Cheshire3 database based on parameters in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid)
)
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
return 2
else:
# Allow for multiple data arguments
docFac = db.get_object(session, 'defaultDocumentFactory')
for dataArg in args.data:
try:
docFac.load(session,
dataArg,
args.cache,
args.format,
args.tagname,
args.codec
)
except MissingDependencyException as e:
server.log_critical(session, e.reason)
missingDependencies = e.dependencies
raise MissingDependencyException('cheshire3-load script',
missingDependencies
)
wf = db.get_object(session, 'buildIndexWorkflow')
wf.process(session, docFac)
def main(argv=None):
"""Search a Cheshire3 database based on query in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid)
)
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
return 2
else:
qFac = db.get_object(session, 'defaultQueryFactory')
query = qFac.get_query(session, args.query, format=args.format)
resultSet = db.search(session, query)
return _format_resultSet(resultSet,
maximumRecords=args.maxRecs,
startRecord=args.startRec)
def getCheshire3Env(args):
"""Init and return Cheshire3 Session, Server and Database.
Intialize Cheshire3 Session, Server and Database objects based on
``args``.
"""
# Create a Session
session = Session()
# Get the Server based on given serverConfig file
server = SimpleServer(session, args.serverconfig)
# Try to get the Database
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
raise
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid)
)
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
raise
else:
# Attach a default Logger to the Session
session.logger = db.get_path(session, 'defaultLogger')
return session, server, db
def main(argv=None):
"""Initialize a Cheshire 3 database based on parameters in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
if args.directory.endswith(os.path.sep):
args.directory = args.directory[:-1]
# Find local database name to use as basis of database id
dbid = "db_{0}".format(os.path.basename(args.directory))
server.log_debug(session,
("database identifier not specified, defaulting to: "
"{0}".format(dbid)))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
# Doesn't exists, so OK to init it
pass
else:
# TODO: check for --force ?
msg = """database with id '{0}' has already been init'd. \
Please specify a different id using the --database option.""".format(dbid)
server.log_critical(session, msg)
raise ValueError(msg)
# Create a .cheshire3 directory and populate it
c3_dir = os.path.join(os.path.abspath(args.directory), '.cheshire3')
for dir_path in [
c3_dir,
os.path.join(c3_dir, 'stores'),
os.path.join(c3_dir, 'indexes'),
os.path.join(c3_dir, 'logs')
]:
try:
os.makedirs(dir_path)
except OSError:
# Directory already exists
server.log_warning(session,
"directory already exists {0}".format(dir_path))
# Generate config file(s)
xmlFilesToWrite = {}
# Generate Protocol Map(s) (ZeeRex)
zrx = create_defaultZeerex(dbid, args)
zrxPath = os.path.join(c3_dir, 'zeerex_sru.xml')
args.zeerexPath = zrxPath
xmlFilesToWrite[zrxPath] = zrx
# Generate generic database config
dbConfig = create_defaultConfig(dbid, args)
dbConfigPath = os.path.join(c3_dir, 'config.xml')
xmlFilesToWrite[dbConfigPath] = dbConfig
# Generate config for generic selectors
selectorConfig = create_defaultConfigSelectors()
path = os.path.join(c3_dir, 'configSelectors.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = selectorConfig
# Generate config for generic indexes
indexConfig = create_defaultConfigIndexes()
path = os.path.join(c3_dir, 'configIndexes.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = indexConfig
# Generate config for default Workflows
workflowConfig = create_defaultConfigWorkflows()
path = os.path.join(c3_dir, 'configWorkflows.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = workflowConfig
# Write configs to files
for path, node in xmlFilesToWrite.iteritems():
with open(path, 'w') as conffh:
conffh.write(
etree.tostring(node, pretty_print=True, encoding="utf-8"))
# Tell the server to register the config file
server.register_databaseConfigFile(session, dbConfigPath)
return 0
def main(argv=None):
"""Load data into a Cheshire3 database based on parameters in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
if irods is None:
raise MissingDependencyException('icheshire3-load script',
'irods (PyRods)'
)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
try:
dbid = identify_database(session, os.getcwd())
except EnvironmentError as e:
server.log_critical(session, e.message)
return 1
server.log_debug(
session,
"database identifier not specified, discovered: {0}".format(dbid))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
msg = """Cheshire3 database {0} does not exist.
Please provide a different database identifier using the --database option.
""".format(dbid)
server.log_critical(session, msg)
return 2
else:
# Allow for multiple data arguments
docFac = db.get_object(session, 'defaultDocumentFactory')
for dataArg in args.data:
if dataArg.startswith('irods://'):
parsed = urlsplit(dataArg)
else:
# Examine current environment
status, myEnv = irods.getRodsEnv()
try:
host = myEnv.getRodsHost()
except AttributeError:
host = myEnv.rodsHost
# Port
try:
myEnv.getRodsPort()
except AttributeError:
port = myEnv.rodsPort
# User
try:
username = myEnv.getRodsUserName()
except AttributeError:
username = myEnv.rodsUserName
netloc = '{0}@{1}:{2}'.format(username, host, port)
try:
cqm = myEnv.getRodsCwd()
except AttributeError:
cwd = myEnv.rodsCwd
path = '/'.join([cwd, dataArg])
parsed = SplitResult('irods', netloc, path, None, None)
dataArg = urlunsplit(parsed)
server.log_debug(session, dataArg)
if args.format is None or not args.format.startswith('i'):
fmt = 'irods'
else:
fmt = args.format
server.log_debug(session, fmt)
try:
docFac.load(session, dataArg,
args.cache, fmt, args.tagname, args.codec)
except MissingDependencyException as e:
server.log_critical(session, e.reason)
missingDependencies = e.dependencies
raise MissingDependencyException('cheshire3-load script',
missingDependencies)
wf = db.get_object(session, 'buildIndexWorkflow')
wf.process(session, docFac)
def main(argv=None):
"""Initialize a Cheshire 3 database based on parameters in argv."""
global argparser, session, server, db
if argv is None:
args = argparser.parse_args()
else:
args = argparser.parse_args(argv)
session = Session()
server = SimpleServer(session, args.serverconfig)
if args.database is None:
if args.directory.endswith(os.path.sep):
args.directory = args.directory[:-1]
# Find local database name to use as basis of database id
dbid = "db_{0}".format(os.path.basename(args.directory))
server.log_debug(session,
("database identifier not specified, defaulting to: "
"{0}".format(dbid)))
else:
dbid = args.database
try:
db = server.get_object(session, dbid)
except ObjectDoesNotExistException:
# Doesn't exists, so OK to init it
pass
else:
# TODO: check for --force ?
msg = """database with id '{0}' has already been init'd. \
Please specify a different id using the --database option.""".format(dbid)
server.log_critical(session, msg)
raise ValueError(msg)
# Create a .cheshire3 directory and populate it
c3_dir = os.path.join(os.path.abspath(args.directory), '.cheshire3')
for dir_path in [c3_dir,
os.path.join(c3_dir, 'stores'),
os.path.join(c3_dir, 'indexes'),
os.path.join(c3_dir, 'logs')]:
try:
os.makedirs(dir_path)
except OSError:
# Directory already exists
server.log_warning(
session,
"directory already exists {0}".format(dir_path)
)
# Generate config file(s)
xmlFilesToWrite = {}
# Generate Protocol Map(s) (ZeeRex)
zrx = create_defaultZeerex(dbid, args)
zrxPath = os.path.join(c3_dir, 'zeerex_sru.xml')
args.zeerexPath = zrxPath
xmlFilesToWrite[zrxPath] = zrx
# Generate generic database config
dbConfig = create_defaultConfig(dbid, args)
dbConfigPath = os.path.join(c3_dir, 'config.xml')
xmlFilesToWrite[dbConfigPath] = dbConfig
# Generate config for generic selectors
selectorConfig = create_defaultConfigSelectors()
path = os.path.join(c3_dir, 'configSelectors.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = selectorConfig
# Generate config for generic indexes
indexConfig = create_defaultConfigIndexes()
path = os.path.join(c3_dir, 'configIndexes.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = indexConfig
# Generate config for default Workflows
workflowConfig = create_defaultConfigWorkflows()
path = os.path.join(c3_dir, 'configWorkflows.xml')
dbConfig = include_configByPath(dbConfig, path)
xmlFilesToWrite[path] = workflowConfig
# Write configs to files
for path, node in xmlFilesToWrite.iteritems():
with open(path, 'w') as conffh:
conffh.write(etree.tostring(node,
pretty_print=True,
encoding="utf-8"
)
)
# Tell the server to register the config file
server.register_databaseConfigFile(session, dbConfigPath)
return 0
