id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
232,800 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.disable_hdfs_ha | def disable_hdfs_ha(self, active_name, secondary_name,
start_dependent_services=True, deploy_client_configs=True,
disable_quorum_storage=False):
"""
Disable high availability for an HDFS NameNode.
This command is no longer supported with API v6 onwards. Use disable_nn_ha instead.
@param active_name: Name of the NameNode to keep.
@param secondary_name: Name of (existing) SecondaryNameNode to link to
remaining NameNode.
@param start_dependent_services: whether to re-start dependent services.
@param deploy_client_configs: whether to re-deploy client configurations.
@param disable_quorum_storage: whether to disable Quorum-based Storage. Available since API v2.
Quorum-based Storage will be disabled for all
nameservices that have Quorum-based Storage
enabled.
@return: Reference to the submitted command.
"""
args = dict(
activeName = active_name,
secondaryName = secondary_name,
startDependentServices = start_dependent_services,
deployClientConfigs = deploy_client_configs,
)
version = self._get_resource_root().version
if version < 2:
if disable_quorum_storage:
raise AttributeError("Quorum-based Storage requires at least API version 2 available in Cloudera Manager 4.1.")
else:
args['disableQuorumStorage'] = disable_quorum_storage
return self._cmd('hdfsDisableHa', data=args) | python | def disable_hdfs_ha(self, active_name, secondary_name,
start_dependent_services=True, deploy_client_configs=True,
disable_quorum_storage=False):
args = dict(
activeName = active_name,
secondaryName = secondary_name,
startDependentServices = start_dependent_services,
deployClientConfigs = deploy_client_configs,
)
version = self._get_resource_root().version
if version < 2:
if disable_quorum_storage:
raise AttributeError("Quorum-based Storage requires at least API version 2 available in Cloudera Manager 4.1.")
else:
args['disableQuorumStorage'] = disable_quorum_storage
return self._cmd('hdfsDisableHa', data=args) | [
"def",
"disable_hdfs_ha",
"(",
"self",
",",
"active_name",
",",
"secondary_name",
",",
"start_dependent_services",
"=",
"True",
",",
"deploy_client_configs",
"=",
"True",
",",
"disable_quorum_storage",
"=",
"False",
")",
":",
"args",
"=",
"dict",
"(",
"activeName"... | Disable high availability for an HDFS NameNode.
This command is no longer supported with API v6 onwards. Use disable_nn_ha instead.
@param active_name: Name of the NameNode to keep.
@param secondary_name: Name of (existing) SecondaryNameNode to link to
remaining NameNode.
@param start_dependent_services: whether to re-start dependent services.
@param deploy_client_configs: whether to re-deploy client configurations.
@param disable_quorum_storage: whether to disable Quorum-based Storage. Available since API v2.
Quorum-based Storage will be disabled for all
nameservices that have Quorum-based Storage
enabled.
@return: Reference to the submitted command. | [
"Disable",
"high",
"availability",
"for",
"an",
"HDFS",
"NameNode",
".",
"This",
"command",
"is",
"no",
"longer",
"supported",
"with",
"API",
"v6",
"onwards",
".",
"Use",
"disable_nn_ha",
"instead",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L886-L918 |
232,801 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enable_hdfs_auto_failover | def enable_hdfs_auto_failover(self, nameservice, active_fc_name,
standby_fc_name, zk_service):
"""
Enable auto-failover for an HDFS nameservice.
This command is no longer supported with API v6 onwards. Use enable_nn_ha instead.
@param nameservice: Nameservice for which to enable auto-failover.
@param active_fc_name: Name of failover controller to create for active node.
@param standby_fc_name: Name of failover controller to create for stand-by node.
@param zk_service: ZooKeeper service to use.
@return: Reference to the submitted command.
"""
version = self._get_resource_root().version
args = dict(
nameservice = nameservice,
activeFCName = active_fc_name,
standByFCName = standby_fc_name,
zooKeeperService = dict(
clusterName = zk_service.clusterRef.clusterName,
serviceName = zk_service.name,
),
)
return self._cmd('hdfsEnableAutoFailover', data=args) | python | def enable_hdfs_auto_failover(self, nameservice, active_fc_name,
standby_fc_name, zk_service):
version = self._get_resource_root().version
args = dict(
nameservice = nameservice,
activeFCName = active_fc_name,
standByFCName = standby_fc_name,
zooKeeperService = dict(
clusterName = zk_service.clusterRef.clusterName,
serviceName = zk_service.name,
),
)
return self._cmd('hdfsEnableAutoFailover', data=args) | [
"def",
"enable_hdfs_auto_failover",
"(",
"self",
",",
"nameservice",
",",
"active_fc_name",
",",
"standby_fc_name",
",",
"zk_service",
")",
":",
"version",
"=",
"self",
".",
"_get_resource_root",
"(",
")",
".",
"version",
"args",
"=",
"dict",
"(",
"nameservice",... | Enable auto-failover for an HDFS nameservice.
This command is no longer supported with API v6 onwards. Use enable_nn_ha instead.
@param nameservice: Nameservice for which to enable auto-failover.
@param active_fc_name: Name of failover controller to create for active node.
@param standby_fc_name: Name of failover controller to create for stand-by node.
@param zk_service: ZooKeeper service to use.
@return: Reference to the submitted command. | [
"Enable",
"auto",
"-",
"failover",
"for",
"an",
"HDFS",
"nameservice",
".",
"This",
"command",
"is",
"no",
"longer",
"supported",
"with",
"API",
"v6",
"onwards",
".",
"Use",
"enable_nn_ha",
"instead",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L920-L943 |
232,802 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enable_hdfs_ha | def enable_hdfs_ha(self, active_name, active_shared_path, standby_name,
standby_shared_path, nameservice, start_dependent_services=True,
deploy_client_configs=True, enable_quorum_storage=False):
"""
Enable high availability for an HDFS NameNode.
This command is no longer supported with API v6 onwards. Use enable_nn_ha instead.
@param active_name: name of active NameNode.
@param active_shared_path: shared edits path for active NameNode.
Ignored if Quorum-based Storage is being enabled.
@param standby_name: name of stand-by NameNode.
@param standby_shared_path: shared edits path for stand-by NameNode.
Ignored if Quourm Journal is being enabled.
@param nameservice: nameservice for the HA pair.
@param start_dependent_services: whether to re-start dependent services.
@param deploy_client_configs: whether to re-deploy client configurations.
@param enable_quorum_storage: whether to enable Quorum-based Storage. Available since API v2.
Quorum-based Storage will be enabled for all
nameservices except those configured with NFS High
Availability.
@return: Reference to the submitted command.
"""
version = self._get_resource_root().version
args = dict(
activeName = active_name,
standByName = standby_name,
nameservice = nameservice,
startDependentServices = start_dependent_services,
deployClientConfigs = deploy_client_configs,
)
if enable_quorum_storage:
if version < 2:
raise AttributeError("Quorum-based Storage is not supported prior to Cloudera Manager 4.1.")
else:
args['enableQuorumStorage'] = enable_quorum_storage
else:
if active_shared_path is None or standby_shared_path is None:
raise AttributeError("Active and standby shared paths must be specified if not enabling Quorum-based Storage")
args['activeSharedEditsPath'] = active_shared_path
args['standBySharedEditsPath'] = standby_shared_path
return self._cmd('hdfsEnableHa', data=args) | python | def enable_hdfs_ha(self, active_name, active_shared_path, standby_name,
standby_shared_path, nameservice, start_dependent_services=True,
deploy_client_configs=True, enable_quorum_storage=False):
version = self._get_resource_root().version
args = dict(
activeName = active_name,
standByName = standby_name,
nameservice = nameservice,
startDependentServices = start_dependent_services,
deployClientConfigs = deploy_client_configs,
)
if enable_quorum_storage:
if version < 2:
raise AttributeError("Quorum-based Storage is not supported prior to Cloudera Manager 4.1.")
else:
args['enableQuorumStorage'] = enable_quorum_storage
else:
if active_shared_path is None or standby_shared_path is None:
raise AttributeError("Active and standby shared paths must be specified if not enabling Quorum-based Storage")
args['activeSharedEditsPath'] = active_shared_path
args['standBySharedEditsPath'] = standby_shared_path
return self._cmd('hdfsEnableHa', data=args) | [
"def",
"enable_hdfs_ha",
"(",
"self",
",",
"active_name",
",",
"active_shared_path",
",",
"standby_name",
",",
"standby_shared_path",
",",
"nameservice",
",",
"start_dependent_services",
"=",
"True",
",",
"deploy_client_configs",
"=",
"True",
",",
"enable_quorum_storage... | Enable high availability for an HDFS NameNode.
This command is no longer supported with API v6 onwards. Use enable_nn_ha instead.
@param active_name: name of active NameNode.
@param active_shared_path: shared edits path for active NameNode.
Ignored if Quorum-based Storage is being enabled.
@param standby_name: name of stand-by NameNode.
@param standby_shared_path: shared edits path for stand-by NameNode.
Ignored if Quourm Journal is being enabled.
@param nameservice: nameservice for the HA pair.
@param start_dependent_services: whether to re-start dependent services.
@param deploy_client_configs: whether to re-deploy client configurations.
@param enable_quorum_storage: whether to enable Quorum-based Storage. Available since API v2.
Quorum-based Storage will be enabled for all
nameservices except those configured with NFS High
Availability.
@return: Reference to the submitted command. | [
"Enable",
"high",
"availability",
"for",
"an",
"HDFS",
"NameNode",
".",
"This",
"command",
"is",
"no",
"longer",
"supported",
"with",
"API",
"v6",
"onwards",
".",
"Use",
"enable_nn_ha",
"instead",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L945-L988 |
232,803 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.disable_nn_ha | def disable_nn_ha(self, active_name, snn_host_id, snn_check_point_dir_list,
snn_name=None):
"""
Disable high availability with automatic failover for an HDFS NameNode.
@param active_name: Name of the NamdeNode role that is going to be active after
High Availability is disabled.
@param snn_host_id: Id of the host where the new SecondaryNameNode will be created.
@param snn_check_point_dir_list : List of directories used for checkpointing
by the new SecondaryNameNode.
@param snn_name: Name of the new SecondaryNameNode role (Optional).
@return: Reference to the submitted command.
@since: API v6
"""
args = dict(
activeNnName = active_name,
snnHostId = snn_host_id,
snnCheckpointDirList = snn_check_point_dir_list,
snnName = snn_name
)
return self._cmd('hdfsDisableNnHa', data=args, api_version=6) | python | def disable_nn_ha(self, active_name, snn_host_id, snn_check_point_dir_list,
snn_name=None):
args = dict(
activeNnName = active_name,
snnHostId = snn_host_id,
snnCheckpointDirList = snn_check_point_dir_list,
snnName = snn_name
)
return self._cmd('hdfsDisableNnHa', data=args, api_version=6) | [
"def",
"disable_nn_ha",
"(",
"self",
",",
"active_name",
",",
"snn_host_id",
",",
"snn_check_point_dir_list",
",",
"snn_name",
"=",
"None",
")",
":",
"args",
"=",
"dict",
"(",
"activeNnName",
"=",
"active_name",
",",
"snnHostId",
"=",
"snn_host_id",
",",
"snnC... | Disable high availability with automatic failover for an HDFS NameNode.
@param active_name: Name of the NamdeNode role that is going to be active after
High Availability is disabled.
@param snn_host_id: Id of the host where the new SecondaryNameNode will be created.
@param snn_check_point_dir_list : List of directories used for checkpointing
by the new SecondaryNameNode.
@param snn_name: Name of the new SecondaryNameNode role (Optional).
@return: Reference to the submitted command.
@since: API v6 | [
"Disable",
"high",
"availability",
"with",
"automatic",
"failover",
"for",
"an",
"HDFS",
"NameNode",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1047-L1067 |
232,804 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enable_jt_ha | def enable_jt_ha(self, new_jt_host_id, force_init_znode=True, zk_service_name=None,
new_jt_name=None, fc1_name=None, fc2_name=None):
"""
Enable high availability for a MR JobTracker.
@param zk_service_name: Name of the ZooKeeper service to use for auto-failover.
If MapReduce service depends on a ZooKeeper service then that ZooKeeper
service will be used for auto-failover and in that case this parameter
can be omitted.
@param new_jt_host_id: id of the host where the second JobTracker
will be added.
@param force_init_znode: Initialize the ZNode used for auto-failover even if
it already exists. This can happen if JobTracker HA
was enabled before and then disabled. Disable operation
doesn't delete this ZNode. Defaults to true.
@param new_jt_name: Name of the second JobTracker role to be created.
@param fc1_name: Name of the Failover Controller role that is co-located with
the existing JobTracker.
@param fc2_name: Name of the Failover Controller role that is co-located with
the new JobTracker.
@return: Reference to the submitted command.
@since: API v5
"""
args = dict(
newJtHostId = new_jt_host_id,
forceInitZNode = force_init_znode,
zkServiceName = zk_service_name,
newJtRoleName = new_jt_name,
fc1RoleName = fc1_name,
fc2RoleName = fc2_name
)
return self._cmd('enableJtHa', data=args) | python | def enable_jt_ha(self, new_jt_host_id, force_init_znode=True, zk_service_name=None,
new_jt_name=None, fc1_name=None, fc2_name=None):
args = dict(
newJtHostId = new_jt_host_id,
forceInitZNode = force_init_znode,
zkServiceName = zk_service_name,
newJtRoleName = new_jt_name,
fc1RoleName = fc1_name,
fc2RoleName = fc2_name
)
return self._cmd('enableJtHa', data=args) | [
"def",
"enable_jt_ha",
"(",
"self",
",",
"new_jt_host_id",
",",
"force_init_znode",
"=",
"True",
",",
"zk_service_name",
"=",
"None",
",",
"new_jt_name",
"=",
"None",
",",
"fc1_name",
"=",
"None",
",",
"fc2_name",
"=",
"None",
")",
":",
"args",
"=",
"dict"... | Enable high availability for a MR JobTracker.
@param zk_service_name: Name of the ZooKeeper service to use for auto-failover.
If MapReduce service depends on a ZooKeeper service then that ZooKeeper
service will be used for auto-failover and in that case this parameter
can be omitted.
@param new_jt_host_id: id of the host where the second JobTracker
will be added.
@param force_init_znode: Initialize the ZNode used for auto-failover even if
it already exists. This can happen if JobTracker HA
was enabled before and then disabled. Disable operation
doesn't delete this ZNode. Defaults to true.
@param new_jt_name: Name of the second JobTracker role to be created.
@param fc1_name: Name of the Failover Controller role that is co-located with
the existing JobTracker.
@param fc2_name: Name of the Failover Controller role that is co-located with
the new JobTracker.
@return: Reference to the submitted command.
@since: API v5 | [
"Enable",
"high",
"availability",
"for",
"a",
"MR",
"JobTracker",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1069-L1100 |
232,805 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.disable_jt_ha | def disable_jt_ha(self, active_name):
"""
Disable high availability for a MR JobTracker active-standby pair.
@param active_name: name of the JobTracker that will be active after
the disable operation. The other JobTracker and
Failover Controllers will be removed.
@return: Reference to the submitted command.
"""
args = dict(
activeName = active_name,
)
return self._cmd('disableJtHa', data=args) | python | def disable_jt_ha(self, active_name):
args = dict(
activeName = active_name,
)
return self._cmd('disableJtHa', data=args) | [
"def",
"disable_jt_ha",
"(",
"self",
",",
"active_name",
")",
":",
"args",
"=",
"dict",
"(",
"activeName",
"=",
"active_name",
",",
")",
"return",
"self",
".",
"_cmd",
"(",
"'disableJtHa'",
",",
"data",
"=",
"args",
")"
] | Disable high availability for a MR JobTracker active-standby pair.
@param active_name: name of the JobTracker that will be active after
the disable operation. The other JobTracker and
Failover Controllers will be removed.
@return: Reference to the submitted command. | [
"Disable",
"high",
"availability",
"for",
"a",
"MR",
"JobTracker",
"active",
"-",
"standby",
"pair",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1102-L1114 |
232,806 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enable_rm_ha | def enable_rm_ha(self, new_rm_host_id, zk_service_name=None):
"""
Enable high availability for a YARN ResourceManager.
@param new_rm_host_id: id of the host where the second ResourceManager
will be added.
@param zk_service_name: Name of the ZooKeeper service to use for auto-failover.
If YARN service depends on a ZooKeeper service then that ZooKeeper
service will be used for auto-failover and in that case this parameter
can be omitted.
@return: Reference to the submitted command.
@since: API v6
"""
args = dict(
newRmHostId = new_rm_host_id,
zkServiceName = zk_service_name
)
return self._cmd('enableRmHa', data=args) | python | def enable_rm_ha(self, new_rm_host_id, zk_service_name=None):
args = dict(
newRmHostId = new_rm_host_id,
zkServiceName = zk_service_name
)
return self._cmd('enableRmHa', data=args) | [
"def",
"enable_rm_ha",
"(",
"self",
",",
"new_rm_host_id",
",",
"zk_service_name",
"=",
"None",
")",
":",
"args",
"=",
"dict",
"(",
"newRmHostId",
"=",
"new_rm_host_id",
",",
"zkServiceName",
"=",
"zk_service_name",
")",
"return",
"self",
".",
"_cmd",
"(",
"... | Enable high availability for a YARN ResourceManager.
@param new_rm_host_id: id of the host where the second ResourceManager
will be added.
@param zk_service_name: Name of the ZooKeeper service to use for auto-failover.
If YARN service depends on a ZooKeeper service then that ZooKeeper
service will be used for auto-failover and in that case this parameter
can be omitted.
@return: Reference to the submitted command.
@since: API v6 | [
"Enable",
"high",
"availability",
"for",
"a",
"YARN",
"ResourceManager",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1116-L1133 |
232,807 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.disable_rm_ha | def disable_rm_ha(self, active_name):
"""
Disable high availability for a YARN ResourceManager active-standby pair.
@param active_name: name of the ResourceManager that will be active after
the disable operation. The other ResourceManager
will be removed.
@return: Reference to the submitted command.
@since: API v6
"""
args = dict(
activeName = active_name
)
return self._cmd('disableRmHa', data=args) | python | def disable_rm_ha(self, active_name):
args = dict(
activeName = active_name
)
return self._cmd('disableRmHa', data=args) | [
"def",
"disable_rm_ha",
"(",
"self",
",",
"active_name",
")",
":",
"args",
"=",
"dict",
"(",
"activeName",
"=",
"active_name",
")",
"return",
"self",
".",
"_cmd",
"(",
"'disableRmHa'",
",",
"data",
"=",
"args",
")"
] | Disable high availability for a YARN ResourceManager active-standby pair.
@param active_name: name of the ResourceManager that will be active after
the disable operation. The other ResourceManager
will be removed.
@return: Reference to the submitted command.
@since: API v6 | [
"Disable",
"high",
"availability",
"for",
"a",
"YARN",
"ResourceManager",
"active",
"-",
"standby",
"pair",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1135-L1148 |
232,808 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enable_oozie_ha | def enable_oozie_ha(self, new_oozie_server_host_ids, new_oozie_server_role_names=None,
zk_service_name=None, load_balancer_host_port=None):
"""
Enable high availability for Oozie.
@param new_oozie_server_host_ids: List of IDs of the hosts on which new Oozie Servers
will be added.
@param new_oozie_server_role_names: List of names of the new Oozie Servers. This is an
optional argument, but if provided, it should
match the length of host IDs provided.
@param zk_service_name: Name of the ZooKeeper service that will be used for Oozie HA.
This is an optional parameter if the Oozie to ZooKeeper
dependency is already set.
@param load_balancer_host_port: Address and port of the load balancer used for Oozie HA.
This is an optional parameter if this config is already set.
@return: Reference to the submitted command.
@since: API v6
"""
args = dict(
newOozieServerHostIds = new_oozie_server_host_ids,
newOozieServerRoleNames = new_oozie_server_role_names,
zkServiceName = zk_service_name,
loadBalancerHostPort = load_balancer_host_port
)
return self._cmd('oozieEnableHa', data=args, api_version=6) | python | def enable_oozie_ha(self, new_oozie_server_host_ids, new_oozie_server_role_names=None,
zk_service_name=None, load_balancer_host_port=None):
args = dict(
newOozieServerHostIds = new_oozie_server_host_ids,
newOozieServerRoleNames = new_oozie_server_role_names,
zkServiceName = zk_service_name,
loadBalancerHostPort = load_balancer_host_port
)
return self._cmd('oozieEnableHa', data=args, api_version=6) | [
"def",
"enable_oozie_ha",
"(",
"self",
",",
"new_oozie_server_host_ids",
",",
"new_oozie_server_role_names",
"=",
"None",
",",
"zk_service_name",
"=",
"None",
",",
"load_balancer_host_port",
"=",
"None",
")",
":",
"args",
"=",
"dict",
"(",
"newOozieServerHostIds",
"... | Enable high availability for Oozie.
@param new_oozie_server_host_ids: List of IDs of the hosts on which new Oozie Servers
will be added.
@param new_oozie_server_role_names: List of names of the new Oozie Servers. This is an
optional argument, but if provided, it should
match the length of host IDs provided.
@param zk_service_name: Name of the ZooKeeper service that will be used for Oozie HA.
This is an optional parameter if the Oozie to ZooKeeper
dependency is already set.
@param load_balancer_host_port: Address and port of the load balancer used for Oozie HA.
This is an optional parameter if this config is already set.
@return: Reference to the submitted command.
@since: API v6 | [
"Enable",
"high",
"availability",
"for",
"Oozie",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1150-L1174 |
232,809 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.disable_oozie_ha | def disable_oozie_ha(self, active_name):
"""
Disable high availability for Oozie
@param active_name: Name of the Oozie Server that will be active after
High Availability is disabled.
@return: Reference to the submitted command.
@since: API v6
"""
args = dict(
activeName = active_name
)
return self._cmd('oozieDisableHa', data=args, api_version=6) | python | def disable_oozie_ha(self, active_name):
args = dict(
activeName = active_name
)
return self._cmd('oozieDisableHa', data=args, api_version=6) | [
"def",
"disable_oozie_ha",
"(",
"self",
",",
"active_name",
")",
":",
"args",
"=",
"dict",
"(",
"activeName",
"=",
"active_name",
")",
"return",
"self",
".",
"_cmd",
"(",
"'oozieDisableHa'",
",",
"data",
"=",
"args",
",",
"api_version",
"=",
"6",
")"
] | Disable high availability for Oozie
@param active_name: Name of the Oozie Server that will be active after
High Availability is disabled.
@return: Reference to the submitted command.
@since: API v6 | [
"Disable",
"high",
"availability",
"for",
"Oozie"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1176-L1188 |
232,810 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.failover_hdfs | def failover_hdfs(self, active_name, standby_name, force=False):
"""
Initiate a failover of an HDFS NameNode HA pair.
This will make the given stand-by NameNode active, and vice-versa.
@param active_name: name of currently active NameNode.
@param standby_name: name of NameNode currently in stand-by.
@param force: whether to force failover.
@return: Reference to the submitted command.
"""
params = { "force" : "true" and force or "false" }
args = { ApiList.LIST_KEY : [ active_name, standby_name ] }
return self._cmd('hdfsFailover', data=[ active_name, standby_name ],
params = { "force" : "true" and force or "false" }) | python | def failover_hdfs(self, active_name, standby_name, force=False):
params = { "force" : "true" and force or "false" }
args = { ApiList.LIST_KEY : [ active_name, standby_name ] }
return self._cmd('hdfsFailover', data=[ active_name, standby_name ],
params = { "force" : "true" and force or "false" }) | [
"def",
"failover_hdfs",
"(",
"self",
",",
"active_name",
",",
"standby_name",
",",
"force",
"=",
"False",
")",
":",
"params",
"=",
"{",
"\"force\"",
":",
"\"true\"",
"and",
"force",
"or",
"\"false\"",
"}",
"args",
"=",
"{",
"ApiList",
".",
"LIST_KEY",
":... | Initiate a failover of an HDFS NameNode HA pair.
This will make the given stand-by NameNode active, and vice-versa.
@param active_name: name of currently active NameNode.
@param standby_name: name of NameNode currently in stand-by.
@param force: whether to force failover.
@return: Reference to the submitted command. | [
"Initiate",
"a",
"failover",
"of",
"an",
"HDFS",
"NameNode",
"HA",
"pair",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1190-L1204 |
232,811 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.roll_edits_hdfs | def roll_edits_hdfs(self, nameservice=None):
"""
Roll the edits of an HDFS NameNode or Nameservice.
@param nameservice: Nameservice whose edits should be rolled.
Required only with a federated HDFS.
@return: Reference to the submitted command.
@since: API v3
"""
args = dict()
if nameservice:
args['nameservice'] = nameservice
return self._cmd('hdfsRollEdits', data=args) | python | def roll_edits_hdfs(self, nameservice=None):
args = dict()
if nameservice:
args['nameservice'] = nameservice
return self._cmd('hdfsRollEdits', data=args) | [
"def",
"roll_edits_hdfs",
"(",
"self",
",",
"nameservice",
"=",
"None",
")",
":",
"args",
"=",
"dict",
"(",
")",
"if",
"nameservice",
":",
"args",
"[",
"'nameservice'",
"]",
"=",
"nameservice",
"return",
"self",
".",
"_cmd",
"(",
"'hdfsRollEdits'",
",",
... | Roll the edits of an HDFS NameNode or Nameservice.
@param nameservice: Nameservice whose edits should be rolled.
Required only with a federated HDFS.
@return: Reference to the submitted command.
@since: API v3 | [
"Roll",
"the",
"edits",
"of",
"an",
"HDFS",
"NameNode",
"or",
"Nameservice",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1235-L1248 |
232,812 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.sync_hue_db | def sync_hue_db(self, *servers):
"""
Synchronize the Hue server's database.
@param servers: Name of Hue Server roles to synchronize. Not required starting with API v10.
@return: List of submitted commands.
"""
actual_version = self._get_resource_root().version
if actual_version < 10:
return self._role_cmd('hueSyncDb', servers)
return self._cmd('hueSyncDb', api_version=10) | python | def sync_hue_db(self, *servers):
actual_version = self._get_resource_root().version
if actual_version < 10:
return self._role_cmd('hueSyncDb', servers)
return self._cmd('hueSyncDb', api_version=10) | [
"def",
"sync_hue_db",
"(",
"self",
",",
"*",
"servers",
")",
":",
"actual_version",
"=",
"self",
".",
"_get_resource_root",
"(",
")",
".",
"version",
"if",
"actual_version",
"<",
"10",
":",
"return",
"self",
".",
"_role_cmd",
"(",
"'hueSyncDb'",
",",
"serv... | Synchronize the Hue server's database.
@param servers: Name of Hue Server roles to synchronize. Not required starting with API v10.
@return: List of submitted commands. | [
"Synchronize",
"the",
"Hue",
"server",
"s",
"database",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1337-L1349 |
232,813 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.enter_maintenance_mode | def enter_maintenance_mode(self):
"""
Put the service in maintenance mode.
@return: Reference to the completed command.
@since: API v2
"""
cmd = self._cmd('enterMaintenanceMode')
if cmd.success:
self._update(_get_service(self._get_resource_root(), self._path()))
return cmd | python | def enter_maintenance_mode(self):
cmd = self._cmd('enterMaintenanceMode')
if cmd.success:
self._update(_get_service(self._get_resource_root(), self._path()))
return cmd | [
"def",
"enter_maintenance_mode",
"(",
"self",
")",
":",
"cmd",
"=",
"self",
".",
"_cmd",
"(",
"'enterMaintenanceMode'",
")",
"if",
"cmd",
".",
"success",
":",
"self",
".",
"_update",
"(",
"_get_service",
"(",
"self",
".",
"_get_resource_root",
"(",
")",
",... | Put the service in maintenance mode.
@return: Reference to the completed command.
@since: API v2 | [
"Put",
"the",
"service",
"in",
"maintenance",
"mode",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1412-L1422 |
232,814 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.create_replication_schedule | def create_replication_schedule(self,
start_time, end_time, interval_unit, interval, paused, arguments,
alert_on_start=False, alert_on_success=False, alert_on_fail=False,
alert_on_abort=False):
"""
Create a new replication schedule for this service.
The replication argument type varies per service type. The following types
are recognized:
- HDFS: ApiHdfsReplicationArguments
- Hive: ApiHiveReplicationArguments
@type start_time: datetime.datetime
@param start_time: The time at which the schedule becomes active and first executes.
@type end_time: datetime.datetime
@param end_time: The time at which the schedule will expire.
@type interval_unit: str
@param interval_unit: The unit of time the `interval` represents. Ex. MINUTE, HOUR,
DAY. See the server documentation for a full list of values.
@type interval: int
@param interval: The number of time units to wait until triggering the next replication.
@type paused: bool
@param paused: Should the schedule be paused? Useful for on-demand replication.
@param arguments: service type-specific arguments for the replication job.
@param alert_on_start: whether to generate alerts when the job is started.
@param alert_on_success: whether to generate alerts when the job succeeds.
@param alert_on_fail: whether to generate alerts when the job fails.
@param alert_on_abort: whether to generate alerts when the job is aborted.
@return: The newly created schedule.
@since: API v3
"""
schedule = ApiReplicationSchedule(self._get_resource_root(),
startTime=start_time, endTime=end_time, intervalUnit=interval_unit, interval=interval,
paused=paused, alertOnStart=alert_on_start, alertOnSuccess=alert_on_success,
alertOnFail=alert_on_fail, alertOnAbort=alert_on_abort)
if self.type == 'HDFS':
if isinstance(arguments, ApiHdfsCloudReplicationArguments):
schedule.hdfsCloudArguments = arguments
elif isinstance(arguments, ApiHdfsReplicationArguments):
schedule.hdfsArguments = arguments
else:
raise TypeError, 'Unexpected type for HDFS replication argument.'
elif self.type == 'HIVE':
if not isinstance(arguments, ApiHiveReplicationArguments):
raise TypeError, 'Unexpected type for Hive replication argument.'
schedule.hiveArguments = arguments
else:
raise TypeError, 'Replication is not supported for service type ' + self.type
return self._post("replications", ApiReplicationSchedule, True, [schedule],
api_version=3)[0] | python | def create_replication_schedule(self,
start_time, end_time, interval_unit, interval, paused, arguments,
alert_on_start=False, alert_on_success=False, alert_on_fail=False,
alert_on_abort=False):
schedule = ApiReplicationSchedule(self._get_resource_root(),
startTime=start_time, endTime=end_time, intervalUnit=interval_unit, interval=interval,
paused=paused, alertOnStart=alert_on_start, alertOnSuccess=alert_on_success,
alertOnFail=alert_on_fail, alertOnAbort=alert_on_abort)
if self.type == 'HDFS':
if isinstance(arguments, ApiHdfsCloudReplicationArguments):
schedule.hdfsCloudArguments = arguments
elif isinstance(arguments, ApiHdfsReplicationArguments):
schedule.hdfsArguments = arguments
else:
raise TypeError, 'Unexpected type for HDFS replication argument.'
elif self.type == 'HIVE':
if not isinstance(arguments, ApiHiveReplicationArguments):
raise TypeError, 'Unexpected type for Hive replication argument.'
schedule.hiveArguments = arguments
else:
raise TypeError, 'Replication is not supported for service type ' + self.type
return self._post("replications", ApiReplicationSchedule, True, [schedule],
api_version=3)[0] | [
"def",
"create_replication_schedule",
"(",
"self",
",",
"start_time",
",",
"end_time",
",",
"interval_unit",
",",
"interval",
",",
"paused",
",",
"arguments",
",",
"alert_on_start",
"=",
"False",
",",
"alert_on_success",
"=",
"False",
",",
"alert_on_fail",
"=",
... | Create a new replication schedule for this service.
The replication argument type varies per service type. The following types
are recognized:
- HDFS: ApiHdfsReplicationArguments
- Hive: ApiHiveReplicationArguments
@type start_time: datetime.datetime
@param start_time: The time at which the schedule becomes active and first executes.
@type end_time: datetime.datetime
@param end_time: The time at which the schedule will expire.
@type interval_unit: str
@param interval_unit: The unit of time the `interval` represents. Ex. MINUTE, HOUR,
DAY. See the server documentation for a full list of values.
@type interval: int
@param interval: The number of time units to wait until triggering the next replication.
@type paused: bool
@param paused: Should the schedule be paused? Useful for on-demand replication.
@param arguments: service type-specific arguments for the replication job.
@param alert_on_start: whether to generate alerts when the job is started.
@param alert_on_success: whether to generate alerts when the job succeeds.
@param alert_on_fail: whether to generate alerts when the job fails.
@param alert_on_abort: whether to generate alerts when the job is aborted.
@return: The newly created schedule.
@since: API v3 | [
"Create",
"a",
"new",
"replication",
"schedule",
"for",
"this",
"service",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1484-L1535 |
232,815 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.update_replication_schedule | def update_replication_schedule(self, schedule_id, schedule):
"""
Update a replication schedule.
@param schedule_id: The id of the schedule to update.
@param schedule: The modified schedule.
@return: The updated replication schedule.
@since: API v3
"""
return self._put("replications/%s" % schedule_id, ApiReplicationSchedule,
data=schedule, api_version=3) | python | def update_replication_schedule(self, schedule_id, schedule):
return self._put("replications/%s" % schedule_id, ApiReplicationSchedule,
data=schedule, api_version=3) | [
"def",
"update_replication_schedule",
"(",
"self",
",",
"schedule_id",
",",
"schedule",
")",
":",
"return",
"self",
".",
"_put",
"(",
"\"replications/%s\"",
"%",
"schedule_id",
",",
"ApiReplicationSchedule",
",",
"data",
"=",
"schedule",
",",
"api_version",
"=",
... | Update a replication schedule.
@param schedule_id: The id of the schedule to update.
@param schedule: The modified schedule.
@return: The updated replication schedule.
@since: API v3 | [
"Update",
"a",
"replication",
"schedule",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1569-L1579 |
232,816 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.get_replication_command_history | def get_replication_command_history(self, schedule_id, limit=20, offset=0,
view=None):
"""
Retrieve a list of commands for a replication schedule.
@param schedule_id: The id of the replication schedule.
@param limit: Maximum number of commands to retrieve.
@param offset: Index of first command to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: List of commands executed for a replication schedule.
@since: API v4
"""
params = {
'limit': limit,
'offset': offset,
}
if view:
params['view'] = view
return self._get("replications/%s/history" % schedule_id,
ApiReplicationCommand, True, params=params, api_version=4) | python | def get_replication_command_history(self, schedule_id, limit=20, offset=0,
view=None):
params = {
'limit': limit,
'offset': offset,
}
if view:
params['view'] = view
return self._get("replications/%s/history" % schedule_id,
ApiReplicationCommand, True, params=params, api_version=4) | [
"def",
"get_replication_command_history",
"(",
"self",
",",
"schedule_id",
",",
"limit",
"=",
"20",
",",
"offset",
"=",
"0",
",",
"view",
"=",
"None",
")",
":",
"params",
"=",
"{",
"'limit'",
":",
"limit",
",",
"'offset'",
":",
"offset",
",",
"}",
"if"... | Retrieve a list of commands for a replication schedule.
@param schedule_id: The id of the replication schedule.
@param limit: Maximum number of commands to retrieve.
@param offset: Index of first command to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: List of commands executed for a replication schedule.
@since: API v4 | [
"Retrieve",
"a",
"list",
"of",
"commands",
"for",
"a",
"replication",
"schedule",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1581-L1601 |
232,817 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.trigger_replication_schedule | def trigger_replication_schedule(self, schedule_id, dry_run=False):
"""
Trigger replication immediately. Start and end dates on the schedule will be
ignored.
@param schedule_id: The id of the schedule to trigger.
@param dry_run: Whether to execute a dry run.
@return: The command corresponding to the replication job.
@since: API v3
"""
return self._post("replications/%s/run" % schedule_id, ApiCommand,
params=dict(dryRun=dry_run),
api_version=3) | python | def trigger_replication_schedule(self, schedule_id, dry_run=False):
return self._post("replications/%s/run" % schedule_id, ApiCommand,
params=dict(dryRun=dry_run),
api_version=3) | [
"def",
"trigger_replication_schedule",
"(",
"self",
",",
"schedule_id",
",",
"dry_run",
"=",
"False",
")",
":",
"return",
"self",
".",
"_post",
"(",
"\"replications/%s/run\"",
"%",
"schedule_id",
",",
"ApiCommand",
",",
"params",
"=",
"dict",
"(",
"dryRun",
"=... | Trigger replication immediately. Start and end dates on the schedule will be
ignored.
@param schedule_id: The id of the schedule to trigger.
@param dry_run: Whether to execute a dry run.
@return: The command corresponding to the replication job.
@since: API v3 | [
"Trigger",
"replication",
"immediately",
".",
"Start",
"and",
"end",
"dates",
"on",
"the",
"schedule",
"will",
"be",
"ignored",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1603-L1615 |
232,818 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.get_snapshot_policies | def get_snapshot_policies(self, view=None):
"""
Retrieve a list of snapshot policies.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: A list of snapshot policies.
@since: API v6
"""
return self._get("snapshots/policies", ApiSnapshotPolicy, True,
params=view and dict(view=view) or None, api_version=6) | python | def get_snapshot_policies(self, view=None):
return self._get("snapshots/policies", ApiSnapshotPolicy, True,
params=view and dict(view=view) or None, api_version=6) | [
"def",
"get_snapshot_policies",
"(",
"self",
",",
"view",
"=",
"None",
")",
":",
"return",
"self",
".",
"_get",
"(",
"\"snapshots/policies\"",
",",
"ApiSnapshotPolicy",
",",
"True",
",",
"params",
"=",
"view",
"and",
"dict",
"(",
"view",
"=",
"view",
")",
... | Retrieve a list of snapshot policies.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: A list of snapshot policies.
@since: API v6 | [
"Retrieve",
"a",
"list",
"of",
"snapshot",
"policies",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1627-L1636 |
232,819 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.get_snapshot_policy | def get_snapshot_policy(self, name, view=None):
"""
Retrieve a single snapshot policy.
@param name: The name of the snapshot policy to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: The requested snapshot policy.
@since: API v6
"""
return self._get("snapshots/policies/%s" % name, ApiSnapshotPolicy,
params=view and dict(view=view) or None, api_version=6) | python | def get_snapshot_policy(self, name, view=None):
return self._get("snapshots/policies/%s" % name, ApiSnapshotPolicy,
params=view and dict(view=view) or None, api_version=6) | [
"def",
"get_snapshot_policy",
"(",
"self",
",",
"name",
",",
"view",
"=",
"None",
")",
":",
"return",
"self",
".",
"_get",
"(",
"\"snapshots/policies/%s\"",
"%",
"name",
",",
"ApiSnapshotPolicy",
",",
"params",
"=",
"view",
"and",
"dict",
"(",
"view",
"=",... | Retrieve a single snapshot policy.
@param name: The name of the snapshot policy to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: The requested snapshot policy.
@since: API v6 | [
"Retrieve",
"a",
"single",
"snapshot",
"policy",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1638-L1648 |
232,820 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.update_snapshot_policy | def update_snapshot_policy(self, name, policy):
"""
Update a snapshot policy.
@param name: The name of the snapshot policy to update.
@param policy: The modified snapshot policy.
@return: The updated snapshot policy.
@since: API v6
"""
return self._put("snapshots/policies/%s" % name, ApiSnapshotPolicy, data=policy,
api_version=6) | python | def update_snapshot_policy(self, name, policy):
return self._put("snapshots/policies/%s" % name, ApiSnapshotPolicy, data=policy,
api_version=6) | [
"def",
"update_snapshot_policy",
"(",
"self",
",",
"name",
",",
"policy",
")",
":",
"return",
"self",
".",
"_put",
"(",
"\"snapshots/policies/%s\"",
"%",
"name",
",",
"ApiSnapshotPolicy",
",",
"data",
"=",
"policy",
",",
"api_version",
"=",
"6",
")"
] | Update a snapshot policy.
@param name: The name of the snapshot policy to update.
@param policy: The modified snapshot policy.
@return: The updated snapshot policy.
@since: API v6 | [
"Update",
"a",
"snapshot",
"policy",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1660-L1670 |
232,821 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiService.get_snapshot_command_history | def get_snapshot_command_history(self, name, limit=20, offset=0, view=None):
"""
Retrieve a list of commands triggered by a snapshot policy.
@param name: The name of the snapshot policy.
@param limit: Maximum number of commands to retrieve.
@param offset: Index of first command to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: List of commands triggered by a snapshot policy.
@since: API v6
"""
params = {
'limit': limit,
'offset': offset,
}
if view:
params['view'] = view
return self._get("snapshots/policies/%s/history" % name, ApiSnapshotCommand, True,
params=params, api_version=6) | python | def get_snapshot_command_history(self, name, limit=20, offset=0, view=None):
params = {
'limit': limit,
'offset': offset,
}
if view:
params['view'] = view
return self._get("snapshots/policies/%s/history" % name, ApiSnapshotCommand, True,
params=params, api_version=6) | [
"def",
"get_snapshot_command_history",
"(",
"self",
",",
"name",
",",
"limit",
"=",
"20",
",",
"offset",
"=",
"0",
",",
"view",
"=",
"None",
")",
":",
"params",
"=",
"{",
"'limit'",
":",
"limit",
",",
"'offset'",
":",
"offset",
",",
"}",
"if",
"view"... | Retrieve a list of commands triggered by a snapshot policy.
@param name: The name of the snapshot policy.
@param limit: Maximum number of commands to retrieve.
@param offset: Index of first command to retrieve.
@param view: View to materialize. Valid values are 'full', 'summary', 'export', 'export_redacted'.
@return: List of commands triggered by a snapshot policy.
@since: API v6 | [
"Retrieve",
"a",
"list",
"of",
"commands",
"triggered",
"by",
"a",
"snapshot",
"policy",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1672-L1691 |
232,822 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiServiceSetupInfo.set_config | def set_config(self, config):
"""
Set the service configuration.
@param config: A dictionary of config key/value
"""
if self.config is None:
self.config = { }
self.config.update(config_to_api_list(config)) | python | def set_config(self, config):
if self.config is None:
self.config = { }
self.config.update(config_to_api_list(config)) | [
"def",
"set_config",
"(",
"self",
",",
"config",
")",
":",
"if",
"self",
".",
"config",
"is",
"None",
":",
"self",
".",
"config",
"=",
"{",
"}",
"self",
".",
"config",
".",
"update",
"(",
"config_to_api_list",
"(",
"config",
")",
")"
] | Set the service configuration.
@param config: A dictionary of config key/value | [
"Set",
"the",
"service",
"configuration",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1940-L1948 |
232,823 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiServiceSetupInfo.add_role_type_info | def add_role_type_info(self, role_type, config):
"""
Add a role type setup info.
@param role_type: Role type
@param config: A dictionary of role type configuration
"""
rt_config = config_to_api_list(config)
rt_config['roleType'] = role_type
if self.config is None:
self.config = { }
if not self.config.has_key(ROLETYPES_CFG_KEY):
self.config[ROLETYPES_CFG_KEY] = [ ]
self.config[ROLETYPES_CFG_KEY].append(rt_config) | python | def add_role_type_info(self, role_type, config):
rt_config = config_to_api_list(config)
rt_config['roleType'] = role_type
if self.config is None:
self.config = { }
if not self.config.has_key(ROLETYPES_CFG_KEY):
self.config[ROLETYPES_CFG_KEY] = [ ]
self.config[ROLETYPES_CFG_KEY].append(rt_config) | [
"def",
"add_role_type_info",
"(",
"self",
",",
"role_type",
",",
"config",
")",
":",
"rt_config",
"=",
"config_to_api_list",
"(",
"config",
")",
"rt_config",
"[",
"'roleType'",
"]",
"=",
"role_type",
"if",
"self",
".",
"config",
"is",
"None",
":",
"self",
... | Add a role type setup info.
@param role_type: Role type
@param config: A dictionary of role type configuration | [
"Add",
"a",
"role",
"type",
"setup",
"info",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1950-L1964 |
232,824 | cloudera/cm_api | python/src/cm_api/endpoints/services.py | ApiServiceSetupInfo.add_role_info | def add_role_info(self, role_name, role_type, host_id, config=None):
"""
Add a role info. The role will be created along with the service setup.
@param role_name: Role name
@param role_type: Role type
@param host_id: The host where the role should run
@param config: (Optional) A dictionary of role config values
"""
if self.roles is None:
self.roles = [ ]
api_config_list = config is not None and config_to_api_list(config) or None
self.roles.append({
'name' : role_name,
'type' : role_type,
'hostRef' : { 'hostId' : host_id },
'config' : api_config_list }) | python | def add_role_info(self, role_name, role_type, host_id, config=None):
if self.roles is None:
self.roles = [ ]
api_config_list = config is not None and config_to_api_list(config) or None
self.roles.append({
'name' : role_name,
'type' : role_type,
'hostRef' : { 'hostId' : host_id },
'config' : api_config_list }) | [
"def",
"add_role_info",
"(",
"self",
",",
"role_name",
",",
"role_type",
",",
"host_id",
",",
"config",
"=",
"None",
")",
":",
"if",
"self",
".",
"roles",
"is",
"None",
":",
"self",
".",
"roles",
"=",
"[",
"]",
"api_config_list",
"=",
"config",
"is",
... | Add a role info. The role will be created along with the service setup.
@param role_name: Role name
@param role_type: Role type
@param host_id: The host where the role should run
@param config: (Optional) A dictionary of role config values | [
"Add",
"a",
"role",
"info",
".",
"The",
"role",
"will",
"be",
"created",
"along",
"with",
"the",
"service",
"setup",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/services.py#L1966-L1982 |
232,825 | cloudera/cm_api | python/src/cm_api/endpoints/hosts.py | create_host | def create_host(resource_root, host_id, name, ipaddr, rack_id=None):
"""
Create a host
@param resource_root: The root Resource object.
@param host_id: Host id
@param name: Host name
@param ipaddr: IP address
@param rack_id: Rack id. Default None
@return: An ApiHost object
"""
apihost = ApiHost(resource_root, host_id, name, ipaddr, rack_id)
return call(resource_root.post, HOSTS_PATH, ApiHost, True, data=[apihost])[0] | python | def create_host(resource_root, host_id, name, ipaddr, rack_id=None):
apihost = ApiHost(resource_root, host_id, name, ipaddr, rack_id)
return call(resource_root.post, HOSTS_PATH, ApiHost, True, data=[apihost])[0] | [
"def",
"create_host",
"(",
"resource_root",
",",
"host_id",
",",
"name",
",",
"ipaddr",
",",
"rack_id",
"=",
"None",
")",
":",
"apihost",
"=",
"ApiHost",
"(",
"resource_root",
",",
"host_id",
",",
"name",
",",
"ipaddr",
",",
"rack_id",
")",
"return",
"ca... | Create a host
@param resource_root: The root Resource object.
@param host_id: Host id
@param name: Host name
@param ipaddr: IP address
@param rack_id: Rack id. Default None
@return: An ApiHost object | [
"Create",
"a",
"host"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/hosts.py#L25-L36 |
232,826 | cloudera/cm_api | python/src/cm_api/endpoints/hosts.py | get_all_hosts | def get_all_hosts(resource_root, view=None):
"""
Get all hosts
@param resource_root: The root Resource object.
@return: A list of ApiHost objects.
"""
return call(resource_root.get, HOSTS_PATH, ApiHost, True,
params=view and dict(view=view) or None) | python | def get_all_hosts(resource_root, view=None):
return call(resource_root.get, HOSTS_PATH, ApiHost, True,
params=view and dict(view=view) or None) | [
"def",
"get_all_hosts",
"(",
"resource_root",
",",
"view",
"=",
"None",
")",
":",
"return",
"call",
"(",
"resource_root",
".",
"get",
",",
"HOSTS_PATH",
",",
"ApiHost",
",",
"True",
",",
"params",
"=",
"view",
"and",
"dict",
"(",
"view",
"=",
"view",
"... | Get all hosts
@param resource_root: The root Resource object.
@return: A list of ApiHost objects. | [
"Get",
"all",
"hosts"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/hosts.py#L47-L54 |
232,827 | cloudera/cm_api | python/src/cm_api/endpoints/hosts.py | ApiHost.enter_maintenance_mode | def enter_maintenance_mode(self):
"""
Put the host in maintenance mode.
@return: Reference to the completed command.
@since: API v2
"""
cmd = self._cmd('enterMaintenanceMode')
if cmd.success:
self._update(get_host(self._get_resource_root(), self.hostId))
return cmd | python | def enter_maintenance_mode(self):
cmd = self._cmd('enterMaintenanceMode')
if cmd.success:
self._update(get_host(self._get_resource_root(), self.hostId))
return cmd | [
"def",
"enter_maintenance_mode",
"(",
"self",
")",
":",
"cmd",
"=",
"self",
".",
"_cmd",
"(",
"'enterMaintenanceMode'",
")",
"if",
"cmd",
".",
"success",
":",
"self",
".",
"_update",
"(",
"get_host",
"(",
"self",
".",
"_get_resource_root",
"(",
")",
",",
... | Put the host in maintenance mode.
@return: Reference to the completed command.
@since: API v2 | [
"Put",
"the",
"host",
"in",
"maintenance",
"mode",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/hosts.py#L161-L171 |
232,828 | cloudera/cm_api | python/src/cm_api/endpoints/hosts.py | ApiHost.migrate_roles | def migrate_roles(self, role_names_to_migrate, destination_host_id,
clear_stale_role_data):
"""
Migrate roles from this host to a different host.
Currently, this command applies only to HDFS NameNode, JournalNode,
and Failover Controller roles. In order to migrate these roles:
- HDFS High Availability must be enabled, using quorum-based storage.
- HDFS must not be configured to use a federated nameservice.
I{B{Migrating a NameNode role requires cluster downtime.}} HDFS, along
with all of its dependent services, will be stopped at the beginning
of the migration process, and restarted at its conclusion.
If the active NameNode is selected for migration, a manual failover
will be performed before the role is migrated. The role will remain in
standby mode after the migration is complete.
When migrating a NameNode role, the co-located Failover Controller
role must be migrated as well. The Failover Controller role name must
be included in the list of role names to migrate specified in the
arguments to this command (it will not be included implicitly). This
command does not allow a Failover Controller role to be moved by itself,
although it is possible to move a JournalNode independently.
@param role_names_to_migrate: list of role names to migrate.
@param destination_host_id: the id of the host to which the roles
should be migrated.
@param clear_stale_role_data: true to delete existing stale role data,
if any. For example, when migrating a
NameNode, if the destination host has
stale data in the NameNode data
directories (possibly because a NameNode
role was previously located there), this
stale data will be deleted before migrating
the role.
@return: Reference to the submitted command.
@since: API v10
"""
args = dict(
roleNamesToMigrate = role_names_to_migrate,
destinationHostId = destination_host_id,
clearStaleRoleData = clear_stale_role_data)
return self._cmd('migrateRoles', data=args, api_version=10) | python | def migrate_roles(self, role_names_to_migrate, destination_host_id,
clear_stale_role_data):
args = dict(
roleNamesToMigrate = role_names_to_migrate,
destinationHostId = destination_host_id,
clearStaleRoleData = clear_stale_role_data)
return self._cmd('migrateRoles', data=args, api_version=10) | [
"def",
"migrate_roles",
"(",
"self",
",",
"role_names_to_migrate",
",",
"destination_host_id",
",",
"clear_stale_role_data",
")",
":",
"args",
"=",
"dict",
"(",
"roleNamesToMigrate",
"=",
"role_names_to_migrate",
",",
"destinationHostId",
"=",
"destination_host_id",
","... | Migrate roles from this host to a different host.
Currently, this command applies only to HDFS NameNode, JournalNode,
and Failover Controller roles. In order to migrate these roles:
- HDFS High Availability must be enabled, using quorum-based storage.
- HDFS must not be configured to use a federated nameservice.
I{B{Migrating a NameNode role requires cluster downtime.}} HDFS, along
with all of its dependent services, will be stopped at the beginning
of the migration process, and restarted at its conclusion.
If the active NameNode is selected for migration, a manual failover
will be performed before the role is migrated. The role will remain in
standby mode after the migration is complete.
When migrating a NameNode role, the co-located Failover Controller
role must be migrated as well. The Failover Controller role name must
be included in the list of role names to migrate specified in the
arguments to this command (it will not be included implicitly). This
command does not allow a Failover Controller role to be moved by itself,
although it is possible to move a JournalNode independently.
@param role_names_to_migrate: list of role names to migrate.
@param destination_host_id: the id of the host to which the roles
should be migrated.
@param clear_stale_role_data: true to delete existing stale role data,
if any. For example, when migrating a
NameNode, if the destination host has
stale data in the NameNode data
directories (possibly because a NameNode
role was previously located there), this
stale data will be deleted before migrating
the role.
@return: Reference to the submitted command.
@since: API v10 | [
"Migrate",
"roles",
"from",
"this",
"host",
"to",
"a",
"different",
"host",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/hosts.py#L185-L229 |
232,829 | cloudera/cm_api | nagios/cm_nagios.py | get_host_map | def get_host_map(root):
''' Gets a mapping between CM hostId and Nagios host information
The key is the CM hostId
The value is an object containing the Nagios hostname and host address
'''
hosts_map = {}
for host in root.get_all_hosts():
hosts_map[host.hostId] = {"hostname": NAGIOS_HOSTNAME_FORMAT % (host.hostname,),
"address": host.ipAddress}
''' Also define "virtual hosts" for the CM clusters- they will be the hosts
to which CM services are mapped
'''
for cluster in root.get_all_clusters():
hosts_map[cluster.name] = {"hostname": cluster.name,
"address": quote(cluster.name)}
hosts_map[CM_DUMMY_HOST] = {"hostname": CM_DUMMY_HOST,
"address": CM_DUMMY_HOST}
return hosts_map | python | def get_host_map(root):
''' Gets a mapping between CM hostId and Nagios host information
The key is the CM hostId
The value is an object containing the Nagios hostname and host address
'''
hosts_map = {}
for host in root.get_all_hosts():
hosts_map[host.hostId] = {"hostname": NAGIOS_HOSTNAME_FORMAT % (host.hostname,),
"address": host.ipAddress}
''' Also define "virtual hosts" for the CM clusters- they will be the hosts
to which CM services are mapped
'''
for cluster in root.get_all_clusters():
hosts_map[cluster.name] = {"hostname": cluster.name,
"address": quote(cluster.name)}
hosts_map[CM_DUMMY_HOST] = {"hostname": CM_DUMMY_HOST,
"address": CM_DUMMY_HOST}
return hosts_map | [
"def",
"get_host_map",
"(",
"root",
")",
":",
"hosts_map",
"=",
"{",
"}",
"for",
"host",
"in",
"root",
".",
"get_all_hosts",
"(",
")",
":",
"hosts_map",
"[",
"host",
".",
"hostId",
"]",
"=",
"{",
"\"hostname\"",
":",
"NAGIOS_HOSTNAME_FORMAT",
"%",
"(",
... | Gets a mapping between CM hostId and Nagios host information
The key is the CM hostId
The value is an object containing the Nagios hostname and host address | [
"Gets",
"a",
"mapping",
"between",
"CM",
"hostId",
"and",
"Nagios",
"host",
"information"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/nagios/cm_nagios.py#L199-L218 |
232,830 | cloudera/cm_api | nagios/cm_nagios.py | get_services | def get_services(root, hosts_map, view=None):
''' Gets a list of objects representing the Nagios services.
Each object contains the Nagios hostname, service name, service display
name, and service health summary.
'''
services_list = []
mgmt_service = root.get_cloudera_manager().get_service()
services_list.append({"hostname": CM_DUMMY_HOST,
"name": mgmt_service.name,
"display_name": "CM Managed Service: %s" % (mgmt_service.name,),
"status": get_status(mgmt_service),
"url": mgmt_service.serviceUrl,
"health_summary": mgmt_service.healthSummary})
for cm_role in root.get_cloudera_manager().get_service().get_all_roles(view):
services_list.append({"hostname": hosts_map[cm_role.hostRef.hostId]["hostname"],
"name": cm_role.name,
"display_name": "CM Management Service: %s" % (cm_role.name,),
"status": get_status(cm_role),
"url": cm_role.roleUrl,
"health_summary": cm_role.healthSummary})
for cm_host in root.get_all_hosts(view):
services_list.append({"hostname": hosts_map[cm_host.hostId]["hostname"],
"name": "cm-host-%s" % (cm_host.hostname,),
"display_name": "CM Managed Host: %s" % (cm_host.hostname,),
"status": get_status(cm_host),
"url": cm_host.hostUrl,
"health_summary": cm_host.healthSummary})
for cluster in root.get_all_clusters(view):
for service in cluster.get_all_services(view):
services_list.append({"hostname": cluster.name,
"name": service.name,
"display_name": "CM Managed Service: %s" % (service.name,),
"status": get_status(service),
"url": service.serviceUrl,
"health_summary": service.healthSummary})
for role in service.get_all_roles(view):
services_list.append({"hostname": hosts_map[role.hostRef.hostId]["hostname"],
"name": role.name,
"display_name": "%s:%s" % (cluster.name, role.name,),
"status": get_status(role),
"url": role.roleUrl,
"health_summary": role.healthSummary})
return services_list | python | def get_services(root, hosts_map, view=None):
''' Gets a list of objects representing the Nagios services.
Each object contains the Nagios hostname, service name, service display
name, and service health summary.
'''
services_list = []
mgmt_service = root.get_cloudera_manager().get_service()
services_list.append({"hostname": CM_DUMMY_HOST,
"name": mgmt_service.name,
"display_name": "CM Managed Service: %s" % (mgmt_service.name,),
"status": get_status(mgmt_service),
"url": mgmt_service.serviceUrl,
"health_summary": mgmt_service.healthSummary})
for cm_role in root.get_cloudera_manager().get_service().get_all_roles(view):
services_list.append({"hostname": hosts_map[cm_role.hostRef.hostId]["hostname"],
"name": cm_role.name,
"display_name": "CM Management Service: %s" % (cm_role.name,),
"status": get_status(cm_role),
"url": cm_role.roleUrl,
"health_summary": cm_role.healthSummary})
for cm_host in root.get_all_hosts(view):
services_list.append({"hostname": hosts_map[cm_host.hostId]["hostname"],
"name": "cm-host-%s" % (cm_host.hostname,),
"display_name": "CM Managed Host: %s" % (cm_host.hostname,),
"status": get_status(cm_host),
"url": cm_host.hostUrl,
"health_summary": cm_host.healthSummary})
for cluster in root.get_all_clusters(view):
for service in cluster.get_all_services(view):
services_list.append({"hostname": cluster.name,
"name": service.name,
"display_name": "CM Managed Service: %s" % (service.name,),
"status": get_status(service),
"url": service.serviceUrl,
"health_summary": service.healthSummary})
for role in service.get_all_roles(view):
services_list.append({"hostname": hosts_map[role.hostRef.hostId]["hostname"],
"name": role.name,
"display_name": "%s:%s" % (cluster.name, role.name,),
"status": get_status(role),
"url": role.roleUrl,
"health_summary": role.healthSummary})
return services_list | [
"def",
"get_services",
"(",
"root",
",",
"hosts_map",
",",
"view",
"=",
"None",
")",
":",
"services_list",
"=",
"[",
"]",
"mgmt_service",
"=",
"root",
".",
"get_cloudera_manager",
"(",
")",
".",
"get_service",
"(",
")",
"services_list",
".",
"append",
"(",... | Gets a list of objects representing the Nagios services.
Each object contains the Nagios hostname, service name, service display
name, and service health summary. | [
"Gets",
"a",
"list",
"of",
"objects",
"representing",
"the",
"Nagios",
"services",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/nagios/cm_nagios.py#L237-L280 |
232,831 | cloudera/cm_api | nagios/cm_nagios.py | submit_status_external_cmd | def submit_status_external_cmd(cmd_file, status_file):
''' Submits the status lines in the status_file to Nagios' external cmd file.
'''
try:
with open(cmd_file, 'a') as cmd_file:
cmd_file.write(status_file.read())
except IOError:
exit("Fatal error: Unable to write to Nagios external command file '%s'.\n"
"Make sure that the file exists and is writable." % (cmd_file,)) | python | def submit_status_external_cmd(cmd_file, status_file):
''' Submits the status lines in the status_file to Nagios' external cmd file.
'''
try:
with open(cmd_file, 'a') as cmd_file:
cmd_file.write(status_file.read())
except IOError:
exit("Fatal error: Unable to write to Nagios external command file '%s'.\n"
"Make sure that the file exists and is writable." % (cmd_file,)) | [
"def",
"submit_status_external_cmd",
"(",
"cmd_file",
",",
"status_file",
")",
":",
"try",
":",
"with",
"open",
"(",
"cmd_file",
",",
"'a'",
")",
"as",
"cmd_file",
":",
"cmd_file",
".",
"write",
"(",
"status_file",
".",
"read",
"(",
")",
")",
"except",
"... | Submits the status lines in the status_file to Nagios' external cmd file. | [
"Submits",
"the",
"status",
"lines",
"in",
"the",
"status_file",
"to",
"Nagios",
"external",
"cmd",
"file",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/nagios/cm_nagios.py#L283-L291 |
232,832 | cloudera/cm_api | python/src/cm_api/resource.py | Resource.invoke | def invoke(self, method, relpath=None, params=None, data=None, headers=None):
"""
Invoke an API method.
@return: Raw body or JSON dictionary (if response content type is JSON).
"""
path = self._join_uri(relpath)
resp = self._client.execute(method,
path,
params=params,
data=data,
headers=headers)
try:
body = resp.read()
except Exception, ex:
raise Exception("Command '%s %s' failed: %s" %
(method, path, ex))
self._client.logger.debug(
"%s Got response: %s%s" %
(method, body[:32], len(body) > 32 and "..." or ""))
# Is the response application/json?
if len(body) != 0 and \
resp.info().getmaintype() == "application" and \
resp.info().getsubtype() == "json":
try:
json_dict = json.loads(body)
return json_dict
except Exception, ex:
self._client.logger.exception('JSON decode error: %s' % (body,))
raise ex
else:
return body | python | def invoke(self, method, relpath=None, params=None, data=None, headers=None):
path = self._join_uri(relpath)
resp = self._client.execute(method,
path,
params=params,
data=data,
headers=headers)
try:
body = resp.read()
except Exception, ex:
raise Exception("Command '%s %s' failed: %s" %
(method, path, ex))
self._client.logger.debug(
"%s Got response: %s%s" %
(method, body[:32], len(body) > 32 and "..." or ""))
# Is the response application/json?
if len(body) != 0 and \
resp.info().getmaintype() == "application" and \
resp.info().getsubtype() == "json":
try:
json_dict = json.loads(body)
return json_dict
except Exception, ex:
self._client.logger.exception('JSON decode error: %s' % (body,))
raise ex
else:
return body | [
"def",
"invoke",
"(",
"self",
",",
"method",
",",
"relpath",
"=",
"None",
",",
"params",
"=",
"None",
",",
"data",
"=",
"None",
",",
"headers",
"=",
"None",
")",
":",
"path",
"=",
"self",
".",
"_join_uri",
"(",
"relpath",
")",
"resp",
"=",
"self",
... | Invoke an API method.
@return: Raw body or JSON dictionary (if response content type is JSON). | [
"Invoke",
"an",
"API",
"method",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/resource.py#L63-L95 |
232,833 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | create_host_template | def create_host_template(resource_root, name, cluster_name):
"""
Create a host template.
@param resource_root: The root Resource object.
@param name: Host template name
@param cluster_name: Cluster name
@return: An ApiHostTemplate object for the created host template.
@since: API v3
"""
apitemplate = ApiHostTemplate(resource_root, name, [])
return call(resource_root.post,
HOST_TEMPLATES_PATH % (cluster_name,),
ApiHostTemplate, True, data=[apitemplate], api_version=3)[0] | python | def create_host_template(resource_root, name, cluster_name):
apitemplate = ApiHostTemplate(resource_root, name, [])
return call(resource_root.post,
HOST_TEMPLATES_PATH % (cluster_name,),
ApiHostTemplate, True, data=[apitemplate], api_version=3)[0] | [
"def",
"create_host_template",
"(",
"resource_root",
",",
"name",
",",
"cluster_name",
")",
":",
"apitemplate",
"=",
"ApiHostTemplate",
"(",
"resource_root",
",",
"name",
",",
"[",
"]",
")",
"return",
"call",
"(",
"resource_root",
".",
"post",
",",
"HOST_TEMPL... | Create a host template.
@param resource_root: The root Resource object.
@param name: Host template name
@param cluster_name: Cluster name
@return: An ApiHostTemplate object for the created host template.
@since: API v3 | [
"Create",
"a",
"host",
"template",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L26-L38 |
232,834 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | get_host_template | def get_host_template(resource_root, name, cluster_name):
"""
Lookup a host template by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@return: An ApiHostTemplate object.
@since: API v3
"""
return call(resource_root.get,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, api_version=3) | python | def get_host_template(resource_root, name, cluster_name):
return call(resource_root.get,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, api_version=3) | [
"def",
"get_host_template",
"(",
"resource_root",
",",
"name",
",",
"cluster_name",
")",
":",
"return",
"call",
"(",
"resource_root",
".",
"get",
",",
"HOST_TEMPLATE_PATH",
"%",
"(",
"cluster_name",
",",
"name",
")",
",",
"ApiHostTemplate",
",",
"api_version",
... | Lookup a host template by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@return: An ApiHostTemplate object.
@since: API v3 | [
"Lookup",
"a",
"host",
"template",
"by",
"name",
"in",
"the",
"specified",
"cluster",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L40-L51 |
232,835 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | get_all_host_templates | def get_all_host_templates(resource_root, cluster_name="default"):
"""
Get all host templates in a cluster.
@param cluster_name: Cluster name.
@return: ApiList of ApiHostTemplate objects for all host templates in a cluster.
@since: API v3
"""
return call(resource_root.get,
HOST_TEMPLATES_PATH % (cluster_name,),
ApiHostTemplate, True, api_version=3) | python | def get_all_host_templates(resource_root, cluster_name="default"):
return call(resource_root.get,
HOST_TEMPLATES_PATH % (cluster_name,),
ApiHostTemplate, True, api_version=3) | [
"def",
"get_all_host_templates",
"(",
"resource_root",
",",
"cluster_name",
"=",
"\"default\"",
")",
":",
"return",
"call",
"(",
"resource_root",
".",
"get",
",",
"HOST_TEMPLATES_PATH",
"%",
"(",
"cluster_name",
",",
")",
",",
"ApiHostTemplate",
",",
"True",
","... | Get all host templates in a cluster.
@param cluster_name: Cluster name.
@return: ApiList of ApiHostTemplate objects for all host templates in a cluster.
@since: API v3 | [
"Get",
"all",
"host",
"templates",
"in",
"a",
"cluster",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L53-L62 |
232,836 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | delete_host_template | def delete_host_template(resource_root, name, cluster_name):
"""
Delete a host template identified by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@return: The deleted ApiHostTemplate object.
@since: API v3
"""
return call(resource_root.delete,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, api_version=3) | python | def delete_host_template(resource_root, name, cluster_name):
return call(resource_root.delete,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, api_version=3) | [
"def",
"delete_host_template",
"(",
"resource_root",
",",
"name",
",",
"cluster_name",
")",
":",
"return",
"call",
"(",
"resource_root",
".",
"delete",
",",
"HOST_TEMPLATE_PATH",
"%",
"(",
"cluster_name",
",",
"name",
")",
",",
"ApiHostTemplate",
",",
"api_versi... | Delete a host template identified by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@return: The deleted ApiHostTemplate object.
@since: API v3 | [
"Delete",
"a",
"host",
"template",
"identified",
"by",
"name",
"in",
"the",
"specified",
"cluster",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L64-L75 |
232,837 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | update_host_template | def update_host_template(resource_root, name, cluster_name, api_host_template):
"""
Update a host template identified by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@param api_host_template: The updated host template.
@return: The updated ApiHostTemplate.
@since: API v3
"""
return call(resource_root.put,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, data=api_host_template, api_version=3) | python | def update_host_template(resource_root, name, cluster_name, api_host_template):
return call(resource_root.put,
HOST_TEMPLATE_PATH % (cluster_name, name),
ApiHostTemplate, data=api_host_template, api_version=3) | [
"def",
"update_host_template",
"(",
"resource_root",
",",
"name",
",",
"cluster_name",
",",
"api_host_template",
")",
":",
"return",
"call",
"(",
"resource_root",
".",
"put",
",",
"HOST_TEMPLATE_PATH",
"%",
"(",
"cluster_name",
",",
"name",
")",
",",
"ApiHostTem... | Update a host template identified by name in the specified cluster.
@param resource_root: The root Resource object.
@param name: Host template name.
@param cluster_name: Cluster name.
@param api_host_template: The updated host template.
@return: The updated ApiHostTemplate.
@since: API v3 | [
"Update",
"a",
"host",
"template",
"identified",
"by",
"name",
"in",
"the",
"specified",
"cluster",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L77-L89 |
232,838 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | ApiHostTemplate.rename | def rename(self, new_name):
"""
Rename a host template.
@param new_name: New host template name.
@return: An ApiHostTemplate object.
"""
update = copy.copy(self)
update.name = new_name
return self._do_update(update) | python | def rename(self, new_name):
update = copy.copy(self)
update.name = new_name
return self._do_update(update) | [
"def",
"rename",
"(",
"self",
",",
"new_name",
")",
":",
"update",
"=",
"copy",
".",
"copy",
"(",
"self",
")",
"update",
".",
"name",
"=",
"new_name",
"return",
"self",
".",
"_do_update",
"(",
"update",
")"
] | Rename a host template.
@param new_name: New host template name.
@return: An ApiHostTemplate object. | [
"Rename",
"a",
"host",
"template",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L136-L144 |
232,839 | cloudera/cm_api | python/src/cm_api/endpoints/host_templates.py | ApiHostTemplate.set_role_config_groups | def set_role_config_groups(self, role_config_group_refs):
"""
Updates the role config groups in a host template.
@param role_config_group_refs: List of role config group refs.
@return: An ApiHostTemplate object.
"""
update = copy.copy(self)
update.roleConfigGroupRefs = role_config_group_refs
return self._do_update(update) | python | def set_role_config_groups(self, role_config_group_refs):
update = copy.copy(self)
update.roleConfigGroupRefs = role_config_group_refs
return self._do_update(update) | [
"def",
"set_role_config_groups",
"(",
"self",
",",
"role_config_group_refs",
")",
":",
"update",
"=",
"copy",
".",
"copy",
"(",
"self",
")",
"update",
".",
"roleConfigGroupRefs",
"=",
"role_config_group_refs",
"return",
"self",
".",
"_do_update",
"(",
"update",
... | Updates the role config groups in a host template.
@param role_config_group_refs: List of role config group refs.
@return: An ApiHostTemplate object. | [
"Updates",
"the",
"role",
"config",
"groups",
"in",
"a",
"host",
"template",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/host_templates.py#L146-L154 |
232,840 | cloudera/cm_api | python/examples/aws.py | list_supported_categories | def list_supported_categories():
"""
Prints a list of supported external account category names.
For example, "AWS" is a supported external account category name.
"""
categories = get_supported_categories(api)
category_names = [category.name for category in categories]
print ("Supported account categories by name: {0}".format(
COMMA_WITH_SPACE.join(map(str, category_names)))) | python | def list_supported_categories():
categories = get_supported_categories(api)
category_names = [category.name for category in categories]
print ("Supported account categories by name: {0}".format(
COMMA_WITH_SPACE.join(map(str, category_names)))) | [
"def",
"list_supported_categories",
"(",
")",
":",
"categories",
"=",
"get_supported_categories",
"(",
"api",
")",
"category_names",
"=",
"[",
"category",
".",
"name",
"for",
"category",
"in",
"categories",
"]",
"print",
"(",
"\"Supported account categories by name: {... | Prints a list of supported external account category names.
For example, "AWS" is a supported external account category name. | [
"Prints",
"a",
"list",
"of",
"supported",
"external",
"account",
"category",
"names",
".",
"For",
"example",
"AWS",
"is",
"a",
"supported",
"external",
"account",
"category",
"name",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L73-L81 |
232,841 | cloudera/cm_api | python/examples/aws.py | list_supported_types | def list_supported_types(category_name):
"""
Prints a list of supported external account type names for the given
category_name. For example, "AWS_ACCESS_KEY_AUTH" is a supported external
account type name for external account category "AWS".
"""
types = get_supported_types(api, category_name)
type_names = [type.name for type in types]
print ("Supported account types by name for '{0}': [{1}]".format(
category_name, COMMA_WITH_SPACE.join(map(str, type_names)))) | python | def list_supported_types(category_name):
types = get_supported_types(api, category_name)
type_names = [type.name for type in types]
print ("Supported account types by name for '{0}': [{1}]".format(
category_name, COMMA_WITH_SPACE.join(map(str, type_names)))) | [
"def",
"list_supported_types",
"(",
"category_name",
")",
":",
"types",
"=",
"get_supported_types",
"(",
"api",
",",
"category_name",
")",
"type_names",
"=",
"[",
"type",
".",
"name",
"for",
"type",
"in",
"types",
"]",
"print",
"(",
"\"Supported account types by... | Prints a list of supported external account type names for the given
category_name. For example, "AWS_ACCESS_KEY_AUTH" is a supported external
account type name for external account category "AWS". | [
"Prints",
"a",
"list",
"of",
"supported",
"external",
"account",
"type",
"names",
"for",
"the",
"given",
"category_name",
".",
"For",
"example",
"AWS_ACCESS_KEY_AUTH",
"is",
"a",
"supported",
"external",
"account",
"type",
"name",
"for",
"external",
"account",
"... | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L84-L93 |
232,842 | cloudera/cm_api | python/examples/aws.py | list_credentials_by_name | def list_credentials_by_name(type_name):
"""
Prints a list of available credential names for the given type_name.
"""
accounts = get_all_external_accounts(api, type_name)
account_names = [account.name for account in accounts]
print ("List of credential names for '{0}': [{1}]".format(
type_name, COMMA_WITH_SPACE.join(map(str, account_names)))) | python | def list_credentials_by_name(type_name):
accounts = get_all_external_accounts(api, type_name)
account_names = [account.name for account in accounts]
print ("List of credential names for '{0}': [{1}]".format(
type_name, COMMA_WITH_SPACE.join(map(str, account_names)))) | [
"def",
"list_credentials_by_name",
"(",
"type_name",
")",
":",
"accounts",
"=",
"get_all_external_accounts",
"(",
"api",
",",
"type_name",
")",
"account_names",
"=",
"[",
"account",
".",
"name",
"for",
"account",
"in",
"accounts",
"]",
"print",
"(",
"\"List of c... | Prints a list of available credential names for the given type_name. | [
"Prints",
"a",
"list",
"of",
"available",
"credential",
"names",
"for",
"the",
"given",
"type_name",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L96-L103 |
232,843 | cloudera/cm_api | python/examples/aws.py | call_s3guard_prune | def call_s3guard_prune(credential_name):
"""
Runs S3Guard prune command on external account associated with the
given credential_name.
""" # Get the AWS credential account associated with the credential
account = get_external_account(api, credential_name)
# Invoke the prune command for the account by its name
cmd = account.external_account_cmd_by_name('S3GuardPrune')
print ("Issued '{0}' command with id '{1}'".format(cmd.name, cmd.id))
print ("Waiting for command {0} to finish...".format(cmd.id))
cmd = cmd.wait()
print ("Command succeeded: {0}".format(cmd.success)) | python | def call_s3guard_prune(credential_name):
# Get the AWS credential account associated with the credential
account = get_external_account(api, credential_name)
# Invoke the prune command for the account by its name
cmd = account.external_account_cmd_by_name('S3GuardPrune')
print ("Issued '{0}' command with id '{1}'".format(cmd.name, cmd.id))
print ("Waiting for command {0} to finish...".format(cmd.id))
cmd = cmd.wait()
print ("Command succeeded: {0}".format(cmd.success)) | [
"def",
"call_s3guard_prune",
"(",
"credential_name",
")",
":",
"# Get the AWS credential account associated with the credential",
"account",
"=",
"get_external_account",
"(",
"api",
",",
"credential_name",
")",
"# Invoke the prune command for the account by its name",
"cmd",
"=",
... | Runs S3Guard prune command on external account associated with the
given credential_name. | [
"Runs",
"S3Guard",
"prune",
"command",
"on",
"external",
"account",
"associated",
"with",
"the",
"given",
"credential_name",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L106-L117 |
232,844 | cloudera/cm_api | python/examples/aws.py | initialize_api | def initialize_api(args):
"""
Initializes the global API instance using the given arguments.
@param args: arguments provided to the script.
"""
global api
api = ApiResource(server_host=args.hostname, server_port=args.port,
username=args.username, password=args.password,
version=args.api_version, use_tls=args.use_tls) | python | def initialize_api(args):
global api
api = ApiResource(server_host=args.hostname, server_port=args.port,
username=args.username, password=args.password,
version=args.api_version, use_tls=args.use_tls) | [
"def",
"initialize_api",
"(",
"args",
")",
":",
"global",
"api",
"api",
"=",
"ApiResource",
"(",
"server_host",
"=",
"args",
".",
"hostname",
",",
"server_port",
"=",
"args",
".",
"port",
",",
"username",
"=",
"args",
".",
"username",
",",
"password",
"=... | Initializes the global API instance using the given arguments.
@param args: arguments provided to the script. | [
"Initializes",
"the",
"global",
"API",
"instance",
"using",
"the",
"given",
"arguments",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L129-L137 |
232,845 | cloudera/cm_api | python/examples/aws.py | validate_api_compatibility | def validate_api_compatibility(args):
"""
Validates the API version.
@param args: arguments provided to the script.
"""
if args.api_version and args.api_version < MINIMUM_SUPPORTED_API_VERSION:
print("ERROR: Given API version: {0}. Minimum supported API version: {1}"
.format(args.api_version, MINIMUM_SUPPORTED_API_VERSION)) | python | def validate_api_compatibility(args):
if args.api_version and args.api_version < MINIMUM_SUPPORTED_API_VERSION:
print("ERROR: Given API version: {0}. Minimum supported API version: {1}"
.format(args.api_version, MINIMUM_SUPPORTED_API_VERSION)) | [
"def",
"validate_api_compatibility",
"(",
"args",
")",
":",
"if",
"args",
".",
"api_version",
"and",
"args",
".",
"api_version",
"<",
"MINIMUM_SUPPORTED_API_VERSION",
":",
"print",
"(",
"\"ERROR: Given API version: {0}. Minimum supported API version: {1}\"",
".",
"format",
... | Validates the API version.
@param args: arguments provided to the script. | [
"Validates",
"the",
"API",
"version",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L140-L147 |
232,846 | cloudera/cm_api | python/examples/aws.py | get_login_credentials | def get_login_credentials(args):
"""
Gets the login credentials from the user, if not specified while invoking
the script.
@param args: arguments provided to the script.
"""
if not args.username:
args.username = raw_input("Enter Username: ")
if not args.password:
args.password = getpass.getpass("Enter Password: ") | python | def get_login_credentials(args):
if not args.username:
args.username = raw_input("Enter Username: ")
if not args.password:
args.password = getpass.getpass("Enter Password: ") | [
"def",
"get_login_credentials",
"(",
"args",
")",
":",
"if",
"not",
"args",
".",
"username",
":",
"args",
".",
"username",
"=",
"raw_input",
"(",
"\"Enter Username: \"",
")",
"if",
"not",
"args",
".",
"password",
":",
"args",
".",
"password",
"=",
"getpass... | Gets the login credentials from the user, if not specified while invoking
the script.
@param args: arguments provided to the script. | [
"Gets",
"the",
"login",
"credentials",
"from",
"the",
"user",
"if",
"not",
"specified",
"while",
"invoking",
"the",
"script",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L150-L159 |
232,847 | cloudera/cm_api | python/examples/aws.py | main | def main():
"""
The "main" entry that controls the flow of the script based
on the provided arguments.
"""
setup_logging(logging.INFO)
# Parse arguments
parser = argparse.ArgumentParser(
description="A utility to interact with AWS using Cloudera Manager.")
parser.add_argument('-H', '--hostname', action='store', dest='hostname',
required=True,
help='The hostname of the Cloudera Manager server.')
parser.add_argument('-p', action='store', dest='port', type=int,
help='The port of the Cloudera Manager server. Defaults '
'to 7180 (http) or 7183 (https).')
parser.add_argument('-u', '--username', action='store', dest='username',
help='Login name.')
parser.add_argument('--password', action='store', dest='password',
help='Login password.')
parser.add_argument('--api-version', action='store', dest='api_version',
type=int,
default=MINIMUM_SUPPORTED_API_VERSION,
help='API version to be used. Defaults to {0}.'.format(
MINIMUM_SUPPORTED_API_VERSION))
parser.add_argument('--tls', action='store_const', dest='use_tls',
const=True, default=False,
help='Whether to use tls (https).')
parser.add_argument('-c', '--show-categories', action='store_true',
default=False, dest='show_categories',
help='Prints a list of supported external account '
'category names. For example, "AWS" is a supported '
'external account category name.')
parser.add_argument('-t', '--show-types', action='store',
dest='category_name',
help='Prints a list of supported external account type '
'names for the given CATEGORY_NAME. For example, '
'"AWS_ACCESS_KEY_AUTH" is a supported external '
'account type name for external account category '
'"AWS".')
parser.add_argument('-n', '--show-credentials', action='store',
dest='type_name',
help='Prints a list of available credential names for '
'the given TYPE_NAME.')
parser.add_argument('--prune', action='store', dest='credential_name',
help='Runs S3Guard prune command on external account '
'associated with the given CREDENTIAL_NAME.')
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
args = parser.parse_args()
# Use the default port if required.
if not args.port:
if args.use_tls:
args.port = DEFAULT_HTTPS_PORT
else:
args.port = DEFAULT_HTTP_PORT
validate_api_compatibility(args)
get_login_credentials(args)
initialize_api(args)
# Perform the AWS operation based on the input arguments.
if args.show_categories:
list_supported_categories()
elif args.category_name:
list_supported_types(args.category_name)
elif args.type_name:
list_credentials_by_name(args.type_name)
elif args.credential_name:
call_s3guard_prune(args.credential_name)
else:
print ("ERROR: No arguments given to perform any AWS operation.")
parser.print_help()
sys.exit(1) | python | def main():
setup_logging(logging.INFO)
# Parse arguments
parser = argparse.ArgumentParser(
description="A utility to interact with AWS using Cloudera Manager.")
parser.add_argument('-H', '--hostname', action='store', dest='hostname',
required=True,
help='The hostname of the Cloudera Manager server.')
parser.add_argument('-p', action='store', dest='port', type=int,
help='The port of the Cloudera Manager server. Defaults '
'to 7180 (http) or 7183 (https).')
parser.add_argument('-u', '--username', action='store', dest='username',
help='Login name.')
parser.add_argument('--password', action='store', dest='password',
help='Login password.')
parser.add_argument('--api-version', action='store', dest='api_version',
type=int,
default=MINIMUM_SUPPORTED_API_VERSION,
help='API version to be used. Defaults to {0}.'.format(
MINIMUM_SUPPORTED_API_VERSION))
parser.add_argument('--tls', action='store_const', dest='use_tls',
const=True, default=False,
help='Whether to use tls (https).')
parser.add_argument('-c', '--show-categories', action='store_true',
default=False, dest='show_categories',
help='Prints a list of supported external account '
'category names. For example, "AWS" is a supported '
'external account category name.')
parser.add_argument('-t', '--show-types', action='store',
dest='category_name',
help='Prints a list of supported external account type '
'names for the given CATEGORY_NAME. For example, '
'"AWS_ACCESS_KEY_AUTH" is a supported external '
'account type name for external account category '
'"AWS".')
parser.add_argument('-n', '--show-credentials', action='store',
dest='type_name',
help='Prints a list of available credential names for '
'the given TYPE_NAME.')
parser.add_argument('--prune', action='store', dest='credential_name',
help='Runs S3Guard prune command on external account '
'associated with the given CREDENTIAL_NAME.')
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
args = parser.parse_args()
# Use the default port if required.
if not args.port:
if args.use_tls:
args.port = DEFAULT_HTTPS_PORT
else:
args.port = DEFAULT_HTTP_PORT
validate_api_compatibility(args)
get_login_credentials(args)
initialize_api(args)
# Perform the AWS operation based on the input arguments.
if args.show_categories:
list_supported_categories()
elif args.category_name:
list_supported_types(args.category_name)
elif args.type_name:
list_credentials_by_name(args.type_name)
elif args.credential_name:
call_s3guard_prune(args.credential_name)
else:
print ("ERROR: No arguments given to perform any AWS operation.")
parser.print_help()
sys.exit(1) | [
"def",
"main",
"(",
")",
":",
"setup_logging",
"(",
"logging",
".",
"INFO",
")",
"# Parse arguments",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"description",
"=",
"\"A utility to interact with AWS using Cloudera Manager.\"",
")",
"parser",
".",
"add_argu... | The "main" entry that controls the flow of the script based
on the provided arguments. | [
"The",
"main",
"entry",
"that",
"controls",
"the",
"flow",
"of",
"the",
"script",
"based",
"on",
"the",
"provided",
"arguments",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/examples/aws.py#L162-L235 |
232,848 | cloudera/cm_api | python/src/cm_api/api_client.py | get_root_resource | def get_root_resource(server_host, server_port=None,
username="admin", password="admin",
use_tls=False, version=API_CURRENT_VERSION):
"""
See ApiResource.
"""
return ApiResource(server_host, server_port, username, password, use_tls,
version) | python | def get_root_resource(server_host, server_port=None,
username="admin", password="admin",
use_tls=False, version=API_CURRENT_VERSION):
return ApiResource(server_host, server_port, username, password, use_tls,
version) | [
"def",
"get_root_resource",
"(",
"server_host",
",",
"server_port",
"=",
"None",
",",
"username",
"=",
"\"admin\"",
",",
"password",
"=",
"\"admin\"",
",",
"use_tls",
"=",
"False",
",",
"version",
"=",
"API_CURRENT_VERSION",
")",
":",
"return",
"ApiResource",
... | See ApiResource. | [
"See",
"ApiResource",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/api_client.py#L392-L399 |
232,849 | cloudera/cm_api | python/src/cm_api/api_client.py | ApiResource.create_cluster | def create_cluster(self, name, version=None, fullVersion=None):
"""
Create a new cluster.
@param name: Cluster name.
@param version: Cluster major CDH version, e.g. 'CDH5'. Ignored if
fullVersion is specified.
@param fullVersion: Complete CDH version, e.g. '5.1.2'. Overrides major
version if both specified.
@return: The created cluster.
"""
return clusters.create_cluster(self, name, version, fullVersion) | python | def create_cluster(self, name, version=None, fullVersion=None):
return clusters.create_cluster(self, name, version, fullVersion) | [
"def",
"create_cluster",
"(",
"self",
",",
"name",
",",
"version",
"=",
"None",
",",
"fullVersion",
"=",
"None",
")",
":",
"return",
"clusters",
".",
"create_cluster",
"(",
"self",
",",
"name",
",",
"version",
",",
"fullVersion",
")"
] | Create a new cluster.
@param name: Cluster name.
@param version: Cluster major CDH version, e.g. 'CDH5'. Ignored if
fullVersion is specified.
@param fullVersion: Complete CDH version, e.g. '5.1.2'. Overrides major
version if both specified.
@return: The created cluster. | [
"Create",
"a",
"new",
"cluster",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/api_client.py#L103-L114 |
232,850 | cloudera/cm_api | python/src/cm_api/api_client.py | ApiResource.create_host | def create_host(self, host_id, name, ipaddr, rack_id = None):
"""
Create a host.
@param host_id: The host id.
@param name: Host name
@param ipaddr: IP address
@param rack_id: Rack id. Default None.
@return: An ApiHost object
"""
return hosts.create_host(self, host_id, name, ipaddr, rack_id) | python | def create_host(self, host_id, name, ipaddr, rack_id = None):
return hosts.create_host(self, host_id, name, ipaddr, rack_id) | [
"def",
"create_host",
"(",
"self",
",",
"host_id",
",",
"name",
",",
"ipaddr",
",",
"rack_id",
"=",
"None",
")",
":",
"return",
"hosts",
".",
"create_host",
"(",
"self",
",",
"host_id",
",",
"name",
",",
"ipaddr",
",",
"rack_id",
")"
] | Create a host.
@param host_id: The host id.
@param name: Host name
@param ipaddr: IP address
@param rack_id: Rack id. Default None.
@return: An ApiHost object | [
"Create",
"a",
"host",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/api_client.py#L144-L154 |
232,851 | cloudera/cm_api | python/src/cm_api/api_client.py | ApiResource.get_metrics | def get_metrics(self, path, from_time, to_time, metrics, view, params=None):
"""
Generic function for querying metrics.
@param from_time: A datetime; start of the period to query (optional).
@param to_time: A datetime; end of the period to query (default = now).
@param metrics: List of metrics to query (default = all).
@param view: View to materialize ('full' or 'summary')
@param params: Other query parameters.
@return: List of metrics and their readings.
"""
if not params:
params = { }
if from_time:
params['from'] = from_time.isoformat()
if to_time:
params['to'] = to_time.isoformat()
if metrics:
params['metrics'] = metrics
if view:
params['view'] = view
resp = self.get(path, params=params)
return types.ApiList.from_json_dict(resp, self, types.ApiMetric) | python | def get_metrics(self, path, from_time, to_time, metrics, view, params=None):
if not params:
params = { }
if from_time:
params['from'] = from_time.isoformat()
if to_time:
params['to'] = to_time.isoformat()
if metrics:
params['metrics'] = metrics
if view:
params['view'] = view
resp = self.get(path, params=params)
return types.ApiList.from_json_dict(resp, self, types.ApiMetric) | [
"def",
"get_metrics",
"(",
"self",
",",
"path",
",",
"from_time",
",",
"to_time",
",",
"metrics",
",",
"view",
",",
"params",
"=",
"None",
")",
":",
"if",
"not",
"params",
":",
"params",
"=",
"{",
"}",
"if",
"from_time",
":",
"params",
"[",
"'from'",... | Generic function for querying metrics.
@param from_time: A datetime; start of the period to query (optional).
@param to_time: A datetime; end of the period to query (default = now).
@param metrics: List of metrics to query (default = all).
@param view: View to materialize ('full' or 'summary')
@param params: Other query parameters.
@return: List of metrics and their readings. | [
"Generic",
"function",
"for",
"querying",
"metrics",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/api_client.py#L263-L285 |
232,852 | cloudera/cm_api | python/src/cm_api/api_client.py | ApiResource.query_timeseries | def query_timeseries(self, query, from_time=None, to_time=None, by_post=False):
"""
Query time series.
@param query: Query string.
@param from_time: Start of the period to query (optional).
@param to_time: End of the period to query (default = now).
@return: A list of ApiTimeSeriesResponse.
"""
return timeseries.query_timeseries(self, query, from_time, to_time, by_post=by_post) | python | def query_timeseries(self, query, from_time=None, to_time=None, by_post=False):
return timeseries.query_timeseries(self, query, from_time, to_time, by_post=by_post) | [
"def",
"query_timeseries",
"(",
"self",
",",
"query",
",",
"from_time",
"=",
"None",
",",
"to_time",
"=",
"None",
",",
"by_post",
"=",
"False",
")",
":",
"return",
"timeseries",
".",
"query_timeseries",
"(",
"self",
",",
"query",
",",
"from_time",
",",
"... | Query time series.
@param query: Query string.
@param from_time: Start of the period to query (optional).
@param to_time: End of the period to query (default = now).
@return: A list of ApiTimeSeriesResponse. | [
"Query",
"time",
"series",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/api_client.py#L287-L295 |
232,853 | cloudera/cm_api | python/src/cm_api/endpoints/tools.py | echo | def echo(root_resource, message):
"""Have the server echo our message back."""
params = dict(message=message)
return root_resource.get(ECHO_PATH, params) | python | def echo(root_resource, message):
params = dict(message=message)
return root_resource.get(ECHO_PATH, params) | [
"def",
"echo",
"(",
"root_resource",
",",
"message",
")",
":",
"params",
"=",
"dict",
"(",
"message",
"=",
"message",
")",
"return",
"root_resource",
".",
"get",
"(",
"ECHO_PATH",
",",
"params",
")"
] | Have the server echo our message back. | [
"Have",
"the",
"server",
"echo",
"our",
"message",
"back",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/tools.py#L23-L26 |
232,854 | cloudera/cm_api | python/src/cm_api/endpoints/tools.py | echo_error | def echo_error(root_resource, message):
"""Generate an error, but we get to set the error message."""
params = dict(message=message)
return root_resource.get(ECHO_ERROR_PATH, params) | python | def echo_error(root_resource, message):
params = dict(message=message)
return root_resource.get(ECHO_ERROR_PATH, params) | [
"def",
"echo_error",
"(",
"root_resource",
",",
"message",
")",
":",
"params",
"=",
"dict",
"(",
"message",
"=",
"message",
")",
"return",
"root_resource",
".",
"get",
"(",
"ECHO_ERROR_PATH",
",",
"params",
")"
] | Generate an error, but we get to set the error message. | [
"Generate",
"an",
"error",
"but",
"we",
"get",
"to",
"set",
"the",
"error",
"message",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/tools.py#L28-L31 |
232,855 | cloudera/cm_api | python/src/cm_shell/cmps.py | ClouderaShell.service_action | def service_action(self, service, action):
"Perform given action on service for the selected cluster"
try:
service = api.get_cluster(self.cluster).get_service(service)
except ApiException:
print("Service not found")
return None
if action == "start":
service.start()
if action == "restart":
service.restart()
if action == "stop":
service.stop()
return True | python | def service_action(self, service, action):
"Perform given action on service for the selected cluster"
try:
service = api.get_cluster(self.cluster).get_service(service)
except ApiException:
print("Service not found")
return None
if action == "start":
service.start()
if action == "restart":
service.restart()
if action == "stop":
service.stop()
return True | [
"def",
"service_action",
"(",
"self",
",",
"service",
",",
"action",
")",
":",
"try",
":",
"service",
"=",
"api",
".",
"get_cluster",
"(",
"self",
".",
"cluster",
")",
".",
"get_service",
"(",
"service",
")",
"except",
"ApiException",
":",
"print",
"(",
... | Perform given action on service for the selected cluster | [
"Perform",
"given",
"action",
"on",
"service",
"for",
"the",
"selected",
"cluster"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_shell/cmps.py#L277-L292 |
232,856 | cloudera/cm_api | python/src/cm_shell/cmps.py | ClouderaShell.cluster_autocomplete | def cluster_autocomplete(self, text, line, start_index, end_index):
"autocomplete for the use command, obtain list of clusters first"
if not self.CACHED_CLUSTERS:
clusters = [cluster.name for cluster in api.get_all_clusters()]
self.CACHED_CLUSTERS = clusters
if text:
return [cluster for cluster in self.CACHED_CLUSTERS if cluster.startswith(text)]
else:
return self.CACHED_CLUSTERS | python | def cluster_autocomplete(self, text, line, start_index, end_index):
"autocomplete for the use command, obtain list of clusters first"
if not self.CACHED_CLUSTERS:
clusters = [cluster.name for cluster in api.get_all_clusters()]
self.CACHED_CLUSTERS = clusters
if text:
return [cluster for cluster in self.CACHED_CLUSTERS if cluster.startswith(text)]
else:
return self.CACHED_CLUSTERS | [
"def",
"cluster_autocomplete",
"(",
"self",
",",
"text",
",",
"line",
",",
"start_index",
",",
"end_index",
")",
":",
"if",
"not",
"self",
".",
"CACHED_CLUSTERS",
":",
"clusters",
"=",
"[",
"cluster",
".",
"name",
"for",
"cluster",
"in",
"api",
".",
"get... | autocomplete for the use command, obtain list of clusters first | [
"autocomplete",
"for",
"the",
"use",
"command",
"obtain",
"list",
"of",
"clusters",
"first"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_shell/cmps.py#L370-L379 |
232,857 | cloudera/cm_api | python/src/cm_shell/cmps.py | ClouderaShell.roles_autocomplete | def roles_autocomplete(self, text, line, start_index, end_index):
"Return full list of roles"
if '-' not in line:
# Append a dash to each service, makes for faster autocompletion of
# roles
return [s + '-' for s in self.services_autocomplete(text, line, start_index, end_index)]
else:
key, role = line.split()[1].split('-', 1)
if key not in self.CACHED_ROLES:
service = api.get_cluster(self.cluster).get_service(key)
roles = []
for t in service.get_role_types():
for r in service.get_roles_by_type(t):
roles.append(r.name)
self.CACHED_ROLES[key] = roles
if not role:
return self.CACHED_ROLES[key]
else:
return [r for r in self.CACHED_ROLES[key] if r.startswith(line.split()[1])] | python | def roles_autocomplete(self, text, line, start_index, end_index):
"Return full list of roles"
if '-' not in line:
# Append a dash to each service, makes for faster autocompletion of
# roles
return [s + '-' for s in self.services_autocomplete(text, line, start_index, end_index)]
else:
key, role = line.split()[1].split('-', 1)
if key not in self.CACHED_ROLES:
service = api.get_cluster(self.cluster).get_service(key)
roles = []
for t in service.get_role_types():
for r in service.get_roles_by_type(t):
roles.append(r.name)
self.CACHED_ROLES[key] = roles
if not role:
return self.CACHED_ROLES[key]
else:
return [r for r in self.CACHED_ROLES[key] if r.startswith(line.split()[1])] | [
"def",
"roles_autocomplete",
"(",
"self",
",",
"text",
",",
"line",
",",
"start_index",
",",
"end_index",
")",
":",
"if",
"'-'",
"not",
"in",
"line",
":",
"# Append a dash to each service, makes for faster autocompletion of",
"# roles",
"return",
"[",
"s",
"+",
"'... | Return full list of roles | [
"Return",
"full",
"list",
"of",
"roles"
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_shell/cmps.py#L424-L444 |
232,858 | cloudera/cm_api | python/src/cm_api/endpoints/events.py | query_events | def query_events(resource_root, query_str=None):
"""
Search for events.
@param query_str: Query string.
@return: A list of ApiEvent.
"""
params = None
if query_str:
params = dict(query=query_str)
return call(resource_root.get, EVENTS_PATH, ApiEventQueryResult,
params=params) | python | def query_events(resource_root, query_str=None):
params = None
if query_str:
params = dict(query=query_str)
return call(resource_root.get, EVENTS_PATH, ApiEventQueryResult,
params=params) | [
"def",
"query_events",
"(",
"resource_root",
",",
"query_str",
"=",
"None",
")",
":",
"params",
"=",
"None",
"if",
"query_str",
":",
"params",
"=",
"dict",
"(",
"query",
"=",
"query_str",
")",
"return",
"call",
"(",
"resource_root",
".",
"get",
",",
"EVE... | Search for events.
@param query_str: Query string.
@return: A list of ApiEvent. | [
"Search",
"for",
"events",
"."
] | 5d2512375bd94684b4da36df9e0d9177865ffcbb | https://github.com/cloudera/cm_api/blob/5d2512375bd94684b4da36df9e0d9177865ffcbb/python/src/cm_api/endpoints/events.py#L23-L33 |
232,859 | ivankorobkov/python-inject | src/inject.py | configure | def configure(config=None, bind_in_runtime=True):
"""Create an injector with a callable config or raise an exception when already configured."""
global _INJECTOR
with _INJECTOR_LOCK:
if _INJECTOR:
raise InjectorException('Injector is already configured')
_INJECTOR = Injector(config, bind_in_runtime=bind_in_runtime)
logger.debug('Created and configured an injector, config=%s', config)
return _INJECTOR | python | def configure(config=None, bind_in_runtime=True):
global _INJECTOR
with _INJECTOR_LOCK:
if _INJECTOR:
raise InjectorException('Injector is already configured')
_INJECTOR = Injector(config, bind_in_runtime=bind_in_runtime)
logger.debug('Created and configured an injector, config=%s', config)
return _INJECTOR | [
"def",
"configure",
"(",
"config",
"=",
"None",
",",
"bind_in_runtime",
"=",
"True",
")",
":",
"global",
"_INJECTOR",
"with",
"_INJECTOR_LOCK",
":",
"if",
"_INJECTOR",
":",
"raise",
"InjectorException",
"(",
"'Injector is already configured'",
")",
"_INJECTOR",
"=... | Create an injector with a callable config or raise an exception when already configured. | [
"Create",
"an",
"injector",
"with",
"a",
"callable",
"config",
"or",
"raise",
"an",
"exception",
"when",
"already",
"configured",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L95-L105 |
232,860 | ivankorobkov/python-inject | src/inject.py | configure_once | def configure_once(config=None, bind_in_runtime=True):
"""Create an injector with a callable config if not present, otherwise, do nothing."""
with _INJECTOR_LOCK:
if _INJECTOR:
return _INJECTOR
return configure(config, bind_in_runtime=bind_in_runtime) | python | def configure_once(config=None, bind_in_runtime=True):
with _INJECTOR_LOCK:
if _INJECTOR:
return _INJECTOR
return configure(config, bind_in_runtime=bind_in_runtime) | [
"def",
"configure_once",
"(",
"config",
"=",
"None",
",",
"bind_in_runtime",
"=",
"True",
")",
":",
"with",
"_INJECTOR_LOCK",
":",
"if",
"_INJECTOR",
":",
"return",
"_INJECTOR",
"return",
"configure",
"(",
"config",
",",
"bind_in_runtime",
"=",
"bind_in_runtime"... | Create an injector with a callable config if not present, otherwise, do nothing. | [
"Create",
"an",
"injector",
"with",
"a",
"callable",
"config",
"if",
"not",
"present",
"otherwise",
"do",
"nothing",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L108-L114 |
232,861 | ivankorobkov/python-inject | src/inject.py | clear_and_configure | def clear_and_configure(config=None, bind_in_runtime=True):
"""Clear an existing injector and create another one with a callable config."""
with _INJECTOR_LOCK:
clear()
return configure(config, bind_in_runtime=bind_in_runtime) | python | def clear_and_configure(config=None, bind_in_runtime=True):
with _INJECTOR_LOCK:
clear()
return configure(config, bind_in_runtime=bind_in_runtime) | [
"def",
"clear_and_configure",
"(",
"config",
"=",
"None",
",",
"bind_in_runtime",
"=",
"True",
")",
":",
"with",
"_INJECTOR_LOCK",
":",
"clear",
"(",
")",
"return",
"configure",
"(",
"config",
",",
"bind_in_runtime",
"=",
"bind_in_runtime",
")"
] | Clear an existing injector and create another one with a callable config. | [
"Clear",
"an",
"existing",
"injector",
"and",
"create",
"another",
"one",
"with",
"a",
"callable",
"config",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L117-L121 |
232,862 | ivankorobkov/python-inject | src/inject.py | autoparams | def autoparams(*selected_args):
"""Return a decorator that will inject args into a function using type annotations, Python >= 3.5 only.
For example::
@inject.autoparams()
def refresh_cache(cache: RedisCache, db: DbInterface):
pass
There is an option to specify which arguments we want to inject without attempts of injecting everything:
For example::
@inject.autoparams('cache', 'db')
def sign_up(name, email, cache, db):
pass
"""
def autoparams_decorator(func):
if sys.version_info[:2] < (3, 5):
raise InjectorException('autoparams are supported from Python 3.5 onwards')
full_args_spec = inspect.getfullargspec(func)
annotations_items = full_args_spec.annotations.items()
all_arg_names = frozenset(full_args_spec.args + full_args_spec.kwonlyargs)
args_to_check = frozenset(selected_args) or all_arg_names
args_annotated_types = {
arg_name: annotated_type for arg_name, annotated_type in annotations_items
if arg_name in args_to_check
}
return _ParametersInjection(**args_annotated_types)(func)
return autoparams_decorator | python | def autoparams(*selected_args):
def autoparams_decorator(func):
if sys.version_info[:2] < (3, 5):
raise InjectorException('autoparams are supported from Python 3.5 onwards')
full_args_spec = inspect.getfullargspec(func)
annotations_items = full_args_spec.annotations.items()
all_arg_names = frozenset(full_args_spec.args + full_args_spec.kwonlyargs)
args_to_check = frozenset(selected_args) or all_arg_names
args_annotated_types = {
arg_name: annotated_type for arg_name, annotated_type in annotations_items
if arg_name in args_to_check
}
return _ParametersInjection(**args_annotated_types)(func)
return autoparams_decorator | [
"def",
"autoparams",
"(",
"*",
"selected_args",
")",
":",
"def",
"autoparams_decorator",
"(",
"func",
")",
":",
"if",
"sys",
".",
"version_info",
"[",
":",
"2",
"]",
"<",
"(",
"3",
",",
"5",
")",
":",
"raise",
"InjectorException",
"(",
"'autoparams are s... | Return a decorator that will inject args into a function using type annotations, Python >= 3.5 only.
For example::
@inject.autoparams()
def refresh_cache(cache: RedisCache, db: DbInterface):
pass
There is an option to specify which arguments we want to inject without attempts of injecting everything:
For example::
@inject.autoparams('cache', 'db')
def sign_up(name, email, cache, db):
pass | [
"Return",
"a",
"decorator",
"that",
"will",
"inject",
"args",
"into",
"a",
"function",
"using",
"type",
"annotations",
"Python",
">",
"=",
"3",
".",
"5",
"only",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L169-L200 |
232,863 | ivankorobkov/python-inject | src/inject.py | Binder.bind | def bind(self, cls, instance):
"""Bind a class to an instance."""
self._check_class(cls)
self._bindings[cls] = lambda: instance
logger.debug('Bound %s to an instance %s', cls, instance)
return self | python | def bind(self, cls, instance):
self._check_class(cls)
self._bindings[cls] = lambda: instance
logger.debug('Bound %s to an instance %s', cls, instance)
return self | [
"def",
"bind",
"(",
"self",
",",
"cls",
",",
"instance",
")",
":",
"self",
".",
"_check_class",
"(",
"cls",
")",
"self",
".",
"_bindings",
"[",
"cls",
"]",
"=",
"lambda",
":",
"instance",
"logger",
".",
"debug",
"(",
"'Bound %s to an instance %s'",
",",
... | Bind a class to an instance. | [
"Bind",
"a",
"class",
"to",
"an",
"instance",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L226-L231 |
232,864 | ivankorobkov/python-inject | src/inject.py | Binder.bind_to_constructor | def bind_to_constructor(self, cls, constructor):
"""Bind a class to a callable singleton constructor."""
self._check_class(cls)
if constructor is None:
raise InjectorException('Constructor cannot be None, key=%s' % cls)
self._bindings[cls] = _ConstructorBinding(constructor)
logger.debug('Bound %s to a constructor %s', cls, constructor)
return self | python | def bind_to_constructor(self, cls, constructor):
self._check_class(cls)
if constructor is None:
raise InjectorException('Constructor cannot be None, key=%s' % cls)
self._bindings[cls] = _ConstructorBinding(constructor)
logger.debug('Bound %s to a constructor %s', cls, constructor)
return self | [
"def",
"bind_to_constructor",
"(",
"self",
",",
"cls",
",",
"constructor",
")",
":",
"self",
".",
"_check_class",
"(",
"cls",
")",
"if",
"constructor",
"is",
"None",
":",
"raise",
"InjectorException",
"(",
"'Constructor cannot be None, key=%s'",
"%",
"cls",
")",... | Bind a class to a callable singleton constructor. | [
"Bind",
"a",
"class",
"to",
"a",
"callable",
"singleton",
"constructor",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L233-L241 |
232,865 | ivankorobkov/python-inject | src/inject.py | Binder.bind_to_provider | def bind_to_provider(self, cls, provider):
"""Bind a class to a callable instance provider executed for each injection."""
self._check_class(cls)
if provider is None:
raise InjectorException('Provider cannot be None, key=%s' % cls)
self._bindings[cls] = provider
logger.debug('Bound %s to a provider %s', cls, provider)
return self | python | def bind_to_provider(self, cls, provider):
self._check_class(cls)
if provider is None:
raise InjectorException('Provider cannot be None, key=%s' % cls)
self._bindings[cls] = provider
logger.debug('Bound %s to a provider %s', cls, provider)
return self | [
"def",
"bind_to_provider",
"(",
"self",
",",
"cls",
",",
"provider",
")",
":",
"self",
".",
"_check_class",
"(",
"cls",
")",
"if",
"provider",
"is",
"None",
":",
"raise",
"InjectorException",
"(",
"'Provider cannot be None, key=%s'",
"%",
"cls",
")",
"self",
... | Bind a class to a callable instance provider executed for each injection. | [
"Bind",
"a",
"class",
"to",
"a",
"callable",
"instance",
"provider",
"executed",
"for",
"each",
"injection",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L243-L251 |
232,866 | ivankorobkov/python-inject | src/inject.py | Injector.get_instance | def get_instance(self, cls):
"""Return an instance for a class."""
binding = self._bindings.get(cls)
if binding:
return binding()
# Try to create a runtime binding.
with _BINDING_LOCK:
binding = self._bindings.get(cls)
if binding:
return binding()
if not self._bind_in_runtime:
raise InjectorException('No binding was found for key=%s' % cls)
if not callable(cls):
raise InjectorException(
'Cannot create a runtime binding, the key is not callable, key=%s' % cls)
instance = cls()
self._bindings[cls] = lambda: instance
logger.debug('Created a runtime binding for key=%s, instance=%s', cls, instance)
return instance | python | def get_instance(self, cls):
binding = self._bindings.get(cls)
if binding:
return binding()
# Try to create a runtime binding.
with _BINDING_LOCK:
binding = self._bindings.get(cls)
if binding:
return binding()
if not self._bind_in_runtime:
raise InjectorException('No binding was found for key=%s' % cls)
if not callable(cls):
raise InjectorException(
'Cannot create a runtime binding, the key is not callable, key=%s' % cls)
instance = cls()
self._bindings[cls] = lambda: instance
logger.debug('Created a runtime binding for key=%s, instance=%s', cls, instance)
return instance | [
"def",
"get_instance",
"(",
"self",
",",
"cls",
")",
":",
"binding",
"=",
"self",
".",
"_bindings",
".",
"get",
"(",
"cls",
")",
"if",
"binding",
":",
"return",
"binding",
"(",
")",
"# Try to create a runtime binding.",
"with",
"_BINDING_LOCK",
":",
"binding... | Return an instance for a class. | [
"Return",
"an",
"instance",
"for",
"a",
"class",
"."
] | e2f04f91fbcfd0b38e628cbeda97bd8449038d36 | https://github.com/ivankorobkov/python-inject/blob/e2f04f91fbcfd0b38e628cbeda97bd8449038d36/src/inject.py#L271-L294 |
232,867 | theislab/anndata | anndata/readwrite/read.py | read_csv | def read_csv(
filename: Union[PathLike, Iterator[str]],
delimiter: Optional[str]=',',
first_column_names: Optional[bool]=None,
dtype: str='float32',
) -> AnnData:
"""Read ``.csv`` file.
Same as :func:`~anndata.read_text` but with default delimiter ``','``.
Parameters
----------
filename
Data file.
delimiter
Delimiter that separates data within text file. If ``None``, will split at
arbitrary number of white spaces, which is different from enforcing
splitting at single white space ``' '``.
first_column_names
Assume the first column stores row names.
dtype
Numpy data type.
"""
return read_text(filename, delimiter, first_column_names, dtype) | python | def read_csv(
filename: Union[PathLike, Iterator[str]],
delimiter: Optional[str]=',',
first_column_names: Optional[bool]=None,
dtype: str='float32',
) -> AnnData:
return read_text(filename, delimiter, first_column_names, dtype) | [
"def",
"read_csv",
"(",
"filename",
":",
"Union",
"[",
"PathLike",
",",
"Iterator",
"[",
"str",
"]",
"]",
",",
"delimiter",
":",
"Optional",
"[",
"str",
"]",
"=",
"','",
",",
"first_column_names",
":",
"Optional",
"[",
"bool",
"]",
"=",
"None",
",",
... | Read ``.csv`` file.
Same as :func:`~anndata.read_text` but with default delimiter ``','``.
Parameters
----------
filename
Data file.
delimiter
Delimiter that separates data within text file. If ``None``, will split at
arbitrary number of white spaces, which is different from enforcing
splitting at single white space ``' '``.
first_column_names
Assume the first column stores row names.
dtype
Numpy data type. | [
"Read",
".",
"csv",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L16-L39 |
232,868 | theislab/anndata | anndata/readwrite/read.py | read_umi_tools | def read_umi_tools(filename: PathLike, dtype: str='float32') -> AnnData:
"""Read a gzipped condensed count matrix from umi_tools.
Parameters
----------
filename
File name to read from.
"""
# import pandas for conversion of a dict of dicts into a matrix
# import gzip to read a gzipped file :-)
import gzip
from pandas import DataFrame
dod = {} # this will contain basically everything
fh = gzip.open(fspath(filename))
header = fh.readline() # read the first line
for line in fh:
t = line.decode('ascii').split('\t') # gzip read bytes, hence the decoding
try:
dod[t[1]].update({t[0]:int(t[2])})
except KeyError:
dod[t[1]] = {t[0]:int(t[2])}
df = DataFrame.from_dict(dod, orient='index') # build the matrix
df.fillna(value=0., inplace=True) # many NaN, replace with zeros
return AnnData(np.array(df), {'obs_names': df.index}, {'var_names': df.columns}, dtype=dtype) | python | def read_umi_tools(filename: PathLike, dtype: str='float32') -> AnnData:
# import pandas for conversion of a dict of dicts into a matrix
# import gzip to read a gzipped file :-)
import gzip
from pandas import DataFrame
dod = {} # this will contain basically everything
fh = gzip.open(fspath(filename))
header = fh.readline() # read the first line
for line in fh:
t = line.decode('ascii').split('\t') # gzip read bytes, hence the decoding
try:
dod[t[1]].update({t[0]:int(t[2])})
except KeyError:
dod[t[1]] = {t[0]:int(t[2])}
df = DataFrame.from_dict(dod, orient='index') # build the matrix
df.fillna(value=0., inplace=True) # many NaN, replace with zeros
return AnnData(np.array(df), {'obs_names': df.index}, {'var_names': df.columns}, dtype=dtype) | [
"def",
"read_umi_tools",
"(",
"filename",
":",
"PathLike",
",",
"dtype",
":",
"str",
"=",
"'float32'",
")",
"->",
"AnnData",
":",
"# import pandas for conversion of a dict of dicts into a matrix",
"# import gzip to read a gzipped file :-)",
"import",
"gzip",
"from",
"pandas... | Read a gzipped condensed count matrix from umi_tools.
Parameters
----------
filename
File name to read from. | [
"Read",
"a",
"gzipped",
"condensed",
"count",
"matrix",
"from",
"umi_tools",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L68-L94 |
232,869 | theislab/anndata | anndata/readwrite/read.py | read_loom | def read_loom(filename: PathLike, sparse: bool = True, cleanup: bool = False, X_name: str = 'spliced',
obs_names: str = 'CellID', var_names: str = 'Gene', dtype: str='float32', **kwargs) -> AnnData:
"""Read ``.loom``-formatted hdf5 file.
This reads the whole file into memory.
Beware that you have to explicitly state when you want to read the file as
sparse data.
Parameters
----------
filename
The filename.
sparse
Whether to read the data matrix as sparse.
cleanup:
Whether to remove all obs/var keys that do not store more than one unique value.
X_name:
Loompy key where the data matrix is stored.
obs_names:
Loompy key where the observation/cell names are stored.
var_names:
Loompy key where the variable/gene names are stored.
**kwargs:
Arguments to loompy.connect
"""
filename = fspath(filename) # allow passing pathlib.Path objects
from loompy import connect
with connect(filename, 'r', **kwargs) as lc:
if X_name not in lc.layers.keys(): X_name = ''
X = lc.layers[X_name].sparse().T.tocsr() if sparse else lc.layers[X_name][()].T
layers = OrderedDict()
if X_name != '': layers['matrix'] = lc.layers[''].sparse().T.tocsr() if sparse else lc.layers[''][()].T
for key in lc.layers.keys():
if key != '': layers[key] = lc.layers[key].sparse().T.tocsr() if sparse else lc.layers[key][()].T
obs = dict(lc.col_attrs)
if obs_names in obs.keys(): obs['obs_names'] = obs.pop(obs_names)
obsm_attrs = [k for k, v in obs.items() if v.ndim > 1 and v.shape[1] > 1]
obsm = {}
for key in obsm_attrs:
obsm[key] = obs.pop(key)
var = dict(lc.row_attrs)
if var_names in var.keys(): var['var_names'] = var.pop(var_names)
varm_attrs = [k for k, v in var.items() if v.ndim > 1 and v.shape[1] > 1]
varm = {}
for key in varm_attrs:
varm[key] = var.pop(key)
if cleanup:
for key in list(obs.keys()):
if len(set(obs[key])) == 1:
del obs[key]
for key in list(var.keys()):
if len(set(var[key])) == 1:
del var[key]
adata = AnnData(
X,
obs=obs, # not ideal: make the generator a dict...
var=var,
layers=layers,
obsm=obsm if obsm else None,
varm=varm if varm else None,
dtype=dtype)
return adata | python | def read_loom(filename: PathLike, sparse: bool = True, cleanup: bool = False, X_name: str = 'spliced',
obs_names: str = 'CellID', var_names: str = 'Gene', dtype: str='float32', **kwargs) -> AnnData:
filename = fspath(filename) # allow passing pathlib.Path objects
from loompy import connect
with connect(filename, 'r', **kwargs) as lc:
if X_name not in lc.layers.keys(): X_name = ''
X = lc.layers[X_name].sparse().T.tocsr() if sparse else lc.layers[X_name][()].T
layers = OrderedDict()
if X_name != '': layers['matrix'] = lc.layers[''].sparse().T.tocsr() if sparse else lc.layers[''][()].T
for key in lc.layers.keys():
if key != '': layers[key] = lc.layers[key].sparse().T.tocsr() if sparse else lc.layers[key][()].T
obs = dict(lc.col_attrs)
if obs_names in obs.keys(): obs['obs_names'] = obs.pop(obs_names)
obsm_attrs = [k for k, v in obs.items() if v.ndim > 1 and v.shape[1] > 1]
obsm = {}
for key in obsm_attrs:
obsm[key] = obs.pop(key)
var = dict(lc.row_attrs)
if var_names in var.keys(): var['var_names'] = var.pop(var_names)
varm_attrs = [k for k, v in var.items() if v.ndim > 1 and v.shape[1] > 1]
varm = {}
for key in varm_attrs:
varm[key] = var.pop(key)
if cleanup:
for key in list(obs.keys()):
if len(set(obs[key])) == 1:
del obs[key]
for key in list(var.keys()):
if len(set(var[key])) == 1:
del var[key]
adata = AnnData(
X,
obs=obs, # not ideal: make the generator a dict...
var=var,
layers=layers,
obsm=obsm if obsm else None,
varm=varm if varm else None,
dtype=dtype)
return adata | [
"def",
"read_loom",
"(",
"filename",
":",
"PathLike",
",",
"sparse",
":",
"bool",
"=",
"True",
",",
"cleanup",
":",
"bool",
"=",
"False",
",",
"X_name",
":",
"str",
"=",
"'spliced'",
",",
"obs_names",
":",
"str",
"=",
"'CellID'",
",",
"var_names",
":",... | Read ``.loom``-formatted hdf5 file.
This reads the whole file into memory.
Beware that you have to explicitly state when you want to read the file as
sparse data.
Parameters
----------
filename
The filename.
sparse
Whether to read the data matrix as sparse.
cleanup:
Whether to remove all obs/var keys that do not store more than one unique value.
X_name:
Loompy key where the data matrix is stored.
obs_names:
Loompy key where the observation/cell names are stored.
var_names:
Loompy key where the variable/gene names are stored.
**kwargs:
Arguments to loompy.connect | [
"Read",
".",
"loom",
"-",
"formatted",
"hdf5",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L129-L199 |
232,870 | theislab/anndata | anndata/readwrite/read.py | read_mtx | def read_mtx(filename: PathLike, dtype: str='float32') -> AnnData:
"""Read ``.mtx`` file.
Parameters
----------
filename
The filename.
dtype
Numpy data type.
"""
from scipy.io import mmread
# could be rewritten accounting for dtype to be more performant
X = mmread(fspath(filename)).astype(dtype)
from scipy.sparse import csr_matrix
X = csr_matrix(X)
return AnnData(X, dtype=dtype) | python | def read_mtx(filename: PathLike, dtype: str='float32') -> AnnData:
from scipy.io import mmread
# could be rewritten accounting for dtype to be more performant
X = mmread(fspath(filename)).astype(dtype)
from scipy.sparse import csr_matrix
X = csr_matrix(X)
return AnnData(X, dtype=dtype) | [
"def",
"read_mtx",
"(",
"filename",
":",
"PathLike",
",",
"dtype",
":",
"str",
"=",
"'float32'",
")",
"->",
"AnnData",
":",
"from",
"scipy",
".",
"io",
"import",
"mmread",
"# could be rewritten accounting for dtype to be more performant",
"X",
"=",
"mmread",
"(",
... | Read ``.mtx`` file.
Parameters
----------
filename
The filename.
dtype
Numpy data type. | [
"Read",
".",
"mtx",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L202-L217 |
232,871 | theislab/anndata | anndata/readwrite/read.py | iter_lines | def iter_lines(file_like: Iterable[str]) -> Generator[str, None, None]:
""" Helper for iterating only nonempty lines without line breaks"""
for line in file_like:
line = line.rstrip('\r\n')
if line:
yield line | python | def iter_lines(file_like: Iterable[str]) -> Generator[str, None, None]:
for line in file_like:
line = line.rstrip('\r\n')
if line:
yield line | [
"def",
"iter_lines",
"(",
"file_like",
":",
"Iterable",
"[",
"str",
"]",
")",
"->",
"Generator",
"[",
"str",
",",
"None",
",",
"None",
"]",
":",
"for",
"line",
"in",
"file_like",
":",
"line",
"=",
"line",
".",
"rstrip",
"(",
"'\\r\\n'",
")",
"if",
... | Helper for iterating only nonempty lines without line breaks | [
"Helper",
"for",
"iterating",
"only",
"nonempty",
"lines",
"without",
"line",
"breaks"
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L258-L263 |
232,872 | theislab/anndata | anndata/readwrite/read.py | read_zarr | def read_zarr(store):
"""Read from a hierarchical Zarr array store.
Parameters
----------
store
The filename, a :class:`~typing.MutableMapping`, or a Zarr storage class.
"""
if isinstance(store, Path):
store = str(store)
import zarr
f = zarr.open(store, mode='r')
d = {}
for key in f.keys():
_read_key_value_from_zarr(f, d, key)
return AnnData(*AnnData._args_from_dict(d)) | python | def read_zarr(store):
if isinstance(store, Path):
store = str(store)
import zarr
f = zarr.open(store, mode='r')
d = {}
for key in f.keys():
_read_key_value_from_zarr(f, d, key)
return AnnData(*AnnData._args_from_dict(d)) | [
"def",
"read_zarr",
"(",
"store",
")",
":",
"if",
"isinstance",
"(",
"store",
",",
"Path",
")",
":",
"store",
"=",
"str",
"(",
"store",
")",
"import",
"zarr",
"f",
"=",
"zarr",
".",
"open",
"(",
"store",
",",
"mode",
"=",
"'r'",
")",
"d",
"=",
... | Read from a hierarchical Zarr array store.
Parameters
----------
store
The filename, a :class:`~typing.MutableMapping`, or a Zarr storage class. | [
"Read",
"from",
"a",
"hierarchical",
"Zarr",
"array",
"store",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L369-L384 |
232,873 | theislab/anndata | anndata/readwrite/read.py | read_h5ad | def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000):
"""Read ``.h5ad``-formatted hdf5 file.
Parameters
----------
filename
File name of data file.
backed : {``None``, ``'r'``, ``'r+'``}
If ``'r'``, load :class:`~anndata.AnnData` in ``backed`` mode instead
of fully loading it into memory (`memory` mode). If you want to modify
backed attributes of the AnnData object, you need to choose ``'r+'``.
chunk_size
Used only when loading sparse dataset that is stored as dense.
Loading iterates through chunks of the dataset of this row size
until it reads the whole dataset.
Higher size means higher memory consumption and higher loading speed.
"""
if isinstance(backed, bool):
# We pass `None`s through to h5py.File, and its default is “a”
# (=“r+”, but create the file if it doesn’t exist)
backed = 'r+' if backed else None
warnings.warn(
"In a future version, read_h5ad will no longer explicitly support "
"boolean arguments. Specify the read mode, or leave `backed=None`.",
DeprecationWarning,
)
if backed:
# open in backed-mode
return AnnData(filename=filename, filemode=backed)
else:
# load everything into memory
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
X = constructor_args[0]
dtype = None
if X is not None:
dtype = X.dtype.name # maintain dtype, since 0.7
return AnnData(*_read_args_from_h5ad(filename=filename, chunk_size=chunk_size), dtype=dtype) | python | def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000):
if isinstance(backed, bool):
# We pass `None`s through to h5py.File, and its default is “a”
# (=“r+”, but create the file if it doesn’t exist)
backed = 'r+' if backed else None
warnings.warn(
"In a future version, read_h5ad will no longer explicitly support "
"boolean arguments. Specify the read mode, or leave `backed=None`.",
DeprecationWarning,
)
if backed:
# open in backed-mode
return AnnData(filename=filename, filemode=backed)
else:
# load everything into memory
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
X = constructor_args[0]
dtype = None
if X is not None:
dtype = X.dtype.name # maintain dtype, since 0.7
return AnnData(*_read_args_from_h5ad(filename=filename, chunk_size=chunk_size), dtype=dtype) | [
"def",
"read_h5ad",
"(",
"filename",
",",
"backed",
":",
"Optional",
"[",
"str",
"]",
"=",
"None",
",",
"chunk_size",
":",
"int",
"=",
"6000",
")",
":",
"if",
"isinstance",
"(",
"backed",
",",
"bool",
")",
":",
"# We pass `None`s through to h5py.File, and it... | Read ``.h5ad``-formatted hdf5 file.
Parameters
----------
filename
File name of data file.
backed : {``None``, ``'r'``, ``'r+'``}
If ``'r'``, load :class:`~anndata.AnnData` in ``backed`` mode instead
of fully loading it into memory (`memory` mode). If you want to modify
backed attributes of the AnnData object, you need to choose ``'r+'``.
chunk_size
Used only when loading sparse dataset that is stored as dense.
Loading iterates through chunks of the dataset of this row size
until it reads the whole dataset.
Higher size means higher memory consumption and higher loading speed. | [
"Read",
".",
"h5ad",
"-",
"formatted",
"hdf5",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L427-L463 |
232,874 | theislab/anndata | anndata/readwrite/read.py | _read_args_from_h5ad | def _read_args_from_h5ad(
adata: AnnData = None,
filename: Optional[PathLike] = None,
mode: Optional[str] = None,
chunk_size: int = 6000
):
"""Return a tuple with the parameters for initializing AnnData.
Parameters
----------
filename
Defaults to the objects filename if ``None``.
"""
if filename is None and (adata is None or adata.filename is None):
raise ValueError('Need either a filename or an AnnData object with file backing')
# we need to be able to call the function without reference to self when
# not reading in backed mode
backed = mode is not None
if filename is None and not backed:
filename = adata.filename
d = {}
if backed:
f = adata.file._file
else:
f = h5py.File(filename, 'r')
for key in f.keys():
if backed and key in AnnData._BACKED_ATTRS:
d[key] = None
else:
_read_key_value_from_h5(f, d, key, chunk_size=chunk_size)
# backwards compat: save X with the correct name
if 'X' not in d:
if backed == 'r+':
for key in AnnData._H5_ALIASES['X']:
if key in d:
del f[key]
f.create_dataset('X', data=d[key])
break
# backwards compat: store sparse matrices properly
csr_keys = [key.replace('_csr_data', '')
for key in d if '_csr_data' in key]
for key in csr_keys:
d = load_sparse_csr(d, key=key)
if not backed:
f.close()
return AnnData._args_from_dict(d) | python | def _read_args_from_h5ad(
adata: AnnData = None,
filename: Optional[PathLike] = None,
mode: Optional[str] = None,
chunk_size: int = 6000
):
if filename is None and (adata is None or adata.filename is None):
raise ValueError('Need either a filename or an AnnData object with file backing')
# we need to be able to call the function without reference to self when
# not reading in backed mode
backed = mode is not None
if filename is None and not backed:
filename = adata.filename
d = {}
if backed:
f = adata.file._file
else:
f = h5py.File(filename, 'r')
for key in f.keys():
if backed and key in AnnData._BACKED_ATTRS:
d[key] = None
else:
_read_key_value_from_h5(f, d, key, chunk_size=chunk_size)
# backwards compat: save X with the correct name
if 'X' not in d:
if backed == 'r+':
for key in AnnData._H5_ALIASES['X']:
if key in d:
del f[key]
f.create_dataset('X', data=d[key])
break
# backwards compat: store sparse matrices properly
csr_keys = [key.replace('_csr_data', '')
for key in d if '_csr_data' in key]
for key in csr_keys:
d = load_sparse_csr(d, key=key)
if not backed:
f.close()
return AnnData._args_from_dict(d) | [
"def",
"_read_args_from_h5ad",
"(",
"adata",
":",
"AnnData",
"=",
"None",
",",
"filename",
":",
"Optional",
"[",
"PathLike",
"]",
"=",
"None",
",",
"mode",
":",
"Optional",
"[",
"str",
"]",
"=",
"None",
",",
"chunk_size",
":",
"int",
"=",
"6000",
")",
... | Return a tuple with the parameters for initializing AnnData.
Parameters
----------
filename
Defaults to the objects filename if ``None``. | [
"Return",
"a",
"tuple",
"with",
"the",
"parameters",
"for",
"initializing",
"AnnData",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/readwrite/read.py#L466-L513 |
232,875 | theislab/anndata | anndata/utils.py | make_index_unique | def make_index_unique(index: pd.Index, join: str = '-'):
"""Makes the index unique by appending '1', '2', etc.
The first occurance of a non-unique value is ignored.
Parameters
----------
join
The connecting string between name and integer.
Examples
--------
>>> adata1 = sc.AnnData(np.ones((3, 2)), {'obs_names': ['a', 'b', 'c']})
>>> adata2 = sc.AnnData(np.zeros((3, 2)), {'obs_names': ['d', 'b', 'b']})
>>> adata = adata1.concatenate(adata2)
>>> adata.obs_names
Index(['a', 'b', 'c', 'd', 'b', 'b'], dtype='object')
>>> adata.obs_names_make_unique()
>>> adata.obs_names
Index(['a', 'b', 'c', 'd', 'b-1', 'b-2'], dtype='object')
"""
if index.is_unique:
return index
from collections import defaultdict
values = index.values
indices_dup = index.duplicated(keep='first')
values_dup = values[indices_dup]
counter = defaultdict(lambda: 0)
for i, v in enumerate(values_dup):
counter[v] += 1
values_dup[i] += join + str(counter[v])
values[indices_dup] = values_dup
index = pd.Index(values)
return index | python | def make_index_unique(index: pd.Index, join: str = '-'):
if index.is_unique:
return index
from collections import defaultdict
values = index.values
indices_dup = index.duplicated(keep='first')
values_dup = values[indices_dup]
counter = defaultdict(lambda: 0)
for i, v in enumerate(values_dup):
counter[v] += 1
values_dup[i] += join + str(counter[v])
values[indices_dup] = values_dup
index = pd.Index(values)
return index | [
"def",
"make_index_unique",
"(",
"index",
":",
"pd",
".",
"Index",
",",
"join",
":",
"str",
"=",
"'-'",
")",
":",
"if",
"index",
".",
"is_unique",
":",
"return",
"index",
"from",
"collections",
"import",
"defaultdict",
"values",
"=",
"index",
".",
"value... | Makes the index unique by appending '1', '2', etc.
The first occurance of a non-unique value is ignored.
Parameters
----------
join
The connecting string between name and integer.
Examples
--------
>>> adata1 = sc.AnnData(np.ones((3, 2)), {'obs_names': ['a', 'b', 'c']})
>>> adata2 = sc.AnnData(np.zeros((3, 2)), {'obs_names': ['d', 'b', 'b']})
>>> adata = adata1.concatenate(adata2)
>>> adata.obs_names
Index(['a', 'b', 'c', 'd', 'b', 'b'], dtype='object')
>>> adata.obs_names_make_unique()
>>> adata.obs_names
Index(['a', 'b', 'c', 'd', 'b-1', 'b-2'], dtype='object') | [
"Makes",
"the",
"index",
"unique",
"by",
"appending",
"1",
"2",
"etc",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/utils.py#L15-L48 |
232,876 | theislab/anndata | anndata/base.py | _find_corresponding_multicol_key | def _find_corresponding_multicol_key(key, keys_multicol):
"""Find the corresponding multicolumn key."""
for mk in keys_multicol:
if key.startswith(mk) and 'of' in key:
return mk
return None | python | def _find_corresponding_multicol_key(key, keys_multicol):
for mk in keys_multicol:
if key.startswith(mk) and 'of' in key:
return mk
return None | [
"def",
"_find_corresponding_multicol_key",
"(",
"key",
",",
"keys_multicol",
")",
":",
"for",
"mk",
"in",
"keys_multicol",
":",
"if",
"key",
".",
"startswith",
"(",
"mk",
")",
"and",
"'of'",
"in",
"key",
":",
"return",
"mk",
"return",
"None"
] | Find the corresponding multicolumn key. | [
"Find",
"the",
"corresponding",
"multicolumn",
"key",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L177-L182 |
232,877 | theislab/anndata | anndata/base.py | _gen_keys_from_multicol_key | def _gen_keys_from_multicol_key(key_multicol, n_keys):
"""Generates single-column keys from multicolumn key."""
keys = [('{}{:03}of{:03}')
.format(key_multicol, i+1, n_keys) for i in range(n_keys)]
return keys | python | def _gen_keys_from_multicol_key(key_multicol, n_keys):
keys = [('{}{:03}of{:03}')
.format(key_multicol, i+1, n_keys) for i in range(n_keys)]
return keys | [
"def",
"_gen_keys_from_multicol_key",
"(",
"key_multicol",
",",
"n_keys",
")",
":",
"keys",
"=",
"[",
"(",
"'{}{:03}of{:03}'",
")",
".",
"format",
"(",
"key_multicol",
",",
"i",
"+",
"1",
",",
"n_keys",
")",
"for",
"i",
"in",
"range",
"(",
"n_keys",
")",... | Generates single-column keys from multicolumn key. | [
"Generates",
"single",
"-",
"column",
"keys",
"from",
"multicolumn",
"key",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L186-L190 |
232,878 | theislab/anndata | anndata/base.py | _check_2d_shape | def _check_2d_shape(X):
"""Check shape of array or sparse matrix.
Assure that X is always 2D: Unlike numpy we always deal with 2D arrays.
"""
if X.dtype.names is None and len(X.shape) != 2:
raise ValueError('X needs to be 2-dimensional, not '
'{}-dimensional.'.format(len(X.shape))) | python | def _check_2d_shape(X):
if X.dtype.names is None and len(X.shape) != 2:
raise ValueError('X needs to be 2-dimensional, not '
'{}-dimensional.'.format(len(X.shape))) | [
"def",
"_check_2d_shape",
"(",
"X",
")",
":",
"if",
"X",
".",
"dtype",
".",
"names",
"is",
"None",
"and",
"len",
"(",
"X",
".",
"shape",
")",
"!=",
"2",
":",
"raise",
"ValueError",
"(",
"'X needs to be 2-dimensional, not '",
"'{}-dimensional.'",
".",
"form... | Check shape of array or sparse matrix.
Assure that X is always 2D: Unlike numpy we always deal with 2D arrays. | [
"Check",
"shape",
"of",
"array",
"or",
"sparse",
"matrix",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L225-L232 |
232,879 | theislab/anndata | anndata/base.py | BoundRecArr.to_df | def to_df(self) -> pd.DataFrame:
"""Convert to pandas dataframe."""
df = pd.DataFrame(index=RangeIndex(0, self.shape[0], name=None))
for key in self.keys():
value = self[key]
for icolumn, column in enumerate(value.T):
df['{}{}'.format(key, icolumn+1)] = column
return df | python | def to_df(self) -> pd.DataFrame:
df = pd.DataFrame(index=RangeIndex(0, self.shape[0], name=None))
for key in self.keys():
value = self[key]
for icolumn, column in enumerate(value.T):
df['{}{}'.format(key, icolumn+1)] = column
return df | [
"def",
"to_df",
"(",
"self",
")",
"->",
"pd",
".",
"DataFrame",
":",
"df",
"=",
"pd",
".",
"DataFrame",
"(",
"index",
"=",
"RangeIndex",
"(",
"0",
",",
"self",
".",
"shape",
"[",
"0",
"]",
",",
"name",
"=",
"None",
")",
")",
"for",
"key",
"in",... | Convert to pandas dataframe. | [
"Convert",
"to",
"pandas",
"dataframe",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L166-L173 |
232,880 | theislab/anndata | anndata/base.py | AnnDataFileManager.isopen | def isopen(self) -> bool:
"""State of backing file."""
if self._file is None:
return False
# try accessing the id attribute to see if the file is open
return bool(self._file.id) | python | def isopen(self) -> bool:
if self._file is None:
return False
# try accessing the id attribute to see if the file is open
return bool(self._file.id) | [
"def",
"isopen",
"(",
"self",
")",
"->",
"bool",
":",
"if",
"self",
".",
"_file",
"is",
"None",
":",
"return",
"False",
"# try accessing the id attribute to see if the file is open",
"return",
"bool",
"(",
"self",
".",
"_file",
".",
"id",
")"
] | State of backing file. | [
"State",
"of",
"backing",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L366-L371 |
232,881 | theislab/anndata | anndata/base.py | AnnData.transpose | def transpose(self) -> 'AnnData':
"""Transpose whole object.
Data matrix is transposed, observations and variables are interchanged.
"""
if not self.isbacked: X = self._X
else: X = self.file['X']
if self.isview:
raise ValueError(
'You\'re trying to transpose a view of an `AnnData`, which is currently not implemented. '
'Call `.copy()` before transposing.')
layers = {k:(v.T.tocsr() if sparse.isspmatrix_csr(v) else v.T) for (k, v) in self.layers.items(copy=False)}
if sparse.isspmatrix_csr(X):
return AnnData(X.T.tocsr(), self._var, self._obs, self._uns,
self._varm.flipped(), self._obsm.flipped(),
filename=self.filename, layers=layers, dtype=self.X.dtype.name)
return AnnData(X.T, self._var, self._obs, self._uns,
self._varm.flipped(), self._obsm.flipped(),
filename=self.filename, layers=layers, dtype=self.X.dtype.name) | python | def transpose(self) -> 'AnnData':
if not self.isbacked: X = self._X
else: X = self.file['X']
if self.isview:
raise ValueError(
'You\'re trying to transpose a view of an `AnnData`, which is currently not implemented. '
'Call `.copy()` before transposing.')
layers = {k:(v.T.tocsr() if sparse.isspmatrix_csr(v) else v.T) for (k, v) in self.layers.items(copy=False)}
if sparse.isspmatrix_csr(X):
return AnnData(X.T.tocsr(), self._var, self._obs, self._uns,
self._varm.flipped(), self._obsm.flipped(),
filename=self.filename, layers=layers, dtype=self.X.dtype.name)
return AnnData(X.T, self._var, self._obs, self._uns,
self._varm.flipped(), self._obsm.flipped(),
filename=self.filename, layers=layers, dtype=self.X.dtype.name) | [
"def",
"transpose",
"(",
"self",
")",
"->",
"'AnnData'",
":",
"if",
"not",
"self",
".",
"isbacked",
":",
"X",
"=",
"self",
".",
"_X",
"else",
":",
"X",
"=",
"self",
".",
"file",
"[",
"'X'",
"]",
"if",
"self",
".",
"isview",
":",
"raise",
"ValueEr... | Transpose whole object.
Data matrix is transposed, observations and variables are interchanged. | [
"Transpose",
"whole",
"object",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L1526-L1544 |
232,882 | theislab/anndata | anndata/base.py | AnnData.copy | def copy(self, filename: Optional[PathLike] = None) -> 'AnnData':
"""Full copy, optionally on disk."""
if not self.isbacked:
return AnnData(self._X.copy() if self._X is not None else None,
self._obs.copy(),
self._var.copy(),
# deepcopy on DictView does not work and is unnecessary
# as uns was copied already before
self._uns.copy() if isinstance(self._uns, DictView) else deepcopy(self._uns),
self._obsm.copy(), self._varm.copy(),
raw=None if self._raw is None else self._raw.copy(),
layers=self.layers.as_dict(),
dtype=self._X.dtype.name if self._X is not None else 'float32')
else:
if filename is None:
raise ValueError(
'To copy an AnnData object in backed mode, '
'pass a filename: `.copy(filename=\'myfilename.h5ad\')`.')
if self.isview:
self.write(filename)
else:
from shutil import copyfile
copyfile(self.filename, filename)
return AnnData(filename=filename) | python | def copy(self, filename: Optional[PathLike] = None) -> 'AnnData':
if not self.isbacked:
return AnnData(self._X.copy() if self._X is not None else None,
self._obs.copy(),
self._var.copy(),
# deepcopy on DictView does not work and is unnecessary
# as uns was copied already before
self._uns.copy() if isinstance(self._uns, DictView) else deepcopy(self._uns),
self._obsm.copy(), self._varm.copy(),
raw=None if self._raw is None else self._raw.copy(),
layers=self.layers.as_dict(),
dtype=self._X.dtype.name if self._X is not None else 'float32')
else:
if filename is None:
raise ValueError(
'To copy an AnnData object in backed mode, '
'pass a filename: `.copy(filename=\'myfilename.h5ad\')`.')
if self.isview:
self.write(filename)
else:
from shutil import copyfile
copyfile(self.filename, filename)
return AnnData(filename=filename) | [
"def",
"copy",
"(",
"self",
",",
"filename",
":",
"Optional",
"[",
"PathLike",
"]",
"=",
"None",
")",
"->",
"'AnnData'",
":",
"if",
"not",
"self",
".",
"isbacked",
":",
"return",
"AnnData",
"(",
"self",
".",
"_X",
".",
"copy",
"(",
")",
"if",
"self... | Full copy, optionally on disk. | [
"Full",
"copy",
"optionally",
"on",
"disk",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L1564-L1587 |
232,883 | theislab/anndata | anndata/base.py | AnnData.write_h5ad | def write_h5ad(
self,
filename: Optional[PathLike] = None,
compression: Optional[str] = None,
compression_opts: Union[int, Any] = None,
force_dense: Optional[bool] = None
):
"""Write ``.h5ad``-formatted hdf5 file.
.. note::
Setting compression to ``'gzip'`` can save disk space but
will slow down writing and subsequent reading. Prior to
v0.6.16, this was the default for parameter
``compression``.
Generally, if you have sparse data that are stored as a dense
matrix, you can dramatically improve performance and reduce
disk space by converting to a :class:`~scipy.sparse.csr_matrix`::
from scipy.sparse import csr_matrix
adata.X = csr_matrix(adata.X)
Parameters
----------
filename
Filename of data file. Defaults to backing file.
compression : ``None``, {``'gzip'``, ``'lzf'``} (default: ``None``)
See the h5py :ref:`dataset_compression`.
compression_opts
See the h5py :ref:`dataset_compression`.
force_dense
Write sparse data as a dense matrix. Defaults to ``True`` if object is
backed, otherwise to ``False``.
"""
from .readwrite.write import _write_h5ad
if filename is None and not self.isbacked:
raise ValueError('Provide a filename!')
if filename is None:
filename = self.filename
if force_dense is None:
force_dense = self.isbacked
_write_h5ad(filename, self, compression=compression,
compression_opts=compression_opts, force_dense=force_dense)
if self.isbacked:
self.file.close() | python | def write_h5ad(
self,
filename: Optional[PathLike] = None,
compression: Optional[str] = None,
compression_opts: Union[int, Any] = None,
force_dense: Optional[bool] = None
):
from .readwrite.write import _write_h5ad
if filename is None and not self.isbacked:
raise ValueError('Provide a filename!')
if filename is None:
filename = self.filename
if force_dense is None:
force_dense = self.isbacked
_write_h5ad(filename, self, compression=compression,
compression_opts=compression_opts, force_dense=force_dense)
if self.isbacked:
self.file.close() | [
"def",
"write_h5ad",
"(",
"self",
",",
"filename",
":",
"Optional",
"[",
"PathLike",
"]",
"=",
"None",
",",
"compression",
":",
"Optional",
"[",
"str",
"]",
"=",
"None",
",",
"compression_opts",
":",
"Union",
"[",
"int",
",",
"Any",
"]",
"=",
"None",
... | Write ``.h5ad``-formatted hdf5 file.
.. note::
Setting compression to ``'gzip'`` can save disk space but
will slow down writing and subsequent reading. Prior to
v0.6.16, this was the default for parameter
``compression``.
Generally, if you have sparse data that are stored as a dense
matrix, you can dramatically improve performance and reduce
disk space by converting to a :class:`~scipy.sparse.csr_matrix`::
from scipy.sparse import csr_matrix
adata.X = csr_matrix(adata.X)
Parameters
----------
filename
Filename of data file. Defaults to backing file.
compression : ``None``, {``'gzip'``, ``'lzf'``} (default: ``None``)
See the h5py :ref:`dataset_compression`.
compression_opts
See the h5py :ref:`dataset_compression`.
force_dense
Write sparse data as a dense matrix. Defaults to ``True`` if object is
backed, otherwise to ``False``. | [
"Write",
".",
"h5ad",
"-",
"formatted",
"hdf5",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L1962-L2010 |
232,884 | theislab/anndata | anndata/base.py | AnnData.write_csvs | def write_csvs(self, dirname: PathLike, skip_data: bool = True, sep: str = ','):
"""Write annotation to ``.csv`` files.
It is not possible to recover the full :class:`~anndata.AnnData` from the
output of this function. Use :meth:`~anndata.AnnData.write` for this.
Parameters
----------
dirname
Name of directory to which to export.
skip_data
Skip the data matrix :attr:`X`.
sep
Separator for the data.
"""
from .readwrite.write import write_csvs
write_csvs(dirname, self, skip_data=skip_data, sep=sep) | python | def write_csvs(self, dirname: PathLike, skip_data: bool = True, sep: str = ','):
from .readwrite.write import write_csvs
write_csvs(dirname, self, skip_data=skip_data, sep=sep) | [
"def",
"write_csvs",
"(",
"self",
",",
"dirname",
":",
"PathLike",
",",
"skip_data",
":",
"bool",
"=",
"True",
",",
"sep",
":",
"str",
"=",
"','",
")",
":",
"from",
".",
"readwrite",
".",
"write",
"import",
"write_csvs",
"write_csvs",
"(",
"dirname",
"... | Write annotation to ``.csv`` files.
It is not possible to recover the full :class:`~anndata.AnnData` from the
output of this function. Use :meth:`~anndata.AnnData.write` for this.
Parameters
----------
dirname
Name of directory to which to export.
skip_data
Skip the data matrix :attr:`X`.
sep
Separator for the data. | [
"Write",
"annotation",
"to",
".",
"csv",
"files",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L2014-L2030 |
232,885 | theislab/anndata | anndata/base.py | AnnData.write_loom | def write_loom(self, filename: PathLike, write_obsm_varm: bool = False):
"""Write ``.loom``-formatted hdf5 file.
Parameters
----------
filename
The filename.
"""
from .readwrite.write import write_loom
write_loom(filename, self, write_obsm_varm = write_obsm_varm) | python | def write_loom(self, filename: PathLike, write_obsm_varm: bool = False):
from .readwrite.write import write_loom
write_loom(filename, self, write_obsm_varm = write_obsm_varm) | [
"def",
"write_loom",
"(",
"self",
",",
"filename",
":",
"PathLike",
",",
"write_obsm_varm",
":",
"bool",
"=",
"False",
")",
":",
"from",
".",
"readwrite",
".",
"write",
"import",
"write_loom",
"write_loom",
"(",
"filename",
",",
"self",
",",
"write_obsm_varm... | Write ``.loom``-formatted hdf5 file.
Parameters
----------
filename
The filename. | [
"Write",
".",
"loom",
"-",
"formatted",
"hdf5",
"file",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L2032-L2041 |
232,886 | theislab/anndata | anndata/base.py | AnnData.write_zarr | def write_zarr(
self,
store: Union[MutableMapping, PathLike],
chunks: Union[bool, int, Tuple[int, ...]],
):
"""Write a hierarchical Zarr array store.
Parameters
----------
store
The filename, a :class:`~typing.MutableMapping`, or a Zarr storage class.
chunks
Chunk shape.
"""
from .readwrite.write import write_zarr
write_zarr(store, self, chunks=chunks) | python | def write_zarr(
self,
store: Union[MutableMapping, PathLike],
chunks: Union[bool, int, Tuple[int, ...]],
):
from .readwrite.write import write_zarr
write_zarr(store, self, chunks=chunks) | [
"def",
"write_zarr",
"(",
"self",
",",
"store",
":",
"Union",
"[",
"MutableMapping",
",",
"PathLike",
"]",
",",
"chunks",
":",
"Union",
"[",
"bool",
",",
"int",
",",
"Tuple",
"[",
"int",
",",
"...",
"]",
"]",
",",
")",
":",
"from",
".",
"readwrite"... | Write a hierarchical Zarr array store.
Parameters
----------
store
The filename, a :class:`~typing.MutableMapping`, or a Zarr storage class.
chunks
Chunk shape. | [
"Write",
"a",
"hierarchical",
"Zarr",
"array",
"store",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L2043-L2058 |
232,887 | theislab/anndata | anndata/base.py | AnnData._to_dict_fixed_width_arrays | def _to_dict_fixed_width_arrays(self, var_len_str=True):
"""A dict of arrays that stores data and annotation.
It is sufficient for reconstructing the object.
"""
self.strings_to_categoricals()
obs_rec, uns_obs = df_to_records_fixed_width(self._obs, var_len_str)
var_rec, uns_var = df_to_records_fixed_width(self._var, var_len_str)
layers = self.layers.as_dict()
d = {
'X': self._X,
'obs': obs_rec,
'var': var_rec,
'obsm': self._obsm,
'varm': self._varm,
'layers': layers,
# add the categories to the unstructured annotation
'uns': {**self._uns, **uns_obs, **uns_var}}
if self.raw is not None:
self.strings_to_categoricals(self.raw._var)
var_rec, uns_var = df_to_records_fixed_width(self.raw._var, var_len_str)
d['raw.X'] = self.raw.X
d['raw.var'] = var_rec
d['raw.varm'] = self.raw.varm
d['raw.cat'] = uns_var
return d | python | def _to_dict_fixed_width_arrays(self, var_len_str=True):
self.strings_to_categoricals()
obs_rec, uns_obs = df_to_records_fixed_width(self._obs, var_len_str)
var_rec, uns_var = df_to_records_fixed_width(self._var, var_len_str)
layers = self.layers.as_dict()
d = {
'X': self._X,
'obs': obs_rec,
'var': var_rec,
'obsm': self._obsm,
'varm': self._varm,
'layers': layers,
# add the categories to the unstructured annotation
'uns': {**self._uns, **uns_obs, **uns_var}}
if self.raw is not None:
self.strings_to_categoricals(self.raw._var)
var_rec, uns_var = df_to_records_fixed_width(self.raw._var, var_len_str)
d['raw.X'] = self.raw.X
d['raw.var'] = var_rec
d['raw.varm'] = self.raw.varm
d['raw.cat'] = uns_var
return d | [
"def",
"_to_dict_fixed_width_arrays",
"(",
"self",
",",
"var_len_str",
"=",
"True",
")",
":",
"self",
".",
"strings_to_categoricals",
"(",
")",
"obs_rec",
",",
"uns_obs",
"=",
"df_to_records_fixed_width",
"(",
"self",
".",
"_obs",
",",
"var_len_str",
")",
"var_r... | A dict of arrays that stores data and annotation.
It is sufficient for reconstructing the object. | [
"A",
"dict",
"of",
"arrays",
"that",
"stores",
"data",
"and",
"annotation",
"."
] | 34f4eb63710628fbc15e7050e5efcac1d7806062 | https://github.com/theislab/anndata/blob/34f4eb63710628fbc15e7050e5efcac1d7806062/anndata/base.py#L2239-L2266 |
232,888 | biocommons/hgvs | hgvs/parser.py | Parser._expose_rule_functions | def _expose_rule_functions(self, expose_all_rules=False):
"""add parse functions for public grammar rules
Defines a function for each public grammar rule, based on
introspecting the grammar. For example, the `c_interval` rule
is exposed as a method `parse_c_interval` and used like this::
Parser.parse_c_interval('26+2_57-3') -> Interval(...)
"""
def make_parse_rule_function(rule_name):
"builds a wrapper function that parses a string with the specified rule"
def rule_fxn(s):
try:
return self._grammar(s).__getattr__(rule_name)()
except ometa.runtime.ParseError as exc:
raise HGVSParseError("{s}: char {exc.position}: {reason}".format(
s=s, exc=exc, reason=exc.formatReason()))
rule_fxn.__doc__ = "parse string s using `%s' rule" % rule_name
return rule_fxn
exposed_rule_re = re.compile(r"hgvs_(variant|position)|(c|g|m|n|p|r)"
r"_(edit|hgvs_position|interval|pos|posedit|variant)")
exposed_rules = [
m.replace("rule_", "") for m in dir(self._grammar._grammarClass)
if m.startswith("rule_")
]
if not expose_all_rules:
exposed_rules = [
rule_name for rule_name in exposed_rules if exposed_rule_re.match(rule_name)
]
for rule_name in exposed_rules:
att_name = "parse_" + rule_name
rule_fxn = make_parse_rule_function(rule_name)
self.__setattr__(att_name, rule_fxn)
self._logger.debug("Exposed {n} rules ({rules})".format(
n=len(exposed_rules), rules=", ".join(exposed_rules))) | python | def _expose_rule_functions(self, expose_all_rules=False):
def make_parse_rule_function(rule_name):
"builds a wrapper function that parses a string with the specified rule"
def rule_fxn(s):
try:
return self._grammar(s).__getattr__(rule_name)()
except ometa.runtime.ParseError as exc:
raise HGVSParseError("{s}: char {exc.position}: {reason}".format(
s=s, exc=exc, reason=exc.formatReason()))
rule_fxn.__doc__ = "parse string s using `%s' rule" % rule_name
return rule_fxn
exposed_rule_re = re.compile(r"hgvs_(variant|position)|(c|g|m|n|p|r)"
r"_(edit|hgvs_position|interval|pos|posedit|variant)")
exposed_rules = [
m.replace("rule_", "") for m in dir(self._grammar._grammarClass)
if m.startswith("rule_")
]
if not expose_all_rules:
exposed_rules = [
rule_name for rule_name in exposed_rules if exposed_rule_re.match(rule_name)
]
for rule_name in exposed_rules:
att_name = "parse_" + rule_name
rule_fxn = make_parse_rule_function(rule_name)
self.__setattr__(att_name, rule_fxn)
self._logger.debug("Exposed {n} rules ({rules})".format(
n=len(exposed_rules), rules=", ".join(exposed_rules))) | [
"def",
"_expose_rule_functions",
"(",
"self",
",",
"expose_all_rules",
"=",
"False",
")",
":",
"def",
"make_parse_rule_function",
"(",
"rule_name",
")",
":",
"\"builds a wrapper function that parses a string with the specified rule\"",
"def",
"rule_fxn",
"(",
"s",
")",
":... | add parse functions for public grammar rules
Defines a function for each public grammar rule, based on
introspecting the grammar. For example, the `c_interval` rule
is exposed as a method `parse_c_interval` and used like this::
Parser.parse_c_interval('26+2_57-3') -> Interval(...) | [
"add",
"parse",
"functions",
"for",
"public",
"grammar",
"rules"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/parser.py#L114-L153 |
232,889 | biocommons/hgvs | hgvs/utils/context.py | format_sequence | def format_sequence(seq, start=None, end=None, group_size=3):
"""print seq from [start, end) in groups of size
3 6 9 12 15
| | | | |
2001 AAA BBB CCC DDD EEE
"""
width = 100
loc_width = 9
sep = " "
body_sep = " : "
start = start or 0
end = end or len(seq)
bw = width - loc_width - len(body_sep)
assert group_size <= bw, "group size must be less than available line width"
gpl = int((bw + len(sep)) / (group_size + len(sep))) # groups per line
gpl = int(gpl / 5) * 5 if gpl > 20 else gpl
rpl = group_size * gpl
line_fmt = "{{l:>{lw}s}}{body_sep}{{body}}".format(lw=loc_width, body_sep=body_sep)
ge_fmt = "{{ge:>{gs}}}".format(gs=group_size)
blocks = []
for ls in range(start, end, rpl):
le = ls + rpl
groups = [
ge_fmt.format(ge=str(gs + group_size)[-group_size + 1:])
for gs in range(ls, le, group_size)
]
blocks += [line_fmt.format(l="", body=sep.join(groups)) + "\n"]
groups = [seq[gs:min(gs + group_size, end)] for gs in range(ls, le, group_size)]
blocks += [line_fmt.format(l=str(ls + 1), body=sep.join(groups)) + "\n"]
blocks += ["\n"]
return blocks | python | def format_sequence(seq, start=None, end=None, group_size=3):
width = 100
loc_width = 9
sep = " "
body_sep = " : "
start = start or 0
end = end or len(seq)
bw = width - loc_width - len(body_sep)
assert group_size <= bw, "group size must be less than available line width"
gpl = int((bw + len(sep)) / (group_size + len(sep))) # groups per line
gpl = int(gpl / 5) * 5 if gpl > 20 else gpl
rpl = group_size * gpl
line_fmt = "{{l:>{lw}s}}{body_sep}{{body}}".format(lw=loc_width, body_sep=body_sep)
ge_fmt = "{{ge:>{gs}}}".format(gs=group_size)
blocks = []
for ls in range(start, end, rpl):
le = ls + rpl
groups = [
ge_fmt.format(ge=str(gs + group_size)[-group_size + 1:])
for gs in range(ls, le, group_size)
]
blocks += [line_fmt.format(l="", body=sep.join(groups)) + "\n"]
groups = [seq[gs:min(gs + group_size, end)] for gs in range(ls, le, group_size)]
blocks += [line_fmt.format(l=str(ls + 1), body=sep.join(groups)) + "\n"]
blocks += ["\n"]
return blocks | [
"def",
"format_sequence",
"(",
"seq",
",",
"start",
"=",
"None",
",",
"end",
"=",
"None",
",",
"group_size",
"=",
"3",
")",
":",
"width",
"=",
"100",
"loc_width",
"=",
"9",
"sep",
"=",
"\" \"",
"body_sep",
"=",
"\" : \"",
"start",
"=",
"start",
"or",... | print seq from [start, end) in groups of size
3 6 9 12 15
| | | | |
2001 AAA BBB CCC DDD EEE | [
"print",
"seq",
"from",
"[",
"start",
"end",
")",
"in",
"groups",
"of",
"size"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/utils/context.py#L182-L222 |
232,890 | biocommons/hgvs | hgvs/dataproviders/ncbi.py | _stage_from_version | def _stage_from_version(version):
"""return "prd", "stg", or "dev" for the given version string. A value is always returned"""
if version:
m = re.match(r"^(?P<xyz>\d+\.\d+\.\d+)(?P<extra>.*)", version)
if m:
return "stg" if m.group("extra") else "prd"
return "dev" | python | def _stage_from_version(version):
if version:
m = re.match(r"^(?P<xyz>\d+\.\d+\.\d+)(?P<extra>.*)", version)
if m:
return "stg" if m.group("extra") else "prd"
return "dev" | [
"def",
"_stage_from_version",
"(",
"version",
")",
":",
"if",
"version",
":",
"m",
"=",
"re",
".",
"match",
"(",
"r\"^(?P<xyz>\\d+\\.\\d+\\.\\d+)(?P<extra>.*)\"",
",",
"version",
")",
"if",
"m",
":",
"return",
"\"stg\"",
"if",
"m",
".",
"group",
"(",
"\"extr... | return "prd", "stg", or "dev" for the given version string. A value is always returned | [
"return",
"prd",
"stg",
"or",
"dev",
"for",
"the",
"given",
"version",
"string",
".",
"A",
"value",
"is",
"always",
"returned"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/dataproviders/ncbi.py#L25-L31 |
232,891 | biocommons/hgvs | hgvs/dataproviders/ncbi.py | _get_ncbi_db_url | def _get_ncbi_db_url():
"""returns NCBI DB URL based on environment variables and code version
* if NCBI_DB_URL is set, use that
* Otherwise, if _NCBI_URL_KEY is set, use that as the name of a
config file entry and use the corresponding URL
* Otherwise,
"""
if "NCBI_DB_URL" in os.environ:
return os.environ["NCBI_DB_URL"]
if "_NCBI_URL_KEY" in os.environ:
url_key = os.environ["_NCBI_URL_KEY"]
else:
sdlc = _stage_from_version(hgvs.__version__)
url_key = "public_{sdlc}".format(sdlc=sdlc)
return hgvs.global_config['NCBI'][url_key] | python | def _get_ncbi_db_url():
if "NCBI_DB_URL" in os.environ:
return os.environ["NCBI_DB_URL"]
if "_NCBI_URL_KEY" in os.environ:
url_key = os.environ["_NCBI_URL_KEY"]
else:
sdlc = _stage_from_version(hgvs.__version__)
url_key = "public_{sdlc}".format(sdlc=sdlc)
return hgvs.global_config['NCBI'][url_key] | [
"def",
"_get_ncbi_db_url",
"(",
")",
":",
"if",
"\"NCBI_DB_URL\"",
"in",
"os",
".",
"environ",
":",
"return",
"os",
".",
"environ",
"[",
"\"NCBI_DB_URL\"",
"]",
"if",
"\"_NCBI_URL_KEY\"",
"in",
"os",
".",
"environ",
":",
"url_key",
"=",
"os",
".",
"environ... | returns NCBI DB URL based on environment variables and code version
* if NCBI_DB_URL is set, use that
* Otherwise, if _NCBI_URL_KEY is set, use that as the name of a
config file entry and use the corresponding URL
* Otherwise, | [
"returns",
"NCBI",
"DB",
"URL",
"based",
"on",
"environment",
"variables",
"and",
"code",
"version"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/dataproviders/ncbi.py#L34-L52 |
232,892 | biocommons/hgvs | hgvs/dataproviders/ncbi.py | NCBI_postgresql._get_cursor | def _get_cursor(self, n_retries=1):
"""Returns a context manager for obtained from a single or pooled
connection, and sets the PostgreSQL search_path to the schema
specified in the connection URL.
Although *connections* are threadsafe, *cursors* are bound to
connections and are *not* threadsafe. Do not share cursors
across threads.
Use this funciton like this::
with hdp._get_cursor() as cur:
# your code
Do not call this function outside a contextmanager.
"""
n_tries_rem = n_retries + 1
while n_tries_rem > 0:
try:
conn = self._pool.getconn() if self.pooling else self._conn
# autocommit=True obviates closing explicitly
conn.autocommit = True
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
cur.execute("set search_path = {self.url.schema};".format(self=self))
yield cur
# contextmanager executes these when context exits
cur.close()
if self.pooling:
self._pool.putconn(conn)
break
except psycopg2.OperationalError:
_logger.warning(
"Lost connection to {url}; attempting reconnect".format(url=self.url))
if self.pooling:
self._pool.closeall()
self._connect()
_logger.warning("Reconnected to {url}".format(url=self.url))
n_tries_rem -= 1
else:
# N.B. Probably never reached
raise HGVSError("Permanently lost connection to {url} ({n} retries)".format(
url=self.url, n=n_retries)) | python | def _get_cursor(self, n_retries=1):
n_tries_rem = n_retries + 1
while n_tries_rem > 0:
try:
conn = self._pool.getconn() if self.pooling else self._conn
# autocommit=True obviates closing explicitly
conn.autocommit = True
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
cur.execute("set search_path = {self.url.schema};".format(self=self))
yield cur
# contextmanager executes these when context exits
cur.close()
if self.pooling:
self._pool.putconn(conn)
break
except psycopg2.OperationalError:
_logger.warning(
"Lost connection to {url}; attempting reconnect".format(url=self.url))
if self.pooling:
self._pool.closeall()
self._connect()
_logger.warning("Reconnected to {url}".format(url=self.url))
n_tries_rem -= 1
else:
# N.B. Probably never reached
raise HGVSError("Permanently lost connection to {url} ({n} retries)".format(
url=self.url, n=n_retries)) | [
"def",
"_get_cursor",
"(",
"self",
",",
"n_retries",
"=",
"1",
")",
":",
"n_tries_rem",
"=",
"n_retries",
"+",
"1",
"while",
"n_tries_rem",
">",
"0",
":",
"try",
":",
"conn",
"=",
"self",
".",
"_pool",
".",
"getconn",
"(",
")",
"if",
"self",
".",
"... | Returns a context manager for obtained from a single or pooled
connection, and sets the PostgreSQL search_path to the schema
specified in the connection URL.
Although *connections* are threadsafe, *cursors* are bound to
connections and are *not* threadsafe. Do not share cursors
across threads.
Use this funciton like this::
with hdp._get_cursor() as cur:
# your code
Do not call this function outside a contextmanager. | [
"Returns",
"a",
"context",
"manager",
"for",
"obtained",
"from",
"a",
"single",
"or",
"pooled",
"connection",
"and",
"sets",
"the",
"PostgreSQL",
"search_path",
"to",
"the",
"schema",
"specified",
"in",
"the",
"connection",
"URL",
"."
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/dataproviders/ncbi.py#L295-L349 |
232,893 | biocommons/hgvs | hgvs/projector.py | Projector.project_interval_forward | def project_interval_forward(self, c_interval):
"""
project c_interval on the source transcript to the
destination transcript
:param c_interval: an :class:`hgvs.interval.Interval` object on the source transcript
:returns: c_interval: an :class:`hgvs.interval.Interval` object on the destination transcript
"""
return self.dst_tm.g_to_c(self.src_tm.c_to_g(c_interval)) | python | def project_interval_forward(self, c_interval):
return self.dst_tm.g_to_c(self.src_tm.c_to_g(c_interval)) | [
"def",
"project_interval_forward",
"(",
"self",
",",
"c_interval",
")",
":",
"return",
"self",
".",
"dst_tm",
".",
"g_to_c",
"(",
"self",
".",
"src_tm",
".",
"c_to_g",
"(",
"c_interval",
")",
")"
] | project c_interval on the source transcript to the
destination transcript
:param c_interval: an :class:`hgvs.interval.Interval` object on the source transcript
:returns: c_interval: an :class:`hgvs.interval.Interval` object on the destination transcript | [
"project",
"c_interval",
"on",
"the",
"source",
"transcript",
"to",
"the",
"destination",
"transcript"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/projector.py#L44-L52 |
232,894 | biocommons/hgvs | hgvs/projector.py | Projector.project_interval_backward | def project_interval_backward(self, c_interval):
"""
project c_interval on the destination transcript to the
source transcript
:param c_interval: an :class:`hgvs.interval.Interval` object on the destination transcript
:returns: c_interval: an :class:`hgvs.interval.Interval` object on the source transcript
"""
return self.src_tm.g_to_c(self.dst_tm.c_to_g(c_interval)) | python | def project_interval_backward(self, c_interval):
return self.src_tm.g_to_c(self.dst_tm.c_to_g(c_interval)) | [
"def",
"project_interval_backward",
"(",
"self",
",",
"c_interval",
")",
":",
"return",
"self",
".",
"src_tm",
".",
"g_to_c",
"(",
"self",
".",
"dst_tm",
".",
"c_to_g",
"(",
"c_interval",
")",
")"
] | project c_interval on the destination transcript to the
source transcript
:param c_interval: an :class:`hgvs.interval.Interval` object on the destination transcript
:returns: c_interval: an :class:`hgvs.interval.Interval` object on the source transcript | [
"project",
"c_interval",
"on",
"the",
"destination",
"transcript",
"to",
"the",
"source",
"transcript"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/projector.py#L54-L62 |
232,895 | biocommons/hgvs | hgvs/variantmapper.py | VariantMapper._convert_edit_check_strand | def _convert_edit_check_strand(strand, edit_in):
"""
Convert an edit from one type to another, based on the stand and type
"""
if isinstance(edit_in, hgvs.edit.NARefAlt):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
try:
# if smells like an int, do nothing
# TODO: should use ref_n, right?
int(edit_in.ref)
ref = edit_in.ref
except (ValueError, TypeError):
ref = reverse_complement(edit_in.ref)
edit_out = hgvs.edit.NARefAlt(
ref=ref,
alt=reverse_complement(edit_in.alt),
)
elif isinstance(edit_in, hgvs.edit.Dup):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
edit_out = hgvs.edit.Dup(ref=reverse_complement(edit_in.ref))
elif isinstance(edit_in, hgvs.edit.Inv):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
try:
int(edit_in.ref)
ref = edit_in.ref
except (ValueError, TypeError):
ref = reverse_complement(edit_in.ref)
edit_out = hgvs.edit.Inv(ref=ref)
else:
raise NotImplementedError("Only NARefAlt/Dup/Inv types are currently implemented")
return edit_out | python | def _convert_edit_check_strand(strand, edit_in):
if isinstance(edit_in, hgvs.edit.NARefAlt):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
try:
# if smells like an int, do nothing
# TODO: should use ref_n, right?
int(edit_in.ref)
ref = edit_in.ref
except (ValueError, TypeError):
ref = reverse_complement(edit_in.ref)
edit_out = hgvs.edit.NARefAlt(
ref=ref,
alt=reverse_complement(edit_in.alt),
)
elif isinstance(edit_in, hgvs.edit.Dup):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
edit_out = hgvs.edit.Dup(ref=reverse_complement(edit_in.ref))
elif isinstance(edit_in, hgvs.edit.Inv):
if strand == 1:
edit_out = copy.deepcopy(edit_in)
else:
try:
int(edit_in.ref)
ref = edit_in.ref
except (ValueError, TypeError):
ref = reverse_complement(edit_in.ref)
edit_out = hgvs.edit.Inv(ref=ref)
else:
raise NotImplementedError("Only NARefAlt/Dup/Inv types are currently implemented")
return edit_out | [
"def",
"_convert_edit_check_strand",
"(",
"strand",
",",
"edit_in",
")",
":",
"if",
"isinstance",
"(",
"edit_in",
",",
"hgvs",
".",
"edit",
".",
"NARefAlt",
")",
":",
"if",
"strand",
"==",
"1",
":",
"edit_out",
"=",
"copy",
".",
"deepcopy",
"(",
"edit_in... | Convert an edit from one type to another, based on the stand and type | [
"Convert",
"an",
"edit",
"from",
"one",
"type",
"to",
"another",
"based",
"on",
"the",
"stand",
"and",
"type"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/variantmapper.py#L457-L493 |
232,896 | biocommons/hgvs | hgvs/assemblymapper.py | AssemblyMapper.t_to_p | def t_to_p(self, var_t):
"""Return a protein variant, or "non-coding" for non-coding variant types
CAUTION: Unlike other x_to_y methods that always return
SequenceVariant instances, this method returns a string when
the variant type is ``n``. This is intended as a convenience,
particularly when looping over ``relevant_transcripts``,
projecting with ``g_to_t``, then desiring a protein
representation for coding transcripts.
"""
if var_t.type == "n":
return "non-coding"
if var_t.type == "c":
return self.c_to_p(var_t)
raise HGVSInvalidVariantError("Expected a coding (c.) or non-coding (n.) variant; got " +
str(var_t)) | python | def t_to_p(self, var_t):
if var_t.type == "n":
return "non-coding"
if var_t.type == "c":
return self.c_to_p(var_t)
raise HGVSInvalidVariantError("Expected a coding (c.) or non-coding (n.) variant; got " +
str(var_t)) | [
"def",
"t_to_p",
"(",
"self",
",",
"var_t",
")",
":",
"if",
"var_t",
".",
"type",
"==",
"\"n\"",
":",
"return",
"\"non-coding\"",
"if",
"var_t",
".",
"type",
"==",
"\"c\"",
":",
"return",
"self",
".",
"c_to_p",
"(",
"var_t",
")",
"raise",
"HGVSInvalidV... | Return a protein variant, or "non-coding" for non-coding variant types
CAUTION: Unlike other x_to_y methods that always return
SequenceVariant instances, this method returns a string when
the variant type is ``n``. This is intended as a convenience,
particularly when looping over ``relevant_transcripts``,
projecting with ``g_to_t``, then desiring a protein
representation for coding transcripts. | [
"Return",
"a",
"protein",
"variant",
"or",
"non",
"-",
"coding",
"for",
"non",
"-",
"coding",
"variant",
"types"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/assemblymapper.py#L124-L140 |
232,897 | biocommons/hgvs | hgvs/assemblymapper.py | AssemblyMapper._fetch_AlignmentMapper | def _fetch_AlignmentMapper(self, tx_ac, alt_ac=None, alt_aln_method=None):
"""convenience version of VariantMapper._fetch_AlignmentMapper that
derives alt_ac from transcript, assembly, and alt_aln_method
used to instantiate the AssemblyMapper instance
"""
if alt_ac is None:
alt_ac = self._alt_ac_for_tx_ac(tx_ac)
if alt_aln_method is None:
alt_aln_method = self.alt_aln_method
return super(AssemblyMapper, self)._fetch_AlignmentMapper(tx_ac, alt_ac, alt_aln_method) | python | def _fetch_AlignmentMapper(self, tx_ac, alt_ac=None, alt_aln_method=None):
if alt_ac is None:
alt_ac = self._alt_ac_for_tx_ac(tx_ac)
if alt_aln_method is None:
alt_aln_method = self.alt_aln_method
return super(AssemblyMapper, self)._fetch_AlignmentMapper(tx_ac, alt_ac, alt_aln_method) | [
"def",
"_fetch_AlignmentMapper",
"(",
"self",
",",
"tx_ac",
",",
"alt_ac",
"=",
"None",
",",
"alt_aln_method",
"=",
"None",
")",
":",
"if",
"alt_ac",
"is",
"None",
":",
"alt_ac",
"=",
"self",
".",
"_alt_ac_for_tx_ac",
"(",
"tx_ac",
")",
"if",
"alt_aln_meth... | convenience version of VariantMapper._fetch_AlignmentMapper that
derives alt_ac from transcript, assembly, and alt_aln_method
used to instantiate the AssemblyMapper instance | [
"convenience",
"version",
"of",
"VariantMapper",
".",
"_fetch_AlignmentMapper",
"that",
"derives",
"alt_ac",
"from",
"transcript",
"assembly",
"and",
"alt_aln_method",
"used",
"to",
"instantiate",
"the",
"AssemblyMapper",
"instance"
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/assemblymapper.py#L208-L219 |
232,898 | biocommons/hgvs | hgvs/assemblymapper.py | AssemblyMapper._maybe_normalize | def _maybe_normalize(self, var):
"""normalize variant if requested, and ignore HGVSUnsupportedOperationError
This is better than checking whether the variant is intronic because
future UTAs will support LRG, which will enable checking intronic variants.
"""
if self.normalize:
try:
return self._norm.normalize(var)
except HGVSUnsupportedOperationError as e:
_logger.warning(str(e) + "; returning unnormalized variant")
# fall through to return unnormalized variant
return var | python | def _maybe_normalize(self, var):
if self.normalize:
try:
return self._norm.normalize(var)
except HGVSUnsupportedOperationError as e:
_logger.warning(str(e) + "; returning unnormalized variant")
# fall through to return unnormalized variant
return var | [
"def",
"_maybe_normalize",
"(",
"self",
",",
"var",
")",
":",
"if",
"self",
".",
"normalize",
":",
"try",
":",
"return",
"self",
".",
"_norm",
".",
"normalize",
"(",
"var",
")",
"except",
"HGVSUnsupportedOperationError",
"as",
"e",
":",
"_logger",
".",
"... | normalize variant if requested, and ignore HGVSUnsupportedOperationError
This is better than checking whether the variant is intronic because
future UTAs will support LRG, which will enable checking intronic variants. | [
"normalize",
"variant",
"if",
"requested",
"and",
"ignore",
"HGVSUnsupportedOperationError",
"This",
"is",
"better",
"than",
"checking",
"whether",
"the",
"variant",
"is",
"intronic",
"because",
"future",
"UTAs",
"will",
"support",
"LRG",
"which",
"will",
"enable",
... | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/assemblymapper.py#L221-L232 |
232,899 | biocommons/hgvs | hgvs/alignmentmapper.py | AlignmentMapper._parse_cigar | def _parse_cigar(self, cigar):
"""For a given CIGAR string, return the start positions of
each aligned segment in ref and tgt, and a list of CIGAR operators.
"""
ces = [m.groupdict() for m in cigar_re.finditer(cigar)]
ref_pos = [None] * len(ces)
tgt_pos = [None] * len(ces)
cigar_op = [None] * len(ces)
ref_cur = tgt_cur = 0
for i, ce in enumerate(ces):
ref_pos[i] = ref_cur
tgt_pos[i] = tgt_cur
cigar_op[i] = ce["op"]
step = int(ce["len"])
if ce["op"] in "=MINX":
ref_cur += step
if ce["op"] in "=MDX":
tgt_cur += step
ref_pos.append(ref_cur)
tgt_pos.append(tgt_cur)
return ref_pos, tgt_pos, cigar_op | python | def _parse_cigar(self, cigar):
ces = [m.groupdict() for m in cigar_re.finditer(cigar)]
ref_pos = [None] * len(ces)
tgt_pos = [None] * len(ces)
cigar_op = [None] * len(ces)
ref_cur = tgt_cur = 0
for i, ce in enumerate(ces):
ref_pos[i] = ref_cur
tgt_pos[i] = tgt_cur
cigar_op[i] = ce["op"]
step = int(ce["len"])
if ce["op"] in "=MINX":
ref_cur += step
if ce["op"] in "=MDX":
tgt_cur += step
ref_pos.append(ref_cur)
tgt_pos.append(tgt_cur)
return ref_pos, tgt_pos, cigar_op | [
"def",
"_parse_cigar",
"(",
"self",
",",
"cigar",
")",
":",
"ces",
"=",
"[",
"m",
".",
"groupdict",
"(",
")",
"for",
"m",
"in",
"cigar_re",
".",
"finditer",
"(",
"cigar",
")",
"]",
"ref_pos",
"=",
"[",
"None",
"]",
"*",
"len",
"(",
"ces",
")",
... | For a given CIGAR string, return the start positions of
each aligned segment in ref and tgt, and a list of CIGAR operators. | [
"For",
"a",
"given",
"CIGAR",
"string",
"return",
"the",
"start",
"positions",
"of",
"each",
"aligned",
"segment",
"in",
"ref",
"and",
"tgt",
"and",
"a",
"list",
"of",
"CIGAR",
"operators",
"."
] | 4d16efb475e1802b2531a2f1c373e8819d8e533b | https://github.com/biocommons/hgvs/blob/4d16efb475e1802b2531a2f1c373e8819d8e533b/hgvs/alignmentmapper.py#L93-L113 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.