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gabstopper/smc-python | smc/routing/bgp.py | BGPProfile.subnet_distance | def subnet_distance(self):
"""
Specific subnet administrative distances
:return: list of tuple (subnet, distance)
"""
return [(Element.from_href(entry.get('subnet')), entry.get('distance'))
for entry in self.data.get('distance_entry')] | python | def subnet_distance(self):
"""
Specific subnet administrative distances
:return: list of tuple (subnet, distance)
"""
return [(Element.from_href(entry.get('subnet')), entry.get('distance'))
for entry in self.data.get('distance_entry')] | [
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:return: list of tuple (subnet, distance) | [
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gabstopper/smc-python | smc/routing/bgp.py | ExternalBGPPeer.create | def create(cls, name, neighbor_as, neighbor_ip,
neighbor_port=179, comment=None):
"""
Create an external BGP Peer.
:param str name: name of peer
:param str,AutonomousSystem neighbor_as_ref: AutonomousSystem
element or href.
:param str neighbor_ip: ip address of BGP peer
:param int neighbor_port: port for BGP, default 179.
:raises CreateElementFailed: failed creating
:return: instance with meta
:rtype: ExternalBGPPeer
"""
json = {'name': name,
'neighbor_ip': neighbor_ip,
'neighbor_port': neighbor_port,
'comment': comment}
neighbor_as_ref = element_resolver(neighbor_as)
json.update(neighbor_as=neighbor_as_ref)
return ElementCreator(cls, json) | python | def create(cls, name, neighbor_as, neighbor_ip,
neighbor_port=179, comment=None):
"""
Create an external BGP Peer.
:param str name: name of peer
:param str,AutonomousSystem neighbor_as_ref: AutonomousSystem
element or href.
:param str neighbor_ip: ip address of BGP peer
:param int neighbor_port: port for BGP, default 179.
:raises CreateElementFailed: failed creating
:return: instance with meta
:rtype: ExternalBGPPeer
"""
json = {'name': name,
'neighbor_ip': neighbor_ip,
'neighbor_port': neighbor_port,
'comment': comment}
neighbor_as_ref = element_resolver(neighbor_as)
json.update(neighbor_as=neighbor_as_ref)
return ElementCreator(cls, json) | [
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gabstopper/smc-python | smc/routing/bgp.py | BGPPeering.create | def create(cls, name, connection_profile_ref=None,
md5_password=None, local_as_option='not_set',
max_prefix_option='not_enabled', send_community='no',
connected_check='disabled', orf_option='disabled',
next_hop_self=True, override_capability=False,
dont_capability_negotiate=False, remote_private_as=False,
route_reflector_client=False, soft_reconfiguration=True,
ttl_option='disabled', comment=None):
"""
Create a new BGPPeering configuration.
:param str name: name of peering
:param str,BGPConnectionProfile connection_profile_ref: required BGP
connection profile. System default used if not provided.
:param str md5_password: optional md5_password
:param str local_as_option: the local AS mode. Valid options are:
'not_set', 'prepend', 'no_prepend', 'replace_as'
:param str max_prefix_option: The max prefix mode. Valid options are:
'not_enabled', 'enabled', 'warning_only'
:param str send_community: the send community mode. Valid options are:
'no', 'standard', 'extended', 'standard_and_extended'
:param str connected_check: the connected check mode. Valid options are:
'disabled', 'enabled', 'automatic'
:param str orf_option: outbound route filtering mode. Valid options are:
'disabled', 'send', 'receive', 'both'
:param bool next_hop_self: next hop self setting
:param bool override_capability: is override received capabilities
:param bool dont_capability_negotiate: do not send capabilities
:param bool remote_private_as: is remote a private AS
:param bool route_reflector_client: Route Reflector Client (iBGP only)
:param bool soft_reconfiguration: do soft reconfiguration inbound
:param str ttl_option: ttl check mode. Valid options are: 'disabled',
'ttl-security'
:raises CreateElementFailed: failed creating profile
:return: instance with meta
:rtype: BGPPeering
"""
json = {'name': name,
'local_as_option': local_as_option,
'max_prefix_option': max_prefix_option,
'send_community': send_community,
'connected_check': connected_check,
'orf_option': orf_option,
'next_hop_self': next_hop_self,
'override_capability': override_capability,
'dont_capability_negotiate': dont_capability_negotiate,
'soft_reconfiguration': soft_reconfiguration,
'remove_private_as': remote_private_as,
'route_reflector_client': route_reflector_client,
'ttl_option': ttl_option,
'comment': comment}
if md5_password:
json.update(md5_password=md5_password)
connection_profile_ref = element_resolver(connection_profile_ref) or \
BGPConnectionProfile('Default BGP Connection Profile').href
json.update(connection_profile=connection_profile_ref)
return ElementCreator(cls, json) | python | def create(cls, name, connection_profile_ref=None,
md5_password=None, local_as_option='not_set',
max_prefix_option='not_enabled', send_community='no',
connected_check='disabled', orf_option='disabled',
next_hop_self=True, override_capability=False,
dont_capability_negotiate=False, remote_private_as=False,
route_reflector_client=False, soft_reconfiguration=True,
ttl_option='disabled', comment=None):
"""
Create a new BGPPeering configuration.
:param str name: name of peering
:param str,BGPConnectionProfile connection_profile_ref: required BGP
connection profile. System default used if not provided.
:param str md5_password: optional md5_password
:param str local_as_option: the local AS mode. Valid options are:
'not_set', 'prepend', 'no_prepend', 'replace_as'
:param str max_prefix_option: The max prefix mode. Valid options are:
'not_enabled', 'enabled', 'warning_only'
:param str send_community: the send community mode. Valid options are:
'no', 'standard', 'extended', 'standard_and_extended'
:param str connected_check: the connected check mode. Valid options are:
'disabled', 'enabled', 'automatic'
:param str orf_option: outbound route filtering mode. Valid options are:
'disabled', 'send', 'receive', 'both'
:param bool next_hop_self: next hop self setting
:param bool override_capability: is override received capabilities
:param bool dont_capability_negotiate: do not send capabilities
:param bool remote_private_as: is remote a private AS
:param bool route_reflector_client: Route Reflector Client (iBGP only)
:param bool soft_reconfiguration: do soft reconfiguration inbound
:param str ttl_option: ttl check mode. Valid options are: 'disabled',
'ttl-security'
:raises CreateElementFailed: failed creating profile
:return: instance with meta
:rtype: BGPPeering
"""
json = {'name': name,
'local_as_option': local_as_option,
'max_prefix_option': max_prefix_option,
'send_community': send_community,
'connected_check': connected_check,
'orf_option': orf_option,
'next_hop_self': next_hop_self,
'override_capability': override_capability,
'dont_capability_negotiate': dont_capability_negotiate,
'soft_reconfiguration': soft_reconfiguration,
'remove_private_as': remote_private_as,
'route_reflector_client': route_reflector_client,
'ttl_option': ttl_option,
'comment': comment}
if md5_password:
json.update(md5_password=md5_password)
connection_profile_ref = element_resolver(connection_profile_ref) or \
BGPConnectionProfile('Default BGP Connection Profile').href
json.update(connection_profile=connection_profile_ref)
return ElementCreator(cls, json) | [
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:param str orf_option: outbound route filtering mode. Valid options are:
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:param bool next_hop_self: next hop self setting
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:param bool dont_capability_negotiate: do not send capabilities
:param bool remote_private_as: is remote a private AS
:param bool route_reflector_client: Route Reflector Client (iBGP only)
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gabstopper/smc-python | smc/routing/bgp.py | BGPConnectionProfile.create | def create(cls, name, md5_password=None, connect_retry=120,
session_hold_timer=180, session_keep_alive=60):
"""
Create a new BGP Connection Profile.
:param str name: name of profile
:param str md5_password: optional md5 password
:param int connect_retry: The connect retry timer, in seconds
:param int session_hold_timer: The session hold timer, in seconds
:param int session_keep_alive: The session keep alive timer, in seconds
:raises CreateElementFailed: failed creating profile
:return: instance with meta
:rtype: BGPConnectionProfile
"""
json = {'name': name,
'connect': connect_retry,
'session_hold_timer': session_hold_timer,
'session_keep_alive': session_keep_alive}
if md5_password:
json.update(md5_password=md5_password)
return ElementCreator(cls, json) | python | def create(cls, name, md5_password=None, connect_retry=120,
session_hold_timer=180, session_keep_alive=60):
"""
Create a new BGP Connection Profile.
:param str name: name of profile
:param str md5_password: optional md5 password
:param int connect_retry: The connect retry timer, in seconds
:param int session_hold_timer: The session hold timer, in seconds
:param int session_keep_alive: The session keep alive timer, in seconds
:raises CreateElementFailed: failed creating profile
:return: instance with meta
:rtype: BGPConnectionProfile
"""
json = {'name': name,
'connect': connect_retry,
'session_hold_timer': session_hold_timer,
'session_keep_alive': session_keep_alive}
if md5_password:
json.update(md5_password=md5_password)
return ElementCreator(cls, json) | [
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gabstopper/smc-python | smc/policy/rule_nat.py | IPv4NATRule.create | def create(self, name, sources=None, destinations=None, services=None,
dynamic_src_nat=None, dynamic_src_nat_ports=(1024, 65535),
static_src_nat=None, static_dst_nat=None,
static_dst_nat_ports=None, is_disabled=False, used_on=None,
add_pos=None, after=None, before=None, comment=None):
"""
Create a NAT rule.
When providing sources/destinations or services, you can provide the
element href, network element or services from ``smc.elements``.
You can also mix href strings with Element types in these fields.
:param str name: name of NAT rule
:param list sources: list of sources by href or Element
:type sources: list(str,Element)
:param list destinations: list of destinations by href or Element
:type destinations: list(str,Element)
:param list services: list of services by href or Element
:type services: list(str,Element)
:param dynamic_src_nat: str ip or Element for dest NAT
:type dynamic_src_nat: str,Element
:param tuple dynamic_src_nat_ports: starting and ending ports for PAT.
Default: (1024, 65535)
:param str static_src_nat: ip or element href of used for source NAT
:param str static_dst_nat: destination NAT IP address or element href
:param tuple static_dst_nat_ports: ports or port range used for original
and destination ports (only needed if a different destination port
is used and does not match the rules service port)
:param bool is_disabled: whether to disable rule or not
:param str,href used_on: Can be a str href of an Element or Element of type
AddressRange('ANY'), AddressRange('NONE') or an engine element.
:type used_on: str,Element
:param int add_pos: position to insert the rule, starting with position 1. If
the position value is greater than the number of rules, the rule is inserted at
the bottom. If add_pos is not provided, rule is inserted in position 1. Mutually
exclusive with ``after`` and ``before`` params.
:param str after: Rule tag to add this rule after. Mutually exclusive with ``add_pos``
and ``before`` params.
:param str before: Rule tag to add this rule before. Mutually exclusive with ``add_pos``
and ``after`` params.
:param str comment: optional comment for the NAT rule
:raises InvalidRuleValue: if rule requirements are not met
:raises CreateRuleFailed: rule creation failure
:return: newly created NAT rule
:rtype: IPv4NATRule
"""
rule_values = self.update_targets(sources, destinations, services)
rule_values.update(name=name, comment=comment)
rule_values.update(is_disabled=is_disabled)
rule_values.update(used_on=element_resolver(used_on) if used_on else used_on)
#rule_values.update(used_on=element_resolver(AddressRange('ANY') if not \
# used_on else element_resolver(used_on)))
if dynamic_src_nat:
nat = DynamicSourceNAT()
start_port, end_port = dynamic_src_nat_ports
nat.update_field(dynamic_src_nat, start_port=start_port,
end_port=end_port)
rule_values.update(options=nat)
elif static_src_nat:
sources = rule_values['sources']
if 'any' in sources or 'none' in sources:
raise InvalidRuleValue('Source field cannot be none or any for '
'static source NAT.')
nat = StaticSourceNAT()
nat.update_field(static_src_nat,
original_value=sources.get('src')[0])
rule_values.update(options=nat)
if static_dst_nat:
destinations = rule_values['destinations']
if 'any' in destinations or 'none' in destinations:
raise InvalidRuleValue('Destination field cannot be none or any for '
'destination NAT.')
nat = StaticDestNAT()
original_port, translated_port = None, None
if static_dst_nat_ports:
original_port, translated_port = static_dst_nat_ports
nat.update_field(static_dst_nat,
original_value=destinations.get('dst')[0],
original_port=original_port,
translated_port=translated_port)
rule_values.setdefault('options', {}).update(nat)
if 'options' not in rule_values: # No NAT
rule_values.update(options=LogOptions())
params = None
href = self.href
if add_pos is not None:
href = self.add_at_position(add_pos)
elif before or after:
params = self.add_before_after(before, after)
return ElementCreator(
self.__class__,
exception=CreateRuleFailed,
href=href,
params=params,
json=rule_values) | python | def create(self, name, sources=None, destinations=None, services=None,
dynamic_src_nat=None, dynamic_src_nat_ports=(1024, 65535),
static_src_nat=None, static_dst_nat=None,
static_dst_nat_ports=None, is_disabled=False, used_on=None,
add_pos=None, after=None, before=None, comment=None):
"""
Create a NAT rule.
When providing sources/destinations or services, you can provide the
element href, network element or services from ``smc.elements``.
You can also mix href strings with Element types in these fields.
:param str name: name of NAT rule
:param list sources: list of sources by href or Element
:type sources: list(str,Element)
:param list destinations: list of destinations by href or Element
:type destinations: list(str,Element)
:param list services: list of services by href or Element
:type services: list(str,Element)
:param dynamic_src_nat: str ip or Element for dest NAT
:type dynamic_src_nat: str,Element
:param tuple dynamic_src_nat_ports: starting and ending ports for PAT.
Default: (1024, 65535)
:param str static_src_nat: ip or element href of used for source NAT
:param str static_dst_nat: destination NAT IP address or element href
:param tuple static_dst_nat_ports: ports or port range used for original
and destination ports (only needed if a different destination port
is used and does not match the rules service port)
:param bool is_disabled: whether to disable rule or not
:param str,href used_on: Can be a str href of an Element or Element of type
AddressRange('ANY'), AddressRange('NONE') or an engine element.
:type used_on: str,Element
:param int add_pos: position to insert the rule, starting with position 1. If
the position value is greater than the number of rules, the rule is inserted at
the bottom. If add_pos is not provided, rule is inserted in position 1. Mutually
exclusive with ``after`` and ``before`` params.
:param str after: Rule tag to add this rule after. Mutually exclusive with ``add_pos``
and ``before`` params.
:param str before: Rule tag to add this rule before. Mutually exclusive with ``add_pos``
and ``after`` params.
:param str comment: optional comment for the NAT rule
:raises InvalidRuleValue: if rule requirements are not met
:raises CreateRuleFailed: rule creation failure
:return: newly created NAT rule
:rtype: IPv4NATRule
"""
rule_values = self.update_targets(sources, destinations, services)
rule_values.update(name=name, comment=comment)
rule_values.update(is_disabled=is_disabled)
rule_values.update(used_on=element_resolver(used_on) if used_on else used_on)
#rule_values.update(used_on=element_resolver(AddressRange('ANY') if not \
# used_on else element_resolver(used_on)))
if dynamic_src_nat:
nat = DynamicSourceNAT()
start_port, end_port = dynamic_src_nat_ports
nat.update_field(dynamic_src_nat, start_port=start_port,
end_port=end_port)
rule_values.update(options=nat)
elif static_src_nat:
sources = rule_values['sources']
if 'any' in sources or 'none' in sources:
raise InvalidRuleValue('Source field cannot be none or any for '
'static source NAT.')
nat = StaticSourceNAT()
nat.update_field(static_src_nat,
original_value=sources.get('src')[0])
rule_values.update(options=nat)
if static_dst_nat:
destinations = rule_values['destinations']
if 'any' in destinations or 'none' in destinations:
raise InvalidRuleValue('Destination field cannot be none or any for '
'destination NAT.')
nat = StaticDestNAT()
original_port, translated_port = None, None
if static_dst_nat_ports:
original_port, translated_port = static_dst_nat_ports
nat.update_field(static_dst_nat,
original_value=destinations.get('dst')[0],
original_port=original_port,
translated_port=translated_port)
rule_values.setdefault('options', {}).update(nat)
if 'options' not in rule_values: # No NAT
rule_values.update(options=LogOptions())
params = None
href = self.href
if add_pos is not None:
href = self.add_at_position(add_pos)
elif before or after:
params = self.add_before_after(before, after)
return ElementCreator(
self.__class__,
exception=CreateRuleFailed,
href=href,
params=params,
json=rule_values) | [
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:param str name: name of NAT rule
:param list sources: list of sources by href or Element
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:param list destinations: list of destinations by href or Element
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:param list services: list of services by href or Element
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:param tuple dynamic_src_nat_ports: starting and ending ports for PAT.
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:param str static_src_nat: ip or element href of used for source NAT
:param str static_dst_nat: destination NAT IP address or element href
:param tuple static_dst_nat_ports: ports or port range used for original
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:param bool is_disabled: whether to disable rule or not
:param str,href used_on: Can be a str href of an Element or Element of type
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:type used_on: str,Element
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:param str after: Rule tag to add this rule after. Mutually exclusive with ``add_pos``
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:param str before: Rule tag to add this rule before. Mutually exclusive with ``add_pos``
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:param str comment: optional comment for the NAT rule
:raises InvalidRuleValue: if rule requirements are not met
:raises CreateRuleFailed: rule creation failure
:return: newly created NAT rule
:rtype: IPv4NATRule | [
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] | e027b8a5dcfaf884eada32d113d41c1e56b32457 | https://github.com/gabstopper/smc-python/blob/e027b8a5dcfaf884eada32d113d41c1e56b32457/smc/policy/rule_nat.py#L535-L640 | train | 38,804 |
GoogleCloudPlatform/google-auth-library-python-httplib2 | google_auth_httplib2.py | AuthorizedHttp.request | def request(self, uri, method='GET', body=None, headers=None,
**kwargs):
"""Implementation of httplib2's Http.request."""
_credential_refresh_attempt = kwargs.pop(
'_credential_refresh_attempt', 0)
# Make a copy of the headers. They will be modified by the credentials
# and we want to pass the original headers if we recurse.
request_headers = headers.copy() if headers is not None else {}
self.credentials.before_request(
self._request, method, uri, request_headers)
# Check if the body is a file-like stream, and if so, save the body
# stream position so that it can be restored in case of refresh.
body_stream_position = None
if all(getattr(body, stream_prop, None) for stream_prop in
_STREAM_PROPERTIES):
body_stream_position = body.tell()
# Make the request.
response, content = self.http.request(
uri, method, body=body, headers=request_headers, **kwargs)
# If the response indicated that the credentials needed to be
# refreshed, then refresh the credentials and re-attempt the
# request.
# A stored token may expire between the time it is retrieved and
# the time the request is made, so we may need to try twice.
if (response.status in self._refresh_status_codes
and _credential_refresh_attempt < self._max_refresh_attempts):
_LOGGER.info(
'Refreshing credentials due to a %s response. Attempt %s/%s.',
response.status, _credential_refresh_attempt + 1,
self._max_refresh_attempts)
self.credentials.refresh(self._request)
# Restore the body's stream position if needed.
if body_stream_position is not None:
body.seek(body_stream_position)
# Recurse. Pass in the original headers, not our modified set.
return self.request(
uri, method, body=body, headers=headers,
_credential_refresh_attempt=_credential_refresh_attempt + 1,
**kwargs)
return response, content | python | def request(self, uri, method='GET', body=None, headers=None,
**kwargs):
"""Implementation of httplib2's Http.request."""
_credential_refresh_attempt = kwargs.pop(
'_credential_refresh_attempt', 0)
# Make a copy of the headers. They will be modified by the credentials
# and we want to pass the original headers if we recurse.
request_headers = headers.copy() if headers is not None else {}
self.credentials.before_request(
self._request, method, uri, request_headers)
# Check if the body is a file-like stream, and if so, save the body
# stream position so that it can be restored in case of refresh.
body_stream_position = None
if all(getattr(body, stream_prop, None) for stream_prop in
_STREAM_PROPERTIES):
body_stream_position = body.tell()
# Make the request.
response, content = self.http.request(
uri, method, body=body, headers=request_headers, **kwargs)
# If the response indicated that the credentials needed to be
# refreshed, then refresh the credentials and re-attempt the
# request.
# A stored token may expire between the time it is retrieved and
# the time the request is made, so we may need to try twice.
if (response.status in self._refresh_status_codes
and _credential_refresh_attempt < self._max_refresh_attempts):
_LOGGER.info(
'Refreshing credentials due to a %s response. Attempt %s/%s.',
response.status, _credential_refresh_attempt + 1,
self._max_refresh_attempts)
self.credentials.refresh(self._request)
# Restore the body's stream position if needed.
if body_stream_position is not None:
body.seek(body_stream_position)
# Recurse. Pass in the original headers, not our modified set.
return self.request(
uri, method, body=body, headers=headers,
_credential_refresh_attempt=_credential_refresh_attempt + 1,
**kwargs)
return response, content | [
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.connect | def connect(self, broker, port=1883, client_id="", clean_session=True):
""" Connect to an MQTT broker. This is a pre-requisite step for publish
and subscribe keywords.
`broker` MQTT broker host
`port` broker port (default 1883)
`client_id` if not specified, a random id is generated
`clean_session` specifies the clean session flag for the connection
Examples:
Connect to a broker with default port and client id
| Connect | 127.0.0.1 |
Connect to a broker by specifying the port and client id explicitly
| Connect | 127.0.0.1 | 1883 | test.client |
Connect to a broker with clean session flag set to false
| Connect | 127.0.0.1 | clean_session=${false} |
"""
logger.info('Connecting to %s at port %s' % (broker, port))
self._connected = False
self._unexpected_disconnect = False
self._mqttc = mqtt.Client(client_id, clean_session)
# set callbacks
self._mqttc.on_connect = self._on_connect
self._mqttc.on_disconnect = self._on_disconnect
if self._username:
self._mqttc.username_pw_set(self._username, self._password)
self._mqttc.connect(broker, int(port))
timer_start = time.time()
while time.time() < timer_start + self._loop_timeout:
if self._connected or self._unexpected_disconnect:
break;
self._mqttc.loop()
if self._unexpected_disconnect:
raise RuntimeError("The client disconnected unexpectedly")
logger.debug('client_id: %s' % self._mqttc._client_id)
return self._mqttc | python | def connect(self, broker, port=1883, client_id="", clean_session=True):
""" Connect to an MQTT broker. This is a pre-requisite step for publish
and subscribe keywords.
`broker` MQTT broker host
`port` broker port (default 1883)
`client_id` if not specified, a random id is generated
`clean_session` specifies the clean session flag for the connection
Examples:
Connect to a broker with default port and client id
| Connect | 127.0.0.1 |
Connect to a broker by specifying the port and client id explicitly
| Connect | 127.0.0.1 | 1883 | test.client |
Connect to a broker with clean session flag set to false
| Connect | 127.0.0.1 | clean_session=${false} |
"""
logger.info('Connecting to %s at port %s' % (broker, port))
self._connected = False
self._unexpected_disconnect = False
self._mqttc = mqtt.Client(client_id, clean_session)
# set callbacks
self._mqttc.on_connect = self._on_connect
self._mqttc.on_disconnect = self._on_disconnect
if self._username:
self._mqttc.username_pw_set(self._username, self._password)
self._mqttc.connect(broker, int(port))
timer_start = time.time()
while time.time() < timer_start + self._loop_timeout:
if self._connected or self._unexpected_disconnect:
break;
self._mqttc.loop()
if self._unexpected_disconnect:
raise RuntimeError("The client disconnected unexpectedly")
logger.debug('client_id: %s' % self._mqttc._client_id)
return self._mqttc | [
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.publish | def publish(self, topic, message=None, qos=0, retain=False):
""" Publish a message to a topic with specified qos and retained flag.
It is required that a connection has been established using `Connect`
keyword before using this keyword.
`topic` topic to which the message will be published
`message` message payload to publish
`qos` qos of the message
`retain` retained flag
Examples:
| Publish | test/test | test message | 1 | ${false} |
"""
logger.info('Publish topic: %s, message: %s, qos: %s, retain: %s'
% (topic, message, qos, retain))
self._mid = -1
self._mqttc.on_publish = self._on_publish
result, mid = self._mqttc.publish(topic, message, int(qos), retain)
if result != 0:
raise RuntimeError('Error publishing: %s' % result)
timer_start = time.time()
while time.time() < timer_start + self._loop_timeout:
if mid == self._mid:
break;
self._mqttc.loop()
if mid != self._mid:
logger.warn('mid wasn\'t matched: %s' % mid) | python | def publish(self, topic, message=None, qos=0, retain=False):
""" Publish a message to a topic with specified qos and retained flag.
It is required that a connection has been established using `Connect`
keyword before using this keyword.
`topic` topic to which the message will be published
`message` message payload to publish
`qos` qos of the message
`retain` retained flag
Examples:
| Publish | test/test | test message | 1 | ${false} |
"""
logger.info('Publish topic: %s, message: %s, qos: %s, retain: %s'
% (topic, message, qos, retain))
self._mid = -1
self._mqttc.on_publish = self._on_publish
result, mid = self._mqttc.publish(topic, message, int(qos), retain)
if result != 0:
raise RuntimeError('Error publishing: %s' % result)
timer_start = time.time()
while time.time() < timer_start + self._loop_timeout:
if mid == self._mid:
break;
self._mqttc.loop()
if mid != self._mid:
logger.warn('mid wasn\'t matched: %s' % mid) | [
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.subscribe | def subscribe(self, topic, qos, timeout=1, limit=1):
""" Subscribe to a topic and return a list of message payloads received
within the specified time.
`topic` topic to subscribe to
`qos` quality of service for the subscription
`timeout` duration of subscription. Specify 0 to enable background looping (async)
`limit` the max number of payloads that will be returned. Specify 0
for no limit
Examples:
Subscribe and get a list of all messages received within 5 seconds
| ${messages}= | Subscribe | test/test | qos=1 | timeout=5 | limit=0 |
Subscribe and get 1st message received within 60 seconds
| @{messages}= | Subscribe | test/test | qos=1 | timeout=60 | limit=1 |
| Length should be | ${messages} | 1 |
"""
seconds = convert_time(timeout)
self._messages[topic] = []
limit = int(limit)
self._subscribed = False
logger.info('Subscribing to topic: %s' % topic)
self._mqttc.on_subscribe = self._on_subscribe
self._mqttc.subscribe(str(topic), int(qos))
self._mqttc.on_message = self._on_message_list
if seconds == 0:
logger.info('Starting background loop')
self._background_mqttc = self._mqttc
self._background_mqttc.loop_start()
return self._messages[topic]
timer_start = time.time()
while time.time() < timer_start + seconds:
if limit == 0 or len(self._messages[topic]) < limit:
self._mqttc.loop()
else:
# workaround for client to ack the publish. Otherwise,
# it seems that if client disconnects quickly, broker
# will not get the ack and publish the message again on
# next connect.
time.sleep(1)
break
return self._messages[topic] | python | def subscribe(self, topic, qos, timeout=1, limit=1):
""" Subscribe to a topic and return a list of message payloads received
within the specified time.
`topic` topic to subscribe to
`qos` quality of service for the subscription
`timeout` duration of subscription. Specify 0 to enable background looping (async)
`limit` the max number of payloads that will be returned. Specify 0
for no limit
Examples:
Subscribe and get a list of all messages received within 5 seconds
| ${messages}= | Subscribe | test/test | qos=1 | timeout=5 | limit=0 |
Subscribe and get 1st message received within 60 seconds
| @{messages}= | Subscribe | test/test | qos=1 | timeout=60 | limit=1 |
| Length should be | ${messages} | 1 |
"""
seconds = convert_time(timeout)
self._messages[topic] = []
limit = int(limit)
self._subscribed = False
logger.info('Subscribing to topic: %s' % topic)
self._mqttc.on_subscribe = self._on_subscribe
self._mqttc.subscribe(str(topic), int(qos))
self._mqttc.on_message = self._on_message_list
if seconds == 0:
logger.info('Starting background loop')
self._background_mqttc = self._mqttc
self._background_mqttc.loop_start()
return self._messages[topic]
timer_start = time.time()
while time.time() < timer_start + seconds:
if limit == 0 or len(self._messages[topic]) < limit:
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else:
# workaround for client to ack the publish. Otherwise,
# it seems that if client disconnects quickly, broker
# will not get the ack and publish the message again on
# next connect.
time.sleep(1)
break
return self._messages[topic] | [
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.listen | def listen(self, topic, timeout=1, limit=1):
""" Listen to a topic and return a list of message payloads received
within the specified time. Requires an async Subscribe to have been called previously.
`topic` topic to listen to
`timeout` duration to listen
`limit` the max number of payloads that will be returned. Specify 0
for no limit
Examples:
Listen and get a list of all messages received within 5 seconds
| ${messages}= | Listen | test/test | timeout=5 | limit=0 |
Listen and get 1st message received within 60 seconds
| @{messages}= | Listen | test/test | timeout=60 | limit=1 |
| Length should be | ${messages} | 1 |
"""
if not self._subscribed:
logger.warn('Cannot listen when not subscribed to a topic')
return []
if topic not in self._messages:
logger.warn('Cannot listen when not subscribed to topic: %s' % topic)
return []
# If enough messages have already been gathered, return them
if limit != 0 and len(self._messages[topic]) >= limit:
messages = self._messages[topic][:] # Copy the list's contents
self._messages[topic] = []
return messages[-limit:]
seconds = convert_time(timeout)
limit = int(limit)
logger.info('Listening on topic: %s' % topic)
timer_start = time.time()
while time.time() < timer_start + seconds:
if limit == 0 or len(self._messages[topic]) < limit:
# If the loop is running in the background
# merely sleep here for a second or so and continue
# otherwise, do the loop ourselves
if self._background_mqttc:
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else:
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else:
# workaround for client to ack the publish. Otherwise,
# it seems that if client disconnects quickly, broker
# will not get the ack and publish the message again on
# next connect.
time.sleep(1)
break
messages = self._messages[topic][:] # Copy the list's contents
self._messages[topic] = []
return messages[-limit:] if limit != 0 else messages | python | def listen(self, topic, timeout=1, limit=1):
""" Listen to a topic and return a list of message payloads received
within the specified time. Requires an async Subscribe to have been called previously.
`topic` topic to listen to
`timeout` duration to listen
`limit` the max number of payloads that will be returned. Specify 0
for no limit
Examples:
Listen and get a list of all messages received within 5 seconds
| ${messages}= | Listen | test/test | timeout=5 | limit=0 |
Listen and get 1st message received within 60 seconds
| @{messages}= | Listen | test/test | timeout=60 | limit=1 |
| Length should be | ${messages} | 1 |
"""
if not self._subscribed:
logger.warn('Cannot listen when not subscribed to a topic')
return []
if topic not in self._messages:
logger.warn('Cannot listen when not subscribed to topic: %s' % topic)
return []
# If enough messages have already been gathered, return them
if limit != 0 and len(self._messages[topic]) >= limit:
messages = self._messages[topic][:] # Copy the list's contents
self._messages[topic] = []
return messages[-limit:]
seconds = convert_time(timeout)
limit = int(limit)
logger.info('Listening on topic: %s' % topic)
timer_start = time.time()
while time.time() < timer_start + seconds:
if limit == 0 or len(self._messages[topic]) < limit:
# If the loop is running in the background
# merely sleep here for a second or so and continue
# otherwise, do the loop ourselves
if self._background_mqttc:
time.sleep(1)
else:
self._mqttc.loop()
else:
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# it seems that if client disconnects quickly, broker
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time.sleep(1)
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messages = self._messages[topic][:] # Copy the list's contents
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.subscribe_and_validate | def subscribe_and_validate(self, topic, qos, payload, timeout=1):
""" Subscribe to a topic and validate that the specified payload is
received within timeout. It is required that a connection has been
established using `Connect` keyword. The payload can be specified as
a python regular expression. If the specified payload is not received
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`topic` topic to subscribe to
`qos` quality of service for the subscription
`payload` payload (message) that is expected to arrive
`timeout` time to wait for the payload to arrive
Examples:
| Subscribe And Validate | test/test | 1 | test message |
"""
seconds = convert_time(timeout)
self._verified = False
logger.info('Subscribing to topic: %s' % topic)
self._mqttc.subscribe(str(topic), int(qos))
self._payload = str(payload)
self._mqttc.on_message = self._on_message
timer_start = time.time()
while time.time() < timer_start + seconds:
if self._verified:
break
self._mqttc.loop()
if not self._verified:
raise AssertionError("The expected payload didn't arrive in the topic") | python | def subscribe_and_validate(self, topic, qos, payload, timeout=1):
""" Subscribe to a topic and validate that the specified payload is
received within timeout. It is required that a connection has been
established using `Connect` keyword. The payload can be specified as
a python regular expression. If the specified payload is not received
within timeout, an AssertionError is thrown.
`topic` topic to subscribe to
`qos` quality of service for the subscription
`payload` payload (message) that is expected to arrive
`timeout` time to wait for the payload to arrive
Examples:
| Subscribe And Validate | test/test | 1 | test message |
"""
seconds = convert_time(timeout)
self._verified = False
logger.info('Subscribing to topic: %s' % topic)
self._mqttc.subscribe(str(topic), int(qos))
self._payload = str(payload)
self._mqttc.on_message = self._on_message
timer_start = time.time()
while time.time() < timer_start + seconds:
if self._verified:
break
self._mqttc.loop()
if not self._verified:
raise AssertionError("The expected payload didn't arrive in the topic") | [
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`payload` payload (message) that is expected to arrive
`timeout` time to wait for the payload to arrive
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.unsubscribe | def unsubscribe(self, topic):
""" Unsubscribe the client from the specified topic.
`topic` topic to unsubscribe from
Example:
| Unsubscribe | test/mqtt_test |
"""
try:
tmp = self._mqttc
except AttributeError:
logger.info('No MQTT Client instance found so nothing to unsubscribe from.')
return
if self._background_mqttc:
logger.info('Closing background loop')
self._background_mqttc.loop_stop()
self._background_mqttc = None
if topic in self._messages:
del self._messages[topic]
logger.info('Unsubscribing from topic: %s' % topic)
self._unsubscribed = False
self._mqttc.on_unsubscribe = self._on_unsubscribe
self._mqttc.unsubscribe(str(topic))
timer_start = time.time()
while (not self._unsubscribed and
time.time() < timer_start + self._loop_timeout):
self._mqttc.loop()
if not self._unsubscribed:
logger.warn('Client didn\'t receive an unsubscribe callback') | python | def unsubscribe(self, topic):
""" Unsubscribe the client from the specified topic.
`topic` topic to unsubscribe from
Example:
| Unsubscribe | test/mqtt_test |
"""
try:
tmp = self._mqttc
except AttributeError:
logger.info('No MQTT Client instance found so nothing to unsubscribe from.')
return
if self._background_mqttc:
logger.info('Closing background loop')
self._background_mqttc.loop_stop()
self._background_mqttc = None
if topic in self._messages:
del self._messages[topic]
logger.info('Unsubscribing from topic: %s' % topic)
self._unsubscribed = False
self._mqttc.on_unsubscribe = self._on_unsubscribe
self._mqttc.unsubscribe(str(topic))
timer_start = time.time()
while (not self._unsubscribed and
time.time() < timer_start + self._loop_timeout):
self._mqttc.loop()
if not self._unsubscribed:
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randomsync/robotframework-mqttlibrary | src/MQTTLibrary/MQTTKeywords.py | MQTTKeywords.disconnect | def disconnect(self):
""" Disconnect from MQTT Broker.
Example:
| Disconnect |
"""
try:
tmp = self._mqttc
except AttributeError:
logger.info('No MQTT Client instance found so nothing to disconnect from.')
return
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""" Disconnect from MQTT Broker.
Example:
| Disconnect |
"""
try:
tmp = self._mqttc
except AttributeError:
logger.info('No MQTT Client instance found so nothing to disconnect from.')
return
self._disconnected = False
self._unexpected_disconnect = False
self._mqttc.on_disconnect = self._on_disconnect
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timer_start = time.time()
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self._mqttc.loop()
if self._unexpected_disconnect:
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imbolc/aiohttp-login | aiohttp_login/decorators.py | user_to_request | def user_to_request(handler):
'''Add user to request if user logged in'''
@wraps(handler)
async def decorator(*args):
request = _get_request(args)
request[cfg.REQUEST_USER_KEY] = await get_cur_user(request)
return await handler(*args)
return decorator | python | def user_to_request(handler):
'''Add user to request if user logged in'''
@wraps(handler)
async def decorator(*args):
request = _get_request(args)
request[cfg.REQUEST_USER_KEY] = await get_cur_user(request)
return await handler(*args)
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brandon-rhodes/python-adventure | adventure/model.py | Word.add_synonym | def add_synonym(self, other):
"""Every word in a group of synonyms shares the same list."""
self.synonyms.extend(other.synonyms)
other.synonyms = self.synonyms | python | def add_synonym(self, other):
"""Every word in a group of synonyms shares the same list."""
self.synonyms.extend(other.synonyms)
other.synonyms = self.synonyms | [
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imbolc/aiohttp-login | aiohttp_login/sql.py | _split_dict | def _split_dict(dic):
'''Split dict into sorted keys and values
>>> _split_dict({'b': 2, 'a': 1})
(['a', 'b'], [1, 2])
'''
keys = sorted(dic.keys())
return keys, [dic[k] for k in keys] | python | def _split_dict(dic):
'''Split dict into sorted keys and values
>>> _split_dict({'b': 2, 'a': 1})
(['a', 'b'], [1, 2])
'''
keys = sorted(dic.keys())
return keys, [dic[k] for k in keys] | [
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brandon-rhodes/python-adventure | adventure/__init__.py | play | def play(seed=None):
"""Turn the Python prompt into an Adventure game.
With optional the `seed` argument the caller can supply an integer
to start the Python random number generator at a known state.
"""
global _game
from .game import Game
from .prompt import install_words
_game = Game(seed)
load_advent_dat(_game)
install_words(_game)
_game.start()
print(_game.output[:-1]) | python | def play(seed=None):
"""Turn the Python prompt into an Adventure game.
With optional the `seed` argument the caller can supply an integer
to start the Python random number generator at a known state.
"""
global _game
from .game import Game
from .prompt import install_words
_game = Game(seed)
load_advent_dat(_game)
install_words(_game)
_game.start()
print(_game.output[:-1]) | [
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brandon-rhodes/python-adventure | adventure/game.py | Game.write | def write(self, more):
"""Append the Unicode representation of `s` to our output."""
if more:
self.output += str(more).upper()
self.output += '\n' | python | def write(self, more):
"""Append the Unicode representation of `s` to our output."""
if more:
self.output += str(more).upper()
self.output += '\n' | [
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brandon-rhodes/python-adventure | adventure/game.py | Game.yesno | def yesno(self, s, yesno_callback, casual=False):
"""Ask a question and prepare to receive a yes-or-no answer."""
self.write(s)
self.yesno_callback = yesno_callback
self.yesno_casual = casual | python | def yesno(self, s, yesno_callback, casual=False):
"""Ask a question and prepare to receive a yes-or-no answer."""
self.write(s)
self.yesno_callback = yesno_callback
self.yesno_casual = casual | [
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brandon-rhodes/python-adventure | adventure/game.py | Game.start2 | def start2(self, yes):
"""Display instructions if the user wants them."""
if yes:
self.write_message(1)
self.hints[3].used = True
self.lamp_turns = 1000
self.oldloc2 = self.oldloc = self.loc = self.rooms[1]
self.dwarves = [ Dwarf(self.rooms[n]) for n in (19, 27, 33, 44, 64) ]
self.pirate = Pirate(self.chest_room)
treasures = self.treasures
self.treasures_not_found = len(treasures)
for treasure in treasures:
treasure.prop = -1
self.describe_location() | python | def start2(self, yes):
"""Display instructions if the user wants them."""
if yes:
self.write_message(1)
self.hints[3].used = True
self.lamp_turns = 1000
self.oldloc2 = self.oldloc = self.loc = self.rooms[1]
self.dwarves = [ Dwarf(self.rooms[n]) for n in (19, 27, 33, 44, 64) ]
self.pirate = Pirate(self.chest_room)
treasures = self.treasures
self.treasures_not_found = len(treasures)
for treasure in treasures:
treasure.prop = -1
self.describe_location() | [
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brandon-rhodes/python-adventure | adventure/game.py | Game.do_command | def do_command(self, words):
"""Parse and act upon the command in the list of strings `words`."""
self.output = ''
self._do_command(words)
return self.output | python | def do_command(self, words):
"""Parse and act upon the command in the list of strings `words`."""
self.output = ''
self._do_command(words)
return self.output | [
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brandon-rhodes/python-adventure | adventure/game.py | Game.resume | def resume(self, obj):
"""Returns an Adventure game saved to the given file."""
if isinstance(obj, str):
savefile = open(obj, 'rb')
else:
savefile = obj
game = pickle.loads(zlib.decompress(savefile.read()))
if savefile is not obj:
savefile.close()
# Reinstate the random number generator.
game.random_generator = random.Random()
game.random_generator.setstate(game.random_state)
del game.random_state
return game | python | def resume(self, obj):
"""Returns an Adventure game saved to the given file."""
if isinstance(obj, str):
savefile = open(obj, 'rb')
else:
savefile = obj
game = pickle.loads(zlib.decompress(savefile.read()))
if savefile is not obj:
savefile.close()
# Reinstate the random number generator.
game.random_generator = random.Random()
game.random_generator.setstate(game.random_state)
del game.random_state
return game | [
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brandon-rhodes/python-adventure | adventure/data.py | parse | def parse(data, datafile):
"""Read the Adventure data file and return a ``Data`` object."""
data._last_travel = [0, [0]] # x and verbs used by section 3
while True:
section_number = int(datafile.readline())
if not section_number: # no further sections
break
store = globals().get('section%d' % section_number)
while True:
fields = [ (int(field) if field.lstrip('-').isdigit() else field)
for field in datafile.readline().strip().split('\t') ]
if fields[0] == -1: # end-of-section marker
break
store(data, *fields)
del data._last_travel # state used by section 3
del data._object # state used by section 5
data.object_list = sorted(set(data.objects.values()), key=attrgetter('n'))
#data.room_list = sorted(set(data.rooms.values()), key=attrgetter('n'))
for obj in data.object_list:
name = obj.names[0]
if hasattr(data, name):
name = name + '2' # create identifiers like ROD2, PLANT2
setattr(data, name, obj)
return data | python | def parse(data, datafile):
"""Read the Adventure data file and return a ``Data`` object."""
data._last_travel = [0, [0]] # x and verbs used by section 3
while True:
section_number = int(datafile.readline())
if not section_number: # no further sections
break
store = globals().get('section%d' % section_number)
while True:
fields = [ (int(field) if field.lstrip('-').isdigit() else field)
for field in datafile.readline().strip().split('\t') ]
if fields[0] == -1: # end-of-section marker
break
store(data, *fields)
del data._last_travel # state used by section 3
del data._object # state used by section 5
data.object_list = sorted(set(data.objects.values()), key=attrgetter('n'))
#data.room_list = sorted(set(data.rooms.values()), key=attrgetter('n'))
for obj in data.object_list:
name = obj.names[0]
if hasattr(data, name):
name = name + '2' # create identifiers like ROD2, PLANT2
setattr(data, name, obj)
return data | [
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BradWhittington/django-mailgun | django_mailgun.py | MailgunBackend._map_smtp_headers_to_api_parameters | def _map_smtp_headers_to_api_parameters(self, email_message):
"""
Map the values passed in SMTP headers to API-ready
2-item tuples present in HEADERS_MAP
header values must be a single string or list or tuple of strings
:return: 2-item tuples of the form (api_name, api_values)
"""
api_data = []
for smtp_key, api_transformer in six.iteritems(self._headers_map):
data_to_transform = email_message.extra_headers.pop(smtp_key, None)
if data_to_transform is not None:
if isinstance(data_to_transform, (list, tuple)):
# map each value in the tuple/list
for data in data_to_transform:
api_data.append((api_transformer[0], api_transformer[1](data)))
elif isinstance(data_to_transform, dict):
for data in six.iteritems(data_to_transform):
api_data.append(api_transformer(data))
else:
# we only have one value
api_data.append((api_transformer[0], api_transformer[1](data_to_transform)))
return api_data | python | def _map_smtp_headers_to_api_parameters(self, email_message):
"""
Map the values passed in SMTP headers to API-ready
2-item tuples present in HEADERS_MAP
header values must be a single string or list or tuple of strings
:return: 2-item tuples of the form (api_name, api_values)
"""
api_data = []
for smtp_key, api_transformer in six.iteritems(self._headers_map):
data_to_transform = email_message.extra_headers.pop(smtp_key, None)
if data_to_transform is not None:
if isinstance(data_to_transform, (list, tuple)):
# map each value in the tuple/list
for data in data_to_transform:
api_data.append((api_transformer[0], api_transformer[1](data)))
elif isinstance(data_to_transform, dict):
for data in six.iteritems(data_to_transform):
api_data.append(api_transformer(data))
else:
# we only have one value
api_data.append((api_transformer[0], api_transformer[1](data_to_transform)))
return api_data | [
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Stanford-Online/xblock-image-modal | imagemodal/views.py | ImageModalViewMixin.student_view | def student_view(self, context=None):
"""
Build the fragment for the default student view
"""
context = context or {}
context.update({
'display_name': self.display_name,
'image_url': self.image_url,
'thumbnail_url': self.thumbnail_url or self.image_url,
'description': self.description,
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fragment = self.build_fragment(
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css=[
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],
js=[
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'view.js',
],
js_init='ImageModalView',
)
return fragment | python | def student_view(self, context=None):
"""
Build the fragment for the default student view
"""
context = context or {}
context.update({
'display_name': self.display_name,
'image_url': self.image_url,
'thumbnail_url': self.thumbnail_url or self.image_url,
'description': self.description,
'xblock_id': text_type(self.scope_ids.usage_id),
'alt_text': self.alt_text or self.display_name,
})
fragment = self.build_fragment(
template='view.html',
context=context,
css=[
'view.less.css',
URL_FONT_AWESOME_CSS,
],
js=[
'draggabilly.pkgd.js',
'view.js',
],
js_init='ImageModalView',
)
return fragment | [
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Stanford-Online/xblock-image-modal | imagemodal/mixins/fragment.py | XBlockFragmentBuilderMixin.build_fragment | def build_fragment(
self,
template='',
context=None,
css=None,
js=None,
js_init=None,
):
"""
Creates a fragment for display.
"""
template = 'templates/' + template
context = context or {}
css = css or []
js = js or []
rendered_template = ''
if template:
rendered_template = self.loader.render_django_template(
template,
context=Context(context),
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)
fragment = Fragment(rendered_template)
for item in css:
if item.startswith('/'):
url = item
else:
item = 'public/' + item
url = self.runtime.local_resource_url(self, item)
fragment.add_css_url(url)
for item in js:
item = 'public/' + item
url = self.runtime.local_resource_url(self, item)
fragment.add_javascript_url(url)
if js_init:
fragment.initialize_js(js_init)
return fragment | python | def build_fragment(
self,
template='',
context=None,
css=None,
js=None,
js_init=None,
):
"""
Creates a fragment for display.
"""
template = 'templates/' + template
context = context or {}
css = css or []
js = js or []
rendered_template = ''
if template:
rendered_template = self.loader.render_django_template(
template,
context=Context(context),
i18n_service=self.runtime.service(self, 'i18n'),
)
fragment = Fragment(rendered_template)
for item in css:
if item.startswith('/'):
url = item
else:
item = 'public/' + item
url = self.runtime.local_resource_url(self, item)
fragment.add_css_url(url)
for item in js:
item = 'public/' + item
url = self.runtime.local_resource_url(self, item)
fragment.add_javascript_url(url)
if js_init:
fragment.initialize_js(js_init)
return fragment | [
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Stanford-Online/xblock-image-modal | imagemodal/mixins/scenario.py | _parse_title | def _parse_title(file_path):
"""
Parse a title from a file name
"""
title = file_path
title = title.split('/')[-1]
title = '.'.join(title.split('.')[:-1])
title = ' '.join(title.split('-'))
title = ' '.join([
word.capitalize()
for word in title.split(' ')
])
return title | python | def _parse_title(file_path):
"""
Parse a title from a file name
"""
title = file_path
title = title.split('/')[-1]
title = '.'.join(title.split('.')[:-1])
title = ' '.join(title.split('-'))
title = ' '.join([
word.capitalize()
for word in title.split(' ')
])
return title | [
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Stanford-Online/xblock-image-modal | imagemodal/mixins/scenario.py | _read_files | def _read_files(files):
"""
Read the contents of a list of files
"""
file_contents = [
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_read_file(file_path),
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for file_path in files
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return file_contents | python | def _read_files(files):
"""
Read the contents of a list of files
"""
file_contents = [
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_read_file(file_path),
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for file_path in files
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return file_contents | [
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Stanford-Online/xblock-image-modal | imagemodal/mixins/scenario.py | _find_files | def _find_files(directory):
"""
Find XML files in the directory
"""
pattern = "{directory}/*.xml".format(
directory=directory,
)
files = glob(pattern)
return files | python | def _find_files(directory):
"""
Find XML files in the directory
"""
pattern = "{directory}/*.xml".format(
directory=directory,
)
files = glob(pattern)
return files | [
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Stanford-Online/xblock-image-modal | imagemodal/mixins/scenario.py | XBlockWorkbenchMixin.workbench_scenarios | def workbench_scenarios(cls):
"""
Gather scenarios to be displayed in the workbench
"""
module = cls.__module__
module = module.split('.')[0]
directory = pkg_resources.resource_filename(module, 'scenarios')
files = _find_files(directory)
scenarios = _read_files(files)
return scenarios | python | def workbench_scenarios(cls):
"""
Gather scenarios to be displayed in the workbench
"""
module = cls.__module__
module = module.split('.')[0]
directory = pkg_resources.resource_filename(module, 'scenarios')
files = _find_files(directory)
scenarios = _read_files(files)
return scenarios | [
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broadinstitute/fiss | firecloud/api.py | _check_response_code | def _check_response_code(response, codes):
"""
Throws an exception if the http response is not expected. Can check single
integer or list of valid responses.
Example usage:
>>> r = api.get_workspace("broad-firecloud-testing", "Fake-Bucket")
>>> _check_response_code(r, 200)
... FireCloudServerError ...
"""
if type(codes) == int:
codes = [codes]
if response.status_code not in codes:
raise FireCloudServerError(response.status_code, response.content) | python | def _check_response_code(response, codes):
"""
Throws an exception if the http response is not expected. Can check single
integer or list of valid responses.
Example usage:
>>> r = api.get_workspace("broad-firecloud-testing", "Fake-Bucket")
>>> _check_response_code(r, 200)
... FireCloudServerError ...
"""
if type(codes) == int:
codes = [codes]
if response.status_code not in codes:
raise FireCloudServerError(response.status_code, response.content) | [
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broadinstitute/fiss | firecloud/api.py | list_entity_types | def list_entity_types(namespace, workspace):
"""List the entity types present in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Entities/getEntityTypes
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "workspaces/{0}/{1}/entities".format(namespace, workspace)
return __get(uri, headers=headers) | python | def list_entity_types(namespace, workspace):
"""List the entity types present in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Entities/getEntityTypes
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "workspaces/{0}/{1}/entities".format(namespace, workspace)
return __get(uri, headers=headers) | [
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namespace (str): project to which workspace belongs
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broadinstitute/fiss | firecloud/api.py | upload_entities | def upload_entities(namespace, workspace, entity_data):
"""Upload entities from tab-delimited string.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
entity_data (str): TSV string describing entites
Swagger:
https://api.firecloud.org/#!/Entities/importEntities
"""
body = urlencode({"entities" : entity_data})
headers = _fiss_agent_header({
'Content-type': "application/x-www-form-urlencoded"
})
uri = "workspaces/{0}/{1}/importEntities".format(namespace, workspace)
return __post(uri, headers=headers, data=body) | python | def upload_entities(namespace, workspace, entity_data):
"""Upload entities from tab-delimited string.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
entity_data (str): TSV string describing entites
Swagger:
https://api.firecloud.org/#!/Entities/importEntities
"""
body = urlencode({"entities" : entity_data})
headers = _fiss_agent_header({
'Content-type': "application/x-www-form-urlencoded"
})
uri = "workspaces/{0}/{1}/importEntities".format(namespace, workspace)
return __post(uri, headers=headers, data=body) | [
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broadinstitute/fiss | firecloud/api.py | upload_entities_tsv | def upload_entities_tsv(namespace, workspace, entities_tsv):
"""Upload entities from a tsv loadfile.
File-based wrapper for api.upload_entities().
A loadfile is a tab-separated text file with a header row
describing entity type and attribute names, followed by
rows of entities and their attribute values.
Ex:
entity:participant_id age alive
participant_23 25 Y
participant_27 35 N
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
entities_tsv (file): FireCloud loadfile, see format above
"""
if isinstance(entities_tsv, string_types):
with open(entities_tsv, "r") as tsv:
entity_data = tsv.read()
elif isinstance(entities_tsv, io.StringIO):
entity_data = entities_tsv.getvalue()
else:
raise ValueError('Unsupported input type.')
return upload_entities(namespace, workspace, entity_data) | python | def upload_entities_tsv(namespace, workspace, entities_tsv):
"""Upload entities from a tsv loadfile.
File-based wrapper for api.upload_entities().
A loadfile is a tab-separated text file with a header row
describing entity type and attribute names, followed by
rows of entities and their attribute values.
Ex:
entity:participant_id age alive
participant_23 25 Y
participant_27 35 N
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
entities_tsv (file): FireCloud loadfile, see format above
"""
if isinstance(entities_tsv, string_types):
with open(entities_tsv, "r") as tsv:
entity_data = tsv.read()
elif isinstance(entities_tsv, io.StringIO):
entity_data = entities_tsv.getvalue()
else:
raise ValueError('Unsupported input type.')
return upload_entities(namespace, workspace, entity_data) | [
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broadinstitute/fiss | firecloud/api.py | copy_entities | def copy_entities(from_namespace, from_workspace, to_namespace,
to_workspace, etype, enames, link_existing_entities=False):
"""Copy entities between workspaces
Args:
from_namespace (str): project (namespace) to which source workspace belongs
from_workspace (str): Source workspace name
to_namespace (str): project (namespace) to which target workspace belongs
to_workspace (str): Target workspace name
etype (str): Entity type
enames (list(str)): List of entity names to copy
link_existing_entities (boolean): Link all soft conflicts to the entities that already exist.
Swagger:
https://api.firecloud.org/#!/Entities/copyEntities
"""
uri = "workspaces/{0}/{1}/entities/copy".format(to_namespace, to_workspace)
body = {
"sourceWorkspace": {
"namespace": from_namespace,
"name": from_workspace
},
"entityType": etype,
"entityNames": enames
}
return __post(uri, json=body, params={'linkExistingEntities':
str(link_existing_entities).lower()}) | python | def copy_entities(from_namespace, from_workspace, to_namespace,
to_workspace, etype, enames, link_existing_entities=False):
"""Copy entities between workspaces
Args:
from_namespace (str): project (namespace) to which source workspace belongs
from_workspace (str): Source workspace name
to_namespace (str): project (namespace) to which target workspace belongs
to_workspace (str): Target workspace name
etype (str): Entity type
enames (list(str)): List of entity names to copy
link_existing_entities (boolean): Link all soft conflicts to the entities that already exist.
Swagger:
https://api.firecloud.org/#!/Entities/copyEntities
"""
uri = "workspaces/{0}/{1}/entities/copy".format(to_namespace, to_workspace)
body = {
"sourceWorkspace": {
"namespace": from_namespace,
"name": from_workspace
},
"entityType": etype,
"entityNames": enames
}
return __post(uri, json=body, params={'linkExistingEntities':
str(link_existing_entities).lower()}) | [
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broadinstitute/fiss | firecloud/api.py | get_entities | def get_entities(namespace, workspace, etype):
"""List entities of given type in a workspace.
Response content will be in JSON format.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
Swagger:
https://api.firecloud.org/#!/Entities/getEntities
"""
uri = "workspaces/{0}/{1}/entities/{2}".format(namespace, workspace, etype)
return __get(uri) | python | def get_entities(namespace, workspace, etype):
"""List entities of given type in a workspace.
Response content will be in JSON format.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
Swagger:
https://api.firecloud.org/#!/Entities/getEntities
"""
uri = "workspaces/{0}/{1}/entities/{2}".format(namespace, workspace, etype)
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broadinstitute/fiss | firecloud/api.py | get_entities_tsv | def get_entities_tsv(namespace, workspace, etype):
"""List entities of given type in a workspace as a TSV.
Identical to get_entities(), but the response is a TSV.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
Swagger:
https://api.firecloud.org/#!/Entities/browserDownloadEntitiesTSV
"""
uri = "workspaces/{0}/{1}/entities/{2}/tsv".format(namespace,
workspace, etype)
return __get(uri) | python | def get_entities_tsv(namespace, workspace, etype):
"""List entities of given type in a workspace as a TSV.
Identical to get_entities(), but the response is a TSV.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
Swagger:
https://api.firecloud.org/#!/Entities/browserDownloadEntitiesTSV
"""
uri = "workspaces/{0}/{1}/entities/{2}/tsv".format(namespace,
workspace, etype)
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | get_entity | def get_entity(namespace, workspace, etype, ename):
"""Request entity information.
Gets entity metadata and attributes.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str): The entity's unique id
Swagger:
https://api.firecloud.org/#!/Entities/getEntity
"""
uri = "workspaces/{0}/{1}/entities/{2}/{3}".format(namespace,
workspace, etype, ename)
return __get(uri) | python | def get_entity(namespace, workspace, etype, ename):
"""Request entity information.
Gets entity metadata and attributes.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str): The entity's unique id
Swagger:
https://api.firecloud.org/#!/Entities/getEntity
"""
uri = "workspaces/{0}/{1}/entities/{2}/{3}".format(namespace,
workspace, etype, ename)
return __get(uri) | [
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Swagger:
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broadinstitute/fiss | firecloud/api.py | get_entities_query | def get_entities_query(namespace, workspace, etype, page=1,
page_size=100, sort_direction="asc",
filter_terms=None):
"""Paginated version of get_entities_with_type.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Entities/entityQuery
"""
# Initial parameters for pagination
params = {
"page" : page,
"pageSize" : page_size,
"sortDirection" : sort_direction
}
if filter_terms:
params['filterTerms'] = filter_terms
uri = "workspaces/{0}/{1}/entityQuery/{2}".format(namespace,workspace,etype)
return __get(uri, params=params) | python | def get_entities_query(namespace, workspace, etype, page=1,
page_size=100, sort_direction="asc",
filter_terms=None):
"""Paginated version of get_entities_with_type.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Entities/entityQuery
"""
# Initial parameters for pagination
params = {
"page" : page,
"pageSize" : page_size,
"sortDirection" : sort_direction
}
if filter_terms:
params['filterTerms'] = filter_terms
uri = "workspaces/{0}/{1}/entityQuery/{2}".format(namespace,workspace,etype)
return __get(uri, params=params) | [
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broadinstitute/fiss | firecloud/api.py | update_entity | def update_entity(namespace, workspace, etype, ename, updates):
""" Update entity attributes in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str): Entity name
updates (list(dict)): List of updates to entity from _attr_set, e.g.
Swagger:
https://api.firecloud.org/#!/Entities/update_entity
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "{0}workspaces/{1}/{2}/entities/{3}/{4}".format(fcconfig.root_url,
namespace, workspace, etype, ename)
# FIXME: create __patch method, akin to __get, __delete etc
return __SESSION.patch(uri, headers=headers, json=updates) | python | def update_entity(namespace, workspace, etype, ename, updates):
""" Update entity attributes in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str): Entity name
updates (list(dict)): List of updates to entity from _attr_set, e.g.
Swagger:
https://api.firecloud.org/#!/Entities/update_entity
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "{0}workspaces/{1}/{2}/entities/{3}/{4}".format(fcconfig.root_url,
namespace, workspace, etype, ename)
# FIXME: create __patch method, akin to __get, __delete etc
return __SESSION.patch(uri, headers=headers, json=updates) | [
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broadinstitute/fiss | firecloud/api.py | list_workspace_configs | def list_workspace_configs(namespace, workspace, allRepos=False):
"""List method configurations in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/listWorkspaceMethodConfigs
DUPLICATE: https://api.firecloud.org/#!/Workspaces/listWorkspaceMethodConfigs
"""
uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
return __get(uri, params={'allRepos': allRepos}) | python | def list_workspace_configs(namespace, workspace, allRepos=False):
"""List method configurations in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/listWorkspaceMethodConfigs
DUPLICATE: https://api.firecloud.org/#!/Workspaces/listWorkspaceMethodConfigs
"""
uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
return __get(uri, params={'allRepos': allRepos}) | [
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broadinstitute/fiss | firecloud/api.py | create_workspace_config | def create_workspace_config(namespace, workspace, body):
"""Create method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
body (json) : a filled-in JSON object for the new method config
(e.g. see return value of get_workspace_config)
Swagger:
https://api.firecloud.org/#!/Method_Configurations/postWorkspaceMethodConfig
DUPLICATE: https://api.firecloud.org/#!/Workspaces/postWorkspaceMethodConfig
"""
#json_body = {
# "namespace" : mnamespace,
# "name" : method,
# "rootEntityType" : root_etype,
# "inputs" : {},
# "outputs" : {},
# "prerequisites" : {}
#}
uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
return __post(uri, json=body) | python | def create_workspace_config(namespace, workspace, body):
"""Create method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
body (json) : a filled-in JSON object for the new method config
(e.g. see return value of get_workspace_config)
Swagger:
https://api.firecloud.org/#!/Method_Configurations/postWorkspaceMethodConfig
DUPLICATE: https://api.firecloud.org/#!/Workspaces/postWorkspaceMethodConfig
"""
#json_body = {
# "namespace" : mnamespace,
# "name" : method,
# "rootEntityType" : root_etype,
# "inputs" : {},
# "outputs" : {},
# "prerequisites" : {}
#}
uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | delete_workspace_config | def delete_workspace_config(namespace, workspace, cnamespace, config):
"""Delete method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
mnamespace (str): Method namespace
method (str): Method name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/deleteWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, config)
return __delete(uri) | python | def delete_workspace_config(namespace, workspace, cnamespace, config):
"""Delete method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
mnamespace (str): Method namespace
method (str): Method name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/deleteWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, config)
return __delete(uri) | [
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broadinstitute/fiss | firecloud/api.py | get_workspace_config | def get_workspace_config(namespace, workspace, cnamespace, config):
"""Get method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Config namespace
config (str): Config name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/getWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
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return __get(uri) | python | def get_workspace_config(namespace, workspace, cnamespace, config):
"""Get method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Config namespace
config (str): Config name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/getWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
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broadinstitute/fiss | firecloud/api.py | overwrite_workspace_config | def overwrite_workspace_config(namespace, workspace, cnamespace, configname, body):
"""Add or overwrite method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
configname (str): Configuration name
body (json): new body (definition) of the method config
Swagger:
https://api.firecloud.org/#!/Method_Configurations/overwriteWorkspaceMethodConfig
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, configname)
return __put(uri, headers=headers, json=body) | python | def overwrite_workspace_config(namespace, workspace, cnamespace, configname, body):
"""Add or overwrite method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
configname (str): Configuration name
body (json): new body (definition) of the method config
Swagger:
https://api.firecloud.org/#!/Method_Configurations/overwriteWorkspaceMethodConfig
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, configname)
return __put(uri, headers=headers, json=body) | [
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broadinstitute/fiss | firecloud/api.py | update_workspace_config | def update_workspace_config(namespace, workspace, cnamespace, configname, body):
"""Update method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
configname (str): Configuration name
body (json): new body (definition) of the method config
Swagger:
https://api.firecloud.org/#!/Method_Configurations/updateWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, configname)
return __post(uri, json=body) | python | def update_workspace_config(namespace, workspace, cnamespace, configname, body):
"""Update method configuration in workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
configname (str): Configuration name
body (json): new body (definition) of the method config
Swagger:
https://api.firecloud.org/#!/Method_Configurations/updateWorkspaceMethodConfig
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
workspace, cnamespace, configname)
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | validate_config | def validate_config(namespace, workspace, cnamespace, config):
"""Get syntax validation for a configuration.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
config (str): Configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/validate_method_configuration
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/validate".format(namespace,
workspace, cnamespace, config)
return __get(uri) | python | def validate_config(namespace, workspace, cnamespace, config):
"""Get syntax validation for a configuration.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Configuration namespace
config (str): Configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/validate_method_configuration
"""
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/validate".format(namespace,
workspace, cnamespace, config)
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | rename_workspace_config | def rename_workspace_config(namespace, workspace, cnamespace, config,
new_namespace, new_name):
"""Rename a method configuration in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
mnamespace (str): Config namespace
config (str): Config name
new_namespace (str): Updated config namespace
new_name (str): Updated method name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/renameWorkspaceMethodConfig
"""
body = {
"namespace" : new_namespace,
"name" : new_name,
# I have no idea why this is required by FC, but it is...
"workspaceName" : {
"namespace" : namespace,
"name" : workspace
}
}
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/rename".format(namespace,
workspace, cnamespace, config)
return __post(uri, json=body) | python | def rename_workspace_config(namespace, workspace, cnamespace, config,
new_namespace, new_name):
"""Rename a method configuration in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
mnamespace (str): Config namespace
config (str): Config name
new_namespace (str): Updated config namespace
new_name (str): Updated method name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/renameWorkspaceMethodConfig
"""
body = {
"namespace" : new_namespace,
"name" : new_name,
# I have no idea why this is required by FC, but it is...
"workspaceName" : {
"namespace" : namespace,
"name" : workspace
}
}
uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/rename".format(namespace,
workspace, cnamespace, config)
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | copy_config_from_repo | def copy_config_from_repo(namespace, workspace, from_cnamespace,
from_config, from_snapshot_id, to_cnamespace,
to_config):
"""Copy a method config from the methods repository to a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
from_cnamespace (str): Source configuration namespace
from_config (str): Source configuration name
from_snapshot_id (int): Source configuration snapshot_id
to_cnamespace (str): Target configuration namespace
to_config (str): Target configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/copyFromMethodRepo
DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyFromMethodRepo
"""
body = {
"configurationNamespace" : from_cnamespace,
"configurationName" : from_config,
"configurationSnapshotId" : from_snapshot_id,
"destinationNamespace" : to_cnamespace,
"destinationName" : to_config
}
uri = "workspaces/{0}/{1}/method_configs/copyFromMethodRepo".format(
namespace, workspace)
return __post(uri, json=body) | python | def copy_config_from_repo(namespace, workspace, from_cnamespace,
from_config, from_snapshot_id, to_cnamespace,
to_config):
"""Copy a method config from the methods repository to a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
from_cnamespace (str): Source configuration namespace
from_config (str): Source configuration name
from_snapshot_id (int): Source configuration snapshot_id
to_cnamespace (str): Target configuration namespace
to_config (str): Target configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/copyFromMethodRepo
DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyFromMethodRepo
"""
body = {
"configurationNamespace" : from_cnamespace,
"configurationName" : from_config,
"configurationSnapshotId" : from_snapshot_id,
"destinationNamespace" : to_cnamespace,
"destinationName" : to_config
}
uri = "workspaces/{0}/{1}/method_configs/copyFromMethodRepo".format(
namespace, workspace)
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | copy_config_to_repo | def copy_config_to_repo(namespace, workspace, from_cnamespace,
from_config, to_cnamespace, to_config):
"""Copy a method config from a workspace to the methods repository.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
from_cnamespace (str): Source configuration namespace
from_config (str): Source configuration name
to_cnamespace (str): Target configuration namespace
to_config (str): Target configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/copyToMethodRepo
DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyToMethodRepo
"""
body = {
"configurationNamespace" : to_cnamespace,
"configurationName" : to_config,
"sourceNamespace" : from_cnamespace,
"sourceName" : from_config
}
uri = "workspaces/{0}/{1}/method_configs/copyToMethodRepo".format(
namespace, workspace)
return __post(uri, json=body) | python | def copy_config_to_repo(namespace, workspace, from_cnamespace,
from_config, to_cnamespace, to_config):
"""Copy a method config from a workspace to the methods repository.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
from_cnamespace (str): Source configuration namespace
from_config (str): Source configuration name
to_cnamespace (str): Target configuration namespace
to_config (str): Target configuration name
Swagger:
https://api.firecloud.org/#!/Method_Configurations/copyToMethodRepo
DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyToMethodRepo
"""
body = {
"configurationNamespace" : to_cnamespace,
"configurationName" : to_config,
"sourceNamespace" : from_cnamespace,
"sourceName" : from_config
}
uri = "workspaces/{0}/{1}/method_configs/copyToMethodRepo".format(
namespace, workspace)
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | get_config_template | def get_config_template(namespace, method, version):
"""Get the configuration template for a method.
The method should exist in the methods repository.
Args:
namespace (str): Method's namespace
method (str): method name
version (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/createMethodTemplate
"""
body = {
"methodNamespace" : namespace,
"methodName" : method,
"methodVersion" : int(version)
}
return __post("template", json=body) | python | def get_config_template(namespace, method, version):
"""Get the configuration template for a method.
The method should exist in the methods repository.
Args:
namespace (str): Method's namespace
method (str): method name
version (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/createMethodTemplate
"""
body = {
"methodNamespace" : namespace,
"methodName" : method,
"methodVersion" : int(version)
}
return __post("template", json=body) | [
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broadinstitute/fiss | firecloud/api.py | get_inputs_outputs | def get_inputs_outputs(namespace, method, snapshot_id):
"""Get a description of the inputs and outputs for a method.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodIO
"""
body = {
"methodNamespace" : namespace,
"methodName" : method,
"methodVersion" : snapshot_id
}
return __post("inputsOutputs", json=body) | python | def get_inputs_outputs(namespace, method, snapshot_id):
"""Get a description of the inputs and outputs for a method.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodIO
"""
body = {
"methodNamespace" : namespace,
"methodName" : method,
"methodVersion" : snapshot_id
}
return __post("inputsOutputs", json=body) | [
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broadinstitute/fiss | firecloud/api.py | get_repository_config | def get_repository_config(namespace, config, snapshot_id):
"""Get a method configuration from the methods repository.
Args:
namespace (str): Methods namespace
config (str): config name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodRepositoryConfiguration
"""
uri = "configurations/{0}/{1}/{2}".format(namespace, config, snapshot_id)
return __get(uri) | python | def get_repository_config(namespace, config, snapshot_id):
"""Get a method configuration from the methods repository.
Args:
namespace (str): Methods namespace
config (str): config name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodRepositoryConfiguration
"""
uri = "configurations/{0}/{1}/{2}".format(namespace, config, snapshot_id)
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | get_repository_method | def get_repository_method(namespace, method, snapshot_id, wdl_only=False):
"""Get a method definition from the method repository.
Args:
namespace (str): Methods namespace
method (str): method name
version (int): snapshot_id of the method
wdl_only (bool): Exclude metadata
Swagger:
https://api.firecloud.org/#!/Method_Repository/get_api_methods_namespace_name_snapshotId
"""
uri = "methods/{0}/{1}/{2}?onlyPayload={3}".format(namespace, method,
snapshot_id,
str(wdl_only).lower())
return __get(uri) | python | def get_repository_method(namespace, method, snapshot_id, wdl_only=False):
"""Get a method definition from the method repository.
Args:
namespace (str): Methods namespace
method (str): method name
version (int): snapshot_id of the method
wdl_only (bool): Exclude metadata
Swagger:
https://api.firecloud.org/#!/Method_Repository/get_api_methods_namespace_name_snapshotId
"""
uri = "methods/{0}/{1}/{2}?onlyPayload={3}".format(namespace, method,
snapshot_id,
str(wdl_only).lower())
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | delete_repository_method | def delete_repository_method(namespace, name, snapshot_id):
"""Redacts a method and all of its associated configurations.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/delete_api_methods_namespace_name_snapshotId
"""
uri = "methods/{0}/{1}/{2}".format(namespace, name, snapshot_id)
return __delete(uri) | python | def delete_repository_method(namespace, name, snapshot_id):
"""Redacts a method and all of its associated configurations.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/delete_api_methods_namespace_name_snapshotId
"""
uri = "methods/{0}/{1}/{2}".format(namespace, name, snapshot_id)
return __delete(uri) | [
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broadinstitute/fiss | firecloud/api.py | delete_repository_config | def delete_repository_config(namespace, name, snapshot_id):
"""Redacts a configuration and all of its associated configurations.
The configuration should exist in the methods repository.
Args:
namespace (str): configuration namespace
configuration (str): configuration name
snapshot_id (int): snapshot_id of the configuration
Swagger:
https://api.firecloud.org/#!/Method_Repository/delete_api_configurations_namespace_name_snapshotId
"""
uri = "configurations/{0}/{1}/{2}".format(namespace, name, snapshot_id)
return __delete(uri) | python | def delete_repository_config(namespace, name, snapshot_id):
"""Redacts a configuration and all of its associated configurations.
The configuration should exist in the methods repository.
Args:
namespace (str): configuration namespace
configuration (str): configuration name
snapshot_id (int): snapshot_id of the configuration
Swagger:
https://api.firecloud.org/#!/Method_Repository/delete_api_configurations_namespace_name_snapshotId
"""
uri = "configurations/{0}/{1}/{2}".format(namespace, name, snapshot_id)
return __delete(uri) | [
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broadinstitute/fiss | firecloud/api.py | get_repository_method_acl | def get_repository_method_acl(namespace, method, snapshot_id):
"""Get permissions for a method.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
version (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodACL
"""
uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
return __get(uri) | python | def get_repository_method_acl(namespace, method, snapshot_id):
"""Get permissions for a method.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
version (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getMethodACL
"""
uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
return __get(uri) | [
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Swagger:
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broadinstitute/fiss | firecloud/api.py | update_repository_method_acl | def update_repository_method_acl(namespace, method, snapshot_id, acl_updates):
"""Set method permissions.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
acl_updates (list(dict)): List of access control updates
Swagger:
https://api.firecloud.org/#!/Method_Repository/setMethodACL
"""
uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
return __post(uri, json=acl_updates) | python | def update_repository_method_acl(namespace, method, snapshot_id, acl_updates):
"""Set method permissions.
The method should exist in the methods repository.
Args:
namespace (str): Methods namespace
method (str): method name
snapshot_id (int): snapshot_id of the method
acl_updates (list(dict)): List of access control updates
Swagger:
https://api.firecloud.org/#!/Method_Repository/setMethodACL
"""
uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
return __post(uri, json=acl_updates) | [
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broadinstitute/fiss | firecloud/api.py | get_repository_config_acl | def get_repository_config_acl(namespace, config, snapshot_id):
"""Get configuration permissions.
The configuration should exist in the methods repository.
Args:
namespace (str): Configuration namespace
config (str): Configuration name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getConfigACL
"""
uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
config, snapshot_id)
return __get(uri) | python | def get_repository_config_acl(namespace, config, snapshot_id):
"""Get configuration permissions.
The configuration should exist in the methods repository.
Args:
namespace (str): Configuration namespace
config (str): Configuration name
snapshot_id (int): snapshot_id of the method
Swagger:
https://api.firecloud.org/#!/Method_Repository/getConfigACL
"""
uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
config, snapshot_id)
return __get(uri) | [
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Swagger:
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broadinstitute/fiss | firecloud/api.py | update_repository_config_acl | def update_repository_config_acl(namespace, config, snapshot_id, acl_updates):
"""Set configuration permissions.
The configuration should exist in the methods repository.
Args:
namespace (str): Configuration namespace
config (str): Configuration name
snapshot_id (int): snapshot_id of the method
acl_updates (list(dict)): List of access control updates
Swagger:
https://api.firecloud.org/#!/Method_Repository/setConfigACL
"""
uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
config, snapshot_id)
return __post(uri, json=acl_updates) | python | def update_repository_config_acl(namespace, config, snapshot_id, acl_updates):
"""Set configuration permissions.
The configuration should exist in the methods repository.
Args:
namespace (str): Configuration namespace
config (str): Configuration name
snapshot_id (int): snapshot_id of the method
acl_updates (list(dict)): List of access control updates
Swagger:
https://api.firecloud.org/#!/Method_Repository/setConfigACL
"""
uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
config, snapshot_id)
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Swagger:
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broadinstitute/fiss | firecloud/api.py | create_submission | def create_submission(wnamespace, workspace, cnamespace, config,
entity, etype, expression=None, use_callcache=True):
"""Submit job in FireCloud workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Method configuration namespace
config (str): Method configuration name
entity (str): Entity to submit job on. Should be the same type as
the root entity type of the method config, unless an
expression is used
etype (str): Entity type of root_entity
expression (str): Instead of using entity as the root entity,
evaluate the root entity from this expression.
use_callcache (bool): use call cache if applicable (default: true)
Swagger:
https://api.firecloud.org/#!/Submissions/createSubmission
"""
uri = "workspaces/{0}/{1}/submissions".format(wnamespace, workspace)
body = {
"methodConfigurationNamespace" : cnamespace,
"methodConfigurationName" : config,
"entityType" : etype,
"entityName" : entity,
"useCallCache" : use_callcache
}
if expression:
body['expression'] = expression
return __post(uri, json=body) | python | def create_submission(wnamespace, workspace, cnamespace, config,
entity, etype, expression=None, use_callcache=True):
"""Submit job in FireCloud workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
cnamespace (str): Method configuration namespace
config (str): Method configuration name
entity (str): Entity to submit job on. Should be the same type as
the root entity type of the method config, unless an
expression is used
etype (str): Entity type of root_entity
expression (str): Instead of using entity as the root entity,
evaluate the root entity from this expression.
use_callcache (bool): use call cache if applicable (default: true)
Swagger:
https://api.firecloud.org/#!/Submissions/createSubmission
"""
uri = "workspaces/{0}/{1}/submissions".format(wnamespace, workspace)
body = {
"methodConfigurationNamespace" : cnamespace,
"methodConfigurationName" : config,
"entityType" : etype,
"entityName" : entity,
"useCallCache" : use_callcache
}
if expression:
body['expression'] = expression
return __post(uri, json=body) | [
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broadinstitute/fiss | firecloud/api.py | abort_submission | def abort_submission(namespace, workspace, submission_id):
"""Abort running job in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
Swagger:
https://api.firecloud.org/#!/Submissions/deleteSubmission
"""
uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
workspace, submission_id)
return __delete(uri) | python | def abort_submission(namespace, workspace, submission_id):
"""Abort running job in a workspace.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
Swagger:
https://api.firecloud.org/#!/Submissions/deleteSubmission
"""
uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
workspace, submission_id)
return __delete(uri) | [
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Swagger:
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broadinstitute/fiss | firecloud/api.py | get_submission | def get_submission(namespace, workspace, submission_id):
"""Request submission information.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
Swagger:
https://api.firecloud.org/#!/Submissions/monitorSubmission
"""
uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
workspace, submission_id)
return __get(uri) | python | def get_submission(namespace, workspace, submission_id):
"""Request submission information.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
Swagger:
https://api.firecloud.org/#!/Submissions/monitorSubmission
"""
uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
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return __get(uri) | [
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submission_id (str): Submission's unique identifier
Swagger:
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broadinstitute/fiss | firecloud/api.py | get_workflow_metadata | def get_workflow_metadata(namespace, workspace, submission_id, workflow_id):
"""Request the metadata for a workflow in a submission.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
workflow_id (str): Workflow's unique identifier.
Swagger:
https://api.firecloud.org/#!/Submissions/workflowMetadata
"""
uri = "workspaces/{0}/{1}/submissions/{2}/workflows/{3}".format(namespace,
workspace, submission_id, workflow_id)
return __get(uri) | python | def get_workflow_metadata(namespace, workspace, submission_id, workflow_id):
"""Request the metadata for a workflow in a submission.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
workflow_id (str): Workflow's unique identifier.
Swagger:
https://api.firecloud.org/#!/Submissions/workflowMetadata
"""
uri = "workspaces/{0}/{1}/submissions/{2}/workflows/{3}".format(namespace,
workspace, submission_id, workflow_id)
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | get_workflow_outputs | def get_workflow_outputs(namespace, workspace, submission_id, workflow_id):
"""Request the outputs for a workflow in a submission.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
workflow_id (str): Workflow's unique identifier.
Swagger:
https://api.firecloud.org/#!/Submissions/workflowOutputsInSubmission
"""
uri = "workspaces/{0}/{1}/".format(namespace, workspace)
uri += "submissions/{0}/workflows/{1}/outputs".format(submission_id,
workflow_id)
return __get(uri) | python | def get_workflow_outputs(namespace, workspace, submission_id, workflow_id):
"""Request the outputs for a workflow in a submission.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
workflow_id (str): Workflow's unique identifier.
Swagger:
https://api.firecloud.org/#!/Submissions/workflowOutputsInSubmission
"""
uri = "workspaces/{0}/{1}/".format(namespace, workspace)
uri += "submissions/{0}/workflows/{1}/outputs".format(submission_id,
workflow_id)
return __get(uri) | [
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broadinstitute/fiss | firecloud/api.py | create_workspace | def create_workspace(namespace, name, authorizationDomain="", attributes=None):
"""Create a new FireCloud Workspace.
Args:
namespace (str): project to which workspace belongs
name (str): Workspace name
protected (bool): If True, this workspace is protected by dbGaP
credentials. This option is only available if your FireCloud
account is linked to your NIH account.
attributes (dict): Workspace attributes as key value pairs
Swagger:
https://api.firecloud.org/#!/Workspaces/createWorkspace
"""
if not attributes:
attributes = dict()
body = {
"namespace": namespace,
"name": name,
"attributes": attributes
}
if authorizationDomain:
authDomain = [{"membersGroupName": authorizationDomain}]
else:
authDomain = []
body["authorizationDomain"] = authDomain
return __post("workspaces", json=body) | python | def create_workspace(namespace, name, authorizationDomain="", attributes=None):
"""Create a new FireCloud Workspace.
Args:
namespace (str): project to which workspace belongs
name (str): Workspace name
protected (bool): If True, this workspace is protected by dbGaP
credentials. This option is only available if your FireCloud
account is linked to your NIH account.
attributes (dict): Workspace attributes as key value pairs
Swagger:
https://api.firecloud.org/#!/Workspaces/createWorkspace
"""
if not attributes:
attributes = dict()
body = {
"namespace": namespace,
"name": name,
"attributes": attributes
}
if authorizationDomain:
authDomain = [{"membersGroupName": authorizationDomain}]
else:
authDomain = []
body["authorizationDomain"] = authDomain
return __post("workspaces", json=body) | [
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broadinstitute/fiss | firecloud/api.py | update_workspace_acl | def update_workspace_acl(namespace, workspace, acl_updates, invite_users_not_found=False):
"""Update workspace access control list.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
acl_updates (list(dict)): Acl updates as dicts with two keys:
"email" - Firecloud user email
"accessLevel" - one of "OWNER", "READER", "WRITER", "NO ACCESS"
Example: {"email":"user1@mail.com", "accessLevel":"WRITER"}
invite_users_not_found (bool): true to invite unregistered users, false to ignore
Swagger:
https://api.firecloud.org/#!/Workspaces/updateWorkspaceACL
"""
uri = "{0}workspaces/{1}/{2}/acl?inviteUsersNotFound={3}".format(fcconfig.root_url,
namespace, workspace, str(invite_users_not_found).lower())
headers = _fiss_agent_header({"Content-type": "application/json"})
# FIXME: create __patch method, akin to __get, __delete etc
return __SESSION.patch(uri, headers=headers, data=json.dumps(acl_updates)) | python | def update_workspace_acl(namespace, workspace, acl_updates, invite_users_not_found=False):
"""Update workspace access control list.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
acl_updates (list(dict)): Acl updates as dicts with two keys:
"email" - Firecloud user email
"accessLevel" - one of "OWNER", "READER", "WRITER", "NO ACCESS"
Example: {"email":"user1@mail.com", "accessLevel":"WRITER"}
invite_users_not_found (bool): true to invite unregistered users, false to ignore
Swagger:
https://api.firecloud.org/#!/Workspaces/updateWorkspaceACL
"""
uri = "{0}workspaces/{1}/{2}/acl?inviteUsersNotFound={3}".format(fcconfig.root_url,
namespace, workspace, str(invite_users_not_found).lower())
headers = _fiss_agent_header({"Content-type": "application/json"})
# FIXME: create __patch method, akin to __get, __delete etc
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broadinstitute/fiss | firecloud/api.py | clone_workspace | def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
authorizationDomain=""):
"""Clone a FireCloud workspace.
A clone is a shallow copy of a FireCloud workspace, enabling
easy sharing of data, such as TCGA data, without duplication.
Args:
from_namespace (str): project (namespace) to which source workspace belongs
from_workspace (str): Source workspace's name
to_namespace (str): project to which target workspace belongs
to_workspace (str): Target workspace's name
authorizationDomain: (str) required authorization domains
Swagger:
https://api.firecloud.org/#!/Workspaces/cloneWorkspace
"""
if authorizationDomain:
if isinstance(authorizationDomain, string_types):
authDomain = [{"membersGroupName": authorizationDomain}]
else:
authDomain = [{"membersGroupName": authDomain} for authDomain in authorizationDomain]
else:
authDomain = []
body = {
"namespace": to_namespace,
"name": to_workspace,
"attributes": dict(),
"authorizationDomain": authDomain,
}
uri = "workspaces/{0}/{1}/clone".format(from_namespace, from_workspace)
return __post(uri, json=body) | python | def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
authorizationDomain=""):
"""Clone a FireCloud workspace.
A clone is a shallow copy of a FireCloud workspace, enabling
easy sharing of data, such as TCGA data, without duplication.
Args:
from_namespace (str): project (namespace) to which source workspace belongs
from_workspace (str): Source workspace's name
to_namespace (str): project to which target workspace belongs
to_workspace (str): Target workspace's name
authorizationDomain: (str) required authorization domains
Swagger:
https://api.firecloud.org/#!/Workspaces/cloneWorkspace
"""
if authorizationDomain:
if isinstance(authorizationDomain, string_types):
authDomain = [{"membersGroupName": authorizationDomain}]
else:
authDomain = [{"membersGroupName": authDomain} for authDomain in authorizationDomain]
else:
authDomain = []
body = {
"namespace": to_namespace,
"name": to_workspace,
"attributes": dict(),
"authorizationDomain": authDomain,
}
uri = "workspaces/{0}/{1}/clone".format(from_namespace, from_workspace)
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broadinstitute/fiss | firecloud/api.py | update_workspace_attributes | def update_workspace_attributes(namespace, workspace, attrs):
"""Update or remove workspace attributes.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
attrs (list(dict)): List of update operations for workspace attributes.
Use the helper dictionary construction functions to create these:
_attr_set() : Set/Update attribute
_attr_rem() : Remove attribute
_attr_ladd() : Add list member to attribute
_attr_lrem() : Remove list member from attribute
Swagger:
https://api.firecloud.org/#!/Workspaces/updateAttributes
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "{0}workspaces/{1}/{2}/updateAttributes".format(fcconfig.root_url,
namespace, workspace)
body = json.dumps(attrs)
# FIXME: create __patch method, akin to __get, __delete etc
return __SESSION.patch(uri, headers=headers, data=body) | python | def update_workspace_attributes(namespace, workspace, attrs):
"""Update or remove workspace attributes.
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
attrs (list(dict)): List of update operations for workspace attributes.
Use the helper dictionary construction functions to create these:
_attr_set() : Set/Update attribute
_attr_rem() : Remove attribute
_attr_ladd() : Add list member to attribute
_attr_lrem() : Remove list member from attribute
Swagger:
https://api.firecloud.org/#!/Workspaces/updateAttributes
"""
headers = _fiss_agent_header({"Content-type": "application/json"})
uri = "{0}workspaces/{1}/{2}/updateAttributes".format(fcconfig.root_url,
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body = json.dumps(attrs)
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broadinstitute/fiss | firecloud/api.py | add_user_to_group | def add_user_to_group(group, role, email):
"""Add a user to a group the caller owns
Args:
group (str): Group name
role (str) : Role of user for group; either 'member' or 'admin'
email (str): Email of user or group to add
Swagger:
https://api.firecloud.org/#!/Groups/addUserToGroup
"""
uri = "groups/{0}/{1}/{2}".format(group, role, email)
return __put(uri) | python | def add_user_to_group(group, role, email):
"""Add a user to a group the caller owns
Args:
group (str): Group name
role (str) : Role of user for group; either 'member' or 'admin'
email (str): Email of user or group to add
Swagger:
https://api.firecloud.org/#!/Groups/addUserToGroup
"""
uri = "groups/{0}/{1}/{2}".format(group, role, email)
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broadinstitute/fiss | firecloud/api.py | remove_user_from_group | def remove_user_from_group(group, role, email):
"""Remove a user from a group the caller owns
Args:
group (str): Group name
role (str) : Role of user for group; either 'member' or 'admin'
email (str): Email of user or group to remove
Swagger:
https://api.firecloud.org/#!/Groups/removeUserFromGroup
"""
uri = "groups/{0}/{1}/{2}".format(group, role, email)
return __delete(uri) | python | def remove_user_from_group(group, role, email):
"""Remove a user from a group the caller owns
Args:
group (str): Group name
role (str) : Role of user for group; either 'member' or 'admin'
email (str): Email of user or group to remove
Swagger:
https://api.firecloud.org/#!/Groups/removeUserFromGroup
"""
uri = "groups/{0}/{1}/{2}".format(group, role, email)
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broadinstitute/fiss | plugins/dev_plugin.py | GDACFissfcPlugin.register_commands | def register_commands(self, subparsers):
"""
Add commands to a list of subparsers. This will be called by
Fissfc to add additional command targets from this plugin.
Each command added should follow the pattern:
parser = subparsers.add_parser('cmd', ...)
parser.add_argument(...)
...
parser.set_defaults(func=do_my_cmd)
where do_my_cmd is a function that takes one argument "args":
def do_my_cmd(args):
pass
"""
#print_("DEV PLUGIN: Loaded commands")
prsr = subparsers.add_parser(
'upload', description='Copy the file or directory into the given')
prsr.add_argument('workspace', help='Workspace name')
prsr.add_argument('source', help='File or directory to upload')
prsr.add_argument('-s', '--show', action='store_true',
help="Show the gsutil command, but don't run it")
dest_help = 'Destination relative to the bucket root. '
dest_help += 'If omitted the file will be placed in the root directory'
prsr.add_argument('-d', '--destination', help=dest_help)
prsr.set_defaults(func=upload) | python | def register_commands(self, subparsers):
"""
Add commands to a list of subparsers. This will be called by
Fissfc to add additional command targets from this plugin.
Each command added should follow the pattern:
parser = subparsers.add_parser('cmd', ...)
parser.add_argument(...)
...
parser.set_defaults(func=do_my_cmd)
where do_my_cmd is a function that takes one argument "args":
def do_my_cmd(args):
pass
"""
#print_("DEV PLUGIN: Loaded commands")
prsr = subparsers.add_parser(
'upload', description='Copy the file or directory into the given')
prsr.add_argument('workspace', help='Workspace name')
prsr.add_argument('source', help='File or directory to upload')
prsr.add_argument('-s', '--show', action='store_true',
help="Show the gsutil command, but don't run it")
dest_help = 'Destination relative to the bucket root. '
dest_help += 'If omitted the file will be placed in the root directory'
prsr.add_argument('-d', '--destination', help=dest_help)
prsr.set_defaults(func=upload) | [
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broadinstitute/fiss | firecloud/method.py | Method.new | def new(namespace, name, wdl, synopsis,
documentation=None, api_url=fapi.PROD_API_ROOT):
"""Create new FireCloud method.
If the namespace + name already exists, a new snapshot is created.
Args:
namespace (str): Method namespace for this method
name (str): Method name
wdl (file): WDL description
synopsis (str): Short description of task
documentation (file): Extra documentation for method
"""
r = fapi.update_workflow(namespace, name, synopsis,
wdl, documentation, api_url)
fapi._check_response_code(r, 201)
d = r.json()
return Method(namespace, name, d["snapshotId"]) | python | def new(namespace, name, wdl, synopsis,
documentation=None, api_url=fapi.PROD_API_ROOT):
"""Create new FireCloud method.
If the namespace + name already exists, a new snapshot is created.
Args:
namespace (str): Method namespace for this method
name (str): Method name
wdl (file): WDL description
synopsis (str): Short description of task
documentation (file): Extra documentation for method
"""
r = fapi.update_workflow(namespace, name, synopsis,
wdl, documentation, api_url)
fapi._check_response_code(r, 201)
d = r.json()
return Method(namespace, name, d["snapshotId"]) | [
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broadinstitute/fiss | firecloud/method.py | Method.template | def template(self):
"""Return a method template for this method."""
r = fapi.get_config_template(self.namespace, self.name,
self.snapshot_id, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | python | def template(self):
"""Return a method template for this method."""
r = fapi.get_config_template(self.namespace, self.name,
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fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/method.py | Method.inputs_outputs | def inputs_outputs(self):
"""Get information on method inputs & outputs."""
r = fapi.get_inputs_outputs(self.namespace, self.name,
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fapi._check_response_code(r, 200)
return r.json() | python | def inputs_outputs(self):
"""Get information on method inputs & outputs."""
r = fapi.get_inputs_outputs(self.namespace, self.name,
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broadinstitute/fiss | firecloud/method.py | Method.acl | def acl(self):
"""Get the access control list for this method."""
r = fapi.get_repository_method_acl(
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fapi._check_response_code(r, 200)
return r.json() | python | def acl(self):
"""Get the access control list for this method."""
r = fapi.get_repository_method_acl(
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fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/method.py | Method.set_acl | def set_acl(self, role, users):
"""Set permissions for this method.
Args:
role (str): Access level
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"""Set permissions for this method.
Args:
role (str): Access level
one of {one of "OWNER", "READER", "WRITER", "NO ACCESS"}
users (list(str)): List of users to give role to
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broadinstitute/fiss | firecloud/workspace.py | Workspace.new | def new(namespace, name, protected=False,
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"""Create a new FireCloud workspace.
Returns:
Workspace: A new FireCloud workspace
Raises:
FireCloudServerError: API call failed.
"""
r = fapi.create_workspace(namespace, name, protected, attributes, api_url)
fapi._check_response_code(r, 201)
return Workspace(namespace, name, api_url) | python | def new(namespace, name, protected=False,
attributes=dict(), api_url=fapi.PROD_API_ROOT):
"""Create a new FireCloud workspace.
Returns:
Workspace: A new FireCloud workspace
Raises:
FireCloudServerError: API call failed.
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r = fapi.create_workspace(namespace, name, protected, attributes, api_url)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.refresh | def refresh(self):
"""Reload workspace metadata from firecloud.
Workspace metadata is cached in the data attribute of a Workspace,
and may become stale, requiring a refresh().
"""
r = fapi.get_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
self.data = r.json()
return self | python | def refresh(self):
"""Reload workspace metadata from firecloud.
Workspace metadata is cached in the data attribute of a Workspace,
and may become stale, requiring a refresh().
"""
r = fapi.get_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
self.data = r.json()
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broadinstitute/fiss | firecloud/workspace.py | Workspace.delete | def delete(self):
"""Delete the workspace from FireCloud.
Note:
This action cannot be undone. Be careful!
"""
r = fapi.delete_workspace(self.namespace, self.name)
fapi._check_response_code(r, 202) | python | def delete(self):
"""Delete the workspace from FireCloud.
Note:
This action cannot be undone. Be careful!
"""
r = fapi.delete_workspace(self.namespace, self.name)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.lock | def lock(self):
"""Lock this Workspace.
This causes the workspace to behave in a read-only way,
regardless of access permissions.
"""
r = fapi.lock_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 204)
self.data['workspace']['isLocked'] = True
return self | python | def lock(self):
"""Lock this Workspace.
This causes the workspace to behave in a read-only way,
regardless of access permissions.
"""
r = fapi.lock_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 204)
self.data['workspace']['isLocked'] = True
return self | [
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broadinstitute/fiss | firecloud/workspace.py | Workspace.unlock | def unlock(self):
"""Unlock this Workspace."""
r = fapi.unlock_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 204)
self.data['workspace']['isLocked'] = False
return self | python | def unlock(self):
"""Unlock this Workspace."""
r = fapi.unlock_workspace(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 204)
self.data['workspace']['isLocked'] = False
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broadinstitute/fiss | firecloud/workspace.py | Workspace.update_attribute | def update_attribute(self, attr, value):
"""Set the value of a workspace attribute."""
update = [fapi._attr_up(attr, value)]
r = fapi.update_workspace_attributes(self.namespace, self.name,
update, self.api_url)
fapi._check_response_code(r, 200) | python | def update_attribute(self, attr, value):
"""Set the value of a workspace attribute."""
update = [fapi._attr_up(attr, value)]
r = fapi.update_workspace_attributes(self.namespace, self.name,
update, self.api_url)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.remove_attribute | def remove_attribute(self, attr):
"""Remove attribute from a workspace.
Args:
attr (str): attribute name
"""
update = [fapi._attr_rem(attr)]
r = fapi.update_workspace_attributes(self.namespace, self.name,
update, self.api_url)
self.data["workspace"]["attributes"].pop(attr, None)
fapi._check_response_code(r, 200) | python | def remove_attribute(self, attr):
"""Remove attribute from a workspace.
Args:
attr (str): attribute name
"""
update = [fapi._attr_rem(attr)]
r = fapi.update_workspace_attributes(self.namespace, self.name,
update, self.api_url)
self.data["workspace"]["attributes"].pop(attr, None)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.import_tsv | def import_tsv(self, tsv_file):
"""Upload entity data to workspace from tsv loadfile.
Args:
tsv_file (file): Tab-delimited file of entity data
"""
r = fapi.upload_entities_tsv(self.namespace, self.name,
self.tsv_file, self.api_url)
fapi._check_response_code(r, 201) | python | def import_tsv(self, tsv_file):
"""Upload entity data to workspace from tsv loadfile.
Args:
tsv_file (file): Tab-delimited file of entity data
"""
r = fapi.upload_entities_tsv(self.namespace, self.name,
self.tsv_file, self.api_url)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.get_entity | def get_entity(self, etype, entity_id):
"""Return entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
"""
r = fapi.get_entity(self.namespace, self.name, etype,
entity_id, self.api_url)
fapi._check_response_code(r, 200)
dresp = r.json()
return Entity(etype, entity_id, dresp['attributes']) | python | def get_entity(self, etype, entity_id):
"""Return entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
"""
r = fapi.get_entity(self.namespace, self.name, etype,
entity_id, self.api_url)
fapi._check_response_code(r, 200)
dresp = r.json()
return Entity(etype, entity_id, dresp['attributes']) | [
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broadinstitute/fiss | firecloud/workspace.py | Workspace.delete_entity | def delete_entity(self, etype, entity_id):
"""Delete an entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
"""
r = fapi.delete_entity(self.namespace, self.name, etype,
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fapi._check_response_code(r, 202) | python | def delete_entity(self, etype, entity_id):
"""Delete an entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
"""
r = fapi.delete_entity(self.namespace, self.name, etype,
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broadinstitute/fiss | firecloud/workspace.py | Workspace.import_entities | def import_entities(self, entities):
"""Upload entity objects.
Args:
entities: iterable of firecloud.Entity objects.
"""
edata = Entity.create_payload(entities)
r = fapi.upload_entities(self.namespace, self.name,
edata, self.api_url)
fapi._check_response_code(r, 201) | python | def import_entities(self, entities):
"""Upload entity objects.
Args:
entities: iterable of firecloud.Entity objects.
"""
edata = Entity.create_payload(entities)
r = fapi.upload_entities(self.namespace, self.name,
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broadinstitute/fiss | firecloud/workspace.py | Workspace.create_set | def create_set(self, set_id, etype, entities):
"""Create a set of entities and upload to FireCloud.
Args
etype (str): one of {"sample, "pair", "participant"}
entities: iterable of firecloud.Entity objects.
"""
if etype not in {"sample", "pair", "participant"}:
raise ValueError("Unsupported entity type:" + str(etype))
payload = "membership:" + etype + "_set_id\t" + etype + "_id\n"
for e in entities:
if e.etype != etype:
msg = "Entity type '" + e.etype + "' does not match "
msg += "set type '" + etype + "'"
raise ValueError(msg)
payload += set_id + '\t' + e.entity_id + '\n'
r = fapi.upload_entities(self.namespace, self.name,
payload, self.api_url)
fapi._check_response_code(r, 201) | python | def create_set(self, set_id, etype, entities):
"""Create a set of entities and upload to FireCloud.
Args
etype (str): one of {"sample, "pair", "participant"}
entities: iterable of firecloud.Entity objects.
"""
if etype not in {"sample", "pair", "participant"}:
raise ValueError("Unsupported entity type:" + str(etype))
payload = "membership:" + etype + "_set_id\t" + etype + "_id\n"
for e in entities:
if e.etype != etype:
msg = "Entity type '" + e.etype + "' does not match "
msg += "set type '" + etype + "'"
raise ValueError(msg)
payload += set_id + '\t' + e.entity_id + '\n'
r = fapi.upload_entities(self.namespace, self.name,
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broadinstitute/fiss | firecloud/workspace.py | Workspace.submissions | def submissions(self):
"""List job submissions in workspace."""
r = fapi.get_submissions(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | python | def submissions(self):
"""List job submissions in workspace."""
r = fapi.get_submissions(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.entity_types | def entity_types(self):
"""List entity types in workspace."""
r = fapi.get_entity_types(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
return r.json().keys() | python | def entity_types(self):
"""List entity types in workspace."""
r = fapi.get_entity_types(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/workspace.py | Workspace.entities | def entities(self):
"""List all entities in workspace."""
r = fapi.get_entities_with_type(self.namespace,
self.name, self.api_url)
fapi._check_response_code(r, 200)
edicts = r.json()
return [Entity(e['entityType'], e['name'], e['attributes'])
for e in edicts] | python | def entities(self):
"""List all entities in workspace."""
r = fapi.get_entities_with_type(self.namespace,
self.name, self.api_url)
fapi._check_response_code(r, 200)
edicts = r.json()
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broadinstitute/fiss | firecloud/workspace.py | Workspace.__get_entities | def __get_entities(self, etype):
"""Helper to get entities for a given type."""
r = fapi.get_entities(self.namespace, self.name,
etype, self.api_url)
fapi._check_response_code(r, 200)
return [Entity(e['entityType'], e['name'], e['attributes'])
for e in r.json()] | python | def __get_entities(self, etype):
"""Helper to get entities for a given type."""
r = fapi.get_entities(self.namespace, self.name,
etype, self.api_url)
fapi._check_response_code(r, 200)
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] | dddf91547479506dbbafb69ec84d44dcc4a94ab4 | https://github.com/broadinstitute/fiss/blob/dddf91547479506dbbafb69ec84d44dcc4a94ab4/firecloud/workspace.py#L235-L241 | train | 38,892 |
broadinstitute/fiss | firecloud/workspace.py | Workspace.copy_entities | def copy_entities(self, from_namespace, from_workspace, etype, enames):
"""Copy entities from another workspace.
Args:
from_namespace (str): Source workspace namespace
from_workspace (str): Source workspace name
etype (str): Entity type
enames (list(str)): List of entity names to copy
"""
r = fapi.copy_entities(from_namespace, from_workspace,
self.namespace, self.name, etype, enames,
self.api_url)
fapi._check_response_code(r, 201) | python | def copy_entities(self, from_namespace, from_workspace, etype, enames):
"""Copy entities from another workspace.
Args:
from_namespace (str): Source workspace namespace
from_workspace (str): Source workspace name
etype (str): Entity type
enames (list(str)): List of entity names to copy
"""
r = fapi.copy_entities(from_namespace, from_workspace,
self.namespace, self.name, etype, enames,
self.api_url)
fapi._check_response_code(r, 201) | [
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broadinstitute/fiss | firecloud/workspace.py | Workspace.configs | def configs(self):
"""Get method configurations in a workspace."""
raise NotImplementedError
r = fapi.get_configs(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
cdata = r.json()
configs = []
for c in cdata:
cnamespace = c['namespace']
cname = c['name']
root_etype = c['rootEntityType']
method_namespace = c['methodRepoMethod']['methodNamespace']
method_name = c['methodRepoMethod']['methodName']
method_version = c['methodRepoMethod']['methodVersion'] | python | def configs(self):
"""Get method configurations in a workspace."""
raise NotImplementedError
r = fapi.get_configs(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
cdata = r.json()
configs = []
for c in cdata:
cnamespace = c['namespace']
cname = c['name']
root_etype = c['rootEntityType']
method_namespace = c['methodRepoMethod']['methodNamespace']
method_name = c['methodRepoMethod']['methodName']
method_version = c['methodRepoMethod']['methodVersion'] | [
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broadinstitute/fiss | firecloud/workspace.py | Workspace.acl | def acl(self):
"""Get the access control list for this workspace."""
r = fapi.get_workspace_acl(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | python | def acl(self):
"""Get the access control list for this workspace."""
r = fapi.get_workspace_acl(self.namespace, self.name, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | [
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broadinstitute/fiss | firecloud/workspace.py | Workspace.clone | def clone(self, to_namespace, to_name):
"""Clone this workspace.
Args:
to_namespace (str): Target workspace namespace
to_name (str): Target workspace name
"""
r = fapi.clone_workspace(self.namespace, self.name,
to_namespace, to_name, self.api_url)
fapi._check_response_code(r, 201)
return Workspace(to_namespace, to_name, self.api_url) | python | def clone(self, to_namespace, to_name):
"""Clone this workspace.
Args:
to_namespace (str): Target workspace namespace
to_name (str): Target workspace name
"""
r = fapi.clone_workspace(self.namespace, self.name,
to_namespace, to_name, self.api_url)
fapi._check_response_code(r, 201)
return Workspace(to_namespace, to_name, self.api_url) | [
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broadinstitute/fiss | firecloud/supervisor.py | supervise | def supervise(project, workspace, namespace, workflow,
sample_sets, recovery_file):
""" Supervise submission of jobs from a Firehose-style workflow of workflows"""
# Get arguments
logging.info("Initializing FireCloud Supervisor...")
logging.info("Saving recovery checkpoints to " + recovery_file)
# Parse workflow description
# these three objects must be saved in order to recover the supervisor
args = {
'project' : project,
'workspace': workspace,
'namespace': namespace,
'workflow' : workflow,
'sample_sets': sample_sets
}
monitor_data, dependencies = init_supervisor_data(workflow, sample_sets)
recovery_data = {
'args' : args,
'monitor_data' : monitor_data,
'dependencies' : dependencies
}
# Monitor loop. Keep going until all nodes have been evaluated
supervise_until_complete(monitor_data, dependencies, args, recovery_file) | python | def supervise(project, workspace, namespace, workflow,
sample_sets, recovery_file):
""" Supervise submission of jobs from a Firehose-style workflow of workflows"""
# Get arguments
logging.info("Initializing FireCloud Supervisor...")
logging.info("Saving recovery checkpoints to " + recovery_file)
# Parse workflow description
# these three objects must be saved in order to recover the supervisor
args = {
'project' : project,
'workspace': workspace,
'namespace': namespace,
'workflow' : workflow,
'sample_sets': sample_sets
}
monitor_data, dependencies = init_supervisor_data(workflow, sample_sets)
recovery_data = {
'args' : args,
'monitor_data' : monitor_data,
'dependencies' : dependencies
}
# Monitor loop. Keep going until all nodes have been evaluated
supervise_until_complete(monitor_data, dependencies, args, recovery_file) | [
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broadinstitute/fiss | firecloud/supervisor.py | validate_monitor_tasks | def validate_monitor_tasks(dependencies, args):
""" Validate that all entries in the supervisor are valid task configurations and
that all permissions requirements are satisfied.
"""
# Make a list of all task configurations needed to supervise
sup_configs = sorted(dependencies.keys())
try:
logging.info("Validating supervisor data...")
# Make an api call to list task configurations in the workspace
r = fapi.list_workspace_configs(args['project'], args['workspace'])
fapi._check_response_code(r, 200)
space_configs = r.json()
# Make a dict for easy lookup later
space_configs = { c["name"]: c for c in space_configs}
# Also make an api call to list methods you have view permissions for
r = fapi.list_repository_methods()
fapi._check_response_code(r, 200)
repo_methods = r.json()
## Put in a form that is more easily searchable: namespace/name:snapshot
repo_methods = {m['namespace'] + '/' + m['name'] + ':' + str(m['snapshotId'])
for m in repo_methods if m['entityType'] == 'Workflow'}
valid = True
for config in sup_configs:
# ensure config exists in the workspace
if config not in space_configs:
logging.error("No task configuration for "
+ config + " found in " + args['project'] + "/"
+ args['workspace'])
valid = False
else:
# Check access permissions for the referenced method
m = space_configs[config]['methodRepoMethod']
ref_method = m['methodNamespace'] + "/" + m['methodName'] + ":" + str(m['methodVersion'])
if ref_method not in repo_methods:
logging.error(config+ " -- You don't have permisson to run the referenced method: "
+ ref_method)
valid = False
except Exception as e:
logging.error("Exception occurred while validating supervisor: " + str(e))
raise
return False
return valid | python | def validate_monitor_tasks(dependencies, args):
""" Validate that all entries in the supervisor are valid task configurations and
that all permissions requirements are satisfied.
"""
# Make a list of all task configurations needed to supervise
sup_configs = sorted(dependencies.keys())
try:
logging.info("Validating supervisor data...")
# Make an api call to list task configurations in the workspace
r = fapi.list_workspace_configs(args['project'], args['workspace'])
fapi._check_response_code(r, 200)
space_configs = r.json()
# Make a dict for easy lookup later
space_configs = { c["name"]: c for c in space_configs}
# Also make an api call to list methods you have view permissions for
r = fapi.list_repository_methods()
fapi._check_response_code(r, 200)
repo_methods = r.json()
## Put in a form that is more easily searchable: namespace/name:snapshot
repo_methods = {m['namespace'] + '/' + m['name'] + ':' + str(m['snapshotId'])
for m in repo_methods if m['entityType'] == 'Workflow'}
valid = True
for config in sup_configs:
# ensure config exists in the workspace
if config not in space_configs:
logging.error("No task configuration for "
+ config + " found in " + args['project'] + "/"
+ args['workspace'])
valid = False
else:
# Check access permissions for the referenced method
m = space_configs[config]['methodRepoMethod']
ref_method = m['methodNamespace'] + "/" + m['methodName'] + ":" + str(m['methodVersion'])
if ref_method not in repo_methods:
logging.error(config+ " -- You don't have permisson to run the referenced method: "
+ ref_method)
valid = False
except Exception as e:
logging.error("Exception occurred while validating supervisor: " + str(e))
raise
return False
return valid | [
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broadinstitute/fiss | firecloud/supervisor.py | recover_and_supervise | def recover_and_supervise(recovery_file):
""" Retrieve monitor data from recovery_file and resume monitoring """
try:
logging.info("Attempting to recover Supervisor data from " + recovery_file)
with open(recovery_file) as rf:
recovery_data = json.load(rf)
monitor_data = recovery_data['monitor_data']
dependencies = recovery_data['dependencies']
args = recovery_data['args']
except:
logging.error("Could not recover monitor data, exiting...")
return 1
logging.info("Data successfully loaded, resuming Supervisor")
supervise_until_complete(monitor_data, dependencies, args, recovery_file) | python | def recover_and_supervise(recovery_file):
""" Retrieve monitor data from recovery_file and resume monitoring """
try:
logging.info("Attempting to recover Supervisor data from " + recovery_file)
with open(recovery_file) as rf:
recovery_data = json.load(rf)
monitor_data = recovery_data['monitor_data']
dependencies = recovery_data['dependencies']
args = recovery_data['args']
except:
logging.error("Could not recover monitor data, exiting...")
return 1
logging.info("Data successfully loaded, resuming Supervisor")
supervise_until_complete(monitor_data, dependencies, args, recovery_file) | [
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