sentence1 stringlengths 52 3.87M | sentence2 stringlengths 1 47.2k | label stringclasses 1
value |
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def _find_files(directory):
"""
Find XML files in the directory
"""
pattern = "{directory}/*.xml".format(
directory=directory,
)
files = glob(pattern)
return files | Find XML files in the directory | entailment |
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_... | Gather scenarios to be displayed in the workbench | entailment |
def _set_session():
""" Sets global __SESSION and __USER_ID if they haven't been set """
global __SESSION
global __USER_ID
if __SESSION is None:
try:
__SESSION = AuthorizedSession(google.auth.default(['https://www.googleapis.com/auth/userinfo.profile',
... | Sets global __SESSION and __USER_ID if they haven't been set | entailment |
def _fiss_agent_header(headers=None):
""" Return request headers for fiss.
Inserts FISS as the User-Agent.
Initializes __SESSION if it hasn't been set.
Args:
headers (dict): Include additional headers as key-value pairs
"""
_set_session()
fiss_headers = {"User-Agent" : FIS... | Return request headers for fiss.
Inserts FISS as the User-Agent.
Initializes __SESSION if it hasn't been set.
Args:
headers (dict): Include additional headers as key-value pairs | entailment |
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)
... ... | 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 ... | entailment |
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_he... | 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 | entailment |
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.or... | 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 | entailment |
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 v... | 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
... | entailment |
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 worksp... | 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
... | entailment |
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://ap... | 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 | entailment |
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
... | 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/br... | entailment |
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
... | 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/ge... | entailment |
def delete_entities(namespace, workspace, json_body):
"""Delete entities in a workspace.
Note: This action is not reversible. Be careful!
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
json_body:
[
{
"entityTy... | Delete entities in a workspace.
Note: This action is not reversible. Be careful!
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
json_body:
[
{
"entityType": "string",
"entityName": "string"
}... | entailment |
def delete_entity_type(namespace, workspace, etype, ename):
"""Delete entities in a workspace.
Note: This action is not reversible. Be careful!
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str, or ... | Delete entities in a workspace.
Note: This action is not reversible. Be careful!
Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
etype (str): Entity type
ename (str, or iterable of str): unique entity id(s)
Swagger:
https:/... | entailment |
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... | 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 | entailment |
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 (lis... | 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:
... | entailment |
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/listWorkspaceMethodCon... | 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/listWorks... | entailment |
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... | 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:
htt... | entailment |
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... | 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/deleteWorkspaceMe... | entailment |
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:
... | 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/getWorkspaceMethodCo... | entailment |
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
config... | 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 metho... | entailment |
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): C... | 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
... | entailment |
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
... | 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/va... | entailment |
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
mnamespa... | 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 ... | entailment |
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
... | 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... | entailment |
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
fr... | 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): ... | entailment |
def list_repository_methods(namespace=None, name=None, snapshotId=None):
"""List method(s) in the methods repository.
Args:
namespace (str): Method Repository namespace
name (str): method name
snapshotId (int): method snapshot ID
Swagger:
https://api.firecloud.org/#!/Method... | List method(s) in the methods repository.
Args:
namespace (str): Method Repository namespace
name (str): method name
snapshotId (int): method snapshot ID
Swagger:
https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryMethods | entailment |
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:
... | 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/createMethod... | entailment |
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
... | 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_Reposit... | entailment |
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... | 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 | entailment |
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
Sw... | 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_name... | entailment |
def update_repository_method(namespace, method, synopsis, wdl, doc=None,
comment=""):
"""Create/Update workflow definition.
FireCloud will create a new snapshot_id for the given workflow.
Args:
namespace (str): Methods namespace
method (str): method name
... | Create/Update workflow definition.
FireCloud will create a new snapshot_id for the given workflow.
Args:
namespace (str): Methods namespace
method (str): method name
synopsis (str): short (<80 char) description of method
wdl (file): Workflow Description Language file
do... | entailment |
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 meth... | 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_Reposi... | entailment |
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... | 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:
h... | entailment |
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... | 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 | entailment |
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_u... | 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.... | entailment |
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
... | 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/get... | entailment |
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 ... | 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
Sw... | entailment |
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): M... | 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 typ... | entailment |
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/#... | 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 | entailment |
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/#!/Su... | 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 | entailment |
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
work... | 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.firec... | entailment |
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
workfl... | 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.firecl... | entailment |
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
credentia... | 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 yo... | entailment |
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:
... | 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", "WRI... | entailment |
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_nam... | 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
t... | entailment |
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 h... | 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:
... | entailment |
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/addU... | 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 | entailment |
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/#... | 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 | entailment |
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_argum... | 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_c... | entailment |
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): Me... | 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
... | entailment |
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() | Return a method template for this method. | entailment |
def inputs_outputs(self):
"""Get information on method inputs & outputs."""
r = fapi.get_inputs_outputs(self.namespace, self.name,
self.snapshot_id, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | Get information on method inputs & outputs. | entailment |
def acl(self):
"""Get the access control list for this method."""
r = fapi.get_repository_method_acl(
self.namespace, self.name, self.snapshot_id, self.api_url)
fapi._check_response_code(r, 200)
return r.json() | Get the access control list for this method. | entailment |
def set_acl(self, role, users):
"""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
"""
acl_updates = [{"user": user, "role": ... | 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 | entailment |
def __ensure_gcloud():
"""The *NIX installer is not guaranteed to add the google cloud sdk to the
user's PATH (the Windows installer does). This ensures that if the default
directory for the executables exists, it is added to the PATH for the
duration of this package's use."""
if which('gcloud') is ... | The *NIX installer is not guaranteed to add the google cloud sdk to the
user's PATH (the Windows installer does). This ensures that if the default
directory for the executables exists, it is added to the PATH for the
duration of this package's use. | entailment |
def config_parse(files=None, config=None, config_profile=".fissconfig", **kwargs):
'''
Read initial configuration state, from named config files; store
this state within a config dictionary (which may be nested) whose keys may
also be referenced as attributes (safely, defaulting to None if unset). A
... | Read initial configuration state, from named config files; store
this state within a config dictionary (which may be nested) whose keys may
also be referenced as attributes (safely, defaulting to None if unset). A
config object may be passed in, as a way of accumulating or overwriting
configuration sta... | entailment |
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.
"""
r = fapi.create_wo... | Create a new FireCloud workspace.
Returns:
Workspace: A new FireCloud workspace
Raises:
FireCloudServerError: API call failed. | entailment |
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... | Reload workspace metadata from firecloud.
Workspace metadata is cached in the data attribute of a Workspace,
and may become stale, requiring a refresh(). | entailment |
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) | Delete the workspace from FireCloud.
Note:
This action cannot be undone. Be careful! | entailment |
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']['isLock... | Lock this Workspace.
This causes the workspace to behave in a read-only way,
regardless of access permissions. | entailment |
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 | Unlock this Workspace. | entailment |
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... | Set the value of a workspace attribute. | entailment |
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.a... | Remove attribute from a workspace.
Args:
attr (str): attribute name | entailment |
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)
... | Upload entity data to workspace from tsv loadfile.
Args:
tsv_file (file): Tab-delimited file of entity data | entailment |
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)
... | Return entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id | entailment |
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,
entity_id, self.... | Delete an entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id | entailment |
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)
... | Upload entity objects.
Args:
entities: iterable of firecloud.Entity objects. | entailment |
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"}:
... | Create a set of entities and upload to FireCloud.
Args
etype (str): one of {"sample, "pair", "participant"}
entities: iterable of firecloud.Entity objects. | entailment |
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() | List job submissions in workspace. | entailment |
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() | List entity types in workspace. | entailment |
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'... | List all entities in workspace. | entailment |
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'])
... | Helper to get entities for a given type. | entailment |
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))... | 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 | entailment |
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['n... | Get method configurations in a workspace. | entailment |
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() | Get the access control list for this workspace. | entailment |
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_na... | Clone this workspace.
Args:
to_namespace (str): Target workspace namespace
to_name (str): Target workspace name | entailment |
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 " + recover... | Supervise submission of jobs from a Firehose-style workflow of workflows | entailment |
def init_supervisor_data(dotfile, sample_sets):
""" Parse a workflow description written in DOT (like Firehose)"""
with open(dotfile) as wf:
graph_data = wf.read()
graph = pydot.graph_from_dot_data(graph_data)[0]
nodes = [n.get_name().strip('"') for n in graph.get_nodes()]
monitor_data = d... | Parse a workflow description written in DOT (like Firehose) | entailment |
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:... | Validate that all entries in the supervisor are valid task configurations and
that all permissions requirements are satisfied. | entailment |
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 = r... | Retrieve monitor data from recovery_file and resume monitoring | entailment |
def supervise_until_complete(monitor_data, dependencies, args, recovery_file):
""" Supervisor loop. Loop forever until all tasks are evaluated or completed """
project = args['project']
workspace = args['workspace']
namespace = args['namespace']
sample_sets = args['sample_sets']
recovery_data = ... | Supervisor loop. Loop forever until all tasks are evaluated or completed | entailment |
def space_list(args):
''' List accessible workspaces, in TSV form: <namespace><TAB>workspace'''
r = fapi.list_workspaces()
fapi._check_response_code(r, 200)
spaces = []
project = args.project
if project:
project = re.compile('^' + project)
for space in r.json():
ns = space... | List accessible workspaces, in TSV form: <namespace><TAB>workspace | entailment |
def space_exists(args):
""" Determine if the named space exists in the given project (namespace)"""
# The return value is the INVERSE of UNIX exit status semantics, (where
# 0 = good/true, 1 = bad/false), so to check existence in UNIX one would do
# if ! fissfc space_exists blah ; then
# ...
... | Determine if the named space exists in the given project (namespace) | entailment |
def space_lock(args):
""" Lock a workspace """
r = fapi.lock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Locked workspace {0}/{1}'.format(args.project, args.workspace))
return 0 | Lock a workspace | entailment |
def space_unlock(args):
""" Unlock a workspace """
r = fapi.unlock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Unlocked workspace {0}/{1}'.format(args.project,args.workspace))
return 0 | Unlock a workspace | entailment |
def space_new(args):
""" Create a new workspace. """
r = fapi.create_workspace(args.project, args.workspace,
args.authdomain, dict())
fapi._check_response_code(r, 201)
if fcconfig.verbosity:
eprint(r.content)
return 0 | Create a new workspace. | entailment |
def space_info(args):
""" Get metadata for a workspace. """
r = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.text | Get metadata for a workspace. | entailment |
def space_delete(args):
""" Delete a workspace. """
message = "WARNING: this will delete workspace: \n\t{0}/{1}".format(
args.project, args.workspace)
if not args.yes and not _confirm_prompt(message):
return 0
r = fapi.delete_workspace(args.project, args.workspace)
fapi._check_respo... | Delete a workspace. | entailment |
def space_clone(args):
""" Replicate a workspace """
# FIXME: add --deep copy option (shallow by default)
# add aliasing capability, then make space_copy alias
if not args.to_workspace:
args.to_workspace = args.workspace
if not args.to_project:
args.to_project = args.project
... | Replicate a workspace | entailment |
def space_acl(args):
''' Retrieve access control list for a workspace'''
r = fapi.get_workspace_acl(args.project, args.workspace)
fapi._check_response_code(r, 200)
result = dict()
for user, info in sorted(r.json()['acl'].items()):
result[user] = info['accessLevel']
return result | Retrieve access control list for a workspace | entailment |
def space_set_acl(args):
""" Assign an ACL role to list of users for a workspace """
acl_updates = [{"email": user,
"accessLevel": args.role} for user in args.users]
r = fapi.update_workspace_acl(args.project, args.workspace, acl_updates)
fapi._check_response_code(r, 200)
errors =... | Assign an ACL role to list of users for a workspace | entailment |
def space_search(args):
""" Search for workspaces matching certain criteria """
r = fapi.list_workspaces()
fapi._check_response_code(r, 200)
# Parse the JSON for workspace + namespace; then filter by
# search terms: each term is treated as a regular expression
workspaces = r.json()
extra_te... | Search for workspaces matching certain criteria | entailment |
def entity_import(args):
""" Upload an entity loadfile. """
project = args.project
workspace = args.workspace
chunk_size = args.chunk_size
with open(args.tsvfile) as tsvf:
headerline = tsvf.readline().strip()
entity_data = [l.rstrip('\n') for l in tsvf]
return _batch_load(proje... | Upload an entity loadfile. | entailment |
def set_export(args):
'''Return a list of lines in TSV form that would suffice to reconstitute a
container (set) entity, if passed to entity_import. The first line in
the list is the header, and subsequent lines are the container members.
'''
r = fapi.get_entity(args.project, args.workspace,... | Return a list of lines in TSV form that would suffice to reconstitute a
container (set) entity, if passed to entity_import. The first line in
the list is the header, and subsequent lines are the container members. | entailment |
def entity_types(args):
""" List entity types in a workspace """
r = fapi.list_entity_types(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.json().keys() | List entity types in a workspace | entailment |
def entity_list(args):
""" List entities in a workspace. """
r = fapi.get_entities_with_type(args.project, args.workspace)
fapi._check_response_code(r, 200)
return [ '{0}\t{1}'.format(e['entityType'], e['name']) for e in r.json() ] | List entities in a workspace. | entailment |
def participant_list(args):
''' List participants within a container'''
# Case 1: retrieve participants within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for participant within participant (itself)
if args.entity_type == 'participant':
ret... | List participants within a container | entailment |
def pair_list(args):
''' List pairs within a container. '''
# Case 1: retrieve pairs within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for pair within a pair (itself)
if args.entity_type == 'pair':
return [ args.entity.strip() ]
# ... | List pairs within a container. | entailment |
def sample_list(args):
''' List samples within a container. '''
# Case 1: retrieve samples within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for samples within a sample (itself)
if args.entity_type == 'sample':
return [ args.entity.strip()... | List samples within a container. | entailment |
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