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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
... | 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
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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
mnamespa... | python | def rename_workspace_config(namespace, workspace, cnamespace, config,
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Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
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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
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namespace (str): project to which workspace belongs
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Args:
namespace (str): project to which workspace belongs
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broadinstitute/fiss | firecloud/api.py | list_repository_methods | 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... | python | 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
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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:
... | 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:
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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
... | 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
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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... | 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:
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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
Sw... | 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
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broadinstitute/fiss | firecloud/api.py | update_repository_method | 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
... | python | 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
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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 meth... | 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.
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namespace (str): Methods namespace
method (str): method name
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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... | 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
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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... | 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
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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_u... | python | def update_repository_method_acl(namespace, method, snapshot_id, acl_updates):
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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
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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
... | python | def get_repository_config_acl(namespace, config, snapshot_id):
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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
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broadinstitute/fiss | firecloud/api.py | update_repository_config_acl | def update_repository_config_acl(namespace, config, snapshot_id, acl_updates):
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The configuration should exist in the methods repository.
Args:
namespace (str): Configuration namespace
config (str): Configuration name
snapshot_id (int): snapshot_id ... | python | def update_repository_config_acl(namespace, config, snapshot_id, acl_updates):
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namespace (str): Configuration namespace
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Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
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namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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broadinstitute/fiss | firecloud/api.py | get_submission | def get_submission(namespace, workspace, submission_id):
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namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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broadinstitute/fiss | firecloud/api.py | get_workflow_metadata | def get_workflow_metadata(namespace, workspace, submission_id, workflow_id):
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namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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broadinstitute/fiss | firecloud/api.py | get_workflow_outputs | def get_workflow_outputs(namespace, workspace, submission_id, workflow_id):
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Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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namespace (str): project to which workspace belongs
workspace (str): Workspace name
submission_id (str): Submission's unique identifier
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broadinstitute/fiss | firecloud/api.py | create_workspace | def create_workspace(namespace, name, authorizationDomain="", attributes=None):
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Args:
namespace (str): project to which workspace belongs
name (str): Workspace name
protected (bool): If True, this workspace is protected by dbGaP
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namespace (str): project to which workspace belongs
name (str): Workspace name
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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):
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Args:
namespace (str): project to which workspace belongs
workspace (str): Workspace name
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namespace (str): project to which workspace belongs
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broadinstitute/fiss | firecloud/api.py | clone_workspace | def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
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"""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:
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broadinstitute/fiss | firecloud/api.py | update_workspace_attributes | def update_workspace_attributes(namespace, workspace, attrs):
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namespace (str): project to which workspace belongs
workspace (str): Workspace name
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broadinstitute/fiss | firecloud/api.py | add_user_to_group | def add_user_to_group(group, role, email):
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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:
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"""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
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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/#... | 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
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broadinstitute/fiss | plugins/dev_plugin.py | GDACFissfcPlugin.register_commands | def register_commands(self, subparsers):
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Add commands to a list of subparsers. This will be called by
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parser = subparsers.add_parser('cmd', ...)
parser.add_argum... | python | def register_commands(self, subparsers):
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broadinstitute/fiss | firecloud/method.py | Method.new | def new(namespace, name, wdl, synopsis,
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If the namespace + name already exists, a new snapshot is created.
Args:
namespace (str): Method namespace for this method
name (str): Me... | python | def new(namespace, name, wdl, synopsis,
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broadinstitute/fiss | firecloud/method.py | Method.template | def template(self):
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broadinstitute/fiss | firecloud/method.py | Method.inputs_outputs | def inputs_outputs(self):
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broadinstitute/fiss | firecloud/method.py | Method.acl | def acl(self):
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broadinstitute/fiss | firecloud/method.py | Method.set_acl | def set_acl(self, role, users):
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role (str): Access level
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Args:
role (str): Access level
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users (list(str)): List of users to give role to
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broadinstitute/fiss | firecloud/__init__.py | __ensure_gcloud | def __ensure_gcloud():
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directory for the executables exists, it is added to the PATH for the
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broadinstitute/fiss | firecloud/fccore.py | config_parse | def config_parse(files=None, config=None, config_profile=".fissconfig", **kwargs):
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Read initial configuration state, from named config files; store
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Read initial configuration state, from named config files; store
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broadinstitute/fiss | firecloud/workspace.py | Workspace.new | 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... | 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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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)
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"""Reload workspace metadata from firecloud.
Workspace metadata is cached in the data attribute of a Workspace,
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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']['isLock... | 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)
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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)
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"""Set the value of a workspace attribute."""
update = [fapi._attr_up(attr, value)]
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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.a... | python | def remove_attribute(self, attr):
"""Remove attribute from a workspace.
Args:
attr (str): attribute name
"""
update = [fapi._attr_rem(attr)]
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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)
... | 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,
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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)
... | 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,
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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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"""Delete an entity in this workspace.
Args:
etype (str): Entity type
entity_id (str): Entity name/unique id
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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,
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"""Upload entity objects.
Args:
entities: iterable of firecloud.Entity objects.
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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"}:
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"""Create a set of entities and upload to FireCloud.
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etype (str): one of {"sample, "pair", "participant"}
entities: iterable of firecloud.Entity objects.
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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'... | 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):
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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
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from_namespace (str): Source workspace namespace
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broadinstitute/fiss | firecloud/workspace.py | Workspace.configs | def configs(self):
"""Get method configurations in a workspace."""
raise NotImplementedError
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fapi._check_response_code(r, 200)
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"""Get method configurations in a workspace."""
raise NotImplementedError
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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)
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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,
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"""Clone this workspace.
Args:
to_namespace (str): Target workspace namespace
to_name (str): Target workspace name
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r = fapi.clone_workspace(self.namespace, self.name,
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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 " + recover... | 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...")
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broadinstitute/fiss | firecloud/supervisor.py | init_supervisor_data | def init_supervisor_data(dotfile, sample_sets):
""" Parse a workflow description written in DOT (like Firehose)"""
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graph_data = wf.read()
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""" Parse a workflow description written in DOT (like Firehose)"""
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graph_data = wf.read()
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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())
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""" Validate that all entries in the supervisor are valid task configurations and
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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)
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recovery_data = json.load(rf)
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""" Retrieve monitor data from recovery_file and resume monitoring """
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broadinstitute/fiss | firecloud/supervisor.py | supervise_until_complete | 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']
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broadinstitute/fiss | firecloud/fiss.py | space_list | 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... | python | def space_list(args):
''' List accessible workspaces, in TSV form: <namespace><TAB>workspace'''
r = fapi.list_workspaces()
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broadinstitute/fiss | firecloud/fiss.py | space_exists | 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
# ...
... | python | 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
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broadinstitute/fiss | firecloud/fiss.py | space_lock | 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 | python | 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))
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broadinstitute/fiss | firecloud/fiss.py | space_unlock | def space_unlock(args):
""" Unlock a workspace """
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""" Unlock a workspace """
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broadinstitute/fiss | firecloud/fiss.py | space_new | def space_new(args):
""" Create a new workspace. """
r = fapi.create_workspace(args.project, args.workspace,
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fapi._check_response_code(r, 201)
if fcconfig.verbosity:
eprint(r.content)
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broadinstitute/fiss | firecloud/fiss.py | space_info | 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 | python | def space_info(args):
""" Get metadata for a workspace. """
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broadinstitute/fiss | firecloud/fiss.py | space_delete | 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)
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""" 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)
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broadinstitute/fiss | firecloud/fiss.py | space_clone | 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
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args.to_project = args.project
... | python | def space_clone(args):
""" Replicate a workspace """
# FIXME: add --deep copy option (shallow by default)
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if not args.to_workspace:
args.to_workspace = args.workspace
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broadinstitute/fiss | firecloud/fiss.py | space_acl | 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 | python | 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']
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broadinstitute/fiss | firecloud/fiss.py | space_set_acl | 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)
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""" Assign an ACL role to list of users for a workspace """
acl_updates = [{"email": user,
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broadinstitute/fiss | firecloud/fiss.py | space_search | 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... | python | 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
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broadinstitute/fiss | firecloud/fiss.py | entity_import | 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... | python | 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]
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broadinstitute/fiss | firecloud/fiss.py | set_export | 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,... | python | def set_export(args):
'''Return a list of lines in TSV form that would suffice to reconstitute a
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the list is the header, and subsequent lines are the container members.
'''
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broadinstitute/fiss | firecloud/fiss.py | entity_types | 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() | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | entity_list | 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() ] | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | participant_list | 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... | python | 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':
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broadinstitute/fiss | firecloud/fiss.py | pair_list | 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':
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''' List pairs within a container. '''
# Case 1: retrieve pairs within a named data entity
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# Edge case: caller asked for pair within a pair (itself)
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broadinstitute/fiss | firecloud/fiss.py | sample_list | 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()... | python | def sample_list(args):
''' List samples within a container. '''
# Case 1: retrieve samples within a named data entity
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broadinstitute/fiss | firecloud/fiss.py | entity_delete | def entity_delete(args):
""" Delete entity in a workspace. """
msg = "WARNING: this will delete {0} {1} in {2}/{3}".format(
args.entity_type, args.entity, args.project, args.workspace)
if not (args.yes or _confirm_prompt(msg)):
return
json_body=[{"entityType": args.entity_type,
... | python | def entity_delete(args):
""" Delete entity in a workspace. """
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broadinstitute/fiss | firecloud/fiss.py | meth_new | def meth_new(args):
""" Submit a new workflow (or update) to the methods repository. """
r = fapi.update_repository_method(args.namespace, args.method,
args.synopsis, args.wdl, args.doc,
args.comment)
fapi._check_response_code(r, 20... | python | def meth_new(args):
""" Submit a new workflow (or update) to the methods repository. """
r = fapi.update_repository_method(args.namespace, args.method,
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args.comment)
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broadinstitute/fiss | firecloud/fiss.py | meth_delete | def meth_delete(args):
""" Remove (redact) a method from the method repository """
message = "WARNING: this will delete workflow \n\t{0}/{1}:{2}".format(
args.namespace, args.method, args.snapshot_id)
if not args.yes and not _confirm_prompt(message):
return
r... | python | def meth_delete(args):
""" Remove (redact) a method from the method repository """
message = "WARNING: this will delete workflow \n\t{0}/{1}:{2}".format(
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broadinstitute/fiss | firecloud/fiss.py | meth_wdl | def meth_wdl(args):
''' Retrieve WDL for given version of a repository method'''
r = fapi.get_repository_method(args.namespace, args.method,
args.snapshot_id, True)
fapi._check_response_code(r, 200)
return r.text | python | def meth_wdl(args):
''' Retrieve WDL for given version of a repository method'''
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broadinstitute/fiss | firecloud/fiss.py | meth_acl | def meth_acl(args):
''' Retrieve access control list for given version of a repository method'''
r = fapi.get_repository_method_acl(args.namespace, args.method,
args.snapshot_id)
fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/fiss.py | meth_set_acl | def meth_set_acl(args):
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# get the lat... | python | def meth_set_acl(args):
""" Assign an ACL role to a list of users for a workflow. """
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broadinstitute/fiss | firecloud/fiss.py | expand_fc_groups | def expand_fc_groups(users):
""" If user is a firecloud group, return all members of the group.
Caveat is that only group admins may do this.
"""
groups = None
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Caveat is that only group admins may do this.
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broadinstitute/fiss | firecloud/fiss.py | meth_list | def meth_list(args):
""" List workflows in the methods repository """
r = fapi.list_repository_methods(namespace=args.namespace,
name=args.method,
snapshotId=args.snapshot_id)
fapi._check_response_code(r, 200)
# Parse the JSON fo... | python | def meth_list(args):
""" List workflows in the methods repository """
r = fapi.list_repository_methods(namespace=args.namespace,
name=args.method,
snapshotId=args.snapshot_id)
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broadinstitute/fiss | firecloud/fiss.py | config_start | def config_start(args):
'''Invoke a task (method configuration), on given entity in given space'''
# Try to use call caching (job avoidance)? Flexibly accept range of answers
cache = getattr(args, "cache", True)
cache = cache is True or (cache.lower() in ["y", "true", "yes", "t", "1"])
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'''Invoke a task (method configuration), on given entity in given space'''
# Try to use call caching (job avoidance)? Flexibly accept range of answers
cache = getattr(args, "cache", True)
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broadinstitute/fiss | firecloud/fiss.py | config_stop | def config_stop(args):
'''Abort a task (method configuration) by submission ID in given space'''
r = fapi.abort_submission(args.project, args.workspace,
args.submission_id)
fapi._check_response_code(r, 204)
return ("Aborted {0} in {1}/{2}".format(args.submission_id,
... | python | def config_stop(args):
'''Abort a task (method configuration) by submission ID in given space'''
r = fapi.abort_submission(args.project, args.workspace,
args.submission_id)
fapi._check_response_code(r, 204)
return ("Aborted {0} in {1}/{2}".format(args.submission_id,
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broadinstitute/fiss | firecloud/fiss.py | config_list | def config_list(args):
""" List configuration(s) in the methods repository or a workspace. """
verbose = fcconfig.verbosity
if args.workspace:
if verbose:
print("Retrieving method configs from space {0}".format(args.workspace))
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""" List configuration(s) in the methods repository or a workspace. """
verbose = fcconfig.verbosity
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broadinstitute/fiss | firecloud/fiss.py | config_acl | def config_acl(args):
''' Retrieve access control list for a method configuration'''
r = fapi.get_repository_config_acl(args.namespace, args.config,
args.snapshot_id)
fapi._check_response_code(r, 200)
acls = sorted(r.json(), key=lambda k: k['user'])
... | python | def config_acl(args):
''' Retrieve access control list for a method configuration'''
r = fapi.get_repository_config_acl(args.namespace, args.config,
args.snapshot_id)
fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/fiss.py | config_set_acl | def config_set_acl(args):
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broadinstitute/fiss | firecloud/fiss.py | config_get | def config_get(args):
""" Retrieve a method config from a workspace, send stdout """
r = fapi.get_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, 200)
# Setting ensure_ascii to False ensures unicode string r... | python | def config_get(args):
""" Retrieve a method config from a workspace, send stdout """
r = fapi.get_workspace_config(args.project, args.workspace,
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fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/fiss.py | config_wdl | def config_wdl(args):
""" Retrieve the WDL for a method config in a workspace, send stdout """
r = fapi.get_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, 200)
method = r.json()["methodRepoMethod"]
args.... | python | def config_wdl(args):
""" Retrieve the WDL for a method config in a workspace, send stdout """
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broadinstitute/fiss | firecloud/fiss.py | config_diff | def config_diff(args):
"""Compare method configuration definitions across workspaces. Ignores
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config_1 = config_get(args).splitlines()
args.project = args.Project
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broadinstitute/fiss | firecloud/fiss.py | config_delete | def config_delete(args):
""" Remove a method config from a workspace """
r = fapi.delete_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, [200,204])
return r.text if r.text else None | python | def config_delete(args):
""" Remove a method config from a workspace """
r = fapi.delete_workspace_config(args.project, args.workspace,
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fapi._check_response_code(r, [200,204])
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broadinstitute/fiss | firecloud/fiss.py | config_copy | def config_copy(args):
""" Copy a method config to new name/space/namespace/project (or all 4) """
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"attribu... | train | https://github.com/broadinstitute/fiss/blob/dddf91547479506dbbafb69ec84d44dcc4a94ab4/firecloud/fiss.py#L815-L867 |
broadinstitute/fiss | firecloud/fiss.py | attr_list | def attr_list(args):
'''Retrieve names of all attributes attached to a given object, either
an entity (if entity type+name is provided) or workspace (if not)'''
args.attributes = None
result = attr_get(args)
names = result.get("__header__",[])
if names:
names = names[1:]
else:
... | python | def attr_list(args):
'''Retrieve names of all attributes attached to a given object, either
an entity (if entity type+name is provided) or workspace (if not)'''
args.attributes = None
result = attr_get(args)
names = result.get("__header__",[])
if names:
names = names[1:]
else:
... | [
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... | Retrieve names of all attributes attached to a given object, either
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