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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.add_tags | def add_tags(self, tags, **kwargs):
"""
:param tags: Tags to add to the job
:type tags: list of strings
Adds each of the specified tags to the job. Takes no
action for tags that are already listed for the job.
"""
dxpy.api.job_add_tags(self._dxid, {"tags": tags... | python | def add_tags(self, tags, **kwargs):
"""
:param tags: Tags to add to the job
:type tags: list of strings
Adds each of the specified tags to the job. Takes no
action for tags that are already listed for the job.
"""
dxpy.api.job_add_tags(self._dxid, {"tags": tags... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.remove_tags | def remove_tags(self, tags, **kwargs):
"""
:param tags: Tags to remove from the job
:type tags: list of strings
Removes each of the specified tags from the job. Takes
no action for tags that the job does not currently have.
"""
dxpy.api.job_remove_tags(self._dx... | python | def remove_tags(self, tags, **kwargs):
"""
:param tags: Tags to remove from the job
:type tags: list of strings
Removes each of the specified tags from the job. Takes
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.set_properties | def set_properties(self, properties, **kwargs):
"""
:param properties: Property names and values given as key-value pairs of strings
:type properties: dict
Given key-value pairs in *properties* for property names and
values, the properties are set on the job for the given
... | python | def set_properties(self, properties, **kwargs):
"""
:param properties: Property names and values given as key-value pairs of strings
:type properties: dict
Given key-value pairs in *properties* for property names and
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.wait_on_done | def wait_on_done(self, interval=2, timeout=3600*24*7, **kwargs):
'''
:param interval: Number of seconds between queries to the job's state
:type interval: integer
:param timeout: Maximum amount of time to wait, in seconds, until the job is done running
:type timeout: integer
... | python | def wait_on_done(self, interval=2, timeout=3600*24*7, **kwargs):
'''
:param interval: Number of seconds between queries to the job's state
:type interval: integer
:param timeout: Maximum amount of time to wait, in seconds, until the job is done running
:type timeout: integer
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob._get_state | def _get_state(self, **kwargs):
'''
:returns: State of the remote object
:rtype: string
Queries the API server for the job's state.
Note that this function is shorthand for:
dxjob.describe(io=False, **kwargs)["state"]
'''
return self.describe(fiel... | python | def _get_state(self, **kwargs):
'''
:returns: State of the remote object
:rtype: string
Queries the API server for the job's state.
Note that this function is shorthand for:
dxjob.describe(io=False, **kwargs)["state"]
'''
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dnanexus/dx-toolkit | src/python/dxpy/cli/org.py | get_user_id | def get_user_id(user_id_or_username):
"""Gets the user ID based on the value `user_id_or_username` specified on
the command-line, being extra lenient and lowercasing the value in all
cases.
"""
user_id_or_username = user_id_or_username.lower()
if not user_id_or_username.startswith("user-"):
... | python | def get_user_id(user_id_or_username):
"""Gets the user ID based on the value `user_id_or_username` specified on
the command-line, being extra lenient and lowercasing the value in all
cases.
"""
user_id_or_username = user_id_or_username.lower()
if not user_id_or_username.startswith("user-"):
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dnanexus/dx-toolkit | src/python/dxpy/cli/org.py | get_org_invite_args | def get_org_invite_args(user_id, args):
"""
Used by:
- `dx new user`
- `dx add member`
PRECONDITION:
- If /org-x/invite is being called in conjunction with /user/new, then
`_validate_new_user_input()` has been called on `args`; otherwise,
the parser must perform ... | python | def get_org_invite_args(user_id, args):
"""
Used by:
- `dx new user`
- `dx add member`
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- If /org-x/invite is being called in conjunction with /user/new, then
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dnanexus/dx-toolkit | src/python/dxpy/scripts/dx.py | _get_user_new_args | def _get_user_new_args(args):
"""
PRECONDITION: `_validate_new_user_input()` has been called on `args`.
"""
user_new_args = {"username": args.username,
"email": args.email}
if args.first is not None:
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if args.last is not None:
... | python | def _get_user_new_args(args):
"""
PRECONDITION: `_validate_new_user_input()` has been called on `args`.
"""
user_new_args = {"username": args.username,
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dnanexus/dx-toolkit | src/python/dxpy/scripts/dx.py | _get_input_for_run | def _get_input_for_run(args, executable, preset_inputs=None, input_name_prefix=None):
"""
Returns an input dictionary that can be passed to executable.run()
"""
# The following may throw if the executable is a workflow with no
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exec_inputs ... | python | def _get_input_for_run(args, executable, preset_inputs=None, input_name_prefix=None):
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Returns an input dictionary that can be passed to executable.run()
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dnanexus/dx-toolkit | src/python/dxpy/scripts/dx.py | register_parser | def register_parser(parser, subparsers_action=None, categories=('other', ), add_help=True):
"""Attaches `parser` to the global ``parser_map``. If `add_help` is truthy,
then adds the helpstring of `parser` into the output of ``dx help...``, for
each category in `categories`.
:param subparsers_action: A ... | python | def register_parser(parser, subparsers_action=None, categories=('other', ), add_help=True):
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | _is_retryable_exception | def _is_retryable_exception(e):
"""Returns True if the exception is always safe to retry.
This is True if the client was never able to establish a connection
to the server (for example, name resolution failed or the connection
could otherwise not be initialized).
Conservatively, if we can't tell w... | python | def _is_retryable_exception(e):
"""Returns True if the exception is always safe to retry.
This is True if the client was never able to establish a connection
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | _extract_msg_from_last_exception | def _extract_msg_from_last_exception():
''' Extract a useful error message from the last thrown exception '''
last_exc_type, last_error, last_traceback = sys.exc_info()
if isinstance(last_error, exceptions.DXAPIError):
# Using the same code path as below would not
# produce a useful message ... | python | def _extract_msg_from_last_exception():
''' Extract a useful error message from the last thrown exception '''
last_exc_type, last_error, last_traceback = sys.exc_info()
if isinstance(last_error, exceptions.DXAPIError):
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | _calculate_retry_delay | def _calculate_retry_delay(response, num_attempts):
'''
Returns the time in seconds that we should wait.
:param num_attempts: number of attempts that have been made to the
resource, including the most recent failed one
:type num_attempts: int
'''
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | DXHTTPRequest | def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
timeout=DEFAULT_TIMEOUT,
use_compression=None, jsonify_data=True, want_full_response=False,
decode_response_body=True, prepend_srv=True, session_handler=None,
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timeout=DEFAULT_TIMEOUT,
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | set_api_server_info | def set_api_server_info(host=None, port=None, protocol=None):
'''
:param host: API server hostname
:type host: string
:param port: API server port. If not specified, *port* is guessed based on *protocol*.
:type port: string
:param protocol: Either "http" or "https"
:type protocol: string
... | python | def set_api_server_info(host=None, port=None, protocol=None):
'''
:param host: API server hostname
:type host: string
:param port: API server port. If not specified, *port* is guessed based on *protocol*.
:type port: string
:param protocol: Either "http" or "https"
:type protocol: string
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | get_auth_server_name | def get_auth_server_name(host_override=None, port_override=None, protocol='https'):
"""
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Raises DXError if the auth server name cannot be guessed and the overrides
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | append_underlying_workflow_describe | def append_underlying_workflow_describe(globalworkflow_desc):
"""
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workflow in that region.
"""
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"""
Adds the "workflowDescribe" field to the config for each region of
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dnanexus/dx-toolkit | src/python/dxpy/cli/exec_io.py | _construct_jbor | def _construct_jbor(job_id, field_name_and_maybe_index):
'''
:param job_id: Job ID
:type job_id: string
:param field_name_and_maybe_index: Field name, plus possibly ".N" where N is an array index
:type field_name_and_maybe_index: string
:returns: dict of JBOR
'''
link = {"$dnanexus_link"... | python | def _construct_jbor(job_id, field_name_and_maybe_index):
'''
:param job_id: Job ID
:type job_id: string
:param field_name_and_maybe_index: Field name, plus possibly ".N" where N is an array index
:type field_name_and_maybe_index: string
:returns: dict of JBOR
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dnanexus/dx-toolkit | src/python/dxpy/cli/exec_io.py | ExecutableInputs.update | def update(self, new_inputs, strip_prefix=True):
"""
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"""
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dnanexus/dx-toolkit | src/python/dxpy/cli/exec_io.py | ExecutableInputs._update_requires_resolution_inputs | def _update_requires_resolution_inputs(self):
"""
Updates self.inputs with resolved input values (the input values that were provided
as paths to items that require resolutions, eg. folder or job/analyses ids)
"""
input_paths = [quad[1] for quad in self.requires_resolution]
... | python | def _update_requires_resolution_inputs(self):
"""
Updates self.inputs with resolved input values (the input values that were provided
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"""
input_paths = [quad[1] for quad in self.requires_resolution]
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dnanexus/dx-toolkit | src/python/dxpy/utils/pretty_print.py | escape_unicode_string | def escape_unicode_string(u):
"""
Escapes the nonprintable chars 0-31 and 127, and backslash;
preferably with a friendly equivalent such as '\n' if available, but
otherwise with a Python-style backslashed hex escape.
"""
def replacer(matchobj):
if ord(matchobj.group(1)) == 127:
... | python | def escape_unicode_string(u):
"""
Escapes the nonprintable chars 0-31 and 127, and backslash;
preferably with a friendly equivalent such as '\n' if available, but
otherwise with a Python-style backslashed hex escape.
"""
def replacer(matchobj):
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dnanexus/dx-toolkit | src/python/dxpy/utils/pretty_print.py | format_tree | def format_tree(tree, root=None):
''' Tree pretty printer.
Expects trees to be given as mappings (dictionaries). Keys will be printed; values will be traversed if they are
mappings. To preserve order, use collections.OrderedDict.
Example:
print format_tree(collections.OrderedDict({'foo': 0, 'b... | python | def format_tree(tree, root=None):
''' Tree pretty printer.
Expects trees to be given as mappings (dictionaries). Keys will be printed; values will be traversed if they are
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dnanexus/dx-toolkit | src/python/dxpy/utils/pretty_print.py | format_table | def format_table(table, column_names=None, column_specs=None, max_col_width=32,
report_dimensions=False):
''' Table pretty printer.
Expects tables to be given as arrays of arrays.
Example:
print format_table([[1, "2"], [3, "456"]], column_names=['A', 'B'])
'''
if len(tabl... | python | def format_table(table, column_names=None, column_specs=None, max_col_width=32,
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''' Table pretty printer.
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dnanexus/dx-toolkit | src/python/dxpy/utils/pretty_print.py | flatten_json_array | def flatten_json_array(json_string, array_name):
"""
Flattens all arrays with the same name in the JSON string
:param json_string: JSON string
:type json_string: str
:param array_name: Array name to flatten
:type array_name: str
"""
result = re.sub('"{}": \\[\r?\n\\s*'.format(array_nam... | python | def flatten_json_array(json_string, array_name):
"""
Flattens all arrays with the same name in the JSON string
:param json_string: JSON string
:type json_string: str
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | new_dxworkflow | def new_dxworkflow(title=None, summary=None, description=None, output_folder=None, init_from=None, **kwargs):
'''
:param title: Workflow title (optional)
:type title: string
:param summary: Workflow summary (optional)
:type summary: string
:param description: Workflow description (optional)
... | python | def new_dxworkflow(title=None, summary=None, description=None, output_folder=None, init_from=None, **kwargs):
'''
:param title: Workflow title (optional)
:type title: string
:param summary: Workflow summary (optional)
:type summary: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow._new | def _new(self, dx_hash, **kwargs):
"""
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:param title: Workflow title (optional)
:type title: string
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow._get_stage_id | def _get_stage_id(self, stage):
'''
:param stage: A stage ID, name, or index (stage index is the number n for the nth stage, starting from 0; can be provided as an int or a string)
:type stage: int or string
:returns: The stage ID (this is a no-op if it was already a stage ID)
:r... | python | def _get_stage_id(self, stage):
'''
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.get_stage | def get_stage(self, stage, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.update | def update(self, title=None, unset_title=False, summary=None, description=None,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow._get_input_name | def _get_input_name(self, input_str, region=None, describe_output=None):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.run | def run(self, workflow_input, *args, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/utils/completer.py | get_folder_matches | def get_folder_matches(text, delim_pos, dxproj, folderpath):
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dnanexus/dx-toolkit | src/python/dxpy/utils/completer.py | get_data_matches | def get_data_matches(text, delim_pos, dxproj, folderpath, classname=None,
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dnanexus/dx-toolkit | src/python/dxpy/utils/completer.py | path_completer | def path_completer(text, expected=None, classes=None, perm_level=None,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | verify_string_dxid | def verify_string_dxid(dxid, expected_classes):
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:param expected_classes: Single string or list of strings of allowed classes of the ID, e.g. "file" or ["project", "container"]
:type expected_classes: string or list of strings
... | python | def verify_string_dxid(dxid, expected_classes):
'''
:param dxid: Value to verify as a DNAnexus ID of class *expected_class*
:param expected_classes: Single string or list of strings of allowed classes of the ID, e.g. "file" or ["project", "container"]
:type expected_classes: string or list of strings
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXObject.set_id | def set_id(self, dxid):
'''
:param dxid: New ID to be associated with the handler
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
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self._dxid = d... | python | def set_id(self, dxid):
'''
:param dxid: New ID to be associated with the handler
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.new | def new(self, **kwargs):
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:param project: Project ID in which to create the new remote object
:type project: string
:param name: Name for the object
:type name: string
:param tags: Tags to add for the object
:type tags: list of strings
:param types: Typ... | python | def new(self, **kwargs):
'''
:param project: Project ID in which to create the new remote object
:type project: string
:param name: Name for the object
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.set_ids | def set_ids(self, dxid, project=None):
'''
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:type dxid: string or dict
:param project: ... | python | def set_ids(self, dxid, project=None):
'''
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.describe | def describe(self, incl_properties=False, incl_details=False, fields=None, default_fields=None, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.add_types | def add_types(self, types, **kwargs):
"""
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:type types: list of strings
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
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action f... | python | def add_types(self, types, **kwargs):
"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.remove_types | def remove_types(self, types, **kwargs):
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:type types: list of strings
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
Removes each the specified types from the remote object. Takes
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.set_details | def set_details(self, details, **kwargs):
"""
:param details: Details to set for the object
:type details: dict or list
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
Sets the details for the remote object with the specified value.
... | python | def set_details(self, details, **kwargs):
"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.rename | def rename(self, name, **kwargs):
"""
:param name: New name for the object
:type name: string
Renames the remote object.
The name is changed on the copy of the object in the project
associated with the handler.
"""
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"""
:param name: New name for the object
:type name: string
Renames the remote object.
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.set_properties | def set_properties(self, properties, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.add_tags | def add_tags(self, tags, **kwargs):
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:type tags: list of strings
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.remove_tags | def remove_tags(self, tags, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.remove | def remove(self, **kwargs):
'''
:raises: :exc:`~dxpy.exceptions.DXError` if no project is associated with the object
Permanently removes the associated remote object from the
associated project.
'''
if self._proj is None:
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'''
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.move | def move(self, folder, **kwargs):
'''
:param folder: Folder route to which to move the object
:type folder: string
:raises: :exc:`~dxpy.exceptions.DXError` if no project is associated with the object
Moves the associated remote object to *folder*.
'''
if self._... | python | def move(self, folder, **kwargs):
'''
:param folder: Folder route to which to move the object
:type folder: string
:raises: :exc:`~dxpy.exceptions.DXError` if no project is associated with the object
Moves the associated remote object to *folder*.
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.clone | def clone(self, project, folder="/", **kwargs):
'''
:param project: Destination project ID
:type project: string
:param folder: Folder route to which to move the object
:type folder: string
:raises: :exc:`~dxpy.exceptions.DXError` if no project is associated with the obje... | python | def clone(self, project, folder="/", **kwargs):
'''
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:type project: string
:param folder: Folder route to which to move the object
:type folder: string
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dnanexus/dx-toolkit | src/python/dxpy/utils/config.py | DXConfig.get_session_conf_dir | def get_session_conf_dir(self, cleanup=False):
"""
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where <PID> is pid of the parent of this process, then its parent, and so on.
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxdataobject_functions.py | dxlink | def dxlink(object_id, project_id=None, field=None):
'''
:param object_id: Object ID or the object handler itself
:type object_id: string or :class:`~dxpy.bindings.DXDataObject`
:param project_id: A project ID, if creating a cross-project DXLink
:type project_id: string
:param field: A field name... | python | def dxlink(object_id, project_id=None, field=None):
'''
:param object_id: Object ID or the object handler itself
:type object_id: string or :class:`~dxpy.bindings.DXDataObject`
:param project_id: A project ID, if creating a cross-project DXLink
:type project_id: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxdataobject_functions.py | is_dxlink | def is_dxlink(x):
'''
:param x: A potential DNAnexus link
Returns whether *x* appears to be a DNAnexus link (is a dict with
key ``"$dnanexus_link"``) with a referenced data object.
'''
if not isinstance(x, dict):
return False
if '$dnanexus_link' not in x:
return False
li... | python | def is_dxlink(x):
'''
:param x: A potential DNAnexus link
Returns whether *x* appears to be a DNAnexus link (is a dict with
key ``"$dnanexus_link"``) with a referenced data object.
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxdataobject_functions.py | get_dxlink_ids | def get_dxlink_ids(link):
'''
:param link: A DNAnexus link
:type link: dict
:returns: (Object ID, Project ID) if the link is to a data object (or :const:`None`
if no project specified in the link), or (Job ID, Field) if the link is
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:rtype: tuple
... | python | def get_dxlink_ids(link):
'''
:param link: A DNAnexus link
:type link: dict
:returns: (Object ID, Project ID) if the link is to a data object (or :const:`None`
if no project specified in the link), or (Job ID, Field) if the link is
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxdataobject_functions.py | get_handler | def get_handler(id_or_link, project=None):
'''
:param id_or_link: String containing an object ID or dict containing a DXLink
:type id_or_link: string or dict
:param project: String project ID to use as the context if the the object is a data object
:type project: string
:rtype: :class:`~dxpy.bin... | python | def get_handler(id_or_link, project=None):
'''
:param id_or_link: String containing an object ID or dict containing a DXLink
:type id_or_link: string or dict
:param project: String project ID to use as the context if the the object is a data object
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxdataobject_functions.py | describe | def describe(id_or_link, **kwargs):
'''
:param id_or_link: String containing an object ID or dict containing a DXLink,
or a list of object IDs or dicts containing a DXLink.
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d... | python | def describe(id_or_link, **kwargs):
'''
:param id_or_link: String containing an object ID or dict containing a DXLink,
or a list of object IDs or dicts containing a DXLink.
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.describe | def describe(self, **kwargs):
"""
:returns: A hash containing attributes of the project or container.
:rtype: dict
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.new_folder | def new_folder(self, folder, parents=False, **kwargs):
"""
:param folder: Full path to the new folder to create
:type folder: string
:param parents: If True, recursively create any parent folders that are missing
:type parents: boolean
Creates a new folder in the project... | python | def new_folder(self, folder, parents=False, **kwargs):
"""
:param folder: Full path to the new folder to create
:type folder: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.list_folder | def list_folder(self, folder="/", describe=False, only="all", includeHidden=False, **kwargs):
"""
:param folder: Full path to the folder to list
:type folder: string
:param describe: If True, returns the output of ``/describe`` on each object (see below for notes)
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"""
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:type folder: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.move | def move(self, destination, objects=[], folders=[], **kwargs):
"""
:param destination: Path of destination folder
:type destination: string
:param objects: List of object IDs to move
:type objects: list of strings
:param folders: List of full paths to folders to move
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"""
:param destination: Path of destination folder
:type destination: string
:param objects: List of object IDs to move
:type objects: list of strings
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.move_folder | def move_folder(self, folder, destination, **kwargs):
"""
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:type folder: string
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:type destination: string
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.remove_objects | def remove_objects(self, objects, force=False, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.clone | def clone(self, container, destination="/", objects=[], folders=[], parents=False, **kwargs):
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:param destination: Path of destination folder in the destination container
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.new | def new(self, name, summary=None, description=None, protected=None,
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properties=None, bill_to=None, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.update | def update(self, name=None, summary=None, description=None, protected=None,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.invite | def invite(self, invitee, level, send_email=True, **kwargs):
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.decrease_perms | def decrease_perms(self, member, level, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.set_properties | def set_properties(self, properties, **kwargs):
"""
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dnanexus/dx-toolkit | src/python/dxpy/exceptions.py | format_exception | def format_exception(e):
"""Returns a string containing the type and text of the exception.
"""
from .utils.printing import fill
return '\n'.join(fill(line) for line in traceback.format_exception_only(type(e), e)) | python | def format_exception(e):
"""Returns a string containing the type and text of the exception.
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dnanexus/dx-toolkit | src/python/dxpy/exceptions.py | exit_with_exc_info | def exit_with_exc_info(code=1, message='', print_tb=False, exception=None):
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:param code: Exit code.
:type code: integer (valid exit code, 0-255)
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dnanexus/dx-toolkit | src/python/dxpy/exceptions.py | err_exit | def err_exit(message='', code=None, expected_exceptions=default_expected_exceptions, arg_parser=None,
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'''Exits the program, printing information about the last exception (if
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dnanexus/dx-toolkit | src/python/dxpy/exceptions.py | DXAPIError.error_message | def error_message(self):
"Returns a one-line description of the error."
output = self.msg + ", code " + str(self.code)
output += ". Request Time={}, Request ID={}".format(self.timestamp, self.req_id)
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output = self.name + ": " + output
... | python | def error_message(self):
"Returns a one-line description of the error."
output = self.msg + ", code " + str(self.code)
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow.publish | def publish(self, **kwargs):
"""
Publishes the global workflow, so all users can find it and use it on the platform.
The current user must be a developer of the workflow.
"""
if self._dxid is not None:
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow.describe_underlying_workflow | def describe_underlying_workflow(self, region, describe_output=None):
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:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
:returns: object description of a workflow
:rtype: : dict... | python | def describe_underlying_workflow(self, region, describe_output=None):
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:type region: string
:param describe_output: description of a global workflow
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow.append_underlying_workflow_desc | def append_underlying_workflow_desc(self, describe_output, region):
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:param region: region name
:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
:returns: object description of the global workflow
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:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
:returns: object description of the global workflow
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow._get_run_input | def _get_run_input(self, workflow_input, project=None, **kwargs):
"""
Checks the region in which the global workflow is run
and returns the input associated with the underlying workflow
from that region.
"""
region = dxpy.api.project_describe(project,
... | python | def _get_run_input(self, workflow_input, project=None, **kwargs):
"""
Checks the region in which the global workflow is run
and returns the input associated with the underlying workflow
from that region.
"""
region = dxpy.api.project_describe(project,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow.run | def run(self, workflow_input, *args, **kwargs):
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:param workflow_input: Dictionary of the workflow's input arguments; see below for more details
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'''
:param workflow_input: Dictionary of the workflow's input arguments; see below for more details
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dnanexus/dx-toolkit | src/python/dxpy/compat.py | unwrap_stream | def unwrap_stream(stream_name):
"""
Temporarily unwraps a given stream (stdin, stdout, or stderr) to undo the effects of wrap_stdio_in_codecs().
"""
wrapped_stream = None
try:
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if hasattr(wrapped_stream, '_original_stream'):
setat... | python | def unwrap_stream(stream_name):
"""
Temporarily unwraps a given stream (stdin, stdout, or stderr) to undo the effects of wrap_stdio_in_codecs().
"""
wrapped_stream = None
try:
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | open_dxfile | def open_dxfile(dxid, project=None, mode=None, read_buffer_size=dxfile.DEFAULT_BUFFER_SIZE):
'''
:param dxid: file ID
:type dxid: string
:rtype: :class:`~dxpy.bindings.dxfile.DXFile`
Given the object ID of an uploaded file, returns a remote file
handler that is a Python file-like object.
E... | python | def open_dxfile(dxid, project=None, mode=None, read_buffer_size=dxfile.DEFAULT_BUFFER_SIZE):
'''
:param dxid: file ID
:type dxid: string
:rtype: :class:`~dxpy.bindings.dxfile.DXFile`
Given the object ID of an uploaded file, returns a remote file
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | new_dxfile | def new_dxfile(mode=None, write_buffer_size=dxfile.DEFAULT_BUFFER_SIZE, expected_file_size=None, file_is_mmapd=False,
**kwargs):
'''
:param mode: One of "w" or "a" for write and append modes, respectively
:type mode: string
:rtype: :class:`~dxpy.bindings.dxfile.DXFile`
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | download_dxfile | def download_dxfile(dxid, filename, chunksize=dxfile.DEFAULT_BUFFER_SIZE, append=False, show_progress=False,
project=None, describe_output=None, **kwargs):
'''
:param dxid: DNAnexus file ID or DXFile (file handler) object
:type dxid: string or DXFile
:param filename: Local filename
... | python | def download_dxfile(dxid, filename, chunksize=dxfile.DEFAULT_BUFFER_SIZE, append=False, show_progress=False,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | _download_dxfile | def _download_dxfile(dxid, filename, part_retry_counter,
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | upload_local_file | def upload_local_file(filename=None, file=None, media_type=None, keep_open=False,
wait_on_close=False, use_existing_dxfile=None, show_progress=False,
write_buffer_size=None, multithread=True, **kwargs):
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... | python | def upload_local_file(filename=None, file=None, media_type=None, keep_open=False,
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write_buffer_size=None, multithread=True, **kwargs):
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | upload_string | def upload_string(to_upload, media_type=None, keep_open=False, wait_on_close=False, **kwargs):
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | list_subfolders | def list_subfolders(project, path, recurse=True):
'''
:param project: Project ID to use as context for the listing
:type project: string
:param path: Subtree root path
:type path: string
:param recurse: Return a complete subfolders tree
:type recurse: boolean
Returns a list of subfolder... | python | def list_subfolders(project, path, recurse=True):
'''
:param project: Project ID to use as context for the listing
:type project: string
:param path: Subtree root path
:type path: string
:param recurse: Return a complete subfolders tree
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | download_folder | def download_folder(project, destdir, folder="/", overwrite=False, chunksize=dxfile.DEFAULT_BUFFER_SIZE,
show_progress=False, **kwargs):
'''
:param project: Project ID to use as context for this download.
:type project: string
:param destdir: Local destination location
:type dest... | python | def download_folder(project, destdir, folder="/", overwrite=False, chunksize=dxfile.DEFAULT_BUFFER_SIZE,
show_progress=False, **kwargs):
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:param project: Project ID to use as context for this download.
:type project: string
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | build | def build(src_dir, parallel_build=True):
"""
Runs any build scripts that are found in the specified directory.
In particular, runs ``./configure`` if it exists, followed by ``make -jN``
if it exists (building with as many parallel tasks as there are CPUs on the
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"""
# TODO: use Gent... | python | def build(src_dir, parallel_build=True):
"""
Runs any build scripts that are found in the specified directory.
In particular, runs ``./configure`` if it exists, followed by ``make -jN``
if it exists (building with as many parallel tasks as there are CPUs on the
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | is_link_local | def is_link_local(link_target):
"""
:param link_target: The target of a symbolic link, as given by os.readlink()
:type link_target: string
:returns: A boolean indicating the link is local to the current directory.
This is defined to mean that os.path.isabs(link_target) == False
... | python | def is_link_local(link_target):
"""
:param link_target: The target of a symbolic link, as given by os.readlink()
:type link_target: string
:returns: A boolean indicating the link is local to the current directory.
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | _fix_perms | def _fix_perms(perm_obj):
"""
:param perm_obj: A permissions object, as given by os.stat()
:type perm_obj: integer
:returns: A permissions object that is the result of "chmod a+rX" on the
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bitwise or-ed with... | python | def _fix_perms(perm_obj):
"""
:param perm_obj: A permissions object, as given by os.stat()
:type perm_obj: integer
:returns: A permissions object that is the result of "chmod a+rX" on the
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | upload_resources | def upload_resources(src_dir, project=None, folder='/', ensure_upload=False, force_symlinks=False):
"""
:param ensure_upload: If True, will bypass checksum of resources directory
and upload resources bundle unconditionally;
will NOT be able to reuse this bundl... | python | def upload_resources(src_dir, project=None, folder='/', ensure_upload=False, force_symlinks=False):
"""
:param ensure_upload: If True, will bypass checksum of resources directory
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | upload_applet | def upload_applet(src_dir, uploaded_resources, check_name_collisions=True, overwrite=False, archive=False, project=None, override_folder=None, override_name=None, dx_toolkit_autodep="stable", dry_run=False, **kwargs):
"""
Creates a new applet object.
:param project: ID of container in which to create the a... | python | def upload_applet(src_dir, uploaded_resources, check_name_collisions=True, overwrite=False, archive=False, project=None, override_folder=None, override_name=None, dx_toolkit_autodep="stable", dry_run=False, **kwargs):
"""
Creates a new applet object.
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | _create_or_update_version | def _create_or_update_version(app_name, version, app_spec, try_update=True):
"""
Creates a new version of the app. Returns an app_id, or None if the app has
already been created and published.
"""
# This has a race condition since the app could have been created or
# published since we last look... | python | def _create_or_update_version(app_name, version, app_spec, try_update=True):
"""
Creates a new version of the app. Returns an app_id, or None if the app has
already been created and published.
"""
# This has a race condition since the app could have been created or
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | _update_version | def _update_version(app_name, version, app_spec, try_update=True):
"""
Updates a version of the app in place. Returns an app_id, or None if the
app has already been published.
"""
if not try_update:
return None
try:
app_id = dxpy.api.app_update("app-" + app_name, version, app_spe... | python | def _update_version(app_name, version, app_spec, try_update=True):
"""
Updates a version of the app in place. Returns an app_id, or None if the
app has already been published.
"""
if not try_update:
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | create_app_multi_region | def create_app_multi_region(regional_options, app_name, src_dir, publish=False, set_default=False, billTo=None,
try_versions=None, try_update=True, confirm=True):
"""
Creates a new app object from the specified applet(s).
:param regional_options: Region-specific options for the ... | python | def create_app_multi_region(regional_options, app_name, src_dir, publish=False, set_default=False, billTo=None,
try_versions=None, try_update=True, confirm=True):
"""
Creates a new app object from the specified applet(s).
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dnanexus/dx-toolkit | src/python/dxpy/app_builder.py | create_app | def create_app(applet_id, applet_name, src_dir, publish=False, set_default=False, billTo=None, try_versions=None,
try_update=True, confirm=True, regional_options=None):
"""
Creates a new app object from the specified applet.
.. deprecated:: 0.204.0
Use :func:`create_app_multi_region()... | python | def create_app(applet_id, applet_name, src_dir, publish=False, set_default=False, billTo=None, try_versions=None,
try_update=True, confirm=True, regional_options=None):
"""
Creates a new app object from the specified applet.
.. deprecated:: 0.204.0
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