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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.new | def new(self, fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: ... | python | def new(self, fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: ... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.set_id | def set_id(self, dxid):
'''
:param dxid: New job ID to be associated with the handler (localjob IDs also accepted for local runs)
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
if dxid is not None:
if not (isins... | python | def set_id(self, dxid):
'''
:param dxid: New job ID to be associated with the handler (localjob IDs also accepted for local runs)
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
if dxid is not None:
if not (isins... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.describe | def describe(self, fields=None, io=None, **kwargs):
"""
:param fields: dict where the keys are field names that should
be returned, and values should be set to True (by default,
all fields are returned)
:type fields: dict
:param io: Include input and output fields... | python | def describe(self, fields=None, io=None, **kwargs):
"""
:param fields: dict where the keys are field names that should
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:type fields: dict
:param io: Include input and output fields... | [
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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
no action for tags that the job does not currently have.
"""
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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
values, the properties are set on the job for the given
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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"]
'''
return self.describe(fiel... | [
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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`
PRECONDITION:
- If /org-x/invite is being called in conjunction with /user/new, then
`_validate_new_user_input()` has been called on `args`; otherwise,
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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:
user_new_args["first"] = args.first
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,
"email": args.email}
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user_new_args["first"] = args.first
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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
# input spec available (because a stage is inaccessible)
exec_inputs ... | python | 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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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):
"""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
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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
to the server (for example, name resolution failed or the 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):
# Using the same code path as below would not
# produce a useful message ... | [
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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
'''
if response is not None and response.sta... | python | 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
'''
if response is not None and response.sta... | [
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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,
max_retries=DEF... | python | 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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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'):
"""
Chooses the auth server name from the currently configured API server name.
Raises DXError if the auth server name cannot be guessed and the overrides
are not provided (or improperly provided).
"""
if host_o... | python | def get_auth_server_name(host_override=None, port_override=None, protocol='https'):
"""
Chooses the auth server name from the currently configured API server name.
Raises DXError if the auth server name cannot be guessed and the overrides
are not provided (or improperly provided).
"""
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dnanexus/dx-toolkit | src/python/dxpy/__init__.py | append_underlying_workflow_describe | def append_underlying_workflow_describe(globalworkflow_desc):
"""
Adds the "workflowDescribe" field to the config for each region of
the global workflow. The value is the description of an underlying
workflow in that region.
"""
if not globalworkflow_desc or \
globalworkflow_desc['cl... | python | def append_underlying_workflow_describe(globalworkflow_desc):
"""
Adds the "workflowDescribe" field to the config for each region of
the global workflow. The value is the description of an underlying
workflow in that region.
"""
if not globalworkflow_desc or \
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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 = {"$dnanexus_link"... | python | def _construct_jbor(job_id, field_name_and_maybe_index):
'''
:param job_id: Job ID
:type job_id: string
:param field_name_and_maybe_index: Field name, plus possibly ".N" where N is an array index
:type field_name_and_maybe_index: string
:returns: dict of JBOR
'''
link = {"$dnanexus_link"... | [
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dnanexus/dx-toolkit | src/python/dxpy/cli/exec_io.py | ExecutableInputs.update | def update(self, new_inputs, strip_prefix=True):
"""
Updates the inputs dictionary with the key/value pairs from new_inputs, overwriting existing keys.
"""
if strip_prefix and self.input_name_prefix is not None:
for i in new_inputs:
if i.startswith(self.input_... | python | def update(self, new_inputs, strip_prefix=True):
"""
Updates the inputs dictionary with the key/value pairs from new_inputs, overwriting existing keys.
"""
if strip_prefix and self.input_name_prefix is not None:
for i in new_inputs:
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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
as paths to items that require resolutions, eg. folder or job/analyses ids)
"""
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
mappings. To preserve order, use collections.OrderedDict.
Example:
print format_tree(collections.OrderedDict({'foo': 0, 'b... | [
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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,
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'])
'''
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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
:param array_name: Array name to flatten
:type array_name: str
"""
result = re.sub('"{}": \\[\r?\n\\s*'.format(array_nam... | [
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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
:param description: Workflow description (optional)
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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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:type dx_hash: dict
:param title: Workflow title (optional)
:type title: string
:param summa... | python | def _new(self, dx_hash, **kwargs):
"""
:param dx_hash: Standard hash populated in :func:`dxpy.bindings.DXDataObject.new()` containing attributes common to all data object classes.
:type dx_hash: dict
:param title: Workflow title (optional)
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow._get_stage_id | def _get_stage_id(self, stage):
'''
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: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):
'''
: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)
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.add_stage | def add_stage(self, executable, stage_id=None, name=None, folder=None, stage_input=None, instance_type=None,
edit_version=None, **kwargs):
'''
:param executable: string or a handler for an app or applet
:type executable: string, DXApplet, or DXApp
:param stage_id: id fo... | python | def add_stage(self, executable, stage_id=None, name=None, folder=None, stage_input=None, instance_type=None,
edit_version=None, **kwargs):
'''
:param executable: string or a handler for an app or applet
:type executable: string, DXApplet, or DXApp
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.get_stage | def get_stage(self, stage, **kwargs):
'''
:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
:type stage: int or string
:returns: Hash of stage descriptor in workflow
'''
stage_id = self._get_stage_... | python | def get_stage(self, stage, **kwargs):
'''
:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
:type stage: int or string
:returns: Hash of stage descriptor in workflow
'''
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.remove_stage | def remove_stage(self, stage, edit_version=None, **kwargs):
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:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
:type stage: int or string
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'''
:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.move_stage | def move_stage(self, stage, new_index, edit_version=None, **kwargs):
'''
:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
:type stage: int or string
:param new_index: The new position in the order of stages that ... | python | def move_stage(self, stage, new_index, edit_version=None, **kwargs):
'''
:param stage: A number for the stage index (for the nth stage, starting from 0), or a string of the stage index, name, or ID
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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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workflow_inputs=None, unset_workflow_inputs=False,
workflow_outputs=None, unset_workflow_outputs=False,
stages=None, edit_version=Non... | python | def update(self, title=None, unset_title=False, summary=None, description=None,
output_folder=None, unset_output_folder=False,
workflow_inputs=None, unset_workflow_inputs=False,
workflow_outputs=None, unset_workflow_outputs=False,
stages=None, edit_version=Non... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.update_stage | def update_stage(self, stage, executable=None, force=False,
name=None, unset_name=False, folder=None, unset_folder=False, stage_input=None,
instance_type=None, edit_version=None, **kwargs):
'''
:param stage: A number for the stage index (for the nth stage, start... | python | def update_stage(self, stage, executable=None, force=False,
name=None, unset_name=False, folder=None, unset_folder=False, stage_input=None,
instance_type=None, edit_version=None, **kwargs):
'''
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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):
'''
:param input_str: A string of one of the forms: "<exported input field name>", "<explicit workflow input field name>", "<stage ID>.<input field name>", "<stage index>.<input field name>", "<stage name>.<input field name>"
... | python | def _get_input_name(self, input_str, region=None, describe_output=None):
'''
:param input_str: A string of one of the forms: "<exported input field name>", "<explicit workflow input field name>", "<stage ID>.<input field name>", "<stage index>.<input field name>", "<stage name>.<input field name>"
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxworkflow.py | DXWorkflow.run | def run(self, workflow_input, *args, **kwargs):
'''
:param workflow_input: Dictionary of the workflow's input arguments; see below for more details
:type workflow_input: dict
:param instance_type: Instance type on which all stages' jobs will be run, or a dict mapping function names to in... | python | def run(self, workflow_input, *args, **kwargs):
'''
:param workflow_input: Dictionary of the workflow's input arguments; see below for more details
:type workflow_input: dict
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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):
'''
:param text: String to be tab-completed; still in escaped form
:type text: string
:param delim_pos: index of last unescaped "/" in text
:type delim_pos: int
:param dxproj: DXProject handler to use
:type dxproj: DXProject
:p... | python | def get_folder_matches(text, delim_pos, dxproj, folderpath):
'''
:param text: String to be tab-completed; still in escaped form
:type text: string
:param delim_pos: index of last unescaped "/" in text
:type delim_pos: int
:param dxproj: DXProject handler to use
:type dxproj: DXProject
:p... | [
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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,
typespec=None, visibility=None):
'''
:param text: String to be tab-completed; still in escaped form
:type text: string
:param delim_pos: index of last unescaped "/" or ":" in text
:type delim_pos: int
... | python | def get_data_matches(text, delim_pos, dxproj, folderpath, classname=None,
typespec=None, visibility=None):
'''
:param text: String to be tab-completed; still in escaped form
:type text: string
:param delim_pos: index of last unescaped "/" or ":" in text
:type delim_pos: int
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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,
include_current_proj=False, typespec=None, visibility=None):
'''
:param text: String to tab-complete to a path matching the syntax project-name:folder/entity_or_folder_name
:type text: string
:param expected: "fold... | python | def path_completer(text, expected=None, classes=None, perm_level=None,
include_current_proj=False, typespec=None, visibility=None):
'''
:param text: String to tab-complete to a path matching the syntax project-name:folder/entity_or_folder_name
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | verify_string_dxid | 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
... | 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*
'''
if dxid is not None:
verify_string_dxid(dxid, self._class)
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*
'''
if dxid is not None:
verify_string_dxid(dxid, self._class)
self._dxid = d... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.new | 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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"""
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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):
"""
:param types: Types to remove from the object
:type types: list of strings
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
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n... | python | def remove_types(self, types, **kwargs):
"""
:param types: Types to remove from the object
:type types: list of strings
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.set_details | def set_details(self, details, **kwargs):
"""
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:type details: dict or list
:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
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... | python | def set_details(self, details, **kwargs):
"""
:param details: Details to set for the object
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:raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state
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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
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The name is changed on the copy of the object in the project
associated with the handler.
"""
return self._rename(self._dxid, {"pro... | python | def rename(self, name, **kwargs):
"""
:param name: New name for the 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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:type properties: dict
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values, the properties are set on the object for the given
... | python | def set_properties(self, properties, **kwargs):
"""
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:type properties: dict
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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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action for tags that are already listed for the object.
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"""
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dnanexus/dx-toolkit | src/python/dxpy/bindings/__init__.py | DXDataObject.remove_tags | def remove_tags(self, tags, **kwargs):
"""
:param tags: Tags to remove from the object
:type tags: list of strings
Removes each of the specified tags from the remote object. Takes
no action for tags that the object does not currently have.
The tags are removed from the ... | python | def remove_tags(self, tags, **kwargs):
"""
:param tags: Tags to remove from the object
:type tags: list of strings
Removes each of the specified tags from the remote object. Takes
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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:
raise DXError("Remove called when a ... | python | 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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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):
'''
: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... | [
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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.
If none of those exist, the path for the immediate parent is... | python | def get_session_conf_dir(self, cleanup=False):
"""
Tries to find the session configuration directory by looking in ~/.dnanexus_config/sessions/<PID>,
where <PID> is pid of the parent of this process, then its parent, and so on.
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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
:param field: A field name... | [
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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 ``"$dnanexus_link"``) with a referenced data object.
'''
if not isinstance(x, dict):
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if '$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 ``"$dnanexus_link"``) with a referenced data object.
'''
if not isinstance(x, dict):
return False
if '$dnanexus_link' not in x:
return False
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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
a job-based object reference (JBOR).
: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
a job-based object reference (JBOR).
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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
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: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
:type project: string
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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.
Given an object ID, calls :meth:`~dxpy.bindings.DXDataObject.describe` on the object.
Example::
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.
Given an object ID, calls :meth:`~dxpy.bindings.DXDataObject.describe` on the object.
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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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specification for the `/project-xxxx/describe
<https://wiki.dnanexus.com/API-Specification-v1.0.... | python | def describe(self, **kwargs):
"""
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: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
:param parents: If True, recursively create any parent folders that are missing
:type parents: boolean
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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)
:type describe:... | python | 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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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
... | python | 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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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.move_folder | def move_folder(self, folder, destination, **kwargs):
"""
:param folder: Full path to the folder to move
:type folder: string
:param destination: Full path to the destination folder that will contain *folder*
:type destination: string
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"""
:param folder: Full path to the folder to move
:type folder: string
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:type destination: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXContainer.remove_folder | def remove_folder(self, folder, recurse=False, force=False, **kwargs):
"""
:param folder: Full path to the folder to remove
:type folder: string
:param recurse: If True, recursively remove all objects and subfolders in the folder
:type recurse: bool
:param force: If True,... | python | def remove_folder(self, folder, recurse=False, force=False, **kwargs):
"""
:param folder: Full path to the folder to remove
:type folder: string
:param recurse: If True, recursively remove all objects and subfolders in the folder
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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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:type objects: list of strings
:param force: If True, will suppress errors for objects that do not exist
:type force: bool
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"""
:param objects: List of object IDs to remove from the project or container
:type objects: list of strings
:param force: If True, will suppress errors for objects that do not exist
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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):
"""
:param container: Destination container ID
:type container: string
:param destination: Path of destination folder in the destination container
:type destination: string
:para... | python | def clone(self, container, destination="/", objects=[], folders=[], parents=False, **kwargs):
"""
:param container: Destination container ID
:type container: string
:param destination: Path of destination folder in the destination container
:type destination: string
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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,
restricted=None, download_restricted=None, contains_phi=None, tags=None,
properties=None, bill_to=None, **kwargs):
"""
:param name: The name of the project
:type name: string
:param summary: If pr... | python | def new(self, name, summary=None, description=None, protected=None,
restricted=None, download_restricted=None, contains_phi=None, tags=None,
properties=None, bill_to=None, **kwargs):
"""
:param name: The name of the project
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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,
restricted=None, download_restricted=None, version=None, **kwargs):
"""
:param name: If provided, the new project name
:type name: string
:param summary: If provided, the new project summary
... | python | def update(self, name=None, summary=None, description=None, protected=None,
restricted=None, download_restricted=None, version=None, **kwargs):
"""
:param name: If provided, the new project name
:type name: string
:param summary: If provided, the new project summary
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.invite | def invite(self, invitee, level, send_email=True, **kwargs):
"""
:param invitee: Username (of the form "user-USERNAME") or email address of person to be invited to the project; use "PUBLIC" to make the project publicly available (in which case level must be set to "VIEW").
:type invitee: string
... | python | def invite(self, invitee, level, send_email=True, **kwargs):
"""
:param invitee: Username (of the form "user-USERNAME") or email address of person to be invited to the project; use "PUBLIC" to make the project publicly available (in which case level must be set to "VIEW").
:type invitee: string
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.decrease_perms | def decrease_perms(self, member, level, **kwargs):
"""
:param member: Username (of the form "user-USERNAME") of the project member whose permissions will be decreased.
:type member: string
:param level: Permissions level that the member will have after this operation (None, "VIEW", "UPLO... | python | def decrease_perms(self, member, level, **kwargs):
"""
:param member: Username (of the form "user-USERNAME") of the project member whose permissions will be decreased.
:type member: string
:param level: Permissions level that the member will have after this operation (None, "VIEW", "UPLO... | [
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxproject.py | DXProject.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 project 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
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values, the properties are set on the project for the given
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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.
"""
from .utils.printing import fill
return '\n'.join(fill(line) for line in traceback.format_exception_only(type(e), e)) | [
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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):
'''Exits the program, printing information about the last exception (if
any) and an optional error message. Uses *exception* instead if provided.
:param code: Exit code.
:type code: integer (valid exit code, 0-255)
:param ... | python | def exit_with_exc_info(code=1, message='', print_tb=False, exception=None):
'''Exits the program, printing information about the last exception (if
any) and an optional error message. Uses *exception* instead if provided.
:param code: Exit code.
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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,
ignore_sigpipe=True, exception=None):
'''Exits the program, printing information about the last exception (if
any) and an optional error message. Uses *exception* instead if provided.
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ignore_sigpipe=True, exception=None):
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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)
if self.name != self.__class__.__name__:
output = self.name + ": " + output
... | python | 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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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:
return dxpy.api.global_workflow_publish(self._dxid, **kwargs)
... | python | 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:
return dxpy.api.global_workflow_publish(self._dxid, **kwargs)
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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):
"""
:param region: region name
: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):
"""
:param region: region name
:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
:returns: object description of a workflow
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxglobalworkflow.py | DXGlobalWorkflow.get_underlying_workflow | def get_underlying_workflow(self, region, describe_output=None):
"""
:param region: region name
:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
:returns: object handler of a workflow
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"""
:param region: region name
:type region: string
:param describe_output: description of a global workflow
:type describe_output: dict
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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):
"""
: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
:rtype:... | python | def append_underlying_workflow_desc(self, describe_output, region):
"""
: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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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):
'''
:param workflow_input: Dictionary of the workflow's input arguments; see below for more details
:type workflow_input: dict
:param instance_type: Instance type on which all stages' jobs will be run, or a dict mapping function names to in... | python | def run(self, workflow_input, *args, **kwargs):
'''
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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:
wrapped_stream = getattr(sys, stream_name)
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:
wrapped_stream = getattr(sys, stream_name)
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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
handler that is a Python file-like object.
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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`
Additional opt... | python | 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,
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
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dnanexus/dx-toolkit | src/python/dxpy/bindings/dxfile_functions.py | _download_dxfile | def _download_dxfile(dxid, filename, part_retry_counter,
chunksize=dxfile.DEFAULT_BUFFER_SIZE, append=False, show_progress=False,
project=None, describe_output=None, **kwargs):
'''
Core of download logic. Download file-id *dxid* and store it in
a local file *filenam... | python | def _download_dxfile(dxid, filename, part_retry_counter,
chunksize=dxfile.DEFAULT_BUFFER_SIZE, append=False, show_progress=False,
project=None, describe_output=None, **kwargs):
'''
Core of download logic. Download file-id *dxid* and store it in
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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):
'''
:param filename: Local filename
:type filename: string
... | python | 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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:type filename: string
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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):
"""
:param to_upload: String to upload into a file
:type to_upload: string
:param media_type: Internet Media Type
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... | python | def upload_string(to_upload, media_type=None, keep_open=False, wait_on_close=False, **kwargs):
"""
:param to_upload: String to upload into a file
:type to_upload: string
:param media_type: Internet Media Type
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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):
'''
: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):
"""
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if it exists (building with as many parallel tasks as there are CPUs on the
system).
"""
# 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.
This is defined to mean that os.path.isabs(link_target) == False
... | [
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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
given permission object. This is defined to be the permission object
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
given permission object. This is defined to be the permission object
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"+... | 74befb53ad90fcf902d8983ae6d74580f402d619 | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/app_builder.py#L167-L182 | train | Fixes permissions for the
. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJU... |
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
and upload resources bundle unconditionally;
will NOT be able to reuse this bundl... | [
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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.
:param project: ID of container in which to create the a... | [
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] | 74befb53ad90fcf902d8983ae6d74580f402d619 | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/app_builder.py#L427-L666 | train | Uploads a applet to the app builder. | GiP5xwVCF98Z,B3LV8Eo811Ma,bIsJhlpYrrU2,UtiWT6f6p9yZ,sY2ClS3bs_Vs,cXy7eDEmqBLX,WBIJpxagI_Bm,oiYQtqKByLVy,pKtZbyLPTF7M,N5KuUvtbiyqB,Y8CO_HpFZe1H,lFpHwHL3xiEO,QT_5wdIFQ3WX,gn988v5t9NEf,dVZxwLTOCtbO,RjQP07DYIdkf,Wun5u3i1rn23,m64e4RQAlmFd,zfo2Sgkz3IVJ,aWb0eXvJHTT7,s2y8nAB4S7UF,znAfcqx_89tO,ZnHlCcECsuOK,TdYHRT1SBW60,mBmBrDJU... |
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
# published since we last look... | [
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