JorgeVB/code_unlearning_dataset · Data Studio

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Returns the memory byte size of a Numpy array as an integer. def bytesize(arr): """ Returns the memory byte size of a Numpy array as an integer. """ byte_size = np.prod(arr.shape) * np.dtype(arr.dtype).itemsize return byte_size
Similar to `numpy.apply_over_axes`, except this performs the operation over a flattened version of all the axes, meaning that the function will only be called once. This only makes a difference for non-linear functions. Parameters ---------- func : callback Function that operates well on Nu...
Argmax that returns an index tuple. Note that `numpy.argmax` will return a scalar index as if you had flattened the array. Parameters ---------- a : array_like Input array. Returns ------- index : tuple Tuple of index, even if `a` is one-dimensional. Note that this can ...
Context manager to make it easy to time the execution of a piece of code. This timer will never run your code several times and is meant more for simple in-production timing, instead of benchmarking. Reports the wall-clock time (using `time.time`) and not the processor time. Parameters ---------- ...
Pad an array with a specific value. Parameters ---------- data : ndarray Numpy array of any dimension and type. padwidth : int or tuple If int, it will pad using this amount at the beginning and end of all dimensions. If it is a tuple (of same length as `ndim`), then the ...
This is similar to `pad`, except you specify the final shape of the array. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.ndim``. If it has to pad unevenly, it will pad one m...
Similar to `pad`, except the border value from ``data`` is used to pad. Parameters ---------- data : ndarray Numpy array of any dimension and type. padwidth : int or tuple If int, it will pad using this amount at the beginning and end of all dimensions. If it is a tuple (of same...
Similar to `pad_repeat_border`, except the padding is always done on the upper end of each axis and the target size is specified. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.n...
This checks if a dictionary can be saved natively as HDF5 groups. If it can't, it will be pickled. def _dict_native_ok(d): """ This checks if a dictionary can be saved natively as HDF5 groups. If it can't, it will be pickled. """ if len(d) >= 256: return False # All keys must be ...
Loads level and builds appropriate type, without handling softlinks def _load_nonlink_level(handler, level, pathtable, pathname): """ Loads level and builds appropriate type, without handling softlinks """ if isinstance(level, tables.Group): if _sns and (level._v_title.startswith('SimpleNamespa...
Loads level and builds appropriate type, handling softlinks if necessary def _load_level(handler, level, pathtable): """ Loads level and builds appropriate type, handling softlinks if necessary """ if isinstance(level, tables.link.SoftLink): # this is a link, so see if target is already loaded,...
Save any Python structure to an HDF5 file. It is particularly suited for Numpy arrays. This function works similar to ``numpy.save``, except if you save a Python object at the top level, you do not need to issue ``data.flat[0]`` to retrieve it from inside a Numpy array of type ``object``. Some type...
Loads an HDF5 saved with `save`. This function requires the `PyTables <http://www.pytables.org/>`_ module to be installed. Parameters ---------- path : string Filename from which to load the data. group : string or list Load a specific group in the HDF5 hierarchy. If `group` is...
Sorts x with numeric semantics if all keys are nonnegative integers. Otherwise uses standard string sorting. def sorted_maybe_numeric(x): """ Sorts x with numeric semantics if all keys are nonnegative integers. Otherwise uses standard string sorting. """ all_numeric = all(map(str.isdigit, x)) ...
Color-aware abbreviator def abbreviate(s, maxlength=25): """Color-aware abbreviator""" assert maxlength >= 4 skip = False abbrv = None i = 0 for j, c in enumerate(s): if c == '\033': skip = True elif skip: if c == 'm': skip = False ...
Extend the settings the manager will serialize. :param data_id: The :class:`~resolwe.flow.models.Data` object id being prepared for. :param files: The settings dictionary to be serialized. Keys are filenames, values are the objects that will be serialized into those ...
Get tools' paths. def get_tools_paths(self): """Get tools' paths.""" if settings.DEBUG or is_testing(): return list(get_apps_tools().values()) else: tools_root = settings.FLOW_TOOLS_ROOT subdirs = next(os.walk(tools_root))[1] return [os.path.joi...
Resolve data path for use with the executor. :param data: Data object instance :param filename: Filename to resolve :return: Resolved filename, which can be used to access the given data file in programs executed using this executor def resolve_data_path(self, data=None, filename=N...
Resolve upload path for use with the executor. :param filename: Filename to resolve :return: Resolved filename, which can be used to access the given uploaded file in programs executed using this executor def resolve_upload_path(self, filename=None): """Resolve upload p...
Work with the AccessPolicy in a SystemMetadata PyXB object. Args: access_pyxb : AccessPolicy PyXB object The AccessPolicy to modify. read_only: bool Do not update the wrapped AccessPolicy. When only a single AccessPolicy operation is needed, there's no need to use this context...
Work with the AccessPolicy in a SystemMetadata PyXB object. Args: sysmeta_pyxb : SystemMetadata PyXB object SystemMetadata containing the AccessPolicy to modify. read_only: bool Do not update the wrapped AccessPolicy. When only a single AccessPolicy operation is needed, there's no...
Args: subj_str : str Subject for which to retrieve the highest permission. Return: The highest permission for subject or None if subject does not have any permissions. def get_highest_perm_str(self, subj_str): """ Args: subj_str : str Subject for which to retrieve th...
Args: subj_str : str Subject for which to retrieve the effective permissions. Returns: list of str: List of permissions up to and including the highest permission for subject, ordered lower to higher, or empty list if subject does not have any permissions. E.g.: If 'write' is...
Args: perm_str : str Permission, ``read``, ``write`` or ``changePermission``. Returns: set of str : Subj that have perm equal or higher than ``perm_str``. Since the lowest permission a subject can have is ``read``, passing ``read`` will return all subjects. def get_subjects_with_e...
Dump the current state to debug level log. def dump(self): """Dump the current state to debug level log.""" logging.debug('AccessPolicy:') map( logging.debug, [ ' {}'.format(s) for s in pprint.pformat(self.get_normalized_perm_list()).spli...
Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. def subj_has_perm(self, subj_str, perm_str): """Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. """ self._assert_valid_permission(perm_str) re...
Add ``read`` perm for all authenticated subj. Public ``read`` is removed if present. def add_authenticated_read(self): """Add ``read`` perm for all authenticated subj. Public ``read`` is removed if present. """ self.remove_perm(d1_common.const.SUBJECT_PUBLIC, 'read') ...
Add ``read`` perm for all verified subj. Public ``read`` is removed if present. def add_verified_read(self): """Add ``read`` perm for all verified subj. Public ``read`` is removed if present. """ self.remove_perm(d1_common.const.SUBJECT_PUBLIC, 'read') self.add_perm(d...
Add a permission for a subject. Args: subj_str : str Subject for which to add permission(s) perm_str : str Permission to add. Implicitly adds all lower permissions. E.g., ``write`` will also add ``read``. def add_perm(self, subj_str, perm_str): ...
Remove permission from a subject. Args: subj_str : str Subject for which to remove permission(s) perm_str : str Permission to remove. Implicitly removes all higher permissions. E.g., ``write`` will also remove ``changePermission`` if previously granted. ...
Remove all permissions for subject. Args: subj_str : str Subject for which to remove all permissions. Since subjects can only be present in the AccessPolicy when they have one or more permissions, this removes the subject itself as well. The subject ma...
Return dict representation of AccessPolicy PyXB obj. def _perm_dict_from_pyxb(self, access_pyxb): """Return dict representation of AccessPolicy PyXB obj.""" subj_dict = self._subj_dict_from_pyxb(access_pyxb) return self._perm_dict_from_subj_dict(subj_dict)
Return dict where keys and values of ``subj_dict`` have been flipped around. def _perm_dict_from_subj_dict(self, subj_dict): """Return dict where keys and values of ``subj_dict`` have been flipped around.""" perm_dict = {} for subj_str, perm_set in list(subj_dict.items()): ...
Return an AccessPolicy PyXB representation of ``perm_dict`` - If ``norm_perm_list`` is empty, None is returned. The schema does not allow AccessPolicy to be empty, but in SystemMetadata, it can be left out altogether. So returning None instead of an empty AccessPolicy allows the result ...
Return an AccessPolicy PyXB representation of ``norm_perm_list`` def _pyxb_from_norm_perm_list(self, norm_perm_list): """Return an AccessPolicy PyXB representation of ``norm_perm_list``""" # Using accessPolicy() instead of AccessPolicy() and accessRule() instead of # AccessRule() gives PyXB the...
Return a dict representation of ``access_pyxb``, which is an AccessPolicy PyXB object. This also remove any duplicate subjects and permissions in the PyXB object. def _subj_dict_from_pyxb(self, access_pyxb): """Return a dict representation of ``access_pyxb``, which is an AccessPolicy P...
Return a perm_dict where only the highest permission for each subject is included. def _highest_perm_dict_from_perm_dict(self, perm_dict): """Return a perm_dict where only the highest permission for each subject is included.""" highest_perm_dict = copy.copy(perm_dict) for ordere...
Return a minimal, ordered, hashable list of subjects and permissions. def _norm_perm_list_from_perm_dict(self, perm_dict): """Return a minimal, ordered, hashable list of subjects and permissions.""" high_perm_dict = self._highest_perm_dict_from_perm_dict(perm_dict) return [ [k, list...
Return list of effective permissions for for highest permission in ``perm_iter``, ordered lower to higher, or None if ``perm_iter`` is empty. def _effective_perm_list_from_iter(self, perm_iter): """Return list of effective permissions for for highest permission in ``perm_iter``, ordered lower t...
Return a set containing only the permissions that are present in the ``perm_dict`` for ``subj_str`` def _present_perm_set_for_subj(self, perm_dict, subj_str): """Return a set containing only the permissions that are present in the ``perm_dict`` for ``subj_str``""" return {p for p, s in ...
Return the highest perm present in ``perm_iter`` or None if ``perm_iter`` is empty. def _highest_perm_from_iter(self, perm_iter): """Return the highest perm present in ``perm_iter`` or None if ``perm_iter`` is empty.""" perm_set = set(perm_iter) for perm_str in reversed(ORDERED_...
Return the ordered index of ``perm_str`` or None if ``perm_str`` is not a valid permission. def _ordered_idx_from_perm(self, perm_str): """Return the ordered index of ``perm_str`` or None if ``perm_str`` is not a valid permission.""" for i, ordered_str in enumerate(ORDERED_PERM_LIST): ...
Raise D1 exception if ``perm_str`` is not a valid permission. def _assert_valid_permission(self, perm_str): """Raise D1 exception if ``perm_str`` is not a valid permission.""" if perm_str not in ORDERED_PERM_LIST: raise d1_common.types.exceptions.InvalidRequest( 0, ...
Suppress stack traces for common errors and provide hints for how to resolve them. def handle_unexpected_exception(max_traceback_levels=100): """Suppress stack traces for common errors and provide hints for how to resolve them.""" exc_type, exc_msgs = sys.exc_info()[:2] if exc_type.__name__ == "SSL...
Create object file and database entries for a new native locally stored (non- proxied) science object. This method takes a request object and is only called from the views that handle: - MNStorage.create() - MNStorage.update() Various sanity checking is performed. Raises D1 exceptions that ar...
Django stores small uploads in memory and streams large uploads directly to disk. Uploads stored in memory are represented by UploadedFile and on disk, TemporaryUploadedFile. To store an UploadedFile on disk, it's iterated and saved in chunks. To store a TemporaryUploadedFile, it's moved from the temporary...
See the description of TRUST_CLIENT_* in settings.py. def set_mn_controlled_values(request, sysmeta_pyxb, is_modification): """See the description of TRUST_CLIENT_* in settings.py.""" now_datetime = d1_common.date_time.utc_now() default_value_list = [ ('originMemberNode', django.conf.settings.NODE...
Duplicate (make a copy) ``Entity`` objects. :param contributor: Duplication user :param inherit_collections: If ``True`` then duplicated entities will be added to collections the original entity is part of. Duplicated entities' data objects will also be added to the ...
Move entities from source to destination collection. def move_to_collection(self, source_collection, destination_collection): """Move entities from source to destination collection.""" for entity in self: entity.move_to_collection(source_collection, destination_collection)
Duplicate (make a copy). def duplicate(self, contributor=None, inherit_collections=False): """Duplicate (make a copy).""" duplicate = Entity.objects.get(id=self.id) duplicate.pk = None duplicate.slug = None duplicate.name = 'Copy of {}'.format(self.name) duplicate.duplic...
Move entity from source to destination collection. def move_to_collection(self, source_collection, destination_collection): """Move entity from source to destination collection.""" # Remove from collection. self.collections.remove(source_collection) # pylint: disable=no-member source_c...
unquote('abc%20def') -> 'abc def'. def unquote(s): """unquote('abc%20def') -> 'abc def'.""" res = s.split('%') # fastpath if len(res) == 1: return s s = res[0] for item in res[1:]: try: s += _hextochr[item[:2]] + item[2:] except KeyError: s += '%'...
Pass in a dictionary that has unsafe characters as the keys, and the percent encoded value as the value. def quote(s, unsafe='/'): """Pass in a dictionary that has unsafe characters as the keys, and the percent encoded value as the value.""" res = s.replace('%', '%25') for c in unsafe: res ...
Return dependencies, which should trigger updates of this model. def get_dependencies(self): """Return dependencies, which should trigger updates of this model.""" # pylint: disable=no-member return super().get_dependencies() + [ Data.collection_set, Data.entity_set, ...
3-loop computation of alpha_s for f flavours with initial condition alpha_s(MZ) = 0.1185 def alpha_s(scale, f, alphasMZ=0.1185, loop=3): """3-loop computation of alpha_s for f flavours with initial condition alpha_s(MZ) = 0.1185""" if scale == MZ and f == 5: return alphasMZ # nothing to do ...
r"""Get running b quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_b(m_b)$ def m_b(mbmb, scale, f, alphasMZ=0.1185, loop=3): r"""Get running b quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavo...
r"""Get running c quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_c(m_c)$ def m_c(mcmc, scale, f, alphasMZ=0.1185, loop=3): r"""Get running c quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavo...
r"""Get running s quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_s(2 \,\text{GeV})$ def m_s(ms2, scale, f, alphasMZ=0.1185, loop=3): r"""Get running s quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical q...
Get user confirmation to proceed. def get_confirmation(self): """Get user confirmation to proceed.""" if self.clear: action = 'This will DELETE ALL FILES in this location!' else: action = 'This will overwrite existing files!' message = ( "\n" ...
Delete contents of the directory on the given path. def clear_dir(self): """Delete contents of the directory on the given path.""" self.stdout.write("Deleting contents of '{}'.".format(self.destination_path)) for filename in os.listdir(self.destination_path): if os.path.isfile(file...
Change path prefix and include app name. def change_path_prefix(self, path, old_prefix, new_prefix, app_name): """Change path prefix and include app name.""" relative_path = os.path.relpath(path, old_prefix) return os.path.join(new_prefix, app_name, relative_path)
Get tools' locations and copy them to a single location. def collect(self): """Get tools' locations and copy them to a single location.""" for app_name, tools_path in get_apps_tools().items(): self.stdout.write("Copying files from '{}'.".format(tools_path)) app_name = app_name....
Collect tools. def handle(self, options): """Collect tools.""" self.set_options(options) os.makedirs(self.destination_path, exist_ok=True) if self.interactive and any(os.listdir(self.destination_path)): self.get_confirmation() if self.clear: self.c...
Compute checksum of processor inputs, name and version. def get_data_checksum(proc_input, proc_slug, proc_version): """Compute checksum of processor inputs, name and version.""" checksum = hashlib.sha256() checksum.update(json.dumps(proc_input, sort_keys=True).encode('utf-8')) checksum.update(proc_slug...
Get or set value using a dot-notation key in a multilevel dict. def dict_dot(d, k, val=None, default=None): """Get or set value using a dot-notation key in a multilevel dict.""" if val is None and k == '': return d def set_default(dict_or_model, key, default_value): """Set default field va...
Get applications' tools and their paths. Return a dict with application names as keys and paths to tools' directories as values. Applications without tools are omitted. def get_apps_tools(): """Get applications' tools and their paths. Return a dict with application names as keys and paths to tools' ...
Rewire inputs of provided data objects. Input parameter is a list of original and copied data object model instances: ``[{'original': original, 'copy': copy}]``. This function finds which objects reference other objects (in the list) on the input and replaces original objects with the copies (mutates ...
Parse the given XML and use the document element to create a Python instance. @param xml_text An XML document. This should be data (Python 2 str or Python 3 bytes), or a text (Python 2 unicode or Python 3 str) in the L{pyxb._InputEncoding} encoding. @keyword default_namespace The L{pyxb.Namespace} in...
Create a Python instance from the given DOM node. The node tag must correspond to an element declaration in this module. @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}. def CreateFromDOM(node, default_namespace=None): """Create a Python instance from the given DOM node...
Take care of any unfinished business. Despite the claims in the Cmd documentation, Cmd.postloop() is not a stub. def postloop(self): """Take care of any unfinished business. Despite the claims in the Cmd documentation, Cmd.postloop() is not a stub. """ cmd.Cmd.postloop(self) ...
This method is called after the line has been input but before it has been interpreted. If you want to modify the input line before execution (for example, variable substitution) do it here. def precmd(self, line): """This method is called after the line has been input but before it ha...
Called on an input line when the command prefix is not recognized. def default(self, line): """Called on an input line when the command prefix is not recognized.""" args = self._split_args(line, 0, 99) d1_cli.impl.util.print_error("Unknown command: {}".format(args[0]))
Get help on commands "help" or "?" with no arguments displays a list_objects of commands for which help is available "help <command>" or "? <command>" gives help on <command> def do_help(self, line): """Get help on commands "help" or "?" with no arguments displays a list_objects of com...
history Display a list of commands that have been entered. def do_history(self, line): """history Display a list of commands that have been entered.""" self._split_args(line, 0, 0) for idx, item in enumerate(self._history): d1_cli.impl.util.print_info("{0: 3d} {1}".format(idx, item)...
exit Exit from the CLI. def do_exit(self, line): """exit Exit from the CLI.""" n_remaining_operations = len(self._command_processor.get_operation_queue()) if n_remaining_operations: d1_cli.impl.util.print_warn( """There are {} unperformed operations in the write oper...
Exit on system EOF character. def do_eof(self, line): """Exit on system EOF character.""" d1_cli.impl.util.print_info("") self.do_exit(line)
set [parameter [value]] set (without parameters): Display the value of all session variables. set <session variable>: Display the value of a single session variable. set <session variable> <value>: Set the value of a session variable. def do_set(self, line): """set [parameter [value]] ...
load [file] Load session variables from file load (without parameters): Load session from default file ~/.dataone_cli.conf load. <file>: Load session from specified file. def do_load(self, line): """load [file] Load session variables from file load (without parameters): Load session fr...
save [config_file] Save session variables to file save (without parameters): Save session to default file ~/.dataone_cli.conf save. <file>: Save session to specified file. def do_save(self, line): """save [config_file] Save session variables to file save (without parameters): Save sess...
reset Set all session variables to their default values. def do_reset(self, line): """reset Set all session variables to their default values.""" self._split_args(line, 0, 0) self._command_processor.get_session().reset() self._print_info_if_verbose("Successfully reset session variables"...
allowaccess <subject> [access-level] Set the access level for subject Access level is "read", "write" or "changePermission". Access level defaults to "read" if not specified. Special subjects: public: Any subject, authenticated and not authenticated authenticatedUser: Any subject th...
denyaccess <subject> Remove subject from access policy. def do_denyaccess(self, line): """denyaccess <subject> Remove subject from access policy.""" subject, = self._split_args(line, 1, 0) self._command_processor.get_session().get_access_control().remove_allowed_subject( subject ...
clearaccess Remove all subjects from access policy Only the submitter will have access to the object. def do_clearaccess(self, line): """clearaccess Remove all subjects from access policy Only the submitter will have access to the object.""" self._split_args(line, 0, 0) self._co...
allowrep Allow new objects to be replicated. def do_allowrep(self, line): """allowrep Allow new objects to be replicated.""" self._split_args(line, 0, 0) self._command_processor.get_session().get_replication_policy().set_replication_allowed( True ) self._print_info_i...
denyrep Prevent new objects from being replicated. def do_denyrep(self, line): """denyrep Prevent new objects from being replicated.""" self._split_args(line, 0, 0) self._command_processor.get_session().get_replication_policy().set_replication_allowed( False ) self._...
preferrep <member node> [member node ...] Add one or more preferred Member Nodes to replication policy. def do_preferrep(self, line): """preferrep <member node> [member node ...] Add one or more preferred Member Nodes to replication policy.""" mns = self._split_args(line, 1, -1) ...
blockrep <member node> [member node ...] Add one or more blocked Member Node to replication policy. def do_blockrep(self, line): """blockrep <member node> [member node ...] Add one or more blocked Member Node to replication policy.""" mns = self._split_args(line, 1, -1) self._co...
removerep <member node> [member node ...] Remove one or more Member Nodes from replication policy. def do_removerep(self, line): """removerep <member node> [member node ...] Remove one or more Member Nodes from replication policy.""" mns = self._split_args(line, 1, -1) self._com...
numberrep <number of replicas> Set preferred number of replicas for new objects If the preferred number of replicas is set to zero, replication is also disallowed. def do_numberrep(self, line): """numberrep <number of replicas> Set preferred number of replicas for new objects If the pre...
clearrep Set the replication policy to default. The default replication policy has no preferred or blocked member nodes, allows replication and sets the preferred number of replicas to 3. def do_clearrep(self, line): """clearrep Set the replication policy to default. The default repli...
get <identifier> <file> Get an object from a Member Node. The object is saved to <file>. def do_get(self, line): """get <identifier> <file> Get an object from a Member Node. The object is saved to <file>. """ pid, output_file = self._split_args(line, 2, 0) self._comma...
meta <identifier> [file] Get the System Metadata that is associated with a Science Object. If the metadata is not on the Coordinating Node, the Member Node is checked. Provide ``file`` to save the System Metada to disk instead of displaying it. def do_meta(self, line): """meta <identi...
list [path] Retrieve a list of available Science Data Objects from Member Node The response is filtered by the from-date, to-date, search, start and count session variables. See also: search def do_list(self, line): """list [path] Retrieve a list of available Science Data Objects from ...
log [path] Retrieve event log from Member Node The response is filtered by the from-date, to-date, start and count session parameters. def do_log(self, line): """log [path] Retrieve event log from Member Node The response is filtered by the from-date, to-date, start and count session parameters...
resolve <identifier> Find all locations from which the given Science Object can be downloaded. def do_resolve(self, line): """resolve <identifier> Find all locations from which the given Science Object can be downloaded.""" pid, = self._split_args(line, 1, 0) self._command_proce...
create <identifier> <file> Create a new Science Object on a Member Node. The System Metadata that becomes associated with the new Science Object is generated from the session variables. def do_create(self, line): """create <identifier> <file> Create a new Science Object on a Member Node. ...
update <old-pid> <new-pid> <file> Replace an existing Science Object in a. :term:`MN` with another. def do_update(self, line): """update <old-pid> <new-pid> <file> Replace an existing Science Object in a. :term:`MN` with another. """ curr_pid, pid_new, input_file = self._spli...
package <package-pid> <science-metadata-pid> <science-pid> [science- pid. ...] Create a simple OAI-ORE Resource Map on a Member Node. def do_package(self, line): """package <package-pid> <science-metadata-pid> <science-pid> [science- pid. ...] Create a simple OAI-ORE Resource Map on a Member ...
archive <identifier> [identifier ...] Mark one or more existing Science Objects as archived. def do_archive(self, line): """archive <identifier> [identifier ...] Mark one or more existing Science Objects as archived.""" pids = self._split_args(line, 1, -1) self._command_processo...
updateaccess <identifier> [identifier ...] Update the Access Policy on one or more existing Science Data Objects. def do_updateaccess(self, line): """updateaccess <identifier> [identifier ...] Update the Access Policy on one or more existing Science Data Objects.""" pids = self._split_a...

Returns the memory byte size of a Numpy array as an integer. def bytesize(arr): """ Returns the memory byte size of a Numpy array as an integer. """ byte_size = np.prod(arr.shape) * np.dtype(arr.dtype).itemsize return byte_size

Similar to `numpy.apply_over_axes`, except this performs the operation over a flattened version of all the axes, meaning that the function will only be called once. This only makes a difference for non-linear functions. Parameters ---------- func : callback Function that operates well on Nu...

Argmax that returns an index tuple. Note that `numpy.argmax` will return a scalar index as if you had flattened the array. Parameters ---------- a : array_like Input array. Returns ------- index : tuple Tuple of index, even if `a` is one-dimensional. Note that this can ...

Context manager to make it easy to time the execution of a piece of code. This timer will never run your code several times and is meant more for simple in-production timing, instead of benchmarking. Reports the wall-clock time (using `time.time`) and not the processor time. Parameters ---------- ...

Pad an array with a specific value. Parameters ---------- data : ndarray Numpy array of any dimension and type. padwidth : int or tuple If int, it will pad using this amount at the beginning and end of all dimensions. If it is a tuple (of same length as `ndim`), then the ...

This is similar to `pad`, except you specify the final shape of the array. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.ndim``. If it has to pad unevenly, it will pad one m...

Similar to `pad`, except the border value from ``data`` is used to pad. Parameters ---------- data : ndarray Numpy array of any dimension and type. padwidth : int or tuple If int, it will pad using this amount at the beginning and end of all dimensions. If it is a tuple (of same...

Similar to `pad_repeat_border`, except the padding is always done on the upper end of each axis and the target size is specified. Parameters ---------- data : ndarray Numpy array of any dimension and type. shape : tuple Final shape of padded array. Should be tuple of length ``data.n...

This checks if a dictionary can be saved natively as HDF5 groups. If it can't, it will be pickled. def _dict_native_ok(d): """ This checks if a dictionary can be saved natively as HDF5 groups. If it can't, it will be pickled. """ if len(d) >= 256: return False # All keys must be ...

Loads level and builds appropriate type, without handling softlinks def _load_nonlink_level(handler, level, pathtable, pathname): """ Loads level and builds appropriate type, without handling softlinks """ if isinstance(level, tables.Group): if _sns and (level._v_title.startswith('SimpleNamespa...

Loads level and builds appropriate type, handling softlinks if necessary def _load_level(handler, level, pathtable): """ Loads level and builds appropriate type, handling softlinks if necessary """ if isinstance(level, tables.link.SoftLink): # this is a link, so see if target is already loaded,...

Save any Python structure to an HDF5 file. It is particularly suited for Numpy arrays. This function works similar to ``numpy.save``, except if you save a Python object at the top level, you do not need to issue ``data.flat[0]`` to retrieve it from inside a Numpy array of type ``object``. Some type...

Loads an HDF5 saved with `save`. This function requires the `PyTables <http://www.pytables.org/>`_ module to be installed. Parameters ---------- path : string Filename from which to load the data. group : string or list Load a specific group in the HDF5 hierarchy. If `group` is...

Sorts x with numeric semantics if all keys are nonnegative integers. Otherwise uses standard string sorting. def sorted_maybe_numeric(x): """ Sorts x with numeric semantics if all keys are nonnegative integers. Otherwise uses standard string sorting. """ all_numeric = all(map(str.isdigit, x)) ...

Color-aware abbreviator def abbreviate(s, maxlength=25): """Color-aware abbreviator""" assert maxlength >= 4 skip = False abbrv = None i = 0 for j, c in enumerate(s): if c == '\033': skip = True elif skip: if c == 'm': skip = False ...

Extend the settings the manager will serialize. :param data_id: The :class:`~resolwe.flow.models.Data` object id being prepared for. :param files: The settings dictionary to be serialized. Keys are filenames, values are the objects that will be serialized into those ...

Get tools' paths. def get_tools_paths(self): """Get tools' paths.""" if settings.DEBUG or is_testing(): return list(get_apps_tools().values()) else: tools_root = settings.FLOW_TOOLS_ROOT subdirs = next(os.walk(tools_root))[1] return [os.path.joi...

Resolve data path for use with the executor. :param data: Data object instance :param filename: Filename to resolve :return: Resolved filename, which can be used to access the given data file in programs executed using this executor def resolve_data_path(self, data=None, filename=N...

Resolve upload path for use with the executor. :param filename: Filename to resolve :return: Resolved filename, which can be used to access the given uploaded file in programs executed using this executor def resolve_upload_path(self, filename=None): """Resolve upload p...

Work with the AccessPolicy in a SystemMetadata PyXB object. Args: access_pyxb : AccessPolicy PyXB object The AccessPolicy to modify. read_only: bool Do not update the wrapped AccessPolicy. When only a single AccessPolicy operation is needed, there's no need to use this context...

Work with the AccessPolicy in a SystemMetadata PyXB object. Args: sysmeta_pyxb : SystemMetadata PyXB object SystemMetadata containing the AccessPolicy to modify. read_only: bool Do not update the wrapped AccessPolicy. When only a single AccessPolicy operation is needed, there's no...

Args: subj_str : str Subject for which to retrieve the highest permission. Return: The highest permission for subject or None if subject does not have any permissions. def get_highest_perm_str(self, subj_str): """ Args: subj_str : str Subject for which to retrieve th...

Args: subj_str : str Subject for which to retrieve the effective permissions. Returns: list of str: List of permissions up to and including the highest permission for subject, ordered lower to higher, or empty list if subject does not have any permissions. E.g.: If 'write' is...

Args: perm_str : str Permission, ``read``, ``write`` or ``changePermission``. Returns: set of str : Subj that have perm equal or higher than ``perm_str``. Since the lowest permission a subject can have is ``read``, passing ``read`` will return all subjects. def get_subjects_with_e...

Dump the current state to debug level log. def dump(self): """Dump the current state to debug level log.""" logging.debug('AccessPolicy:') map( logging.debug, [ ' {}'.format(s) for s in pprint.pformat(self.get_normalized_perm_list()).spli...

Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. def subj_has_perm(self, subj_str, perm_str): """Returns: bool: ``True`` if ``subj_str`` has perm equal to or higher than ``perm_str``. """ self._assert_valid_permission(perm_str) re...

Add ``read`` perm for all authenticated subj. Public ``read`` is removed if present. def add_authenticated_read(self): """Add ``read`` perm for all authenticated subj. Public ``read`` is removed if present. """ self.remove_perm(d1_common.const.SUBJECT_PUBLIC, 'read') ...

Add ``read`` perm for all verified subj. Public ``read`` is removed if present. def add_verified_read(self): """Add ``read`` perm for all verified subj. Public ``read`` is removed if present. """ self.remove_perm(d1_common.const.SUBJECT_PUBLIC, 'read') self.add_perm(d...

Add a permission for a subject. Args: subj_str : str Subject for which to add permission(s) perm_str : str Permission to add. Implicitly adds all lower permissions. E.g., ``write`` will also add ``read``. def add_perm(self, subj_str, perm_str): ...

Remove permission from a subject. Args: subj_str : str Subject for which to remove permission(s) perm_str : str Permission to remove. Implicitly removes all higher permissions. E.g., ``write`` will also remove ``changePermission`` if previously granted. ...

Remove all permissions for subject. Args: subj_str : str Subject for which to remove all permissions. Since subjects can only be present in the AccessPolicy when they have one or more permissions, this removes the subject itself as well. The subject ma...

Return dict representation of AccessPolicy PyXB obj. def _perm_dict_from_pyxb(self, access_pyxb): """Return dict representation of AccessPolicy PyXB obj.""" subj_dict = self._subj_dict_from_pyxb(access_pyxb) return self._perm_dict_from_subj_dict(subj_dict)

Return dict where keys and values of ``subj_dict`` have been flipped around. def _perm_dict_from_subj_dict(self, subj_dict): """Return dict where keys and values of ``subj_dict`` have been flipped around.""" perm_dict = {} for subj_str, perm_set in list(subj_dict.items()): ...

Return an AccessPolicy PyXB representation of ``perm_dict`` - If ``norm_perm_list`` is empty, None is returned. The schema does not allow AccessPolicy to be empty, but in SystemMetadata, it can be left out altogether. So returning None instead of an empty AccessPolicy allows the result ...

Return an AccessPolicy PyXB representation of ``norm_perm_list`` def _pyxb_from_norm_perm_list(self, norm_perm_list): """Return an AccessPolicy PyXB representation of ``norm_perm_list``""" # Using accessPolicy() instead of AccessPolicy() and accessRule() instead of # AccessRule() gives PyXB the...

Return a dict representation of ``access_pyxb``, which is an AccessPolicy PyXB object. This also remove any duplicate subjects and permissions in the PyXB object. def _subj_dict_from_pyxb(self, access_pyxb): """Return a dict representation of ``access_pyxb``, which is an AccessPolicy P...

Return a perm_dict where only the highest permission for each subject is included. def _highest_perm_dict_from_perm_dict(self, perm_dict): """Return a perm_dict where only the highest permission for each subject is included.""" highest_perm_dict = copy.copy(perm_dict) for ordere...

Return a minimal, ordered, hashable list of subjects and permissions. def _norm_perm_list_from_perm_dict(self, perm_dict): """Return a minimal, ordered, hashable list of subjects and permissions.""" high_perm_dict = self._highest_perm_dict_from_perm_dict(perm_dict) return [ [k, list...

Return list of effective permissions for for highest permission in ``perm_iter``, ordered lower to higher, or None if ``perm_iter`` is empty. def _effective_perm_list_from_iter(self, perm_iter): """Return list of effective permissions for for highest permission in ``perm_iter``, ordered lower t...

Return a set containing only the permissions that are present in the ``perm_dict`` for ``subj_str`` def _present_perm_set_for_subj(self, perm_dict, subj_str): """Return a set containing only the permissions that are present in the ``perm_dict`` for ``subj_str``""" return {p for p, s in ...

Return the highest perm present in ``perm_iter`` or None if ``perm_iter`` is empty. def _highest_perm_from_iter(self, perm_iter): """Return the highest perm present in ``perm_iter`` or None if ``perm_iter`` is empty.""" perm_set = set(perm_iter) for perm_str in reversed(ORDERED_...

Return the ordered index of ``perm_str`` or None if ``perm_str`` is not a valid permission. def _ordered_idx_from_perm(self, perm_str): """Return the ordered index of ``perm_str`` or None if ``perm_str`` is not a valid permission.""" for i, ordered_str in enumerate(ORDERED_PERM_LIST): ...

Raise D1 exception if ``perm_str`` is not a valid permission. def _assert_valid_permission(self, perm_str): """Raise D1 exception if ``perm_str`` is not a valid permission.""" if perm_str not in ORDERED_PERM_LIST: raise d1_common.types.exceptions.InvalidRequest( 0, ...

Suppress stack traces for common errors and provide hints for how to resolve them. def handle_unexpected_exception(max_traceback_levels=100): """Suppress stack traces for common errors and provide hints for how to resolve them.""" exc_type, exc_msgs = sys.exc_info()[:2] if exc_type.__name__ == "SSL...

Create object file and database entries for a new native locally stored (non- proxied) science object. This method takes a request object and is only called from the views that handle: - MNStorage.create() - MNStorage.update() Various sanity checking is performed. Raises D1 exceptions that ar...

Django stores small uploads in memory and streams large uploads directly to disk. Uploads stored in memory are represented by UploadedFile and on disk, TemporaryUploadedFile. To store an UploadedFile on disk, it's iterated and saved in chunks. To store a TemporaryUploadedFile, it's moved from the temporary...

See the description of TRUST_CLIENT_* in settings.py. def set_mn_controlled_values(request, sysmeta_pyxb, is_modification): """See the description of TRUST_CLIENT_* in settings.py.""" now_datetime = d1_common.date_time.utc_now() default_value_list = [ ('originMemberNode', django.conf.settings.NODE...

Duplicate (make a copy) ``Entity`` objects. :param contributor: Duplication user :param inherit_collections: If ``True`` then duplicated entities will be added to collections the original entity is part of. Duplicated entities' data objects will also be added to the ...

Move entities from source to destination collection. def move_to_collection(self, source_collection, destination_collection): """Move entities from source to destination collection.""" for entity in self: entity.move_to_collection(source_collection, destination_collection)

Duplicate (make a copy). def duplicate(self, contributor=None, inherit_collections=False): """Duplicate (make a copy).""" duplicate = Entity.objects.get(id=self.id) duplicate.pk = None duplicate.slug = None duplicate.name = 'Copy of {}'.format(self.name) duplicate.duplic...

Move entity from source to destination collection. def move_to_collection(self, source_collection, destination_collection): """Move entity from source to destination collection.""" # Remove from collection. self.collections.remove(source_collection) # pylint: disable=no-member source_c...

unquote('abc%20def') -> 'abc def'. def unquote(s): """unquote('abc%20def') -> 'abc def'.""" res = s.split('%') # fastpath if len(res) == 1: return s s = res[0] for item in res[1:]: try: s += _hextochr[item[:2]] + item[2:] except KeyError: s += '%'...

Pass in a dictionary that has unsafe characters as the keys, and the percent encoded value as the value. def quote(s, unsafe='/'): """Pass in a dictionary that has unsafe characters as the keys, and the percent encoded value as the value.""" res = s.replace('%', '%25') for c in unsafe: res ...

Return dependencies, which should trigger updates of this model. def get_dependencies(self): """Return dependencies, which should trigger updates of this model.""" # pylint: disable=no-member return super().get_dependencies() + [ Data.collection_set, Data.entity_set, ...

3-loop computation of alpha_s for f flavours with initial condition alpha_s(MZ) = 0.1185 def alpha_s(scale, f, alphasMZ=0.1185, loop=3): """3-loop computation of alpha_s for f flavours with initial condition alpha_s(MZ) = 0.1185""" if scale == MZ and f == 5: return alphasMZ # nothing to do ...

r"""Get running b quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_b(m_b)$ def m_b(mbmb, scale, f, alphasMZ=0.1185, loop=3): r"""Get running b quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavo...

r"""Get running c quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_c(m_c)$ def m_c(mcmc, scale, f, alphasMZ=0.1185, loop=3): r"""Get running c quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavo...

r"""Get running s quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical quark flavours starting from $m_s(2 \,\text{GeV})$ def m_s(ms2, scale, f, alphasMZ=0.1185, loop=3): r"""Get running s quark mass in the MSbar scheme at the scale `scale` in the theory with `f` dynamical q...

Get user confirmation to proceed. def get_confirmation(self): """Get user confirmation to proceed.""" if self.clear: action = 'This will DELETE ALL FILES in this location!' else: action = 'This will overwrite existing files!' message = ( "\n" ...

Delete contents of the directory on the given path. def clear_dir(self): """Delete contents of the directory on the given path.""" self.stdout.write("Deleting contents of '{}'.".format(self.destination_path)) for filename in os.listdir(self.destination_path): if os.path.isfile(file...

Change path prefix and include app name. def change_path_prefix(self, path, old_prefix, new_prefix, app_name): """Change path prefix and include app name.""" relative_path = os.path.relpath(path, old_prefix) return os.path.join(new_prefix, app_name, relative_path)

Get tools' locations and copy them to a single location. def collect(self): """Get tools' locations and copy them to a single location.""" for app_name, tools_path in get_apps_tools().items(): self.stdout.write("Copying files from '{}'.".format(tools_path)) app_name = app_name....

Collect tools. def handle(self, **options): """Collect tools.""" self.set_options(**options) os.makedirs(self.destination_path, exist_ok=True) if self.interactive and any(os.listdir(self.destination_path)): self.get_confirmation() if self.clear: self.c...

Compute checksum of processor inputs, name and version. def get_data_checksum(proc_input, proc_slug, proc_version): """Compute checksum of processor inputs, name and version.""" checksum = hashlib.sha256() checksum.update(json.dumps(proc_input, sort_keys=True).encode('utf-8')) checksum.update(proc_slug...

Get or set value using a dot-notation key in a multilevel dict. def dict_dot(d, k, val=None, default=None): """Get or set value using a dot-notation key in a multilevel dict.""" if val is None and k == '': return d def set_default(dict_or_model, key, default_value): """Set default field va...

Get applications' tools and their paths. Return a dict with application names as keys and paths to tools' directories as values. Applications without tools are omitted. def get_apps_tools(): """Get applications' tools and their paths. Return a dict with application names as keys and paths to tools' ...

Rewire inputs of provided data objects. Input parameter is a list of original and copied data object model instances: ``[{'original': original, 'copy': copy}]``. This function finds which objects reference other objects (in the list) on the input and replaces original objects with the copies (mutates ...

Parse the given XML and use the document element to create a Python instance. @param xml_text An XML document. This should be data (Python 2 str or Python 3 bytes), or a text (Python 2 unicode or Python 3 str) in the L{pyxb._InputEncoding} encoding. @keyword default_namespace The L{pyxb.Namespace} in...

Create a Python instance from the given DOM node. The node tag must correspond to an element declaration in this module. @deprecated: Forcing use of DOM interface is unnecessary; use L{CreateFromDocument}. def CreateFromDOM(node, default_namespace=None): """Create a Python instance from the given DOM node...

Take care of any unfinished business. Despite the claims in the Cmd documentation, Cmd.postloop() is not a stub. def postloop(self): """Take care of any unfinished business. Despite the claims in the Cmd documentation, Cmd.postloop() is not a stub. """ cmd.Cmd.postloop(self) ...

This method is called after the line has been input but before it has been interpreted. If you want to modify the input line before execution (for example, variable substitution) do it here. def precmd(self, line): """This method is called after the line has been input but before it ha...

Called on an input line when the command prefix is not recognized. def default(self, line): """Called on an input line when the command prefix is not recognized.""" args = self._split_args(line, 0, 99) d1_cli.impl.util.print_error("Unknown command: {}".format(args[0]))

Get help on commands "help" or "?" with no arguments displays a list_objects of commands for which help is available "help <command>" or "? <command>" gives help on <command> def do_help(self, line): """Get help on commands "help" or "?" with no arguments displays a list_objects of com...

history Display a list of commands that have been entered. def do_history(self, line): """history Display a list of commands that have been entered.""" self._split_args(line, 0, 0) for idx, item in enumerate(self._history): d1_cli.impl.util.print_info("{0: 3d} {1}".format(idx, item)...

exit Exit from the CLI. def do_exit(self, line): """exit Exit from the CLI.""" n_remaining_operations = len(self._command_processor.get_operation_queue()) if n_remaining_operations: d1_cli.impl.util.print_warn( """There are {} unperformed operations in the write oper...

Exit on system EOF character. def do_eof(self, line): """Exit on system EOF character.""" d1_cli.impl.util.print_info("") self.do_exit(line)

set [parameter [value]] set (without parameters): Display the value of all session variables. set <session variable>: Display the value of a single session variable. set <session variable> <value>: Set the value of a session variable. def do_set(self, line): """set [parameter [value]] ...

load [file] Load session variables from file load (without parameters): Load session from default file ~/.dataone_cli.conf load. <file>: Load session from specified file. def do_load(self, line): """load [file] Load session variables from file load (without parameters): Load session fr...

save [config_file] Save session variables to file save (without parameters): Save session to default file ~/.dataone_cli.conf save. <file>: Save session to specified file. def do_save(self, line): """save [config_file] Save session variables to file save (without parameters): Save sess...

reset Set all session variables to their default values. def do_reset(self, line): """reset Set all session variables to their default values.""" self._split_args(line, 0, 0) self._command_processor.get_session().reset() self._print_info_if_verbose("Successfully reset session variables"...

allowaccess <subject> [access-level] Set the access level for subject Access level is "read", "write" or "changePermission". Access level defaults to "read" if not specified. Special subjects: public: Any subject, authenticated and not authenticated authenticatedUser: Any subject th...

denyaccess <subject> Remove subject from access policy. def do_denyaccess(self, line): """denyaccess <subject> Remove subject from access policy.""" subject, = self._split_args(line, 1, 0) self._command_processor.get_session().get_access_control().remove_allowed_subject( subject ...

clearaccess Remove all subjects from access policy Only the submitter will have access to the object. def do_clearaccess(self, line): """clearaccess Remove all subjects from access policy Only the submitter will have access to the object.""" self._split_args(line, 0, 0) self._co...

allowrep Allow new objects to be replicated. def do_allowrep(self, line): """allowrep Allow new objects to be replicated.""" self._split_args(line, 0, 0) self._command_processor.get_session().get_replication_policy().set_replication_allowed( True ) self._print_info_i...

denyrep Prevent new objects from being replicated. def do_denyrep(self, line): """denyrep Prevent new objects from being replicated.""" self._split_args(line, 0, 0) self._command_processor.get_session().get_replication_policy().set_replication_allowed( False ) self._...

preferrep <member node> [member node ...] Add one or more preferred Member Nodes to replication policy. def do_preferrep(self, line): """preferrep <member node> [member node ...] Add one or more preferred Member Nodes to replication policy.""" mns = self._split_args(line, 1, -1) ...

blockrep <member node> [member node ...] Add one or more blocked Member Node to replication policy. def do_blockrep(self, line): """blockrep <member node> [member node ...] Add one or more blocked Member Node to replication policy.""" mns = self._split_args(line, 1, -1) self._co...

removerep <member node> [member node ...] Remove one or more Member Nodes from replication policy. def do_removerep(self, line): """removerep <member node> [member node ...] Remove one or more Member Nodes from replication policy.""" mns = self._split_args(line, 1, -1) self._com...

numberrep <number of replicas> Set preferred number of replicas for new objects If the preferred number of replicas is set to zero, replication is also disallowed. def do_numberrep(self, line): """numberrep <number of replicas> Set preferred number of replicas for new objects If the pre...

clearrep Set the replication policy to default. The default replication policy has no preferred or blocked member nodes, allows replication and sets the preferred number of replicas to 3. def do_clearrep(self, line): """clearrep Set the replication policy to default. The default repli...

get <identifier> <file> Get an object from a Member Node. The object is saved to <file>. def do_get(self, line): """get <identifier> <file> Get an object from a Member Node. The object is saved to <file>. """ pid, output_file = self._split_args(line, 2, 0) self._comma...

meta <identifier> [file] Get the System Metadata that is associated with a Science Object. If the metadata is not on the Coordinating Node, the Member Node is checked. Provide ``file`` to save the System Metada to disk instead of displaying it. def do_meta(self, line): """meta <identi...

list [path] Retrieve a list of available Science Data Objects from Member Node The response is filtered by the from-date, to-date, search, start and count session variables. See also: search def do_list(self, line): """list [path] Retrieve a list of available Science Data Objects from ...

log [path] Retrieve event log from Member Node The response is filtered by the from-date, to-date, start and count session parameters. def do_log(self, line): """log [path] Retrieve event log from Member Node The response is filtered by the from-date, to-date, start and count session parameters...

resolve <identifier> Find all locations from which the given Science Object can be downloaded. def do_resolve(self, line): """resolve <identifier> Find all locations from which the given Science Object can be downloaded.""" pid, = self._split_args(line, 1, 0) self._command_proce...

create <identifier> <file> Create a new Science Object on a Member Node. The System Metadata that becomes associated with the new Science Object is generated from the session variables. def do_create(self, line): """create <identifier> <file> Create a new Science Object on a Member Node. ...

update <old-pid> <new-pid> <file> Replace an existing Science Object in a. :term:`MN` with another. def do_update(self, line): """update <old-pid> <new-pid> <file> Replace an existing Science Object in a. :term:`MN` with another. """ curr_pid, pid_new, input_file = self._spli...

package <package-pid> <science-metadata-pid> <science-pid> [science- pid. ...] Create a simple OAI-ORE Resource Map on a Member Node. def do_package(self, line): """package <package-pid> <science-metadata-pid> <science-pid> [science- pid. ...] Create a simple OAI-ORE Resource Map on a Member ...

archive <identifier> [identifier ...] Mark one or more existing Science Objects as archived. def do_archive(self, line): """archive <identifier> [identifier ...] Mark one or more existing Science Objects as archived.""" pids = self._split_args(line, 1, -1) self._command_processo...

updateaccess <identifier> [identifier ...] Update the Access Policy on one or more existing Science Data Objects. def do_updateaccess(self, line): """updateaccess <identifier> [identifier ...] Update the Access Policy on one or more existing Science Data Objects.""" pids = self._split_a...