JorgeVB/code_unlearning_dataset · Data Studio

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Check whether the outputs of the pipeline are present in all sessions in the project repository and were generated with matching provenance. Return an 2D boolean array (subjects: rows, visits: cols) with the sessions to process marked True. Parameters ---------- pipeline...
'Dialates' a to_process/to_protect array to include all subject and/or visits if the pipeline contains any joins over the corresponding iterators. Parameters ---------- array : np.array[M, N] The array to potentially dialate iterators : set[str] T...
Intercept calls to get template and return our own node-specific template def _get_args(self, node, keywords): """ Intercept calls to get template and return our own node-specific template """ args = super(ArcanaSlurmGraphPlugin, self)._get_args( node, keywor...
Returns the wall time in the format required for the sbatch script def wall_time_str(self, wall_time): """ Returns the wall time in the format required for the sbatch script """ days = int(wall_time // 1440) hours = int((wall_time - days * 1440) // 60) minutes = int(math...
Retrieve panel information from ElkM1 def sync(self): """Retrieve panel information from ElkM1""" self._elk.add_handler('VN', self._vn_handler) self._elk.add_handler('XK', self._xk_handler) self._elk.add_handler('RP', self._rp_handler) self._elk.add_handler('IE', self._elk.call_...
(Helper) Set thermostat def set(self, element_to_set, value): """(Helper) Set thermostat""" self._elk.send(ts_encode(self.index, value, element_to_set))
Duplicate the datum and rename it def renamed(self, name): """ Duplicate the datum and rename it """ duplicate = copy(self) duplicate._name = name return duplicate
Compares the version with another Parameters ---------- other : Version The version to compare to def compare(self, other): """ Compares the version with another Parameters ---------- other : Version The version to compare to ...
Splits a typical version string (e.g. <MAJOR>.<MINOR>.<MICRO>) into a tuple that can be sorted properly. Ignores all leading and trailing characters by using a regex search (instead of match) so as to pick the version string out of a block of text. Parameters ---------- ...
A single version can also be interpreted as an open range (i.e. no maximum version) def within(self, version): """ A single version can also be interpreted as an open range (i.e. no maximum version) """ if not isinstance(version, Version): version = type(self...
Returns either a single requirement version or a requirement version range depending on whether two arguments are supplied or one Parameters ---------- version : str \| Version Either a version of the requirement, or the first version in a range of acceptable vers...
Open a connection to the database. If a connection appears to be open already, transactions are committed and it is closed before proceeding. After establishing the connection, the searchIndex table is prepared (and dropped if it already exists). def open(self): '''Open a connection to...
Insert an entry into the Zeal database. Args: name: A string representing the name of the entry. entry_type: A string representing the entry type. filename: A string representing the filename of the documentation for the entry. Raises: Ru...
A simple wrapper of Django's serializer with defaults for JSON and natural keys. Note: use_natural_primary_keys is False as once a pk is set, it should not be changed throughout the distributed data. def serialize(objects=None): """A simple wrapper of Django's serializer with defaults for JSON...
Returns the Fileset(s) or Field(s) associated with the provided spec name(s), generating derived filesets as required. Multiple names in a list can be provided, to allow their workflows to be combined into a single workflow. Parameters ---------- name : str \| List[str] ...
Checks whether the given switch matches the value provided Parameters ---------- name : str The name of the parameter to retrieve value : str \| None The value(s) of the switch to match if a non-boolean switch def branch(self, name, values=None): # @UnusedVariab...
Convenient method for raising exception if a pipeline doesn't handle a particular switch value Parameters ---------- name : str Name of the switch value : str Value of the switch which hasn't been handled def unhandled_branch(self, name): """ ...
Saves a graph of the workflow to generate the requested spec_name Parameters ---------- spec_name : str Name of the spec to generate the graph for fname : str The filename for the saved graph style : str The style of the graph, can be one of c...
Returns either the input corresponding to a fileset or field field spec or a spec or parameter that has either been passed to the study as an input or can be derived. Parameters ---------- name : Str \| BaseData \| Parameter A parameter, fileset or field or name of one...
Returns an input selector or derived spec bound to the study, i.e. where the repository tree is checked for existing outputs Parameters ---------- name : Str A name of a fileset or field def bound_spec(self, name): """ Returns an input selector or derived sp...
Return the fileset_spec, i.e. the template of the fileset expected to be supplied or generated corresponding to the fileset_spec name. Parameters ---------- name : Str Name of the fileset_spec to return def data_spec(cls, name): """ Return the fileset_spec, ...
Runs the Study's repository source node for each of the inputs of the study, thereby caching any data required from remote repositorys. Useful when launching many parallel jobs that will all try to concurrently access the remote repository, and probably lead to timeout errors. def cache...
Checks to see whether the corresponding data spec was provided an explicit input, as opposed to derivatives or missing optional inputs Parameters ---------- spec_name : str Name of a data spec def provided(self, spec_name, default_okay=True): """ Checks to s...
Returns the frequency corresponding to the given iterators def freq_from_iterators(cls, iterators): """ Returns the frequency corresponding to the given iterators """ return { set(it): f for f, it in cls.FREQUENCIES.items()}[set(iterators)]
Extracts provenance information from the study for storage alongside generated derivatives. Typically for reference purposes only as only the pipeline workflow, inputs and outputs are checked by default when determining which sessions require reprocessing. Returns ------- ...
(Helper) Arm system at specified level (away, vacation, etc) def arm(self, level, code): """(Helper) Arm system at specified level (away, vacation, etc)""" self._elk.send(al_encode(level, self._index, code))
Display a message on all of the keypads in this area. def display_message(self, clear, beep, timeout, line1, line2): """Display a message on all of the keypads in this area.""" self._elk.send( dm_encode(self._index, clear, beep, timeout, line1, line2) )
Retrieve areas from ElkM1 def sync(self): """Retrieve areas from ElkM1""" self.elk.send(as_encode()) self.get_descriptions(TextDescriptions.AREA.value)
(Helper) Set light to specified level def level(self, level, time=0): """(Helper) Set light to specified level""" if level <= 0: self._elk.send(pf_encode(self._index)) elif level >= 98: self._elk.send(pn_encode(self._index)) else: self._elk.send(pc_en...
Retrieve lights from ElkM1 def sync(self): """Retrieve lights from ElkM1""" for i in range(4): self.elk.send(ps_encode(i)) self.get_descriptions(TextDescriptions.LIGHT.value)
Returns the latest modification time of all files/subdirectories in a directory def dir_modtime(dpath): """ Returns the latest modification time of all files/subdirectories in a directory """ return max(os.path.getmtime(d) for d, _, _ in os.walk(dpath))
A extension splitter that checks for compound extensions such as 'file.nii.gz' Parameters ---------- filename : str A filename to split into base and extension Returns ------- base : str The base part of the string, i.e. 'file' of 'file.nii.gz' ext : str The ext...
Tries to convert to int, float and then gives up and assumes the value is of type string. Useful when excepting values that may be string representations of numerical values def parse_single_value(value): """ Tries to convert to int, float and then gives up and assumes the value is of type string. ...
Checks whether all the provided items are containers (i.e of class list, dict, tuple, etc...) def iscontainer(*items): """ Checks whether all the provided items are containers (i.e of class list, dict, tuple, etc...) """ return all(isinstance(i, Iterable) and not isinstance(i, basestring) ...
Finds where two objects differ, iterating down into nested containers (i.e. dicts, lists and tuples) They can be nested containers any combination of primary dtypes, str, int, float, dict and lists Parameters ---------- first : dict \| list \| tuple \| str \| int \| float The first object to com...
Returns a generator of deserialized objects. Wraps django deserialize with defaults for JSON and natural keys. See https://docs.djangoproject.com/en/2.1/topics/serialization/ def deserialize(json_text=None): """Returns a generator of deserialized objects. Wraps django deserialize with defaults f...
Create token when a user is created (from rest_framework). def create_auth_token(sender, instance, raw, created, **kwargs): """Create token when a user is created (from rest_framework). """ if not raw: if created: sender.objects.create(user=instance)
Part of the serialize transaction process that ensures m2m are serialized correctly. Skip those not registered. def serialize_m2m_on_save(sender, action, instance, using, **kwargs): """ Part of the serialize transaction process that ensures m2m are serialized correctly. Skip those not registered....
Serialize the model instance as an OutgoingTransaction. Skip those not registered. def serialize_on_save(sender, instance, raw, created, using, **kwargs): """ Serialize the model instance as an OutgoingTransaction. Skip those not registered. """ if not raw: if "historical" not in instance...
Serialize the history instance as an OutgoingTransaction. Skip those not registered. def serialize_history_on_post_create(history_instance, using, **kwargs): """ Serialize the history instance as an OutgoingTransaction. Skip those not registered. """ try: wrapped_instance = site_offline_m...
Creates a serialized OutgoingTransaction when a model instance is deleted. Skip those not registered. def serialize_on_post_delete(sender, instance, using, **kwargs): """Creates a serialized OutgoingTransaction when a model instance is deleted. Skip those not registered. """ try: ...
(Helper) Set custom value. def set(self, value): """(Helper) Set custom value.""" self._elk.send(cw_encode(self._index, value, self.value_format))
Retrieve custom values from ElkM1 def sync(self): """Retrieve custom values from ElkM1""" self.elk.send(cp_encode()) self.get_descriptions(TextDescriptions.SETTING.value)
Iterates through all files in the set def paths(self): """Iterates through all files in the set""" if self.format is None: raise ArcanaFileFormatError( "Cannot get paths of fileset ({}) that hasn't had its format " "set".format(self)) if self.format.d...
Detects the format of the fileset from a list of possible candidates. If multiple candidates match the potential files, e.g. NiFTI-X (see dcm2niix) and NiFTI, then the first matching candidate is selected. If a 'format_name' was specified when the fileset was created then that i...
Test the equality of the fileset contents with another fileset. If the fileset's format implements a 'contents_equal' method than that is used to determine the equality, otherwise a straight comparison of the checksums is used. Parameters ---------- other : Fileset ...
Returns a copy of the AcquiredSpec bound to the given study Parameters ---------- study : Study A study to bind the fileset spec to (should happen in the study __init__) def bind(self, study, **kwargs): # @UnusedVariable """ Returns a copy of the Acquir...
Returns a copy of the Spec bound to the given study Parameters ---------- study : Study A study to bind the fileset spec to (should happen in the study __init__) def bind(self, study, **kwargs): # @UnusedVariable """ Returns a copy of the Spec bound to ...
Returns the relevant nodes for the spec's frequency def nodes(self, tree): """ Returns the relevant nodes for the spec's frequency """ # Run the match against the tree if self.frequency == 'per_session': nodes = [] for subject in tree.subjects: ...
Whether the spec (only valid for derived specs) can be derived given the inputs and switches provided to the study def derivable(self): """ Whether the spec (only valid for derived specs) can be derived given the inputs and switches provided to the study """ try: ...
Re-establish connection to all instances def reconnect_all(self): """ Re-establish connection to all instances """ for role in self.Instances.keys(): for connection in self.Instances[role]: connection.reconnect()
Add instance to the setup @param role: instance's role @type role: str @param instance: host parameters we would like to establish connection to @type instance: dict @param username: user name for creating ssh connection @type username: str ...
Setup from yaml config @param yamlfile: path to yaml config file @type yamlfile: str @param output_shell: write output from this connection to standard output @type output_shell: bool def setup_from_yamlfile(self, yamlfile, output_shell=False): """...
helper function to iterate over a process stdout and report error messages when done def process_iter(proc, cmd=""): """ helper function to iterate over a process stdout and report error messages when done """ try: for l in proc.stdout: yield l finally: if proc.p...
just grab the header from a given file def header(fname, sep="\t"): """ just grab the header from a given file """ fh = iter(nopen(fname)) h = tokens(next(fh), sep) h[0] = h[0].lstrip("#") return h
r""" for each row in the file `fname` generate dicts If `header` is True or lists if `header` is False. The dict keys are drawn from the first line. If `header` is a list of names, those will be used as the dict keys. If `header` is 'ordered', the function will yield ordered dicts. If `header` i...
check that all b files have been modified more recently than a def is_newer_b(a, bfiles): """ check that all b files have been modified more recently than a """ if isinstance(bfiles, basestring): bfiles = [bfiles] if not op.exists(a): return False if not all(op.exists(b) for b in bfile...
Expect a list of expressions @param connection: Connection to the host @type connection: L{Connection} @param regexp_list: regular expressions and associated return values @type regexp_list: list of (regexp, return value) @param timeout: timeout for performing expect operation...
Expect one expression @param connection: Connection to the host @type connection: L{Connection} @param strexp: string to convert to expression (.string.) @type strexp: str @param timeout: timeout for performing expect operation @type timeout: int @return: Tr...
Match against an expression @param connection: Connection to the host @type connection: L{Connection} @param regexp: compiled regular expression @type regexp: L{SRE_Pattern} @param grouplist: list of groups to return @type group: list of int @param timeout: ti...
Enter a command and wait for something to happen (enter + expect combined) @param connection: connection to the host @type connection: L{Connection} @param command: command to execute @type command: str @param strexp: string to convert to expression (.string.) ...
Run command and expect specified return valud @param connection: connection to the host @type connection: L{Connection} @param command: command to execute @type command: str @param expected_status: expected return value @type expected_status: int @param timeou...
Retrieve areas from ElkM1 def sync(self): """Retrieve areas from ElkM1""" self.elk.send(ka_encode()) self.get_descriptions(TextDescriptions.KEYPAD.value)
Yield tags matching the tag criterion from a soup. There is no need to override this if you are satisfied with finding tags that match match_criterion. Args: soup: A BeautifulSoup to search through. Yields: BeautifulSoup Tags that match the criterion. def find...
Extract and return a representative "name" from a tag. Override as necessary. get_name's output can be controlled through keyword arguments that are provided when initializing a TagProcessor. For instance, a member of a class or namespace can have its parent scope included in the name b...
Extract and return a documentation filename from a tag. Override as necessary, though this default implementation probably covers all the cases of interest. Args: tag: A BeautifulSoup Tag that satisfies match_criterion. Returns: A string that would be appropria...
Override. Determine if a tag has the desired name and kind attribute value. Args: tag: A BeautifulSoup Tag. Returns: True if tag has the desired name and kind, otherwise False. def match_criterion(self, tag): '''Override. Determine if a tag has the desired name...
Override. Extract a representative "name" from a function tag. get_name's output can be controlled through keyword arguments that are provided when initializing a functionTagProcessor. For instance, function arguments and return types can be included by passing include_function_signatur...
Override that returns u'Method' for class/struct methods. Override as necessary. Args: tag: A BeautifulSoup Tag for a function. Returns: If this is a class/struct method, returns u'Method', otherwise returns the value from the inherited implementation of ...
create a multiprocessing pool that responds to interrupts. def pool(n=None, dummy=False): """ create a multiprocessing pool that responds to interrupts. """ if dummy: from multiprocessing.dummy import Pool else: from multiprocessing import Pool if n is None: import mult...
parallel map of a function to an iterable if each item in iterable is itself an iterable, then automatically call f(*item) instead of f(item) Arguments: f: function iterable: any iterable where each item is sent to f n: number of cpus (default is number on machine) dummy: use dummy ...
Callbacks when attribute of element changes def _call_callbacks(self): """Callbacks when attribute of element changes""" for callback in self._callbacks: callback(self, self._changeset) self._changeset = {}
If attribute value has changed then set it and call the callbacks def setattr(self, attr, new_value, close_the_changeset=True): """If attribute value has changed then set it and call the callbacks""" existing_value = getattr(self, attr, None) if existing_value != new_value: setattr(...
Return a default name for based on class and index of element def default_name(self, separator='-'): """Return a default name for based on class and index of element""" return self.__class__.__name__ + '{}{:03d}'.format( separator, self._index+1)
Package up the public attributes as a dict. def as_dict(self): """Package up the public attributes as a dict.""" attrs = vars(self) return {key: attrs[key] for key in attrs if not key.startswith('_')}
Gets the descriptions for specified type. When complete the callback is called with a list of descriptions def get_descriptions(self, description_type): """ Gets the descriptions for specified type. When complete the callback is called with a list of descriptions """ (de...
(:class:`str`) The canonical url of the page. def page_url(self) -> str: """(:class:`str`) The canonical url of the page.""" url = self.attributes['canonicalurl'] assert isinstance(url, str) return url
r"""(:class:`~typing.Optional`\ [:class:`str`]) The image url. It may be :const:`None` if it's not an image. def image_url(self) -> Optional[str]: r"""(:class:`~typing.Optional`\ [:class:`str`]) The image url. It may be :const:`None` if it's not an image. """ images = self.attr...
r"""(:class:`~typing.Optional`\ [:class:`~typing.Tuple`\ [:class:`int`, :class:`int`]]) The (width, height) pair of the image. It may be :const:`None` if it's not an image. def image_resolution(self) -> Optional[Tuple[int, int]]: r"""(:class:`~typing.Optional`\ [:class:`~typing.Tuple`\ [:class:...
r"""(:class:`~typing.Optional`\ [:class:`int`]) The size of the image in bytes. It may be :const:`None` if it's not an image. def image_size(self) -> Optional[int]: r"""(:class:`~typing.Optional`\ [:class:`int`]) The size of the image in bytes. It may be :const:`None` if it's not an image. ...
Determine the normalized locale code string. >>> normalize_locale_code('ko-kr') 'ko_KR' >>> normalize_locale_code('zh_TW') 'zh_Hant_TW' >>> normalize_locale_code(Locale.parse('en_US')) 'en_US' def normalize_locale_code(locale: Union[Locale, str]) -> str: """Determine the normalized locale ...
Get a Wikidata entity by its :class:`~.entity.EntityId`. :param entity_id: The :attr:`~.entity.Entity.id` of the :class:`~.entity.Entity` to find. :type eneity_id: :class:`~.entity.EntityId` :param load: Eager loading on :const:`True`. Lazy loading...
r"""Guess :class:`~.entity.EntityType` from the given :class:`~.entity.EntityId`. It could return :const:`None` when it fails to guess. .. note:: It always fails to guess when :attr:`entity_type_guess` is configued to :const:`False`. :return: The guessed :class:...
Decode the given ``datavalue`` using the configured :attr:`datavalue_decoder`. .. versionadded:: 0.3.0 def decode_datavalue(self, datatype: str, datavalue: Mapping[str, object]) -> object: """Decode the given ``datavalue`` using the configured ...
r"""Create or update a cache. :param key: A key string to create or update. :type key: :const:`CacheKey` :param value: A value to cache. :const:`None` to remove cache. :type value: :class:`~typing.Optional`\ [:const:`CacheValue`] def set(self, key: CacheKey, value: Optional[CacheValue...
r"""Return all values associated to the given ``key`` property in sequence. :param key: The property entity. :type key: :class:`Entity` :return: A sequence of all values associated to the given ``key`` property. It can be empty if nothing is associated to ...
(:class:`EntityType`) The type of entity, :attr:`~EntityType.item` or :attr:`~EntityType.property`. .. versionadded:: 0.2.0 def type(self) -> EntityType: """(:class:`EntityType`) The type of entity, :attr:`~EntityType.item` or :attr:`~EntityType.property`. .. versionadded:: 0....
Create the user-role association table so that it correctly references your own UserMixin subclass. def make_user_role_table(table_name='user', id_column_name='id'): """ Create the user-role association table so that it correctly references your own UserMixin subclass. """ return ...
Takes an ability (a string name of either a role or an ability) and returns the function if the user has that ability def user_has(ability, get_user=import_user): """ Takes an ability (a string name of either a role or an ability) and returns the function if the user has that ability """ def wrapper(fu...
Takes an role (a string name of either a role or an ability) and returns the function if the user has that role def user_is(role, get_user=import_user): """ Takes an role (a string name of either a role or an ability) and returns the function if the user has that role """ def wrapper(func): @wr...
Handles generating a 'combo' file for the given path. This is similar to what happens when we upload to S3. Processors are applied, and we get the value that we would if we were serving from S3. This is a good way to make sure combo files work as intended before rolling out to production. def combo_ser...
Given a URL path, massage it into a key we can perform a lookup on the MEDIASYNC['JOINED'] dict with. This mostly involves figuring into account the CSS_PATH and JS_PATH settings, if they have been set. def _form_key_str(path): """ Given a URL path, massage it into a key we can perform a looku...
Calculate the key to check the MEDIASYNC['JOINED'] dict for, perform the lookup, and return the matching key string if a match is found. If no match is found, return None instead. def _find_combo_match(path): """ Calculate the key to check the MEDIASYNC['JOINED'] dict for, perform the lookup, and r...
Given a request for a media asset, this view does the necessary wrangling to get the correct thing delivered to the user. This can also emulate the combo behavior seen when SERVE_REMOTE == False and EMULATE_COMBO == True. def static_serve(request, path, client): """ Given a request for a media asset, t...
Create a HTTP server and start it. :param int port_number: the port number to bind the server to :param int number_of_procs: number of processes to pass to Tornado's ``httpserver.HTTPServer.start``. If the application's ``debug`` setting is ``True``, then we are going to ru...
Create the server and run the IOLoop. :param int port_number: the port number to bind the server to :param int number_of_procs: number of processes to pass to Tornado's ``httpserver.HTTPServer.start``. If the application's ``debug`` setting is ``True``, then we are going to...
Sets 'short_description' attribute (this attribute is in exports to generate header name). def short_description(description): """ Sets 'short_description' attribute (this attribute is in exports to generate header name). """ def decorator(func): if isinstance(func, property): func ...
Adds configuration parameters from a Python module. def add_module(self, module): ''' Adds configuration parameters from a Python module. ''' for key, value in module.__dict__.iteritems(): if key[0:2] != '__': self.__setattr__(attr=key, value=value)
Redirects the user to the login page, passing the given 'next' page def redirect_to_login(next, redirect_field_name=REDIRECT_FIELD_NAME): """ Redirects the user to the login page, passing the given 'next' page """ resolved_url = reverse('IS:login') login_url_parts = list(urlparse(resolved_url)) ...
If customer is not authorized he should not get information that object is exists. Therefore 403 is returned if object was not found or is redirected to the login page. If custmer is authorized and object was not found is returned 404. If object was found and user is not authorized is returned 4...

Check whether the outputs of the pipeline are present in all sessions in the project repository and were generated with matching provenance. Return an 2D boolean array (subjects: rows, visits: cols) with the sessions to process marked True. Parameters ---------- pipeline...

'Dialates' a to_process/to_protect array to include all subject and/or visits if the pipeline contains any joins over the corresponding iterators. Parameters ---------- array : np.array[M, N] The array to potentially dialate iterators : set[str] T...

Intercept calls to get template and return our own node-specific template def _get_args(self, node, keywords): """ Intercept calls to get template and return our own node-specific template """ args = super(ArcanaSlurmGraphPlugin, self)._get_args( node, keywor...

Returns the wall time in the format required for the sbatch script def wall_time_str(self, wall_time): """ Returns the wall time in the format required for the sbatch script """ days = int(wall_time // 1440) hours = int((wall_time - days * 1440) // 60) minutes = int(math...

Retrieve panel information from ElkM1 def sync(self): """Retrieve panel information from ElkM1""" self._elk.add_handler('VN', self._vn_handler) self._elk.add_handler('XK', self._xk_handler) self._elk.add_handler('RP', self._rp_handler) self._elk.add_handler('IE', self._elk.call_...

(Helper) Set thermostat def set(self, element_to_set, value): """(Helper) Set thermostat""" self._elk.send(ts_encode(self.index, value, element_to_set))

Duplicate the datum and rename it def renamed(self, name): """ Duplicate the datum and rename it """ duplicate = copy(self) duplicate._name = name return duplicate

Compares the version with another Parameters ---------- other : Version The version to compare to def compare(self, other): """ Compares the version with another Parameters ---------- other : Version The version to compare to ...

Splits a typical version string (e.g. <MAJOR>.<MINOR>.<MICRO>) into a tuple that can be sorted properly. Ignores all leading and trailing characters by using a regex search (instead of match) so as to pick the version string out of a block of text. Parameters ---------- ...

A single version can also be interpreted as an open range (i.e. no maximum version) def within(self, version): """ A single version can also be interpreted as an open range (i.e. no maximum version) """ if not isinstance(version, Version): version = type(self...

Returns either a single requirement version or a requirement version range depending on whether two arguments are supplied or one Parameters ---------- version : str | Version Either a version of the requirement, or the first version in a range of acceptable vers...

Open a connection to the database. If a connection appears to be open already, transactions are committed and it is closed before proceeding. After establishing the connection, the searchIndex table is prepared (and dropped if it already exists). def open(self): '''Open a connection to...

Insert an entry into the Zeal database. Args: name: A string representing the name of the entry. entry_type: A string representing the entry type. filename: A string representing the filename of the documentation for the entry. Raises: Ru...

A simple wrapper of Django's serializer with defaults for JSON and natural keys. Note: use_natural_primary_keys is False as once a pk is set, it should not be changed throughout the distributed data. def serialize(objects=None): """A simple wrapper of Django's serializer with defaults for JSON...

Returns the Fileset(s) or Field(s) associated with the provided spec name(s), generating derived filesets as required. Multiple names in a list can be provided, to allow their workflows to be combined into a single workflow. Parameters ---------- name : str | List[str] ...

Checks whether the given switch matches the value provided Parameters ---------- name : str The name of the parameter to retrieve value : str | None The value(s) of the switch to match if a non-boolean switch def branch(self, name, values=None): # @UnusedVariab...

Convenient method for raising exception if a pipeline doesn't handle a particular switch value Parameters ---------- name : str Name of the switch value : str Value of the switch which hasn't been handled def unhandled_branch(self, name): """ ...

Saves a graph of the workflow to generate the requested spec_name Parameters ---------- spec_name : str Name of the spec to generate the graph for fname : str The filename for the saved graph style : str The style of the graph, can be one of c...

Returns either the input corresponding to a fileset or field field spec or a spec or parameter that has either been passed to the study as an input or can be derived. Parameters ---------- name : Str | BaseData | Parameter A parameter, fileset or field or name of one...

Returns an input selector or derived spec bound to the study, i.e. where the repository tree is checked for existing outputs Parameters ---------- name : Str A name of a fileset or field def bound_spec(self, name): """ Returns an input selector or derived sp...

Return the fileset_spec, i.e. the template of the fileset expected to be supplied or generated corresponding to the fileset_spec name. Parameters ---------- name : Str Name of the fileset_spec to return def data_spec(cls, name): """ Return the fileset_spec, ...

Runs the Study's repository source node for each of the inputs of the study, thereby caching any data required from remote repositorys. Useful when launching many parallel jobs that will all try to concurrently access the remote repository, and probably lead to timeout errors. def cache...

Checks to see whether the corresponding data spec was provided an explicit input, as opposed to derivatives or missing optional inputs Parameters ---------- spec_name : str Name of a data spec def provided(self, spec_name, default_okay=True): """ Checks to s...

Returns the frequency corresponding to the given iterators def freq_from_iterators(cls, iterators): """ Returns the frequency corresponding to the given iterators """ return { set(it): f for f, it in cls.FREQUENCIES.items()}[set(iterators)]

Extracts provenance information from the study for storage alongside generated derivatives. Typically for reference purposes only as only the pipeline workflow, inputs and outputs are checked by default when determining which sessions require reprocessing. Returns ------- ...

(Helper) Arm system at specified level (away, vacation, etc) def arm(self, level, code): """(Helper) Arm system at specified level (away, vacation, etc)""" self._elk.send(al_encode(level, self._index, code))

Display a message on all of the keypads in this area. def display_message(self, clear, beep, timeout, line1, line2): """Display a message on all of the keypads in this area.""" self._elk.send( dm_encode(self._index, clear, beep, timeout, line1, line2) )

Retrieve areas from ElkM1 def sync(self): """Retrieve areas from ElkM1""" self.elk.send(as_encode()) self.get_descriptions(TextDescriptions.AREA.value)

(Helper) Set light to specified level def level(self, level, time=0): """(Helper) Set light to specified level""" if level <= 0: self._elk.send(pf_encode(self._index)) elif level >= 98: self._elk.send(pn_encode(self._index)) else: self._elk.send(pc_en...

Retrieve lights from ElkM1 def sync(self): """Retrieve lights from ElkM1""" for i in range(4): self.elk.send(ps_encode(i)) self.get_descriptions(TextDescriptions.LIGHT.value)

Returns the latest modification time of all files/subdirectories in a directory def dir_modtime(dpath): """ Returns the latest modification time of all files/subdirectories in a directory """ return max(os.path.getmtime(d) for d, _, _ in os.walk(dpath))

A extension splitter that checks for compound extensions such as 'file.nii.gz' Parameters ---------- filename : str A filename to split into base and extension Returns ------- base : str The base part of the string, i.e. 'file' of 'file.nii.gz' ext : str The ext...

Tries to convert to int, float and then gives up and assumes the value is of type string. Useful when excepting values that may be string representations of numerical values def parse_single_value(value): """ Tries to convert to int, float and then gives up and assumes the value is of type string. ...

Checks whether all the provided items are containers (i.e of class list, dict, tuple, etc...) def iscontainer(*items): """ Checks whether all the provided items are containers (i.e of class list, dict, tuple, etc...) """ return all(isinstance(i, Iterable) and not isinstance(i, basestring) ...

Finds where two objects differ, iterating down into nested containers (i.e. dicts, lists and tuples) They can be nested containers any combination of primary dtypes, str, int, float, dict and lists Parameters ---------- first : dict | list | tuple | str | int | float The first object to com...

Returns a generator of deserialized objects. Wraps django deserialize with defaults for JSON and natural keys. See https://docs.djangoproject.com/en/2.1/topics/serialization/ def deserialize(json_text=None): """Returns a generator of deserialized objects. Wraps django deserialize with defaults f...

Create token when a user is created (from rest_framework). def create_auth_token(sender, instance, raw, created, **kwargs): """Create token when a user is created (from rest_framework). """ if not raw: if created: sender.objects.create(user=instance)

Part of the serialize transaction process that ensures m2m are serialized correctly. Skip those not registered. def serialize_m2m_on_save(sender, action, instance, using, **kwargs): """ Part of the serialize transaction process that ensures m2m are serialized correctly. Skip those not registered....

Serialize the model instance as an OutgoingTransaction. Skip those not registered. def serialize_on_save(sender, instance, raw, created, using, **kwargs): """ Serialize the model instance as an OutgoingTransaction. Skip those not registered. """ if not raw: if "historical" not in instance...

Serialize the history instance as an OutgoingTransaction. Skip those not registered. def serialize_history_on_post_create(history_instance, using, **kwargs): """ Serialize the history instance as an OutgoingTransaction. Skip those not registered. """ try: wrapped_instance = site_offline_m...

Creates a serialized OutgoingTransaction when a model instance is deleted. Skip those not registered. def serialize_on_post_delete(sender, instance, using, **kwargs): """Creates a serialized OutgoingTransaction when a model instance is deleted. Skip those not registered. """ try: ...

(Helper) Set custom value. def set(self, value): """(Helper) Set custom value.""" self._elk.send(cw_encode(self._index, value, self.value_format))

Retrieve custom values from ElkM1 def sync(self): """Retrieve custom values from ElkM1""" self.elk.send(cp_encode()) self.get_descriptions(TextDescriptions.SETTING.value)

Iterates through all files in the set def paths(self): """Iterates through all files in the set""" if self.format is None: raise ArcanaFileFormatError( "Cannot get paths of fileset ({}) that hasn't had its format " "set".format(self)) if self.format.d...

Detects the format of the fileset from a list of possible candidates. If multiple candidates match the potential files, e.g. NiFTI-X (see dcm2niix) and NiFTI, then the first matching candidate is selected. If a 'format_name' was specified when the fileset was created then that i...

Test the equality of the fileset contents with another fileset. If the fileset's format implements a 'contents_equal' method than that is used to determine the equality, otherwise a straight comparison of the checksums is used. Parameters ---------- other : Fileset ...

Returns a copy of the AcquiredSpec bound to the given study Parameters ---------- study : Study A study to bind the fileset spec to (should happen in the study __init__) def bind(self, study, **kwargs): # @UnusedVariable """ Returns a copy of the Acquir...

Returns a copy of the Spec bound to the given study Parameters ---------- study : Study A study to bind the fileset spec to (should happen in the study __init__) def bind(self, study, **kwargs): # @UnusedVariable """ Returns a copy of the Spec bound to ...

Returns the relevant nodes for the spec's frequency def nodes(self, tree): """ Returns the relevant nodes for the spec's frequency """ # Run the match against the tree if self.frequency == 'per_session': nodes = [] for subject in tree.subjects: ...

Whether the spec (only valid for derived specs) can be derived given the inputs and switches provided to the study def derivable(self): """ Whether the spec (only valid for derived specs) can be derived given the inputs and switches provided to the study """ try: ...

Re-establish connection to all instances def reconnect_all(self): """ Re-establish connection to all instances """ for role in self.Instances.keys(): for connection in self.Instances[role]: connection.reconnect()

Add instance to the setup @param role: instance's role @type role: str @param instance: host parameters we would like to establish connection to @type instance: dict @param username: user name for creating ssh connection @type username: str ...

Setup from yaml config @param yamlfile: path to yaml config file @type yamlfile: str @param output_shell: write output from this connection to standard output @type output_shell: bool def setup_from_yamlfile(self, yamlfile, output_shell=False): """...

helper function to iterate over a process stdout and report error messages when done def process_iter(proc, cmd=""): """ helper function to iterate over a process stdout and report error messages when done """ try: for l in proc.stdout: yield l finally: if proc.p...

just grab the header from a given file def header(fname, sep="\t"): """ just grab the header from a given file """ fh = iter(nopen(fname)) h = tokens(next(fh), sep) h[0] = h[0].lstrip("#") return h

r""" for each row in the file `fname` generate dicts If `header` is True or lists if `header` is False. The dict keys are drawn from the first line. If `header` is a list of names, those will be used as the dict keys. If `header` is 'ordered', the function will yield ordered dicts. If `header` i...

check that all b files have been modified more recently than a def is_newer_b(a, bfiles): """ check that all b files have been modified more recently than a """ if isinstance(bfiles, basestring): bfiles = [bfiles] if not op.exists(a): return False if not all(op.exists(b) for b in bfile...

Expect a list of expressions @param connection: Connection to the host @type connection: L{Connection} @param regexp_list: regular expressions and associated return values @type regexp_list: list of (regexp, return value) @param timeout: timeout for performing expect operation...

Expect one expression @param connection: Connection to the host @type connection: L{Connection} @param strexp: string to convert to expression (.*string.*) @type strexp: str @param timeout: timeout for performing expect operation @type timeout: int @return: Tr...

Match against an expression @param connection: Connection to the host @type connection: L{Connection} @param regexp: compiled regular expression @type regexp: L{SRE_Pattern} @param grouplist: list of groups to return @type group: list of int @param timeout: ti...

Enter a command and wait for something to happen (enter + expect combined) @param connection: connection to the host @type connection: L{Connection} @param command: command to execute @type command: str @param strexp: string to convert to expression (.*string.*) ...

Run command and expect specified return valud @param connection: connection to the host @type connection: L{Connection} @param command: command to execute @type command: str @param expected_status: expected return value @type expected_status: int @param timeou...

Retrieve areas from ElkM1 def sync(self): """Retrieve areas from ElkM1""" self.elk.send(ka_encode()) self.get_descriptions(TextDescriptions.KEYPAD.value)

Yield tags matching the tag criterion from a soup. There is no need to override this if you are satisfied with finding tags that match match_criterion. Args: soup: A BeautifulSoup to search through. Yields: BeautifulSoup Tags that match the criterion. def find...

Extract and return a representative "name" from a tag. Override as necessary. get_name's output can be controlled through keyword arguments that are provided when initializing a TagProcessor. For instance, a member of a class or namespace can have its parent scope included in the name b...

Extract and return a documentation filename from a tag. Override as necessary, though this default implementation probably covers all the cases of interest. Args: tag: A BeautifulSoup Tag that satisfies match_criterion. Returns: A string that would be appropria...

Override. Determine if a tag has the desired name and kind attribute value. Args: tag: A BeautifulSoup Tag. Returns: True if tag has the desired name and kind, otherwise False. def match_criterion(self, tag): '''Override. Determine if a tag has the desired name...

Override. Extract a representative "name" from a function tag. get_name's output can be controlled through keyword arguments that are provided when initializing a functionTagProcessor. For instance, function arguments and return types can be included by passing include_function_signatur...

Override that returns u'Method' for class/struct methods. Override as necessary. Args: tag: A BeautifulSoup Tag for a function. Returns: If this is a class/struct method, returns u'Method', otherwise returns the value from the inherited implementation of ...

create a multiprocessing pool that responds to interrupts. def pool(n=None, dummy=False): """ create a multiprocessing pool that responds to interrupts. """ if dummy: from multiprocessing.dummy import Pool else: from multiprocessing import Pool if n is None: import mult...

parallel map of a function to an iterable if each item in iterable is itself an iterable, then automatically call f(*item) instead of f(item) Arguments: f: function iterable: any iterable where each item is sent to f n: number of cpus (default is number on machine) dummy: use dummy ...

Callbacks when attribute of element changes def _call_callbacks(self): """Callbacks when attribute of element changes""" for callback in self._callbacks: callback(self, self._changeset) self._changeset = {}

If attribute value has changed then set it and call the callbacks def setattr(self, attr, new_value, close_the_changeset=True): """If attribute value has changed then set it and call the callbacks""" existing_value = getattr(self, attr, None) if existing_value != new_value: setattr(...

Return a default name for based on class and index of element def default_name(self, separator='-'): """Return a default name for based on class and index of element""" return self.__class__.__name__ + '{}{:03d}'.format( separator, self._index+1)

Package up the public attributes as a dict. def as_dict(self): """Package up the public attributes as a dict.""" attrs = vars(self) return {key: attrs[key] for key in attrs if not key.startswith('_')}

Gets the descriptions for specified type. When complete the callback is called with a list of descriptions def get_descriptions(self, description_type): """ Gets the descriptions for specified type. When complete the callback is called with a list of descriptions """ (de...

(:class:`str`) The canonical url of the page. def page_url(self) -> str: """(:class:`str`) The canonical url of the page.""" url = self.attributes['canonicalurl'] assert isinstance(url, str) return url

r"""(:class:`~typing.Optional`\ [:class:`str`]) The image url. It may be :const:`None` if it's not an image. def image_url(self) -> Optional[str]: r"""(:class:`~typing.Optional`\ [:class:`str`]) The image url. It may be :const:`None` if it's not an image. """ images = self.attr...

r"""(:class:`~typing.Optional`\ [:class:`~typing.Tuple`\ [:class:`int`, :class:`int`]]) The (width, height) pair of the image. It may be :const:`None` if it's not an image. def image_resolution(self) -> Optional[Tuple[int, int]]: r"""(:class:`~typing.Optional`\ [:class:`~typing.Tuple`\ [:class:...

r"""(:class:`~typing.Optional`\ [:class:`int`]) The size of the image in bytes. It may be :const:`None` if it's not an image. def image_size(self) -> Optional[int]: r"""(:class:`~typing.Optional`\ [:class:`int`]) The size of the image in bytes. It may be :const:`None` if it's not an image. ...

Determine the normalized locale code string. >>> normalize_locale_code('ko-kr') 'ko_KR' >>> normalize_locale_code('zh_TW') 'zh_Hant_TW' >>> normalize_locale_code(Locale.parse('en_US')) 'en_US' def normalize_locale_code(locale: Union[Locale, str]) -> str: """Determine the normalized locale ...

Get a Wikidata entity by its :class:`~.entity.EntityId`. :param entity_id: The :attr:`~.entity.Entity.id` of the :class:`~.entity.Entity` to find. :type eneity_id: :class:`~.entity.EntityId` :param load: Eager loading on :const:`True`. Lazy loading...

r"""Guess :class:`~.entity.EntityType` from the given :class:`~.entity.EntityId`. It could return :const:`None` when it fails to guess. .. note:: It always fails to guess when :attr:`entity_type_guess` is configued to :const:`False`. :return: The guessed :class:...

Decode the given ``datavalue`` using the configured :attr:`datavalue_decoder`. .. versionadded:: 0.3.0 def decode_datavalue(self, datatype: str, datavalue: Mapping[str, object]) -> object: """Decode the given ``datavalue`` using the configured ...

r"""Create or update a cache. :param key: A key string to create or update. :type key: :const:`CacheKey` :param value: A value to cache. :const:`None` to remove cache. :type value: :class:`~typing.Optional`\ [:const:`CacheValue`] def set(self, key: CacheKey, value: Optional[CacheValue...

r"""Return all values associated to the given ``key`` property in sequence. :param key: The property entity. :type key: :class:`Entity` :return: A sequence of all values associated to the given ``key`` property. It can be empty if nothing is associated to ...

(:class:`EntityType`) The type of entity, :attr:`~EntityType.item` or :attr:`~EntityType.property`. .. versionadded:: 0.2.0 def type(self) -> EntityType: """(:class:`EntityType`) The type of entity, :attr:`~EntityType.item` or :attr:`~EntityType.property`. .. versionadded:: 0....

Create the user-role association table so that it correctly references your own UserMixin subclass. def make_user_role_table(table_name='user', id_column_name='id'): """ Create the user-role association table so that it correctly references your own UserMixin subclass. """ return ...

Takes an ability (a string name of either a role or an ability) and returns the function if the user has that ability def user_has(ability, get_user=import_user): """ Takes an ability (a string name of either a role or an ability) and returns the function if the user has that ability """ def wrapper(fu...

Takes an role (a string name of either a role or an ability) and returns the function if the user has that role def user_is(role, get_user=import_user): """ Takes an role (a string name of either a role or an ability) and returns the function if the user has that role """ def wrapper(func): @wr...

Handles generating a 'combo' file for the given path. This is similar to what happens when we upload to S3. Processors are applied, and we get the value that we would if we were serving from S3. This is a good way to make sure combo files work as intended before rolling out to production. def combo_ser...

Given a URL path, massage it into a key we can perform a lookup on the MEDIASYNC['JOINED'] dict with. This mostly involves figuring into account the CSS_PATH and JS_PATH settings, if they have been set. def _form_key_str(path): """ Given a URL path, massage it into a key we can perform a looku...

Calculate the key to check the MEDIASYNC['JOINED'] dict for, perform the lookup, and return the matching key string if a match is found. If no match is found, return None instead. def _find_combo_match(path): """ Calculate the key to check the MEDIASYNC['JOINED'] dict for, perform the lookup, and r...

Given a request for a media asset, this view does the necessary wrangling to get the correct thing delivered to the user. This can also emulate the combo behavior seen when SERVE_REMOTE == False and EMULATE_COMBO == True. def static_serve(request, path, client): """ Given a request for a media asset, t...

Create a HTTP server and start it. :param int port_number: the port number to bind the server to :param int number_of_procs: number of processes to pass to Tornado's ``httpserver.HTTPServer.start``. If the application's ``debug`` setting is ``True``, then we are going to ru...

Create the server and run the IOLoop. :param int port_number: the port number to bind the server to :param int number_of_procs: number of processes to pass to Tornado's ``httpserver.HTTPServer.start``. If the application's ``debug`` setting is ``True``, then we are going to...

Sets 'short_description' attribute (this attribute is in exports to generate header name). def short_description(description): """ Sets 'short_description' attribute (this attribute is in exports to generate header name). """ def decorator(func): if isinstance(func, property): func ...

Adds configuration parameters from a Python module. def add_module(self, module): ''' Adds configuration parameters from a Python module. ''' for key, value in module.__dict__.iteritems(): if key[0:2] != '__': self.__setattr__(attr=key, value=value)

Redirects the user to the login page, passing the given 'next' page def redirect_to_login(next, redirect_field_name=REDIRECT_FIELD_NAME): """ Redirects the user to the login page, passing the given 'next' page """ resolved_url = reverse('IS:login') login_url_parts = list(urlparse(resolved_url)) ...

If customer is not authorized he should not get information that object is exists. Therefore 403 is returned if object was not found or is redirected to the login page. If custmer is authorized and object was not found is returned 404. If object was found and user is not authorized is returned 4...