hdmf.spec.catalog module

class hdmf.spec.catalog.SpecCatalog

Bases: object

Create a new catalog for storing specifications

** Private Instance Variables **

Variables:

__specs – Dict with the specification of each registered type
__parent_types – Dict with parent types for each registered type
__spec_source_files – Dict with the path to the source files (if available) for each registered type
__hierarchy – Dict describing the hierarchy for each registered type. NOTE: Always use SpecCatalog.get_hierarchy(…) to retrieve the hierarchy as this dictionary is used like a cache, i.e., to avoid repeated calculation of the hierarchy but the contents are computed on first request by SpecCatalog.get_hierarchy(…)

register_spec(spec, source_file=None)

Associate a specified object type with a specification

Parameters:

spec (BaseStorageSpec) – a Spec object
source_file (str) – path to the source file from which the spec was loaded

get_spec(data_type)

Get the Spec object for the given type

Parameters:: data_type (str) – the data_type to get the Spec for
Returns:: the specification for writing the given object type to HDF5
Return type:: Spec

get_registered_types(): Return all registered specifications

get_spec_source_file(data_type)

Return the path to the source file from which the spec for the given: type was loaded from. None is returned if no file path is available for the spec. Note: The spec in the file may not be identical to the object in case the spec is modified after load.

Parameters:: data_type (str) – the data_type of the spec to get the source file for
Returns:: the path to source specification file from which the spec was originally loaded or None
Return type:: str

auto_register(spec, source_file=None)

Register this specification and all sub-specification using data_type as object type name

Parameters:

spec (BaseStorageSpec) – the Spec object to register
source_file (str) – path to the source file from which the spec was loaded

Returns:

the types that were registered with this spec

Return type:

tuple

get_hierarchy(data_type)

For a given type get the type inheritance hierarchy for that type.

E.g., if we have a type MyContainer that inherits from BaseContainer then the result will be a tuple with the strings (‘MyContainer’, ‘BaseContainer’)

Parameters:: data_type (str or type) – the data_type to get the hierarchy of
Returns:: Tuple of strings with the names of the types the given data_type inherits from.
Return type:: tuple

get_full_hierarchy()

Get the complete hierarchy of all types. The function attempts to sort types by name using: standard Python sorted.

Returns:: Hierarchically nested OrderedDict with the hierarchy of all the types
Return type:: OrderedDict

get_subtypes(data_type, recursive=True)

For a given data type recursively find all the subtypes that inherit from it.

E.g., assume we have the following inheritance hierarchy:
-BaseContainer--+-->AContainer--->ADContainer
                |
                +-->BContainer
In this case, the subtypes of BaseContainer would be (AContainer, ADContainer, BContainer), the subtypes of AContainer would be (ADContainer), and the subtypes of BContainer would be empty ().

Parameters:

data_type (str or type) – the data_type to get the subtypes for
recursive (bool) – recursively get all subtypes. Set to False to only get the direct subtypes

Returns:

Tuple of strings with the names of all types of the given data_type.

Return type:

tuple