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 calcuation 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