hdmf.spec.namespace module

class hdmf.spec.namespace.SpecNamespace(doc, name, schema, full_name=None, version=None, date=None, author=None, contact=None, catalog=None)

Bases: dict

A namespace for specifications

Parameters:

doc (str) – a description about what this namespace represents
name (str) – the name of this namespace
schema (list) – location of schema specification files or other Namespaces
full_name (str) – extended full name of this namespace
version (str or tuple or list) – Version number of the namespace
date (datetime or str) – Date last modified or released. Formatting is %Y-%m-%d %H:%M:%S, e.g, 2017-04-25 17:14:13
author (str or list) – Author or list of authors.
contact (str or list) – List of emails. Ordering should be the same as for author
catalog (SpecCatalog) – The SpecCatalog object for this SpecNamespace

UNVERSIONED = None

classmethod types_key()

Get the key used for specifying types to include from a file or namespace

Override this method to use a different name for ‘data_types’

property full_name: String with full name or None

property contact: String or list of strings with the contacts or None

property author: String or list of strings with the authors or None

property version: String, list, or tuple with the version or SpecNamespace.UNVERSIONED if the version is missing or empty

property date

Date last modified or released.

Returns:: datetime object, string, or None

property name: String with short name or None

property doc

property schema

get_source_files(): Get the list of names of the source files included the schema of the namespace

get_source_description(sourcefile)

Get the description of a source file as described in the namespace. The result is a dict which contains the ‘source’ and optionally ‘title’, ‘doc’ and ‘data_types’ imported from the source file

Parameters:: sourcefile (str) – Name of the source file
Returns:: Dict with the source file documentation
Return type:: dict

property catalog: The SpecCatalog containing all the Specs

get_spec(data_type)

Get the Spec object for the given data type

Parameters:: data_type (str or type) – the data_type to get the spec for

get_registered_types()

Get the available types in this namespace

Returns:: the a tuple of the available data types
Return type:: tuple

get_hierarchy(data_type)

Get the extension hierarchy for the given data_type in this namespace

Parameters:: data_type (str or type) – the data_type to get the hierarchy of
Returns:: a tuple with the type hierarchy
Return type:: tuple

classmethod build_namespace(**spec_dict)

class hdmf.spec.namespace.SpecReader(source)

Bases: object

Parameters:: source (str) – the source from which this reader reads from

property source

abstractmethod read_spec()

abstractmethod read_namespace()

class hdmf.spec.namespace.YAMLSpecReader(indir='.')

Bases: SpecReader

Parameters:: indir (str) – the path spec files are relative to

read_namespace(namespace_path)

read_spec(spec_path)

class hdmf.spec.namespace.NamespaceCatalog(group_spec_cls=<class 'hdmf.spec.spec.GroupSpec'>, dataset_spec_cls=<class 'hdmf.spec.spec.DatasetSpec'>, spec_namespace_cls=<class 'hdmf.spec.namespace.SpecNamespace'>, core_namespaces=[])

Bases: object

Create a catalog for storing multiple Namespaces

Parameters:

group_spec_cls (type) – the class to use for group specifications
dataset_spec_cls (type) – the class to use for dataset specifications
spec_namespace_cls (type) – the class to use for specification namespaces
core_namespaces (list) – the names of the core namespaces

merge(ns_catalog)

property namespaces

The namespaces in this NamespaceCatalog

Returns:: a tuple of the available namespaces
Return type:: tuple

property dataset_spec_cls: The DatasetSpec class used in this NamespaceCatalog

property group_spec_cls: The GroupSpec class used in this NamespaceCatalog

property spec_namespace_cls: The SpecNamespace class used in this NamespaceCatalog

property core_namespaces: The core namespaces used in this NamespaceCatalog

get_source_types(ns_name)

Get the source types for a namespace.

Returns a tuple of data type names that were loaded from source files for the given namespace.

add_namespace(name, namespace)

Add a namespace to this catalog

Parameters:

name (str) – the name of this namespace
namespace (SpecNamespace) – the SpecNamespace object

get_namespace(name)

Get the a SpecNamespace

Parameters:: name (str) – the name of this namespace
Returns:: the SpecNamespace with the given name
Return type:: SpecNamespace

get_spec(namespace, data_type)

Get the Spec object for the given type from the given Namespace

Parameters:

namespace (str) – the name of the namespace
data_type (str or type) – the data_type to get the spec for

Returns:

the specification for writing the given object type to HDF5

Return type:

Spec

get_hierarchy(namespace, data_type)

Get the type hierarchy for a given data_type in a given namespace

Parameters:

namespace (str) – the name of the namespace
data_type (str or type) – the data_type to get the spec for

Returns:

a tuple with the type hierarchy

Return type:

tuple

is_sub_data_type(namespace, data_type, parent_data_type)

Return whether or not data_type is a sub data_type of parent_data_type

Parameters:

namespace (str) – the name of the namespace containing the data_type
data_type (str) – the data_type to check
parent_data_type (str) – the potential parent data_type

Returns:

True if data_type is a sub data_type of parent_data_type, False otherwise

Return type:

bool

get_sources(): Get all the source specification files that were loaded in this catalog

get_namespace_sources(namespace)

Get all the source specifications that were loaded for a given namespace

Parameters:: namespace (str) – the name of the namespace

get_types(source)

Get the types that were loaded from a given source

Parameters:: source (str) – the name of the source

get_spec_source_dict(source)

Get the unresolved specs for a given source file. Returns a dict with ‘datasets’ and ‘groups’ keys containing lists of unresolved Spec objects (before resolution of inherited fields). Returns None if the source is not found.

Parameters:: source (str) – the name of the source file

resolve_all_specs() → None

Resolve all specs in all namespaces in the catalog.

This method resolves all type-level includes (merging parent type fields into child types) and subspec-level includes (merging included type fields into subspecs). It uses a recursive depth-first approach with cycle detection to handle containment cycles (e.g., DynamicTable contains MeaningsTable, MeaningsTable extends DynamicTable).

load_namespaces(namespace_path, resolve=True, reader=None)

Load the namespaces in the given file

Parameters:

namespace_path (str) – the path to the file containing the namespaces(s) to load
resolve (bool) – whether or not to include objects from included/parent spec objects. In practice, this is False when generating documentation where it is useful to show the unresolved specs
reader (SpecReader or dict) – the SpecReader or dict of SpecReader classes to use for reading specifications

Returns:

a dictionary describing the dependencies of loaded namespaces

Return type:

dict

warn_for_ignored_namespaces(ignored_namespaces)

Warning if namespaces were ignored where a different version was already loaded

Parameters:: ignored_namespaces (list) – name, cached version, and loaded version of the namespace