hdmf.term_set module¶
- class hdmf.term_set.TermSet(term_schema_path: str | None = None, schemasheets_folder: str | None = None, dynamic: bool = False)¶
Bases:
object
Class for implementing term sets from ontologies and other resources used to define the meaning and/or identify of terms.
- Variables:
term_schema_path – The path to the LinkML YAML enumeration schema
sources – The prefixes for the ontologies used in the TermSet
view – SchemaView of the term set schema
schemasheets_folder – The path to the folder containing the LinkML TSV files
expanded_termset_path – The path to the schema with the expanded enumerations
- Parameters:
term_schema_path – The path to the LinkML YAML enumeration schema
schemasheets_folder – The path to the folder containing the LinkML TSV files
dynamic – Boolean parameter denoting whether the schema uses Dynamic Enumerations
- validate(term)¶
Validate term in dataset towards a termset.
- Parameters:
term (
str
) – term to be validated
- property view_set¶
Property method to return a view of all terms in the the LinkML YAML Schema.
- __getitem__(term)¶
Method to retrieve a term and term information (LinkML description and LinkML meaning) from the set of terms.
- class hdmf.term_set.TermSetWrapper(termset, value, field=None)¶
Bases:
object
This class allows any HDF5 dataset or attribute to have a TermSet.
- Parameters:
- property value¶
- property field¶
- property termset¶
- property dtype¶
- __getitem__(val)¶
This is used when we want to index items.
- append(arg)¶
This append resolves the wrapper to use the append of the container using the wrapper.
- extend(arg)¶
This append resolves the wrapper to use the extend of the container using the wrapper.
- class hdmf.term_set.TypeConfigurator(path=None)¶
Bases:
object
This class allows users to toggle on/off a global configuration for defined data types. When toggled on, every instance of a configuration file supported data type will be validated according to the corresponding TermSet.
- Parameters:
path (
str
) – Path to the configuration file.
- get_config(data_type, namespace)¶
Return the config for that data type in the given namespace.
- load_type_config(config_path)¶
Load the configuration file for validation on the fields defined for the objects within the file.
- Parameters:
config_path (
str
) – Path to the configuration file.
- unload_type_config()¶
Remove validation according to termset configuration file.