bluepyemodel.emodel_pipeline.emodel_metadata

EModelMetadata class

Functions

update_metadata_dict(metadata_dict, var, new_key)

Update metadata dict with new key and variable if not None.

Classes

EModelMetadata([emodel, etype, ttype, ...])

Contains the metadata of an emodel such as its e-model name or its brain region.
class EModelMetadata(emodel=None, etype=None, ttype=None, mtype=None, species=None, brain_region=None, iteration_tag=None, synapse_class=None, allen_notation=None)

Bases: object

Contains the metadata of an emodel such as its e-model name or its brain region. These metadata can be understood as a unique identifier of an e-model.

This class is a backend class and is not meant to be used directly by the user.

Constructor

Parameters:

  • emodel (str) – name of the e-model

  • etype (str) – name of the electric type of the e-model.

  • ttype (str) – name of the transcriptomic type of the e-model.

  • mtype (str) – name of the morphology type of the e-model.

  • species (str) – name of the species of the e-model.

  • brain_region (str) – name of the brain location of the e-model.

  • iteration_tag (str) – tag associated to the current run.

  • synapse_class (str) – synapse class (neurotransmitter) of the e-model.

  • allen_notation (str) – Allen acronym for the brain region (Optional). Can be used to replace brain region in as_string().

annotation_list(is_analysis_suitable=False, is_curated=False)

Returns an annotation list containing mtype, etype and ttype annotations.

Parameters:

is_analysis_suitable (bool) – Should be True only when managing metatada for resources of type EModel, for which all data are complete (has FCC, ETC, EMC, etc.).

as_dict()

Metadata as dict.

as_dict_for_resource()

Metadata as a dict, with keys consistent with nexus.

as_dict_for_resource_legacy()

Metadata as a dict, with keys consistent with legacy nexus.

check_emodel_name()

Check if name complies with requirements: https://nrn.readthedocs.io/en/8.2.3/guide/hoc_chapter_11_old_reference.html#names

etype_annotation_dict()

Returns an etype annotation dict to be added to annotations list.

filters_for_resource()

Metadata used for filtering, without the annotation list

filters_for_resource_legacy()

Legacy metadata used for filtering, without the annotation list

for_resource(is_analysis_suitable=False, is_curated=False)

Metadata to add to a resource to register.

DO NOT use for filtering. For filtering, use self.filters_for_resource() instead.

Parameters:

is_analysis_suitable (bool) – Should be True only when managing metatada for resources of type EModel, for which all data are complete (has FCC, ETC, EMC, etc.).

mtype_annotation_dict()

Returns an mtype annotation dict to be added to annotations list.

ttype_annotation_dict()

Returns an ttype annotation dict to be added to annotations list.

update_metadata_dict(metadata_dict, var, new_key)

Update metadata dict with new key and variable if not None.