modos.helpers.schema#

Introspection utilities for the MODO schema.

This module provides helpers for accessing the schema structure and for converting instances to different representations.

Attributes#

SCHEMA_PATH

Classes#

`UserElementType`	Enumeration of element types exposed to the user.
`ElementType`	Enumeration of all element types.

Functions#

`class_from_name`(name)
`dict_to_instance`(element)
`is_full_id`(element_id)	Checks if an element_id contains the element type as prefix.
`set_haspart_relationship`(child_class, child_path, ...)	Add element to the hasPart attribute of a parent zarr group
`update_haspart_id`(element)	update the id of the has_part property of an element to use the full id including its type
`set_data_path`(element[, source_file])	Set the data_path attribute, if it is not specified to the modo root.
`is_uri`(text)	Checks if input is a valid URI.
`load_schema`()	Return a view over the schema structure.
`load_prefixmap`()	Load the prefixmap.
`get_slots`(target_class[, required_only])	Return a list of required slots for a class.
`instance_to_graph`(instance)
`get_slot_range`(slot_name)	Return the class-independent range of a slot.
`get_enum_values`(enum_name)
`get_haspart_property`(child_class)	Return the name of the "has_part" property for a target class.

Module Contents#

modos.helpers.schema.SCHEMA_PATH[source]#

modos.helpers.schema.class_from_name(name)[source]#

Parameters:: name (str)

modos.helpers.schema.dict_to_instance(element)[source]#

Parameters:: element (Mapping[str, Any])
Return type:: Any

modos.helpers.schema.is_full_id(element_id)[source]#

Checks if an element_id contains the element type as prefix.

Examples

>>> is_full_id("sample1")
False
>>> is_full_id("data/test")
True
>>> is_full_id("/assay/test_assay")
True

Parameters:: element_id (str)
Return type:: bool

modos.helpers.schema.set_haspart_relationship(child_class, child_path, parent_group)[source]#

Add element to the hasPart attribute of a parent zarr group

Parameters:

child_class (str)
child_path (str)
parent_group (zarr.hierarchy.Group)

modos.helpers.schema.update_haspart_id(element)[source]#

update the id of the has_part property of an element to use the full id including its type

Parameters:: element (modos_schema.datamodel.DataEntity | modos_schema.datamodel.Sample | modos_schema.datamodel.Assay | modos_schema.datamodel.ReferenceGenome | modos_schema.datamodel.MODO)

modos.helpers.schema.set_data_path(element, source_file=None)[source]#

Set the data_path attribute, if it is not specified to the modo root.

Parameters:

element (dict)
source_file (Optional[Union[pathlib.Path, str]])

Return type:

dict

class modos.helpers.schema.UserElementType[source]#

Bases: str, enum.Enum

Enumeration of element types exposed to the user.

SAMPLE = 'sample'[source]#

ASSAY = 'assay'[source]#

DATA_ENTITY = 'data'[source]#

REFERENCE_GENOME = 'reference'[source]#

get_target_class()[source]#

Return the target class for the element type.

Return type:: type

classmethod from_object(obj)[source]#: Return the element type from an object.

class modos.helpers.schema.ElementType[source]#

Bases: str, enum.Enum

Enumeration of all element types.

SAMPLE = 'sample'[source]#

ASSAY = 'assay'[source]#

DATA_ENTITY = 'data'[source]#

REFERENCE_GENOME = 'reference'[source]#

REFERENCE_SEQUENCE = 'sequence'[source]#

get_target_class()[source]#

Return the target class for the element type.

Return type:: type

classmethod from_object(obj)[source]#: Return the element type from an object.

classmethod from_model_name(name)[source]#

Return the element type from an object name.

Parameters:: name (str)

modos.helpers.schema.is_uri(text)[source]#

Checks if input is a valid URI.

Parameters:: text (str)

modos.helpers.schema.load_schema()[source]#

Return a view over the schema structure.

Return type:: linkml_runtime.utils.schemaview.SchemaView

modos.helpers.schema.load_prefixmap()[source]#

Load the prefixmap.

Return type:: Any

modos.helpers.schema.get_slots(target_class, required_only=False)[source]#

Return a list of required slots for a class.

Parameters:: target_class (type)
Return type:: list[str]

modos.helpers.schema.instance_to_graph(instance)[source]#

Return type:: rdflib.Graph

modos.helpers.schema.get_slot_range(slot_name)[source]#

Return the class-independent range of a slot.

Parameters:: slot_name (str)
Return type:: str

modos.helpers.schema.get_enum_values(enum_name)[source]#

Parameters:: enum_name (str)
Return type:: Optional[list[str]]

modos.helpers.schema.get_haspart_property(child_class)[source]#

Return the name of the “has_part” property for a target class. If no such property is in the schema, return None.

Examples

>>> get_haspart_property('AlignmentSet')
'has_data'
>>> get_haspart_property('Assay')
'has_assay'

Parameters:: child_class (str)
Return type:: Optional[str]