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

DataElement	Facade class to wrap model.DataEntity and include index logic for genomic files
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.
compute_checksum(file_obj)	Generate the BLAKE2b checksum of the file_obj digest.
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

modos.helpers.schema.class_from_name(name)

Parameters:

name (str)

modos.helpers.schema.dict_to_instance(element)

Parameters:

element (Mapping[str, Any])

Return type:

Any

modos.helpers.schema.is_full_id(element_id)

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)

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)

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)

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

Parameters:

• element (modos_schema.datamodel.DataEntity)

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

Return type:

modos_schema.datamodel.DataEntity

class modos.helpers.schema.DataElement(model)

Facade class to wrap model.DataEntity and include index logic for genomic files

Parameters:

model (DataElement.__init__.model)

model

_set_checksum(source_checksum)

process_and_store(storage, source_path)

Parameters:

source_path (pathlib.Path)

modos.helpers.schema.compute_checksum(file_obj)

Generate the BLAKE2b checksum of the file_obj digest.

Parameters:

file_obj (io.RawIOBase)

Return type:

str

class modos.helpers.schema.UserElementType

Bases: str, enum.Enum

Enumeration of element types exposed to the user.

SAMPLE = 'sample'

ASSAY = 'assay'

DATA_ENTITY = 'data'

REFERENCE_GENOME = 'reference'

get_target_class()

Return the target class for the element type.

Return type:

type

classmethod from_object(obj)

Return the element type from an object.

class modos.helpers.schema.ElementType

Bases: str, enum.Enum

Enumeration of all element types.

SAMPLE = 'sample'

ASSAY = 'assay'

DATA_ENTITY = 'data'

REFERENCE_GENOME = 'reference'

REFERENCE_SEQUENCE = 'sequence'

get_target_class()

Return the target class for the element type.

Return type:

type

classmethod from_object(obj)

Return the element type from an object.

classmethod from_model_name(name)

Return the element type from an object name.

Parameters:

name (str)

modos.helpers.schema.is_uri(text)

Checks if input is a valid URI.

Parameters:

text (str)

modos.helpers.schema.load_schema()

Return a view over the schema structure.

Return type:

linkml_runtime.utils.schemaview.SchemaView

modos.helpers.schema.load_prefixmap()

Load the prefixmap.

Return type:

Any

modos.helpers.schema.get_slots(target_class, required_only=False)

Return a list of required slots for a class.

Parameters:

target_class (type)

Return type:

list[str]

modos.helpers.schema.instance_to_graph(instance)

Return type:

rdflib.Graph

modos.helpers.schema.get_slot_range(slot_name)

Return the class-independent range of a slot.

Parameters:

slot_name (str)

Return type:

str

modos.helpers.schema.get_enum_values(enum_name)

Parameters:

enum_name (str)

Return type:

Optional[list[str]]

modos.helpers.schema.get_haspart_property(child_class)

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]