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 to facilitate file handling (including index 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)
update_metadata_from_model(group, element)	Update the metadata of a zarr group with the metadata of a model 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.update_metadata_from_model(group, element)

Update the metadata of a zarr group with the metadata of a model element.

Parameters:

• group (zarr.hierarchy.group)

• element (modos_schema.datamodel.DataEntity | modos_schema.datamodel.Sample | modos_schema.datamodel.Assay | modos_schema.datamodel.ReferenceGenome)

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, storage)

Facade class to wrap model DataEntity to facilitate file handling (including index files).

Parameters:

model (DataElement.__init__.model)

model

storage

_set_metadata(**kwargs)

_update_checksum(source_path)

Parameters:

source_path (pathlib.Path)

property is_genomic: bool

Check if the data element is genomic.

Return type:

bool

add_file(source_path, target_path)

Add a file to target_path to the storage. If existing also add the index file and update data_path and checksum in metadata

Parameters:

• source_path (pathlib.Path)

• target_path (pathlib.Path)

move_file(target_path)

Move a file from the path specified in metadata to the target_path. If existing also move the index file.

Parameters:

target_path (pathlib.Path)

remove_file(rm_path)

Remove a file and its related index from the storage.

Parameters:

rm_path (pathlib.Path)

update_file(new_path, source_file=None)

Update file, its corresponding index file and metadata, based on new data_path and source_file.

There are four cases: 1. Neither path nor contents changed –> do nothing. 2. Only contents changed –> overwrite the file(s). 3. Only path changed -> move file(s). 4. Both path and contents changed -> add new file(s) and remove old ones.

Parameters:

• new_path (pathlib.Path) – Path to where the file should be placed.

• source_file (pathlib.Path | None) – Path to the file that shall be added. If None the file already associated to the DataElement will be used.

encrypt(recipient_pubkeys, seckey_path=None, passphrase=None, delete=True)

Encrypt data path linked to the DataElement. Works for genomic files and their index files.

Parameters:

• recipient_pubkeys (list[os.PathLike] | os.PathLike)

• seckey_path (Optional[os.PathLike])

• passphrase (Optional[str])

• delete (bool)

decrypt(seckey_path, sender_pubkey=None, passphrase=None)

Decrypt data path linked to the DataElement. Works for genomic files and their index files.

Parameters:

• seckey_path (os.PathLike)

• sender_pubkey (Optional[os.PathLike])

• passphrase (Optional[str])

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]