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Adapter

fieldz_kb.biocypher.adapter

BioCypher adapter for fieldz_kb.

Converts fieldz objects to BioCypher-compatible node and relationship tuples.

Classes:

Name Description
Adapter

Adapter for converting fieldz objects to BioCypher format.

Adapter 

Adapter(obj: object)

Adapter for converting fieldz objects to BioCypher format.

Takes a fieldz object and converts it to BioCypher-compatible nodes and relationships using the LPG conversion layer.

Parameters:

Name Type Description Default
obj object

The object to convert to BioCypher format.

 required
Example

import dataclasses import fieldz_kb.biocypher.adapter

@dataclasses.dataclass ... class Gene: ... name: str ... chromosome: int

adapter = fieldz_kb.biocypher.adapter.Adapter(Gene(name="TP53", chromosome=17)) nodes, relationships = adapter.make_nodes_and_relationships()

Initialize the adapter with an object.

Parameters:

Name Type Description Default
obj object

The object to convert to BioCypher format.

 required

Methods:

Name Description
make_nodes_and_relationships

Convert the object to BioCypher nodes and relationships.
Source code in src/fieldz_kb/biocypher/adapter.py 
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def __init__(self, obj: object) -> None:
    """Initialize the adapter with an object.

    Args:
        obj: The object to convert to BioCypher format.
    """
    self.obj = obj
    self._context = fieldz_kb.lpg.core.get_default_context()

make_nodes_and_relationships 

make_nodes_and_relationships() -> tuple[list[tuple], list[tuple]]

Convert the object to BioCypher nodes and relationships.

Returns:

Type Description
list[tuple]

A tuple of (biocypher_nodes, biocypher_relationships) where:
list[tuple]
  • biocypher_nodes: List of (id, label, properties) tuples.
tuple[list[tuple], list[tuple]]
  • biocypher_relationships: List of (source_id, target_id, label, properties) tuples.
Source code in src/fieldz_kb/biocypher/adapter.py 
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def make_nodes_and_relationships(
    self,
) -> tuple[list[tuple], list[tuple]]:
    """Convert the object to BioCypher nodes and relationships.

    Returns:
        A tuple of (biocypher_nodes, biocypher_relationships) where:
        - biocypher_nodes: List of (id, label, properties) tuples.
        - biocypher_relationships: List of (source_id, target_id, label, properties) tuples.
    """
    nodes, relationships = fieldz_kb.lpg.core.make_nodes_from_object(
        self._context, self.obj
    )
    biocypher_nodes = []
    for node in nodes:
        label = node.__class__.__name__
        properties = node.to_dict()
        biocypher_nodes.append((id(node), label, properties))
    biocypher_relationships = []
    for relationship in relationships:
        label = type(relationship).__type__
        relationship_properties = {}
        for property_name in type(relationship).__primitive_properties__:
            property_value = getattr(relationship, property_name)
            if property_value is not None:
                relationship_properties[property_name] = property_value
        biocypher_relationships.append((
            id(relationship.source),
            id(relationship.target),
            label,
            relationship_properties,
        ))
    return biocypher_nodes, biocypher_relationships