pyobo 0.12.2__py3-none-any.whl → 0.12.3__py3-none-any.whl

pyobo/obographs.py

@@ -1,152 +0,0 @@
-"""Convert PyOBO into OBO Graph."""
-
-from __future__ import annotations
-
-import logging
-from collections.abc import Iterable
-from typing import TYPE_CHECKING
-
-import bioregistry
-from bioontologies.obograph import (
-    Definition,
-    Edge,
-    Graph,
-    GraphDocument,
-    Meta,
-    Node,
-    Synonym,
-    Xref,
-)
-from tqdm import tqdm
-
-from pyobo.struct import Obo, OBOLiteral, Reference, Term
-from pyobo.struct.typedef import definition_source, is_a
-
-if TYPE_CHECKING:
-    from bioontologies.robot import ParseResults
-
-__all__ = [
-    "graph_from_obo",
-    "parse_results_from_obo",
-]
-
-logger = logging.getLogger(__name__)
-
-
-def parse_results_from_obo(obo: Obo) -> ParseResults:
-    """Get parse results from an OBO graph."""
-    graph = graph_from_obo(obo)
-    from bioontologies.robot import ParseResults
-
-    return ParseResults(graph_document=GraphDocument(graphs=[graph]))
-
-
-def graph_from_obo(obo: Obo, use_tqdm: bool = True) -> Graph:
-    """Get an OBO Graph object from a PyOBO object."""
-    nodes: list[Node] = []
-    edges: list[Edge] = []
-    for term in tqdm(
-        obo,
-        disable=not use_tqdm,
-        unit="term",
-        unit_scale=True,
-        desc=f"[{obo._prefix_version}] to OBO Graph JSON",
-    ):
-        nodes.append(_get_class_node(term))
-        edges.extend(_iter_edges(term))
-    return Graph(
-        id=bioregistry.get_bioregistry_iri("bioregistry", obo.ontology),
-        prefix=obo.ontology,
-        meta=_get_meta(obo),
-        nodes=nodes,
-        edges=edges,
-        standardized=True,  # from construction :)
-    )
-
-
-def _get_meta(obo: Obo) -> Meta:
-    return Meta(
-        version=obo.data_version,
-    )
-
-
-def _get_class_node(term: Term) -> Node:
-    if term.provenance or term.definition:
-        definition = Definition.from_parsed(
-            value=term.definition, references=_prep_prov(term.provenance)
-        )
-    else:
-        definition = None
-    xrefs = [
-        Xref.from_parsed(
-            predicate=Reference.from_reference(mapping_predicate),
-            value=Reference.from_reference(mapping_object),
-        )
-        for mapping_predicate, mapping_object in term.get_mappings(
-            include_xrefs=True, add_context=False
-        )
-    ]
-    synonyms = [
-        Synonym.from_parsed(
-            name=synonym.name,
-            predicate=Reference.from_reference(synonym.predicate),
-            synonym_type=Reference.from_reference(synonym.type) if synonym.type else None,
-            references=_prep_prov(synonym.provenance),
-        )
-        for synonym in term.synonyms
-    ]
-
-    meta = Meta(
-        definition=definition,
-        xrefs=xrefs,
-        synonyms=synonyms,
-        basicPropertyValues=None,  # TODO properties
-        deprecated=term.is_obsolete or False,
-    )
-    return Node(
-        # FIXME do expansion same as for OFN
-        id=f"https://bioregistry.io/{term.curie}",
-        lbl=term.name,
-        meta=meta,
-        type="CLASS",
-        reference=Reference.from_reference(term.reference),
-        standardized=True,
-    )
-
-
-def _prep_prov(provenance):
-    rv = []
-    for x in provenance:
-        match x:
-            case Reference():
-                rv.append(Reference.from_reference(x))
-            case OBOLiteral():
-                logger.debug("not implemented to convert literal provenance")
-                continue
-    return rv
-
-
-def _iter_edges(term: Term) -> Iterable[Edge]:
-    for parent in term.parents:
-        yield Edge.from_parsed(
-            Reference.from_reference(term.reference),
-            Reference.from_reference(is_a.reference),
-            Reference.from_reference(parent),
-        )
-
-    for typedef, targets in term.relationships.items():
-        for target in targets:
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(typedef),
-                Reference.from_reference(target),
-            )
-
-    for provenance_reference in term.provenance:
-        if isinstance(provenance_reference, Reference):
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(definition_source.reference),
-                Reference.from_reference(provenance_reference),
-            )
-    # TODO also look through xrefs and seealso to get provenance xrefs?