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* Adding d3viz json tree export * Adding ability to output d3viz json. Also added graph transformers to allow for dynamic generation of SEP-style grouping classes. Fixes #696 * reformat
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| from dataclasses import dataclass | ||
| from typing import Any, Collection | ||
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| from oaklib.transformers.ontology_transformer import OntologyTransformer | ||
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| @dataclass | ||
| class ChainedOntologyTransformer(OntologyTransformer): | ||
| """ | ||
| An ontology graph transformer that chains multiple other transformers | ||
| """ | ||
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| chained_transformers: Collection[OntologyTransformer] | ||
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| def transform(self, source_ontology: Any, **kwargs) -> Any: | ||
| for transformer in self.chained_transformers: | ||
| source_ontology = transformer.transform(source_ontology, **kwargs) | ||
| return source_ontology |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| from dataclasses import dataclass | ||
| from typing import Collection, Optional | ||
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| from oaklib.datamodels.obograph import Graph | ||
| from oaklib.datamodels.vocabulary import IS_A | ||
| from oaklib.transformers.graph_transformer import GraphTransformer | ||
| from oaklib.types import PRED_CURIE | ||
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| @dataclass | ||
| class EdgeFilterTransformer(GraphTransformer): | ||
| """ | ||
| An ontology graph transformer that filters edges | ||
| """ | ||
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| include_predicates: Optional[Collection[PRED_CURIE]] = None | ||
| """A collection of predicates to include""" | ||
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| exclude_predicates: Optional[Collection[PRED_CURIE]] = None | ||
| """A collection of predicates to exclude""" | ||
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| filter_function: Optional[callable] = None | ||
| """A function that takes an edge and returns True if it should be included""" | ||
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| def transform(self, source_ontology: Graph, **kwargs) -> Graph: | ||
| """ | ||
| Filters edges from a graph. | ||
| Example: | ||
| >>> from oaklib import get_adapter | ||
| >>> from oaklib.transformers.transformers_factory import get_ontology_transformer | ||
| >>> from oaklib.datamodels.vocabulary import IS_A | ||
| >>> adapter = get_adapter("tests/input/go-nucleus.obo") | ||
| >>> graph = adapter.as_obograph() | ||
| >>> transformer = get_ontology_transformer("EdgeFilterTransformer", include_predicates=[IS_A]) | ||
| >>> filtered_graph = transformer.transform(graph) | ||
| >>> set([e.pred for e in filtered_graph.edges]) | ||
| {'is_a'} | ||
| :param graph: | ||
| :return: | ||
| """ | ||
| include_predicates = self.include_predicates | ||
| exclude_predicates = self.exclude_predicates | ||
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| if include_predicates is None and exclude_predicates is None: | ||
| return source_ontology | ||
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| def _normalize_id(pred: PRED_CURIE) -> PRED_CURIE: | ||
| if pred == IS_A: | ||
| return "is_a" | ||
| else: | ||
| return pred | ||
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| if include_predicates is not None: | ||
| include_predicates = {_normalize_id(pred) for pred in include_predicates} | ||
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| if exclude_predicates is not None: | ||
| exclude_predicates = {_normalize_id(pred) for pred in exclude_predicates} | ||
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| new_edges = [] | ||
| for edge in source_ontology.edges: | ||
| if include_predicates is not None: | ||
| if edge.pred not in include_predicates: | ||
| continue | ||
| if exclude_predicates is not None: | ||
| if edge.pred in exclude_predicates: | ||
| continue | ||
| if self.filter_function is not None: | ||
| if not self.filter_function(edge): | ||
| continue | ||
| new_edges.append(edge) | ||
| new_graph = Graph(id=source_ontology.id, nodes=source_ontology.nodes, edges=new_edges) | ||
| return self._post_process(new_graph) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| from dataclasses import dataclass | ||
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| from oaklib.datamodels.obograph import Graph | ||
| from oaklib.transformers.ontology_transformer import OntologyTransformer | ||
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| @dataclass | ||
| class GraphTransformer(OntologyTransformer): | ||
| """ | ||
| An ontology transformer that operates on a graph | ||
| """ | ||
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| remove_dangling_edges: bool = False | ||
| """If true, removes edges that point to nodes that are not in the graph""" | ||
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| def transform(self, source_ontology: Graph, **kwargs) -> Graph: | ||
| """ | ||
| Transforms a graph into an ontology | ||
| :param graph: | ||
| :return: | ||
| """ | ||
| raise NotImplementedError | ||
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| def apply_remove_dangling_edges(self, graph: Graph): | ||
| """ | ||
| Removes edges that point to nodes that are not in the graph. | ||
| :param graph: | ||
| :return: | ||
| """ | ||
| node_ids = {n.id for n in graph.nodes} | ||
| new_edges = [] | ||
| for edge in graph.edges: | ||
| if edge.sub in node_ids and edge.obj in node_ids: | ||
| new_edges.append(edge) | ||
| return Graph(id=graph.id, nodes=graph.nodes, edges=new_edges) | ||
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| def _post_process(self, graph: Graph): | ||
| if self.remove_dangling_edges: | ||
| return self.apply_remove_dangling_edges(graph) | ||
| else: | ||
| return graph |
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