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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.drop_edges | def drop_edges(self) -> None:
"""Drop all edges in the database."""
t = time.time()
self.session.query(Edge).delete()
self.session.commit()
log.info('dropped all edges in %.2f seconds', time.time() - t) | python | def drop_edges(self) -> None:
"""Drop all edges in the database."""
t = time.time()
self.session.query(Edge).delete()
self.session.commit()
log.info('dropped all edges in %.2f seconds', time.time() - t) | [
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.get_or_create_edge | def get_or_create_edge(self,
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sha512: str,
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evidence: Optional[E... | python | def get_or_create_edge(self,
source: Node,
target: Node,
relation: str,
bel: str,
sha512: str,
data: EdgeData,
evidence: Optional[E... | [
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.get_or_create_citation | def get_or_create_citation(self,
reference: str,
type: Optional[str] = None,
name: Optional[str] = None,
title: Optional[str] = None,
volume: Optional[str] = None,
... | python | def get_or_create_citation(self,
reference: str,
type: Optional[str] = None,
name: Optional[str] = None,
title: Optional[str] = None,
volume: Optional[str] = None,
... | [
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:param title: Title of article
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.get_or_create_author | def get_or_create_author(self, name: str) -> Author:
"""Get an author by name, or creates one if it does not exist."""
author = self.object_cache_author.get(name)
if author is not None:
self.session.add(author)
return author
author = self.get_author_by_name(name... | python | def get_or_create_author(self, name: str) -> Author:
"""Get an author by name, or creates one if it does not exist."""
author = self.object_cache_author.get(name)
if author is not None:
self.session.add(author)
return author
author = self.get_author_by_name(name... | [
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.get_modification_by_hash | def get_modification_by_hash(self, sha512: str) -> Optional[Modification]:
"""Get a modification by a SHA512 hash."""
return self.session.query(Modification).filter(Modification.sha512 == sha512).one_or_none() | python | def get_modification_by_hash(self, sha512: str) -> Optional[Modification]:
"""Get a modification by a SHA512 hash."""
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager.get_property_by_hash | def get_property_by_hash(self, property_hash: str) -> Optional[Property]:
"""Get a property by its hash if it exists."""
return self.session.query(Property).filter(Property.sha512 == property_hash).one_or_none() | python | def get_property_by_hash(self, property_hash: str) -> Optional[Property]:
"""Get a property by its hash if it exists."""
return self.session.query(Property).filter(Property.sha512 == property_hash).one_or_none() | [
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pybel/pybel | src/pybel/manager/cache_manager.py | InsertManager._make_property_from_dict | def _make_property_from_dict(self, property_def: Dict) -> Property:
"""Build an edge property from a dictionary."""
property_hash = hash_dump(property_def)
edge_property_model = self.object_cache_property.get(property_hash)
if edge_property_model is None:
edge_property_model... | python | def _make_property_from_dict(self, property_def: Dict) -> Property:
"""Build an edge property from a dictionary."""
property_hash = hash_dump(property_def)
edge_property_model = self.object_cache_property.get(property_hash)
if edge_property_model is None:
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pybel/pybel | src/pybel/struct/graph.py | _clean_annotations | def _clean_annotations(annotations_dict: AnnotationsHint) -> AnnotationsDict:
"""Fix the formatting of annotation dict."""
return {
key: (
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{v: True for v in values} if isinstance(values, set) else
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"""Fix the formatting of annotation dict."""
return {
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{v: True for v in values} if isinstance(values, set) else
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.defined_namespace_keywords | def defined_namespace_keywords(self) -> Set[str]: # noqa: D401
"""The set of all keywords defined as namespaces in this graph."""
return set(self.namespace_pattern) | set(self.namespace_url) | python | def defined_namespace_keywords(self) -> Set[str]: # noqa: D401
"""The set of all keywords defined as namespaces in this graph."""
return set(self.namespace_pattern) | set(self.namespace_url) | [
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.defined_annotation_keywords | def defined_annotation_keywords(self) -> Set[str]:
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"""Get the set of all keywords defined as annotations in this graph."""
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.skip_storing_namespace | def skip_storing_namespace(self, namespace: Optional[str]) -> bool:
"""Check if the namespace should be skipped.
:param namespace: The keyword of the namespace to check.
"""
return (
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"""Check if the namespace should be skipped.
:param namespace: The keyword of the namespace to check.
"""
return (
namespace is not None and
namespace in self.namespace_url and
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_warning | def add_warning(self,
exception: BELParserWarning,
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) -> None:
"""Add a warning to the internal warning log in the graph, with optional context information.
:param exception: The exception that occur... | python | def add_warning(self,
exception: BELParserWarning,
context: Optional[Mapping[str, Any]] = None,
) -> None:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph._help_add_edge | def _help_add_edge(self, u: BaseEntity, v: BaseEntity, attr: Mapping) -> str:
"""Help add a pre-built edge."""
self.add_node_from_data(u)
self.add_node_from_data(v)
return self._help_add_edge_helper(u, v, attr) | python | def _help_add_edge(self, u: BaseEntity, v: BaseEntity, attr: Mapping) -> str:
"""Help add a pre-built edge."""
self.add_node_from_data(u)
self.add_node_from_data(v)
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_unqualified_edge | def add_unqualified_edge(self, u: BaseEntity, v: BaseEntity, relation: str) -> str:
"""Add a unique edge that has no annotations.
:param u: The source node
:param v: The target node
:param relation: A relationship label from :mod:`pybel.constants`
:return: The key for this edge ... | python | def add_unqualified_edge(self, u: BaseEntity, v: BaseEntity, relation: str) -> str:
"""Add a unique edge that has no annotations.
:param u: The source node
:param v: The target node
:param relation: A relationship label from :mod:`pybel.constants`
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_transcription | def add_transcription(self, gene: Gene, rna: Union[Rna, MicroRna]) -> str:
"""Add a transcription relation from a gene to an RNA or miRNA node.
:param gene: A gene node
:param rna: An RNA or microRNA node
"""
return self.add_unqualified_edge(gene, rna, TRANSCRIBED_TO) | python | def add_transcription(self, gene: Gene, rna: Union[Rna, MicroRna]) -> str:
"""Add a transcription relation from a gene to an RNA or miRNA node.
:param gene: A gene node
:param rna: An RNA or microRNA node
"""
return self.add_unqualified_edge(gene, rna, TRANSCRIBED_TO) | [
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_translation | def add_translation(self, rna: Rna, protein: Protein) -> str:
"""Add a translation relation from a RNA to a protein.
:param rna: An RNA node
:param protein: A protein node
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:param rna: An RNA node
:param protein: A protein node
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pybel/pybel | src/pybel/struct/graph.py | BELGraph._add_two_way_unqualified_edge | def _add_two_way_unqualified_edge(self, u: BaseEntity, v: BaseEntity, relation: str) -> str:
"""Add an unqualified edge both ways."""
self.add_unqualified_edge(v, u, relation)
return self.add_unqualified_edge(u, v, relation) | python | def _add_two_way_unqualified_edge(self, u: BaseEntity, v: BaseEntity, relation: str) -> str:
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subject_modifier: Optional[Mapping] = None,
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_node_from_data | def add_node_from_data(self, node: BaseEntity) -> BaseEntity:
"""Add an entity to the graph."""
assert isinstance(node, BaseEntity)
if node in self:
return node
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"""Add an entity to the graph."""
assert isinstance(node, BaseEntity)
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return node
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.has_edge_citation | def has_edge_citation(self, u: BaseEntity, v: BaseEntity, key: str) -> bool:
"""Check if the given edge has a citation."""
return self._has_edge_attr(u, v, key, CITATION) | python | def has_edge_citation(self, u: BaseEntity, v: BaseEntity, key: str) -> bool:
"""Check if the given edge has a citation."""
return self._has_edge_attr(u, v, key, CITATION) | [
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.has_edge_evidence | def has_edge_evidence(self, u: BaseEntity, v: BaseEntity, key: str) -> bool:
"""Check if the given edge has an evidence."""
return self._has_edge_attr(u, v, key, EVIDENCE) | python | def has_edge_evidence(self, u: BaseEntity, v: BaseEntity, key: str) -> bool:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.get_edge_citation | def get_edge_citation(self, u: BaseEntity, v: BaseEntity, key: str) -> Optional[CitationDict]:
"""Get the citation for a given edge."""
return self._get_edge_attr(u, v, key, CITATION) | python | def get_edge_citation(self, u: BaseEntity, v: BaseEntity, key: str) -> Optional[CitationDict]:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.get_edge_evidence | def get_edge_evidence(self, u: BaseEntity, v: BaseEntity, key: str) -> Optional[str]:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.edge_to_bel | def edge_to_bel(u: BaseEntity, v: BaseEntity, edge_data: EdgeData, sep: Optional[str] = None) -> str:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph._equivalent_node_iterator_helper | def _equivalent_node_iterator_helper(self, node: BaseEntity, visited: Set[BaseEntity]) -> BaseEntity:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.iter_equivalent_nodes | def iter_equivalent_nodes(self, node: BaseEntity) -> Iterable[BaseEntity]:
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yield node
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yield node
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.get_equivalent_nodes | def get_equivalent_nodes(self, node: BaseEntity) -> Set[BaseEntity]:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph._describe_list | def _describe_list(self) -> List[Tuple[str, float]]:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.summary_str | def summary_str(self) -> str:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.serialize | def serialize(self, *, fmt: str = 'nodelink', file: Union[None, str, TextIO] = None, **kwargs):
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pybel/pybel | src/pybel/struct/mutation/utils.py | remove_isolated_nodes | def remove_isolated_nodes(graph):
"""Remove isolated nodes from the network, in place.
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pybel/pybel | src/pybel/struct/mutation/utils.py | expand_by_edge_filter | def expand_by_edge_filter(source, target, edge_predicates: EdgePredicates):
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.handle_document | def handle_document(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
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:raises: InvalidMetadataException
:raises: VersionFormatWarning
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value = tokens['value']
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.raise_for_redefined_namespace | def raise_for_redefined_namespace(self, line: str, position: int, namespace: str) -> None:
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.handle_namespace_url | def handle_namespace_url(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.raise_for_redefined_annotation | def raise_for_redefined_annotation(self, line: str, position: int, annotation: str) -> None:
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.handle_annotations_url | def handle_annotations_url(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.has_annotation | def has_annotation(self, annotation: str) -> bool:
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.raise_for_version | def raise_for_version(self, line: str, position: int, version: str) -> None:
"""Check that a version string is valid for BEL documents.
This means it's either in the YYYYMMDD or semantic version format.
:param line: The line being parsed
:param position: The position in the line being ... | python | def raise_for_version(self, line: str, position: int, version: str) -> None:
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pybel/pybel | src/pybel/manager/base_manager.py | BaseManager.drop_all | def drop_all(self, checkfirst: bool = True) -> None:
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pybel/pybel | src/pybel/manager/base_manager.py | BaseManager.bind | def bind(self) -> None:
"""Bind the metadata to the engine and session."""
self.base.metadata.bind = self.engine
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"""Bind the metadata to the engine and session."""
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pybel/pybel | src/pybel/manager/base_manager.py | BaseManager._list_model | def _list_model(self, model_cls: Type[X]) -> List[X]:
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return self.session.query(model_cls).all() | python | def _list_model(self, model_cls: Type[X]) -> List[X]:
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pybel/pybel | src/pybel/manager/citation_utils.py | sanitize_date | def sanitize_date(publication_date: str) -> str:
"""Sanitize lots of different date strings into ISO-8601."""
if re1.search(publication_date):
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return datetime.strptime(publication_da... | python | def sanitize_date(publication_date: str) -> str:
"""Sanitize lots of different date strings into ISO-8601."""
if re1.search(publication_date):
return datetime.strptime(publication_date, '%Y %b %d').strftime('%Y-%m-%d')
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pybel/pybel | src/pybel/manager/citation_utils.py | clean_pubmed_identifiers | def clean_pubmed_identifiers(pmids: Iterable[str]) -> List[str]:
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"""Clean a list of PubMed identifiers with string strips, deduplicates, and sorting."""
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pybel/pybel | src/pybel/manager/citation_utils.py | get_pubmed_citation_response | def get_pubmed_citation_response(pubmed_identifiers: Iterable[str]):
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:rtype: dict
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pubmed_identifiers = list(pubmed_identifiers)
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"""Get the response from PubMed E-Utils for a given list of PubMed identifiers.
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pybel/pybel | src/pybel/manager/citation_utils.py | enrich_citation_model | def enrich_citation_model(manager, citation, p) -> bool:
"""Enrich a citation model with the information from PubMed.
:param pybel.manager.Manager manager:
:param Citation citation: A citation model
:param dict p: The dictionary from PubMed E-Utils corresponding to d["result"][pmid]
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pybel/pybel | src/pybel/manager/citation_utils.py | get_citations_by_pmids | def get_citations_by_pmids(manager,
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sleep_time: Optional[int] = None,
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pybel/pybel | src/pybel/manager/citation_utils.py | enrich_pubmed_citations | def enrich_pubmed_citations(manager,
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pybel/pybel | src/pybel/struct/mutation/collapse/protein_rna_origins.py | _build_collapse_to_gene_dict | def _build_collapse_to_gene_dict(graph) -> Dict[BaseEntity, Set[BaseEntity]]:
"""Build a collapse dictionary.
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:return: A dictionary of {node: set of PyBEL node tuples}
"""
collapse_dict = defaultdict(set)
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pybel/pybel | src/pybel/struct/mutation/collapse/protein_rna_origins.py | collapse_to_genes | def collapse_to_genes(graph):
"""Collapse all protein, RNA, and miRNA nodes to their corresponding gene nodes.
:param pybel.BELGraph graph: A BEL graph
"""
enrich_protein_and_rna_origins(graph)
collapse_dict = _build_collapse_to_gene_dict(graph)
collapse_nodes(graph, collapse_dict) | python | def collapse_to_genes(graph):
"""Collapse all protein, RNA, and miRNA nodes to their corresponding gene nodes.
:param pybel.BELGraph graph: A BEL graph
"""
enrich_protein_and_rna_origins(graph)
collapse_dict = _build_collapse_to_gene_dict(graph)
collapse_nodes(graph, collapse_dict) | [
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pybel/pybel | src/pybel/cli.py | main | def main(ctx, connection):
"""Command line interface for PyBEL."""
ctx.obj = Manager(connection=connection)
ctx.obj.bind() | python | def main(ctx, connection):
"""Command line interface for PyBEL."""
ctx.obj = Manager(connection=connection)
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pybel/pybel | src/pybel/cli.py | compile | def compile(manager, path, allow_naked_names, allow_nested, disallow_unqualified_translocations,
no_identifier_validation, no_citation_clearing, required_annotations, skip_tqdm, verbose):
"""Compile a BEL script to a graph."""
if verbose:
logging.basicConfig(level=logging.DEBUG)
log.... | python | def compile(manager, path, allow_naked_names, allow_nested, disallow_unqualified_translocations,
no_identifier_validation, no_citation_clearing, required_annotations, skip_tqdm, verbose):
"""Compile a BEL script to a graph."""
if verbose:
logging.basicConfig(level=logging.DEBUG)
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pybel/pybel | src/pybel/cli.py | insert | def insert(manager, graph: BELGraph):
"""Insert a graph to the database."""
to_database(graph, manager=manager, use_tqdm=True) | python | def insert(manager, graph: BELGraph):
"""Insert a graph to the database."""
to_database(graph, manager=manager, use_tqdm=True) | [
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pybel/pybel | src/pybel/cli.py | post | def post(graph: BELGraph, host: str):
"""Upload a graph to BEL Commons."""
resp = to_web(graph, host=host)
resp.raise_for_status() | python | def post(graph: BELGraph, host: str):
"""Upload a graph to BEL Commons."""
resp = to_web(graph, host=host)
resp.raise_for_status() | [
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pybel/pybel | src/pybel/cli.py | serialize | def serialize(graph: BELGraph, csv, sif, gsea, graphml, json, bel):
"""Serialize a graph to various formats."""
if csv:
log.info('Outputting CSV to %s', csv)
to_csv(graph, csv)
if sif:
log.info('Outputting SIF to %s', sif)
to_sif(graph, sif)
if graphml:
log.info... | python | def serialize(graph: BELGraph, csv, sif, gsea, graphml, json, bel):
"""Serialize a graph to various formats."""
if csv:
log.info('Outputting CSV to %s', csv)
to_csv(graph, csv)
if sif:
log.info('Outputting SIF to %s', sif)
to_sif(graph, sif)
if graphml:
log.info... | [
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pybel/pybel | src/pybel/cli.py | neo | def neo(graph: BELGraph, connection: str, password: str):
"""Upload to neo4j."""
import py2neo
neo_graph = py2neo.Graph(connection, password=password)
to_neo4j(graph, neo_graph) | python | def neo(graph: BELGraph, connection: str, password: str):
"""Upload to neo4j."""
import py2neo
neo_graph = py2neo.Graph(connection, password=password)
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pybel/pybel | src/pybel/cli.py | machine | def machine(manager: Manager, agents: List[str], local: bool, host: str):
"""Get content from the INDRA machine and upload to BEL Commons."""
from indra.sources import indra_db_rest
from pybel import from_indra_statements
statements = indra_db_rest.get_statements(agents=agents)
click.echo('got {} s... | python | def machine(manager: Manager, agents: List[str], local: bool, host: str):
"""Get content from the INDRA machine and upload to BEL Commons."""
from indra.sources import indra_db_rest
from pybel import from_indra_statements
statements = indra_db_rest.get_statements(agents=agents)
click.echo('got {} s... | [
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pybel/pybel | src/pybel/cli.py | examples | def examples(manager: Manager):
"""Load examples to the database."""
for graph in (sialic_acid_graph, statin_graph, homology_graph, braf_graph, egf_graph):
if manager.has_name_version(graph.name, graph.version):
click.echo('already inserted {}'.format(graph))
continue
cli... | python | def examples(manager: Manager):
"""Load examples to the database."""
for graph in (sialic_acid_graph, statin_graph, homology_graph, braf_graph, egf_graph):
if manager.has_name_version(graph.name, graph.version):
click.echo('already inserted {}'.format(graph))
continue
cli... | [
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pybel/pybel | src/pybel/cli.py | ls | def ls(manager: Manager, url: Optional[str], namespace_id: Optional[int]):
"""List cached namespaces."""
if url:
n = manager.get_or_create_namespace(url)
if isinstance(n, Namespace):
_page(n.entries)
else:
click.echo('uncachable namespace')
elif namespace_id i... | python | def ls(manager: Manager, url: Optional[str], namespace_id: Optional[int]):
"""List cached namespaces."""
if url:
n = manager.get_or_create_namespace(url)
if isinstance(n, Namespace):
_page(n.entries)
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click.echo('uncachable namespace')
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pybel/pybel | src/pybel/cli.py | ls | def ls(manager: Manager):
"""List network names, versions, and optionally, descriptions."""
for n in manager.list_networks():
click.echo('{}\t{}\t{}'.format(n.id, n.name, n.version)) | python | def ls(manager: Manager):
"""List network names, versions, and optionally, descriptions."""
for n in manager.list_networks():
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pybel/pybel | src/pybel/cli.py | drop | def drop(manager: Manager, network_id: Optional[int], yes):
"""Drop a network by its identifier or drop all networks."""
if network_id:
manager.drop_network_by_id(network_id)
elif yes or click.confirm('Drop all networks?'):
manager.drop_networks() | python | def drop(manager: Manager, network_id: Optional[int], yes):
"""Drop a network by its identifier or drop all networks."""
if network_id:
manager.drop_network_by_id(network_id)
elif yes or click.confirm('Drop all networks?'):
manager.drop_networks() | [
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pybel/pybel | src/pybel/cli.py | ls | def ls(manager: Manager, offset: Optional[int], limit: Optional[int]):
"""List edges."""
q = manager.session.query(Edge)
if offset:
q = q.offset(offset)
if limit > 0:
q = q.limit(limit)
for e in q:
click.echo(e.bel) | python | def ls(manager: Manager, offset: Optional[int], limit: Optional[int]):
"""List edges."""
q = manager.session.query(Edge)
if offset:
q = q.offset(offset)
if limit > 0:
q = q.limit(limit)
for e in q:
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pybel/pybel | src/pybel/cli.py | prune | def prune(manager: Manager):
"""Prune nodes not belonging to any edges."""
nodes_to_delete = [
node
for node in tqdm(manager.session.query(Node), total=manager.count_nodes())
if not node.networks
]
manager.session.delete(nodes_to_delete)
manager.session.commit() | python | def prune(manager: Manager):
"""Prune nodes not belonging to any edges."""
nodes_to_delete = [
node
for node in tqdm(manager.session.query(Node), total=manager.count_nodes())
if not node.networks
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manager.session.delete(nodes_to_delete)
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pybel/pybel | src/pybel/cli.py | summarize | def summarize(manager: Manager):
"""Summarize the contents of the database."""
click.echo('Networks: {}'.format(manager.count_networks()))
click.echo('Edges: {}'.format(manager.count_edges()))
click.echo('Nodes: {}'.format(manager.count_nodes()))
click.echo('Namespaces: {}'.format(manager.count_name... | python | def summarize(manager: Manager):
"""Summarize the contents of the database."""
click.echo('Networks: {}'.format(manager.count_networks()))
click.echo('Edges: {}'.format(manager.count_edges()))
click.echo('Nodes: {}'.format(manager.count_nodes()))
click.echo('Namespaces: {}'.format(manager.count_name... | [
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pybel/pybel | src/pybel/cli.py | echo_warnings_via_pager | def echo_warnings_via_pager(warnings: List[WarningTuple], sep: str = '\t') -> None:
"""Output the warnings from a BEL graph with Click and the system's pager."""
# Exit if no warnings
if not warnings:
click.echo('Congratulations! No warnings.')
sys.exit(0)
max_line_width = max(
... | python | def echo_warnings_via_pager(warnings: List[WarningTuple], sep: str = '\t') -> None:
"""Output the warnings from a BEL graph with Click and the system's pager."""
# Exit if no warnings
if not warnings:
click.echo('Congratulations! No warnings.')
sys.exit(0)
max_line_width = max(
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pybel/pybel | src/pybel/tokens.py | parse_result_to_dsl | def parse_result_to_dsl(tokens):
"""Convert a ParseResult to a PyBEL DSL object.
:type tokens: dict or pyparsing.ParseResults
:rtype: BaseEntity
"""
if MODIFIER in tokens:
return parse_result_to_dsl(tokens[TARGET])
elif REACTION == tokens[FUNCTION]:
return _reaction_po_to_dict(... | python | def parse_result_to_dsl(tokens):
"""Convert a ParseResult to a PyBEL DSL object.
:type tokens: dict or pyparsing.ParseResults
:rtype: BaseEntity
"""
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:param tokens: A PyParsing data dictionary representing a fusion
:type tokens: ParseResult
"""
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:param tokens: A PyParsing data dictionary representing a fusion
:type tokens: ParseResult
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pybel/pybel | src/pybel/tokens.py | _fusion_range_to_dsl | def _fusion_range_to_dsl(tokens) -> FusionRangeBase:
"""Convert a PyParsing data dictionary into a PyBEL.
:type tokens: ParseResult
"""
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"""Convert a PyParsing data dictionary into a PyBEL.
:type tokens: ParseResult
"""
if FUSION_MISSING in tokens:
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pybel/pybel | src/pybel/tokens.py | _simple_po_to_dict | def _simple_po_to_dict(tokens) -> BaseAbundance:
"""Convert a simple named entity to a DSL object.
:type tokens: ParseResult
"""
dsl = FUNC_TO_DSL.get(tokens[FUNCTION])
if dsl is None:
raise ValueError('invalid tokens: {}'.format(tokens))
return dsl(
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"""Convert a simple named entity to a DSL object.
:type tokens: ParseResult
"""
dsl = FUNC_TO_DSL.get(tokens[FUNCTION])
if dsl is None:
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pybel/pybel | src/pybel/tokens.py | _variant_to_dsl_helper | def _variant_to_dsl_helper(tokens) -> Variant:
"""Convert variant tokens to DSL objects.
:type tokens: ParseResult
"""
kind = tokens[KIND]
if kind == HGVS:
return hgvs(tokens[IDENTIFIER])
if kind == GMOD:
return gmod(
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"""Convert variant tokens to DSL objects.
:type tokens: ParseResult
"""
kind = tokens[KIND]
if kind == HGVS:
return hgvs(tokens[IDENTIFIER])
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pybel/pybel | src/pybel/tokens.py | _reaction_po_to_dict | def _reaction_po_to_dict(tokens) -> Reaction:
"""Convert a reaction parse object to a DSL.
:type tokens: ParseResult
"""
return Reaction(
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products=_reaction_part_po_to_dict(tokens[PRODUCTS]),
) | python | def _reaction_po_to_dict(tokens) -> Reaction:
"""Convert a reaction parse object to a DSL.
:type tokens: ParseResult
"""
return Reaction(
reactants=_reaction_part_po_to_dict(tokens[REACTANTS]),
products=_reaction_part_po_to_dict(tokens[PRODUCTS]),
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:type tokens: ParseResult
"""
func = tokens[FUNCTION]
dsl = FUNC_TO_LIST_DSL[func]
members = [parse_result_to_dsl(token) for token in tokens[MEMBERS]]
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"""Convert a list parse object to a node.
:type tokens: ParseResult
"""
func = tokens[FUNCTION]
dsl = FUNC_TO_LIST_DSL[func]
members = [parse_result_to_dsl(token) for token in tokens[MEMBERS]]
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pybel/pybel | src/pybel/struct/mutation/induction/annotations.py | get_subgraph_by_annotations | def get_subgraph_by_annotations(graph, annotations, or_=None):
"""Induce a sub-graph given an annotations filter.
:param graph: pybel.BELGraph graph: A BEL graph
:param dict[str,iter[str]] annotations: Annotation filters (match all with :func:`pybel.utils.subdict_matches`)
:param boolean or_: if True a... | python | def get_subgraph_by_annotations(graph, annotations, or_=None):
"""Induce a sub-graph given an annotations filter.
:param graph: pybel.BELGraph graph: A BEL graph
:param dict[str,iter[str]] annotations: Annotation filters (match all with :func:`pybel.utils.subdict_matches`)
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pybel/pybel | src/pybel/struct/mutation/induction/annotations.py | get_subgraph_by_annotation_value | def get_subgraph_by_annotation_value(graph, annotation, values):
"""Induce a sub-graph over all edges whose annotations match the given key and value.
:param pybel.BELGraph graph: A BEL graph
:param str annotation: The annotation to group by
:param values: The value(s) for the annotation
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pybel/pybel | src/pybel/struct/filters/edge_filters.py | invert_edge_predicate | def invert_edge_predicate(edge_predicate: EdgePredicate) -> EdgePredicate: # noqa: D202
"""Build an edge predicate that is the inverse of the given edge predicate."""
def _inverse_filter(graph, u, v, k):
return not edge_predicate(graph, u, v, k)
return _inverse_filter | python | def invert_edge_predicate(edge_predicate: EdgePredicate) -> EdgePredicate: # noqa: D202
"""Build an edge predicate that is the inverse of the given edge predicate."""
def _inverse_filter(graph, u, v, k):
return not edge_predicate(graph, u, v, k)
return _inverse_filter | [
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pybel/pybel | src/pybel/struct/filters/edge_filters.py | and_edge_predicates | def and_edge_predicates(edge_predicates: EdgePredicates) -> EdgePredicate:
"""Concatenate multiple edge predicates to a new predicate that requires all predicates to be met."""
# If something that isn't a list or tuple is given, assume it's a function and return it
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pybel/pybel | src/pybel/struct/filters/edge_filters.py | filter_edges | def filter_edges(graph: BELGraph, edge_predicates: EdgePredicates) -> EdgeIterator:
"""Apply a set of filters to the edges iterator of a BEL graph.
:return: An iterable of edges that pass all predicates
"""
compound_edge_predicate = and_edge_predicates(edge_predicates=edge_predicates)
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"""Apply a set of filters to the edges iterator of a BEL graph.
:return: An iterable of edges that pass all predicates
"""
compound_edge_predicate = and_edge_predicates(edge_predicates=edge_predicates)
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pybel/pybel | src/pybel/struct/filters/edge_filters.py | count_passed_edge_filter | def count_passed_edge_filter(graph: BELGraph, edge_predicates: EdgePredicates) -> int:
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"""Return the number of edges passing a given set of predicates."""
return sum(
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pybel/pybel | src/pybel/struct/operations.py | subgraph | def subgraph(graph, nodes: Iterable[BaseEntity]):
"""Induce a sub-graph over the given nodes.
:rtype: BELGraph
"""
sg = graph.subgraph(nodes)
# see implementation for .copy()
result = graph.fresh_copy()
result.graph.update(sg.graph)
for node, data in sg.nodes(data=True):
resul... | python | def subgraph(graph, nodes: Iterable[BaseEntity]):
"""Induce a sub-graph over the given nodes.
:rtype: BELGraph
"""
sg = graph.subgraph(nodes)
# see implementation for .copy()
result = graph.fresh_copy()
result.graph.update(sg.graph)
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pybel/pybel | src/pybel/struct/operations.py | left_full_join | def left_full_join(g, h) -> None:
"""Add all nodes and edges from ``h`` to ``g``, in-place for ``g``.
:param pybel.BELGraph g: A BEL graph
:param pybel.BELGraph h: A BEL graph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_full_j... | python | def left_full_join(g, h) -> None:
"""Add all nodes and edges from ``h`` to ``g``, in-place for ``g``.
:param pybel.BELGraph g: A BEL graph
:param pybel.BELGraph h: A BEL graph
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>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_full_j... | [
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... | Add all nodes and edges from ``h`` to ``g``, in-place for ``g``.
:param pybel.BELGraph g: A BEL graph
:param pybel.BELGraph h: A BEL graph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_full_join(g, h) | [
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pybel/pybel | src/pybel/struct/operations.py | left_outer_join | def left_outer_join(g, h) -> None:
"""Only add components from the ``h`` that are touching ``g``.
Algorithm:
1. Identify all weakly connected components in ``h``
2. Add those that have an intersection with the ``g``
:param BELGraph g: A BEL graph
:param BELGraph h: A BEL graph
Example us... | python | def left_outer_join(g, h) -> None:
"""Only add components from the ``h`` that are touching ``g``.
Algorithm:
1. Identify all weakly connected components in ``h``
2. Add those that have an intersection with the ``g``
:param BELGraph g: A BEL graph
:param BELGraph h: A BEL graph
Example us... | [
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Example usage:
>>> import pybel
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pybel/pybel | src/pybel/struct/operations.py | union | def union(graphs, use_tqdm: bool = False):
"""Take the union over a collection of graphs into a new graph.
Assumes iterator is longer than 2, but not infinite.
:param iter[BELGraph] graphs: An iterator over BEL graphs. Can't be infinite.
:param use_tqdm: Should a progress bar be displayed?
:return... | python | def union(graphs, use_tqdm: bool = False):
"""Take the union over a collection of graphs into a new graph.
Assumes iterator is longer than 2, but not infinite.
:param iter[BELGraph] graphs: An iterator over BEL graphs. Can't be infinite.
:param use_tqdm: Should a progress bar be displayed?
:return... | [
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pybel/pybel | src/pybel/struct/operations.py | left_node_intersection_join | def left_node_intersection_join(g, h):
"""Take the intersection over two graphs.
This intersection of two graphs is defined by the union of the sub-graphs induced over the intersection of their nodes
:param BELGraph g: A BEL graph
:param BELGraph h: A BEL graph
:rtype: BELGraph
Example usage:... | python | def left_node_intersection_join(g, h):
"""Take the intersection over two graphs.
This intersection of two graphs is defined by the union of the sub-graphs induced over the intersection of their nodes
:param BELGraph g: A BEL graph
:param BELGraph h: A BEL graph
:rtype: BELGraph
Example usage:... | [
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:param BELGraph g: A BEL graph
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pybel/pybel | src/pybel/struct/operations.py | node_intersection | def node_intersection(graphs):
"""Take the node intersection over a collection of graphs into a new graph.
This intersection is defined the same way as by :func:`left_node_intersection_join`
:param iter[BELGraph] graphs: An iterable of graphs. Since it's iterated over twice, it gets converted to a
tu... | python | def node_intersection(graphs):
"""Take the node intersection over a collection of graphs into a new graph.
This intersection is defined the same way as by :func:`left_node_intersection_join`
:param iter[BELGraph] graphs: An iterable of graphs. Since it's iterated over twice, it gets converted to a
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pybel/pybel | src/pybel/struct/mutation/metadata.py | strip_annotations | def strip_annotations(graph):
"""Strip all the annotations from a BEL graph.
:param pybel.BELGraph graph: A BEL graph
"""
for u, v, k in graph.edges(keys=True):
if ANNOTATIONS in graph[u][v][k]:
del graph[u][v][k][ANNOTATIONS] | python | def strip_annotations(graph):
"""Strip all the annotations from a BEL graph.
:param pybel.BELGraph graph: A BEL graph
"""
for u, v, k in graph.edges(keys=True):
if ANNOTATIONS in graph[u][v][k]:
del graph[u][v][k][ANNOTATIONS] | [
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pybel/pybel | src/pybel/struct/mutation/metadata.py | remove_citation_metadata | def remove_citation_metadata(graph):
"""Remove the metadata associated with a citation.
Best practice is to add this information programmatically.
"""
for u, v, k in graph.edges(keys=True):
if CITATION not in graph[u][v][k]:
continue
for key in list(graph[u][v][k][CITATION])... | python | def remove_citation_metadata(graph):
"""Remove the metadata associated with a citation.
Best practice is to add this information programmatically.
"""
for u, v, k in graph.edges(keys=True):
if CITATION not in graph[u][v][k]:
continue
for key in list(graph[u][v][k][CITATION])... | [
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pybel/pybel | src/pybel/io/nodelink.py | to_json | def to_json(graph: BELGraph) -> Mapping[str, Any]:
"""Convert this graph to a Node-Link JSON object."""
graph_json_dict = node_link_data(graph)
# Convert annotation list definitions (which are sets) to canonicalized/sorted lists
graph_json_dict['graph'][GRAPH_ANNOTATION_LIST] = {
keyword: list(... | python | def to_json(graph: BELGraph) -> Mapping[str, Any]:
"""Convert this graph to a Node-Link JSON object."""
graph_json_dict = node_link_data(graph)
# Convert annotation list definitions (which are sets) to canonicalized/sorted lists
graph_json_dict['graph'][GRAPH_ANNOTATION_LIST] = {
keyword: list(... | [
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