repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1 value | code stringlengths 75 19.8k | code_tokens listlengths 20 707 | docstring stringlengths 3 17.3k | docstring_tokens listlengths 3 222 | sha stringlengths 40 40 | url stringlengths 87 242 | partition stringclasses 1 value | idx int64 0 252k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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,
source: Node,
target: Node,
relation: str,
bel: str,
sha512: str,
data: EdgeData,
evidence: Optional[Evidence] = None,
annotations: Optional[List[NamespaceEntry]] = None,
properties: Optional[List[Property]] = None,
) -> Edge:
"""Create an edge if it does not exist, or return it if it does.
:param source: Source node of the relation
:param target: Target node of the relation
:param relation: Type of the relation between source and target node
:param bel: BEL statement that describes the relation
:param sha512: The SHA512 hash of the edge as a string
:param data: The PyBEL data dictionary
:param Evidence evidence: Evidence object that proves the given relation
:param properties: List of all properties that belong to the edge
:param annotations: List of all annotations that belong to the edge
"""
if sha512 in self.object_cache_edge:
edge = self.object_cache_edge[sha512]
self.session.add(edge)
return edge
edge = self.get_edge_by_hash(sha512)
if edge is not None:
self.object_cache_edge[sha512] = edge
return edge
edge = Edge(
source=source,
target=target,
relation=relation,
bel=bel,
sha512=sha512,
data=json.dumps(data),
)
if evidence is not None:
edge.evidence = evidence
if properties is not None:
edge.properties = properties
if annotations is not None:
edge.annotations = annotations
self.session.add(edge)
self.object_cache_edge[sha512] = edge
return edge | python | def get_or_create_edge(self,
source: Node,
target: Node,
relation: str,
bel: str,
sha512: str,
data: EdgeData,
evidence: Optional[Evidence] = None,
annotations: Optional[List[NamespaceEntry]] = None,
properties: Optional[List[Property]] = None,
) -> Edge:
"""Create an edge if it does not exist, or return it if it does.
:param source: Source node of the relation
:param target: Target node of the relation
:param relation: Type of the relation between source and target node
:param bel: BEL statement that describes the relation
:param sha512: The SHA512 hash of the edge as a string
:param data: The PyBEL data dictionary
:param Evidence evidence: Evidence object that proves the given relation
:param properties: List of all properties that belong to the edge
:param annotations: List of all annotations that belong to the edge
"""
if sha512 in self.object_cache_edge:
edge = self.object_cache_edge[sha512]
self.session.add(edge)
return edge
edge = self.get_edge_by_hash(sha512)
if edge is not None:
self.object_cache_edge[sha512] = edge
return edge
edge = Edge(
source=source,
target=target,
relation=relation,
bel=bel,
sha512=sha512,
data=json.dumps(data),
)
if evidence is not None:
edge.evidence = evidence
if properties is not None:
edge.properties = properties
if annotations is not None:
edge.annotations = annotations
self.session.add(edge)
self.object_cache_edge[sha512] = edge
return edge | [
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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,
issue: Optional[str] = None,
pages: Optional[str] = None,
date: Optional[str] = None,
first: Optional[str] = None,
last: Optional[str] = None,
authors: Union[None, List[str]] = None,
) -> Citation:
"""Create a citation if it does not exist, or return it if it does.
:param type: Citation type (e.g. PubMed)
:param reference: Identifier of the given citation (e.g. PubMed id)
:param name: Name of the publication
:param title: Title of article
:param volume: Volume of publication
:param issue: Issue of publication
:param pages: Pages of issue
:param date: Date of publication in ISO 8601 (YYYY-MM-DD) format
:param first: Name of first author
:param last: Name of last author
:param authors: Either a list of authors separated by |, or an actual list of authors
"""
if type is None:
type = CITATION_TYPE_PUBMED
sha512 = hash_citation(type=type, reference=reference)
if sha512 in self.object_cache_citation:
citation = self.object_cache_citation[sha512]
self.session.add(citation)
return citation
citation = self.get_citation_by_hash(sha512)
if citation is not None:
self.object_cache_citation[sha512] = citation
return citation
citation = Citation(
type=type,
reference=reference,
sha512=sha512,
name=name,
title=title,
volume=volume,
issue=issue,
pages=pages
)
if date is not None:
citation.date = parse_datetime(date)
if first is not None:
citation.first = self.get_or_create_author(first)
if last is not None:
citation.last = self.get_or_create_author(last)
if authors is not None:
for author in authors:
author_model = self.get_or_create_author(author)
if author_model not in citation.authors:
citation.authors.append(author_model)
self.session.add(citation)
self.object_cache_citation[sha512] = citation
return citation | 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,
issue: Optional[str] = None,
pages: Optional[str] = None,
date: Optional[str] = None,
first: Optional[str] = None,
last: Optional[str] = None,
authors: Union[None, List[str]] = None,
) -> Citation:
"""Create a citation if it does not exist, or return it if it does.
:param type: Citation type (e.g. PubMed)
:param reference: Identifier of the given citation (e.g. PubMed id)
:param name: Name of the publication
:param title: Title of article
:param volume: Volume of publication
:param issue: Issue of publication
:param pages: Pages of issue
:param date: Date of publication in ISO 8601 (YYYY-MM-DD) format
:param first: Name of first author
:param last: Name of last author
:param authors: Either a list of authors separated by |, or an actual list of authors
"""
if type is None:
type = CITATION_TYPE_PUBMED
sha512 = hash_citation(type=type, reference=reference)
if sha512 in self.object_cache_citation:
citation = self.object_cache_citation[sha512]
self.session.add(citation)
return citation
citation = self.get_citation_by_hash(sha512)
if citation is not None:
self.object_cache_citation[sha512] = citation
return citation
citation = Citation(
type=type,
reference=reference,
sha512=sha512,
name=name,
title=title,
volume=volume,
issue=issue,
pages=pages
)
if date is not None:
citation.date = parse_datetime(date)
if first is not None:
citation.first = self.get_or_create_author(first)
if last is not None:
citation.last = self.get_or_create_author(last)
if authors is not None:
for author in authors:
author_model = self.get_or_create_author(author)
if author_model not in citation.authors:
citation.authors.append(author_model)
self.session.add(citation)
self.object_cache_citation[sha512] = citation
return citation | [
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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)
if author is not None:
self.object_cache_author[name] = author
return author
author = self.object_cache_author[name] = Author.from_name(name=name)
self.session.add(author)
return author | 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)
if author is not None:
self.object_cache_author[name] = author
return author
author = self.object_cache_author[name] = Author.from_name(name=name)
self.session.add(author)
return author | [
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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."""
return self.session.query(Modification).filter(Modification.sha512 == sha512).one_or_none() | [
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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 = self.get_property_by_hash(property_hash)
if not edge_property_model:
property_def['sha512'] = property_hash
edge_property_model = Property(**property_def)
self.object_cache_property[property_hash] = edge_property_model
return 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:
edge_property_model = self.get_property_by_hash(property_hash)
if not edge_property_model:
property_def['sha512'] = property_hash
edge_property_model = Property(**property_def)
self.object_cache_property[property_hash] = edge_property_model
return edge_property_model | [
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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: (
values if isinstance(values, dict) else
{v: True for v in values} if isinstance(values, set) else
{values: True}
)
for key, values in annotations_dict.items()
} | python | def _clean_annotations(annotations_dict: AnnotationsHint) -> AnnotationsDict:
"""Fix the formatting of annotation dict."""
return {
key: (
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{values: True}
)
for key, values in annotations_dict.items()
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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]:
"""Get the set of all keywords defined as annotations in this graph."""
return (
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set(self.annotation_url) |
set(self.annotation_list)
) | python | def defined_annotation_keywords(self) -> Set[str]:
"""Get the set of all keywords defined as annotations in this graph."""
return (
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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 (
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_warning | def add_warning(self,
exception: BELParserWarning,
context: Optional[Mapping[str, Any]] = None,
) -> None:
"""Add a warning to the internal warning log in the graph, with optional context information.
:param exception: The exception that occurred
:param context: The context from the parser when the exception occurred
"""
self.warnings.append((
self.path,
exception,
{} if context is None else context,
)) | python | def add_warning(self,
exception: BELParserWarning,
context: Optional[Mapping[str, Any]] = None,
) -> None:
"""Add a warning to the internal warning log in the graph, with optional context information.
:param exception: The exception that occurred
:param context: The context from the parser when the exception occurred
"""
self.warnings.append((
self.path,
exception,
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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."""
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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."""
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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 (a unique hash)
"""
attr = {RELATION: relation}
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"""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 (a unique hash)
"""
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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
"""
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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
"""
return self.add_unqualified_edge(rna, protein, TRANSLATED_TO) | python | 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
"""
return self.add_unqualified_edge(rna, protein, TRANSLATED_TO) | [
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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:
"""Add an unqualified edge both ways."""
self.add_unqualified_edge(v, u, relation)
return self.add_unqualified_edge(u, v, relation) | [
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.add_qualified_edge | def add_qualified_edge(
self,
u,
v,
*,
relation: str,
evidence: str,
citation: Union[str, Mapping[str, str]],
annotations: Optional[AnnotationsHint] = None,
subject_modifier: Optional[Mapping] = None,
object_modifier: Optional[Mapping] = None,
**attr
) -> str:
"""Add a qualified edge.
Qualified edges have a relation, evidence, citation, and optional annotations, subject modifications,
and object modifications.
:param u: The source node
:param v: The target node
:param relation: The type of relation this edge represents
:param evidence: The evidence string from an article
:param citation: The citation data dictionary for this evidence. If a string is given,
assumes it's a PubMed identifier and auto-fills the citation type.
:param annotations: The annotations data dictionary
:param subject_modifier: The modifiers (like activity) on the subject node. See data model documentation.
:param object_modifier: The modifiers (like activity) on the object node. See data model documentation.
:return: The hash of the edge
"""
attr.update({
RELATION: relation,
EVIDENCE: evidence,
})
if isinstance(citation, str):
attr[CITATION] = {
CITATION_TYPE: CITATION_TYPE_PUBMED,
CITATION_REFERENCE: citation,
}
elif isinstance(citation, dict):
attr[CITATION] = citation
else:
raise TypeError
if annotations: # clean up annotations
attr[ANNOTATIONS] = _clean_annotations(annotations)
if subject_modifier:
attr[SUBJECT] = subject_modifier
if object_modifier:
attr[OBJECT] = object_modifier
return self._help_add_edge(u, v, attr) | python | def add_qualified_edge(
self,
u,
v,
*,
relation: str,
evidence: str,
citation: Union[str, Mapping[str, str]],
annotations: Optional[AnnotationsHint] = None,
subject_modifier: Optional[Mapping] = None,
object_modifier: Optional[Mapping] = None,
**attr
) -> str:
"""Add a qualified edge.
Qualified edges have a relation, evidence, citation, and optional annotations, subject modifications,
and object modifications.
:param u: The source node
:param v: The target node
:param relation: The type of relation this edge represents
:param evidence: The evidence string from an article
:param citation: The citation data dictionary for this evidence. If a string is given,
assumes it's a PubMed identifier and auto-fills the citation type.
:param annotations: The annotations data dictionary
:param subject_modifier: The modifiers (like activity) on the subject node. See data model documentation.
:param object_modifier: The modifiers (like activity) on the object node. See data model documentation.
:return: The hash of the edge
"""
attr.update({
RELATION: relation,
EVIDENCE: evidence,
})
if isinstance(citation, str):
attr[CITATION] = {
CITATION_TYPE: CITATION_TYPE_PUBMED,
CITATION_REFERENCE: citation,
}
elif isinstance(citation, dict):
attr[CITATION] = citation
else:
raise TypeError
if annotations: # clean up annotations
attr[ANNOTATIONS] = _clean_annotations(annotations)
if subject_modifier:
attr[SUBJECT] = subject_modifier
if object_modifier:
attr[OBJECT] = object_modifier
return self._help_add_edge(u, v, attr) | [
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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
self.add_node(node)
if VARIANTS in node:
self.add_has_variant(node.get_parent(), node)
elif MEMBERS in node:
for member in node[MEMBERS]:
self.add_has_component(node, member)
elif PRODUCTS in node and REACTANTS in node:
for reactant_tokens in node[REACTANTS]:
self.add_has_reactant(node, reactant_tokens)
for product_tokens in node[PRODUCTS]:
self.add_has_product(node, product_tokens)
return node | python | 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
self.add_node(node)
if VARIANTS in node:
self.add_has_variant(node.get_parent(), node)
elif MEMBERS in node:
for member in node[MEMBERS]:
self.add_has_component(node, member)
elif PRODUCTS in node and REACTANTS in node:
for reactant_tokens in node[REACTANTS]:
self.add_has_reactant(node, reactant_tokens)
for product_tokens in node[PRODUCTS]:
self.add_has_product(node, product_tokens)
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:
"""Check if the given edge has an evidence."""
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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]:
"""Get the citation for a given edge."""
return self._get_edge_attr(u, v, key, CITATION) | [
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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.get_edge_annotations | def get_edge_annotations(self, u, v, key: str) -> Optional[AnnotationsDict]:
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pybel/pybel | src/pybel/struct/graph.py | BELGraph.get_node_description | def get_node_description(self, node: BaseEntity) -> Optional[str]:
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"""Serialize a pair of nodes and related edge data as a BEL relation."""
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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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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]:
"""Get a set of equivalent nodes to this node, excluding the given node."""
if isinstance(node, BaseEntity):
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pybel/pybel | src/pybel/struct/graph.py | BELGraph._node_has_namespace_helper | def _node_has_namespace_helper(node: BaseEntity, namespace: str) -> bool:
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"""Check that the node has namespace information.
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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.summarize | def summarize(self, file: Optional[TextIO] = None) -> None:
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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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For additional I/O, see the :mod:`pybel.io` module.
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self._serialize_file(fmt=fmt, file=file, **kwargs) | python | def serialize(self, *, fmt: str = 'nodelink', file: Union[None, str, TextIO] = None, **kwargs):
"""Serialize the graph to an object or file if given.
For additional I/O, see the :mod:`pybel.io` module.
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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.
:param pybel.BELGraph graph: A BEL graph
"""
nodes = list(nx.isolates(graph))
graph.remove_nodes_from(nodes) | python | def remove_isolated_nodes(graph):
"""Remove isolated nodes from the network, in place.
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nodes = list(nx.isolates(graph))
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pybel/pybel | src/pybel/struct/mutation/utils.py | remove_isolated_nodes_op | def remove_isolated_nodes_op(graph):
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:rtype: pybel.BELGraph
"""
rv = graph.copy()
nodes = list(nx.isolates(rv))
rv.remove_nodes_from(nodes)
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"""Build a new graph excluding the isolated nodes.
:param pybel.BELGraph graph: A BEL graph
:rtype: pybel.BELGraph
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rv = graph.copy()
nodes = list(nx.isolates(rv))
rv.remove_nodes_from(nodes)
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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):
"""Expand a target graph by edges in the source matching the given predicates.
:param pybel.BELGraph source: A BEL graph
:param pybel.BELGraph target: A BEL graph
:param edge_predicates: An edge predicate or list of edge predicates
:return: A BEL sub-graph induced over the edges passing the given filters
:rtype: pybel.BELGraph
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target.add_edges_from(
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update_node_helper(source, target)
update_metadata(source, target) | python | def expand_by_edge_filter(source, target, edge_predicates: EdgePredicates):
"""Expand a target graph by edges in the source matching the given predicates.
:param pybel.BELGraph source: A BEL graph
:param pybel.BELGraph target: A BEL graph
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:rtype: pybel.BELGraph
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update_node_helper(source, target)
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:param pybel.BELGraph target: A BEL graph
:param edge_predicates: An edge predicate or list of edge predicates
:return: A BEL sub-graph induced over the edges passing the given filters
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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:
"""Handle statements like ``SET DOCUMENT X = "Y"``.
:raises: InvalidMetadataException
:raises: VersionFormatWarning
"""
key = tokens['key']
value = tokens['value']
if key not in DOCUMENT_KEYS:
raise InvalidMetadataException(self.get_line_number(), line, position, key, value)
norm_key = DOCUMENT_KEYS[key]
if norm_key in self.document_metadata:
log.warning('Tried to overwrite metadata: %s', key)
return tokens
self.document_metadata[norm_key] = value
if norm_key == METADATA_VERSION:
self.raise_for_version(line, position, value)
return tokens | python | def handle_document(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
"""Handle statements like ``SET DOCUMENT X = "Y"``.
:raises: InvalidMetadataException
:raises: VersionFormatWarning
"""
key = tokens['key']
value = tokens['value']
if key not in DOCUMENT_KEYS:
raise InvalidMetadataException(self.get_line_number(), line, position, key, value)
norm_key = DOCUMENT_KEYS[key]
if norm_key in self.document_metadata:
log.warning('Tried to overwrite metadata: %s', key)
return tokens
self.document_metadata[norm_key] = value
if norm_key == METADATA_VERSION:
self.raise_for_version(line, position, value)
return tokens | [
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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:
"""Raise an exception if a namespace is already defined.
:raises: RedefinedNamespaceError
"""
if self.disallow_redefinition and self.has_namespace(namespace):
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"""Raise an exception if a namespace is already defined.
:raises: RedefinedNamespaceError
"""
if self.disallow_redefinition and self.has_namespace(namespace):
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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:
"""Handle statements like ``DEFINE NAMESPACE X AS URL "Y"``.
:raises: RedefinedNamespaceError
:raises: pybel.resources.exc.ResourceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
url = tokens['url']
self.namespace_url_dict[namespace] = url
if self.skip_validation:
return tokens
namespace_result = self.manager.get_or_create_namespace(url)
if isinstance(namespace_result, dict):
self.namespace_to_term[namespace] = namespace_result
self.uncachable_namespaces.add(url)
else:
self.namespace_to_term[namespace] = self.manager.get_namespace_encoding(url)
return tokens | python | def handle_namespace_url(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
"""Handle statements like ``DEFINE NAMESPACE X AS URL "Y"``.
:raises: RedefinedNamespaceError
:raises: pybel.resources.exc.ResourceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
url = tokens['url']
self.namespace_url_dict[namespace] = url
if self.skip_validation:
return tokens
namespace_result = self.manager.get_or_create_namespace(url)
if isinstance(namespace_result, dict):
self.namespace_to_term[namespace] = namespace_result
self.uncachable_namespaces.add(url)
else:
self.namespace_to_term[namespace] = self.manager.get_namespace_encoding(url)
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.handle_namespace_pattern | def handle_namespace_pattern(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
"""Handle statements like ``DEFINE NAMESPACE X AS PATTERN "Y"``.
:raises: RedefinedNamespaceError
"""
namespace = tokens['name']
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return tokens | python | def handle_namespace_pattern(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
"""Handle statements like ``DEFINE NAMESPACE X AS PATTERN "Y"``.
:raises: RedefinedNamespaceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
self.namespace_to_pattern[namespace] = re.compile(tokens['value'])
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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:
"""Raise an exception if the given annotation is already defined.
:raises: RedefinedAnnotationError
"""
if self.disallow_redefinition and self.has_annotation(annotation):
raise RedefinedAnnotationError(self.get_line_number(), line, position, annotation) | python | def raise_for_redefined_annotation(self, line: str, position: int, annotation: str) -> None:
"""Raise an exception if the given annotation is already defined.
:raises: RedefinedAnnotationError
"""
if self.disallow_redefinition and self.has_annotation(annotation):
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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:
"""Handle statements like ``DEFINE ANNOTATION X AS URL "Y"``.
:raises: RedefinedAnnotationError
"""
keyword = tokens['name']
self.raise_for_redefined_annotation(line, position, keyword)
url = tokens['url']
self.annotation_url_dict[keyword] = url
if self.skip_validation:
return tokens
self.annotation_to_term[keyword] = self.manager.get_annotation_entry_names(url)
return tokens | python | def handle_annotations_url(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
"""Handle statements like ``DEFINE ANNOTATION X AS URL "Y"``.
:raises: RedefinedAnnotationError
"""
keyword = tokens['name']
self.raise_for_redefined_annotation(line, position, keyword)
url = tokens['url']
self.annotation_url_dict[keyword] = url
if self.skip_validation:
return tokens
self.annotation_to_term[keyword] = self.manager.get_annotation_entry_names(url)
return tokens | [
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.handle_annotation_pattern | def handle_annotation_pattern(self, line: str, position: int, tokens: ParseResults) -> ParseResults:
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:raises: RedefinedAnnotationError
"""
annotation = tokens['name']
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"""Handle statements like ``DEFINE ANNOTATION X AS PATTERN "Y"``.
:raises: RedefinedAnnotationError
"""
annotation = tokens['name']
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pybel/pybel | src/pybel/parser/parse_metadata.py | MetadataParser.has_annotation | def has_annotation(self, annotation: str) -> bool:
"""Check if this annotation is defined."""
return (
self.has_enumerated_annotation(annotation) or
self.has_regex_annotation(annotation) or
self.has_local_annotation(annotation)
) | python | def has_annotation(self, annotation: str) -> bool:
"""Check if this annotation is defined."""
return (
self.has_enumerated_annotation(annotation) or
self.has_regex_annotation(annotation) or
self.has_local_annotation(annotation)
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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 parsed
:param str version: A version string
:raises: VersionFormatWarning
"""
if valid_date_version(version):
return
if not SEMANTIC_VERSION_STRING_RE.match(version):
raise VersionFormatWarning(self.get_line_number(), line, position, version) | python | 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 parsed
:param str version: A version string
:raises: VersionFormatWarning
"""
if valid_date_version(version):
return
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raise VersionFormatWarning(self.get_line_number(), line, position, version) | [
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pybel/pybel | src/pybel/dsl/namespaces.py | chebi | def chebi(name=None, identifier=None) -> Abundance:
"""Build a ChEBI abundance node."""
return Abundance(namespace='CHEBI', name=name, identifier=identifier) | python | def chebi(name=None, identifier=None) -> Abundance:
"""Build a ChEBI abundance node."""
return Abundance(namespace='CHEBI', name=name, identifier=identifier) | [
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pybel/pybel | src/pybel/dsl/namespaces.py | hgnc | def hgnc(name=None, identifier=None) -> Protein:
"""Build an HGNC protein node."""
return Protein(namespace='HGNC', name=name, identifier=identifier) | python | def hgnc(name=None, identifier=None) -> Protein:
"""Build an HGNC protein node."""
return Protein(namespace='HGNC', name=name, identifier=identifier) | [
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pybel/pybel | src/pybel/manager/base_manager.py | build_engine_session | def build_engine_session(connection: str,
echo: bool = False,
autoflush: Optional[bool] = None,
autocommit: Optional[bool] = None,
expire_on_commit: Optional[bool] = None,
scopefunc=None) -> Tuple:
"""Build an engine and a session.
:param connection: An RFC-1738 database connection string
:param echo: Turn on echoing SQL
:param autoflush: Defaults to True if not specified in kwargs or configuration.
:param autocommit: Defaults to False if not specified in kwargs or configuration.
:param expire_on_commit: Defaults to False if not specified in kwargs or configuration.
:param scopefunc: Scoped function to pass to :func:`sqlalchemy.orm.scoped_session`
:rtype: tuple[Engine,Session]
From the Flask-SQLAlchemy documentation:
An extra key ``'scopefunc'`` can be set on the ``options`` dict to
specify a custom scope function. If it's not provided, Flask's app
context stack identity is used. This will ensure that sessions are
created and removed with the request/response cycle, and should be fine
in most cases.
"""
if connection is None:
raise ValueError('can not build engine when connection is None')
engine = create_engine(connection, echo=echo)
if autoflush is None:
autoflush = config.get('PYBEL_MANAGER_AUTOFLUSH', False)
if autocommit is None:
autocommit = config.get('PYBEL_MANAGER_AUTOCOMMIT', False)
if expire_on_commit is None:
expire_on_commit = config.get('PYBEL_MANAGER_AUTOEXPIRE', True)
log.debug('auto flush: %s, auto commit: %s, expire on commmit: %s', autoflush, autocommit, expire_on_commit)
#: A SQLAlchemy session maker
session_maker = sessionmaker(
bind=engine,
autoflush=autoflush,
autocommit=autocommit,
expire_on_commit=expire_on_commit,
)
#: A SQLAlchemy session object
session = scoped_session(
session_maker,
scopefunc=scopefunc,
)
return engine, session | python | def build_engine_session(connection: str,
echo: bool = False,
autoflush: Optional[bool] = None,
autocommit: Optional[bool] = None,
expire_on_commit: Optional[bool] = None,
scopefunc=None) -> Tuple:
"""Build an engine and a session.
:param connection: An RFC-1738 database connection string
:param echo: Turn on echoing SQL
:param autoflush: Defaults to True if not specified in kwargs or configuration.
:param autocommit: Defaults to False if not specified in kwargs or configuration.
:param expire_on_commit: Defaults to False if not specified in kwargs or configuration.
:param scopefunc: Scoped function to pass to :func:`sqlalchemy.orm.scoped_session`
:rtype: tuple[Engine,Session]
From the Flask-SQLAlchemy documentation:
An extra key ``'scopefunc'`` can be set on the ``options`` dict to
specify a custom scope function. If it's not provided, Flask's app
context stack identity is used. This will ensure that sessions are
created and removed with the request/response cycle, and should be fine
in most cases.
"""
if connection is None:
raise ValueError('can not build engine when connection is None')
engine = create_engine(connection, echo=echo)
if autoflush is None:
autoflush = config.get('PYBEL_MANAGER_AUTOFLUSH', False)
if autocommit is None:
autocommit = config.get('PYBEL_MANAGER_AUTOCOMMIT', False)
if expire_on_commit is None:
expire_on_commit = config.get('PYBEL_MANAGER_AUTOEXPIRE', True)
log.debug('auto flush: %s, auto commit: %s, expire on commmit: %s', autoflush, autocommit, expire_on_commit)
#: A SQLAlchemy session maker
session_maker = sessionmaker(
bind=engine,
autoflush=autoflush,
autocommit=autocommit,
expire_on_commit=expire_on_commit,
)
#: A SQLAlchemy session object
session = scoped_session(
session_maker,
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pybel/pybel | src/pybel/manager/base_manager.py | BaseManager.create_all | def create_all(self, checkfirst: bool = True) -> None:
"""Create the PyBEL cache's database and tables.
:param checkfirst: Check if the database exists before trying to re-make it
"""
self.base.metadata.create_all(bind=self.engine, checkfirst=checkfirst) | python | def create_all(self, checkfirst: bool = True) -> None:
"""Create the PyBEL cache's database and tables.
:param checkfirst: Check if the database exists before trying to re-make it
"""
self.base.metadata.create_all(bind=self.engine, checkfirst=checkfirst) | [
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pybel/pybel | src/pybel/manager/base_manager.py | BaseManager.drop_all | def drop_all(self, checkfirst: bool = True) -> None:
"""Drop all data, tables, and databases for the PyBEL cache.
:param checkfirst: Check if the database exists before trying to drop it
"""
self.session.close()
self.base.metadata.drop_all(bind=self.engine, checkfirst=checkfirst) | python | def drop_all(self, checkfirst: bool = True) -> None:
"""Drop all data, tables, and databases for the PyBEL cache.
:param checkfirst: Check if the database exists before trying to drop it
"""
self.session.close()
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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
self.base.query = self.session.query_property() | python | def bind(self) -> None:
"""Bind the metadata to the engine and session."""
self.base.metadata.bind = self.engine
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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]:
"""List the models in this class."""
return self.session.query(model_cls).all() | python | def _list_model(self, model_cls: Type[X]) -> List[X]:
"""List the models in this class."""
return self.session.query(model_cls).all() | [
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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):
return datetime.strptime(publication_date, '%Y %b %d').strftime('%Y-%m-%d')
if re2.search(publication_date):
return datetime.strptime(publication_date, '%Y %b').strftime('%Y-%m-01')
if re3.search(publication_date):
return publication_date + "-01-01"
if re4.search(publication_date):
return datetime.strptime(publication_date[:-4], '%Y %b').strftime('%Y-%m-01')
s = re5.search(publication_date)
if s:
year, season = s.groups()
return '{}-{}-01'.format(year, season_map[season])
s = re6.search(publication_date)
if s:
return datetime.strptime(publication_date, '%Y %b %d-{}'.format(s.groups()[0])).strftime('%Y-%m-%d')
s = re7.search(publication_date)
if s:
return datetime.strptime(publication_date, '%Y %b %d-{}'.format(s.groups()[0])).strftime('%Y-%m-%d') | 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')
if re2.search(publication_date):
return datetime.strptime(publication_date, '%Y %b').strftime('%Y-%m-01')
if re3.search(publication_date):
return publication_date + "-01-01"
if re4.search(publication_date):
return datetime.strptime(publication_date[:-4], '%Y %b').strftime('%Y-%m-01')
s = re5.search(publication_date)
if s:
year, season = s.groups()
return '{}-{}-01'.format(year, season_map[season])
s = re6.search(publication_date)
if s:
return datetime.strptime(publication_date, '%Y %b %d-{}'.format(s.groups()[0])).strftime('%Y-%m-%d')
s = re7.search(publication_date)
if s:
return datetime.strptime(publication_date, '%Y %b %d-{}'.format(s.groups()[0])).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]:
"""Clean a list of PubMed identifiers with string strips, deduplicates, and sorting."""
return sorted({str(pmid).strip() for pmid in pmids}) | python | def clean_pubmed_identifiers(pmids: Iterable[str]) -> List[str]:
"""Clean a list of PubMed identifiers with string strips, deduplicates, and sorting."""
return sorted({str(pmid).strip() for pmid in pmids}) | [
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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]):
"""Get the response from PubMed E-Utils for a given list of PubMed identifiers.
:param pubmed_identifiers:
:rtype: dict
"""
pubmed_identifiers = list(pubmed_identifiers)
url = EUTILS_URL_FMT.format(','.join(
pubmed_identifier
for pubmed_identifier in pubmed_identifiers
if pubmed_identifier
))
response = requests.get(url)
return response.json() | python | def get_pubmed_citation_response(pubmed_identifiers: Iterable[str]):
"""Get the response from PubMed E-Utils for a given list of PubMed identifiers.
:param pubmed_identifiers:
:rtype: dict
"""
pubmed_identifiers = list(pubmed_identifiers)
url = EUTILS_URL_FMT.format(','.join(
pubmed_identifier
for pubmed_identifier in pubmed_identifiers
if pubmed_identifier
))
response = requests.get(url)
return response.json() | [
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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]
"""
if 'error' in p:
log.warning('Error downloading PubMed')
return False
citation.name = p['fulljournalname']
citation.title = p['title']
citation.volume = p['volume']
citation.issue = p['issue']
citation.pages = p['pages']
citation.first = manager.get_or_create_author(p['sortfirstauthor'])
citation.last = manager.get_or_create_author(p['lastauthor'])
if 'authors' in p:
for author in p['authors']:
author_model = manager.get_or_create_author(author['name'])
if author_model not in citation.authors:
citation.authors.append(author_model)
publication_date = p['pubdate']
sanitized_publication_date = sanitize_date(publication_date)
if sanitized_publication_date:
citation.date = datetime.strptime(sanitized_publication_date, '%Y-%m-%d')
else:
log.info('result had date with strange format: %s', publication_date)
return True | python | 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]
"""
if 'error' in p:
log.warning('Error downloading PubMed')
return False
citation.name = p['fulljournalname']
citation.title = p['title']
citation.volume = p['volume']
citation.issue = p['issue']
citation.pages = p['pages']
citation.first = manager.get_or_create_author(p['sortfirstauthor'])
citation.last = manager.get_or_create_author(p['lastauthor'])
if 'authors' in p:
for author in p['authors']:
author_model = manager.get_or_create_author(author['name'])
if author_model not in citation.authors:
citation.authors.append(author_model)
publication_date = p['pubdate']
sanitized_publication_date = sanitize_date(publication_date)
if sanitized_publication_date:
citation.date = datetime.strptime(sanitized_publication_date, '%Y-%m-%d')
else:
log.info('result had date with strange format: %s', publication_date)
return True | [
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pybel/pybel | src/pybel/manager/citation_utils.py | get_citations_by_pmids | def get_citations_by_pmids(manager,
pmids: Iterable[Union[str, int]],
group_size: Optional[int] = None,
sleep_time: Optional[int] = None,
) -> Tuple[Dict[str, Dict], Set[str]]:
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:type manager: pybel.Manager
:param pmids: an iterable of PubMed identifiers
:param group_size: The number of PubMed identifiers to query at a time. Defaults to 200 identifiers.
:param sleep_time: Number of seconds to sleep between queries. Defaults to 1 second.
:return: A dictionary of {pmid: pmid data dictionary} or a pair of this dictionary and a set ot erroneous
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"""
group_size = group_size if group_size is not None else 200
sleep_time = sleep_time if sleep_time is not None else 1
pmids = clean_pubmed_identifiers(pmids)
log.info('Ensuring %d PubMed identifiers', len(pmids))
result = {}
unenriched_pmids = {}
for pmid in pmids:
citation = manager.get_or_create_citation(type=CITATION_TYPE_PUBMED, reference=pmid)
if not citation.date or not citation.name or not citation.authors:
unenriched_pmids[pmid] = citation
continue
result[pmid] = citation.to_json()
manager.session.commit()
log.debug('Found %d PubMed identifiers in database', len(pmids) - len(unenriched_pmids))
if not unenriched_pmids:
return result, set()
number_unenriched = len(unenriched_pmids)
log.info('Querying PubMed for %d identifiers', number_unenriched)
errors = set()
t = time.time()
for pmid_group_index, pmid_list in enumerate(grouper(group_size, unenriched_pmids), start=1):
pmid_list = list(pmid_list)
log.info('Getting group %d having %d PubMed identifiers', pmid_group_index, len(pmid_list))
response = get_pubmed_citation_response(pmid_list)
response_pmids = response['result']['uids']
for pmid in response_pmids:
p = response['result'][pmid]
citation = unenriched_pmids[pmid]
successful_enrichment = enrich_citation_model(manager, citation, p)
if not successful_enrichment:
log.warning("Error downloading PubMed identifier: %s", pmid)
errors.add(pmid)
continue
result[pmid] = citation.to_json()
manager.session.add(citation)
manager.session.commit() # commit in groups
# Don't want to hit that rate limit
time.sleep(sleep_time)
log.info('retrieved %d PubMed identifiers in %.02f seconds', len(unenriched_pmids), time.time() - t)
return result, errors | python | def get_citations_by_pmids(manager,
pmids: Iterable[Union[str, int]],
group_size: Optional[int] = None,
sleep_time: Optional[int] = None,
) -> Tuple[Dict[str, Dict], Set[str]]:
"""Get citation information for the given list of PubMed identifiers using the NCBI's eUtils service.
:type manager: pybel.Manager
:param pmids: an iterable of PubMed identifiers
:param group_size: The number of PubMed identifiers to query at a time. Defaults to 200 identifiers.
:param sleep_time: Number of seconds to sleep between queries. Defaults to 1 second.
:return: A dictionary of {pmid: pmid data dictionary} or a pair of this dictionary and a set ot erroneous
pmids if return_errors is :data:`True`
"""
group_size = group_size if group_size is not None else 200
sleep_time = sleep_time if sleep_time is not None else 1
pmids = clean_pubmed_identifiers(pmids)
log.info('Ensuring %d PubMed identifiers', len(pmids))
result = {}
unenriched_pmids = {}
for pmid in pmids:
citation = manager.get_or_create_citation(type=CITATION_TYPE_PUBMED, reference=pmid)
if not citation.date or not citation.name or not citation.authors:
unenriched_pmids[pmid] = citation
continue
result[pmid] = citation.to_json()
manager.session.commit()
log.debug('Found %d PubMed identifiers in database', len(pmids) - len(unenriched_pmids))
if not unenriched_pmids:
return result, set()
number_unenriched = len(unenriched_pmids)
log.info('Querying PubMed for %d identifiers', number_unenriched)
errors = set()
t = time.time()
for pmid_group_index, pmid_list in enumerate(grouper(group_size, unenriched_pmids), start=1):
pmid_list = list(pmid_list)
log.info('Getting group %d having %d PubMed identifiers', pmid_group_index, len(pmid_list))
response = get_pubmed_citation_response(pmid_list)
response_pmids = response['result']['uids']
for pmid in response_pmids:
p = response['result'][pmid]
citation = unenriched_pmids[pmid]
successful_enrichment = enrich_citation_model(manager, citation, p)
if not successful_enrichment:
log.warning("Error downloading PubMed identifier: %s", pmid)
errors.add(pmid)
continue
result[pmid] = citation.to_json()
manager.session.add(citation)
manager.session.commit() # commit in groups
# Don't want to hit that rate limit
time.sleep(sleep_time)
log.info('retrieved %d PubMed identifiers in %.02f seconds', len(unenriched_pmids), time.time() - t)
return result, errors | [
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pybel/pybel | src/pybel/manager/citation_utils.py | enrich_pubmed_citations | def enrich_pubmed_citations(manager,
graph,
group_size: Optional[int] = None,
sleep_time: Optional[int] = None,
) -> Set[str]:
"""Overwrite all PubMed citations with values from NCBI's eUtils lookup service.
Sets authors as list, so probably a good idea to run :func:`pybel_tools.mutation.serialize_authors` before
exporting.
:type manager: pybel.manager.Manager
:type graph: pybel.BELGraph
:param group_size: The number of PubMed identifiers to query at a time. Defaults to 200 identifiers.
:param sleep_time: Number of seconds to sleep between queries. Defaults to 1 second.
:return: A set of PMIDs for which the eUtils service crashed
"""
pmids = get_pubmed_identifiers(graph)
pmid_data, errors = get_citations_by_pmids(manager, pmids=pmids, group_size=group_size, sleep_time=sleep_time)
for u, v, k in filter_edges(graph, has_pubmed):
pmid = graph[u][v][k][CITATION][CITATION_REFERENCE].strip()
if pmid not in pmid_data:
log.warning('Missing data for PubMed identifier: %s', pmid)
errors.add(pmid)
continue
graph[u][v][k][CITATION].update(pmid_data[pmid])
return errors | python | def enrich_pubmed_citations(manager,
graph,
group_size: Optional[int] = None,
sleep_time: Optional[int] = None,
) -> Set[str]:
"""Overwrite all PubMed citations with values from NCBI's eUtils lookup service.
Sets authors as list, so probably a good idea to run :func:`pybel_tools.mutation.serialize_authors` before
exporting.
:type manager: pybel.manager.Manager
:type graph: pybel.BELGraph
:param group_size: The number of PubMed identifiers to query at a time. Defaults to 200 identifiers.
:param sleep_time: Number of seconds to sleep between queries. Defaults to 1 second.
:return: A set of PMIDs for which the eUtils service crashed
"""
pmids = get_pubmed_identifiers(graph)
pmid_data, errors = get_citations_by_pmids(manager, pmids=pmids, group_size=group_size, sleep_time=sleep_time)
for u, v, k in filter_edges(graph, has_pubmed):
pmid = graph[u][v][k][CITATION][CITATION_REFERENCE].strip()
if pmid not in pmid_data:
log.warning('Missing data for PubMed identifier: %s', pmid)
errors.add(pmid)
continue
graph[u][v][k][CITATION].update(pmid_data[pmid])
return errors | [
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:type graph: pybel.BELGraph
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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.
:param pybel.BELGraph graph: A BEL graph
:return: A dictionary of {node: set of PyBEL node tuples}
"""
collapse_dict = defaultdict(set)
r2g = {}
for gene_node, rna_node, d in graph.edges(data=True):
if d[RELATION] != TRANSCRIBED_TO:
continue
collapse_dict[gene_node].add(rna_node)
r2g[rna_node] = gene_node
for rna_node, protein_node, d in graph.edges(data=True):
if d[RELATION] != TRANSLATED_TO:
continue
if rna_node not in r2g:
raise ValueError('Should complete origin before running this function')
collapse_dict[r2g[rna_node]].add(protein_node)
return collapse_dict | python | def _build_collapse_to_gene_dict(graph) -> Dict[BaseEntity, Set[BaseEntity]]:
"""Build a collapse dictionary.
:param pybel.BELGraph graph: A BEL graph
:return: A dictionary of {node: set of PyBEL node tuples}
"""
collapse_dict = defaultdict(set)
r2g = {}
for gene_node, rna_node, d in graph.edges(data=True):
if d[RELATION] != TRANSCRIBED_TO:
continue
collapse_dict[gene_node].add(rna_node)
r2g[rna_node] = gene_node
for rna_node, protein_node, d in graph.edges(data=True):
if d[RELATION] != TRANSLATED_TO:
continue
if rna_node not in r2g:
raise ValueError('Should complete origin before running this function')
collapse_dict[r2g[rna_node]].add(protein_node)
return collapse_dict | [
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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)
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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)
ctx.obj.bind() | [
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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.setLevel(logging.DEBUG)
log.debug('using connection: %s', manager.engine.url)
click.secho('Compilation', fg='red', bold=True)
if skip_tqdm:
click.echo('```')
graph = from_path(
path,
manager=manager,
use_tqdm=(not (skip_tqdm or verbose)),
allow_nested=allow_nested,
allow_naked_names=allow_naked_names,
disallow_unqualified_translocations=disallow_unqualified_translocations,
citation_clearing=(not no_citation_clearing),
required_annotations=required_annotations,
no_identifier_validation=no_identifier_validation,
allow_definition_failures=True,
)
if skip_tqdm:
click.echo('```')
to_pickle(graph, get_corresponding_pickle_path(path))
click.echo('')
_print_summary(graph, ticks=skip_tqdm)
sys.exit(0 if 0 == graph.number_of_warnings() else 1) | 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)
log.setLevel(logging.DEBUG)
log.debug('using connection: %s', manager.engine.url)
click.secho('Compilation', fg='red', bold=True)
if skip_tqdm:
click.echo('```')
graph = from_path(
path,
manager=manager,
use_tqdm=(not (skip_tqdm or verbose)),
allow_nested=allow_nested,
allow_naked_names=allow_naked_names,
disallow_unqualified_translocations=disallow_unqualified_translocations,
citation_clearing=(not no_citation_clearing),
required_annotations=required_annotations,
no_identifier_validation=no_identifier_validation,
allow_definition_failures=True,
)
if skip_tqdm:
click.echo('```')
to_pickle(graph, get_corresponding_pickle_path(path))
click.echo('')
_print_summary(graph, ticks=skip_tqdm)
sys.exit(0 if 0 == graph.number_of_warnings() else 1) | [
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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('Outputting GraphML to %s', graphml)
to_graphml(graph, graphml)
if gsea:
log.info('Outputting GRP to %s', gsea)
to_gsea(graph, gsea)
if json:
log.info('Outputting JSON to %s', json)
to_json_file(graph, json)
if bel:
log.info('Outputting BEL to %s', bel)
to_bel(graph, bel) | 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('Outputting GraphML to %s', graphml)
to_graphml(graph, graphml)
if gsea:
log.info('Outputting GRP to %s', gsea)
to_gsea(graph, gsea)
if json:
log.info('Outputting JSON to %s', json)
to_json_file(graph, json)
if bel:
log.info('Outputting BEL to %s', bel)
to_bel(graph, bel) | [
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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)
to_neo4j(graph, neo_graph) | [
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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 {} statements from INDRA'.format(len(statements)))
graph = from_indra_statements(
statements,
name='INDRA Machine for {}'.format(', '.join(sorted(agents))),
version=time.strftime('%Y%m%d'),
)
click.echo('built BEL graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
if 0 == len(graph):
click.echo('not uploading empty graph')
sys.exit(-1)
if local:
to_database(graph, manager=manager)
else:
resp = to_web(graph, host=host)
resp.raise_for_status() | 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 {} statements from INDRA'.format(len(statements)))
graph = from_indra_statements(
statements,
name='INDRA Machine for {}'.format(', '.join(sorted(agents))),
version=time.strftime('%Y%m%d'),
)
click.echo('built BEL graph with {} nodes and {} edges'.format(graph.number_of_nodes(), graph.number_of_edges()))
if 0 == len(graph):
click.echo('not uploading empty graph')
sys.exit(-1)
if local:
to_database(graph, manager=manager)
else:
resp = to_web(graph, host=host)
resp.raise_for_status() | [
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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
click.echo('inserting {}'.format(graph))
manager.insert_graph(graph, use_tqdm=True) | 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
click.echo('inserting {}'.format(graph))
manager.insert_graph(graph, use_tqdm=True) | [
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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 is not None:
_ls(manager, Namespace, namespace_id)
else:
click.echo('Missing argument -i or -u') | 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)
else:
click.echo('uncachable namespace')
elif namespace_id is not None:
_ls(manager, Namespace, namespace_id)
else:
click.echo('Missing argument -i or -u') | [
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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():
click.echo('{}\t{}\t{}'.format(n.id, n.name, n.version)) | [
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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:
click.echo(e.bel) | [
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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
]
manager.session.delete(nodes_to_delete)
manager.session.commit() | [
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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_namespaces()))
click.echo('Namespaces entries: {}'.format(manager.count_namespace_entries()))
click.echo('Annotations: {}'.format(manager.count_annotations()))
click.echo('Annotation entries: {}'.format(manager.count_annotation_entries())) | 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_namespaces()))
click.echo('Namespaces entries: {}'.format(manager.count_namespace_entries()))
click.echo('Annotations: {}'.format(manager.count_annotations()))
click.echo('Annotation entries: {}'.format(manager.count_annotation_entries())) | [
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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(
len(str(exc.line_number))
for _, exc, _ in warnings
)
max_warning_width = max(
len(exc.__class__.__name__)
for _, exc, _ in warnings
)
s1 = '{:>' + str(max_line_width) + '}' + sep
s2 = '{:>' + str(max_warning_width) + '}' + sep
def _make_line(path: str, exc: BELParserWarning):
s = click.style(path, fg='cyan') + sep
s += click.style(s1.format(exc.line_number), fg='blue', bold=True)
s += click.style(s2.format(exc.__class__.__name__),
fg=('red' if exc.__class__.__name__.endswith('Error') else 'yellow'))
s += click.style(exc.line, bold=True) + sep
s += click.style(str(exc))
return s
click.echo_via_pager('\n'.join(
_make_line(path, exc)
for path, exc, _ in warnings
)) | 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(
len(str(exc.line_number))
for _, exc, _ in warnings
)
max_warning_width = max(
len(exc.__class__.__name__)
for _, exc, _ in warnings
)
s1 = '{:>' + str(max_line_width) + '}' + sep
s2 = '{:>' + str(max_warning_width) + '}' + sep
def _make_line(path: str, exc: BELParserWarning):
s = click.style(path, fg='cyan') + sep
s += click.style(s1.format(exc.line_number), fg='blue', bold=True)
s += click.style(s2.format(exc.__class__.__name__),
fg=('red' if exc.__class__.__name__.endswith('Error') else 'yellow'))
s += click.style(exc.line, bold=True) + sep
s += click.style(str(exc))
return s
click.echo_via_pager('\n'.join(
_make_line(path, exc)
for path, exc, _ in warnings
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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(tokens)
elif VARIANTS in tokens:
return _variant_po_to_dict(tokens)
elif MEMBERS in tokens:
return _list_po_to_dict(tokens)
elif FUSION in tokens:
return _fusion_to_dsl(tokens)
return _simple_po_to_dict(tokens) | python | 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(tokens)
elif VARIANTS in tokens:
return _variant_po_to_dict(tokens)
elif MEMBERS in tokens:
return _list_po_to_dict(tokens)
elif FUSION in tokens:
return _fusion_to_dsl(tokens)
return _simple_po_to_dict(tokens) | [
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pybel/pybel | src/pybel/tokens.py | _fusion_to_dsl | def _fusion_to_dsl(tokens) -> FusionBase:
"""Convert a PyParsing data dictionary to a PyBEL fusion data dictionary.
:param tokens: A PyParsing data dictionary representing a fusion
:type tokens: ParseResult
"""
func = tokens[FUNCTION]
fusion_dsl = FUNC_TO_FUSION_DSL[func]
member_dsl = FUNC_TO_DSL[func]
partner_5p = member_dsl(
namespace=tokens[FUSION][PARTNER_5P][NAMESPACE],
name=tokens[FUSION][PARTNER_5P][NAME]
)
partner_3p = member_dsl(
namespace=tokens[FUSION][PARTNER_3P][NAMESPACE],
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)
range_5p = _fusion_range_to_dsl(tokens[FUSION][RANGE_5P])
range_3p = _fusion_range_to_dsl(tokens[FUSION][RANGE_3P])
return fusion_dsl(
partner_5p=partner_5p,
partner_3p=partner_3p,
range_5p=range_5p,
range_3p=range_3p,
) | python | def _fusion_to_dsl(tokens) -> FusionBase:
"""Convert a PyParsing data dictionary to a PyBEL fusion data dictionary.
:param tokens: A PyParsing data dictionary representing a fusion
:type tokens: ParseResult
"""
func = tokens[FUNCTION]
fusion_dsl = FUNC_TO_FUSION_DSL[func]
member_dsl = FUNC_TO_DSL[func]
partner_5p = member_dsl(
namespace=tokens[FUSION][PARTNER_5P][NAMESPACE],
name=tokens[FUSION][PARTNER_5P][NAME]
)
partner_3p = member_dsl(
namespace=tokens[FUSION][PARTNER_3P][NAMESPACE],
name=tokens[FUSION][PARTNER_3P][NAME]
)
range_5p = _fusion_range_to_dsl(tokens[FUSION][RANGE_5P])
range_3p = _fusion_range_to_dsl(tokens[FUSION][RANGE_3P])
return fusion_dsl(
partner_5p=partner_5p,
partner_3p=partner_3p,
range_5p=range_5p,
range_3p=range_3p,
) | [
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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
"""
if FUSION_MISSING in tokens:
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start=tokens[FUSION_START],
stop=tokens[FUSION_STOP]
) | python | def _fusion_range_to_dsl(tokens) -> FusionRangeBase:
"""Convert a PyParsing data dictionary into a PyBEL.
:type tokens: ParseResult
"""
if FUSION_MISSING in tokens:
return missing_fusion_range()
return fusion_range(
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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(
namespace=tokens[NAMESPACE],
name=tokens.get(NAME),
identifier=tokens.get(IDENTIFIER),
) | python | 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(
namespace=tokens[NAMESPACE],
name=tokens.get(NAME),
identifier=tokens.get(IDENTIFIER),
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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(
name=tokens[IDENTIFIER][NAME],
namespace=tokens[IDENTIFIER][NAMESPACE],
)
if kind == PMOD:
return pmod(
name=tokens[IDENTIFIER][NAME],
namespace=tokens[IDENTIFIER][NAMESPACE],
code=tokens.get(PMOD_CODE),
position=tokens.get(PMOD_POSITION),
)
if kind == FRAGMENT:
start, stop = tokens.get(FRAGMENT_START), tokens.get(FRAGMENT_STOP)
return fragment(
start=start,
stop=stop,
description=tokens.get(FRAGMENT_DESCRIPTION)
)
raise ValueError('invalid fragment kind: {}'.format(kind)) | python | 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(
name=tokens[IDENTIFIER][NAME],
namespace=tokens[IDENTIFIER][NAMESPACE],
)
if kind == PMOD:
return pmod(
name=tokens[IDENTIFIER][NAME],
namespace=tokens[IDENTIFIER][NAMESPACE],
code=tokens.get(PMOD_CODE),
position=tokens.get(PMOD_POSITION),
)
if kind == FRAGMENT:
start, stop = tokens.get(FRAGMENT_START), tokens.get(FRAGMENT_STOP)
return fragment(
start=start,
stop=stop,
description=tokens.get(FRAGMENT_DESCRIPTION)
)
raise ValueError('invalid fragment kind: {}'.format(kind)) | [
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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(
reactants=_reaction_part_po_to_dict(tokens[REACTANTS]),
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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pybel/pybel | src/pybel/tokens.py | _list_po_to_dict | def _list_po_to_dict(tokens) -> ListAbundance:
"""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]]
return dsl(members) | python | def _list_po_to_dict(tokens) -> ListAbundance:
"""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]]
return dsl(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 any annotation should be present, if False all annotations should be present in the
edge. Defaults to True.
:return: A subgraph of the original BEL graph
:rtype: pybel.BELGraph
"""
edge_filter_builder = (
build_annotation_dict_any_filter
if (or_ is None or or_) else
build_annotation_dict_all_filter
)
return get_subgraph_by_edge_filter(graph, edge_filter_builder(annotations)) | 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`)
:param boolean or_: if True any annotation should be present, if False all annotations should be present in the
edge. Defaults to True.
:return: A subgraph of the original BEL graph
:rtype: pybel.BELGraph
"""
edge_filter_builder = (
build_annotation_dict_any_filter
if (or_ is None or or_) else
build_annotation_dict_all_filter
)
return get_subgraph_by_edge_filter(graph, edge_filter_builder(annotations)) | [
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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
:type values: str or iter[str]
:return: A subgraph of the original BEL graph
:rtype: pybel.BELGraph
"""
if isinstance(values, str):
values = {values}
return get_subgraph_by_annotations(graph, {annotation: values}) | python | 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
:type values: str or iter[str]
:return: A subgraph of the original BEL graph
:rtype: pybel.BELGraph
"""
if isinstance(values, str):
values = {values}
return get_subgraph_by_annotations(graph, {annotation: values}) | [
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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
if not isinstance(edge_predicates, Iterable):
return edge_predicates
edge_predicates = tuple(edge_predicates)
# If only one predicate is given, don't bother wrapping it
if 1 == len(edge_predicates):
return edge_predicates[0]
def concatenated_edge_predicate(graph: BELGraph, u: BaseEntity, v: BaseEntity, k: str) -> bool:
"""Pass only for an edge that pass all enclosed predicates.
:return: If the edge passes all enclosed predicates
"""
return all(
edge_predicate(graph, u, v, k)
for edge_predicate in edge_predicates
)
return concatenated_edge_predicate | python | 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
if not isinstance(edge_predicates, Iterable):
return edge_predicates
edge_predicates = tuple(edge_predicates)
# If only one predicate is given, don't bother wrapping it
if 1 == len(edge_predicates):
return edge_predicates[0]
def concatenated_edge_predicate(graph: BELGraph, u: BaseEntity, v: BaseEntity, k: str) -> bool:
"""Pass only for an edge that pass all enclosed predicates.
:return: If the edge passes all enclosed predicates
"""
return all(
edge_predicate(graph, u, v, k)
for edge_predicate in edge_predicates
)
return concatenated_edge_predicate | [
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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)
for u, v, k in graph.edges(keys=True):
if compound_edge_predicate(graph, u, v, k):
yield u, v, k | python | 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)
for u, v, k in graph.edges(keys=True):
if compound_edge_predicate(graph, u, v, k):
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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:
"""Return the number of edges passing a given set of predicates."""
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1
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"""Return the number of edges passing a given set of predicates."""
return sum(
1
for _ in filter_edges(graph, edge_predicates=edge_predicates)
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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):
result.add_node(node, **data)
result.add_edges_from(
(u, v, key, datadict.copy())
for u, v, key, datadict in sg.edges(keys=True, data=True)
)
return result | 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)
for node, data in sg.nodes(data=True):
result.add_node(node, **data)
result.add_edges_from(
(u, v, key, datadict.copy())
for u, v, key, datadict in sg.edges(keys=True, data=True)
)
return result | [
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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_join(g, h)
"""
g.add_nodes_from(
(node, data)
for node, data in h.nodes(data=True)
if node not in g
)
g.add_edges_from(
(u, v, key, data)
for u, v, key, data in h.edges(keys=True, data=True)
if u not in g or v not in g[u] or key not in g[u][v]
)
update_metadata(h, g)
update_node_helper(h, g)
g.warnings.extend(h.warnings) | 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
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_full_join(g, h)
"""
g.add_nodes_from(
(node, data)
for node, data in h.nodes(data=True)
if node not in g
)
g.add_edges_from(
(u, v, key, data)
for u, v, key, data in h.edges(keys=True, data=True)
if u not in g or v not in g[u] or key not in g[u][v]
)
update_metadata(h, g)
update_node_helper(h, g)
g.warnings.extend(h.warnings) | [
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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 usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_outer_join(g, h)
"""
g_nodes = set(g)
for comp in nx.weakly_connected_components(h):
if g_nodes.intersection(comp):
h_subgraph = subgraph(h, comp)
left_full_join(g, h_subgraph) | 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 usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> left_outer_join(g, h)
"""
g_nodes = set(g)
for comp in nx.weakly_connected_components(h):
if g_nodes.intersection(comp):
h_subgraph = subgraph(h, comp)
left_full_join(g, h_subgraph) | [
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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: A merged graph
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = union([g, h, k])
"""
it = iter(graphs)
if use_tqdm:
it = tqdm(it, desc='taking union')
try:
target = next(it)
except StopIteration as e:
raise ValueError('no graphs given') from e
try:
graph = next(it)
except StopIteration:
return target
else:
target = target.copy()
left_full_join(target, graph)
for graph in it:
left_full_join(target, graph)
return target | 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: A merged graph
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = union([g, h, k])
"""
it = iter(graphs)
if use_tqdm:
it = tqdm(it, desc='taking union')
try:
target = next(it)
except StopIteration as e:
raise ValueError('no graphs given') from e
try:
graph = next(it)
except StopIteration:
return target
else:
target = target.copy()
left_full_join(target, graph)
for graph in it:
left_full_join(target, graph)
return target | [
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:param iter[BELGraph] graphs: An iterator over BEL graphs. Can't be infinite.
:param use_tqdm: Should a progress bar be displayed?
:return: A merged graph
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = union([g, h, k]) | [
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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:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> merged = left_node_intersection_join(g, h)
"""
intersecting = set(g).intersection(set(h))
g_inter = subgraph(g, intersecting)
h_inter = subgraph(h, intersecting)
left_full_join(g_inter, h_inter)
return g_inter | 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:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> merged = left_node_intersection_join(g, h)
"""
intersecting = set(g).intersection(set(h))
g_inter = subgraph(g, intersecting)
h_inter = subgraph(h, intersecting)
left_full_join(g_inter, h_inter)
return g_inter | [
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:param BELGraph h: A BEL graph
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> merged = left_node_intersection_join(g, h) | [
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] | c8a7a1bdae4c475fa2a8c77f3a9a5f6d79556ca0 | https://github.com/pybel/pybel/blob/c8a7a1bdae4c475fa2a8c77f3a9a5f6d79556ca0/src/pybel/struct/operations.py#L155-L178 | train | 29,695 |
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
tuple first, so this isn't a safe operation for infinite lists.
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = node_intersection([g, h, k])
"""
graphs = tuple(graphs)
n_graphs = len(graphs)
if n_graphs == 0:
raise ValueError('no graphs given')
if n_graphs == 1:
return graphs[0]
nodes = set(graphs[0].nodes())
for graph in graphs[1:]:
nodes.intersection_update(graph)
return union(
subgraph(graph, nodes)
for graph in graphs
) | 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
tuple first, so this isn't a safe operation for infinite lists.
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = node_intersection([g, h, k])
"""
graphs = tuple(graphs)
n_graphs = len(graphs)
if n_graphs == 0:
raise ValueError('no graphs given')
if n_graphs == 1:
return graphs[0]
nodes = set(graphs[0].nodes())
for graph in graphs[1:]:
nodes.intersection_update(graph)
return union(
subgraph(graph, nodes)
for graph in graphs
) | [
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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
tuple first, so this isn't a safe operation for infinite lists.
:rtype: BELGraph
Example usage:
>>> import pybel
>>> g = pybel.from_path('...')
>>> h = pybel.from_path('...')
>>> k = pybel.from_path('...')
>>> merged = node_intersection([g, h, k]) | [
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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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:param pybel.BELGraph graph: A BEL graph | [
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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]):
if key not in _CITATION_KEEP_KEYS:
del graph[u][v][k][CITATION][key] | 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]):
if key not in _CITATION_KEEP_KEYS:
del graph[u][v][k][CITATION][key] | [
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Best practice is to add this information programmatically. | [
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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(sorted(values))
for keyword, values in graph_json_dict['graph'].get(GRAPH_ANNOTATION_LIST, {}).items()
}
# Convert set to list
graph_json_dict['graph'][GRAPH_UNCACHED_NAMESPACES] = list(
graph_json_dict['graph'].get(GRAPH_UNCACHED_NAMESPACES, [])
)
return graph_json_dict | 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(sorted(values))
for keyword, values in graph_json_dict['graph'].get(GRAPH_ANNOTATION_LIST, {}).items()
}
# Convert set to list
graph_json_dict['graph'][GRAPH_UNCACHED_NAMESPACES] = list(
graph_json_dict['graph'].get(GRAPH_UNCACHED_NAMESPACES, [])
)
return graph_json_dict | [
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] | c8a7a1bdae4c475fa2a8c77f3a9a5f6d79556ca0 | https://github.com/pybel/pybel/blob/c8a7a1bdae4c475fa2a8c77f3a9a5f6d79556ca0/src/pybel/io/nodelink.py#L29-L44 | train | 29,699 |
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