def _to_bel_lines_header(graph) -> Iterable[str]:
"""Iterate the lines of a BEL graph's corresponding BEL script's header.
:param pybel.BELGraph graph: A BEL graph
"""
yield '# This document was created by PyBEL v{} and bel-resources v{} on {}\n'.format(
VERSION, bel_resources.constants.VERSION, time.asctime())
yield from make_knowledge_header(
namespace_url=graph.namespace_url,
namespace_patterns=graph.namespace_pattern,
annotation_url=graph.annotation_url,
annotation_patterns=graph.annotation_pattern,
annotation_list=graph.annotation_list,
**graph.document)
def write_boilerplate(
name: str,
version: Optional[str] = None,
description: Optional[str] = None,
authors: Optional[str] = None,
contact: Optional[str] = None,
copyright: Optional[str] = None,
licenses: Optional[str] = None,
disclaimer: Optional[str] = None,
namespace_url: Optional[Mapping[str, str]] = None,
namespace_patterns: Optional[Mapping[str, str]] = None,
annotation_url: Optional[Mapping[str, str]] = None,
annotation_patterns: Optional[Mapping[str, str]] = None,
annotation_list: Optional[Mapping[str, Set[str]]] = None,
pmids: Optional[Iterable[Union[str, int]]] = None,
entrez_ids: Optional[Iterable[Union[str, int]]] = None,
file: Optional[TextIO] = None,
) -> None:
"""Write a boilerplate BEL document, with standard document metadata, definitions.
:param name: The unique name for this BEL document
:param contact: The email address of the maintainer
:param description: A description of the contents of this document
:param authors: The authors of this document
:param version: The version. Defaults to current date in format ``YYYYMMDD``.
:param copyright: Copyright information about this document
:param licenses: The license applied to this document
:param disclaimer: The disclaimer for this document
:param namespace_url: an optional dictionary of {str name: str URL} of namespaces
:param namespace_patterns: An optional dictionary of {str name: str regex} namespaces
:param annotation_url: An optional dictionary of {str name: str URL} of annotations
:param annotation_patterns: An optional dictionary of {str name: str regex} of regex annotations
:param annotation_list: An optional dictionary of {str name: set of names} of list annotations
:param pmids: A list of PubMed identifiers to auto-populate with citation and abstract
:param entrez_ids: A list of Entrez identifiers to autopopulate the gene summary as evidence
:param file: A writable file or file-like. If None, defaults to :data:`sys.stdout`
"""
lines = make_knowledge_header(
name=name,
version=version or '1.0.0',
description=description,
authors=authors,
contact=contact,
copyright=copyright,
licenses=licenses,
disclaimer=disclaimer,
namespace_url=namespace_url,
namespace_patterns=namespace_patterns,
annotation_url=annotation_url,
annotation_patterns=annotation_patterns,
annotation_list=annotation_list,
)
for line in lines:
print(line, file=file)
if pmids is not None:
for line in make_pubmed_abstract_group(pmids):
print(line, file=file)
if entrez_ids is not None:
for line in make_pubmed_gene_group(entrez_ids):
print(line, file=file)