def __init__(
self,
*,
name: str,
version: str,
repositories: List[Union[BELRepository, BELSheetsRepository]],
directory: Optional[str] = None,
) -> None:
"""Initialize a distributed repository.
:param name: The name of the distributed repository
:param version: The version of the distributed repository, independent of the constituent
repositories' versions
:param repositories: A list of BEL repositories
"""
self.name = name
self.repositories = repositories
self.directory = directory
for repository in self.repositories:
if not hasattr(repository, 'metadata'):
raise TypeError(f'Missing metadata: {repository}')
self.dependency_version = '/'.join(repository.metadata.version
for repository in self.repositories)
self.version = f'{version} ({self.dependency_version})'
self.authors = serialize_authors({
author.strip()
for repository in self.repositories
for author in repository.metadata.authors.split(',')
})
self.description = """A distributed repository of several repositories: {}""".format(
f'{repository.metadata.name} v{repository.metadata.version}'
for repository in self.repositories)
self.metadata = BELMetadata(
name=self.name,
version=self.version,
authors=self.authors,
description=self.description,
)
# Author list will be sorted by name
AUTHORS = [
'Alpha Tom Kodamullil',
'Daniel Domingo-Fernández',
'Martin Hofmann-Apitius',
'Reagon Karki',
'Shounak Baksi',
'Yojana Gadiya',
]
# All metadata is grouped here
metadata = BELMetadata(
name='COVID-19 Knowledge Graph',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description=
"Knowledge graph for analysis of COVID-19 disease and potential drug and drug-targets.",
license='Creative Commons Zero v1.0 Universal',
)
repository = BELRepository(
HERE,
metadata=metadata,
)
get_graph = repository.get_graph
get_graphs = repository.get_graphs
get_summary_df = repository.get_summary_df
'repository',
'main',
]
AUTHORS = [
'Charles Tapley Hoyt',
'Daniel Domingo-Fernández',
'Esther Wollert',
'Sandra Spalek',
'Keerthika Lohanadan',
'Rana Al Disi',
'Lingling Xu',
'Kristian Kolpeja',
]
AUTHOR_STRING = serialize_authors(AUTHORS)
# Folder pointers
HERE = os.path.abspath(os.path.dirname(__file__))
CURATION_DIRECTORY = os.path.join(HERE, 'curation')
VERSION = '0.1.1'
metadata = BELMetadata(
name='HBP Semi-Automated Curation',
version=VERSION,
description="This knowledge graph contains content generated with the semi-automated curation workflow"
"in the Human Brain Pharmacome project.",
authors=AUTHOR_STRING,
contact='*****@*****.**',
license='CC BY 4.0',