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
main = repository.build_cli()
'metadata',
'main',
]
HERE = os.path.dirname(__file__)
VERSION = '0.0.1-dev'
# Author list will be sorted by last name
AUTHORS = [
'Stephan Gebel',
'Vanessa Lage-Rupprecht',
]
# All metadata is grouped here
metadata = BELMetadata(
name='Enzyme Technology Internship 2019',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description=
"BEL Curation from the Enzyme Technology Internship 2019 at B-IT and Fraunhofer SCAI.",
license='CC BY 4.0',
)
repository = BELRepository(
HERE,
bel_metadata=metadata,
)
main = repository.build_cli()
'metadata',
'get_graph',
'get_graphs',
'get_summary_df',
'main',
]
HERE = os.path.dirname(__file__)
VERSION = '20150611'
# All metadata is grouped here
metadata = BELMetadata(
name='Selventa Corpora',
version=VERSION,
authors='Selventa',
contact='*****@*****.**',
description="Selventa Large and Small Corpora.",
license='Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License',
copyright='Copyright (c) 2011-2015, Selventa. All Rights Reserved.',
)
repository = BELRepository(
HERE,
metadata=metadata,
from_path_kwargs=dict(
allow_nested=True,
citation_clearing=False,
),
)
get_graph = repository.get_graph
'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',
)
repository = BELSheetsRepository(
directory=CURATION_DIRECTORY,
output_directory=HERE,
metadata=metadata,
)
main = repository.build_cli()
class DistributedRepo:
"""A repository dependent on several BEL repositories."""
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,
)
def get_graphs(self, use_tqdm: bool = True) -> Mapping[str, BELGraph]:
"""Get a mapping of all BEL graphs in the repository."""
return {
repository.metadata.name: repository.get_graph(use_tqdm=use_tqdm)
for repository in self.repositories
}
def get_graph(
self,
directory: Optional[str] = None,
use_cached: bool = True,
use_tqdm: bool = True,
) -> BELGraph:
"""Get the graph from all sources."""
if directory is None:
if self.directory is None:
raise ValueError
directory = self.directory
pickle_path = os.path.join(directory, f'{self.name}.bel.pickle')
if use_cached and os.path.exists(pickle_path):
return pybel.from_pickle(pickle_path)
rv = union(self.get_graphs(use_tqdm=use_tqdm))
self.metadata.update(rv)
pybel.to_pickle(rv, pickle_path)
nodelink_path = os.path.join(directory,
f'{self.name}.bel.nodelink.json')
pybel.to_json_path(rv, nodelink_path)
sif_path = os.path.join(directory, f'{self.name}.bel.sif')
pybel.to_sif_path(rv, sif_path)
gsea_path = os.path.join(directory, f'{self.name}.bel.gmt')
pybel.to_gsea_path(rv, gsea_path)
graphml_path = os.path.join(directory, f'{self.name}.bel.graphml')
pybel.to_graphml(rv, graphml_path)
try:
statements = pybel.to_indra_statements(rv)
except ImportError:
pass
else:
indra_path = os.path.join(directory, f'{self.name}.indra.pickle')
with open(indra_path, 'wb') as file:
pickle.dump(statements, file)
try:
from pybel_cx import to_cx_file
except ImportError:
pass
else:
cx_path = os.path.join(directory, f'{self.name}.bel.cx.json')
with open(cx_path, 'w') as file:
to_cx_file(rv, file)
try:
from pybel_tools.assembler.html import to_html
except ImportError:
pass
else:
html_path = os.path.join(directory, 'index.html')
with open(html_path, 'w') as file:
print(to_html(rv), file=file)
return rv
def get_indra_statements(
self,
directory: str,
use_cached: bool = True) -> List['indra.statements.Statement']:
"""Get INDRA statements for the graph."""
return pybel.to_indra_statements(
self.get_graph(directory, use_cached=use_cached))
'Kristian Kolpeja',
]
AUTHOR_STRING = serialize_authors(AUTHORS)
# Folder pointers
HERE = os.path.abspath(os.path.dirname(__file__))
ROUNDS_DIRECTORY = os.path.join(HERE, 'rounds')
DATA_DIRECTORY = os.path.join(HERE, 'data')
VERSION = '0.1.0'
metadata = BELMetadata(
name='HBP - INDRA Curation',
version=VERSION,
description="This knowledge graph contains content generated by the rational enrichment approach described by "
"Hoyt et al. (2019) applied to the NeuroMMSig inventory.",
authors=AUTHOR_STRING,
contact='*****@*****.**',
license='CC BY 4.0',
)
repository = BELSheetsRepository(
directory=ROUNDS_DIRECTORY,
output_directory=DATA_DIRECTORY,
metadata=metadata,
prior=neurommsig_knowledge.repository,
)
main = repository.build_cli()
if __name__ == '__main__':
'Yojana Gadiya',
'Trusha Adeshara',
'Stephan Gebel',
'Sepehr Golriz',
]
description = "Mechanistic knowledge surrounding several neurodegenerative diseases," \
" with specific focus on protein aggregation, nicotinic receptor signalling," \
" proteostasis, and other mechanisms."
# All metadata is grouped here
metadata = BELMetadata(
name='Curation of Neurodegeneration in BEL (CONIB)',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description=description,
license='CC BY 4.0',
copyright='Copyright © 2019 Fraunhofer SCAI, All rights reserved.',
)
repository = BELRepository(
HERE,
metadata=metadata,
)
get_graph = repository.get_graph
get_graphs = repository.get_graphs
get_indra_statements = repository.get_indra_statements
get_summary_df = repository.get_summary_df
HERE = os.path.dirname(__file__)
VERSION = '0.0.1-dev'
# Author list will be sorted by last name
AUTHORS = [
'Farah Humayun',
'Daniel Domingo-Fernández',
]
# All metadata is grouped here
metadata = BELMetadata(
name='Heme Curation',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description="Mechanistic knowledge surrounding hemes",
license='Private Ownership to Fraunhofer Institute SCAI',
copyright='Copyright © 2019 Fraunhofer SCAI, All rights reserved.',
)
repository = BELRepository(
HERE,
bel_metadata=metadata,
)
get_graph = repository.get_graph
get_graphs = repository.get_graphs
get_summary_df = repository.get_summary_df
main = repository.build_cli()
HERE = os.path.dirname(__file__)
VERSION = '0.0.1-dev'
# Author list will be sorted by last name
AUTHORS = [
'Farah Humayun',
'Daniel Domingo-Fernández',
]
# All metadata is grouped here
metadata = BELMetadata(
name='HemeKG',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description=
"Mechanistic knowledge surrounding heme and hemolytic disorders.",
license='CC BY 4.0',
)
repository = BELRepository(
HERE,
metadata=metadata,
)
get_graph = repository.get_graph
get_graphs = repository.get_graphs
get_summary_df = repository.get_summary_df
main = repository.build_cli()
HERE = os.path.dirname(__file__)
VERSION = '0.0.1-dev'
# Author list will be sorted by last name
AUTHORS = [
'Farah Humayun',
'Daniel Domingo-Fernández',
]
# All metadata is grouped here
metadata = BELMetadata(
name='Heme Curation',
version=VERSION,
authors=serialize_authors(AUTHORS),
contact='*****@*****.**',
description="Mechanistic knowledge surrounding heme",
license='MIT License',
copyright='',
)
repository = BELRepository(
HERE,
bel_metadata=metadata,
)
get_graph = repository.get_graph
get_graphs = repository.get_graphs
get_summary_df = repository.get_summary_df
main = repository.build_cli()