def to_web(self, host=None, user=None, password=None):
"""Send the model to BEL Commons by wrapping :py:func:`pybel.to_web`
The parameters ``host``, ``user``, and ``password`` all check the
PyBEL configuration, which is located at
``~/.config/pybel/config.json`` by default
Parameters
----------
host : Optional[str]
The host name to use. If none, first checks the PyBEL
configuration entry ``PYBEL_REMOTE_HOST``, then the
environment variable ``PYBEL_REMOTE_HOST``. Finally, defaults
to https://bel-commons.scai.fraunhofer.de.
user : Optional[str]
The username (email) to use. If none, first checks the
PyBEL configuration entry ``PYBEL_REMOTE_USER``,
then the environment variable ``PYBEL_REMOTE_USER``.
password : Optional[str]
The password to use. If none, first checks the PyBEL configuration
entry ``PYBEL_REMOTE_PASSWORD``, then the environment variable
``PYBEL_REMOTE_PASSWORD``.
Returns
-------
response : requests.Response
The response from the BEL Commons network upload endpoint.
"""
response = pybel.to_web(self.model, host=host, user=user,
password=password)
return response
def to_web(self, host=None, user=None, password=None):
"""Send the model to BEL Commons by wrapping :py:func:`pybel.to_web`
The parameters ``host``, ``user``, and ``password`` all check the
PyBEL configuration, which is located at
``~/.config/pybel/config.json`` by default
Parameters
----------
host : Optional[str]
The host name to use. If none, first checks the PyBEL
configuration entry ``PYBEL_REMOTE_HOST``, then the
environment variable ``PYBEL_REMOTE_HOST``. Finally, defaults
to https://bel-commons.scai.fraunhofer.de.
user : Optional[str]
The username (email) to use. If none, first checks the
PyBEL configuration entry ``PYBEL_REMOTE_USER``,
then the environment variable ``PYBEL_REMOTE_USER``.
password : Optional[str]
The password to use. If none, first checks the PyBEL configuration
entry ``PYBEL_REMOTE_PASSWORD``, then the environment variable
``PYBEL_REMOTE_PASSWORD``.
Returns
-------
response : requests.Response
The response from the BEL Commons network upload endpoint.
"""
response = pybel.to_web(self.model, host=host, user=user,
password=password)
return response
def machine(agents, local, connection, host):
"""Get content from the INDRA machine and upload to BEL Commons."""
from indra.sources import indra_db_rest
from pybel import from_indra_statements, to_web
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:
manager = Manager(connection=connection)
to_database(graph, manager=manager)
else:
resp = to_web(graph, host=host)
resp.raise_for_status()
def upload(manager, path, skip_check_version, to_service, service_url,
exclude_directory_pattern, debug):
"""Upload gpickles"""
set_debug_param(debug)
if os.path.isdir(path):
log.info('uploading recursively from: %s', path)
upload_recursive(path,
connection=manager,
exclude_directory_pattern=exclude_directory_pattern)
elif os.path.isfile(path):
from pybel import from_pickle
graph = from_pickle(path, check_version=(not skip_check_version))
if to_service:
from pybel import to_web
to_web(graph, service_url)
else:
from pybel import to_database
to_database(graph, connection=manager, store_parts=True)
def convert_paths(paths,
connection=None,
upload=False,
pickle=False,
canonicalize=True,
infer_central_dogma=True,
enrich_citations=False,
send=False,
version_in_path=False,
**kwargs):
"""Recursively parses and either uploads/pickles graphs in a given set of files
:param iter[str] paths: The paths to convert
:param connection: The connection
:type connection: None or str or pybel.manager.Manager
:param bool upload: Should the networks be uploaded to the cache?
:param bool pickle: Should the networks be saved as pickles?
:param bool canonicalize: Calculate canonical nodes?
:param bool infer_central_dogma: Should the central dogma be inferred for all proteins, RNAs, and miRNAs
:param bool enrich_citations: Should the citations be enriched using Entrez Utils?
:param bool send: Send to PyBEL Web?
:param bool version_in_path: Add the current pybel version to the pathname
:param kwargs: Parameters to pass to :func:`pybel.from_path`
"""
manager = Manager.ensure(connection)
failures = []
for path in paths:
log.info('parsing: %s', path)
try:
graph = from_path(path, manager=manager, **kwargs)
except Exception as e:
log.exception('problem parsing %s', path)
failures.append((path, e))
continue
if canonicalize:
add_canonical_names(graph)
if infer_central_dogma:
infer_central_dogma_mutator(graph)
if enrich_citations:
enrich_pubmed_citations(graph=graph, manager=manager)
if upload:
to_database(graph, connection=manager, store_parts=True)
if pickle:
name = path[:-len(
'.bel')] # gets rid of .bel at the end of the file name
if version_in_path:
new_path = '{}-{}.gpickle'.format(name, get_pybel_version())
else:
new_path = '{}.gpickle'.format(name)
to_pickle(graph, new_path)
log.info('output pickle: %s', new_path)
if send:
response = to_web(graph)
log.info('sent to PyBEL Web with response: %s', response.json())
return failures
def post(path, url, skip_check_version):
"""Posts the given graph to the PyBEL Web Service via JSON"""
from pybel import from_pickle, to_web
graph = from_pickle(path, check_version=(not skip_check_version))
to_web(graph, url)
def upload(manager: BELManagerMixin, host: str):
"""Upload BEL to BEL Commons."""
graph = manager.to_bel()
pybel.to_web(graph, host=host, public=True)
