def setUp(self):
self.fd, self.path = tempfile.mkstemp()
self.connection = 'sqlite:///' + self.path
log.info('Test generated connection string %s', self.connection)
self.manager = Manager(connection=self.connection)
self.manager.create_all()
def test_insert_namespace_persistent(self, mock_get):
self.manager.ensure_namespace(HGNC_URL)
self._help_check_hgnc(self.manager)
alternate_manager = Manager(connection=self.connection)
alternate_manager.ensure_namespace(HGNC_URL)
self._help_check_hgnc(alternate_manager)
class TemporaryCacheMixin(unittest.TestCase):
def setUp(self):
self.fd, self.path = tempfile.mkstemp()
self.connection = 'sqlite:///' + self.path
log.info('Test generated connection string %s', self.connection)
self.manager = Manager(connection=self.connection)
self.manager.create_all()
def tearDown(self):
self.manager.session.close()
os.close(self.fd)
os.remove(self.path)
def setUp(self):
super(ManagerMixin, self).setUp()
self.db_fd, self.db_file = tempfile.mkstemp()
self.connection = 'sqlite:///' + self.db_file
self.manager = Manager(connection=self.connection)
def upload_recursive(directory,
connection=None,
exclude_directory_pattern=None):
"""Recursively uploads all gpickles in a given directory and sub-directories
:param str directory: the directory to traverse
:param connection: A connection string or manager
:type connection: Optional[str or pybel.manage.Manager]
:param Optional[str] exclude_directory_pattern: Any directory names to exclude
"""
manager = Manager.ensure(connection)
paths = list(
get_paths_recursive(
directory,
extension='.gpickle',
exclude_directory_pattern=exclude_directory_pattern))
log.info('Paths to upload: %s', paths)
for path in paths:
try:
network = from_pickle(path)
except (ImportError, ImportVersionWarning):
log.warning(
'%s uses a pickle from an old version of PyBEL. Quitting.',
path)
continue
to_database(network, connection=manager, store_parts=True)
def setUpClass(cls):
if test_connection:
cls.connection = test_connection
else:
cls.fd, cls.path = tempfile.mkstemp()
cls.connection = 'sqlite:///' + cls.path
log.info('Test generated connection string %s', cls.connection)
cls.manager = Manager(connection=cls.connection)
cls.manager.create_all()
def main(manager: Manager, permutations: int = 25):
"""Run the experiments and uploads them."""
network_directory = os.path.join(BMS_BASE, 'aetionomy', 'neurommsig')
gse1297_directory = os.path.join(OMICS_DATA_DIR, 'GSE1297')
gse28146_directory = os.path.join(OMICS_DATA_DIR, 'GSE28146')
gse63063_directory = os.path.join(OMICS_DATA_DIR, 'GSE63063')
omics_directories = [
gse1297_directory,
gse28146_directory,
gse63063_directory,
]
work_group(
network_directory=network_directory,
omics_directories=omics_directories,
manager=manager,
permutations=permutations,
)
if __name__ == '__main__':
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
logger.setLevel(logging.INFO)
main(Manager())
with open(path) as f:
cbn_jgif_dict = json.load(f)
graph = pybel.from_cbn_jgif(cbn_jgif_dict)
out_path = os.path.join(dir_path, jfg_path.replace('.jgf', '.bel'))
with open(out_path, 'w') as o:
pybel.to_bel(graph, o)
strip_annotations(graph)
enrich_pubmed_citations(manager=manager, graph=graph)
pybel.to_database(graph, manager=manager)
log.info('')
log.info('done in %.2f', time.time() - t)
if __name__ == '__main__':
logging.basicConfig(level=logging.INFO)
log.setLevel(logging.INFO)
logging.getLogger('pybel.parser.baseparser').setLevel(logging.WARNING)
bms_base = os.environ['BMS_BASE']
cbn_base = os.path.join(bms_base, 'cbn', 'Human-2.0')
m = Manager()
upload_cbn_dir(cbn_base, m)
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
return
return insert_graph(manager, graph, public=True, use_tqdm=True)
def load_cbn(manager: Manager):
"""Load CBN data as BEL."""
upload_jgf_directory(cbn_human, manager)
upload_jgf_directory(cbn_mouse, manager)
upload_jgf_directory(cbn_rat, manager)
def load_bms(manager: Manager):
"""Load BEL."""
upload_neurommsig_graphs(manager)
upload_bel_directory(selventa_directory, manager)
upload_bel_directory(alzheimer_directory,
manager,
blacklist=['alzheimers'])
upload_bel_directory(parkinsons_directory,
manager,
blacklist=['parkinsons'])
if __name__ == '__main__':
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
logger.setLevel(logging.INFO)
load_bms(Manager())
def main(manager: Optional[Manager] = None):
"""Load BEL."""
if manager is None:
manager = Manager()
upload_bel_directory(alzheimer_directory, manager)