def gene_families(ctx, enrich_authors, use_edge_store, debug):
"""Caches the HGNC Gene Family memberships"""
set_debug_param(debug)
graph = from_url(GENE_FAMILIES, manager=ctx.obj)
if enrich_authors:
fix_pubmed_citations(graph)
ctx.obj.insert_graph(graph, store_parts=use_edge_store)
def named_complexes(ctx, enrich_authors, use_edge_store, debug):
"""Caches GO Named Protein Complexes memberships"""
set_debug_param(debug)
graph = from_url(NAMED_COMPLEXES, manager=ctx.obj)
if enrich_authors:
fix_pubmed_citations(graph)
ctx.obj.insert_graph(graph, store_parts=use_edge_store)
def ensure_large_corpus():
"""Parses the large corpus"""
graph = from_url(LARGE_CORPUS_URL,
manager=manager,
citation_clearing=False,
allow_nested=True)
return try_insert_graph(manager, graph, api)
def ensure_small_corpus():
"""Parses and stores the small corpus"""
graph = from_url(SMALL_CORPUS_URL,
manager=manager,
citation_clearing=False,
allow_nested=True)
return try_insert_graph(manager, graph, api)
def ensure_abstract3():
"""Parses and stores Selventa Example 3"""
url = 'http://resources.openbel.org/belframework/20150611/knowledge/full_abstract3.bel'
graph = from_url(url,
manager=manager,
citation_clearing=False,
allow_nested=True)
return try_insert_graph(manager, graph, api)
def large_corpus(ctx, enrich_authors, use_edge_store, debug):
"""Caches the Selventa Large Corpus"""
set_debug_param(debug)
graph = from_url(LARGE_CORPUS_URL,
manager=ctx.obj,
citation_clearing=False,
allow_nested=True)
if enrich_authors:
fix_pubmed_citations(graph)
ctx.obj.insert_graph(graph, store_parts=use_edge_store)
def help_ensure(debug, url, enrich_authors, manager):
set_debug_param(debug)
from pybel import from_url
graph = from_url(SMALL_CORPUS_URL,
manager=manager,
citation_clearing=False,
allow_nested=True)
if enrich_authors:
from .mutation.metadata import enrich_pubmed_citations
enrich_pubmed_citations(graph, manager=manager)
manager.insert_graph(graph, store_parts=True)
def setUpClass(cls):
"""Set up this class with several pre-loaded BEL graphs."""
super(TestInterchange, cls).setUpClass()
with mock_bel_resources:
cls.thorough_graph = from_path(test_bel_thorough,
manager=cls.manager,
allow_nested=True)
cls.slushy_graph = from_path(test_bel_slushy, manager=cls.manager)
cls.simple_graph = from_url(Path(test_bel_simple).as_uri(),
manager=cls.manager)
cls.isolated_graph = from_path(test_bel_isolated,
manager=cls.manager)
cls.misordered_graph = from_path(test_bel_misordered,
manager=cls.manager,
citation_clearing=False)
def setUp(self):
if 'PYBEL_BASE' in os.environ:
test_bel_simple_path = os.path.join(os.environ['PYBEL_BASE'], 'tests', 'bel', 'test_bel.bel')
self.graph = pybel.from_path(test_bel_simple_path)
else:
test_bel_simple_url = 'https://raw.githubusercontent.com/pybel/pybel/develop/tests/bel/test_bel.bel'
self.graph = pybel.from_url(test_bel_simple_url)
infer_central_dogma(self.graph)
n1 = GENE, 'HGNC', 'AKT1'
n2 = RNA, 'HGNC', 'EGFR'
n3 = GENE, 'HGNC', 'DUMMY1'
self.graph.add_simple_node(*n3)
n4 = GENE, 'HGNC', 'DUMMY2'
self.graph.add_simple_node(*n4)
self.graph.add_edge(n1, n3)
self.graph.add_edge(n2, n4)
def main(connection):
"""Parse a network, load it to the database, then test how fast it drops."""
manager = pybel.Manager(connection)
if os.path.exists(PICKLE):
print(f'opening from {PICKLE}')
graph = pybel.from_pickle(PICKLE)
else:
with time_me(f'opening from {SMALL_CORPUS_URL}'):
graph = pybel.from_url(SMALL_CORPUS_URL, manager=manager, use_tqdm=True, citation_clearing=False)
pybel.to_pickle(graph, PICKLE)
n = 1
# FIXME this fails if you do it with the same manager
times = [
get_numbers(graph, manager)
for _ in range(n)
]
print(times)
print(sum(times) / n)
def get_simple_graph(mock_get):
return from_url(Path(test_bel_simple).as_uri(),
manager=cls.manager)
def ensure_gfam():
"""Parses and stores the HGNC Gene Family Definitions"""
graph = from_url(FRAUNHOFER_RESOURCES + 'gfam_members.bel',
manager=manager)
return try_insert_graph(manager, graph, api)
def ensure_simple():
"""Parses and stores the PyBEL Test BEL Script"""
url = 'https://raw.githubusercontent.com/pybel/pybel/develop/tests/bel/test_bel.bel'
graph = from_url(url, manager=manager)
return try_insert_graph(manager, graph, api)