def test_isolated_upgrade(self):
lines = to_bel_lines(self.isolated_graph)
with mock_bel_resources:
reconstituted = from_lines(lines, manager=self.manager)
self.bel_isolated_reconstituted(reconstituted)
def serialize_namespaces(namespaces, connection, path, directory):
"""Parses a BEL document then serializes the given namespaces (errors and all) to the given directory"""
from pybel import from_lines
from .definition_utils import export_namespaces
graph = from_lines(path, manager=connection)
export_namespaces(namespaces, graph, directory)
def async_compile(lines,
connection,
allow_nested=False,
citation_clearing=False,
store_parts=False):
log.info('starting compilation')
manager = build_manager(connection)
try:
graph = from_lines(lines,
manager=manager,
allow_nested=allow_nested,
citation_clearing=citation_clearing)
add_canonical_names(graph)
except requests.exceptions.ConnectionError as e:
message = 'Connection to resource could not be established.'
log.exception(message)
return message
except InconsistientDefinitionError as e:
message = '{} was defined multiple times.'.format(e.definition)
log.exception(message)
return message
except Exception as e:
message = 'Compilation error: {}'.format(e)
log.exception(message)
return message
try:
network = manager.insert_graph(graph, store_parts=store_parts)
except IntegrityError:
log_graph(graph, current_user, precompiled=False, failed=True)
message = integrity_message.format(graph.name, graph.version)
log.exception(message)
manager.rollback()
return message
except Exception as e:
log_graph(graph, current_user, precompiled=False, failed=True)
message = "Error storing in database: {}".format(e)
log.exception(message)
return message
log.info('done storing [%d]', network.id)
try:
add_network_reporting(manager,
network,
current_user,
graph.number_of_nodes(),
graph.number_of_edges(),
len(graph.warnings),
precompiled=False)
except IntegrityError:
message = 'Problem with reporting service.'
log.exception(message)
manager.rollback()
return message
return network.id
def test_difference(self):
a = pybel.from_lines(test_bel_1.split('\n'))
b = pybel.from_lines(test_bel_2.split('\n'))
self.assertFalse(graph_entities_equal(a, b))
self.assertFalse(graph_topologically_equal(a, b))
self.assertFalse(graph_provenance_equal(a, b))
'''
d_nodes = {
MIA,
AKT1_Ph
}
self.assertEqual(d_nodes, set(d.nodes()))
'''
d_edges = {
(MIA, AKT1_Ph): {
'relation': 'directlyDecreases',
'SupportingText': 'Evidence 2',
'TESTAN2': '3'
},
(FADD, CASP8): {
'relation': 'increases',
'SupportingText': 'Evidence 3',
'TESTAN1': '3'
},
(AKT1, CASP8): {
'relation': 'association',
'SupportingText': 'Evidence 3',
'TESTAN1': '3'
},
(CASP8, AKT1): {
'relation': 'association',
'SupportingText': 'Evidence 3',
'TESTAN1': '3'
}
}
difference = graph_edges_difference(b, a)
self.assertEqual({(AKT1, AKT1_Ph), (MIA, AKT1_Ph)}, difference)
def bel_to_cx(file, connection, output):
"""Convert a BEL Script from STDIN and write a CX document to STDOUT."""
try:
graph = from_lines(file, manager=connection)
except Exception:
log.exception('error occurred while loading BEL.')
sys.exit(1)
try:
to_cx_file(graph, output)
except Exception:
log.exception('error occurred in conversion to CX.')
sys.exit(2)
sys.exit(0)
def test_isolated_upgrade(self, mock):
lines = to_bel_lines(self.isolated_graph)
reconstituted = from_lines(lines, manager=self.manager)
self.bel_isolated_reconstituted(reconstituted)
def test_thorough_upgrade(self):
lines = to_bel_lines(self.thorough_graph)
reconstituted = from_lines(lines, manager=self.manager)
self.bel_thorough_reconstituted(reconstituted,
check_citation_name=False)
def view_compile():
"""An upload form for a BEL script"""
form = CompileForm(save_network=True)
if not form.validate_on_submit():
return render_template('compile.html', form=form, current_user=current_user)
log.info('Running on %s', form.file.data.filename)
t = time.time()
# Decode the file with the given decoding (utf-8 is default)
lines = codecs.iterdecode(form.file.data.stream, form.encoding.data)
try:
graph = from_lines(
lines,
manager=manager,
allow_nested=form.allow_nested.data,
citation_clearing=(not form.citation_clearing.data)
)
add_canonical_names(graph)
except requests.exceptions.ConnectionError as e:
flash("Resource doesn't exist.", category='error')
return render_error(e)
except InconsistientDefinitionError as e:
log.error('%s was defined multiple times', e.definition)
flash('{} was defined multiple times.'.format(e.definition), category='error')
return redirect(url_for('view_compile'))
except Exception as e:
log.exception('compilation error')
flash('Compilation error: {}'.format(e))
return redirect(url_for('view_compile'))
if not enable_cache:
flash('Sorry, graph storage is not currently enabled.', category='warning')
log_graph(graph, current_user, precompiled=False)
return render_graph_summary(0, graph)
if not form.save_network.data and not form.save_edge_store.data:
log_graph(graph, current_user, precompiled=False)
return render_graph_summary(0, graph)
try:
network = manager.insert_graph(graph, store_parts=form.save_edge_store.data)
except IntegrityError:
log_graph(graph, current_user, precompiled=False, failed=True)
log.exception('integrity error')
flash(integrity_message.format(graph.name, graph.version), category='error')
manager.rollback()
return redirect(url_for('view_compile'))
except Exception as e:
log_graph(graph, current_user, precompiled=False, failed=True)
log.exception('general storage error')
flash("Error storing in database: {}".format(e), category='error')
return redirect(url_for('view_compile'))
log.info('done storing %s [%d]', form.file.data.filename, network.id)
try:
add_network_reporting(manager, network, current_user, graph.number_of_nodes(),
graph.number_of_edges(), len(graph.warnings), precompiled=False,
public=form.public.data)
except IntegrityError:
log.exception('integrity error')
flash('problem with reporting service', category='warning')
manager.rollback()
return redirect(url_for('view_summary', graph_id=network.id))
def serialize_namespaces(namespaces, connection, path, directory):
"""Parses a BEL document then serializes the given namespaces (errors and all) to the given directory"""
graph = from_lines(path, manager=connection)
export_namespaces(namespaces, graph, directory)