def upload_to_ndex(self):
"""Upload the assembled model as CX to NDEx"""
assembled_stmts = self.run_assembly()
cxa = CxAssembler(assembled_stmts, network_name=self.name)
cxa.make_model()
cx_str = cxa.print_cx()
ndex_client.update_network(cx_str, self.ndex_network)
def update_to_ndex(self):
"""Update assembled model as CX on NDEx, updates existing network."""
if not self.assembled_stmts:
self.run_assembly()
cxa = CxAssembler(self.assembled_stmts, network_name=self.name)
cxa.make_model()
cx_str = cxa.print_cx()
ndex_client.update_network(cx_str, self.ndex_network)
def upload_cx_to_ndex(cx_str, ndex_cred):
network_id = ndex_cred['network']
provenance = make_ndex_provenance(network_id)
ndex_client.set_provenance(provenance, network_id, ndex_cred)
try:
ndex_client.update_network(cx_str, network_id, ndex_cred)
except Exception as e:
logger.error('NDEx network update failed')
logger.exception(e)
def upload_cx_to_ndex(cx_str, ndex_cred):
network_id = ndex_cred['network']
provenance = make_ndex_provenance(network_id)
ndex_client.set_provenance(provenance, network_id, ndex_cred)
try:
ndex_client.update_network(cx_str, network_id, ndex_cred)
except Exception as e:
logger.error('NDEx network update failed')
logger.exception(e)
def create_upload_model(model_name, full_name, indra_stmts, ndex_id=None):
"""Make and upload an EMMAA model from a list of INDRA Statements.
Parameters
----------
short_name : str
Short name of the model to use on S3.
full_name : str
Human-readable model name to use in EMMAA dashboard.
indra_stmts : list of indra.statement
INDRA Statements to be used to populate the EMMAA model.
ndex_id : str
UUID of the network corresponding to the model on NDex. If provided,
the NDex network will be updated with the latest model content.
If None (default), a new network will be created and the UUID stored
in the model config files on S3.
"""
emmaa_stmts = to_emmaa_stmts(indra_stmts, datetime.datetime.now(), [])
# Get updated CX content for the INDRA Statements
cxa = CxAssembler(indra_stmts)
cx_str = cxa.make_model()
# If we don't have an NDex ID, create network and upload to Ndex
if ndex_id is None:
ndex_id = cxa.upload_model(private=False)
print(f'NDex ID for {model_name} is {ndex_id}.')
# If the NDEx ID is provided, update the existing network
else:
ndex_client.update_network(cx_str, ndex_id)
# Create the config dictionary
config_dict = {'ndex': {'network': ndex_id}, 'search_terms': []}
# Create EMMAA model
emmaa_model = EmmaaModel(model_name, config_dict)
emmaa_model.add_statements(emmaa_stmts)
# Upload model to S3 with config as YAML and JSON
emmaa_model.save_to_s3()
s3_client = boto3.client('s3')
config_json = json.dumps(config_dict)
s3_client.put_object(Body=config_json.encode('utf8'),
Key='models/%s/config.json' % model_name,
Bucket='emmaa')
config_json = json.dumps(config_dict)
s3_client.put_object(Body=config_json.encode('utf8'),
Key='models/%s/config.json' % model_name,
Bucket='emmaa')
username=ndex_cred['user'],
password=ndex_cred['password'])
gene_names = [
hgnc_client.get_hgnc_name(ag.db_refs['HGNC'])
for ag in ncp.get_agents()
]
"""
# Get PMIDs for reading
entrez_pmids = get_pmids(gene_names)
network_pmids = ncp.get_pmids()
pmids = list(set(entrez_pmids + network_pmids))
save_pmids_for_reading(pmids, 'dna_damage_pmids.txt')
"""
# Build the model
prior_stmts = build_prior(gene_names, 'prior_stmts.pkl')
reach_stmts = ac.load_statements('reach_stmts.pkl')
stmts = ncp.statements + reach_stmts + prior_stmts
stmts = run_assembly(stmts, 'unfiltered_assembled_stmts.pkl')
# Filter the statements at different levels
ids_cutoffs = (('4e26a4f0-9388-11e7-a10d-0ac135e8bacf',
0.90), ('527fecf7-9388-11e7-a10d-0ac135e8bacf', 0.95),
('2f0e17bc-9387-11e7-a10d-0ac135e8bacf', 0.99))
for net_id, cutoff in ids_cutoffs:
stmts_filt = filter(stmts, cutoff, 'stmts_%.2f.pkl' % cutoff)
cxa = assemble_cx(stmts_filt, 'dna_damage_%.2f.cx' % cutoff)
cx_str = cxa.print_cx()
ndex_client.update_network(cx_str, net_id, ndex_cred)