def __init__(self,
hosts_filename=None,
num_processes_per_host=0,
bkb_handler=None,
joint_reasoner=None,
dynamic_reasoner=None,
max_results=10):
# Instantiate handler is one was not passed
if bkb_handler is None:
self.bkb_data_handler = BkbDataHandler(
bkb_major_version='darwin',
bkb_minor_version='2.0',
disease='tcga',
)
else:
self.bkb_data_handler = bkb_handler
# Save off other attributes
self.hosts_filename = hosts_filename
self.num_processes_per_host = num_processes_per_host
self.max_results = max_results
self.joint_reasoner = joint_reasoner
self.dynamic_reasoner = dynamic_reasoner
# Run specific handler setup
self._setup_handler()
# Read in curies
with open(self.bkb_data_handler.curies_path, 'r') as f_:
self.curies = json.load(f_)
class ChpBrainApiConfig(AppConfig):
logger.warning('Running CHP Brain API Configuration. May take a minute.')
name = 'chp_core_brain'
# Used for distrbuted reasoning
# Get Hosts File if it exists
#parent_dir = os.path.dirname(os.path.realpath(__file__))
#HOSTS_FILENAME = os.path.join(parent_dir, 'hosts')
#NUM_PROCESSES_PER_HOST = multiprocessing.cpu_count()
#if not os.path.exists(HOSTS_FILENAME):
hosts_filename = None
num_processes_per_host = 0
# Instantiate BKB handler
bkb_handler = BkbDataHandler(disease='tcga_gbm',
bkb_major_version='darwin',
bkb_minor_version='2.0')
logger.info('Instantiating reasoners.')
# Instantiate Reasoners
dynamic_reasoner = ChpDynamicReasoner(
bkb_handler=bkb_handler,
hosts_filename=hosts_filename,
num_processes_per_host=num_processes_per_host)
joint_reasoner = ChpJointReasoner(
bkb_handler=bkb_handler,
hosts_filename=hosts_filename,
num_processes_per_host=num_processes_per_host)
def __init__(self,
query,
hosts_filename=None,
num_processes_per_host=0,
max_results=100,
bkb_handler=None,
joint_reasoner=None,
dynamic_reasoner=None):
# Save initial passed query(s)
self.init_query = query
# Instantiate handler is one was not passed
if bkb_handler is None:
self.bkb_data_handler = BkbDataHandler(bkb_major_version='coulomb',
bkb_minor_version='1.0')
else:
self.bkb_data_handler = bkb_handler
# Save off other attributes
self.hosts_filename = hosts_filename
self.num_processes_per_host = num_processes_per_host
self.max_results = max_results
self.joint_reasoner = joint_reasoner
self.dynamic_reasoner = dynamic_reasoner
# Run specific handler setup
self._setup_handler()
# Read in curies
with open(self.bkb_data_handler.curies_path, 'r') as f_:
self.curies = json.load(f_)
def setUpClass(cls):
super(TestOneHopHandler, cls).setUpClass()
# load in sample query graphs
with open('query_samples/onehop/standard_queries.json', 'r') as f_:
cls.standard_queries = json.load(f_)
with open('query_samples/onehop/wildcard_queries.json', 'r') as f_:
cls.wildcard_queries = json.load(f_)
cls.bkb_handler = BkbDataHandler()
cls.dynamic_reasoner = ChpDynamicReasoner(cls.bkb_handler)
cls.joint_reasoner = ChpJointReasoner(cls.bkb_handler)
def __init__(self,
query,
hosts_filename=None,
num_processes_per_host=0,
max_results=100):
# query graph components
self.query = query
self.max_results = max_results
self.qg = self.query['query_graph']
if 'knowledge_graph' not in list(self.query.keys()):
self.kg = { "edges": {},
"nodes": {}
}
else:
self.kg = self.query['knowledge_graph']
if 'results' not in list(self.query.keys()):
self.results = []
else:
self.results = self.query['results']
self.op = '>='
self.value = 970
# Instiatate Reasoner
self.bkb_data_handler = BkbDataHandler(dataset_version='1.4')
self.reasoner = Reasoner(bkb_data_handler=self.bkb_data_handler,
hosts_filename=hosts_filename,
num_processes_per_host=num_processes_per_host)
# prepare curie gene dict
self.true_gene_contrib = dict()
self.false_gene_contrib = dict()
self.gene_curie_dict = dict()
self.gene_to_curie = dict()
with open(self.bkb_data_handler.gene_curie_path, 'r') as gene_file:
reader = csv.reader(gene_file)
next(reader)
for row in reader:
self.gene_curie_dict[row[1]] = row[0]
self.true_gene_contrib[row[1]] = 0
self.false_gene_contrib[row[1]] = 0
self.gene_to_curie[row[0]] = row[1]
# prepare curie drug dict
self.drug_curie_dict = dict()
with open(self.bkb_data_handler.drug_curie_path, 'r') as drug_file:
reader = csv.reader(drug_file)
next(reader)
for row in reader:
self.drug_curie_dict[row[1]] = row[0]
# default query specification
self.target_strategy = 'explicit'
self.interpolation = 'standard'
def __init__(self, query, hosts_filename=None, num_processes_per_host=0):
self.query = query
self.qg = self.query['query_graph']
self.kg = self.query['knowledge_graph']
self.results = self.query['results']
self.probability_targets = self.query['probability_targets']
#-- Instiatate Reasoner
self.bkb_data_handler = BkbDataHandler()
self.reasoner = Reasoner(bkb_data_handler=self.bkb_data_handler,
hosts_filename=hosts_filename,
num_processes_per_host=num_processes_per_host)
self.gene_curie_dict = dict()
with open(self.bkb_data_handler.gene_curie_path, 'r') as gene_file:
reader = csv.reader(gene_file)
next(reader)
for row in reader:
self.gene_curie_dict[row[1]] = row[0]
self.target_strategy = 'chain'
self.interpolation = 'standard'
def __init__(self, query, hosts_filename=None, num_processes_per_host=0):
# query graph components
self.query = query
self.bkb_data_handler = BkbDataHandler(dataset_version='1.1')
# Only do the rest of this if a query is passed
if self.query is not None:
self.qg = self.query['query_graph']
if 'knowledge_graph' not in list(self.query.keys()):
self.kg = {"edges": [], "nodes": []}
else:
self.kg = self.query['knowledge_graph']
if 'results' not in list(self.query.keys()):
self.results = {"node_bindings": [], "edge_bindings": []}
else:
self.results = self.query['results']
# Instiatate Reasoner
self.reasoner = Reasoner(
bkb_data_handler=self.bkb_data_handler,
hosts_filename=hosts_filename,
num_processes_per_host=num_processes_per_host)
# prepare curie gene dict
self.gene_curie_dict = dict()
with open(self.bkb_data_handler.gene_curie_path, 'r') as gene_file:
reader = csv.reader(gene_file)
next(reader)
for row in reader:
self.gene_curie_dict[row[1]] = row[0]
# prepare curie drug dict
self.drug_curie_dict = dict()
with open(self.bkb_data_handler.drug_curie_path, 'r') as drug_file:
reader = csv.reader(drug_file)
next(reader)
for row in reader:
self.drug_curie_dict[row[1]] = row[0]
# default query specification
self.target_strategy = 'explicit'
self.interpolation = 'standard'
def setUp(self):
self.bkb_handler = BkbDataHandler(
bkb_major_version='coulomb',
bkb_minor_version='1.0',
)
self.dynamic_reasoner = ChpDynamicReasoner(self.bkb_handler)
def setUp(self):
self.bkb_handler = BkbDataHandler()
self.joint_reasoner = ChpJointReasoner(self.bkb_handler)
from chp.query import Query
from chp_data.bkb_handler import BkbDataHandler
#-- Initalize a BKB
fused_bkb = BKB()
'''
#-- Load in the fused bkb from our datafiles
fused_bkb.load('/home/public/data/ncats/AxleBKBS/660Pats6HoldoutSTAGING/fusion.bkb')
#-- Here are the associated patient data files
patient_data_file = '/home/public/data/ncats/AxleBKBS/660Pats6HoldoutSTAGING/patient_data.pk'
withheld_patients_file = '/home/public/data/ncats/AxleBKBS/660Pats6HoldoutSTAGING/withheldPatients.csv'
'''
bkb_data_handler = BkbDataHandler(bkb_version='special',
dataset_version='babel-small-problem')
#-- Instiante reasoner
reasoner = Reasoner(bkb_data_handler=bkb_data_handler)
#-- If you want to see what genetic or demographic evidence is avaliable, uncomment the line below
#print(reasoner.metadata_ranges)
'''
#-- Make a query (evidence is for genetic info, and meta_ is for demographic info)
query0 = Query(evidence={'mut_TMEM245=': 'True'},
targets=list(),
meta_evidence=[('Age_of_Diagnosis', '>=',20000)],
meta_targets=[('Survival_Time', '>=', 300)])
'''
query0 = Query(evidence={'_mut_AADAC': 'True'},
targets=list(),
def setUpClass(cls):
super(TestBaseHandler, cls).setUpClass()
cls.bkb_handler = BkbDataHandler()
cls.dynamic_reasoner = ChpDynamicReasoner(cls.bkb_handler)
cls.joint_reasoner = ChpJointReasoner(cls.bkb_handler)
def setUpClass(cls):
super(TestDynamicReasoner, cls).setUpClass()
cls.bkb_handler = BkbDataHandler(disease='tcga_brca')
cls.dynamic_reasoner = ChpDynamicReasoner(cls.bkb_handler)
def setUpClass(cls):
super(TestJointReasoner, cls).setUpClass()
cls.bkb_handler = BkbDataHandler()
cls.joint_reasoner = ChpJointReasoner(cls.bkb_handler)