def build_onehop_query(
q_object_category,
q_subject_category,
q_subject=None,
q_object=None,
genes=None,
drugs=None,
outcome=None,
outcome_name=None,
outcome_op=None,
outcome_value=None,
disease=None,
trapi_version='1.1',
biolink_version=None,
):
# Initialize query
message = Message(trapi_version, biolink_version)
q = message.query_graph
# Add nodes
subject_node = q.add_node(q_subject, q_subject_category)
object_node = q.add_node(q_object, q_object_category)
# Add edge
try:
edge_predicate = SUBJECT_TO_OBJECT_PREDICATE_MAP[q_subject_category[0]][q_object_category[0]]
except KeyError:
raise QueryBuildError('Edge from {} to {} is not supported.'.format(q_subject_category, q_object_category))
edge_id = q.add_edge(subject_node, object_node, edge_predicate)
# Add constraints
if outcome is not None:
q.add_constraint('predicate_proxy', 'CHP:PredicateProxy', '==', [outcome], edge_id=edge_id)
q.add_constraint(outcome, outcome, outcome_op, outcome_value, edge_id=edge_id)
# Get context
context = []
if genes is not None:
context.append(BIOLINK_GENE)
if drugs is not None:
context.append(BIOLINK_DRUG)
if disease is not None:
context.append(BIOLINK_DISEASE)
# Process context
if len(context) > 0:
q.add_constraint('predicate_context', 'CHP:PredicateContext', '==', context, edge_id=edge_id)
if genes is not None:
q.add_constraint(BIOLINK_GENE, BIOLINK_GENE, 'matches', genes, edge_id=edge_id)
if drugs is not None:
q.add_constraint(BIOLINK_DRUG, BIOLINK_DRUG, 'matches', drugs, edge_id=edge_id)
if disease is not None:
q.add_constraint(BIOLINK_DISEASE, BIOLINK_DISEASE, 'matches', disease, edge_id=edge_id)
query = Query(trapi_version=trapi_version, biolink_version=biolink_version)
query.message = message
return query
def build_standard_query(
genes=None,
drugs=None,
outcome=None,
outcome_name=None,
outcome_op=None,
outcome_value=None,
disease=None,
trapi_version='1.1',
biolink_version=None,
batch_genes=None,
batch_drugs=None,
batch_diseases=None,
):
if outcome is None:
raise QueryBuildError('You must specify an outcome CURIE.')
if outcome_op is None:
raise QueryBuildError("You must specify an outcome operation consistent with \
with your desired TRAPI version's Constraint Object.")
if outcome_value is None:
raise QueryBuildError('You must specify an outcome value to test.')
if disease is None and batch_diseases is None:
raise QueryBuildError('You must specify a disease.')
if disease is not None and batch_diseases is not None:
raise QueryBuildError('Only specify either diseases or batch diseases not both.')
# Initialize Message
message = Message(trapi_version, biolink_version)
q = message.query_graph
# Add disease or batch disease node
if disease is not None:
disease_node = q.add_node(disease, BIOLINK_DISEASE)
else:
disease_node = q.add_node(batch_diseases, BIOLINK_DISEASE)
if genes is not None:
# Add gene nodes
gene_nodes = []
for gene in genes:
gene_nodes.append(q.add_node(gene, BIOLINK_GENE))
# Connect all gene nodes to disease.
for gene_node in gene_nodes:
q.add_edge(gene_node, disease_node, BIOLINK_GENE_ASSOCIATED_WITH_CONDITION)
# Setup batch genes
if batch_genes is not None:
if type(batch_genes) is not list:
raise QueryBuildError('Batch genes must be a list.')
batch_gene_node = q.add_node(batch_genes, BIOLINK_GENE)
q.add_edge(batch_gene_node, disease_node, BIOLINK_GENE_ASSOCIATED_WITH_CONDITION)
if drugs is not None:
# Add drug nodes
if drugs is not None:
drug_nodes = []
for drug in drugs:
drug_nodes.append(q.add_node(drug, BIOLINK_DRUG))
# Connect all drug nodes to disease.
for drug_node in drug_nodes:
q.add_edge(drug_node, disease_node, BIOLINK_TREATS)
# Setup batch drugs
if batch_drugs is not None:
if type(batch_drugs) is not list:
raise QueryBuildError('Batch drugs must be a list.')
batch_drug_node = q.add_node(batch_drugs, BIOLINK_DRUG)
q.add_edge(batch_drug_node, disease_node, BIOLINK_TREATS)
# Connect drug node to outcome node
outcome_node = q.add_node(outcome, BIOLINK_PHENOTYPIC_FEATURE)
phenotype_edge = q.add_edge(disease_node, outcome_node, BIOLINK_HAS_PHENOTYPE)
q.add_constraint(outcome_name, outcome, outcome_op, outcome_value, edge_id=phenotype_edge)
query = Query(trapi_version=trapi_version, biolink_version=biolink_version)
query.message = message
return query