def test_drugcentral(rosetta):
fname='caster.output_filter(mychem~get_drugcentral,disease,typecheck~is_disease)'
func = rosetta.get_ops(fname)
assert func is not None
node = KNode('CHEMBL:CHEMBL159', type=node_types.DRUG)
results = func(node)
for e,n in results:
assert e.edge_source=='mychem.get_drugcentral'
def test_drugcentral(rosetta):
fname = 'caster.output_filter(mychem~get_drugcentral,disease,typecheck~is_disease)'
func = rosetta.get_ops(fname)
assert func is not None
node = KNode('CHEMBL:CHEMBL159', type=node_types.CHEMICAL_SUBSTANCE)
results = func(node)
for e, n in results:
assert e.provided_by == 'mychem.get_drugcentral'
def test_kegg(rosetta):
fname = 'caster.upcast(kegg~enzyme_get_chemicals,chemical_substance)'
func = rosetta.get_ops(fname)
assert func is not None
node = KNode('HGNC:2843', name='gene', type=node_types.GENE)
rosetta.synonymizer.synonymize(node)
results = func(node)
assert len(results) > 0
def x_test_with_pheno_filter(rosetta):
"""This will usually get called with a phenotype filter"""
fname = 'caster.output_filter(mychem~get_adverse_events,phenotypic_feature,typecheck~is_phenotypic_feature)'
func = rosetta.get_ops(fname)
assert func is not None
#Escitalopram
results = func(KNode('CHEMBL:CHEMBL1508', type=node_types.DRUG))
assert len(results) > 0
def test_complicated(rosetta):
"""make sure that a very complicated cast gets everything to the right place"""
fname = 'caster.output_filter(input_filter(upcast(hetio~disease_to_phenotype,disease_or_phenotypic_feature),disease,typecheck~is_disease),disease,typecheck~is_disease)'
func = rosetta.get_ops(fname)
assert func is not None
node = KNode('HP:0007354', type=node_types.PHENOTYPIC_FEATURE)
node.add_synonyms(set([LabeledID(identifier='DOID:332', label='ALS')]))
results = func(node)
assert results is not None
def test_kegg_get_enzyme(rosetta):
fname = 'caster.input_filter(kegg~chemical_get_enzyme,metabolite)'
func = rosetta.get_ops(fname)
node = KNode('CHEBI:29073',
name='chem',
type=node_types.CHEMICAL_SUBSTANCE)
rosetta.synonymizer.synonymize(node)
results = func(node)
assert len(results) > 0
def test_kegg_get_enzyme_norcodeine(rosetta):
fname = 'caster.input_filter(kegg~chemical_get_enzyme,metabolite)'
func = rosetta.get_ops(fname)
node = KNode('CHEBI:80579',
name='norcodeine',
type=node_types.CHEMICAL_SUBSTANCE)
rosetta.synonymizer.synonymize(node)
results = func(node)
for edge, node in results:
print(edge, node.id, node.name)
def test_upcast(rosetta):
"""According to biolink model, pathway is_a biological process. So we should be able to do gene->pathway and
then upcast the result to type biological process"""
fname = 'caster.upcast(biolink~gene_get_pathways,biological_process)'
func = rosetta.get_ops(fname)
assert func is not None
#PPARG
results = func(KNode('HGNC:9236', type=node_types.GENE))
assert len(results) > 0
for edge, node in results:
assert node.type == node_types.BIOLOGICAL_PROCESS
def test_null_input_filter(rosetta):
"""According to biolink model, pathway is_a biological process. So if we have a process, we can try to
call pathway_get_gene, We don't have a function for determining whether an entity is a pathway, so the
filter is a passthrough."""
fname='caster.input_filter(biolink~pathway_get_gene,pathway)'
func = rosetta.get_ops(fname)
assert func is not None
results = func(KNode('KEGG-path:maphsa04211', type=node_types.PROCESS)) #one of the results from the above
assert len(results) > 0
for edge,node in results:
assert node.type == node_types.GENE
gene_ids = [ node.id for edge,node in results]
assert 'HGNC:9236' in gene_ids #PPARG
def test_input_filter(rosetta):
"""We have a typecheck for sell, so we can check for cell->something push_ups. IN this case the only
cell->something function we have is cell->anatomy, and anatomy is also the superclass, so it gets a little
confusing. But basically, this is where we are going to have an anatomy node containing a cell identifier,
and we should be able to call the function. But when we call it with a non-cell anatomy, nothing will happen"""
fname='caster.input_filter(uberongraph~get_anatomy_by_cell_graph,cell,typecheck~is_cell)'
func = rosetta.get_ops(fname)
assert func is not None
results = func(KNode('CL:0000169', type=node_types.ANATOMY)) #Type-B pancreatic cell cast as an anatomy
assert len(results) > 0
anat_ids = [node.id for edge,node in results]
assert 'UBERON:0001264' in anat_ids #pancreas
results = func(KNode('UBERON:0001264', type=node_types.ANATOMY)) #PANCREAS
assert len(results) == 0
def test_kegg_chem_to_chem_carnitine(rosetta):
fname = 'caster.upcast(input_filter(kegg~chemical_get_chemical,metabolite),chemical_substance)'
carn = KNode('CHEBI:16347',
name='L-Carnitine',
type=node_types.CHEMICAL_SUBSTANCE)
rosetta.synonymizer.synonymize(carn)
func = rosetta.get_ops(fname)
assert func is not None
results = func(carn)
other = 'KEGG.COMPOUND:C02990'
ids = []
for edge, node in results:
ids.append(node.id)
#Really, it should be, but this reaction doesn't appear in KEGG (for humans)
assert other in ids
def test_output_filter(rosetta):
"""Test automatic wrapping of gene_get_disease so that outputs are only genetic conditions"""
fname = 'caster.output_filter(biolink~gene_get_disease,genetic_condition,mondo~is_genetic_disease)'
func = rosetta.get_ops(fname)
assert func is not None
#PPARG
results = func(KNode('HGNC:9236', type=node_types.GENE))
for edge, node in results:
assert node.type == node_types.GENETIC_CONDITION
gc_identifiers = [node.id for edge, node in results]
#These are genetic conditions associated with PPARG
assert 'MONDO:0011448' in gc_identifiers
assert 'MONDO:0018883' in gc_identifiers
assert 'MONDO:0019245' in gc_identifiers
#These are diseases associated with PPARG that are not Genetic Conditions (non-comprehensive)
assert 'MONDO:0001106' not in gc_identifiers
def test_nested(rosetta):
"""cell->anatomy should be callable even if the input is upcast to an anatomy and we want a cell as output"""
fname = 'caster.output_filter(input_filter(uberongraph~get_anatomy_by_cell_graph,cell,typecheck~is_cell),cell,typecheck~is_cell)'
#Test that we can actually get a function. This was failing 4/21
func = rosetta.get_ops(fname)