def test_pure_abundances(self):
"""Test validating abundance nodes."""
self.assertTrue(is_valid_node(PROTEIN))
self.assertTrue(is_valid_node(GENE))
abundance = pybel.dsl.Abundance(namespace=NAMESPACE,
name=NAME,
identifier=IDENTIFIER)
self.assertTrue(is_valid_node(abundance))
def test_invalid_amino(self):
"""Test that protein variants with invalid amino acid codes are caught."""
invalid_psub = dict(PROTEIN_SUB)
invalid_psub['hgvs'] = 'p.Aaa0Bbb'
self.assertFalse(is_valid_node(invalid_psub))
invalid_pmod = dict(PROTEIN_MOD)
invalid_pmod['code'] = 'Aaa'
self.assertFalse(is_valid_node(invalid_pmod))
def test_list_abundances(self):
"""Test validating list abundance nodes."""
complex_abundance = pybel.dsl.ComplexAbundance(
[GENE.with_variants(GENE_MOD),
PROTEIN.with_variants(PROTEIN_SUB)],
namespace=NAMESPACE,
name=NAME,
identifier=IDENTIFIER)
composite_abundance = pybel.dsl.CompositeAbundance(
[PROTEIN, complex_abundance])
self.assertTrue(is_valid_node(complex_abundance))
self.assertTrue(is_valid_node(composite_abundance))
def test_matching_variants(self):
"""Test catching invalid abundance/variant pairs, e.g. ProteinModification on a Gene."""
invalid_gmod = PROTEIN.with_variants(GENE_MOD)
self.assertFalse(is_valid_node(invalid_gmod))
invalid_psub = GENE.with_variants(PROTEIN_SUB)
self.assertFalse(is_valid_node(invalid_psub))
invalid_pmod = GENE.with_variants(PROTEIN_MOD)
self.assertFalse(is_valid_node(invalid_pmod))
invalid_frag = GENE.with_variants(FRAGMENT)
self.assertFalse(is_valid_node(invalid_frag))
def test_variant_abundances(self):
"""Test validating abundance nodes with variants."""
gmod = GENE.with_variants(GENE_MOD)
self.assertTrue(is_valid_node(gmod))
psub = PROTEIN.with_variants(PROTEIN_SUB)
self.assertTrue(is_valid_node(psub))
pmod = PROTEIN.with_variants(PROTEIN_MOD)
self.assertTrue(is_valid_node(pmod))
frag = PROTEIN.with_variants(FRAGMENT)
self.assertTrue(is_valid_node(frag))
def test_reaction(self):
"""Test validating a reaction node."""
node = pybel.dsl.Rna(namespace=NAMESPACE,
name=NAME,
identifier=IDENTIFIER)
node_list = [node, PROTEIN, GENE]
rxn = pybel.dsl.Reaction(reactants=node_list, products=node_list)
self.assertTrue(is_valid_node(rxn))
def test_invalid_psub(self):
"""Test that invalid protein substitutions are caught."""
missing_hgvs = dict(PROTEIN_SUB)
# Remove the required "hgvs" property
missing_hgvs.pop("hgvs")
protein = BLANK_ABUNDANCE.copy()
protein["function"] = "Protein"
protein["variants"] = [missing_hgvs]
self.assertFalse(is_valid_node(protein))
def test_fusions(self):
"""Test validating fusion nodes."""
protein = pybel.dsl.Protein(namespace=NAMESPACE,
name=NAME,
identifier=IDENTIFIER)
enum_fusion_range = pybel.dsl.EnumeratedFusionRange("r", 1, 79)
missing_fusion_range = pybel.dsl.MissingFusionRange()
fusion_node = pybel.dsl.FusionBase(protein,
protein,
range_5p=enum_fusion_range,
range_3p=missing_fusion_range)
self.assertTrue(is_valid_node(fusion_node))
def test_invalid_abundances(self):
"""Test that invalid abundances are caught."""
missing_fn = BLANK_ABUNDANCE.copy()
missing_fn.pop("function")
self.assertFalse(is_valid_node(missing_fn))