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# -*- coding: utf-8 -*-
"""Tests for the jsonschema node validation."""
import copy
import json
import os
import unittest
import pybel.dsl
from pybel.schema import is_valid_edge, is_valid_node
from pybel.testing.utils import n
NAMESPACE, NAME, IDENTIFIER = n(), n(), n()
BLANK_ABUNDANCE = {"function": "", "variants": []}
# Abundances
PROTEIN = pybel.dsl.Protein(namespace=NAMESPACE, name=NAME, identifier=IDENTIFIER)
GENE = pybel.dsl.Gene(NAMESPACE, name=NAME, identifier=IDENTIFIER)
# Variants
GENE_MOD = pybel.dsl.GeneModification(NAME, namespace=NAMESPACE, identifier=IDENTIFIER)
PROTEIN_SUB = pybel.dsl.ProteinSubstitution("Ala", 1, "Tyr")
PROTEIN_MOD = pybel.dsl.ProteinModification(NAME, code="Ala", position=1, namespace=NAMESPACE, identifier=IDENTIFIER)
FRAGMENT = pybel.dsl.Fragment(1, 2)
class TestNodeSchema(unittest.TestCase):
"""Tests for the jsonschema node validation."""
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_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_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_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_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_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_abundances(self):
"""Test that invalid abundances are caught."""
missing_fn = BLANK_ABUNDANCE.copy()
missing_fn.pop("function")
self.assertFalse(is_valid_node(missing_fn))
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_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))
class TestEdgeSchema(unittest.TestCase):
"""Tests for the jsonschema edge validation."""
@classmethod
def setUpClass(cls):
"""Load the edge contained in example_edge.json."""
here = os.path.abspath(os.path.dirname(__file__))
example_file = os.path.join(here, "example_edge.json")
with open(example_file) as example_json:
edge = json.load(example_json)
cls.example_edge = edge
def test_predefined_example(self):
"""Test a predefined edge example."""
edge = self.example_edge
self.assertTrue(is_valid_edge(edge))
def test_missing_information(self):
"""Test removing information from the predefined edge."""
edge = self.example_edge
missing_source = copy.deepcopy(edge)
missing_source.pop("source")
self.assertFalse(is_valid_edge(missing_source))
missing_relation = copy.deepcopy(edge)
missing_relation.pop("relation")
self.assertFalse(is_valid_edge(missing_relation))
missing_target = copy.deepcopy(edge)
missing_target.pop("target")
self.assertFalse(is_valid_edge(missing_target))
missing_location = copy.deepcopy(edge)
missing_location["target"]["effect"].pop("fromLoc")
self.assertFalse(is_valid_edge(missing_location))
if __name__ == "__main__":
unittest.main()
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