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# -*- coding: utf-8 -*-
import logging
import unittest
from io import StringIO
from pybel import BELGraph
from pybel.examples.egf_example import egf_graph
from pybel.struct.mutation import enrich_protein_and_rna_origins
from pybel.struct.pipeline import Pipeline
from pybel.struct.pipeline.decorators import get_transformation, mapped
from pybel.struct.pipeline.exc import MetaValueError, MissingPipelineFunctionError
log = logging.getLogger(__name__)
log.setLevel(10)
class TestEgfExample(unittest.TestCase):
"""Random test for mutation functions"""
def setUp(self):
self.graph = egf_graph.copy()
self.original_number_nodes = self.graph.number_of_nodes()
self.original_number_edges = self.graph.number_of_edges()
def check_original_unchanged(self):
self.assertEqual(
self.original_number_nodes,
self.graph.number_of_nodes(),
msg="original graph nodes should remain unchanged",
)
self.assertEqual(
self.original_number_edges,
self.graph.number_of_edges(),
msg="original graph edges should remain unchanged",
)
class TestPipelineFailures(unittest.TestCase):
def test_assert_failure(self):
with self.assertRaises(MissingPipelineFunctionError):
get_transformation("missing function")
def test_assert_success(self):
m = list(mapped)
self.assertLess(0, len(m))
m = m[0]
f = get_transformation(m)
self.assertIsNotNone(f)
def test_append_invalid(self):
"""Test when an invalid type is given to a :class:`pybel.struct.Pipeline`."""
p = Pipeline()
with self.assertRaises(TypeError):
p.append(4)
def test_get_function_failure(self):
p = Pipeline()
with self.assertRaises(MissingPipelineFunctionError):
p._get_function("nonsense name")
def test_build_meta_failure(self):
p1, p2 = Pipeline(), Pipeline()
p = Pipeline._build_meta("wrong", [p1, p2])
with self.assertRaises(MetaValueError):
p(BELGraph())
def test_fail_add(self):
pipeline = Pipeline()
with self.assertRaises(MissingPipelineFunctionError):
pipeline.append("missing function")
class TestPipeline(TestEgfExample):
def test_append(self):
pipeline = Pipeline()
self.assertEqual(0, len(pipeline))
pipeline.append("enrich_protein_and_rna_origins")
self.assertEqual(1, len(pipeline))
def test_extend(self):
p1 = Pipeline.from_functions(["enrich_protein_and_rna_origins"])
self.assertEqual(1, len(p1))
p2 = Pipeline.from_functions(["remove_pathologies"])
p1.extend(p2)
self.assertEqual(2, len(p1))
def test_serialize_string(self):
p = Pipeline.from_functions(["enrich_protein_and_rna_origins"])
s = p.dumps()
p_reconstituted = Pipeline.loads(s)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_serialize_file(self):
p = Pipeline.from_functions(["enrich_protein_and_rna_origins"])
sio = StringIO()
p.dump(sio)
sio.seek(0)
p_reconstituted = Pipeline.load(sio)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_pipeline_by_string(self):
pipeline = Pipeline.from_functions(
[
"enrich_protein_and_rna_origins",
]
)
result = pipeline(self.graph)
self.assertEqual(32, result.number_of_nodes())
for node in self.graph:
self.assertIn(node, result)
self.check_original_unchanged()
def test_pipeline_by_function(self):
pipeline = Pipeline.from_functions(
[
enrich_protein_and_rna_origins,
]
)
result = pipeline(self.graph)
self.assertEqual(32, result.number_of_nodes())
for node in self.graph:
self.assertIn(node, result)
self.check_original_unchanged()
|
