def test_level_2_2(self):
'''
Test that runs with GrandParent - Child Relationship
Expect: Two trees (Two Component Definitions) with two relationships
This is a component that is a child of one of the CDS with a SequenceAnnotation and a child Location.
'''
# Create SBOL from ShortBOL
test_fn = "test_level_2_2.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),3)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
# The tree has two roots
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,3)
self.assertEqual(child_count,5)
self.assertEqual(children["http://sbol_prefix.org/cd1/1"],0)
self.assertEqual(children["http://sbol_prefix.org/cd2/1"],0)
self.assertEqual(children["http://sbol_prefix.org/moduledef_1/1"],5)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,2)
self.assertEqual(depths["http://sbol_prefix.org/cd1/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/cd2/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/moduledef_1/1"],2)
def test_level_1(self):
'''
Test that runs with a single parent-child relationship
Expect: Two trees (Two Component Definitions) but with a relationship triplepack
This is a component that is a child of one of the CDS
'''
# Create SBOL from ShortBOL
test_fn = "test_level_1.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),2)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
# The tree has two roots
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,2)
self.assertEqual(child_count,1)
self.assertEqual(children["http://sbol_prefix.org/pTetR/1"],0)
self.assertEqual(children["http://sbol_prefix.org/tetRInverter/1"],1)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,1)
self.assertEqual(depths["http://sbol_prefix.org/pTetR/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/tetRInverter/1"],1)
def test_large_script_2(self):
'''
Tests a large script as almost like a user-test scenario.
'''
# Create SBOL from ShortBOL
test_fn = "test_large_script_2.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),4)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,4)
self.assertEqual(child_count,13)
self.assertEqual(children["http://sbol_prefix.org/LacI_inverter/1"],8)
self.assertEqual(children["http://sbol_prefix.org/TetR_inverter/1"],5)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,2)
self.assertEqual(depths["http://sbol_prefix.org/LacI_inverter/1"],2)
self.assertEqual(depths["http://sbol_prefix.org/TetR_inverter/1"],2)
def test_sequence(self):
'''
Test Sequences with CD's to ensure that Sequences ARENT identified as children
'''
# Create SBOL from ShortBOL
test_fn = "test_sequence.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),2)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,2)
self.assertEqual(child_count,0)
self.assertEqual(children["http://sbol_prefix.org/seq_1/1"],0)
self.assertEqual(children["http://sbol_prefix.org/pTetR/1"],0)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,0)
self.assertEqual(depths["http://sbol_prefix.org/seq_1/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/pTetR/1"],0)
def produce_sbol(fn, output):
try:
return_code = shortbol_script_runner.parse_from_file(
fn, "sbolxml", [templates], output, [])
except Exception as e:
return e
return return_code
def produce_sbol(fn, output, version):
try:
return_code = shortbol_script_runner.parse_from_file(
fn,
"sbolxml", [templates],
output, [],
no_validation=False,
version=version)
except Exception as e:
return e
return return_code
def test_regression_by_examples(self):
failure_exceptions = []
sbol_validation_errors = []
for path, subdirs, files in os.walk(test_files):
for name in files:
if name == "temporary_runner.shb":
continue
if name.endswith(".shb") or name.endswith(".rdfsh"):
if "sbol_3" in path:
version = "sbol_3"
else:
version = "sbol_2"
file_to_run = os.path.join(path, name)
short_fn = file_to_run.split("\\")
short_fn = "/".join(short_fn[len(short_fn) - 2:])
print("Running with file: " + str(short_fn))
return_code = "Error Thrown."
try:
return_code = run.parse_from_file(file_to_run,
"sbolxml",
[templates],
output_fn, [],
version=version)
except Exception as e:
failure_exceptions.append({file_to_run: e})
if return_code != {"SBOL validator success.": []}:
sbol_validation_errors.append({short_fn: return_code})
print("--------------------Report--------------------\n")
print(
f"Number of failures by exception: {str(len(failure_exceptions))}")
print(
f"Number of failures by validation: {str(len(sbol_validation_errors))}"
)
if len(failure_exceptions) > 0:
for exception in failure_exceptions:
for k, v in exception.items():
print("Failure by Exception on:" + k + ", Exception: " +
str(v))
if len(sbol_validation_errors) > 0:
for validation_error in sbol_validation_errors:
for k, v in validation_error.items():
print("Failure by SBOL Validation on: " + str(k) +
"\nvalidation errors: " + str(v) + "\n")
if len(failure_exceptions) > 0 or len(sbol_validation_errors) > 0:
self.fail("Atleast One Test Failed")
print("\n--------------------------------------------")
def test_level_0(self):
'''
Simplest Test only one triplepack with no children.
Expect: Single tree, cd as root with only a single layer that only contains the properties
of the CD no children references.
'''
# Create SBOL from ShortBOL
test_fn = "test_level_0.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),1)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
single_cd = heirachy_tree[str(list(roots)[0][0])]
expected_type = (rdflib.URIRef('http://sbol_prefix.org/n/1') , rdflib.URIRef('http://sbols.org/v2#type'), rdflib.URIRef('http://www.biopax.org/release/biopax-level3.owl#Dna'))
expected_name = (rdflib.URIRef('http://sbol_prefix.org/n/1') , rdflib.URIRef('http://purl.org/dc/terms/title'), rdflib.term.Literal('LacI CDS'))
expected_description = (rdflib.URIRef('http://sbol_prefix.org/n/1') , rdflib.URIRef('http://purl.org/dc/terms/description'), rdflib.term.Literal('Coding Region for LacI protein'))
expected_role = (rdflib.URIRef('http://sbol_prefix.org/n/1') , rdflib.URIRef('http://sbols.org/v2#role'), rdflib.URIRef('http://identifiers.org/so/SO:0000316'))
self.assertEqual(len(heirachy_tree),1)
self.assertTrue(expected_type in single_cd)
self.assertTrue(expected_name in single_cd)
self.assertTrue(expected_description in single_cd)
self.assertTrue(expected_role in single_cd)
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,1)
self.assertEqual(child_count,0)
self.assertEqual(children["http://sbol_prefix.org/n/1"],0)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,0)
self.assertEqual(depths["http://sbol_prefix.org/n/1"],0)
def test_large_script(self):
'''
Tests a large script as almost like a user-test scenario.
'''
# Create SBOL from ShortBOL
test_fn = "test_large_script.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),30)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,30)
self.assertEqual(child_count,76)
self.assertEqual(children["http://sbol_prefix.org/Gal4VP16_gene/1"],3)
self.assertEqual(children["http://sbol_prefix.org/EYFP_gene/1"],3)
self.assertEqual(children["http://sbol_prefix.org/gRNA_b_gene/1"],5)
self.assertEqual(children["http://sbol_prefix.org/mKate_gene/1"],3)
self.assertEqual(children["http://sbol_prefix.org/cas9m_BFP_gene/1"],3)
self.assertEqual(children["http://sbol_prefix.org/CRISPR_Template/1"],15)
self.assertEqual(children["http://sbol_prefix.org/CRPb_characterization_Circuit/1"],44)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,2)
self.assertEqual(depths["http://sbol_prefix.org/Gal4VP16_gene/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/EYFP_gene/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/gRNA_b_gene/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/mKate_gene/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/cas9m_BFP_gene/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/CRISPR_Template/1"],2)
self.assertEqual(depths["http://sbol_prefix.org/CRPb_characterization_Circuit/1"],2)
def test_many_trees_many_relationships(self):
'''
Test that runs many top-level objects AND with many relationships but all depth-2 level relationships.
Expect: Each Top-Level objects are connected by non-top-level object, parent-child relationships.
'''
# Create SBOL from ShortBOL
test_fn = "test_many_trees_many_relationships.shb"
return_code = shortbol_script_runner.parse_from_file(test_fn,optpaths=[lib_path],out=output_fn)
self.assertEqual(list(return_code.keys())[0], "SBOL validator success.")
test_graph = load_graph(output_fn)
# Run GetRoots
roots = SBOL2ShortBOL.find_graph_roots(test_graph)
self.assertEqual(len(roots),5)
# Test get_tree
heirachy_tree = generate_tree(roots,test_graph)
SBOL2ShortBOL.tree_dump(heirachy_tree, os.path.join(output_dir,test_fn.split(".")[0] + ".txt"))
self.common_tests(heirachy_tree,roots)
# Bespoke tests that can only be done by knowledge of the graph.
# The tree has two roots
top_level_count,children = count_objects(heirachy_tree)
child_count = sum(list(children.values()))
self.assertEqual(top_level_count,5)
self.assertEqual(child_count,6)
self.assertEqual(children["http://sbol_prefix.org/seq_1/1"],0)
self.assertEqual(children["http://sbol_prefix.org/cd_1/1"],0)
self.assertEqual(children["http://sbol_prefix.org/cd_2/1"],4)
self.assertEqual(children["http://sbol_prefix.org/model_1/1"],0)
self.assertEqual(children["http://sbol_prefix.org/mod_def_1/1"],2)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,1)
self.assertEqual(depths["http://sbol_prefix.org/seq_1/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/cd_1/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/cd_2/1"],1)
self.assertEqual(depths["http://sbol_prefix.org/model_1/1"],0)
self.assertEqual(depths["http://sbol_prefix.org/mod_def_1/1"],1)
def run_shortbol(filename):
return_code_shortbol = run.parse_from_file(filename, "sbolxml",
[templates], shortbol_output_fn,
[])
return return_code_shortbol