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_non_shortbol_produced_10(self):
'''
All previous tests are made from ShortBOL produced SBOL.
Should'nt make a difference but potentially some different ways of displaying SBOL.
CollectionOutput
'''
# Create SBOL from ShortBOL
test_fn = "test_non_shortbol_produced_10.rdf"
return_code = SBOL2ShortBOL.general_validation(test_fn)
self.assertTrue(return_code)
test_graph = load_graph(test_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.
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)
max_depth,depths = get_depth(heirachy_tree)
self.assertEqual(max_depth,0)
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 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_non_sbol_produced(self):
# For each example in the examples_dir
diff_errors = []
sbol_validation_errors = {}
for path, subdirs, files in os.walk(test_files):
if "extensions" in path:
continue
for name in files:
if name == "temporary_runner.shb":
continue
if name.endswith(".xml"):
file_to_run = os.path.join(path, name)
log_dir = os.path.join(os.getcwd(), name.split(".")[0])
try:
os.mkdir(log_dir)
except FileExistsError:
pass
print("\n----------------------------------------")
print(f'Running Regression test with {file_to_run}')
shortbol_code = os.path.join(log_dir, "shortbol_code.shb")
second_rdf_fn = os.path.join(log_dir, "final_output.rdf")
try:
SBOL2ShortBOL.produce_shortbol(file_to_run, templates,
shortbol_code, True)
except ValueError:
self.fail("Unable to produce the ShortBOL code.")
# ShortBOL 2 SBOL - Produce RDF from new ShortBOL.
ret_code = produce_sbol(shortbol_code, second_rdf_fn)
if not ret_code == {'SBOL validator success.': []}:
print(
"Test failed due to generated ShortBOL producing Invalid SBOL."
)
sbol_validation_errors[file_to_run] = ret_code
# Load the original RDF and Newer RDF into a graph and compare.
log_fn = os.path.join(log_dir, "error_log.txt")
if rdf_difference_check(file_to_run, second_rdf_fn,
log_fn):
print("Test Passed")
shutil.rmtree(log_dir)
else:
print("Test failed due to differences in SHB files.")
diff_errors.append(file_to_run)
print("----------------------------------------")
if len(list(sbol_validation_errors.keys())) > 0:
print("ERROR:: Produced invalid ShortBOL.")
for k, v in sbol_validation_errors.items():
print(k, v)
if len(diff_errors) != 0:
print(f"Regressed with {len(diff_errors)} number of tests")
print("ERROR:: Differences found during testing")
for e in diff_errors:
print(e)
self.fail("Failed due to differences")
def test_convert_simple(self):
heirachy_tree = {
'http://sbol_prefix.org/tetRInverter/1':
[(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter')),
(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#type'),
rdflib.term.URIRef(
'http://www.biopax.org/release/biopax-level3.owl#Dna')),
(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef('http://sbols.org/v2#ComponentDefinition')),
(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#name'),
rdflib.term.Literal('name')),
(rdflib.term.URIRef('http://sbol_prefix.org/tetRInverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('tetRInverter'))],
'http://sbol_prefix.org/pTetR/1':
[(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('pTetR')),
(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#type'),
rdflib.term.URIRef(
'http://www.biopax.org/release/biopax-level3.owl#Dna')),
(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef('http://sbol_prefix.org/pTetR')),
(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#role'),
rdflib.term.URIRef('http://identifiers.org/so/SO:0000167')),
(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef('http://sbol_prefix.org/pTetR/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef('http://sbols.org/v2#ComponentDefinition'))]
}
shortbol_code = SBOL2ShortBOL.convert(heirachy_tree, lib_path)
summary = summarise_shortbol_code(shortbol_code)
self.assertEqual(
summary['tetRInverter'], {
'type': 'DNAComponent',
'parameters': [''],
'expansion': {
'name': '"name"'
}
})
self.assertEqual(summary['pTetR'], {
'type': 'Promoter',
'parameters': [''],
'expansion': {}
})
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 generate_tree(roots,graph):
heirachy_tree = {}
for root in roots:
heirachy_tree[str(root[0])] = SBOL2ShortBOL.get_tree(graph,root[0])
return heirachy_tree
def test_convert_advanced(self):
heirachy_tree = {
'http://sbol_prefix.org/LacI_inverter/1': [
{
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1':
[(rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib.term.URIRef('http://sbols.org/v2#access'),
rdflib.term.URIRef('http://sbols.org/v2#public')),
(rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('LacI_fc')),
(rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib.term.URIRef('http://sbols.org/v2#definition'),
rdflib.term.URIRef('http://sbol_prefix.org/LacI/1')),
(rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef(
'http://sbols.org/v2#FunctionalComponent')),
(rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacI_fc/1'),
rdflib
.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1'
), rdflib.term.URIRef('http://sbols.org/v2#direction'),
rdflib.term.URIRef('http://sbols.org/v2#none'))]
}, {
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1': [
{
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1':
[
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib
.term.URIRef('http://sbols.org/v2#persistentIdentity'
),
rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part'
)),
(
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib
.term.URIRef('http://sbols.org/v2#participant'
),
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
)),
(
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib
.term.URIRef('http://sbols.org/v2#version'
), rdflib.term.Literal('1')),
(
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib.term.
URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
),
rdflib.term.URIRef(
'http://sbols.org/v2#Participation')
),
(
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib
.term.URIRef('http://sbols.org/v2#role'),
rdflib.term.
URIRef('http://identifiers.org/biomodels.sbo/SBO:0000642'
)),
(
rdflib.term.
URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
),
rdflib.term.URIRef(
'http://sbols.org/v2#displayId'
), rdflib.term.Literal('TetR_lacinv_part'))
]
}, {
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1':
[(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib.term.URIRef('http://sbols.org/v2#version'
), rdflib.term.Literal('1')),
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib
.term.URIRef('http://sbols.org/v2#persistentIdentity'
),
rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part'
)),
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib.term.URIRef('http://sbols.org/v2#role'),
rdflib.
term.URIRef('http://identifiers.org/biomodels.sbo/SBO:0000020'
)),
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib
.term.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
),
rdflib
.term.URIRef('http://sbols.org/v2#Participation'
)),
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib.term.URIRef('http://sbols.org/v2#participant'
),
rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacI_fc/1'
)),
(rdflib
.term.URIRef('http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
),
rdflib.
term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('LacI_lacinv_part'))]
},
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef('http://sbols.org/v2#type'),
rdflib.term.URIRef('http://sbol_prefix.org/inhibition'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef(
'http://sbols.org/v2#persistentIdentity'
),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
), rdflib.term.URIRef('http://sbols.org/v2#version'
),
rdflib.term.Literal('1')),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef('http://sbols.org/v2#participation'
),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/TetR_lacinv_part/1'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('LacITetR_int'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef('http://sbols.org/v2#participation'
),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/LacI_lacinv_part/1'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1'
),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
),
rdflib.term.URIRef('http://sbols.org/v2#Interaction'))
]
}, {
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1':
[(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
), rdflib.term.URIRef('http://sbols.org/v2#direction'
),
rdflib.term.URIRef('http://sbols.org/v2#none'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
),
rdflib.term.URIRef(
'http://sbols.org/v2#FunctionalComponent'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
),
rdflib.term.URIRef(
'http://sbols.org/v2#persistentIdentity'
),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc'
)),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
), rdflib.term.URIRef('http://sbols.org/v2#access'),
rdflib.term.URIRef('http://sbols.org/v2#public')),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
), rdflib.term.URIRef('http://sbols.org/v2#definition'),
rdflib.term.URIRef('http://sbol_prefix.org/TetR/1')),
(rdflib
.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/TetR_fc/1'
), rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('TetR_fc'))]
},
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef(
'http://sbols.org/v2#displayId'),
rdflib.term.Literal('LacI_inverter')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#functionalComponent'),
rdflib.term
.URIRef('http://sbol_prefix.org/LacI_inverter/TetR_fc/1')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef('http://sbols.org/v2#ModuleDefinition')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef(
'http://sbols.org/v2#interaction'),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacITetR_int/1')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef('http://sbols.org/v2#functionalComponent'),
rdflib.term.URIRef(
'http://sbol_prefix.org/LacI_inverter/LacI_fc/1')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI_inverter/1'),
rdflib.term.URIRef('http://purl.org/dc/terms/description'),
rdflib.term.Literal('LacI inverter'))
],
'http://sbol_prefix.org/TetR/1':
[(rdflib.term.URIRef('http://sbol_prefix.org/TetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef('http://sbol_prefix.org/TetR')),
(rdflib.term.URIRef('http://sbol_prefix.org/TetR/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef('http://sbols.org/v2#ComponentDefinition')),
(rdflib.term.URIRef('http://sbol_prefix.org/TetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef('http://sbol_prefix.org/TetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('TetR')),
(rdflib.term.URIRef('http://sbol_prefix.org/TetR/1'),
rdflib.term.URIRef('http://sbols.org/v2#type'),
rdflib.term.URIRef(
'http://www.biopax.org/release/biopax-level3.owl#Protein'))],
'http://sbol_prefix.org/LacI/1':
[(rdflib.term.URIRef('http://sbol_prefix.org/LacI/1'),
rdflib.term.URIRef('http://sbols.org/v2#version'),
rdflib.term.Literal('1')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI/1'),
rdflib.term.URIRef('http://sbols.org/v2#displayId'),
rdflib.term.Literal('LacI')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI/1'),
rdflib.term.URIRef(
'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
rdflib.term.URIRef('http://sbols.org/v2#ComponentDefinition')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI/1'),
rdflib.term.URIRef('http://sbols.org/v2#type'),
rdflib.term.URIRef(
'http://www.biopax.org/release/biopax-level3.owl#Protein')),
(rdflib.term.URIRef('http://sbol_prefix.org/LacI/1'),
rdflib.term.URIRef('http://sbols.org/v2#persistentIdentity'),
rdflib.term.URIRef('http://sbol_prefix.org/LacI'))]
}
shortbol_code = SBOL2ShortBOL.convert(heirachy_tree, lib_path)
summary = summarise_shortbol_code(shortbol_code)
self.assertEqual(summary['TetR'], {
'type': 'ProteinComponent',
'parameters': [''],
'expansion': {}
})
self.assertEqual(summary['LacI'], {
'type': 'ProteinComponent',
'parameters': [''],
'expansion': {}
})
self.assertEqual(summary['TetR_fc'], {
'type': 'NoneComponent',
'parameters': ['TetR'],
'expansion': {}
})
self.assertEqual(summary['LacI_fc'], {
'type': 'NoneComponent',
'parameters': ['LacI'],
'expansion': {}
})
self.assertEqual(summary['LacI_lacinv_part'], {
'type': 'Inhibitor',
'parameters': ['LacI_fc'],
'expansion': {}
})
self.assertEqual(summary['TetR_lacinv_part'], {
'type': 'Inhibited',
'parameters': ['TetR_fc'],
'expansion': {}
})
self.assertEqual(
summary['LacITetR_int'], {
'type': 'Interaction',
'parameters': ['inhibition'],
'expansion': {
'participation': 'TetR_lacinv_part',
'participation': 'LacI_lacinv_part'
}
})
self.assertEqual(
summary['LacI_inverter'], {
'type': 'ModuleDefinition',
'parameters': [''],
'expansion': {
'description': '"LacIinverter"',
"functionalComponent": "TetR_fc",
"functionalComponent": "LacI_fc",
"interaction": "LacITetR_int"
}
})