def test_validation_tloc():
"""Validate reaction"""
assertion = AssertionStr(
subject="tloc(p(MGI:Lipe), fromLoc(GO:0005737), toLoc(GO:0005811))")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
assertion = AssertionStr(
subject=
'tloc(p(HGNC:NFE2L2), fromLoc(MESH:Cytoplasm), toLoc(MESH:"Cell Nucleus"))'
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_complex_nsarg():
assertion = AssertionStr(
subject=
'p(HGNC:PTHLH) increases act(complex(SCOMP:"Nfkb Complex"), ma(tscript))'
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
assertion = AssertionStr(
subject='complex(GO:"transcription factor AP-1 complex")')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_bad_function():
assertion = AssertionStr(subject="ppp(HGNC:PTHLH)")
expected = "Could not parse Assertion - bad relation? HGNC:9607!PTHLH"
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_bad_nsarg():
assertion = AssertionStr(subject="p(HGNC:)")
expected = "Could not match function: proteinAbundance arguments to BEL Specification"
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_missing_right_quote():
assertion = AssertionStr(subject='p(HGNC:"AKT1)')
expected = "Missing right quote after left quote at position 7 and before position 13"
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_missing_left_quote():
assertion = AssertionStr(subject='p(HGNC:AKT1")')
expected = "Missing left quote before right quote at position 11"
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_namespace_using_synonyms():
"""Validate nsarg that doesn't match alt_keys but does match synonyms"""
assertion = AssertionStr(subject="p(MGI:Emr4)", )
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_abundance_namespace():
"""Validate abundance namespace"""
assertion = AssertionStr(subject="a(CHEBI:15377!water)", )
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_pmod_function_errors(test_input, expected):
"""Accept Single or three letter Amino Acid code"""
assertion = AssertionStr(entire=test_input)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_frag_function():
"""Validate functions"""
assertion = AssertionStr(entire='p(HGNC:AKT1, frag("26_141"))')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_strarg():
assertion = AssertionStr(subject='complex("missing")')
expected = "String argument not allowed as an optional or multiple argument. Probably missing a namespace."
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_simple_function():
"""Validate simple function"""
assertion = AssertionStr(entire="p(HGNC:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_nsarg():
"""Validate path()"""
assertion = AssertionStr(subject="path(DO:COVID-19)")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_obsolete_nsarg():
assertion = AssertionStr(subject="r(HGNC:A2MP)")
expected = "BEL Entity name is obsolete - please update to HGNC:8!A2MP1"
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_empty_modifier():
"""Validate empty modifier"""
assertion = AssertionStr(entire="p(HGNC:AKT1, frag())")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == "No arguments in function: fragment"
assert ast.errors[0].severity == "Error"
def test_validate_deg_function():
"""Validate functions"""
assertion = AssertionStr(
entire='deg(a(CHEBI:"intermediate-density lipoprotein"))')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_fus5():
"""Validate fus()"""
assertion = AssertionStr(
subject='r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034"))')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_empty_function():
"""Validate empty function"""
assertion = AssertionStr(entire="p()")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == "No arguments in function: proteinAbundance"
assert ast.errors[0].severity == "Error"
def test_validate_fus2():
"""Validate fus()"""
assertion = AssertionStr(
subject="p(fus(HGNC:EWSR1, start, HGNC:FLI1, end))")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_complex_nsarg_quoted_colon():
assertion = AssertionStr(subject='complex(SCOMP:"KLF1:SWI/SNF complex")')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert (
ast.errors[0].msg ==
'Unknown BEL Entity SCOMP:"KLF1:SWI/SNF complex" - cannot determine if this matches function signature'
)
def test_validate_complex_missing_namespace():
"""Validate path()"""
assertion = AssertionStr(subject="complex(UNKNOWN:test)")
expected = (
"Unknown BEL Entity UNKNOWN:test - cannot determine if this matches function signature"
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors[0].msg == expected
def test_validate_fus1():
"""Validate fus()"""
# HGNC:NPM isn't valid - but it gets converted to updated entity
assertion = AssertionStr(
subject='p(fus(HGNC:NPM, "1_117", HGNC:ALK, end))')
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_nested():
assertion = AssertionStr(
subject="p(HGNC:CCL5)",
relation="decreases",
object='(p(HGNC:CXCL12) increases bp(GO:"platelet aggregation"))',
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_sec():
"""Validate fus()"""
assertion = AssertionStr(
subject='bp(GO:0030168!"platelet activation")',
relation="increases",
object='sec(a(SCHEM:"Thymosin beta(4)"))',
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert ast.errors == []
def test_validate_missing_namespace():
"""Validate simple function"""
assertion = AssertionStr(entire="p(missing:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors", ast.errors)
assert (
ast.errors[0].msg ==
"Unknown BEL Entity 'missing:AKT1' for the proteinAbundance function at position 2"
)
assert ast.errors[0].severity == "Warning"
def test_validate_rxn3():
"""Validate path()"""
assertion = AssertionStr(
subject=
'act(p(HGNC:GPT2), ma(cat)) directlyIncreases rxn(reactants(a(CHEBI:alanine), a(SCHEM:"alpha-Ketoglutaric acid")), products(a(SCHEM:"Propanoic acid, 2-oxo-, ion(1-)"), a(CHEBI:"L-glutamic acid")))'
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors")
for error in ast.errors:
print("Error", error.json())
assert ast.errors == []
def test_validate_rxn2():
"""Validate path()"""
assertion = AssertionStr(
subject=
'rxn(reactants(a(CHEBI:"guanidinoacetic acid"), a(CHEBI:"(S)-S-adenosyl-L-methionine")), products(a(CHEMBL:s-adenosylhomocysteine), a(CHEBI:creatine)))'
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors")
for error in ast.errors:
print("Error", error.json())
assert ast.errors == []
def test_validate_reaction():
"""Validate reaction"""
assertion = AssertionStr(
subject=
'rxn(reactants(a(CHEBI:"vitamin A"), a(CHEBI:NAD)), products(a(SCHEM:Retinaldehyde)))'
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Errors")
for error in ast.errors:
print(" ", error.json(), "\n")
assert ast.errors == []
def test_validate_rxn1():
"""Validate path()"""
assertion = AssertionStr(
subject=
"rxn(reactants(complex(reactome:R-HSA-1112584.1, p(SP:O14543, loc(GO:0005829)))), products(complex(reactome:R-HSA-1112584.1, p(SP:O14543), loc(GO:0005829))))"
)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.validate()
print("Parse Info", ast.parse_info)
print("Errors")
for error in ast.errors:
print("Error", error.json())
assert ast.errors == []
