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_assertion_str():
assertion = AssertionStr(subject=" hello", relation="there", object="world ")
assert assertion.entire == "hello there world"
# Does not update assertion.entire when SRO fields are altered
assertion.entire = ""
assertion.object = ""
assert assertion.entire != "hello there"
def get_bel_canonicalize(bel_assertion: str, version: str = "latest"):
"""Get Canonicalized Assertion"""
assertion = AssertionStr(entire=bel_assertion)
ast = bel.lang.ast.BELAst(assertion=assertion)
canonicalized = ast.canonicalize().to_string()
return {"canonicalized": canonicalized, "original": bel_assertion}
def validate_assertion(bel_assertion: str):
"""Validate BEL Assertion"""
validated = bel.nanopub.validate.validate_assertion(
AssertionStr(entire=bel_assertion))
logger.info(f"Validated: {validated}")
return validated
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_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_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_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_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_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_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_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_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_ast_parse_fus():
assertion = AssertionStr(
entire="act(p(fus(HGNC:EWSR1, start, HGNC:FLI1, end)), ma(tscript))")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("To String", ast.to_string())
assert (
ast.to_string() ==
"act(p(fus(HGNC:3508!EWSR1, start, HGNC:3749!FLI1, end)), ma(tscript))"
)
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_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_get_species():
"""Collect all NSArg species for Assertion"""
assertion = AssertionStr(
entire="p(HGNC:391!AKT1) increases p(MGI:87986!Akt1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
species = ast.get_species_keys()
print("Species", species)
assert species == ["TAX:9606", "TAX:10090"]
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_missing_parts():
"""Test object only or missing object or relation bel assertion"""
assertion = AssertionStr(object="p(HGNC:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("Validation messages - object only")
for error in ast.errors:
print(" ", error.json(), "\n")
assert ast.errors[0].msg == "Missing Assertion Subject or Relation"
assertion = AssertionStr(relation="increases")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("Validation messages - relation only")
for error in ast.errors:
print(" ", error.json(), "\n")
assert ast.errors[0].msg == "Missing Assertion Object"
assertion = AssertionStr(relation="increases", object="p(HGNC:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("Validation messages - relation and object")
for error in ast.errors:
print(" ", error.json(), "\n")
assert ast.errors[0].msg == "Missing Assertion Subject or Relation"
assertion = AssertionStr(subject="p(HGNC:AKT1)", object="p(HGNC:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("Validation messages - subject and object")
for error in ast.errors:
print(" ", error.json(), "\n")
assert ast.errors[0].msg == "Missing Assertion Subject or Relation"
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_ast_subcomponents_simple():
test_input = "path(DO:0080600!COVID-19)"
assertion = AssertionStr(entire=test_input)
ast = bel.lang.ast.BELAst(assertion=assertion)
subcomponents = ast.subcomponents()
print("Subcomponents", subcomponents)
assert subcomponents == [
"path(DO:0080600!COVID-19)", "DO:0080600!COVID-19", "DO:COVID-19"
]
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_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_ast_subcomponents_complex():
test_input = """rxn(reactants(complex(p(HGNC:5241!HSPA8), p(HGNC:6501!LAMP2), p(reactome:R-HSA-9622845.1!"HSP90AA1, HSP90AB1"), loc(GO:0005829!cytosol))), products(complex(p(HGNC:6501!LAMP2), p(reactome:R-HSA-9622845.1!"HSP90AA1, HSP90AB1"), loc(GO:0005765!"lysosomal membrane")), p(HGNC:5241!HSPA8, loc(GO:0005829!cytosol))))"""
assertion = AssertionStr(entire=test_input)
ast = bel.lang.ast.BELAst(assertion=assertion)
subcomponents = ast.subcomponents()
pprint.pprint(subcomponents)
assert subcomponents == [
"path(DO:0080600!COVID-19)", "DO:0080600!COVID-19", "DO:COVID-19"
]