def test_query_term_from_json():
invalid = {}
with pytest.raises(ValueError):
QueryTerm.from_json(invalid)
invalid['term_type'] = 'invalid'
with pytest.raises(ValueError):
QueryTerm.from_json(invalid)
expr = {}
expr['term_type'] = 'expr'
with pytest.raises(ValueError):
QueryTerm.from_json(expr)
expr['category'] = 'type'
expr['term'] = 'nrps'
term = QueryTerm.from_json(expr)
assert term.kind == 'expression'
assert term.category == expr['category']
assert term.term == expr['term']
op = {}
op['term_type'] = 'op'
with pytest.raises(ValueError):
QueryTerm.from_json(op)
op['operation'] = 'or'
op['left'] = expr
op['right'] = expr
term = QueryTerm.from_json(op)
assert term.kind == 'operation'
assert term.operation == op['operation']
assert isinstance(term.left, QueryTerm)
assert isinstance(term.right, QueryTerm)
def test_query_term__generate_tokens():
string = "lanthipeptide"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['lanthipeptide', 'END']
string = "(foo)"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['(', 'foo', ')', 'END']
string = "foo (foo) foo"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['foo', '(', 'foo', ')', 'foo', 'END']
def test_query_term__generate_tokens():
string = "lanthipeptide"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['lanthipeptide', 'END']
string = "(foo)"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['(', 'foo', ')', 'END']
string = "foo (foo) foo"
tokens = QueryTerm._generate_tokens(string)
assert tokens == ['foo', '(', 'foo', ')', 'foo', 'END']
def test_query_term_init_expression():
with pytest.raises(ValueError):
term = QueryTerm('expression')
with pytest.raises(ValueError):
term = QueryTerm('expression', category='type')
with pytest.raises(ValueError):
term = QueryTerm('expression', term='nrps')
term = QueryTerm('expression', category='type', term='nrps')
assert term.kind == 'expression'
assert term.category == 'type'
assert term.term == 'nrps'
assert repr(term) == "QueryTerm(category: 'type', term: 'nrps')"
assert str(term) == "[type]nrps"
def test_query_term_init_operation():
with pytest.raises(ValueError):
term = QueryTerm('operation')
left = QueryTerm('expression', category='type', term='nrps')
right = QueryTerm('expression', category='type', term='nrps')
term = QueryTerm('operation', operation='or', left=left, right=right)
assert term.kind == 'operation'
assert term.operation == 'or'
assert term.left == left
assert term.right == right
expected = "QueryTerm(operation: {!r},\n\tleft: {!r}\n\tright: {!r}\n)".format('or', left, right)
assert repr(term) == expected
assert str(term) == "( [type]nrps OR [type]nrps )"
def test_guess_cluster_category():
tests = [('lantipeptide', 'type'), ('NC_003888', 'acc'),
('Streptomyces', 'genus'), ('coelicolor', 'species'),
('not-in-database', 'unknown')]
for search_term, expected in tests:
term = QueryTerm.from_string(search_term)
assert clusters.guess_cluster_category(term) == expected, search_term
def test_cluster_query_from_term_expression():
term = QueryTerm('expression', category='type', term='lantipeptide')
ret = search.cluster_query_from_term(term)
assert ret.count() == 6
term.category = 'unknown'
ret = search.cluster_query_from_term(term)
assert ret.count() == 6
term.category = 'type'
term.term = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.category = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
def test_cluster_query_from_term_expression():
term = QueryTerm('expression', category='type', term='lantipeptide')
ret = search.cluster_query_from_term(term)
assert ret.count() == 3
term.category = 'unknown'
ret = search.cluster_query_from_term(term)
assert ret.count() == 3
term.category = 'type'
term.term = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.category = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
def test_cluster_query_from_term_invalid():
term = QueryTerm('expression', category='type', term='lantipeptide')
term.kind = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
def test_cluster_query_from_term_operation():
left = QueryTerm('expression', category='type', term='lantipeptide')
right = QueryTerm('expression', category='genus', term='Streptomyces')
term = QueryTerm('operation', operation='and', left=left, right=right)
ret = search.cluster_query_from_term(term)
assert ret.count() == 3
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 29
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
left.category = 'bogus'
term.operation = 'and'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 29
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
left.category = 'type'
right.category = 'bogus'
term.operation = 'and'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 3
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 3
def test_query_term_from_json():
invalid = {}
with pytest.raises(ValueError):
QueryTerm.from_json(invalid)
invalid['term_type'] = 'invalid'
with pytest.raises(ValueError):
QueryTerm.from_json(invalid)
expr = {}
expr['term_type'] = 'expr'
with pytest.raises(ValueError):
QueryTerm.from_json(expr)
expr['category'] = 'type'
expr['term'] = 'nrps'
term = QueryTerm.from_json(expr)
assert term.kind == 'expression'
assert term.category == expr['category']
assert term.term == expr['term']
op = {}
op['term_type'] = 'op'
with pytest.raises(ValueError):
QueryTerm.from_json(op)
op['operation'] = 'or'
op['left'] = expr
op['right'] = expr
term = QueryTerm.from_json(op)
assert term.kind == 'operation'
assert term.operation == op['operation']
assert isinstance(term.left, QueryTerm)
assert isinstance(term.right, QueryTerm)
expr = {
'term_type': 'expr',
'category': 'minimal',
'term': False
}
term = QueryTerm.from_json(expr)
assert term.kind == 'expression'
assert term.category == expr['category']
assert term.term is False
expr['term'] = 'true'
term = QueryTerm.from_json(expr)
assert term.kind == 'expression'
assert term.category == expr['category']
assert term.term is True
def test_query_term_from_string():
string = ""
with pytest.raises(ValueError):
QueryTerm.from_string(string)
string = "nrps"
term = QueryTerm.from_string(string)
assert term.kind == 'expression'
assert term.category == 'unknown'
assert term.term == 'nrps'
string = "[type]nrps"
term = QueryTerm.from_string(string)
assert term.kind == 'expression'
assert term.category == 'type'
assert term.term == 'nrps'
string = "[contigedge]true"
term = QueryTerm.from_string(string)
assert term.kind == 'expression'
assert term.category == 'contigedge'
assert term.term is True
string = "nrps AND 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'and'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps OR 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'or'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps EXCEPT 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'except'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'and'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "ripp AND ( streptomyces OR lactococcus )"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.left.term == 'ripp'
assert term.right.kind == 'operation'
assert term.right.left.term == 'streptomyces'
assert term.right.right.term == 'lactococcus'
string = "lanthipeptide ((Streptomyces coelicolor) OR (Lactococcus lactis))"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.left.term == 'lanthipeptide'
assert term.right.kind == 'operation'
assert term.right.left.kind == 'operation'
assert term.right.left.left.term == 'Streptomyces'
assert term.right.right.kind == 'operation'
assert term.right.right.right.term == 'lactis'
with pytest.raises(ValueError):
string = "AND ripp"
term = QueryTerm.from_string(string)
with pytest.raises(ValueError):
string = "END"
term = QueryTerm.from_string(string)
with pytest.raises(ValueError):
string = "( ripp"
term = QueryTerm.from_string(string)
def test_cluster_query_from_term_invalid():
term = QueryTerm('expression', category='type', term='lantipeptide')
term.kind = 'bogus'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
def test_cluster_query_from_term_operation():
left = QueryTerm('expression', category='type', term='lantipeptide')
right = QueryTerm('expression', category='genus', term='Streptomyces')
term = QueryTerm('operation', operation='and', left=left, right=right)
ret = search.cluster_query_from_term(term)
assert ret.count() == 6
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 120
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
left.category = 'bogus'
term.operation = 'and'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 120
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
left.category = 'type'
right.category = 'bogus'
term.operation = 'and'
ret = search.cluster_query_from_term(term)
assert ret.count() == 0
term.operation = 'or'
ret = search.cluster_query_from_term(term)
assert ret.count() == 6
term.operation = 'except'
ret = search.cluster_query_from_term(term)
assert ret.count() == 6
def test_query_term_init_invalid():
with pytest.raises(ValueError):
QueryTerm('foo')
def test_query_term_from_string():
string = ""
with pytest.raises(ValueError):
QueryTerm.from_string(string)
string = "nrps"
term = QueryTerm.from_string(string)
assert term.kind == 'expression'
assert term.category == 'unknown'
assert term.term == 'nrps'
string = "[type]nrps"
term = QueryTerm.from_string(string)
assert term.kind == 'expression'
assert term.category == 'type'
assert term.term == 'nrps'
string = "nrps AND 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'and'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps OR 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'or'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps EXCEPT 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'except'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "nrps 1234"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.operation == 'and'
assert term.left.term == 'nrps'
assert term.right.term == '1234'
string = "ripp AND ( streptomyces OR lactococcus )"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.left.term == 'ripp'
assert term.right.kind == 'operation'
assert term.right.left.term == 'streptomyces'
assert term.right.right.term == 'lactococcus'
string = "lanthipeptide ((Streptomyces coelicolor) OR (Lactococcus lactis))"
term = QueryTerm.from_string(string)
assert term.kind == 'operation'
assert term.left.term == 'lanthipeptide'
assert term.right.kind == 'operation'
assert term.right.left.kind == 'operation'
assert term.right.left.left.term == 'Streptomyces'
assert term.right.right.kind == 'operation'
assert term.right.right.right.term == 'lactis'
with pytest.raises(ValueError):
string = "AND ripp"
term = QueryTerm.from_string(string)
with pytest.raises(ValueError):
string = "END"
term = QueryTerm.from_string(string)
with pytest.raises(ValueError):
string = "( ripp"
term = QueryTerm.from_string(string)
