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Split sb_api::test_amend_metadata and update for new py3.7 re.sub()
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Core dev has made a modification to how the * match character is
 handled, causing additional insertions at the end of a string as an
 "empty match". This is... unintuitive... behavior, but it is what it is
 I guess...
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@biologyguy
biologyguy committed Dec 27, 2018
1 parent f103820 commit bf6f6e2
Showing 1 changed file with 23 additions and 17 deletions.
40 changes: 23 additions & 17 deletions buddysuite/tests/test_seqbuddy/test_sb_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,52 +36,58 @@ def test_amend_metadata_topo(sb_resources, hf, monkeypatch, capsys):
for value, _hash in [('linear', 'b3feec305beee8243be7f7afb02a909d'),
('circular', '7ff89b41edab0a10b53629a28092e062'),
('', '0a8462e72f64fcd22544bb153b51b2b6')]:
tester = Sb.amend_metadata(tester, "topology", value, ".*")
tester = Sb.amend_metadata(tester, "topology", value, ".+")
assert hf.buddy2hash(tester) == _hash

with pytest.raises(ValueError) as err:
Sb.amend_metadata(tester, "topology", "foo_bar", ".*")
Sb.amend_metadata(tester, "topology", "foo_bar", ".+")

assert "Topology values are limited to ['', 'linear', 'circular']" in str(err)


def test_amend_metadata_str_attr(sb_resources, hf, monkeypatch):
monkeypatch.setattr(br, "clean_regex", lambda regex: [regex])

def test_amend_metadata_str_attr_data_file_division(sb_resources, hf):
"""
There are limited number of values that biopython will accept
["PRI", "ROD", "MAM", "VRT", "INV", "PLN", "BCT",
"VRL", "PHG", "SYN", "UNA", "EST", "PAT", "STS",
"GSS", "HTG", "HTC", "ENV", "CON"]
"""
"""
# data_file_division
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "data_file_division", "PRI", ".*")
tester = Sb.amend_metadata(tester, "data_file_division", "PRI", ".+")
assert hf.buddy2hash(tester) == "68cbefe01be215c373b75ee5cb4b0d4c"

tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "data_file_division", "FOO", ".*")
tester = Sb.amend_metadata(tester, "data_file_division", "FOO", ".+")
assert hf.buddy2hash(tester) == "6d767ae1bdda9ce23ce99cfae35a1a74"


def test_amend_metadata_str_attr_date(sb_resources, hf):
# date
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "date", "21-APR-2000", ".*")
tester = Sb.amend_metadata(tester, "date", "21-APR-2000", ".+")
assert hf.buddy2hash(tester) == "3695432066ca4c61727aa139d40a7b8e"

tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "date", "FOO", ".*")
tester = Sb.amend_metadata(tester, "date", "FOO", ".+")
assert hf.buddy2hash(tester) == "28b8f6425b92755f2936883837b1c452"


def test_amend_metadata_str_attr_source(sb_resources, hf):
# source
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "source", "Mnemiopsis", ".*")
assert hf.buddy2hash(tester) == "ff0d55dc060e28e47440a07414ea62bf"


def test_amend_metadata_str_attr_organism(sb_resources, hf):
# organism
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "organism", "Foo", "leidyi")
assert hf.buddy2hash(tester) == "0494f26e437928e8af96ba6e7cbfb7cf"


def test_amend_metadata_str_attr_comment(sb_resources, hf):
# comment
tester = sb_resources.get_one("p g")
structured_comment = OrderedDict()
Expand Down Expand Up @@ -116,15 +122,15 @@ def test_amend_metadata_list_attr(sb_resources, hf, monkeypatch):
# taxonomy
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "taxonomy", "Eukaryota Opisthokonta Metazoa Eumetazoa Ctenophora Tentaculata"
" Lobata Bolinopsidae Mnemiopsis", ".*")
" Lobata Bolinopsidae Mnemiopsis", ".+")
assert hf.buddy2hash(tester) == "cdc30e7ec65c525bac898bbfaa75a0b7"

tester = Sb.amend_metadata(tester, "taxonomy", "FooBar", "Eukaryota")
assert hf.buddy2hash(tester) == "bb80f495ade4e8a8f62253642f350d22"

# keywords
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "keywords", "Something Else", ".*")
tester = Sb.amend_metadata(tester, "keywords", "Something Else", ".+")
assert hf.buddy2hash(tester) == "bda9a1405d954aa2542d9017ba5c0796"

tester.records[0].annotations["keywords"] = []
Expand All @@ -135,7 +141,7 @@ def test_amend_metadata_list_attr(sb_resources, hf, monkeypatch):
def test_amend_metadata_dbxrefs(sb_resources, hf, monkeypatch):
monkeypatch.setattr(br, "clean_regex", lambda regex: [regex])
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "dbxrefs", "Project:1234 Project:4321", ".*")
tester = Sb.amend_metadata(tester, "dbxrefs", "Project:1234 Project:4321", ".+")
assert hf.buddy2hash(tester) == "342286427f1dc495131610a9c02587cf"

tester.records[0].dbxrefs = []
Expand All @@ -146,15 +152,15 @@ def test_amend_metadata_dbxrefs(sb_resources, hf, monkeypatch):
def test_amend_metadata_version(sb_resources, hf, monkeypatch):
monkeypatch.setattr(br, "clean_regex", lambda regex: [regex])
tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "version", 5, ".*")
tester = Sb.amend_metadata(tester, "version", 5, ".+")
assert hf.buddy2hash(tester) == "d83c18c44529700eaa3ab32da3ec8d08"

tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "sequence_version", 5, ".*")
tester = Sb.amend_metadata(tester, "sequence_version", 5, ".+")
assert hf.buddy2hash(tester) == "d83c18c44529700eaa3ab32da3ec8d08"

tester = sb_resources.get_one("p g")
tester = Sb.amend_metadata(tester, "sequence_version", "foo", ".*")
tester = Sb.amend_metadata(tester, "sequence_version", "foo", ".+")
assert hf.buddy2hash(tester) == "0a8462e72f64fcd22544bb153b51b2b6"


Expand All @@ -164,7 +170,7 @@ def test_amend_metadata_arb_attr(sb_resources, hf, monkeypatch):
tester = Sb.amend_metadata(tester, "id", "Hech", "Mle")
assert hf.buddy2hash(tester) == "c0a9461be6cb3b7e6ad76200f009c4ab"

tester = Sb.amend_metadata(tester, "foobar", "Some stuff", ".*")
tester = Sb.amend_metadata(tester, "foobar", "Some stuff", ".+")
assert tester.records[0].foobar == "Some stuff"


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