diff --git a/buddysuite/tests/test_seqbuddy/test_sb_api.py b/buddysuite/tests/test_seqbuddy/test_sb_api.py index 2f35684..d195a89 100644 --- a/buddysuite/tests/test_seqbuddy/test_sb_api.py +++ b/buddysuite/tests/test_seqbuddy/test_sb_api.py @@ -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() @@ -116,7 +122,7 @@ 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") @@ -124,7 +130,7 @@ def test_amend_metadata_list_attr(sb_resources, hf, monkeypatch): # 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"] = [] @@ -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 = [] @@ -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" @@ -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"