def test_read_metadata_query(self, tmpdir, prepare_file, query,
expected_strains):
prepare_file("""
strain,location,quality
strainA,colorado,good
strainB,colorado,bad
strainC,nevada,good
""")
records, columns = MetadataFile(f"{tmpdir}/metadata.txt", query).read()
assert list(records.keys()) == expected_strains
assert list(columns) == ["strain", "location", "quality"]
def test_read_metadata_no_strain_or_name(self, tmpdir, prepare_file):
prepare_file("""
location,quality
colorado,good
nevada,good
""")
with pytest.raises(ValueError, match="does not contain"):
MetadataFile(f"{tmpdir}/metadata.txt", None).read()
def test_read_metadata_strain_and_name(self, tmpdir, prepare_file):
prepare_file("""
strain,name,quality
strainA,nameA,good
strainB,nameB,good
""")
assert MetadataFile(f"{tmpdir}/metadata.txt",
None).find_key_type() == "strain"
def test_metadata_strain_type(self, tmpdir, prepare_file):
prepare_file("""
strain\tlocation
1\tWashington
2\tOregon
""")
records, columns = MetadataFile(f"{tmpdir}/metadata.txt").read()
assert "1" in records
def test_read_metadata_duplicate_name(self, tmpdir, prepare_file):
prepare_file("""
name,quality
nameA,good
nameA,good
""")
with pytest.raises(ValueError,
match="Duplicated name in metadata: nameA"):
MetadataFile(f"{tmpdir}/metadata.txt", None).read()
def test_read_metadata_duplicate_strain(self, tmpdir, prepare_file):
prepare_file("""
strain,quality
strainA,good
strainA,good
""")
with pytest.raises(ValueError,
match="Duplicated strain in metadata: strainA"):
MetadataFile(f"{tmpdir}/metadata.txt", None).read()
def test_read_metadata_bad_query(self, tmpdir, prepare_file):
prepare_file("""
strain,location,quality
strainA,colorado,good
strainB,colorado,bad
strainC,nevada,good
""")
with pytest.raises(ValueError, match="Error applying pandas query"):
MetadataFile(f"{tmpdir}/metadata.txt", "age=5").read()
def test_metadata_delimiter_autodetect(self, tmpdir, prepare_file):
prepare_file("""
strain\tlocation\tquality
strainA\tcolorado\tgood
strainB\tnevada\tgood
""")
records, columns = MetadataFile(f"{tmpdir}/metadata.txt").read()
assert records == {
"strainA": {
"strain": "strainA",
"location": "colorado",
"quality": "good"
},
"strainB": {
"strain": "strainB",
"location": "nevada",
"quality": "good"
},
}
assert list(columns) == ["strain", "location", "quality"]
def test_read_metadata_file_not_found(self, fname):
with pytest.raises(FileNotFoundError):
MetadataFile(fname, None).read()
def read_metadata(fname, query=None):
return MetadataFile(fname, query).read()
def read_metadata(fname, query=None, as_data_frame=False):
return MetadataFile(fname, query, as_data_frame).read()