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in read_metadata update pandas series object name to reflect name col… #564

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merged 2 commits into from
Jun 26, 2020
Merged

in read_metadata update pandas series object name to reflect name col… #564

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cfa555b
in read_metadata update pandas series object name to reflect name col…
shinespiked Jun 16, 2020
ab9cc74
Merge branch 'master' into FixDuplicateName
shinespiked Jun 23, 2020
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1 change: 1 addition & 0 deletions augur/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@ def read_metadata(fname, query=None):
raise ValueError("Duplicate strain '{}'".format(val.strain))
meta_dict[val.strain] = val.to_dict()
elif hasattr(val, "name"):
val = val.rename(val["name"])
if val.name in meta_dict:
raise ValueError("Duplicate name '{}'".format(val.name))
meta_dict[val.name] = val.to_dict()
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58 changes: 57 additions & 1 deletion tests/test_utils.py
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Expand Up @@ -101,6 +101,24 @@ def test_read_mask_file_drm_file(self, tmpdir):
fh.write("\n".join(drm_lines))
assert utils.read_mask_file(drm_file) == expected_sites

def test_read_metadata_no_filename(self):
expected_result = {}, []
assert utils.read_metadata('') == expected_result

def test_read_metadata_bad_filename(self, tmpdir):
bad_filename = "incorrect_path.tsv"
expected_result = {}, []

meta_fn = str(tmpdir / "metadata.tsv")
meta_lines = ["strain\tlocation\tquality",
"c_good\tcolorado\tgood",
"n_bad\tnevada\tbad",]
with open(meta_fn, "w") as fh:
fh.write("\n".join(meta_lines))

utils.read_metadata(bad_filename, query='quality=="good" & location=="colorado"')
assert utils.read_metadata('') == expected_result

def test_read_metadata_with_good_query(self, tmpdir):
meta_fn = str(tmpdir / "metadata.tsv")
meta_lines = ["strain\tlocation\tquality",
Expand All @@ -121,4 +139,42 @@ def test_read_metadata_bad_query(self, tmpdir):
with open(meta_fn, "w") as fh:
fh.write("\n".join(meta_lines))
with pytest.raises(SystemExit):
utils.read_metadata(meta_fn, query='badcol=="goodval"')
utils.read_metadata(meta_fn, query='badcol=="goodval"')
def test_read_metadata_duplicate_strain(self, tmpdir):
meta_fn = str(tmpdir / "metadata.tsv")
meta_lines = ["strain\tlocation\tquality",
"c_good\tcolorado\tgood",
"c_bad\tcolorado\tbad",
"c_bad\tcolorado\tbad",
"n_good\tnevada\tgood"]
with open(meta_fn, "w") as fh:
fh.write("\n".join(meta_lines))
with pytest.raises(ValueError):
utils.read_metadata(meta_fn, query='location=="colorado"')

def test_read_metadata_duplicate_name(self, tmpdir):
meta_fn = str(tmpdir / "metadata.tsv")
meta_lines = ["name\tlocation\tquality",
"c_good\tcolorado\tgood",
"c_bad\tcolorado\tbad",
"c_bad\tcolorado\tbad",
"n_good\tnevada\tgood"]
with open(meta_fn, "w") as fh:
fh.write("\n".join(meta_lines))

with pytest.raises(ValueError):
utils.read_metadata(meta_fn)

def test_read_metadata_no_strain_or_name(self, tmpdir):
expected_result = {}, []

meta_fn = str(tmpdir / "metadata.tsv")
meta_lines = ["location\tquality",
"colorado\tgood",
"colorado\tbad",
"colorado\tbad",
"nevada\tgood"]
with open(meta_fn, "w") as fh:
fh.write("\n".join(meta_lines))

assert utils.read_metadata('') == expected_result