def test_group_becomes_individuals():
"""Tests that when a group's numbers go to 1 it transforms into an "animal" from a "group" """
df = read_xlsx_data(INPUT_EXAMPLE)
create_enclosures(df)
create_species(df)
animals, groups = find_animals_groups(df)
create_animals(animals)
create_groups(groups)
accession = "111112"
gp = Group.objects.get(accession_number=accession)
assert gp.population_total > 1
# modify the df to have only one population
df.at[df[df["Accession"] == accession].index[0], "Population _Female"] = 0
df.at[df[df["Accession"] == accession].index[0], "Population _Unknown"] = 1
# get_changesets on that dataframe
changeset = get_changesets(df)
# assert we are adding an individual
animal_changes_accession = [
ch_a["object_kwargs"]["Accession"] for ch_a in changeset["animals"]
if ch_a["action"] == "add"
]
assert accession in animal_changes_accession
# assert we are removing the group
group_changes_accession = [
ch_a["object_kwargs"]["accession_number"]
for ch_a in changeset["groups"] if ch_a["action"] == "del"
]
assert accession in group_changes_accession
def test_get_changesets():
# test empty df -- raises an error
empty_df = pd.DataFrame([{}])
with pytest.raises(KeyError):
get_changesets(empty_df)
# test that we get the changeset back as we think we should given the test data
df = read_xlsx_data(INPUT_EXAMPLE)
ch_s = get_changesets(df)
assert ch_s["enclosures"] == ["enc1"]
anim_add_accession = [
ch_a["object_kwargs"]["Accession"] for ch_a in ch_s["animals"]
if ch_a["action"] == "add"
]
animals_acc = [
"111111",
"111113",
"111114",
"111115",
]
assert sorted(anim_add_accession) == sorted(animals_acc)
gp_add_accession = [
ch_a["object_kwargs"]["Accession"] for ch_a in ch_s["groups"]
if ch_a["action"] == "add"
]
# only one group
assert ["111112"] == gp_add_accession
def test_create_species():
df = read_xlsx_data(INPUT_EXAMPLE)
create_species(df)
for common_name in df["Common"]:
sp = Species.objects.get(common_name=common_name)
assert sp is not None
def test_ingest_changesets():
"""Test example ingest from df"""
df = read_xlsx_data(INPUT_EXAMPLE)
ch_s = get_changesets(df)
ingest_changesets(ch_s)
accession_nums = df["Accession"]
for accession_num in accession_nums:
anim = Animal.objects.filter(accession_number=accession_num)
groups = Group.objects.filter(accession_number=accession_num)
assert len(anim) + len(groups) == 1
# only groups
df = read_xlsx_data(ONLY_GROUPS_EXAMPLE)
ch_s = get_changesets(df)
ingest_changesets(ch_s)
accession_nums = df["Accession"]
for accession_num in accession_nums:
# this would raise an exception if it didn't find one
Group.objects.get(accession_number=accession_num)
# only animals
df = read_xlsx_data(ONLY_ANIMALS_EXAMPLE)
ch_s = get_changesets(df)
ingest_changesets(ch_s)
accession_nums = df["Accession"]
for accession_num in accession_nums:
# this would raise an exception if it didn't find one
Animal.objects.get(accession_number=accession_num)
# empty: making sure we don't raise any exceptions
df = read_xlsx_data(INPUT_EXAMPLE)
df_empty = df[0:0]
ch_s = get_changesets(df_empty)
ingest_changesets(ch_s)
def main():
parser = argparse.ArgumentParser(description="Parse csv file for animals")
parser.add_argument("csvfile")
args = parser.parse_args()
df = read_xlsx_data(args.csvfile)
create_enclosures(df)
create_species(df)
animals, groups = find_animals_groups(df)
create_animals(animals)
create_groups(groups)
print(f"Processed {args.csvfile}")
def test_read_xlsx_data():
with pytest.raises(ExcelUploadError, match="No data found in file"):
read_xlsx_data(INPUT_EMPTY)
with pytest.raises(
ExcelUploadError,
match="Not all columns found in file",
):
read_xlsx_data(INPUT_WRONG_COL)
with pytest.raises(ExcelUploadError, match="Unable to read file"):
read_xlsx_data(INPUT_MALFORMED)
df = read_xlsx_data(INPUT_EXAMPLE)
assert df.shape[0] == 5
def test_validate_input():
df = read_xlsx_data(INPUT_ACCESSIONS_BAD)
with pytest.raises(
ExcelUploadError,
match="Accession numbers should only have 6 characters"):
validate_accession_numbers(df)
df_simple_bad = pd.DataFrame({"Accession": "12345"}, index=[0])
with pytest.raises(
ExcelUploadError,
match="Accession numbers should only have 6 characters"):
validate_accession_numbers(df_simple_bad)
df_simple_good = pd.DataFrame([{"Accession": "654321"}])
df_validated = validate_accession_numbers(df_simple_good)
assert df_validated is not None
assert df_validated.loc[0, "Accession"] == "654321"
def test_create_groups():
df = read_xlsx_data(INPUT_EXAMPLE)
create_enclosures(df)
create_species(df)
with pytest.raises(ValueError,
match="Cannot create groups. Not all have a pop. > 1"):
create_groups(df)
animals, groups = find_animals_groups(df)
create_groups(groups)
for acc_num in groups["Accession"]:
g = Group.objects.get(accession_number=acc_num)
assert g.population_total > 1
for acc_num in animals["Accession"]:
with pytest.raises(ObjectDoesNotExist):
Group.objects.get(accession_number=acc_num)
def test_create_animals():
df = read_xlsx_data(INPUT_EXAMPLE)
# need to first create species, enclosures
create_enclosures(df)
create_species(df)
with pytest.raises(
ValueError,
match="Cannot create individuals. Not all have a pop. of 1"):
create_animals(df)
animals, groups = find_animals_groups(df)
create_animals(animals)
for acc_num in animals["Accession"]:
Animal.objects.get(accession_number=acc_num)
for acc_num in groups["Accession"]:
with pytest.raises(ObjectDoesNotExist):
Animal.objects.get(accession_number=acc_num)
def test_individual_becomes_group():
"""Tests that when an individual's numbers go > 1 it transforms into a "group" from an "animal" """
df = read_xlsx_data(INPUT_EXAMPLE)
create_enclosures(df)
create_species(df)
animals, groups = find_animals_groups(df)
create_animals(animals)
create_groups(groups)
accession = "111111"
# this would raise an not found exception if it was not present
Animal.objects.get(accession_number=accession)
# modify the df to have > one population
df.at[df[df["Accession"] == accession].index[0], "Population _Female"] = 1
df.at[df[df["Accession"] == accession].index[0], "Population _Unknown"] = 1
# get_changesets on that dataframe
changeset = get_changesets(df)
# assert we are adding a group
add_accession = [
ch_a["object_kwargs"]["Accession"] for ch_a in changeset["groups"]
if ch_a["action"] == "add"
]
assert accession in add_accession
# assert we are removing the animal
del_accession = [
ch_a["object_kwargs"]["accession_number"]
for ch_a in changeset["animals"] if ch_a["action"] == "del"
]
assert accession in del_accession