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_create_enclosures():
encl_name = "example_enclosure"
df = pd.DataFrame({"Enclosure": encl_name}, index=[0])
create_enclosures(df)
test_enclosure = Enclosure.objects.get(name=encl_name)
assert test_enclosure is not None
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_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