def test_infinite_coord(self):
with open("test/resources/infinite_coord.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(custom_message.exception.message,
"z in row 2 is not finite")
def test_too_many_columns(self):
with open("test/resources/too_many_columns.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(
custom_message.exception.message,
"Incorrect number of columns (15) in row 2",
)
def test_invalid_version(self):
with open("test/resources/invalid_version.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(
custom_message.exception.message,
"Markups fiducial file version 3.5 too low",
)
def test_incorrect_desc(self):
with open("test/resources/incorrect_desc.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(
custom_message.exception.message,
"Row label 2 does not match row description dummy",
)
def test_invalid_content(self):
with open("test/resources/invalid_content.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(
custom_message.exception.message,
"Missing or invalid header in fiducial file",
)
with open("test/resources/invalid_content_valid_header.fcsv",
"r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(custom_message.exception.message,
"Row has no value label")
def test_valid_fcsv_flip(self):
with open("test/resources/valid_flip.fcsv", "r") as fcsv:
fcsv_afids = model.csv_to_afids(fcsv.read())
self.assertTrue(fcsv_afids.validate())
self.assertEqual(
fcsv_afids.AC_x,
-0.07077182344203692,
)
self.assertEqual(fcsv_afids.AC_y, 0.2548674381652525)
def validate():
"""Present the validator form, or validate an AFIDs set."""
form = Average(request.form)
result = ""
distances = []
labels = []
template_afids = None
# Set all dropdown choices
form_choices = os.listdir(current_app.config["AFIDS_DIR"])
form_choices = [choice.capitalize() for choice in form_choices]
form_choices.sort()
# Get time stamp
timestamp = str(
datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S %Z")
)
if not (request.method == "POST" and request.files):
return render_template(
"validator.html",
form=form,
form_choices=form_choices,
result=result,
template_afids=template_afids,
index=[],
labels=labels,
distances=distances,
)
upload = request.files[form.filename.name]
upload_ext, file_check = allowed_file(upload.filename)
if not (upload and file_check):
result = f"Invalid file: extension not allowed ({timestamp})"
return render_template(
"validator.html",
form=form,
form_choices=form_choices,
result=result,
template_afids=template_afids,
index=[],
labels=labels,
distances=distances,
)
try:
if upload_ext in current_app.config["ALLOWED_EXTENSIONS"][:2]:
user_afids = csv_to_afids(upload.read().decode("utf-8"))
else:
user_afids = json_to_afids(upload.read().decode("utf-8"))
except InvalidFileError as err:
result = f"Invalid file: {err.message} ({timestamp})"
return render_template(
"validator.html",
form=form,
form_choices=form_choices,
result=result,
template_afids=template_afids,
index=[],
labels=labels,
distances=distances,
current_user=current_user,
)
if user_afids.validate():
result = f"Valid file ({timestamp})"
else:
result = (
f"Invalid AFIDs set, please double check your file ({timestamp})"
)
fid_species = request.form["fid_species"]
fid_species = fid_species.lower()
fid_template = request.form["fid_template"]
if fid_template == "Validate file structure":
return render_template(
"validator.html",
form=form,
form_choices=form_choices,
result=result,
template_afids=template_afids,
index=[],
labels=labels,
distances=distances,
current_user=current_user,
)
result = f"{result}<br>{fid_template} selected"
# Need to pull from correct folder when more templates are added
template_file_path = f"{current_app.config['AFIDS_DIR']}/{fid_species.lower()}/tpl-{fid_template}_afids.fcsv"
with open(template_file_path, "r") as template_file:
template_afids = csv_to_afids(template_file.read())
if request.form.get("db_checkbox"):
if current_user.is_authenticated:
user_afids.afids_user_id = current_user.id
db.session.add(user_afids)
db.session.commit()
print("Fiducial set added")
else:
print("DB option unchecked, user data not saved")
for desc in EXPECTED_DESCS:
distances.append(
"{:.5f}".format(
np.linalg.norm(
np.array(
[
getattr(
template_afids, desc[-1]
).__composite_values__()
]
)
- np.array(
[getattr(user_afids, desc[-1]).__composite_values__()]
)
)
)
)
labels.append(desc[-1])
return render_template(
"validator.html",
form=form,
form_choices=form_choices,
result=result,
template_afids=template_afids,
index=list(range(len(EXPECTED_DESCS))),
labels=labels,
distances=distances,
timestamp=timestamp,
scatter_html=generate_3d_scatter(template_afids, user_afids),
histogram_html=generate_histogram(template_afids, user_afids),
current_user=current_user,
)
def test_too_many_rows(self):
with open("test/resources/too_many_rows.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(custom_message.exception.message, "Too many rows")
def test_valid_nhp(self):
with open("test/resources/valid_nhp.fcsv", "r") as fcsv:
self.assertTrue(model.csv_to_afids(fcsv.read()).validate())
def test_valid_fcsv(self):
with open("test/resources/valid.fcsv", "r") as fcsv:
afids = model.csv_to_afids(fcsv.read())
self.assertTrue(afids.validate())
def test_missing_row(self):
with open("test/resources/missing_row_10.fcsv", "r") as fcsv:
with self.assertRaises(model.InvalidFileError) as custom_message:
model.csv_to_afids(fcsv.read())
self.assertEqual(custom_message.exception.message, "Too few rows")