def test_extract_custom_form_info_samples_not_ascii_characters(self):
template_path = (os.path.join(
os.path.split(__file__)[0],
"extract_custom_form_info_samples_not_ascii_characters.xml"))
template_path
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3209463", req_soup)
samples = form.samples
for sample in samples:
assert re.search(r"[^0-9A-Za-z-]", sample.con.name) is None
def test_extract_from_grid_tgm_data(self):
template_path = (os.path.join(
os.path.split(__file__)[0], "extract_from_grid_tgm_data.xml"))
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3904550", req_soup)
samples = form.samples
assert len(samples) == 19
for sample in samples:
assert "TGM Assay List" in sample.udf_to_value.keys()
assert sample.udf_to_value["TGM Assay List"][-1] != ','
def test_extract_from_grid_lvs_data(self):
template_path = (os.path.join(
os.path.split(__file__)[0], "extract_from_grid_lvs_primers.xml"))
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3923775", req_soup)
samples = form.samples
assert len(samples) == 7
for sample in samples:
assert "Primer" in sample.udf_to_value.keys()
assert '*' not in sample.udf_to_value["Primer"]
assert len(sample.udf_to_value["Primer"].split(',')) == 3
def test_extract_from_grid_eight_strip_too_many_tubes(self):
template_path = (os.path.join(
os.path.split(__file__)[0],
"extract_from_grid_con_type_eight_strip_too_many_tubes.xml"))
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3220469", req_soup)
samples = form.samples
sample_names = ["A3", "B13", "H11", "F8", "G2", "C3", "C5", "E6"]
assert len(samples) == len(sample_names)
for sample in samples:
assert sample.name in sample_names
assert re.search(r"2220920-[1-8]", sample.con.name) is not None
assert sample.con.con_type == "8-well strip"
assert re.search(r"A:[1-8]", sample.location) is not None
assert "Volume (uL)" in sample.udf_to_value.keys()
def test_extract_custom_form_info_samples_con_type_tube(self):
template_path = (os.path.join(
os.path.split(__file__)[0],
"extract_custom_form_info_samples_con_type_tube.xml"))
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
samples = ua_ilab_tools.extract_custom_form_info(
"0", "3271720", req_soup).samples
sample_names = [
"UA2001111", "UA2002222", "UA2003333", "UA2004444", "UA2005555"
]
assert len(samples) == len(sample_names)
for sample in samples:
assert sample.name in sample_names
assert sample.con.name in sample_names
assert sample.con.con_type == "Tube"
assert sample.location == "1:1"
assert "TGM Assay List" in sample.udf_to_value.keys()
def test_extract_from_grid_container_name_in_form(self):
template_path = (os.path.join(
os.path.split(__file__)[0],
"extract_from_grid_container_name_in_form.xml"))
with open(template_path) as file:
form = file.read()
form_soup = BeautifulSoup(form, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3275577",
form_soup)
samples = form.samples
sample_names = [sample.name for sample in samples]
assert "Empty" not in sample_names
assert len(samples) == 67
assert form.field_to_values["container_name"] == "Test-Plate-Name"
for sample in samples:
assert "AF" in sample.name
assert sample.con.name == "Test-Plate-Name"
assert sample.con.con_type == "96 well plate"
assert re.search(r"[A-H]:[0-9]{1,2}", sample.location) is not None
assert "Dilution" in sample.udf_to_value.keys()
def test_extract_from_grid_container_name_in_grid(self):
template_path = (os.path.join(
os.path.split(__file__)[0],
"extract_from_grid_container_name_in_grid.xml"))
with open(template_path) as file:
req = file.read()
req_soup = BeautifulSoup(req, "xml")
form = ua_ilab_tools.extract_custom_form_info("0", "3256202", req_soup)
samples = form.samples
sample_names = [sample.name for sample in samples]
container_names = [
"Plate-1", "Plate-2", "Plate-3", "Plate-4", "Plate-5", "Plate-6"
]
assert "Empty" not in sample_names
assert len(samples) == 540
assert "Dilution_each_sample" in form.field_to_values.keys()
for sample in samples:
assert '-' in sample.name
assert sample.con.name in container_names
assert sample.con.con_type == "96 well plate"
assert re.search(r"[A-H]:[0-9]{1,2}", sample.location) is not None
assert "Dilution" in sample.udf_to_value.keys()
def harvest_form(prj_data):
"""Get the correct form from iLab.
Arguments:
prj_data (dataclass):
Object that holds important information for transferring projects.
Returns:
custom_form (api_types.CustomForm):
Object that is populated with all of the information gathered
from the iLab form.
None if nothing is found."""
try:
forms_uri_to_soup = ILAB_TOOLS.get_custom_forms(prj_data.req_id)
except ua_ilab_tools.IlabConfigError:
# Requests without forms are Consultation Requests or Custom Projects
# that have not yet had a business form attached, and so the request
# should just be skipped.
return None
except requests.exceptions.HTTPError as error:
# Skip requests that were made with different core ids.
return None
# Make sure the current_form is zeroed out between request id's.
else:
current_form = None
# Get all of the custom forms for the current req_id.
for form_uri, form_soup in forms_uri_to_soup.items():
# Get the form info (including the sample info) before you post
# anything, as this is where most of the errors are thrown.
try:
current_form = ua_ilab_tools.extract_custom_form_info(
prj_data.req_id, form_uri, form_soup)
except TypeError as grid_error:
grid_error = str(grid_error).replace('"', '\'')
LOGGER.error({
"template":
os.path.join("project_transfer", "error.html"),
"content":
(f"The request {prj_data.current_record} has been filled"
f" out incorrectly. The error message is:\n{grid_error}")
})
break
except ValueError as form_error:
LOGGER.error({
"template":
os.path.join("project_transfer", "error.html"),
"content":
form_error
})
continue
# Add the request_type to the form that was just added.
current_form.request_type = prj_data.request_type
# If the request has a non-queryable (NQ) form or Request a Quote A
# Form, skip it.
if ("NQ" in current_form.name.strip()
or "REQUEST A QUOTE" in current_form.name.strip().upper()
or "DATA ANALYSIS INFO" in current_form.name.strip().upper()):
current_form = None
continue
if not current_form.samples:
LOGGER.error({
"template":
os.path.join("project_transfer", "error.html"),
"content": (f"The {current_form.name} form in request"
f" {current_form.req_id} has no samples.")
})
return current_form