def test_create_containers(self):
current_time = str(datetime.now())
prj = api_types.Project(f"Project_TEST_{current_time}", DEFAULT_RES,
str(datetime.today().date()), [], "")
custom_form = api_types.CustomForm(f"TEST_{current_time}", "0000",
"0000")
current_time = []
sample_list = []
for x in range(5):
current_time.append(datetime.now().__str__())
time.sleep(.1)
sample = api_types.Sample("Test_{}".format(current_time[x]))
sample.con = api_types.Container("Test_{}".format(current_time[x]),
"96 well plate", "", "")
sample_list.append(sample)
custom_form.samples = sample_list
con_uris = LIMS_UTIL.create_containers(0000, prj, custom_form)
assert con_uris is not None
cons_soup = BeautifulSoup(LIMS_API.tools.api.get(con_uris), "xml")
cons_soup = cons_soup.find_all("con:container")
con_names = [con_soup.find("name") for con_soup in cons_soup]
for i, con_name in enumerate(con_names):
assert con_name.text.split("_")[-1] in current_time
def extract_project_info(req_soup, full_name=False):
"""Extract the relevant project info from a request.
Arguments:
req_soup (BS4 soup object):
The soup of the request.
full_name (boolean):
Whether or not to capture the entire project name or just the last
hyphenated element.
Returns:
prj_info (Project):
The required info to post a project.
"""
if full_name:
prj_name = req_soup.find("name").string
else:
prj_name = req_soup.find("name").string.split('-')[-1]
res_name = req_soup.find("owner").find("name").string
email = req_soup.find("owner").find("email").string
# NOTE: Change this line to your own institution's email domain.
if "email.arizona.edu" in email:
res_lab = "internal"
else:
res_lab = "external"
# Replace all not ascii chars with ascii ones, and any symbols with '-'.
prj_res = api_types.Researcher(
extract_custom_forms._sanitize_text(res_name.split()[0]),
extract_custom_forms._sanitize_text(res_name.split()[-1]),
extract_custom_forms._sanitize_text(res_lab), email, "")
prj_info = api_types.Project(prj_name, prj_res)
return prj_info
def test_create_project_not_in_system(self):
current_time = str(datetime.now())
prj = api_types.Project(f"Project_TEST_{current_time}", DEFAULT_RES,
str(datetime.today().date()), [], "")
prj_uri = LIMS_UTIL.create_project(0000, prj)
assert prj_uri != ""
prj_soup = BeautifulSoup(LIMS_API.tools.api.get(prj_uri), "xml")
prj_soup = prj_soup.find("prj:project")
assert current_time in prj_soup.find("name").text
def test_create_researcher_not_in_system(self):
current_time = str(datetime.now())
res = api_types.Researcher(f"Researcher_TEST_{current_time}",
"POST_TEST", "internal",
"*****@*****.**", "")
prj = api_types.Project(f"Project_TEST_{current_time}", res,
str(datetime.today().date()), [], "")
res_uri = LIMS_UTIL.create_researcher(0000, prj)
assert res_uri is not None
res_soup = BeautifulSoup(LIMS_API.tools.api.get(res_uri), "xml")
res_soup = res_soup.find("res:researcher")
assert current_time in res_soup.find("first-name").text
def _post_project(prj=None):
"""Method that will post a project and return an api_types.Project."""
template_path = (os.path.join(
os.path.split(__file__)[0], "post_project_template.xml"))
with open(template_path, 'r') as file:
template = Template(file.read())
response_xml = template.render(
name=f"Project_TEST_{datetime.now()}",
open_date=str(datetime.today().date()),
res_uri=f"{LIMS_API.tools.api.host}researchers/1")
prj_response = LIMS_API.tools.api.post(
f"{LIMS_API.tools.api.host}projects", response_xml)
prj_response_soup = BeautifulSoup(prj_response, "xml").find("prj:project")
prj = api_types.Project(prj_response_soup.find("name"), DEFAULT_RES,
datetime.today().date(), [],
prj_response_soup["uri"])
return prj
def test_post_project(self):
prj = api_types.Project(f"Project_TEST_{datetime.now()}", DEFAULT_RES,
str(datetime.today().date()), [], "")
result_uri = LIMS_API.post_project(prj)
assert result_uri is not None
def test_post_project_already_in_system(self):
prj = api_types.Project("Already_in_system", DEFAULT_RES,
str(datetime.today().date()), [], "")
LIMS_API.post_project(prj)
LIMS_API.post_project(prj)
