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_post_researcher(self):
current_time = str(datetime.now())
res = api_types.Researcher(f"Researcher_TEST_{current_time}",
"POST_TEST", "internal",
"*****@*****.**", "")
result_uri = LIMS_API.post_researcher(res)
res_soup = BeautifulSoup(LIMS_API.tools.api.get(result_uri), "xml")
res_soup = res_soup.find("res:researcher")
assert result_uri is not None
assert current_time in res_soup.find("first-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 test_get_researcher_uri_with_one_and_two_existing_researchers(self):
current_time = datetime.now()
res = api_types.Researcher(f"Test-{current_time}", "Last Name",
f"{LIMS_API.tools.api.host}labs/1",
"*****@*****.**", "")
uri_answer = BeautifulSoup(_post_researcher(current_time), "xml")
uri_answer = uri_answer.find("res:researcher")["uri"]
assert len(LIMS_API.get_researcher_uri(res)) == 1
assert LIMS_API.get_researcher_uri(res) == [uri_answer]
uri_answer = BeautifulSoup(_post_researcher(current_time), "xml")
uri_answer = uri_answer.find("res:researcher")["uri"]
assert len(LIMS_API.get_researcher_uri(res)) == 2
def _post_researcher(current_time, res=None):
"""Method that will post a researcher and return a request."""
if res is None:
res = api_types.Researcher(f"Test-{current_time}", "Last Name",
f"{LIMS_API.tools.api.host}labs/1",
"*****@*****.**", "")
template_path = (os.path.join(
os.path.split(__file__)[0], "post_researcher_template.xml"))
with open(template_path, 'r') as file:
template = Template(file.read())
response_xml = template.render(first_name=res.first_name,
last_name=res.last_name,
lab_uri=res.lab_type,
email=res.email)
url = f"{LIMS_API.tools.api.host}researchers"
return LIMS_API.tools.api.post(url, response_xml)
def setUpModule():
creds_path = (os.path.join(
os.path.split(__file__)[0], "lims_dev_token.json"))
with open(creds_path, 'r') as file:
creds = json.load(file)
global LIMS_API
global LIMS_UTIL
global DEFAULT_RES
LIMS_API = project_lims_tools.ProjectLimsApi(host=creds["host"],
username=creds["username"],
password=creds["password"])
LIMS_UTIL = project_lims_tools.LimsUtility(host=creds["host"],
username=creds["username"],
password=creds["password"])
DEFAULT_RES = api_types.Researcher(
"System", "Administrator", "internal", "",
f"{LIMS_API.tools.api.host}researchers/1")
assert LIMS_API is not None
assert LIMS_UTIL is not None
def test_post_researcher_already_in_system(self):
res = api_types.Researcher("Already_In", "System", "internal",
"*****@*****.**", "")
LIMS_API.post_researcher(res)
LIMS_API.post_researcher(res)
def test_get_researcher_uri_with_non_existing_researcher(self):
res = api_types.Researcher("TEST_NOT", "_PRESENT", "internal",
"*****@*****.**", "")
assert len(LIMS_API.get_researcher_uri(res)) == 0