def test_L_wrong_file01(self, tmpdir: py.path.local) -> None:
"A loggingconfig file containing a list should raise an error"
fname = str(tmpdir.join('/bla.yaml'))
data = [1, 2, 3, 4]
yamlutil.writeyamlfile(data, fname)
with pytest.raises(RuntimeError):
serverconfig.read_logging_config(fname)
def setup_class(cls) -> None:
lverb = True
if lverb:
print("SETUP CLASS {}".format(cls))
cls.faulty_session = FaultySession(TESTqai_url)
# --
cls.s = TrackerSession(TESTqai_url)
cls.s.login(TESTauth_uname, TESTauth_password)
if not cls.s.is_logged_in():
raise RuntimeError("login failed")
rcode, cls.reagent_list = cls.s.get_json(PATH_REAGENT_LIST_REAGENTS)
assert rcode == HTTP_OK, "called failed"
# get list of suppliers
rcode, cls.supplierlst = cls.s.get_json(PATH_REAGENT_LIST_SUPPLIERS)
assert rcode == HTTP_OK, "called failed"
if lverb:
yamlutil.writeyamlfile(cls.supplierlst, "./supplierlst.yaml")
# lets choose a supplier from the list. Choose the first name in the list.
cls.selected_supplier_dct = cls.supplierlst[0]
# retrieve the list of locations and choose some for testing.
rcode, cls.loclst = cls.s.get_json(PATH_LOCATION_LIST)
assert rcode == HTTP_OK, "called failed"
if lverb:
yamlutil.writeyamlfile(cls.loclst, "./loclist.yaml")
nameset = frozenset(['SPH\\604\\Research Fridge', 'SPH\\605\\Fridge'])
cls.testlocs = [d for d in cls.loclst if d['name'] in nameset]
if len(cls.testlocs) != len(nameset):
print("loclst '{}'".format(cls.loclst))
raise RuntimeError("error finding location names {}".format(nameset))
cls.establish_test_reagent()
def test_S_wrong_file02(self, tmpdir: py.path.local) -> None:
"A serverconfig file with missing keywords should raise an error."
fname = str(tmpdir.join('/bla.yaml'))
dd = dict(VERSION=99)
yamlutil.writeyamlfile(dd, fname)
with pytest.raises(RuntimeError):
serverconfig.read_server_config(fname)
def test_S_wrong_file01(self, tmpdir: py.path.local) -> None:
"A serverconfig file containing an unknown keyword should raise an error."
fname = str(tmpdir.join('/bla.yaml'))
dd = dict(FUNNY=99)
yamlutil.writeyamlfile(dd, fname)
with pytest.raises(RuntimeError):
serverconfig.read_server_config(fname)
def test_L_wrong_file03(self, tmpdir: py.path.local) -> None:
"A loggingconfig file containing a single dict should pass."
fname = str(tmpdir.join('/bla.yaml'))
data = dict(a=1, b=2, gg=77)
yamlutil.writeyamlfile(data, fname)
retval = serverconfig.read_logging_config(fname)
assert retval == data, "failed to read back data"
def test_S_wrong_file03(self, tmpdir: py.path.local) -> None:
"A serverconfig file containing a list should raise an error."
fname = str(tmpdir.join('/bla.yaml'))
dd = dict(a=1, b=2, gg=77)
data = [1, 2, 3, 4, dd]
yamlutil.writeyamlfile(data, fname)
with pytest.raises(RuntimeError):
serverconfig.read_server_config(fname)
def establish_test_reagent(cls):
lverb = True
# next, retrieve the list of users and choose our testing user.
rcode, userlst = cls.s.get_json(PATH_USER_LIST)
assert rcode == HTTP_OK, "called failed"
if lverb:
yamlutil.writeyamlfile(userlst, "./userlst.yaml")
cls.test_user_login = '******'
fndlst = [d for d in userlst if d['login'] == cls.test_user_login]
if len(fndlst) != 1:
print("userlst: {}".format(userlst))
raise RuntimeError('failed to find test user')
cls.test_user = fndlst[0]
test_user_id = cls.test_user['id']
cls.test_stat_lst = [
{'status': 'MADE',
'occurred': '1956-03-31T00:00:00Z',
'qcs_user_id': test_user_id},
{'status': 'EXPIRED',
'occurred': '1956-03-31T00:00:00Z',
'qcs_user_id': test_user_id},
{'status': 'RUO_EXPIRED',
'occurred': '1956-03-31T00:00:00Z',
'qcs_user_id': test_user_id}]
cls.test_reagent_item_lot_num = 'testlotAAA'
cls.test_reagent_item_notes = "A fictitious stock item for software testing purposes"
cls.test_itema_rfid = random_string(8)
# --- create or retrieve a test reagent
cls.test_reagent_name = "Whisky-Cola"
cls.test_reagent_catnum = '9999'
cls.test_reagent_id = None
# if we have a reagent of this name, lets use it
fndlst = [d for d in cls.reagent_list if d['name'] == cls.test_reagent_name]
if len(fndlst) > 0:
if lverb:
print("found a test reagent {}".format(fndlst[0]))
cls.test_reagent_id = fndlst[0]['id']
else:
pdct = {'basetype': 'stockchem',
'name': cls.test_reagent_name,
'category': 'Other Chemicals',
'notes': 'essential equipment',
'storage': '',
'needs_validation': None,
'expiry_time': 30,
'supplier': cls.selected_supplier_dct['name'],
'catalog_number': cls.test_reagent_catnum,
'date_msds_expires': 'never',
'msds_filename': ''}
rcode, postres = cls.s.post_json(TPATH_REAGENT_SAVE, data=pdct, retries=1)
if lverb:
print("POSTreagent save {}".format(postres))
assert rcode == HTTP_CREATED, "call failed"
cls.test_reagent_id = postres['id']
print("goot ID {}".format(cls.test_reagent_id))
assert cls.test_reagent_id is not None, "cannot get test reagent id"
def check_dump(self, fname: str, data: typing.Any, lverb: bool) -> None:
"""Dump some data, read it back and compare to the original"""
yamlutil.writeyamlfile(data, fname)
if lverb:
with open(fname, "r") as fi:
print("the file is '{}'".format(fi.read()))
# now read it back and compare
newnn = yamlutil.readyamlfile(fname)
print("new time is {}".format(newnn))
assert data == newnn, "saved and restored data is not equal!"
def test_reagent_list_and_show01(self):
"""Get information about a specific reagent"""
lverb = True
reagent_id = self.test_reagent_id
reagent_name = self.test_reagent_name
pdct = {'id': reagent_id}
rcode, reagent_show = self.s.get_json(PATH_REAGENT_SHOW, params=pdct)
assert rcode == HTTP_OK, "call failed"
if lverb:
print("showing reagent: '{}: '{}".format(reagent_id, reagent_name))
for dat, fn in [(reagent_show, "./reagentshow.yaml")]:
yamlutil.writeyamlfile(dat, fn)
def test_location_items(self):
"""Find all reagents at a specific location"""
lverb = False
selected_loc = self.testlocs[0]
loc_id = selected_loc['id']
loc_name = selected_loc['name']
query_dct = {'id': loc_id}
if lverb:
print("search for reagents at locid {}: '{}'".format(loc_id, loc_name))
rcode, rlst = self.s.get_json(PATH_REAGENT_LOCITEMS, params=query_dct)
assert rcode == HTTP_OK, "call failed"
if lverb:
print("goot {}".format(rlst))
for dat, fn in [(rlst, "./locitems.yaml")]:
yamlutil.writeyamlfile(dat, fn)
def test_S_wrong_values01(self, tmpdir: py.path.local) -> None:
"A serverconfig file with the wrong values should raise an error."
fname = str(tmpdir.join('/bla.yaml'))
dd = serverconfig.read_server_config(
get_testfilename('test02.OK.yaml'))
# remove keys that are not meant to be on file...
dnew = dict(
[tt for tt in dd.items() if tt[0] in serverconfig.known_set])
for k, brokenval in [('VERSION', serverconfig.VERSION_FLT + 0.1),
('RFID_REGION_CODE', 'blaa'), ('TIME_ZONE', '?'),
('TIME_ZONE', 'moon')]:
# with mock.patch.dict(dnew, values={k: brokenval}):
with mock.patch.dict(dnew, {k: brokenval}):
yamlutil.writeyamlfile(dnew, fname)
with pytest.raises(RuntimeError):
serverconfig.read_server_config(fname)
def test_qai_dump02(self):
ds = self.s.get_qai_dump()
assert isinstance(ds, qai_helper.QAIDataset), "QAIDataset expected"
yamlutil.writeyamlfile(ds, QAI_DUMP_FILE)
def create_test_reagent(cls) -> None:
"""Create some test data to play with.
If the following do not already exist in the database, we
create a reagent, and a reagent item.
"""
lverb = True
rcode, cls.reagent_dct = cls.s.get_json(PATH_REAGENT_LIST)
assert rcode == HTTP_OK, "called failed"
if lverb:
yamlutil.writeyamlfile(cls.reagent_dct, "./reagentlst.yaml")
cls.reagent_lst = cls.reagent_dct['items']
cls.establish_test_reagent()
# --- create some reagent items
# see whether we have a reagent item with this rfid: create one if not, and set
# the item_id
cls.test_itema_id = None
cls.test_itema_locid = None
rcode, reagitemlst = cls.s.get_json(PATH_REAGITEM_LIST,
params=dict(id=cls.test_reagent_id))
assert rcode == HTTP_OK, "call to PATH_REAGITEM_LIST failed"
if lverb:
yamlutil.writeyamlfile(reagitemlst, "./reagitemlst.yaml")
fndlst = [d for d in reagitemlst if d['rfid'] == cls.test_itema_rfid]
if len(fndlst) == 0:
# if there are items, but not one with the expected RFID, then modify the RFID
# of a record
cls.test_itema_locid = cls.testlocs[0]['id']
if len(reagitemlst) > 0:
print("setting location")
cls.setlocation(reagitemlst[0]['id'], cls.test_itema_locid)
print("SETTING RFID\n")
cls.setRFID(reagitemlst[0]['id'], cls.test_itema_rfid)
else:
# create a reagent item
print("setting new location to {}".format(cls.test_itema_locid))
itema = {'rfid': cls.test_itema_rfid,
'qcs_reag_id': cls.test_reagent_id,
'qcs_location_id': cls.test_itema_locid,
'lot_num': cls.test_reagent_item_lot_num,
'notes': cls.test_reagent_item_notes,
'source_ids': [],
'statuses': cls.test_stat_lst}
rcode, res = cls.s.post_json(TPATH_REAGENT_ITEM, data={'items': [itema]})
assert rcode == HTTP_CREATED, "called failed"
print("postres '{}'".format(res))
itm_rec = cls.get_reagent_item_record(cls.test_itema_rfid, isrfid=True)
cls.test_itema_id = itm_rec['id']
print('LOC2 {}'.format(itm_rec))
# raise RuntimeError("Stopping for a test")
else:
print("Found item with required RFID")
assert len(fndlst) == 1, "Database Error: multiple items with same RFID"
# ensure the required state of an existing reagent item
print("BLAREC {}".format(fndlst[0]))
cls.test_itema_id = fndlst[0]['id']
print("looking for item {}".format(cls.test_itema_id))
itm_rec = cls.get_reagent_item_record(cls.test_itema_id)
print("Found required item")
# ensure that the reagent item is MADE, not IN_USE
if itm_rec['current_status'] == 'IN_USE':
res = cls.s.delete_json(PATH_REAGITEM_STATUS,
params=dict(qcs_reag_item_id=cls.test_itema_id,
status='IN_USE'))
print("got res {}".format(res))
itm_rec = cls.get_reagent_item_record(cls.test_itema_id)
assert itm_rec['current_status'] == 'MADE', 'made status expected'
cls.test_itema_locid = itm_rec['loc_id']
# ensure the RFID is what the tests expected
# if itm_rec['rfid'] != cls.test_itema_rfid:
# rcode, res = cls.s.patch_json(TPATH_REAGENT_ITEM,
# data=dict(id=cls.test_itema_id,
# rfid=cls.test_itema_rfid))
# assert rcode == HTTP_OK, "called failed"
# itm_rec = cls.get_reagent_item_record(cls.test_itema_id)
assert itm_rec['rfid'] == cls.test_itema_rfid, "failed to set RFID"
print("ITEMREC IS {}".format(itm_rec))
if itm_rec['loc_id'] is None:
print("setting item location")
cls.test_itema_locid = cls.testlocs[0]['id']
cls.setlocation(cls.test_itema_id, cls.test_itema_locid)
assert cls.test_itema_id is not None, "failed to determine itema_id"
assert cls.test_itema_locid is not None, "failed to determine itema_locid"