def test_origin_only_tank(self):
# move group with only origin, make sure group is still in original tank
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk)
move_date = datetime.now().date()
utils.create_movement_evnt(self.final_tank, None, self.cleaned_data, move_date, grp_pk=self.grp.pk)
indv_list, grp_list = self.tank.fish_in_cont()
self.assertIn(self.grp, grp_list)
def test_two_grps_one_tank(self):
# put two grps into a single tank, make sure both are located:
second_grp = BioFactoryFloor.GrpFactory()
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk)
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=second_grp.pk)
indv_list, grp_list = self.tank.fish_in_cont()
self.assertEqual(len(grp_list), 2)
self.assertIn(self.grp, grp_list)
self.assertIn(second_grp, grp_list)
def test_move_grp(self):
# grp in one tank, gets moved, is in second tank and not in first tank
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk)
indv_list, grp_list = self.tank.fish_in_cont()
self.assertIn(self.grp, grp_list)
move_date = datetime.now().date()
utils.create_movement_evnt(self.tank, self.final_tank, self.cleaned_data, move_date, grp_pk=self.grp.pk)
indv_list, grp_list = self.tank.fish_in_cont()
self.assertNotIn(self.grp, grp_list)
indv_list, grp_list = self.final_tank.fish_in_cont()
self.assertIn(self.grp, grp_list)
def test_two_cnts_one_grp(self):
# add two counts in different containers and make sure group record proper count
cnt_val = randint(0, 100)
utils.enter_cnt(self.cleaned_data, cnt_val, self.contx.pk, cnt_code="Fish in Container")
contx = utils.enter_contx(self.final_tank, self.cleaned_data, True, grp_pk=self.grp.pk, return_contx=True)
utils.enter_cnt(self.cleaned_data, cnt_val, contx.pk, cnt_code="Fish in Container")
self.assertEqual(self.grp.count_fish_in_group(), 2 * cnt_val)
def setUp(self):
super().setUp() # used to import fixtures
self.grp = BioFactoryFloor.GrpFactory()
self.trof = BioFactoryFloor.TrofFactory(name='-1')
self.trof_two = BioFactoryFloor.TrofFactory(
name='-2', facic_id=self.trof.facic_id)
self.evnt_date = utils.naive_to_aware(datetime.today() -
timedelta(days=100))
self.evnt = BioFactoryFloor.EvntFactory(start_datetime=self.evnt_date,
facic_id=self.trof.facic_id)
self.cleaned_data = {
"facic_id": self.evnt.facic_id,
"evnt_id": self.evnt,
"created_by": self.evnt.created_by,
"created_date": self.evnt.created_date,
}
self.contx, data_entered = utils.enter_contx(self.trof,
self.cleaned_data,
None,
return_contx=True)
self.contx_two, data_entered = utils.enter_contx(self.trof_two,
self.cleaned_data,
None,
return_contx=True)
temp_envc = models.EnvCode.objects.filter(name="Temperature").get()
# add ten days worth of temp data to the trough
for temp in range(0, 10):
env_date = utils.naive_to_aware(self.evnt.start_date +
timedelta(days=temp))
utils.enter_env(temp,
env_date,
self.cleaned_data,
temp_envc,
contx=self.contx)
for temp in range(10, 20):
env_date = utils.naive_to_aware(self.evnt.start_date +
timedelta(days=temp))
utils.enter_env(temp,
env_date,
self.cleaned_data,
temp_envc,
contx=self.contx_two)
def row_parser(self, row):
cleaned_data = self.cleaned_data
row_datetime = utils.get_row_date(row, get_time=True)
trof_list = utils.parse_trof_str(row.get(self.trof_key), cleaned_data["facic_id"])
for trof_id in trof_list:
row_contx, contx_entered = utils.enter_contx(trof_id, cleaned_data, final_flag=None, return_contx=True)
self.row_entered += contx_entered
self.row_entered += utils.enter_env(row[self.temp_key], row_datetime.date(), cleaned_data,
self.envc_id, env_time=row_datetime.time(), contx=row_contx,
save=True, qual_id=self.qual_id)
def test_two_cnts_one_grp(self):
# add two counts in different containers and make sure group record proper count
cnt_val = randint(0, 100)
utils.enter_cnt(self.cleaned_data, cnt_val, self.contx.pk, cnt_code="Fish in Container")
# sometimes factories will reuse an event/tank which will prevent new contx's and cnt's from being entered.
# this loop ensures that new data does get added
data_entered = False
while not data_entered:
contx, data_entered = utils.enter_contx(self.final_tank, self.cleaned_data, True, grp_pk=self.grp.pk,
return_contx=True)
utils.enter_cnt(self.cleaned_data, cnt_val, contx.pk, cnt_code="Fish in Container")
self.assertEqual(self.grp.count_fish_in_group(), 2 * cnt_val)
def data_preper(self):
cleaned_data = self.cleaned_data
self.prog_grp_anidc_id = models.AnimalDetCode.objects.filter(name="Program Group").get()
self.sex_anidc_id = models.AnimalDetCode.objects.filter(name="Gender").get()
self.len_anidc_id = models.AnimalDetCode.objects.filter(name="Length").get()
self.weight_anidc_id = models.AnimalDetCode.objects.filter(name="Weight").get()
self.vial_anidc_id = models.AnimalDetCode.objects.filter(name="Vial").get()
self.ani_health_anidc_id = models.AnimalDetCode.objects.filter(name="Animal Health").get()
self.envelope_anidc_id = models.AnimalDetCode.objects.filter(name="Scale Envelope").get()
self.wr_adsc_id = models.AniDetSubjCode.objects.filter(name="Wild Return").get()
self.locc_id = models.LocCode.objects.filter(name="Adult Collection Site").get()
self.salmon_id = models.SpeciesCode.objects.filter(name="Salmon").get()
self.sampc_id = models.SampleCode.objects.filter(name="Individual Sample").get()
for site_name in self.data[self.site_key].unique():
if utils.nan_to_none(site_name):
self.site_dict[site_name] = models.ReleaseSiteCode.objects.filter(name__icontains=site_name).select_related("rive_id").get()
for tank_name in self.data[self.tank_key].unique():
if utils.nan_to_none(tank_name):
self.tank_dict[tank_name] = models.Tank.objects.filter(name__iexact=tank_name, facic_id=cleaned_data["facic_id"]).get()
utils.enter_contx(self.tank_dict[tank_name], cleaned_data)
def test_aboslute_cnt(self):
# take eggs from a group and then record absolute count the following day.
init_cnt = randint(300, 500)
cnt_one_val = randint(5, 100)
cnt_final_val = randint(0, 5)
next_day_evnt = BioFactoryFloor.EvntFactory()
next_day_evnt.facic_id = self.evnt.facic_id
next_day_evnt.start_datetime = self.evnt.start_datetime + datetime.timedelta(days=1)
next_day_evnt.save()
new_cleaned_data = self.cleaned_data.copy()
new_cleaned_data["evnt_id"] = next_day_evnt
end_contx = utils.enter_contx(self.tank, new_cleaned_data, None, grp_pk=self.grp.pk, return_contx=True)
utils.enter_cnt(self.cleaned_data, init_cnt, self.contx.pk, cnt_code="Eggs Added")
cnt = utils.enter_cnt(self.cleaned_data, 0, self.contx.pk, cnt_code="Eggs Removed")
utils.enter_cnt_det(self.cleaned_data, cnt, cnt_one_val, "Program Group", "EQU")
utils.enter_cnt(new_cleaned_data, cnt_final_val, end_contx.pk, cnt_code="Egg Count")
self.assertEqual(self.grp.count_fish_in_group(), cnt_final_val)
def row_parser(self, row):
# need to: find the pair's group, link it to it's pairing, create a tray, and add the count.
cleaned_data = self.cleaned_data
row_date = utils.get_row_date(row)
pair_list = utils.get_pair(row[self.cross_key],
row["stok_id"],
row[self.year_key],
prog_grp=utils.nan_to_none(
row.get(self.prog_key)),
fail_on_not_found=True)
if len(pair_list) == 1:
pair_id = pair_list[0]
else:
raise Exception("Too many pairs found for row \n{}".format(row))
anix_id = models.AniDetailXref.objects.filter(
pair_id=pair_id,
grp_id__isnull=False).select_related('grp_id').first()
grp_id = anix_id.grp_id
self.row_entered += utils.enter_anix(cleaned_data,
grp_pk=grp_id.pk,
return_sucess=True)
tray_id = utils.create_tray(row["trof_id"], row[self.tray_key],
row_date, cleaned_data)
contx, contx_entered = utils.enter_contx(tray_id,
cleaned_data,
True,
grp_pk=grp_id.pk,
return_contx=True)
self.row_entered += contx_entered
if utils.nan_to_none(row.get(self.fecu_key)):
cnt, cnt_entered = utils.enter_cnt(cleaned_data,
row[self.fecu_key],
contx_pk=contx.pk,
cnt_code="Photo Count")
self.row_entered += cnt_entered
self.row_entered += utils.enter_bulk_grpd(anix_id.pk,
cleaned_data,
row_date,
comments=row.get(
self.comment_key))
def setUp(self):
super().setUp() # used to import fixtures
# create group, put them in a tank:
self.grp = BioFactoryFloor.GrpFactory()
self.evnt = BioFactoryFloor.EvntFactory()
self.tank = BioFactoryFloor.TankFactory()
self.tank.facic_id = self.evnt.facic_id
self.tank.save()
self.final_tank = BioFactoryFloor.TankFactory()
self.final_tank.facic_id = self.evnt.facic_id
self.final_tank.save()
self.cleaned_data = {
"facic_id": self.evnt.facic_id,
"evnt_id": self.evnt,
"created_by": self.evnt.created_by,
"created_date": self.evnt.created_date,
}
self.contx = utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk, return_contx=True)
def clean(self):
cleaned_data = super().clean()
cleaned_data["move_date"] = utils.naive_to_aware(
cleaned_data["move_date"])
cleaned_data["facic_id"] = cleaned_data["evnt_id"].facic_id
if cleaned_data["grp_id"] and not cleaned_data["new_grp_id"]:
grp_id = cleaned_data["grp_id"]
elif not cleaned_data["grp_id"] and cleaned_data["new_grp_id"]:
grp_id = cleaned_data["new_grp_id"]
if cleaned_data["grp_id"] and cleaned_data["new_grp_id"]:
self.add_error('grp_id',
gettext("Can only add to one group at a time"))
self.add_error('new_grp_id',
gettext("Can only add to one group at a time"))
if not self.is_valid():
return cleaned_data
# fish into tank contx
contx, entered = utils.enter_contx(self.cont,
cleaned_data,
True,
grp_pk=grp_id.pk,
return_contx=True)
#fish to event
utils.enter_anix(cleaned_data, grp_pk=grp_id.pk)
# perc contx:
if cleaned_data["perc_id"]:
team_id, entered = utils.add_team_member(cleaned_data["perc_id"],
cleaned_data["evnt_id"],
return_team=True)
utils.enter_anix(cleaned_data,
grp_pk=grp_id.pk,
team_pk=team_id.pk)
# cnt:
utils.enter_cnt(cleaned_data,
cleaned_data["num_fish"],
contx_pk=contx.pk)
def clean(self):
cleaned_data = super(FeedHandlerForm, self).clean()
if self.is_valid():
cleaned_data["feed_date"] = utils.naive_to_aware(
cleaned_data["feed_date"])
cleaned_data["created_date"] = utils.naive_to_aware(
cleaned_data["created_date"])
cleaned_data["evnt_id"] = utils.create_feed_evnt(cleaned_data)
contx_id, entered = utils.enter_contx(self.cont,
cleaned_data,
return_contx=True)
feed_entered = utils.enter_feed(cleaned_data,
contx_id,
cleaned_data["feedc_id"],
cleaned_data["feedm_id"],
cleaned_data["amt"],
freq=cleaned_data["freq"])
if not feed_entered:
raise ValidationError("Feeding instance not entered")
return cleaned_data
def data_preper(self):
cleaned_data = self.cleaned_data
self.sampc_id = models.SampleCode.objects.filter(
name="Individual Sample").get()
self.prnt_grp_anidc_id = models.AnimalDetCode.objects.filter(
name="Parent Group").get()
self.prog_grp_anidc_id = models.AnimalDetCode.objects.filter(
name="Program Group").get()
self.sex_anidc_id = models.AnimalDetCode.objects.filter(
name="Gender").get()
self.len_anidc_id = models.AnimalDetCode.objects.filter(
name="Length").get()
self.weight_anidc_id = models.AnimalDetCode.objects.filter(
name="Weight").get()
self.vial_anidc_id = models.AnimalDetCode.objects.filter(
name="Vial").get()
self.envelope_anidc_id = models.AnimalDetCode.objects.filter(
name="Scale Envelope").get()
self.ani_health_anidc_id = models.AnimalDetCode.objects.filter(
name="Animal Health").get()
self.anidc_ufid_id = models.AnimalDetCode.objects.filter(
name="UFID").get()
self.vax_anidc_id = models.AnimalDetCode.objects.filter(
name="Vaccination").get()
self.mark_anidc_id = models.AnimalDetCode.objects.filter(
name="Mark").get()
self.lifestage_anidc_id = models.AnimalDetCode.objects.filter(
name="Lifestage").get()
self.comment_anidc_id = models.AnimalDetCode.objects.filter(
name="Comment").get()
# The following steps are to set additional columns on each row to facilitate parsing.
# In particular, columns set will be: "datetime", "grp_year", "grp_coll", "start_tank_id",
# "end_tank_id", "grp_key", "end_grp_key".
# The two grp_keys will link to dictionaries of the groups, which are also set below
# set date
self.data = utils.set_row_datetime(self.data)
# split year-coll
self.data["grp_year"] = self.data.apply(
lambda row: utils.year_coll_splitter(row[self.yr_coll_key])[0],
axis=1)
self.data["grp_coll"] = self.data.apply(
lambda row: utils.year_coll_splitter(row[self.yr_coll_key])[1],
axis=1)
# set start and end tank columns:
self.data = utils.set_row_tank(self.data,
cleaned_data,
self.start_tank_key,
col_name="start_tank_id")
self.data = utils.set_row_tank(self.data,
cleaned_data,
self.end_tank_key,
col_name="end_tank_id")
# set the dict keys for groups, use astype(str) to handle anything that might be a nan.
self.data, self.start_grp_dict = utils.set_row_grp(
self.data,
self.rive_key,
self.yr_coll_key,
self.prio_key,
"start_tank_id",
"datetime",
self.grp_mark_key,
grp_col_name="start_grp_id",
return_dict=True)
for item, grp in self.start_grp_dict.items():
utils.enter_anix(cleaned_data, grp_pk=grp.pk)
self.data["end_grp_key"] = self.data[self.rive_key] + self.data[self.yr_coll_key] + \
self.data[self.end_tank_key].astype(str) + self.data[self.prio_key].astype(str) + \
self.data["datetime"].astype(str) + self.data[self.grp_mark_key].astype(str)
# create the end group dict and create, movement event, groups, counts, contxs, etc. necesarry
end_grp_data = self.data.groupby([
self.rive_key, "grp_year", "grp_coll", "end_tank_id",
"start_tank_id", self.prio_key, "datetime", self.grp_mark_key,
"grp_key", "end_grp_key"
],
dropna=False,
sort=False).size().reset_index()
for row in end_grp_data.to_dict('records'):
# check if end tank is set, otherwise, skip this step
if not utils.nan_to_none(row["end_tank_id"]):
self.end_grp_dict[row["end_grp_key"]] = None
continue
grps = utils.get_grp(row[self.rive_key],
row["grp_year"],
row["grp_coll"],
row["end_tank_id"],
at_date=row["datetime"],
prog_str=row[self.prio_key],
mark_str=row[self.grp_mark_key])
start_grp_id = self.start_grp_dict[row["grp_key"]]
start_contx, contx_entered = utils.enter_contx(
row["start_tank_id"],
cleaned_data,
None,
grp_pk=start_grp_id.pk,
return_contx=True)
self.row_entered += utils.enter_cnt(
cleaned_data,
sum(end_grp_data[end_grp_data["grp_key"] == row["grp_key"]]
[0]),
start_contx.pk,
cnt_code="Fish Removed from Container")[1]
if len(grps) > 0:
end_grp_id = grps[0]
self.end_grp_dict[row["end_grp_key"]] = grps[0]
else:
end_grp_id = copy.deepcopy(start_grp_id)
end_grp_id.pk = None
end_grp_id.save()
self.end_grp_dict[row["end_grp_key"]] = end_grp_id
if end_grp_id.pk != start_grp_id.pk:
grp_anix = utils.enter_anix(cleaned_data,
grp_pk=end_grp_id.pk,
return_anix=True)
utils.enter_grpd(grp_anix.pk,
cleaned_data,
row["datetime"],
None,
self.prnt_grp_anidc_id.pk,
frm_grp_id=start_grp_id)
if utils.nan_to_none(row[self.prio_key]):
utils.enter_grpd(grp_anix.pk, cleaned_data,
row["datetime"], row[self.prio_key],
self.prog_grp_anidc_id.pk,
row[self.prio_key])
if utils.nan_to_none(row[self.grp_mark_key]):
utils.enter_grpd(grp_anix.pk, cleaned_data,
row["datetime"], row[self.grp_mark_key],
self.mark_anidc_id.pk,
row[self.grp_mark_key])
end_contx = utils.create_movement_evnt(row["start_tank_id"],
row["end_tank_id"],
cleaned_data,
row["datetime"],
grp_pk=end_grp_id.pk,
return_end_contx=True)
if end_contx:
self.row_entered += utils.enter_cnt(
cleaned_data, row[0], end_contx.pk)[1]
self.data_dict = self.data.to_dict("records")
def row_parser(self, row):
cleaned_data = self.cleaned_data
row_date = row["datetime"].date()
row_start_grp = utils.get_grp(row[self.rive_key],
row["grp_year"],
row["grp_coll"],
row["start_tank_id"],
row_date,
prog_str=row.get(self.prio_key),
mark_str=row.get(self.grp_mark_key),
fail_on_not_found=True)[0]
start_anix, self.row_entered = utils.enter_anix(
cleaned_data, grp_pk=row_start_grp.pk)
start_contx, contx_entered = utils.enter_contx(row["start_tank_id"],
cleaned_data,
None,
return_contx=True)
self.row_entered += contx_entered
whole_grp = utils.y_n_to_bool(row[self.abs_key])
det_anix = start_anix
row["start_contx_pk"] = None
if not whole_grp:
row["start_contx_pk"] = start_contx.pk
if utils.nan_to_none(row["end_tank_id"]):
# 4 possible cases here: group in tank or not and whole group move or not:
row_end_grp_list = utils.get_grp(row[self.rive_key],
row["grp_year"],
row["grp_coll"],
row["end_tank_id"],
row_date,
prog_str=row[self.prio_key],
mark_str=row[self.grp_mark_key])
row_end_grp = None
if not whole_grp and not row_end_grp_list:
# splitting fish group, create end group:
row_end_grp = copy.deepcopy(row_start_grp)
row_end_grp.pk = None
row_end_grp.id = None
row_end_grp.save()
end_grp_anix, anix_entered = utils.enter_anix(
cleaned_data, grp_pk=row_end_grp.pk)
self.row_entered = anix_entered
self.row_entered += utils.enter_bulk_grpd(
end_grp_anix.pk,
cleaned_data,
row_date,
prog_grp=row.get(self.prio_key),
mark=row.get(self.mark_key))
elif not whole_grp:
# splitting fish group, merging to exsisting end group
row_end_grp = row_end_grp_list[0]
if row_end_grp:
move_contx = utils.create_movement_evnt(row["start_tank_id"],
row["end_tank_id"],
cleaned_data,
row_date,
grp_pk=row_end_grp.pk,
return_end_contx=True)
end_grp_anix, anix_entered = utils.enter_anix(
cleaned_data, grp_pk=row_end_grp.pk)
self.row_entered += anix_entered
self.row_entered += utils.enter_grpd(end_grp_anix.pk,
cleaned_data,
row_date,
None,
self.prnt_grp_anidc_id.pk,
frm_grp_id=row_start_grp)
cnt, cnt_entered = utils.enter_cnt(cleaned_data,
row[self.nfish_key],
move_contx.pk)
self.row_entered = cnt_entered
# record details on end tank group
det_anix = end_grp_anix
else:
# move all the fish (whole group, merge to fish at destination if needed)
move_contx = utils.create_movement_evnt(
row["start_tank_id"],
row["end_tank_id"],
cleaned_data,
row_date,
grp_pk=row_start_grp.pk,
return_end_contx=True)
cnt, cnt_entered = utils.enter_cnt(cleaned_data,
row[self.nfish_key],
move_contx.pk,
cnt_code="Fish Count")
self.row_entered = cnt_entered
else:
if utils.nan_to_none(row[self.nfish_key]):
cnt, cnt_entered = utils.enter_cnt(cleaned_data,
row[self.nfish_key],
start_contx.pk,
cnt_code="Fish Count")
self.row_entered = cnt_entered
# add details to det_anix:
self.row_entered += utils.enter_bulk_grpd(
det_anix.pk,
cleaned_data,
row_date,
vaccinated=row.get(self.vax_key),
mark=row.get(self.mark_key),
lifestage=row.get(self.lifestage_key),
comments=row.get(self.comment_key))
self.row_entered += utils.parse_extra_cols(row,
self.cleaned_data,
det_anix,
grp=True)
def clean(self):
cleaned_data = super().clean()
cleaned_data["mort_date"] = utils.naive_to_aware(
cleaned_data["mort_date"])
if not self.is_valid():
return cleaned_data
# grab an event for facility info, etc.
if cleaned_data["indv_mort"]:
cleaned_data["evnt_id"] = models.AniDetailXref.objects.filter(
indv_id_id=cleaned_data["indv_mort"]).last().evnt_id
mort_evntc = models.EventCode.objects.filter(
name="Mortality").get()
else:
cleaned_data["evnt_id"] = models.AniDetailXref.objects.filter(
grp_id_id=cleaned_data["grp_mort"]).last().evnt_id
mort_evntc = models.EventCode.objects.filter(
name="Mortality").get()
mortality_evnt = models.Event(
evntc_id=mort_evntc,
facic_id=cleaned_data["evnt_id"].facic_id,
prog_id=cleaned_data["evnt_id"].prog_id,
perc_id=cleaned_data["evnt_id"].perc_id,
start_datetime=cleaned_data["mort_date"],
end_datetime=cleaned_data["mort_date"],
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
mortality_evnt.clean()
mortality_evnt.save()
except (ValidationError, IntegrityError):
mortality_evnt = models.Event.objects.filter(
evntc_id=mortality_evnt.evntc_id,
facic_id=mortality_evnt.facic_id,
prog_id=mortality_evnt.prog_id,
start_datetime=mortality_evnt.start_datetime,
end_datetime=mortality_evnt.end_datetime,
).get()
cleaned_data["evnt_id"] = mortality_evnt
cleaned_data["facic_id"] = mortality_evnt.facic_id
if cleaned_data["indv_mort"]:
indv = models.Individual.objects.filter(
pk=cleaned_data["indv_mort"]).get()
indv.indv_valid = False
indv.save()
anix, mort_entered = utils.enter_mortality(
indv, cleaned_data, cleaned_data["mort_date"])
utils.enter_bulk_indvd(
anix.pk,
cleaned_data,
cleaned_data["mort_date"],
len_val=cleaned_data["indv_length"],
weight=cleaned_data["indv_mass"],
vial=cleaned_data["indv_vial"],
scale_envelope=cleaned_data["scale_envelope"],
gender=cleaned_data["indv_gender"],
)
if cleaned_data["observations"].count() != 0:
for adsc in cleaned_data["observations"]:
utils.enter_indvd(anix.pk, cleaned_data,
cleaned_data["mort_date"], None,
adsc.anidc_id.pk, adsc.name, None)
if cleaned_data["grp_mort"]:
grp = models.Group.objects.filter(
pk=cleaned_data["grp_mort"]).get()
salmon_pk = models.SpeciesCode.objects.filter(
name__icontains="Salmon").get().pk
mort_sampc = models.SampleCode.objects.filter(
name="Mortality Sample").get().pk
cont = grp.current_cont(at_date=cleaned_data["mort_date"])[0]
# create contx, link to grp and samp:
contx, contx_entered = utils.enter_contx(cont,
cleaned_data,
None,
return_contx=True)
samp_anix, anix_entered = utils.enter_anix(cleaned_data,
grp_pk=grp.pk,
contx_pk=contx.pk)
samp_id, samp_entered = utils.enter_samp(cleaned_data,
cleaned_data["samp_num"],
salmon_pk,
mort_sampc,
anix_pk=samp_anix.pk)
mort_entered = utils.enter_samp_mortality(
samp_id, cleaned_data, cleaned_data["mort_date"])
utils.enter_bulk_sampd(
samp_id.pk,
cleaned_data,
cleaned_data["mort_date"],
len_val=cleaned_data["indv_length"],
weight=cleaned_data["indv_mass"],
vial=cleaned_data["indv_vial"],
scale_envelope=cleaned_data["scale_envelope"],
gender=cleaned_data["indv_gender"],
)
def row_parser(self, row):
cleaned_data = self.cleaned_data
row_date = utils.get_row_date(row)
self.row_entered += utils.enter_contx(row["trof_id"], cleaned_data)
# find group from either cross or tray:
if utils.nan_to_none(row.get(self.hu_key)):
cont_id = utils.get_cont_from_dot(row[self.hu_key], cleaned_data,
row_date)
elif utils.nan_to_none(row.get(self.tray_key)):
cont_id = models.Tray.objects.filter(
trof_id=row["trof_id"],
end_date__isnull=True,
name=row[self.tray_key]).get()
else:
cont_id = row["trof_id"]
if utils.nan_to_none(row.get(self.cross_key)):
pair_id = models.Pairing.objects.filter(
cross=row[self.cross_key],
end_date__isnull=True,
indv_id__stok_id=row["stok_id"],
start_date__year=row[self.year_key]).first()
grp_id = utils.get_tray_group(pair_id, cont_id, row_date)
else:
grp_id = cont_id.fish_in_cont(row_date, get_grp=True)
grp_anix = None
shock = False
for pickc_id in cleaned_data["pickc_id"]:
if utils.nan_to_none(row[pickc_id.name]):
shock = utils.y_n_to_bool(row.get(self.shocking_key))
grp_anix, evnt_entered = utils.create_picks_evnt(
cleaned_data,
cont_id,
grp_id.pk,
row[pickc_id.name],
row_date,
pickc_id.name,
cleaned_data["evnt_id"].perc_id,
shocking=shock,
return_anix=True,
pick_comments=row.get(self.comment_key))
self.row_entered += evnt_entered
for col_name in row.keys():
col_date = utils.get_col_date(col_name)
if col_date:
col_date_str = datetime.strftime(col_date, "%Y-%b-%d")
self.date_dict[col_date_str] = True
if utils.nan_to_none(row.get(col_name)):
self.row_entered += utils.create_picks_evnt(
cleaned_data,
cont_id,
grp_id.pk,
row[col_name],
col_date,
self.default_pickc_id,
cleaned_data["evnt_id"].perc_id,
pick_comments=row.get(self.comment_key))
# record development
if grp_anix and shock:
pick_evnt_cleaned_data = cleaned_data.copy()
pick_evnt_cleaned_data["evnt_id"] = grp_anix.evnt_id
dev_at_pick = grp_id.get_development(row_date)
utils.enter_grpd(grp_anix.pk,
pick_evnt_cleaned_data,
row_date,
dev_at_pick,
None,
anidc_str="Development")
self.row_entered += utils.enter_contx(row["trof_id"], cleaned_data)
def row_parser(self, row):
cleaned_data = self.cleaned_data
# get tray, group, and row date
row_date = utils.get_row_date(row)
tray_qs = models.Tray.objects.filter(trof_id=row["trof_id"],
name=row[self.tray_key])
tray_id = tray_qs.filter(
Q(start_date__lte=row_date, end_date__gte=row_date)
| Q(end_date__isnull=True)).get()
pair_id = models.Pairing.objects.filter(
cross=row[self.cross_key],
end_date__isnull=True,
indv_id__stok_id=row["stok_id"],
start_date__year=row[self.year_key]).first()
grp_id = utils.get_tray_group(pair_id, tray_id, row_date)
# want to shift the hu move event, so that the counting math always works out.
hu_move_date = row_date + timedelta(minutes=1)
hu_cleaned_data = utils.create_new_evnt(cleaned_data, "Allocation",
hu_move_date)
hu_anix, data_entered = utils.enter_anix(hu_cleaned_data,
grp_pk=grp_id.pk)
self.row_entered += data_entered
hu_contx, data_entered = utils.enter_contx(tray_id,
hu_cleaned_data,
None,
grp_pk=grp_id.pk,
return_contx=True)
self.row_entered += data_entered
# record development
dev_at_hu_transfer = grp_id.get_development(hu_move_date)
utils.enter_grpd(hu_anix.pk,
hu_cleaned_data,
hu_move_date,
dev_at_hu_transfer,
None,
anidc_str="Development")
self.row_entered += utils.enter_contx(row["trof_id"], cleaned_data)
# HU Picks:
self.row_entered += utils.enter_cnt(cleaned_data,
row[self.loss_key],
hu_contx.pk,
cnt_code="HU Transfer Loss")[1]
# generate new group, cup, and movement event:
cont = None
if utils.nan_to_none(row[self.end_tray_key]):
trof_id = models.Trough.objects.filter(
facic_id=cleaned_data["facic_id"],
name=row[self.end_trof_key]).get()
tray_qs = models.Tray.objects.filter(trof_id=trof_id,
name=row[self.tray_key])
cont = tray_qs.filter(
Q(start_date__lte=row_date, end_date__gte=row_date)
| Q(end_date__isnull=True)).get()
elif utils.nan_to_none(row[self.end_trof_key]):
cont = models.Trough.objects.filter(
facic_id=cleaned_data["facic_id"],
name=row[self.end_trof_key]).get()
elif utils.nan_to_none(row[self.heatl_key]):
cont = utils.get_cont_from_dot(row[self.cont_key], cleaned_data,
row_date)
elif utils.nan_to_none(row[self.tank_key]):
cont = models.Tank.objects.filter(
facic_id=cleaned_data["facic_id"], name=row[self.tank_key])
self.row_entered += utils.enter_contx(cont, cleaned_data)
if not utils.y_n_to_bool(row[self.final_key]):
# NEW GROUPS TAKEN FROM INITIAL
out_cnt = utils.enter_cnt(cleaned_data,
0,
hu_contx.pk,
cnt_code="Eggs Removed")[0]
utils.enter_cnt_det(cleaned_data, out_cnt, row[self.cnt_key],
"Program Group Split", row[self.prog_key])
indv, final_grp = cont.fish_in_cont(row_date)
if not final_grp:
final_grp = models.Group(
spec_id=grp_id.spec_id,
coll_id=grp_id.coll_id,
grp_year=grp_id.grp_year,
stok_id=grp_id.stok_id,
grp_valid=True,
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
final_grp.clean()
final_grp.save()
except (ValidationError, IntegrityError):
return None
else:
# MAIN GROUP GETTING MOVED
final_grp = final_grp[0]
final_grp_anix = utils.enter_anix(cleaned_data,
grp_pk=final_grp.pk,
return_anix=True)
self.row_entered += utils.enter_anix(hu_cleaned_data,
grp_pk=final_grp.pk,
return_sucess=True)
self.row_entered += utils.enter_bulk_grpd(
final_grp_anix,
cleaned_data,
row_date,
prnt_grp=grp_id,
prog_grp=row.get(self.prog_key),
comments=row.get(self.comment_key))
self.row_entered += utils.enter_grpd(final_grp_anix.pk,
cleaned_data,
row_date,
dev_at_hu_transfer,
None,
anidc_str="Development")
# create movement for the new group, create 2 contx's and 3 anix's
# cup contx is contx used to link the positive counts
cont_contx = utils.create_egg_movement_evnt(tray_id,
cont,
cleaned_data,
row_date,
final_grp.pk,
return_cup_contx=True)
move_cleaned_data = cleaned_data.copy()
move_cleaned_data["evnt_id"] = cont_contx.evnt_id
cnt_contx = cont_contx
cnt_contx.pk = None
cnt_contx.tray_id = tray_id
try:
cnt_contx.save()
except IntegrityError:
cnt_contx = models.ContainerXRef.objects.filter(
pk=cont_contx.pk).get()
self.row_entered += utils.enter_anix(move_cleaned_data,
grp_pk=final_grp.pk,
contx_pk=cnt_contx.pk,
return_sucess=True)
# add the positive counts
cnt = utils.enter_cnt(
move_cleaned_data,
row[self.cnt_key],
cnt_contx.pk,
cnt_code="Eggs Added",
)[0]
if utils.nan_to_none(self.weight_key):
utils.enter_cnt_det(move_cleaned_data, cnt,
row[self.weight_key], "Weight")
utils.enter_cnt_det(move_cleaned_data, cnt, row[self.cnt_key],
"Program Group Split", row[self.prog_key])
else:
# Move main group to drawer, and add end date to tray:
if cont:
end_contx = utils.create_movement_evnt(tray_id,
cont,
cleaned_data,
row_date,
grp_pk=grp_id.pk,
return_end_contx=True)
tray_id.end_date = row_date
tray_id.save()
end_cnt = utils.enter_cnt(cleaned_data,
row[self.cnt_key],
end_contx.pk,
cnt_code="Egg Count")[0]
utils.enter_cnt_det(cleaned_data, end_cnt,
row[self.weight_key], "Weight")
else:
self.log_data += "\n Draw {} from {} not found".format(
cont, row[self.cont_key])
# link cup to egg development event
utils.enter_contx(cont, cleaned_data, None)
def row_parser(self, row):
cleaned_data = self.cleaned_data
row_datetime = utils.get_row_date(row)
relc_id = self.site_dict[row[self.site_key]]
year, coll = utils.year_coll_splitter(row[self.coll_key])
coll_id = utils.coll_getter(coll)
stok_id = models.StockCode.objects.filter(name__iexact=relc_id.rive_id.name).get()
indv_id = None
if utils.nan_to_none(row[self.pit_key]):
indv_id = models.Individual.objects.filter(pit_tag=row[self.pit_key]).first()
if not indv_id:
indv_id = models.Individual(spec_id=self.salmon_id,
stok_id=stok_id,
coll_id=coll_id,
indv_year=year,
pit_tag=row[self.pit_key],
indv_valid=True,
comments=utils.nan_to_none(row.get(self.comment_key)),
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
indv_id.clean()
indv_id.save()
self.row_entered = True
except (ValidationError, IntegrityError):
indv_id = models.Individual.objects.filter(pit_tag=indv_id.pit_tag).get()
indv_anix, data_entered = utils.enter_anix(cleaned_data, indv_pk=indv_id.pk)
self.row_entered += data_entered
# add program group to individual if needed:
loc = models.Location(evnt_id_id=cleaned_data["evnt_id"].pk,
locc_id=self.locc_id,
rive_id=relc_id.rive_id,
relc_id=relc_id,
loc_date=row_datetime,
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
loc.clean()
loc.save()
self.row_entered = True
except ValidationError:
loc = models.Location.objects.filter(evnt_id=loc.evnt_id, locc_id=loc.locc_id,
rive_id=loc.rive_id, subr_id=loc.subr_id,
relc_id=loc.relc_id, loc_lat=loc.loc_lat,
loc_lon=loc.loc_lon, loc_date=loc.loc_date).get()
self.loc = loc
self.team_parser(row[self.crew_key], row, loc_id=loc)
if indv_id:
anix_loc_indv, anix_entered = utils.enter_anix(cleaned_data, loc_pk=loc.pk, indv_pk=indv_id.pk)
self.row_entered += anix_entered
self.row_entered += utils.enter_bulk_indvd(anix_loc_indv.pk, self.cleaned_data, row_datetime,
gender=row.get(self.sex_key),
len_mm=row.get(self.len_key_mm),
len_val=row.get(self.len_key),
weight=row.get(self.weight_key),
weight_kg=row.get(self.weight_key_kg),
vial=row.get(self.vial_key),
scale_envelope=row.get(self.scale_key),
prog_grp=row.get(self.grp_key),
comments=row.get(self.comment_key)
)
if utils.nan_to_none(row.get(self.mort_key)):
if utils.y_n_to_bool(row[self.mort_key]):
mort_anix, mort_entered = utils.enter_mortality(indv_id, self.cleaned_data, row_datetime)
self.row_entered += mort_entered
if utils.nan_to_none(row.get(self.wr_key)):
if utils.y_n_to_bool(row[self.wr_key]):
self.row_entered += utils.enter_indvd(anix_loc_indv.pk, cleaned_data, row_datetime, None,
self.ani_health_anidc_id.pk, adsc_str=self.wr_adsc_id.name)
if utils.nan_to_none(row.get(self.aquaculture_key)):
if utils.y_n_to_bool(row[self.aquaculture_key]):
self.row_entered += utils.enter_indvd(anix_loc_indv.pk, cleaned_data, row_datetime, None,
self.ani_health_anidc_id.pk, adsc_str="Aquaculture")
if utils.nan_to_none(row[self.tank_key]):
self.row_entered += utils.enter_contx(self.tank_dict[row[self.tank_key]], cleaned_data, True, indv_id.pk)
if self.loc.pk not in self.loc_caught_dict:
self.loc_caught_dict[self.loc.pk] = 1
else:
self.loc_caught_dict[self.loc.pk] += 1
else:
if self.loc.pk not in self.loc_obs_dict:
self.loc_obs_dict[self.loc.pk] = 1
else:
self.loc_obs_dict[self.loc.pk] += 1
elif utils.nan_to_none(row.get(self.samp_key)):
samp = models.Sample.objects.filter(anix_id__evnt_id=cleaned_data["evnt_id"],
loc_id=loc,
spec_id=self.salmon_id,
samp_num=row[self.samp_key],
sampc_id=self.sampc_id,
).get()
if not samp:
# create group for sample:
grp_id = models.Group(spec_id=self.salmon_id,
stok_id=stok_id,
coll_id=coll_id,
grp_year=year,
grp_valid=False,
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
grp_id.clean()
grp_id.save()
self.row_entered = True
grp_anix, data_entered = utils.enter_anix(cleaned_data, grp_pk=grp_id.pk)
self.row_entered += data_entered
samp, samp_entered = utils.enter_samp(cleaned_data, row[self.samp_key], self.salmon_id.pk, self.sampc_id.pk,
anix_pk=grp_anix.pk, loc_pk=loc.pk,
comments=utils.nan_to_none(row.get(self.comment_key)))
self.row_entered += samp_entered
self.row_entered += utils.enter_bulk_sampd(samp.pk, self.cleaned_data, row_datetime,
gender=row.get(self.sex_key),
len_mm=row.get(self.len_key_mm),
len_val=row.get(self.len_key),
weight=row.get(self.weight_key),
weight_kg=row.get(self.weight_key_kg),
vial=row.get(self.vial_key),
scale_envelope=row.get(self.scale_key),
prog_grp=row.get(self.grp_key),
comments=row.get(self.comment_key)
)
if utils.nan_to_none(row.get(self.mort_key)):
if utils.y_n_to_bool(row[self.mort_key]):
self.row_entered += utils.enter_samp_mortality(samp, self.cleaned_data, row_datetime)
if utils.nan_to_none(row.get(self.wr_key)):
if utils.y_n_to_bool(row[self.wr_key]):
self.row_entered += utils.enter_sampd(samp.pk, cleaned_data, row_datetime, None,
self.ani_health_anidc_id.pk, adsc_str=self.wr_adsc_id.name)
if utils.nan_to_none(row.get(self.aquaculture_key)):
if utils.y_n_to_bool(row[self.aquaculture_key]):
self.row_entered += utils.enter_sampd(samp.pk, cleaned_data, row_datetime, None,
self.ani_health_anidc_id.pk, adsc_str="Aquaculture")
else:
raise Exception("Fish must either be assigned a sample number or a pit tag.")
def row_parser(self, row):
cleaned_data = self.cleaned_data
year, coll = utils.year_coll_splitter(row[self.coll_key])
row_datetime = utils.get_row_date(row)
row_date = row_datetime.date()
indv_ufid = utils.nan_to_none(row.get(self.ufid_key))
indv = models.Individual(
grp_id=self.grp_id,
spec_id=self.salmon_id,
stok_id=self.stok_id,
coll_id=self.coll_id,
indv_year=year,
pit_tag=row[self.pit_key],
ufid=indv_ufid,
indv_valid=True,
comments=utils.nan_to_none(row.get(self.comment_key)),
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
indv.clean()
indv.save()
self.row_entered = True
except (ValidationError, IntegrityError):
indv = models.Individual.objects.filter(pit_tag=indv.pit_tag).get()
if utils.nan_to_none(row[self.from_tank_id_key]) or utils.nan_to_none(
row[self.to_tank_id_key]):
in_tank = row[self.from_tank_id_key]
out_tank = row[self.to_tank_id_key]
self.row_entered += utils.create_movement_evnt(in_tank,
out_tank,
cleaned_data,
row_datetime,
indv_pk=indv.pk)
# if tagged fish goes back into same tank, still link fish to tank:
if in_tank == out_tank:
utils.enter_contx(in_tank, cleaned_data, True, indv_pk=indv.pk)
anix_indv, anix_entered = utils.enter_anix(cleaned_data,
indv_pk=indv.pk)
self.row_entered += anix_entered
self.anix_indv = anix_indv
utils.enter_bulk_indvd(
anix_indv.pk,
self.cleaned_data,
row_date,
len_mm=row.get(self.len_key_mm),
len_val=row.get(self.len_key),
weight=row.get(self.weight_key),
weight_kg=row.get(self.weight_key_kg),
vial=row.get(self.vial_key),
mark=row.get(self.mark_key),
prog_grp=row.get(self.group_key),
lifestage=row.get(self.lifestage_key),
comments=row.get(self.comment_key),
)
if utils.nan_to_none(row.get(self.precocity_key)):
self.row_entered += utils.enter_indvd(anix_indv.pk, cleaned_data,
row_date, None,
self.ani_health_anidc_id.pk,
"Precocity")
if utils.nan_to_none(row.get(self.crew_key)):
perc_list, inits_not_found = utils.team_list_splitter(
row[self.crew_key])
for perc_id in perc_list:
team_id, team_entered = utils.add_team_member(
perc_id,
cleaned_data["evnt_id"],
role_id=self.tagger_code,
return_team=True)
self.row_entered += team_entered
if team_id:
self.row_entered += utils.enter_anix(cleaned_data,
indv_pk=indv.pk,
team_pk=team_id.pk,
return_sucess=True)
for inits in inits_not_found:
self.log_data += "No valid personnel with initials ({}) for row with pit tag" \
" {}\n".format(inits, row[self.pit_key])
def row_parser(self, row):
cleaned_data = self.cleaned_data
row_date = row["datetime"].date()
row_grp = row["start_grp_id"]
row_end_grp = self.end_grp_dict[row["end_grp_key"]]
if row_end_grp:
row_grp = row_end_grp
row_anix, data_entered = utils.enter_anix(cleaned_data,
grp_pk=row_grp.pk)
self.row_entered += data_entered
row_contx, data_entered = utils.enter_contx(row.get("start_tank_id"),
cleaned_data,
None,
grp_pk=row_grp.pk,
return_contx=True)
self.row_entered += data_entered
samp_anix = row_contx.animal_details.filter(
grp_id=row_grp,
evnt_id=cleaned_data["evnt_id"],
indv_id__isnull=True,
loc_id__isnull=True,
pair_id__isnull=True,
final_contx_flag=None).get()
row_samp, data_entered = utils.enter_samp(cleaned_data,
row[self.samp_key],
row_grp.spec_id.pk,
self.sampc_id.pk,
anix_pk=samp_anix.pk)
self.row_entered += data_entered
if utils.nan_to_none(row.get(self.mort_key)):
if utils.y_n_to_bool(row[self.mort_key]):
self.row_entered += utils.enter_samp_mortality(
row_samp, cleaned_data, row_date)
if row_samp:
self.row_entered += utils.enter_bulk_sampd(
row_samp.pk,
self.cleaned_data,
row_date,
gender=row.get(self.sex_key),
len_mm=row.get(self.len_key_mm),
len_val=row.get(self.len_key),
weight=row.get(self.weight_key),
weight_kg=row.get(self.weight_key_kg),
vial=row.get(self.vial_key),
scale_envelope=row.get(self.envelope_key),
tissue_yn=row.get(self.tissue_key),
mark=row.get(self.mark_key),
vaccinated=row.get(self.vax_key),
lifestage=row.get(self.lifestage_key),
comments=row.get(self.comment_key))
if utils.nan_to_none(row.get(self.precocity_key)):
if utils.y_n_to_bool(row[self.precocity_key]):
self.row_entered += utils.enter_sampd(
row_samp.pk,
cleaned_data,
row_date,
"Precocity",
self.ani_health_anidc_id.pk,
adsc_str="Precocity")
if utils.nan_to_none(row.get(self.ufid_key)):
self.row_entered += utils.enter_sampd(row_samp.pk,
cleaned_data, row_date,
row[self.ufid_key],
self.anidc_ufid_id.pk)
self.row_entered += utils.parse_extra_cols(row,
self.cleaned_data,
row_samp,
samp=True)
else:
self.success = False
def test_cont_has_grp(self):
# test a tank with a contx has one and only one group in it:
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk)
indv_list, grp_list = self.tank.fish_in_cont()
self.assertEqual(len(grp_list), 1)
self.assertIn(self.grp, grp_list)
def test_grp_in_cont(self):
# test a group with a contx is in one and only one tank:
utils.enter_contx(self.tank, self.cleaned_data, True, grp_pk=self.grp.pk)
self.assertEqual(self.grp.current_cont()[0], self.tank)
self.assertEqual(len(self.grp.current_cont()), 1)
