def test_move_and_detail_development(self):
# test grp placed in trof, get a detail recorded and then moved to second trof
entry_date = self.evnt_date - timedelta(days=1)
det_date = self.evnt_date + timedelta(days=5)
move_date = self.evnt_date + timedelta(days=10)
det_evnt_cleaned_data = utils.create_new_evnt(self.cleaned_data,
"Picking", det_date)
anix = utils.enter_anix(det_evnt_cleaned_data,
grp_pk=self.grp.pk,
return_anix=True)
utils.enter_grpd(anix.pk,
det_evnt_cleaned_data,
det_date,
10,
None,
anidc_str="Development")
utils.create_movement_evnt(None,
self.trof,
self.cleaned_data,
entry_date,
grp_pk=self.grp.pk)
utils.create_movement_evnt(self.trof,
self.trof_two,
self.cleaned_data,
move_date,
grp_pk=self.grp.pk)
grp_dev = self.grp.get_development()
self.assertEqual(round(grp_dev, 3), round(Decimal(36.291), 3))
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_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_development(self):
# test grp placed in trof
entry_date = self.evnt_date - timedelta(days=1)
utils.create_movement_evnt(None,
self.trof,
self.cleaned_data,
entry_date,
grp_pk=self.grp.pk)
grp_dev = self.grp.get_development()
# compare to hard coded value corresponding to 10 days of sequential temperature increases:
self.assertEqual(round(grp_dev, 3), round(Decimal(5.579), 3))
def test_movement_development(self):
# test grp placed in trof and moved to second trof
entry_date = self.evnt_date - timedelta(days=1)
move_date = self.evnt_date + timedelta(days=10)
utils.create_movement_evnt(None,
self.trof,
self.cleaned_data,
entry_date,
grp_pk=self.grp.pk)
utils.create_movement_evnt(self.trof,
self.trof_two,
self.cleaned_data,
move_date,
grp_pk=self.grp.pk)
grp_dev = self.grp.get_development()
self.assertEqual(round(grp_dev, 3), round(Decimal(27.854), 3))
def test_fix_jumped_tanks(self):
# simulate accidentally recording group in wrong tank and correcting:
# ie A->B, C->D (fish is in both B and D) ->E should correct this
tank_a = BioFactoryFloor.TankFactory(name="A")
tank_a.facic_id = self.evnt.facic_id
tank_a.save()
tank_b = BioFactoryFloor.TankFactory(name="B")
tank_b.facic_id = self.evnt.facic_id
tank_b.save()
tank_c = BioFactoryFloor.TankFactory(name="C")
tank_c.facic_id = self.evnt.facic_id
tank_c.save()
tank_d = BioFactoryFloor.TankFactory(name="D")
tank_d.facic_id = self.evnt.facic_id
tank_d.save()
tank_e = BioFactoryFloor.TankFactory(name="E")
tank_e.facic_id = self.evnt.facic_id
tank_e.save()
# need three dates to ensure unique moving events, to keep django test env happy
move_a_date = (datetime.now() - timedelta(days=2)).date()
move_b_date = (datetime.now() - timedelta(days=1)).date()
move_c_date = datetime.now().date()
utils.create_movement_evnt(tank_a, tank_b, self.cleaned_data, move_a_date, grp_pk=self.grp.pk)
utils.create_movement_evnt(tank_c, tank_d, self.cleaned_data, move_b_date, grp_pk=self.grp.pk)
self.assertIn(tank_b, self.grp.current_cont())
self.assertIn(tank_d, self.grp.current_cont())
utils.create_movement_evnt(None, tank_e, self.cleaned_data, move_c_date, grp_pk=self.grp.pk)
self.assertIn(tank_e, self.grp.current_cont())
self.assertNotIn(tank_c, self.grp.current_cont())
self.assertNotIn(tank_d, self.grp.current_cont())
def test_development_after_detail(self):
# test grp placed in trof, has development recorded go off of that and don't double count
entry_date = self.evnt_date - timedelta(days=1)
utils.create_movement_evnt(None,
self.trof,
self.cleaned_data,
entry_date,
grp_pk=self.grp.pk)
det_date = self.evnt_date + timedelta(days=5)
det_evnt_cleaned_data = utils.create_new_evnt(self.cleaned_data,
"Picking", det_date)
anix = utils.enter_anix(det_evnt_cleaned_data,
grp_pk=self.grp.pk,
return_anix=True)
utils.enter_grpd(anix.pk,
det_evnt_cleaned_data,
det_date,
10,
None,
anidc_str="Development")
grp_dev = self.grp.get_development()
self.assertEqual(round(grp_dev, 3), round(Decimal(14.015), 3))
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
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
indv_female, samp_female, new_log = utils.get_indv_or_samp(
row, self.pit_key_f, self.samp_key_f, cleaned_data["evnt_id"])
if new_log:
self.log_data += new_log
return self.log_data, False
indv_male, samp_male, new_log = utils.get_indv_or_samp(
row, self.pit_key_m, self.samp_key_m, cleaned_data["evnt_id"])
if new_log:
self.log_data += new_log
return self.log_data, False
if not (indv_female or samp_female) or not (indv_male or samp_male):
raise Exception(
"No Individual or Fish found for row {}".format(row))
if not utils.nan_to_none(row[self.choice_key]):
raise Exception(
"Choice column cannot be empty. Set Fecundity column to zero to indicate Duds."
)
row_date = utils.get_row_date(row)
if indv_female:
anix_female, anix_entered = utils.enter_anix(
cleaned_data, indv_pk=indv_female.pk)
self.row_entered += anix_entered
self.row_entered += utils.enter_bulk_indvd(
anix_female.pk,
cleaned_data,
row_date,
gender="F",
len_mm=row.get(self.len_key_f_mm),
len_val=row.get(self.len_key_f),
weight=row.get(self.weight_key_f),
weight_kg=row.get(self.weight_key_f_kg),
status=row.get(self.status_key_f),
comments=row.get(self.comment_key_f))
if indv_male:
anix_male, anix_entered = utils.enter_anix(cleaned_data,
indv_pk=indv_male.pk)
self.row_entered += anix_entered
self.row_entered += utils.enter_bulk_indvd(
anix_male.pk,
cleaned_data,
row_date,
gender="M",
len_mm=row.get(self.len_key_m_mm),
len_val=row.get(self.len_key_m),
weight=row.get(self.weight_key_m),
weight_kg=row.get(self.weight_key_m_kg),
status=row.get(self.status_key_m),
comments=row.get(self.comment_key_m))
if samp_female:
self.row_entered += utils.enter_bulk_sampd(
samp_female.pk,
cleaned_data,
row_date,
gender="F",
len_mm=row.get(self.len_key_f_mm),
len_val=row.get(self.len_key_f),
weight=row.get(self.weight_key_f),
weight_kg=row.get(self.weight_key_f_kg),
status=row.get(self.status_key_f),
comments=row.get(self.comment_key_f))
if samp_male:
self.row_entered += utils.enter_bulk_sampd(
samp_male.pk,
cleaned_data,
row_date,
gender="M",
len_mm=row.get(self.len_key_m_mm),
len_val=row.get(self.len_key_m),
weight=row.get(self.weight_key_m),
weight_kg=row.get(self.weight_key_m_kg),
status=row.get(self.status_key_m),
comments=row.get(self.comment_key_m))
if utils.nan_to_none(row.get(self.dest_key_f)) and indv_female:
end_tank_id_f = models.Tank.objects.filter(
name=row[self.dest_key_f],
facic_id=cleaned_data["facic_id"]).get()
self.row_entered += utils.create_movement_evnt(
None, end_tank_id_f, cleaned_data, row_date, indv_female.pk)
if utils.nan_to_none(row.get(self.dest_key_m)) and indv_male:
end_tank_id_m = models.Tank.objects.filter(
name=row[self.dest_key_m],
facic_id=cleaned_data["facic_id"]).get()
self.row_entered += utils.create_movement_evnt(
None, end_tank_id_m, cleaned_data, row_date, indv_male.pk)
# pair
pair = models.Pairing(
start_date=row_date,
prio_id=models.PriorityCode.objects.filter(
name__iexact=prio_dict[row[self.prio_key_f]]).get(),
pair_prio_id=models.PriorityCode.objects.filter(
name__iexact=prio_dict[row[self.prio_key_pair]]).get(),
cross=row[self.cross_key],
valid=True,
indv_id=indv_female,
samp_id=samp_female,
comments=utils.nan_to_none(row[self.comment_key_pair]),
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
pair.clean()
pair.save()
self.row_entered = True
except (ValidationError, IntegrityError):
pair = models.Pairing.objects.filter(start_date=row_date,
indv_id=indv_female,
samp_id=samp_female).get()
# sire
sire = models.Sire(
prio_id=models.PriorityCode.objects.filter(
name__iexact=prio_dict[row[self.prio_key_m]]).get(),
pair_id=pair,
indv_id=indv_male,
samp_id=samp_male,
choice=row[self.choice_key],
comments=utils.nan_to_none(row[self.comment_key_m]),
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
sire.clean()
sire.save()
self.row_entered = True
except (ValidationError, IntegrityError):
# don't use sire again anywhere
pass
self.row_entered += utils.enter_anix(cleaned_data,
pair_pk=pair.pk,
return_sucess=True)
# pairing program:
if utils.nan_to_none(row.get(self.prog_key)):
self.row_entered += utils.enter_spwnd(
pair.pk,
cleaned_data,
row[self.prog_key],
self.prog_spwndc_id.pk,
spwnsc_str=row[self.prog_key])
# fecu/dud/extra male
if row[self.egg_est_key] > 0:
self.row_entered += utils.enter_spwnd(pair.pk, cleaned_data,
int(row[self.egg_est_key]),
self.fecu_spwndc_id.pk, None,
"Calculated")
else:
self.row_entered += utils.enter_spwnd(pair.pk, cleaned_data,
row[self.choice_key],
self.dud_spwndc_id.pk, None,
"Good")
# grp
anix_grp_qs = models.AniDetailXref.objects.filter(
evnt_id=cleaned_data["evnt_id"],
grp_id__isnull=False,
pair_id=pair,
indv_id__isnull=True,
contx_id__isnull=True,
loc_id__isnull=True,
)
anix_grp = False
if anix_grp_qs.count() == 0:
if indv_female:
stok_id = indv_female.stok_id
spec_id = indv_female.spec_id
else:
stok_id = samp_female.stok_id
spec_id = samp_female.spec_id
grp = models.Group(
spec_id=spec_id,
stok_id=stok_id,
coll_id=models.Collection.objects.filter(
name="Egg (F1)").get(),
grp_year=row_date.year,
grp_valid=False,
created_by=cleaned_data["created_by"],
created_date=cleaned_data["created_date"],
)
try:
grp.clean()
grp.save()
row_entered = True
anix_grp, anix_entered = utils.enter_anix(cleaned_data,
grp_pk=grp.pk)
row_entered += utils.enter_anix(cleaned_data,
grp_pk=grp.pk,
pair_pk=pair.pk,
return_sucess=True)
grp.grp_valid = True
grp.save()
self.row_entered = True
except ValidationError:
# recovering the group is only doable through the anix with both grp and pair.
# no way to find it here, so only make the group valid after anix's created.
pass
elif anix_grp_qs.count() == 1:
anix_grp = anix_grp_qs.get()
grp = anix_grp.grp_id
if anix_grp:
utils.enter_bulk_grpd(anix_grp,
cleaned_data,
row_date,
prog_grp=row[self.prog_key])
def row_parser(self, row):
row_datetime = utils.get_row_date(row)
row_date = row_datetime.date()
indv_qs = models.Individual.objects.filter(pit_tag=row[self.pit_key])
if len(indv_qs) == 1:
indv = indv_qs.get()
else:
self.log_data += "Error parsing row: \n"
self.log_data += str(row)
self.log_data += "\nFish with PIT {} not found in db\n".format(
row[self.pit_key])
self.success = False
return
anix, anix_entered = utils.enter_anix(self.cleaned_data,
indv_pk=indv.pk)
self.row_entered += anix_entered
self.row_entered += utils.enter_bulk_indvd(
anix.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),
status=row.get(self.status_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_indvd(
anix.pk, self.cleaned_data, row_date, None,
self.ani_health_anidc_id.pk, "Precocity")
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, self.cleaned_data, row_datetime)
self.row_entered += mort_entered
in_tank = None
out_tank = None
if utils.nan_to_none(row[self.start_tank_key]):
in_tank = models.Tank.objects.filter(
name=row[self.start_tank_key]).get()
if utils.nan_to_none(row[self.end_tank_key]):
out_tank = models.Tank.objects.filter(
name=row[self.end_tank_key]).get()
if in_tank or out_tank:
self.row_entered += utils.create_movement_evnt(in_tank,
out_tank,
self.cleaned_data,
row_datetime,
indv_pk=indv.pk)
self.row_entered += utils.parse_extra_cols(row,
self.cleaned_data,
anix,
indv=True)
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 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")
