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_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
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):
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 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