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)