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_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 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 data_preper(self): cleaned_data = self.cleaned_data self.temp_envc_id = models.EnvCode.objects.filter(name="Temperature").get() self.leader_code = models.RoleCode.objects.filter(name__iexact="Crew Lead").get() self.settings_locdc_id = models.LocationDetCode.objects.filter(name__iexact="Electrofishing Settings").get() self.voltage_locdc_id = models.LocationDetCode.objects.filter(name__iexact="Voltage").get() self.fishing_time_locdc_id = models.LocationDetCode.objects.filter(name__iexact="Electrofishing Seconds").get() for river_name in self.data[self.rive_key].unique(): self.river_dict[river_name] = models.RiverCode.objects.filter(name__icontains=river_name).get() if self.cleaned_data["evntc_id"].__str__() == "Electrofishing": self.locc_id = models.LocCode.objects.filter(name__icontains="Electrofishing site").get() elif self.cleaned_data["evntc_id"].__str__() == "Smolt Wheel Collection": self.locc_id = models.LocCode.objects.filter(name__icontains="Smolt Wheel site").get() elif self.cleaned_data["evntc_id"].__str__() == "Bypass Collection": self.locc_id = models.LocCode.objects.filter(name__icontains="Bypass site").get() # assign groups to columns, add generic group data: self.data["grp_id"] = None river_group_data = self.data.groupby([self.rive_key, self.prio_key, self.year_key, self.coll_key, self.tank_key], dropna=False).size().reset_index() if not river_group_data[self.tank_key].is_unique: raise Exception("Too many different groups going into same tank. Create multiple events if needed") for index, row in river_group_data.iterrows(): if not utils.nan_to_none(row[self.tank_key]): # if fish are only observed, don't make a group data_rows = (self.data[self.tank_key].isnull()) self.data.loc[data_rows, "grp_id"] = None self.data.loc[data_rows, "contx_id"] = None break stok_id = models.StockCode.objects.filter(name__icontains=row[self.rive_key]).get() coll_str = row[self.coll_key] if len(coll_str.lstrip(' 0123456789')) == len(coll_str): # year taken from year coll: coll_id = utils.coll_getter(row[self.coll_key]) grp_year = row[self.year_key] else: grp_year, coll_str = utils.year_coll_splitter(row[self.coll_key]) coll_id = utils.coll_getter(coll_str) anix_grp_qs = models.AniDetailXref.objects.filter(evnt_id=cleaned_data["evnt_id"], grp_id__stok_id=stok_id, grp_id__coll_id=coll_id, grp_id__grp_year=grp_year, indv_id__isnull=True, contx_id__isnull=True, loc_id__isnull=True, pair_id__isnull=True) grp_found = False grp = None for anix in anix_grp_qs: anix_prog_grp_names = [adsc.name for adsc in anix.grp_id.prog_group()] if utils.nan_to_none(row[self.prio_key]) and row[self.prio_key] in anix_prog_grp_names: grp_found = True grp = anix.grp_id break elif not utils.nan_to_none(row[self.prio_key]) and not anix_prog_grp_names: grp_found = True grp = anix.grp_id break if not grp_found: grp = models.Group(spec_id=models.SpeciesCode.objects.filter(name__iexact="Salmon").get(), stok_id=stok_id, coll_id=coll_id, grp_year=grp_year, grp_valid=True, created_by=cleaned_data["created_by"], created_date=cleaned_data["created_date"], ) try: grp.clean() grp.save() except ValidationError: grp = models.Group.objects.filter(spec_id=grp.spec_id, stok_id=grp.stok_id, grp_year=grp.grp_year, coll_id=grp.coll_id).get() anix_grp = utils.enter_anix(cleaned_data, grp_pk=grp.pk, return_anix=True) if utils.nan_to_none(row.get(self.prio_key)): utils.enter_grpd(anix_grp.pk, cleaned_data, cleaned_data["evnt_id"].start_date, None, None, anidc_str="Program Group", adsc_str=row[self.prio_key]) # create index column matching all rows in data to this group-tank-prio combination if utils.nan_to_none(row.get(self.prio_key)): data_rows = (self.data[self.rive_key] == row[self.rive_key]) & \ (self.data[self.prio_key] == row[self.prio_key]) & \ (self.data[self.tank_key] == row[self.tank_key]) & \ (self.data[self.coll_key] == row[self.coll_key]) else: data_rows = (self.data[self.rive_key] == row[self.rive_key]) & \ (self.data[self.coll_key] == row[self.coll_key]) & \ (self.data[self.tank_key] == row[self.tank_key]) & \ (self.data[self.prio_key].isnull()) # grp found, assign to all rows: self.data.loc[data_rows, "grp_id"] = grp contx, data_entered = utils.enter_tank_contx(row[self.tank_key], cleaned_data, True, None, grp.pk, return_contx=True) self.data.loc[data_rows, "contx_id"] = contx 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 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")