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Merge pull request #2 from iml-gddaiss/biometrie_hack
Biometrie hack
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| from andes_migrate.andes_helper import AndesHelper | ||
| from andes_migrate.projet_mollusque import ProjetMollusque | ||
| from andes_migrate.table_peche_sentinelle import TablePecheSentinelle | ||
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| class BiometriePetoncle(TablePecheSentinelle): | ||
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| def __init__(self, andes_db: AndesHelper, proj: ProjetMollusque, collection_name:str, *args, **kwargs): | ||
| # super().__init__(*args, **kwargs) | ||
| super().__init__(*args, ref=proj.reference_data, **kwargs) | ||
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| self.andes_db = andes_db | ||
| self.proj: ProjetMollusque = proj | ||
| self.collection_name:str = collection_name | ||
| # self.table_name = "TRAIT_MOLLUSQUE" | ||
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| # call this form outside | ||
| self._init_rows() | ||
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| def populate_data(self): | ||
| """Populate data: run all getters""" | ||
| # secteur trait no taille poids_vif poids_muscle poids_gonade poids_visceres sexe espece comment | ||
| if self.collection_name == 'Conserver le spécimen (Biométrie Centre)': | ||
| secteur = "Centre" | ||
| if self.collection_name == 'Conserver le spécimen (Biométrie Ouest)': | ||
| secteur = "Ouest" | ||
| # if self.collection_name == 'Conserver un specimen': | ||
| # secteur = "16E" | ||
| # secteur = "16E" | ||
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| # print(self.collection_name) | ||
| sexe_dict={'0':"I", | ||
| '1':'M', | ||
| '2':'F', | ||
| } | ||
| self.data["id_specimen"] = self._get_current_row_pk() | ||
| self.data["secteur"] = secteur | ||
| self.data["trait"] = self.get_ident_no_trait() | ||
| self.data["no"] = self.get_observation("Code Collection coquille").strip().split("-")[-1] | ||
| self.data["taille"] = self.get_observation("Longuer (biométrie)").replace(".",",") | ||
| self.data["taille (old)"] = self.get_observation("Longueur").replace(".",",") | ||
| self.data["poids_vif"] = self.get_observation("Poids vif").replace(".",",") | ||
| self.data["poids_muscle"] = self.get_observation("Poids du muscle").replace(".",",") | ||
| self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",") | ||
| self.data["poids_visceres"] = self.get_observation("Poids des viscères").replace(".",",") | ||
| self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",") | ||
| self.data["sexe"] = self.get_observation("Sexe") | ||
| self.data["comment"] = self.get_comment() | ||
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| def __next__(self): | ||
| """ | ||
| Increment to focus on next row | ||
| """ | ||
| # print(self.table_name) | ||
| # print(f"{self._row_idx} of {len(self._row_list)}") | ||
| # print() | ||
| if self._row_idx is not None and self._row_list is not None: | ||
| if self._row_idx < len(self._row_list): | ||
| # increment first, it'l be adjusted in _get_current_row_pk() | ||
| self._row_idx += 1 | ||
| self.populate_data() | ||
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| # self.write_row() | ||
| return self.data | ||
| else: | ||
| raise StopIteration | ||
| else: | ||
| self.logger.error("Row data not initialise, did you run _init_rows()?") | ||
| raise ValueError | ||
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| def _init_rows(self): | ||
| """Initialisation method | ||
| This queries the Andes DB and creates a list of row entries to be added to the current table | ||
| After running this methods initialises the following attribute: | ||
| self._row_list | ||
| self._row_idx (hopefully to self._row_idx=0) | ||
| self._row_list will be populated with the specimen ids belonging in the collection | ||
| self._row_idx will start at 0 | ||
| """ | ||
| query = ( | ||
| "SELECT specimen_id " | ||
| "FROM ecosystem_survey_observation " | ||
| "LEFT JOIN ecosystem_survey_specimen " | ||
| "ON ecosystem_survey_observation.specimen_id = ecosystem_survey_specimen.id " | ||
| "LEFT JOIN ecosystem_survey_basket " | ||
| "ON ecosystem_survey_specimen.basket_id = ecosystem_survey_basket.id " | ||
| "LEFT JOIN ecosystem_survey_catch " | ||
| "ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id " | ||
| "LEFT JOIN shared_models_set " | ||
| "ON shared_models_set.id=ecosystem_survey_catch.set_id " | ||
| "LEFT JOIN shared_models_observationtype " | ||
| "ON shared_models_observationtype.id=observation_type_id " | ||
| f"WHERE shared_models_set.cruise_id = {self.proj._get_current_row_pk()} " | ||
| f"AND (shared_models_observationtype.nom ='{self.collection_name}' AND observation_value=1) " | ||
| ) | ||
| result = self.andes_db.execute_query(query) | ||
| self._assert_not_empty(result) | ||
| self._row_list = [specimen[0] for specimen in result] | ||
| self._row_idx = 0 | ||
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| # @validate_int() | ||
| # @log_results | ||
| def get_ident_no_trait(self) -> int: | ||
| """IDENT_NO_TRAIT INTEGER / NUMBER(5,0) | ||
| Numéro séquentiel d'identification du trait | ||
| Andes | ||
| ----- | ||
| shared_models.set.set_number | ||
| """ | ||
| specimen_pk = self._get_current_row_pk() | ||
| query = ( | ||
| "SELECT shared_models_set.set_number " | ||
| "FROM ecosystem_survey_specimen " | ||
| "LEFT JOIN ecosystem_survey_basket " | ||
| "ON ecosystem_survey_specimen.basket_id=ecosystem_survey_basket.id " | ||
| "LEFT JOIN ecosystem_survey_catch " | ||
| "ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id " | ||
| "LEFT JOIN shared_models_set " | ||
| "ON shared_models_set.id=ecosystem_survey_catch.set_id " | ||
| f"WHERE ecosystem_survey_specimen.id={specimen_pk} " | ||
| ) | ||
| result = self.andes_db.execute_query(query) | ||
| self._assert_one(result) | ||
| to_return = result[0][0] | ||
| return to_return | ||
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| def get_observation(self, name_fr): | ||
| specimen_pk = self._get_current_row_pk() | ||
| query = ( | ||
| "SELECT observation_value " | ||
| "FROM ecosystem_survey_observation " | ||
| "LEFT JOIN shared_models_observationtype " | ||
| "ON ecosystem_survey_observation.observation_type_id=shared_models_observationtype.id " | ||
| f"WHERE ecosystem_survey_observation.specimen_id={specimen_pk} " | ||
| f"AND shared_models_observationtype.nom='{name_fr}' " | ||
| ) | ||
| result = self.andes_db.execute_query(query) | ||
| try: | ||
| self._assert_one(result) | ||
| to_return = result[0][0] | ||
| except ValueError: | ||
| # print('error:', specimen_pk, name_fr,result) | ||
| to_return = None | ||
| if to_return is None: | ||
| to_return="" | ||
| return to_return | ||
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| def get_comment(self): | ||
| specimen_pk = self._get_current_row_pk() | ||
| query = ( | ||
| "SELECT ecosystem_survey_specimen.comment " | ||
| "FROM ecosystem_survey_specimen " | ||
| f"WHERE ecosystem_survey_specimen.id={specimen_pk} " | ||
| ) | ||
| result = self.andes_db.execute_query(query) | ||
| self._assert_one(result) | ||
| to_return = result[0][0] | ||
| if to_return is None: | ||
| to_return="" | ||
| to_return.replace("\n", " ") | ||
| to_return.replace("\r", " ") | ||
| return to_return | ||
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