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Merge pull request #2 from iml-gddaiss/biometrie_hack
Biometrie hack
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‎andes_migrate/biometrie_petoncle.py

+176
Original file line numberDiff line numberDiff line change
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from andes_migrate.andes_helper import AndesHelper
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from andes_migrate.projet_mollusque import ProjetMollusque
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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):
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# super().__init__(*args, **kwargs)
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super().__init__(*args, ref=proj.reference_data, **kwargs)
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self.andes_db = andes_db
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self.proj: ProjetMollusque = proj
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self.collection_name:str = collection_name
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# self.table_name = "TRAIT_MOLLUSQUE"
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# call this form outside
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self._init_rows()
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def populate_data(self):
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"""Populate data: run all getters"""
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# secteur trait no taille poids_vif poids_muscle poids_gonade poids_visceres sexe espece comment
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if self.collection_name == 'Conserver le spécimen (Biométrie Centre)':
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secteur = "Centre"
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if self.collection_name == 'Conserver le spécimen (Biométrie Ouest)':
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secteur = "Ouest"
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# if self.collection_name == 'Conserver un specimen':
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# secteur = "16E"
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# secteur = "16E"
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# print(self.collection_name)
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sexe_dict={'0':"I",
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'1':'M',
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'2':'F',
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}
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self.data["id_specimen"] = self._get_current_row_pk()
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self.data["secteur"] = secteur
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self.data["trait"] = self.get_ident_no_trait()
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self.data["no"] = self.get_observation("Code Collection coquille").strip().split("-")[-1]
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self.data["taille"] = self.get_observation("Longuer (biométrie)").replace(".",",")
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self.data["taille (old)"] = self.get_observation("Longueur").replace(".",",")
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self.data["poids_vif"] = self.get_observation("Poids vif").replace(".",",")
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self.data["poids_muscle"] = self.get_observation("Poids du muscle").replace(".",",")
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self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",")
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self.data["poids_visceres"] = self.get_observation("Poids des viscères").replace(".",",")
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self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",")
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self.data["sexe"] = self.get_observation("Sexe")
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self.data["comment"] = self.get_comment()
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def __next__(self):
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"""
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Increment to focus on next row
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"""
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# print(self.table_name)
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# print(f"{self._row_idx} of {len(self._row_list)}")
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# print()
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if self._row_idx is not None and self._row_list is not None:
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if self._row_idx < len(self._row_list):
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# increment first, it'l be adjusted in _get_current_row_pk()
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self._row_idx += 1
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self.populate_data()
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# self.write_row()
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return self.data
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else:
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raise StopIteration
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else:
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self.logger.error("Row data not initialise, did you run _init_rows()?")
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raise ValueError
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def _init_rows(self):
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"""Initialisation method
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This queries the Andes DB and creates a list of row entries to be added to the current table
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After running this methods initialises the following attribute:
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self._row_list
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self._row_idx (hopefully to self._row_idx=0)
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self._row_list will be populated with the specimen ids belonging in the collection
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self._row_idx will start at 0
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"""
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query = (
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"SELECT specimen_id "
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"FROM ecosystem_survey_observation "
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"LEFT JOIN ecosystem_survey_specimen "
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"ON ecosystem_survey_observation.specimen_id = ecosystem_survey_specimen.id "
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"LEFT JOIN ecosystem_survey_basket "
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"ON ecosystem_survey_specimen.basket_id = ecosystem_survey_basket.id "
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"LEFT JOIN ecosystem_survey_catch "
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"ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id "
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"LEFT JOIN shared_models_set "
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"ON shared_models_set.id=ecosystem_survey_catch.set_id "
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"LEFT JOIN shared_models_observationtype "
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"ON shared_models_observationtype.id=observation_type_id "
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f"WHERE shared_models_set.cruise_id = {self.proj._get_current_row_pk()} "
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f"AND (shared_models_observationtype.nom ='{self.collection_name}' AND observation_value=1) "
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)
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result = self.andes_db.execute_query(query)
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self._assert_not_empty(result)
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self._row_list = [specimen[0] for specimen in result]
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self._row_idx = 0
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# @validate_int()
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# @log_results
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def get_ident_no_trait(self) -> int:
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"""IDENT_NO_TRAIT INTEGER / NUMBER(5,0)
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Numéro séquentiel d'identification du trait
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Andes
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-----
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shared_models.set.set_number
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"""
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specimen_pk = self._get_current_row_pk()
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query = (
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"SELECT shared_models_set.set_number "
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"FROM ecosystem_survey_specimen "
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"LEFT JOIN ecosystem_survey_basket "
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"ON ecosystem_survey_specimen.basket_id=ecosystem_survey_basket.id "
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"LEFT JOIN ecosystem_survey_catch "
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"ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id "
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"LEFT JOIN shared_models_set "
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"ON shared_models_set.id=ecosystem_survey_catch.set_id "
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f"WHERE ecosystem_survey_specimen.id={specimen_pk} "
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)
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result = self.andes_db.execute_query(query)
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self._assert_one(result)
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to_return = result[0][0]
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return to_return
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def get_observation(self, name_fr):
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specimen_pk = self._get_current_row_pk()
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query = (
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"SELECT observation_value "
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"FROM ecosystem_survey_observation "
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"LEFT JOIN shared_models_observationtype "
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"ON ecosystem_survey_observation.observation_type_id=shared_models_observationtype.id "
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f"WHERE ecosystem_survey_observation.specimen_id={specimen_pk} "
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f"AND shared_models_observationtype.nom='{name_fr}' "
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)
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result = self.andes_db.execute_query(query)
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try:
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self._assert_one(result)
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to_return = result[0][0]
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except ValueError:
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# print('error:', specimen_pk, name_fr,result)
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to_return = None
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if to_return is None:
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to_return=""
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return to_return
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def get_comment(self):
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specimen_pk = self._get_current_row_pk()
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query = (
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"SELECT ecosystem_survey_specimen.comment "
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"FROM ecosystem_survey_specimen "
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f"WHERE ecosystem_survey_specimen.id={specimen_pk} "
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)
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result = self.andes_db.execute_query(query)
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self._assert_one(result)
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to_return = result[0][0]
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if to_return is None:
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to_return=""
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to_return.replace("\n", " ")
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to_return.replace("\r", " ")
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return to_return
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‎docs/source/contraintes.md

+2-1
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,6 @@ Doit corréspondre à une entrée de la table `PROJET_MOLLUSQUE` ayant une valeu
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Pour les mission pétoncle, un de ces choix:
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- `Évaluation de stocks IML - Pétoncle I de M`
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- `Évaluation de stocks IML - Pétoncle Minganie`
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Pour les missions buccin:
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- `Relevé buccin Haute Côte-Nord`
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@@ -43,6 +42,8 @@ Doit corréspondre à une entrée de la table `TRAIT_MOLLUSQUE` ayant une valeur
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Pour les mission pétoncle, un de ces choix:
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- `Îles-de-la-Madeleine`
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- `Côte-Nord`
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Pour les missions buccin:
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- `Haute Côte-Nord`
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Pour les missions buccin:
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- `Haute Côte-Nord`

‎run.py

+51-21
Original file line numberDiff line numberDiff line change
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import csv
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import shutil
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import pyodbc
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import logging
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import logging
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from andes_migrate.biometrie_petoncle import BiometriePetoncle
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from andes_migrate.capture_mollusque import CaptureMollusque
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from andes_migrate.oracle_helper import OracleHelper
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# INPUT VALUES
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no_notification = "IML-2023-011"
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zone = "20"
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no_notification = "IML-2024-008E"
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zone = "16E"
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espece = "pétoncle"
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SEQ_peche = 151
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SEQ_peche = 0
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output_fname = f'./{no_notification}.mdb'
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shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
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proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
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for p in proj:
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print(f"Projet: ", p)
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trait = TraitMollusque(andes_db, proj, output_cur)
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for t in trait:
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no_moll = 1
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print(f"Trait: ", t)
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engin = EnginMollusque(trait, output_cur)
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for e in engin:
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# print(f"Engin: ", e)
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capture = CaptureMollusque(engin, output_cur)
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for c in capture:
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# print(f"Capture: ", c)
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freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
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for f in freq:
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# print(f"FreqLong: ", f)
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# if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) :
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no_moll += 1
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collection_name = 'Conserver un specimen'
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# observationgroup_name = 'Biometrie 16E extérieur'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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with open('Biometrie_16E.csv','w') as fp:
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writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
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"secteur",
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"trait",
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"no",
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"taille",
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"taille (old)",
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"poids_vif",
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"poids_muscle",
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"poids_gonade",
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"poids_visceres",
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"poids_gonade",
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"sexe",
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"comment"])
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writer.writeheader()
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for b in biometrie:
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# print(b)
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if b is not None:
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writer.writerow(b)
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exit()
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# trait = TraitMollusque(andes_db, proj, output_cur)
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# for t in trait:
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# no_moll = 1
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# print(f"Trait: ", t)
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# engin = EnginMollusque(trait, output_cur)
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# for e in engin:
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# # print(f"Engin: ", e)
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# capture = CaptureMollusque(engin, output_cur)
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# for c in capture:
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# # print(f"Capture: ", c)
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# freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
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# for f in freq:
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# # print(f"FreqLong: ", f)
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# # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) :
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# no_moll += 1
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# monolithic commit if no errors are found
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output_cur.commit()
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# output_cur.commit()
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