update for whelk eggs in biometry tables

andes_migrate/biometrie_mollusque.py

@@ -0,0 +1,218 @@
+import logging
+import numpy as np
+
+from andes_migrate.capture_mollusque import CaptureMollusque
+from andes_migrate.table_peche_sentinelle import TablePecheSentinelle
+from andes_migrate.decorators import (
+    NotAndes,
+    Computed,
+    HardCoded,
+    Deprecated,
+    AndesCodeLookup,
+    tag,
+    log_results,
+    validate_string,
+    validate_int,
+)
+
+# logging.basicConfig(level=logging.INFO)
+
+
+class BiometrieMollusque(TablePecheSentinelle):
+    """
+    Object model representing the BIOMETRIE_MOLLUSQUE table
+
+    WARNING: only good for getting the weight of whelk eggs, other features (actual biometry) are not implemented
+    """
+
+    def __init__(self, capture: CaptureMollusque, *args, no_moll_init=0, **kwargs):
+        super().__init__(*args, ref=capture.reference_data, **kwargs)
+
+        self.capture: CaptureMollusque = capture
+
+        self.table_name = "BIOMETRIE_MOLLUSQUE"
+        self.andes_db = capture.andes_db
+        self.data = {}
+        self._init_rows()
+        self.no_moll = no_moll_init
+
+    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 associated Andes catch ids for the current set
+        self._row_idx will start at 0
+        For this class, the row will contain a tuple: (specimen_id, length, basket_id)
+
+        """
+
+        # HACK! only choose baskets that are WHELK EGGs size-class (shared_models_sizeclass.code=3)
+        # 3 -> oeufs buccin
+        target_size_class = 3
+
+        # DOUBLE HACK! only choose whelkes species (aphia_id=138878)
+        target_aphia_id = 138878
+
+        query = (
+            "SELECT basket_wt_kg "
+            "FROM ecosystem_survey_catch  "
+            "LEFT JOIN ecosystem_survey_basket  "
+            "ON ecosystem_survey_catch.id=ecosystem_survey_basket.catch_id "
+            "LEFT JOIN shared_models_species "
+            "ON ecosystem_survey_catch.species_id = shared_models_species.id "
+            f"WHERE ecosystem_survey_catch.id={self.capture._get_current_row_pk()} "
+            f"AND shared_models_species.aphia_id = {target_aphia_id} "
+            f"AND ecosystem_survey_basket.size_class = {target_size_class} "
+        )
+        result = self.andes_db.execute_query(query)
+
+        # a list of all the catch pk's (need to unpack a bit)
+        self._row_list = result
+        self._row_idx = 0
+
+    def populate_data(self):
+        """Populate data: run all getters"""
+        self.data["COD_SOURCE_INFO"] = self.get_cod_source_info()
+        self.data["NO_RELEVE"] = self.get_no_releve()
+        self.data["COD_NBPC"] = self.get_cod_nbpc()
+        self.data["IDENT_NO_TRAIT"] = self.get_ident_no_trait()
+        self.data["COD_ENG_GEN"] = self.get_cod_eng_gen()
+        self.data["COD_TYP_PANIER"] = self.get_cod_typ_panier()
+        self.data["NO_ENGIN"] = self.get_no_engin()
+        self.data["COD_ESP_GEN"] = self.get_cod_esp_gen()
+        self.data['NO_MOLLUSQUE'] = self.get_no_mollusque()
+
+        self.data['COD_SEXE'] = self.get_cod_sexe()
+        self.data['VOLUME_GONADE'] = self.get_volume_gonade()
+        self.data['VOLUME_GONADE_P'] = self.get_volume_gonade_p()
+        self.data['NO_CHARGEMENT'] = self.get_no_chargement()
+
+    def get_cod_esp_gen(self) -> int:
+        """COD_ESP_GEN INTEGER / NUMBER(5,0)
+        Identification de l'espèce capturée tel que défini dans la table ESPECE_GENERAL
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CapturenMollusque.get_cod_esp_gen`
+
+        """
+        return self.capture.get_cod_esp_gen()
+
+    def get_cod_eng_gen(self) -> int:
+        """COD_ENG_GEN INTEGER / NUMBER(5,0)
+        Identification de l'engin de pêche utilisé tel que défini dans la table ENGIN_GENERAL
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CapturenMollusque.get_cod_eng_gen`
+
+        """
+        return self.capture.get_cod_eng_gen()
+
+    def get_cod_source_info(self) -> int:
+        """COD_SOURCE_INFO INTEGER / NUMBER(5,0)
+        Identification de la source d'information tel que défini dans la table SOURCE_INFO
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_cod_source_info`
+
+        """
+        return self.capture.get_cod_source_info()
+
+    def get_no_releve(self) -> int:
+        """NO_RELEVE INTEGER / NUMBER(5,0)
+        Numéro séquentiel du relevé
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CAptureMollusque.get_no_releve`
+        """
+        return self.capture.get_no_releve()
+
+    def get_ident_no_trait(self) -> int:
+        """IDENT_NO_TRAIT INTEGER / NUMBER(5,0)
+        Numéro séquentiel d'identification du trait
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_ident_no_trait`
+        """
+        return self.capture.get_ident_no_trait()
+
+    def get_cod_typ_panier(self) -> int:
+        """COD_TYP_PANIER INTEGER / NUMBER(5,0)
+        Identification du type de panier utilisé tel que défini dans la table TYPE_PANIER
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_cod_type_panier`
+
+        """
+
+        return self.capture.get_cod_typ_panier()
+
+    def get_cod_nbpc(self) -> str:
+        """COD_NBPC VARCHAR(6) / VARCHAR2(6)
+        Numéro du navire utilisé pour réaliser le relevé tel que défini dans la table NAVIRE
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_cod_nbpc`
+
+        """
+        return self.capture.get_cod_nbpc()
+
+    def get_no_engin(self) -> int:
+        """NO_ENGIN INTEGER/ NUMBER(5,0)
+        Numéro identifiant l'engin utilisé tel que défini dans la table NO_ENGIN
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_no_engin`
+
+        """
+
+        return self.capture.get_no_engin()
+
+    @tag(HardCoded)
+    @validate_int()
+    def get_cod_sexe(self) -> int:
+        """COD_SEXE INTEGER / NUMBER(5,0)
+        Sexe de l''organisme tel que décrit dans la table SEXE
+
+        Hard-coded: This function always returns 9
+        9 -> inconnu / indéterminé
+        """
+
+        return self._hard_coded_result(9)
+
+    @tag(HardCoded)
+    def get_volume_gonade(self) -> float|None:
+        """VOLUME_GONADE FLOAT / NUMBER
+        Volume occupé par les gonades unité ml
+
+        Hard-coded: This function always returns None
+
+        """
+        return self._hard_coded_result(None)
+
+    @tag(HardCoded)
+    def get_volume_gonade_p(self) -> float|None:
+        """VOLUME_GONADE_P FLOAT / NUMBER
+        Nombre de chiffre après la décimale pour la précision d'affichage associée à "Volume_Gonade"
+
+        Hard-coded: This function always returns None
+
+        """
+        return self._hard_coded_result(None)
+
+    @validate_int()
+    @log_results
+    def get_no_mollusque(self) -> int :
+        """NO_MOLLUSQUE INTEGER / NUMBER(5,0)
+        Numéro séquentiel attribué à l'individus mesuré
+
+        """
+        adjusted_row_idx = self._row_idx-1
+
+        return self.no_moll + adjusted_row_idx
+        # raise NotImplementedError
+
+    @log_results
+    def get_no_chargement(self) -> float|None:
+        """NO_CHARGEMENT DOUBLE / NUMBER
+        Numéro de l'activité de chargement de données dans la base Oracle
+
+        Extrait de la capture ::func:`~andes_migrate.capture_mollusque.CaptureMollusque.get_no_engin`
+
+        """
+        return self.capture.get_no_chargement()

andes_migrate/capture_mollusque.py

@@ -53,9 +53,19 @@ def _init_rows(self):
         #     "ORDER BY ecosystem_survey_catch.id ASC;"
         # )
 
-        # HACK! only choose scallops aphia IDs
+        # HACK! only choose aphia IDs for commercial target species
         placopecten_magellanicus = 156972
         chlamys_islandica = 140692
+        buccinum_undatum = 138878
+        if 'pétoncle'==self.engin.trait.proj.espece:
+            species_filter = f"AND (shared_models_species.aphia_id = {placopecten_magellanicus} OR shared_models_species.aphia_id = {chlamys_islandica}) "
+        elif 'buccin'==self.engin.trait.proj.espece:
+            # NEED other bucinums, glacial, teranovae etc
+            species_filter = f"AND (shared_models_species.aphia_id = {buccinum_undatum}) "
+        else:
+            print("Problem filtering species, need aphia-ids for extraction")
+            raise ValueError
+
 
         # DOUBLE HACK! only choose catches that contain baskets that are NOT an NA size-class (shared_models_sizeclass.code=0)
         # some NA baskets can still exist in a catch that has a non-NA basket
@@ -80,7 +90,7 @@ def _init_rows(self):
             f"AND NOT shared_models_sizeclass.code={size_class_code_NA} "
             f"AND NOT shared_models_sizeclass.code={size_class_code_biodiversity} "
             f"AND ecosystem_survey_catch.set_id={self.engin.trait._get_current_row_pk()} "
-            f"AND (shared_models_species.aphia_id = {placopecten_magellanicus} OR shared_models_species.aphia_id = {chlamys_islandica}) "
+            f"{species_filter} "
             "ORDER BY ecosystem_survey_catch.id ASC "
         )