sizeclass and aphia filters for Capture

andes_migrate/biometrie_mollusque.py

@@ -91,14 +91,14 @@ def populate_data(self):
         self.data['VOLUME_GONADE_P'] = self.get_volume_gonade_p()
         self.data['NO_CHARGEMENT'] = self.get_no_chargement()
 
+    @tag(HardCoded)
     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`
-
+        hard-coded to whelk eggs: 2151
         """
-        return self.capture.get_cod_esp_gen()
+        return self._hard_coded_result(2151)
 
     def get_cod_eng_gen(self) -> int:
         """COD_ENG_GEN INTEGER / NUMBER(5,0)

andes_migrate/capture_mollusque.py

@@ -23,15 +23,17 @@ class CaptureMollusque(TablePecheSentinelle):
     Object model representing the CAPTURE_MOLLUSQUE table
     """
 
-    def __init__(self, engin: EnginMollusque, *args, **kwargs):
+    def __init__(self, engin: EnginMollusque, *args, aphia_id_filter=None, size_class_filter=None, **kwargs):
+
         super().__init__(*args, ref=engin.reference_data, **kwargs)
 
         self.engin: EnginMollusque = engin
         self.table_name = "CAPTURE_MOLLUSQUE"
 
         self.andes_db = engin.andes_db
         self.data = {}
-
+        self.aphia_id_filter = aphia_id_filter
+        self.size_class_filter = size_class_filter
         self._init_rows()
 
     def _init_rows(self):
@@ -53,26 +55,28 @@ def _init_rows(self):
         #     "ORDER BY ecosystem_survey_catch.id ASC;"
         # )
 
-        # 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
-        # The NA basket filter is probably not needed...
-        # also do not consider basket class 9 (biodiversity basket)
-        size_class_code_NA = 0
-        size_class_code_biodiversity = 9
+        # create a SQL query to filter by aphia ids
+        aphia_id_filter_query = None
+        if self.aphia_id_filter:
+            aphia_id_filter_query='AND ('
+            # the first one
+            aphia_id_filter_query += f"shared_models_species.aphia_id = {self.aphia_id_filter[0]}"
+            # the rest
+            for aphia_id in self.aphia_id_filter[1:]:
+                aphia_id_filter_query += f" OR shared_models_species.aphia_id = {aphia_id}"
+            aphia_id_filter_query+=') '
+
+        # create a SQL query to filter by size class codes
+        size_class_filter_query = None
+        if self.size_class_filter:
+            size_class_filter_query='AND ('
+            # the first one
+            size_class_filter_query += f"shared_models_sizeclass.code={self.size_class_filter[0]}"
+            # the rest
+            for size_class_code in self.size_class_filter[1:]:
+                size_class_filter_query += f" OR shared_models_sizeclass.code={size_class_code}"
+            size_class_filter_query+=') '
 
         query = (
             "SELECT DISTINCT ecosystem_survey_catch.id "
@@ -87,17 +91,15 @@ def _init_rows(self):
             "LEFT JOIN shared_models_cruise "
             "ON shared_models_cruise.sampling_protocol_id = shared_models_sizeclass.sampling_protocol_id "
             f"WHERE shared_models_cruise.id={self.engin.trait.proj._get_current_row_pk()} "
-            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"{species_filter} "
+            f"{size_class_filter_query if size_class_filter_query else ''} "
+            f"{aphia_id_filter_query if aphia_id_filter_query else ''} "
             "ORDER BY ecosystem_survey_catch.id ASC "
         )
 
         result = self.andes_db.execute_query(query)
         # a set could be empty,
         # self._assert_not_empty(result)
-
         # a list of all the catch pk's (need to unpack a bit)
         self._row_list = [catch[0] for catch in result]
         self._row_idx = 0
@@ -186,6 +188,13 @@ def get_cod_esp_gen(self) -> int:
 
 
         """
+        oeufs_buccin_size_class = 3
+        espece = "buccin"
+        # HACK for whelk eggs,
+        if self.engin.trait.proj.espece=="buccin" and self.size_class_filter and oeufs_buccin_size_class in self.size_class_filter:
+            self.logger.info("cod_es_gen hack for whelk eggs")
+            return self._hard_coded_result(2151)
+
         query = (
             "SELECT shared_models_species.id, shared_models_species.aphia_id, shared_models_species.code "
             "FROM ecosystem_survey_catch "
@@ -199,7 +208,6 @@ def get_cod_esp_gen(self) -> int:
         andes_id = result[0][0]
         andes_aphia_id = result[0][1]
         andes_code = result[0][2]
-        # print( andes_id, andes_aphia_id, andes_code)
 
         # try to match an aphia_id
         self.logger.info(

make_access_IML-2024008.py

@@ -18,12 +18,26 @@
 access_file = 'andes_migrate/ref_data/access_template.mdb'
 ref = OracleHelper(access_file=access_file)
 
+placopecten_magellanicus = 156972
+chlamys_islandica = 140692
+buccinum_undatum = 138878
+
+na_size_class = 0
+claquette_ouverte=2
+vivant_intact_size_class = 1
+vivant_brisé_size_class = 2
+oeufs_Buccin_size_class = 3
+predateur_size_class = 4
+biodiversite_size_class = 9
+
 
 # INPUT VALUES
 no_notification = "IML-2024-008F"
 zone = "16F"
 espece = "pétoncle"
 SEQ_peche = 151
+aphia_id_filter = [placopecten_magellanicus, chlamys_islandica]
+size_class_filter = [vivant_intact_size_class, claquette_ouverte]
 
 output_fname = f'./{no_notification}.mdb'
 shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)

make_access_IML-2024009.py

@@ -18,12 +18,27 @@
 access_file = 'andes_migrate/ref_data/access_template.mdb'
 ref = OracleHelper(access_file=access_file)
 
+placopecten_magellanicus = 156972
+chlamys_islandica = 140692
+buccinum_undatum = 138878
+
+na_size_class = 0
+claquette_ouverte=2
+vivant_intact_size_class = 1
+vivant_brisé_size_class = 2
+oeufs_Buccin_size_class = 3
+predateur_size_class = 4
+biodiversite_size_class = 9
+
 
 # INPUT VALUES
 no_notification = "IML-2024-009"
 zone = "20"
 espece = "pétoncle"
 SEQ_peche = 151
+aphia_id_filter = [placopecten_magellanicus, chlamys_islandica]
+size_class_filter = [vivant_intact_size_class, claquette_ouverte]
+
 
 output_fname = f'./{no_notification}.mdb'
 shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)

make_access_IML-2024022.py

@@ -21,12 +21,27 @@
 access_file = 'andes_migrate/ref_data/access_template.mdb'
 ref = OracleHelper(access_file=access_file)
 
+# HACK! only choose aphia IDs for commercial target species
+placopecten_magellanicus = 156972
+chlamys_islandica = 140692
+buccinum_undatum = 138878
+
+na_size_class = 0
+claquette_ouverte=2
+vivant_intact_size_class = 1
+vivant_brisé_size_class = 2
+oeufs_buccin_size_class = 3
+predateur_size_class = 4
+biodiversite_size_class = 9
 
 # INPUT VALUES
 no_notification = "IML-2024-022"
 zone = None
 espece = "buccin"
 SEQ_peche = 151
+aphia_id_filter = [buccinum_undatum]
+size_class_filter = [vivant_intact_size_class, vivant_brisé_size_class]
+
 
 output_fname = f'./{no_notification}.mdb'
 shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
@@ -55,7 +70,10 @@
             engin = EnginMollusque(trait, output_cur)
             for e in engin:
                 # print(f"Engin: ", e)
-                capture = CaptureMollusque(engin, output_cur)
+                # capture for freq-long
+                capture = CaptureMollusque(engin, output_cur,
+                                           aphia_id_filter=aphia_id_filter,
+                                           size_class_filter=[vivant_intact_size_class, vivant_brisé_size_class])
                 for c in capture:
                     # print(f"Capture: ", c)
 
@@ -65,6 +83,11 @@
                         # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) : 
                         no_moll_freq_long += 1
 
+                # capture for biometrie (whelk eggs)
+                capture = CaptureMollusque(engin, output_cur,
+                                           aphia_id_filter=aphia_id_filter,
+                                           size_class_filter=[oeufs_buccin_size_class])
+                for c in capture:
                     biometrie = BiometrieMollusque(capture, output_cur, no_moll_init=no_moll_biometrie)
                     for b in biometrie:
                         print(f"biometrie: ", b)