export 2024

andes_migrate/capture_mollusque.py

@@ -57,9 +57,12 @@ def _init_rows(self):
         placopecten_magellanicus = 156972
         chlamys_islandica = 140692
 
-        # DOUBLE HACK! only choose catches that contain baskets that are NOT and NA size-class (shared_models_sizeclass.code=0)
+        # 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
 
         query = (
             "SELECT DISTINCT ecosystem_survey_catch.id "
@@ -74,7 +77,8 @@ 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=0 "
+            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}) "
             "ORDER BY ecosystem_survey_catch.id ASC "
@@ -814,6 +818,8 @@ def _compute_couverture_epibiont(self, catch_id: int) -> int | None:
             f"AND ecosystem_survey_observation.observation_type_id='{observation_coverage_type_id}' "
             f"AND NOT ecosystem_survey_observation.observation_value='{observation_value_no_barnacles}' "
             "AND ecosystem_survey_observation.observation_value IS NOT NULL "
+            "AND NOT ecosystem_survey_observation.observation_value='NaN' "
+
         )
         result = self.andes_db.execute_query(query)
 

andes_migrate/engin_mollusque.py

@@ -121,29 +121,31 @@ def get_no_engin(self) -> int:
         """COD_ENG_GEN INTEGER / NUMBER(5,0)
         Numéro identifiant l'engin utilisé tel que défini dans la table NO_ENGIN
 
-        Andes: shared_models_set.gear_type_id-> shared_models.geartype.code
+        Andes: shared_models_auxiliaryequipment.code
 
         This one would be good to have linked with a regional code lookup
         https://github.com/dfo-gulf-science/andes/issues/988
 
         Code lookup
+        1 -> Engin babord
+        2 -> Engin tribord
+        3 -> Treuil océano
 
         """
 
         set_pk = self.trait._get_current_row_pk()
         query = (
-            "SELECT shared_models_set.winch_code "
+            "SELECT shared_models_auxiliaryequipment.code "
             "FROM shared_models_set "
-            "LEFT JOIN shared_models_set_operations "
-            "ON shared_models_set_operations.set_id = shared_models_set.id "
-            "LEFT JOIN shared_models_operation "
-            "ON shared_models_operation.id = shared_models_set_operations.operation_id "
+            "LEFT JOIN shared_models_auxiliaryequipment "
+            "ON shared_models_set.auxiliary_equipment_id = shared_models_auxiliaryequipment.id "
 
             f"WHERE shared_models_set.id={set_pk} "
         )
         result = self.andes_db.execute_query(query)
         self._assert_one(result)
         to_return = result[0][0]
+
         return to_return
 
     @log_results

andes_migrate/projet_mollusque.py

@@ -2,6 +2,7 @@
 import datetime
 
 from andes_migrate.andes_helper import AndesHelper
+from andes_migrate.oracle_helper import OracleHelper
 from andes_migrate.table_peche_sentinelle import TablePecheSentinelle
 from andes_migrate.decorators import (
     AndesCodeLookup,
@@ -54,7 +55,12 @@ def validate(self):
             )
         if self.zone in ["20"] and not cod_source_info == 19:
             raise ValueError(
-                f"La zone {self.zone} est incompatible avec le COD_SOURCE_INFO: {cod_source_info}"
+                f"La zones {self.zone} est incompatible avec le COD_SOURCE_INFO: {cod_source_info}"
+            )
+
+        if self.zone is None and cod_source_info == 18:
+            raise ValueError(
+                f"Le COD_SOURCE_INFO: {cod_source_info} doit spécifier la zone de peche 16E ou 16F"
             )
 
         # year compatible with start and end dates
@@ -103,12 +109,12 @@ def _init_rows(self):
 
     def init_input(
         self,
-        zone: str = "defaultzone",
+        zone: str|None = None,
         no_notif: str = "IML-2000-001",
         espece: str = "pétoncle",
     ):
         """
-        zone (str): 16E, 16F ou 20
+        zone (str): 16E, 16F or None. ONLY for petoncle minganie 
 
         """
 
@@ -118,7 +124,7 @@ def init_input(
             )
         self.espece = espece
 
-        if zone not in ["16E", "16F", "20"]:
+        if zone not in ["16E", "16F", "20", None]:
             raise ValueError("zone doit etre un de 16E, 16F ou 20")
         self.zone = zone
 
@@ -171,6 +177,8 @@ def get_cod_source_info(self) -> int:
         18 -> Évaluation de stocks IML - Pétoncle Minganie
         19 -> Évaluation de stocks IML - Pétoncle I de M (Access)
         19 -> Évaluation de stocks IML - Pétoncle Îles-de-la-Madeleine (Oracle)
+        22 -> Relevé buccin Haute Côte-Nord
+
         """
         query = (
             f"SELECT shared_models_cruise.description "
@@ -299,6 +307,7 @@ def get_cod_serie_hist(self) -> int:
         15 -> Indice d'abondance zone 16E - pétoncle
         16 -> Indice d'abondance zone 16F - pétoncle
         18 -> Indice d'abondance zone 20 - pétoncle
+        20 -> Indice d'abondance buccin
 
         Valid description should be one of
             Indice d'abondance zone 16E - pétoncle
@@ -311,8 +320,11 @@ def get_cod_serie_hist(self) -> int:
         # TODO: use COD_SERIE_HIST as datainput
         if self.espece == "pétoncle":
             desc = f"Indice d'abondance zone {self.zone} - {self.espece}"
-        else:
+        elif self.espece == "buccin":
             desc = f"Indice d'abondance {self.espece}"
+        else:
+            print("cannot find description for COD_SERIE_HIST")
+            raise ValueError
 
         key = self.reference_data.get_ref_key(
             table="Indice_Suivi_Etat_Stock",
@@ -417,7 +429,7 @@ def get_date_fin_project(self) -> str | None:
 
         return to_return
 
-    @validate_string(max_len=12)
+    @validate_string(max_len=13)
     @log_results
     def get_no_notif_iml(self) -> str | None:
         """NO_NOTIF_IML VARCHAR(12) / VARCHAR2(12)
@@ -572,7 +584,8 @@ def get_dist_chalute_visee(self) -> float | None:
 
         Andes: `shared_models_cruise.targeted_trawl_distance`
 
-        units: meters
+        units: meters Andes stores this in nautical miles, need to convert to m.
+
 
         N.B Andes does not permit setting this value, but will rather calculate it.
 
@@ -591,6 +604,7 @@ def get_dist_chalute_visee(self) -> float | None:
         self._assert_one(result)
         to_return = result[0][0]
         to_return = float(to_return)
+        to_return = OracleHelper.convert_nm_2_km(to_return)*1000
         return to_return
 
     @tag(HardCoded)

andes_migrate/ref_data/stations_BC.csv

@@ -0,0 +1,12 @@
+name,type,latitude,longitude,comments
+101,27,49.20604167,-68.08777778,
+102,1,49.20025,-68.08777778,
+103,1,49.19431944,-68.08777778,
+104,1,49.18855556,-68.08777778,
+105,1,49.18273611,-68.08777778,
+106,1,49.17693056,-68.08777778,
+107,1,49.171,-68.08777778,
+108,1,49.16506944,-68.08777778,
+109,1,49.15927778,-68.09269444,
+110,1,49.15333333,-68.09716667,
+111,27,49.14766667,-68.09716667,

andes_migrate/ref_data/stations_FOR.csv

@@ -0,0 +1,56 @@
+name,type,latitude,longitude,comments
+001,1,48.77044444,-68.94191667,
+002,27,48.764625,-68.95073611,
+003,1,48.764625,-68.95955556,
+004,1,48.75880556,-68.95955556,
+005,1,48.75880556,-68.96855556,
+006,1,48.75880556,-68.977375,
+007,1,48.75298611,-68.95955556,
+008,1,48.75298611,-68.96855556,
+009,1,48.75298611,-68.977375,
+010,1,48.75298611,-68.98618889,
+011,1,48.74715278,-68.96855556,
+012,1,48.74715278,-68.977375,
+013,1,48.74715278,-68.98618889,
+014,1,48.74715278,-68.995,
+015,1,48.74120278,-68.977375,
+016,1,48.74120278,-68.98618889,
+017,1,48.74120278,-68.995,
+018,1,48.74120278,-69.00380556,
+019,1,48.73537778,-68.977375,
+020,1,48.73537778,-68.98618889,
+021,1,48.73537778,-68.995,
+022,1,48.73537778,-69.00380556,
+023,1,48.72955556,-68.98618889,
+024,1,48.72955556,-68.995,
+025,1,48.72955556,-69.00380556,
+026,27,48.72955556,-69.01261111,
+027,1,48.72372222,-68.98618889,
+028,1,48.72372222,-68.995,
+035,1,48.7179,-69.02141667,
+036,1,48.71207222,-69.00380556,
+037,1,48.71207222,-69.01261111,
+038,1,48.71207222,-69.02141667,
+039,1,48.71207222,-69.03040278,
+040,1,48.70611111,-69.00380556,
+041,1,48.70611111,-69.01261111,
+042,1,48.70611111,-69.02141667,
+043,1,48.70611111,-69.03040278,
+044,1,48.70029167,-69.01261111,
+045,1,48.70029167,-69.02141667,
+046,1,48.70029167,-69.03040278,
+047,1,48.69445833,-69.01261111,
+048,1,48.69445833,-69.02141667,
+049,1,48.69445833,-69.03040278,
+050,1,48.68863889,-69.02141667,
+051,1,48.68863889,-69.03040278,
+052,1,48.68280556,-69.02141667,
+053,1,48.68280556,-69.03040278,
+054,1,48.68280556,-69.03918056,
+055,1,48.67698611,-69.03040278,
+056,1,48.67698611,-69.03918056,
+057,1,48.67102778,-69.03918056,
+058,1,48.66519444,-69.03918056,
+059,1,48.66519444,-69.04797222,
+060,27,48.659375,-69.03918056,
+061,1,48.659375,-69.04797222,

andes_migrate/ref_data/stations_PaO.csv

@@ -0,0 +1,27 @@
+name,type,latitude,longitude,comments
+206,1,49.00827778,-68.48127778,
+207,1,49.00527778,-68.49034722,
+208,1,49.00527778,-68.49919444,
+209,1,49.00527778,-68.50802778,
+210,1,49.00527778,-68.51686111,
+211,1,49.00527778,-68.525625,
+212,1,49.00527778,-68.53475,
+213,1,49.00527778,-68.54356944,
+214,1,49.00527778,-68.55258333,
+215,1,49.00527778,-68.56140278,
+216,27,48.99952778,-68.51686111,
+217,1,48.99952778,-68.525625,
+218,1,48.99952778,-68.53475,
+219,1,48.99952778,-68.54356944,
+220,1,48.99952778,-68.55258333,
+251,1,49.00901667,-68.56353333,
+252,1,49.00476667,-68.57445,
+253,1,49.00216667,-68.58161667,
+254,1,48.99853333,-68.58731667,
+255,27,48.99536667,-68.59416667,
+256,1,49.00963333,-68.47291667,
+257,1,49.01090278,-68.46453333,
+258,1,49.01276111,-68.45584722,
+259,1,49.014025,-68.44716944,
+260,27,49.01528889,-68.43849167,
+261,1,49.01703056,-68.43016944,

andes_migrate/ref_data/stations_buccin01.csv

@@ -0,0 +1,80 @@
+name,type,latitude,longitude,comments
+001,1,48.77044444,-68.94191667,
+002,27,48.764625,-68.95073611,
+003,1,48.764625,-68.95955556,
+004,1,48.75880556,-68.95955556,
+005,1,48.75880556,-68.96855556,
+006,1,48.75880556,-68.977375,
+007,1,48.75298611,-68.95955556,
+008,1,48.75298611,-68.96855556,
+009,1,48.75298611,-68.977375,
+010,1,48.75298611,-68.98618889,
+011,1,48.74715278,-68.96855556,
+012,1,48.74715278,-68.977375,
+013,1,48.74715278,-68.98618889,
+014,1,48.74715278,-68.995,
+015,1,48.74120278,-68.977375,
+016,1,48.74120278,-68.98618889,
+017,1,48.74120278,-68.995,
+018,1,48.74120278,-69.00380556,
+019,1,48.73537778,-68.977375,
+020,1,48.73537778,-68.98618889,
+021,1,48.73537778,-68.995,
+022,1,48.73537778,-69.00380556,
+023,1,48.72955556,-68.98618889,
+024,1,48.72955556,-68.995,
+025,1,48.72955556,-69.00380556,
+026,27,48.72955556,-69.01261111,
+027,1,48.72372222,-68.98618889,
+028,1,48.72372222,-68.995,
+035,1,48.7179,-69.02141667,
+036,1,48.71207222,-69.00380556,
+037,1,48.71207222,-69.01261111,
+038,1,48.71207222,-69.02141667,
+039,1,48.71207222,-69.03040278,
+040,1,48.70611111,-69.00380556,
+041,1,48.70611111,-69.01261111,
+042,1,48.70611111,-69.02141667,
+043,1,48.70611111,-69.03040278,
+044,1,48.70029167,-69.01261111,
+045,1,48.70029167,-69.02141667,
+046,1,48.70029167,-69.03040278,
+047,1,48.69445833,-69.01261111,
+048,1,48.69445833,-69.02141667,
+049,1,48.69445833,-69.03040278,
+050,1,48.68863889,-69.02141667,
+051,1,48.68863889,-69.03040278,
+052,1,48.68280556,-69.02141667,
+053,1,48.68280556,-69.03040278,
+054,1,48.68280556,-69.03918056,
+055,1,48.67698611,-69.03040278,
+056,1,48.67698611,-69.03918056,
+057,1,48.67102778,-69.03918056,
+058,1,48.66519444,-69.03918056,
+059,1,48.66519444,-69.04797222,
+060,27,48.659375,-69.03918056,
+061,1,48.659375,-69.04797222,
+206,1,49.00827778,-68.48127778,
+207,1,49.00527778,-68.49034722,
+208,1,49.00527778,-68.49919444,
+209,1,49.00527778,-68.50802778,
+210,1,49.00527778,-68.51686111,
+211,1,49.00527778,-68.525625,
+212,1,49.00527778,-68.53475,
+213,1,49.00527778,-68.54356944,
+214,1,49.00527778,-68.55258333,
+215,1,49.00527778,-68.56140278,
+216,27,48.99952778,-68.51686111,
+217,1,48.99952778,-68.525625,
+218,1,48.99952778,-68.53475,
+219,1,48.99952778,-68.54356944,
+220,1,48.99952778,-68.55258333,
+251,1,49.00901667,-68.56353333,
+252,1,49.00476667,-68.57445,
+253,1,49.00216667,-68.58161667,
+254,1,48.99853333,-68.58731667,
+255,27,48.99536667,-68.59416667,
+256,1,49.00963333,-68.47291667,
+257,1,49.01090278,-68.46453333,
+258,1,49.01276111,-68.45584722,
+259,1,49.014025,-68.44716944,

andes_migrate/ref_data/stations_buccin02.csv

@@ -0,0 +1,14 @@
+name,type,latitude,longitude,comments
+101,27,49.20604167,-68.08777778,
+102,1,49.20025,-68.08777778,
+103,1,49.19431944,-68.08777778,
+104,1,49.18855556,-68.08777778,
+105,1,49.18273611,-68.08777778,
+106,1,49.17693056,-68.08777778,
+107,1,49.171,-68.08777778,
+108,1,49.16506944,-68.08777778,
+109,1,49.15927778,-68.09269444,
+110,1,49.15333333,-68.09716667,
+111,27,49.14766667,-68.09716667,
+260,27,49.01528889,-68.43849167,
+261,1,49.01703056,-68.43016944,