Biometrie hack

andes_migrate/biometrie_petoncle.py

@@ -0,0 +1,176 @@
+
+
+from andes_migrate.andes_helper import AndesHelper
+from andes_migrate.projet_mollusque import ProjetMollusque
+from andes_migrate.table_peche_sentinelle import TablePecheSentinelle
+
+
+class BiometriePetoncle(TablePecheSentinelle):
+
+    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)
+
+        self.andes_db = andes_db
+        self.proj: ProjetMollusque = proj
+        self.collection_name:str = collection_name 
+        # self.table_name = "TRAIT_MOLLUSQUE"
+
+        # call this form outside
+        self._init_rows()
+
+    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"
+
+        # 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()
+
+    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()
+
+                # self.write_row()
+                return self.data
+            else:
+                raise StopIteration
+        else:
+            self.logger.error("Row data not initialise, did you run _init_rows()?")
+            raise ValueError
+
+
+    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
+
+    # @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
+
+
+    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
+
+    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
+
+
+
+
+
+

docs/source/contraintes.md

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

run.py

@@ -1,6 +1,8 @@
+import csv
 import shutil
 import pyodbc
-import logging 
+import logging
+from andes_migrate.biometrie_petoncle import BiometriePetoncle 
 
 from andes_migrate.capture_mollusque import CaptureMollusque
 from andes_migrate.oracle_helper import OracleHelper
@@ -20,10 +22,10 @@
 
 
 # INPUT VALUES
-no_notification = "IML-2023-011"
-zone = "20"
+no_notification = "IML-2024-008E"
+zone = "16E"
 espece = "pétoncle"
-SEQ_peche = 151
+SEQ_peche = 0
 
 output_fname = f'./{no_notification}.mdb'
 shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
@@ -38,28 +40,56 @@
 proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
 
 
+
 for p in proj:
     print(f"Projet: ", p)
-    trait = TraitMollusque(andes_db, proj, output_cur)
-    for t in trait:
-        no_moll = 1
-        print(f"Trait: ", t)
-        engin = EnginMollusque(trait, output_cur)
-        for e in engin:
-            # print(f"Engin: ", e)
-            capture = CaptureMollusque(engin, output_cur)
-            for c in capture:
-                # print(f"Capture: ", c)
-
-                freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
-                for f in freq:
-                    # print(f"FreqLong: ", f)
-                    # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) : 
-                    no_moll += 1
+
+    collection_name = 'Conserver un specimen'
+    # observationgroup_name = 'Biometrie 16E extérieur' 
+    biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+    with open('Biometrie_16E.csv','w') as fp:
+        writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
+                                                                    "secteur",
+                                                                    "trait",
+                                                                    "no",
+                                                                    "taille", 
+                                                                    "taille (old)",
+                                                                    "poids_vif",
+                                                                    "poids_muscle", 
+                                                                    "poids_gonade",
+                                                                    "poids_visceres",
+                                                                    "poids_gonade",
+                                                                    "sexe",
+                                                                    "comment"])
+        writer.writeheader()
+        for b in biometrie:
+            # print(b)
+            if b is not None:
+                writer.writerow(b)
+
+
+
+    exit()
+#     trait = TraitMollusque(andes_db, proj, output_cur)
+#     for t in trait:
+#         no_moll = 1
+#         print(f"Trait: ", t)
+#         engin = EnginMollusque(trait, output_cur)
+#         for e in engin:
+#             # print(f"Engin: ", e)
+#             capture = CaptureMollusque(engin, output_cur)
+#             for c in capture:
+#                 # print(f"Capture: ", c)
+
+#                 freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
+#                 for f in freq:
+#                     # print(f"FreqLong: ", f)
+#                     # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) : 
+#                     no_moll += 1
 
 
 # monolithic commit if no errors are found
-output_cur.commit()
+# output_cur.commit()