From 0fbfd6ee0139493e7828a9da419e097bf71ffe0b Mon Sep 17 00:00:00 2001
From: David Sean <david.sean@gmail.com>
Date: Tue, 20 Feb 2024 10:24:03 -0500
Subject: [PATCH] add runners

---
 make_accessdb.py     | 123 +++++++++++++++++++++++++++++++++++++++++++
 make_biodiversity.py | 123 +++++++++++++++++++++++++++++++++++++++++++
 make_biometry.py     | 123 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 369 insertions(+)
 create mode 100644 make_accessdb.py
 create mode 100644 make_biodiversity.py
 create mode 100644 make_biometry.py

diff --git a/make_accessdb.py b/make_accessdb.py
new file mode 100644
index 0000000..692ccfc
--- /dev/null
+++ b/make_accessdb.py
@@ -0,0 +1,123 @@
+import csv
+import shutil
+import pyodbc
+import logging
+from andes_migrate.biometrie_petoncle import BiometriePetoncle 
+
+from andes_migrate.capture_mollusque import CaptureMollusque
+from andes_migrate.oracle_helper import OracleHelper
+from andes_migrate.projet_mollusque import ProjetMollusque
+from andes_migrate.trait_mollusque import TraitMollusque
+from andes_migrate.engin_mollusque import EnginMollusque
+from andes_migrate.freq_long_mollusque import FreqLongMollusque
+from andes_migrate.andes_helper import AndesHelper
+
+
+logging.basicConfig(level=logging.ERROR)
+
+
+andes_db = AndesHelper()
+access_file = 'andes_migrate/ref_data/access_template.mdb'
+ref = OracleHelper(access_file=access_file)
+
+
+# INPUT VALUES
+no_notification = "IML-2023-011"
+zone = "20"
+espece = "pétoncle"
+SEQ_peche = 151
+
+output_fname = f'./{no_notification}.mdb'
+shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
+con = pyodbc.connect(
+    f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
+)
+output_cur = con.cursor()
+
+
+# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
+# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
+proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
+
+
+
+for p in proj:
+    print(f"Projet: ", p)
+
+    with open('biometrie.csv','w') as fp:
+        writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
+                                                                    "secteur",
+                                                                    "trait",
+                                                                    "no",
+                                                                    "taille", 
+                                                                    "poids_vif",
+                                                                    "poids_muscle", 
+                                                                    "poids_gonade",
+                                                                    "poids_visceres",
+                                                                    "poids_gonade",
+                                                                    "sexe",
+                                                                    "comment"])
+        writer.writeheader()
+        collection_name='Conserver le spécimen (Biométrie Ouest)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            writer.writerow(b)
+
+        collection_name='Conserver le spécimen (Biométrie Centre)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            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()
+
+
+
+
+
+# for i in range(12):
+#     trait._increment_row()
+# print("trait: ", trait.get_ident_no_trait())
+
+# statement = trait.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+
+# statement = engin.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# capture.populate_data()
+# statement = capture.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# freq_long = FreqLongMollusque(capture)
+# print("iterating...")
+# for i in FreqLongMollusque(capture, output_cur):
+#     print(i)
+#     # statement = i.get_insert_statement()
+#     # cur.execute(statement)
+#     # cur.commit()
diff --git a/make_biodiversity.py b/make_biodiversity.py
new file mode 100644
index 0000000..692ccfc
--- /dev/null
+++ b/make_biodiversity.py
@@ -0,0 +1,123 @@
+import csv
+import shutil
+import pyodbc
+import logging
+from andes_migrate.biometrie_petoncle import BiometriePetoncle 
+
+from andes_migrate.capture_mollusque import CaptureMollusque
+from andes_migrate.oracle_helper import OracleHelper
+from andes_migrate.projet_mollusque import ProjetMollusque
+from andes_migrate.trait_mollusque import TraitMollusque
+from andes_migrate.engin_mollusque import EnginMollusque
+from andes_migrate.freq_long_mollusque import FreqLongMollusque
+from andes_migrate.andes_helper import AndesHelper
+
+
+logging.basicConfig(level=logging.ERROR)
+
+
+andes_db = AndesHelper()
+access_file = 'andes_migrate/ref_data/access_template.mdb'
+ref = OracleHelper(access_file=access_file)
+
+
+# INPUT VALUES
+no_notification = "IML-2023-011"
+zone = "20"
+espece = "pétoncle"
+SEQ_peche = 151
+
+output_fname = f'./{no_notification}.mdb'
+shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
+con = pyodbc.connect(
+    f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
+)
+output_cur = con.cursor()
+
+
+# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
+# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
+proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
+
+
+
+for p in proj:
+    print(f"Projet: ", p)
+
+    with open('biometrie.csv','w') as fp:
+        writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
+                                                                    "secteur",
+                                                                    "trait",
+                                                                    "no",
+                                                                    "taille", 
+                                                                    "poids_vif",
+                                                                    "poids_muscle", 
+                                                                    "poids_gonade",
+                                                                    "poids_visceres",
+                                                                    "poids_gonade",
+                                                                    "sexe",
+                                                                    "comment"])
+        writer.writeheader()
+        collection_name='Conserver le spécimen (Biométrie Ouest)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            writer.writerow(b)
+
+        collection_name='Conserver le spécimen (Biométrie Centre)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            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()
+
+
+
+
+
+# for i in range(12):
+#     trait._increment_row()
+# print("trait: ", trait.get_ident_no_trait())
+
+# statement = trait.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+
+# statement = engin.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# capture.populate_data()
+# statement = capture.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# freq_long = FreqLongMollusque(capture)
+# print("iterating...")
+# for i in FreqLongMollusque(capture, output_cur):
+#     print(i)
+#     # statement = i.get_insert_statement()
+#     # cur.execute(statement)
+#     # cur.commit()
diff --git a/make_biometry.py b/make_biometry.py
new file mode 100644
index 0000000..692ccfc
--- /dev/null
+++ b/make_biometry.py
@@ -0,0 +1,123 @@
+import csv
+import shutil
+import pyodbc
+import logging
+from andes_migrate.biometrie_petoncle import BiometriePetoncle 
+
+from andes_migrate.capture_mollusque import CaptureMollusque
+from andes_migrate.oracle_helper import OracleHelper
+from andes_migrate.projet_mollusque import ProjetMollusque
+from andes_migrate.trait_mollusque import TraitMollusque
+from andes_migrate.engin_mollusque import EnginMollusque
+from andes_migrate.freq_long_mollusque import FreqLongMollusque
+from andes_migrate.andes_helper import AndesHelper
+
+
+logging.basicConfig(level=logging.ERROR)
+
+
+andes_db = AndesHelper()
+access_file = 'andes_migrate/ref_data/access_template.mdb'
+ref = OracleHelper(access_file=access_file)
+
+
+# INPUT VALUES
+no_notification = "IML-2023-011"
+zone = "20"
+espece = "pétoncle"
+SEQ_peche = 151
+
+output_fname = f'./{no_notification}.mdb'
+shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
+con = pyodbc.connect(
+    f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
+)
+output_cur = con.cursor()
+
+
+# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
+# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
+proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
+
+
+
+for p in proj:
+    print(f"Projet: ", p)
+
+    with open('biometrie.csv','w') as fp:
+        writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
+                                                                    "secteur",
+                                                                    "trait",
+                                                                    "no",
+                                                                    "taille", 
+                                                                    "poids_vif",
+                                                                    "poids_muscle", 
+                                                                    "poids_gonade",
+                                                                    "poids_visceres",
+                                                                    "poids_gonade",
+                                                                    "sexe",
+                                                                    "comment"])
+        writer.writeheader()
+        collection_name='Conserver le spécimen (Biométrie Ouest)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            writer.writerow(b)
+
+        collection_name='Conserver le spécimen (Biométrie Centre)'
+        biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
+        for b in biometrie:
+            print(b)
+            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()
+
+
+
+
+
+# for i in range(12):
+#     trait._increment_row()
+# print("trait: ", trait.get_ident_no_trait())
+
+# statement = trait.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+
+# statement = engin.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# capture.populate_data()
+# statement = capture.get_insert_statement()
+# cur.execute(statement)
+# cur.commit()
+
+# freq_long = FreqLongMollusque(capture)
+# print("iterating...")
+# for i in FreqLongMollusque(capture, output_cur):
+#     print(i)
+#     # statement = i.get_insert_statement()
+#     # cur.execute(statement)
+#     # cur.commit()