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davidseandavidsean
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add runners
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‎make_accessdb.py

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import csv
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import shutil
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import pyodbc
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import logging
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from andes_migrate.biometrie_petoncle import BiometriePetoncle
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from andes_migrate.capture_mollusque import CaptureMollusque
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from andes_migrate.oracle_helper import OracleHelper
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from andes_migrate.projet_mollusque import ProjetMollusque
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from andes_migrate.trait_mollusque import TraitMollusque
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from andes_migrate.engin_mollusque import EnginMollusque
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from andes_migrate.freq_long_mollusque import FreqLongMollusque
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from andes_migrate.andes_helper import AndesHelper
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logging.basicConfig(level=logging.ERROR)
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andes_db = AndesHelper()
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access_file = 'andes_migrate/ref_data/access_template.mdb'
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ref = OracleHelper(access_file=access_file)
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# INPUT VALUES
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no_notification = "IML-2023-011"
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zone = "20"
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espece = "pétoncle"
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SEQ_peche = 151
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output_fname = f'./{no_notification}.mdb'
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shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
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con = pyodbc.connect(
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f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
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)
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output_cur = con.cursor()
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# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
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# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
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proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
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for p in proj:
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print(f"Projet: ", p)
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with open('biometrie.csv','w') as fp:
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writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
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"secteur",
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"trait",
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"no",
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"taille",
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"poids_vif",
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"poids_muscle",
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"poids_gonade",
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"poids_visceres",
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"poids_gonade",
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"sexe",
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"comment"])
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writer.writeheader()
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collection_name='Conserver le spécimen (Biométrie Ouest)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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collection_name='Conserver le spécimen (Biométrie Centre)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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exit()
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# trait = TraitMollusque(andes_db, proj, output_cur)
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# for t in trait:
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# no_moll = 1
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# print(f"Trait: ", t)
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# engin = EnginMollusque(trait, output_cur)
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# for e in engin:
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# # print(f"Engin: ", e)
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# capture = CaptureMollusque(engin, output_cur)
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# for c in capture:
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# # print(f"Capture: ", c)
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# freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
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# for f in freq:
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# # print(f"FreqLong: ", f)
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# # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) :
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# no_moll += 1
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# monolithic commit if no errors are found
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# output_cur.commit()
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# for i in range(12):
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# trait._increment_row()
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# print("trait: ", trait.get_ident_no_trait())
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# statement = trait.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# statement = engin.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# capture.populate_data()
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# statement = capture.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# freq_long = FreqLongMollusque(capture)
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# print("iterating...")
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# for i in FreqLongMollusque(capture, output_cur):
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# print(i)
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# # statement = i.get_insert_statement()
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# # cur.execute(statement)
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# # cur.commit()

‎make_biodiversity.py

+123
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import csv
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import shutil
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import pyodbc
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import logging
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from andes_migrate.biometrie_petoncle import BiometriePetoncle
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from andes_migrate.capture_mollusque import CaptureMollusque
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from andes_migrate.oracle_helper import OracleHelper
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from andes_migrate.projet_mollusque import ProjetMollusque
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from andes_migrate.trait_mollusque import TraitMollusque
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from andes_migrate.engin_mollusque import EnginMollusque
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from andes_migrate.freq_long_mollusque import FreqLongMollusque
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from andes_migrate.andes_helper import AndesHelper
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logging.basicConfig(level=logging.ERROR)
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andes_db = AndesHelper()
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access_file = 'andes_migrate/ref_data/access_template.mdb'
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ref = OracleHelper(access_file=access_file)
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# INPUT VALUES
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no_notification = "IML-2023-011"
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zone = "20"
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espece = "pétoncle"
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SEQ_peche = 151
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output_fname = f'./{no_notification}.mdb'
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shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
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con = pyodbc.connect(
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f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
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)
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output_cur = con.cursor()
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# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
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# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
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proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
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for p in proj:
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print(f"Projet: ", p)
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with open('biometrie.csv','w') as fp:
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writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
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"secteur",
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"trait",
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"no",
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"taille",
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"poids_vif",
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"poids_muscle",
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"poids_gonade",
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"poids_visceres",
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"poids_gonade",
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"sexe",
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"comment"])
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writer.writeheader()
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collection_name='Conserver le spécimen (Biométrie Ouest)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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collection_name='Conserver le spécimen (Biométrie Centre)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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exit()
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# trait = TraitMollusque(andes_db, proj, output_cur)
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# for t in trait:
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# no_moll = 1
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# print(f"Trait: ", t)
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# engin = EnginMollusque(trait, output_cur)
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# for e in engin:
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# # print(f"Engin: ", e)
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# capture = CaptureMollusque(engin, output_cur)
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# for c in capture:
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# # print(f"Capture: ", c)
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# freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
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# for f in freq:
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# # print(f"FreqLong: ", f)
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# # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) :
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# no_moll += 1
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# monolithic commit if no errors are found
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# output_cur.commit()
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# for i in range(12):
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# trait._increment_row()
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# print("trait: ", trait.get_ident_no_trait())
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# statement = trait.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# statement = engin.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# capture.populate_data()
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# statement = capture.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# freq_long = FreqLongMollusque(capture)
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# print("iterating...")
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# for i in FreqLongMollusque(capture, output_cur):
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# print(i)
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# # statement = i.get_insert_statement()
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# # cur.execute(statement)
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# # cur.commit()

‎make_biometry.py

+123
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import csv
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import shutil
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import pyodbc
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import logging
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from andes_migrate.biometrie_petoncle import BiometriePetoncle
6+
7+
from andes_migrate.capture_mollusque import CaptureMollusque
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from andes_migrate.oracle_helper import OracleHelper
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from andes_migrate.projet_mollusque import ProjetMollusque
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from andes_migrate.trait_mollusque import TraitMollusque
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from andes_migrate.engin_mollusque import EnginMollusque
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from andes_migrate.freq_long_mollusque import FreqLongMollusque
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from andes_migrate.andes_helper import AndesHelper
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logging.basicConfig(level=logging.ERROR)
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andes_db = AndesHelper()
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access_file = 'andes_migrate/ref_data/access_template.mdb'
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ref = OracleHelper(access_file=access_file)
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# INPUT VALUES
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no_notification = "IML-2023-011"
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zone = "20"
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espece = "pétoncle"
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SEQ_peche = 151
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output_fname = f'./{no_notification}.mdb'
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shutil.copyfile('andes_migrate/ref_data/access_template.mdb', output_fname)
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con = pyodbc.connect(
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f"Driver={{Microsoft Access Driver (*.mdb, *.accdb)}};DBQ={output_fname};"
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)
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output_cur = con.cursor()
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# proj = ProjetMollusque(andes_db, output_cur, ref=ref)
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# proj.init_input(zone="20", no_releve=34, no_notif=no_notification, espece="pétoncle")
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proj = ProjetMollusque(andes_db, output_cur, ref=ref, zone=zone, no_notif=no_notification, espece=espece)
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for p in proj:
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print(f"Projet: ", p)
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with open('biometrie.csv','w') as fp:
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writer = csv.DictWriter(fp, lineterminator="\n", fieldnames=["id_specimen",
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"secteur",
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"trait",
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"no",
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"taille",
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"poids_vif",
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"poids_muscle",
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"poids_gonade",
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"poids_visceres",
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"poids_gonade",
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"sexe",
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"comment"])
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writer.writeheader()
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collection_name='Conserver le spécimen (Biométrie Ouest)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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collection_name='Conserver le spécimen (Biométrie Centre)'
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biometrie = BiometriePetoncle(andes_db, proj, collection_name, output_cur)
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for b in biometrie:
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print(b)
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writer.writerow(b)
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exit()
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# trait = TraitMollusque(andes_db, proj, output_cur)
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# for t in trait:
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# no_moll = 1
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# print(f"Trait: ", t)
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# engin = EnginMollusque(trait, output_cur)
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# for e in engin:
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# # print(f"Engin: ", e)
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# capture = CaptureMollusque(engin, output_cur)
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# for c in capture:
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# # print(f"Capture: ", c)
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# freq = FreqLongMollusque(capture, output_cur, no_moll_init=no_moll)
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# for f in freq:
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# # print(f"FreqLong: ", f)
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# # if (c['COD_ESP_GEN'] == 48 or c['COD_ESP_GEN'] == 50) :
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# no_moll += 1
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# monolithic commit if no errors are found
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# output_cur.commit()
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# for i in range(12):
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# trait._increment_row()
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# print("trait: ", trait.get_ident_no_trait())
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# statement = trait.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# statement = engin.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# capture.populate_data()
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# statement = capture.get_insert_statement()
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# cur.execute(statement)
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# cur.commit()
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# freq_long = FreqLongMollusque(capture)
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# print("iterating...")
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# for i in FreqLongMollusque(capture, output_cur):
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# print(i)
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# # statement = i.get_insert_statement()
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# # cur.execute(statement)
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# # cur.commit()

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