Skip to content

Commit

Permalink
add runners
Browse files Browse the repository at this point in the history
davidsean committed Feb 20, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
1 parent c5bd5a9 commit 0fbfd6e
Showing 3 changed files with 369 additions and 0 deletions.
123 changes: 123 additions & 0 deletions make_accessdb.py
Original file line number Diff line number Diff line change
@@ -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()
123 changes: 123 additions & 0 deletions make_biodiversity.py
Original file line number Diff line number Diff line change
@@ -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()
123 changes: 123 additions & 0 deletions make_biometry.py
Original file line number Diff line number Diff line change
@@ -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()

0 comments on commit 0fbfd6e

Please sign in to comment.