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Replace subprocess.call() with check_call() in db.py to prevent silent failures #3580

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Merged
MoralCode merged 2 commits into from
Feb 4, 2026
Merged

Replace subprocess.call() with check_call() in db.py to prevent silent failures #3580

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c39c142
Fix #3579: Replace subprocess.call() with check_call() in db.py to pr…
guptapratykshh Jan 15, 2026
3fef565
Fix docstring for check_for_upgrade() to accurately describe its purpose
guptapratykshh Jan 16, 2026
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12 changes: 6 additions & 6 deletions augur/application/cli/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
from os import environ, chmod, path, getenv
import logging
from sys import exit
from subprocess import call
from subprocess import check_call
import random
import string
import click
Expand Down Expand Up @@ -280,7 +280,7 @@
"""
Get the version of the configured database
"""
call(["alembic", "current"])
check_call(["alembic", "current"])


@cli.command("upgrade-db-version")
Expand All @@ -290,7 +290,7 @@
"""
Upgrade the configured database to the latest version
"""
call(["alembic", "upgrade", "head"])
check_call(["alembic", "upgrade", "head"])


@cli.command("check-for-upgrade")
Expand All @@ -300,7 +300,7 @@
"""
Upgrade the configured database to the latest version
"""
call(["alembic", "history", "-i"])
check_call(["alembic", "history", "-i"])


@cli.command("create-schema")
Expand All @@ -310,7 +310,7 @@
"""
Create schema in the configured database
"""
call(["alembic", "upgrade", "head"])
check_call(["alembic", "upgrade", "head"])


def generate_key(length):
Expand Down Expand Up @@ -443,24 +443,24 @@
}
}
check_pgpass_credentials(config)
run_db_creation_psql_command(

Check warning on line 446 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)

Raw Output:
augur/application/cli/db.py:446:4: E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)
host, port, default_user, default_db_name, f"CREATE DATABASE {target_db_name};"
)
run_db_creation_psql_command(

Check warning on line 449 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)

Raw Output:
augur/application/cli/db.py:449:4: E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)
host,
port,
default_user,
default_db_name,
f"CREATE USER {target_user} WITH ENCRYPTED PASSWORD '{target_password}';",
)
run_db_creation_psql_command(

Check warning on line 456 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)

Raw Output:
augur/application/cli/db.py:456:4: E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)
host,
port,
default_user,
default_db_name,
f"ALTER DATABASE {target_db_name} OWNER TO {target_user};",
)
run_db_creation_psql_command(

Check warning on line 463 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)

Raw Output:
augur/application/cli/db.py:463:4: E0602: Undefined variable 'run_db_creation_psql_command' (undefined-variable)
host,
port,
default_user,
Expand Down Expand Up @@ -513,7 +513,7 @@
db_conn_string = f"postgresql+psycopg2://{db_config['user']}:{db_config['password']}@{db_config['host']}:{db_config['port']}/{db_config['database_name']}"
engine = s.create_engine(db_conn_string)

call(
check_call(
[
"psql",
"-h",
Expand All @@ -521,9 +521,9 @@
"-d",
database_name,
"-U",
user,

Check warning on line 524 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'user' (undefined-variable)

Raw Output:
augur/application/cli/db.py:524:12: E0602: Undefined variable 'user' (undefined-variable)
"-p",
port,

Check warning on line 526 in augur/application/cli/db.py

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GitHub Actions / runner / pylint 

[pylint] reported by reviewdog 🐶
E0602: Undefined variable 'port' (undefined-variable)

Raw Output:
augur/application/cli/db.py:526:12: E0602: Undefined variable 'port' (undefined-variable)
"-a",
"-w",
target_type,
Expand Down
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