diff --git a/README.md b/README.md
index 81b1b0b67f3762753a5688ce4fabd4e0edefcc62..dd9a7dce6b1534fbd04577e8af437a232c3e6334 100644
--- a/README.md
+++ b/README.md
@@ -63,11 +63,13 @@ survey-publisher-2022
## Creating a db migration after editing the sqlalchemy models
```bash
-cd compendium_v2
-alembic revision --autogenerate -m "description"
+flask db migrate -m "description"
```
Then go to the created migration file to make any necessary additions, for example to migrate data.
Also see https://alembic.sqlalchemy.org/en/latest/autogenerate.html#what-does-autogenerate-detect-and-what-does-it-not-detect
+Flask-migrate sets `compare_type=True` by default.
Note that starting the application applies all upgrades.
+This also happens when running `flask db` commands such as `flask db downgrade`,
+so if you want to downgrade 2 or more versions you need to do so in one command, eg by specifying the revision number.
diff --git a/compendium_v2/__init__.py b/compendium_v2/__init__.py
index 7a69bf9eb602680352c2328d8f228a27ee008432..4717a4864e29c398106b79605661e0441d3ea009 100644
--- a/compendium_v2/__init__.py
+++ b/compendium_v2/__init__.py
@@ -6,15 +6,11 @@ import os
from flask import Flask
from flask_cors import CORS # for debugging
+# the currently available stubs for flask_migrate are old (they depend on sqlalchemy 1.4 types)
+from flask_migrate import Migrate, upgrade # type: ignore
from compendium_v2 import config, environment
from compendium_v2.db import db
-from compendium_v2.migrations import migration_utils
-
-
-def migrate_database(config: dict) -> None:
- dsn = config['SQLALCHEMY_DATABASE_URI']
- migration_utils.upgrade(dsn)
def _create_app(app_config) -> Flask:
@@ -56,11 +52,14 @@ def create_app() -> Flask:
app = _create_app_with_db(app_config)
+ Migrate(app, db, directory=os.path.join(os.path.dirname(__file__), 'migrations'))
+
logging.info('Flask app initialized')
environment.setup_logging()
# run migrations on startup
- migrate_database(app_config)
+ with app.app_context():
+ upgrade()
return app
diff --git a/compendium_v2/alembic.ini b/compendium_v2/alembic.ini
deleted file mode 100644
index 2145863baa95551a588dd229ee525abd06f32742..0000000000000000000000000000000000000000
--- a/compendium_v2/alembic.ini
+++ /dev/null
@@ -1,10 +0,0 @@
-# A generic, single database configuration.
-
-# only needed for generating new revision scripts
-[alembic]
-# make sure the right line is un / commented depending on which schema you want
-# a migration for
-script_location = migrations
-# script_location = cachedb_migrations
-# change this to run migrations from the command line
-sqlalchemy.url = postgresql://compendium:compendium321@localhost:65000/compendium
diff --git a/compendium_v2/migrations/README b/compendium_v2/migrations/README
new file mode 100644
index 0000000000000000000000000000000000000000..0e048441597444a7e2850d6d7c4ce15550f79bda
--- /dev/null
+++ b/compendium_v2/migrations/README
@@ -0,0 +1 @@
+Single-database configuration for Flask.
diff --git a/compendium_v2/migrations/__init__.py b/compendium_v2/migrations/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/compendium_v2/migrations/alembic.ini b/compendium_v2/migrations/alembic.ini
new file mode 100644
index 0000000000000000000000000000000000000000..ec9d45c26a6bb54e833fd4e6ce2de29343894f4b
--- /dev/null
+++ b/compendium_v2/migrations/alembic.ini
@@ -0,0 +1,50 @@
+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S
diff --git a/compendium_v2/migrations/env.py b/compendium_v2/migrations/env.py
index 5ea9c8d33d0c06ae30cc8e05740a8f3758d18357..e2408681ba289bd300144dddf1c47f754ba931d1 100644
--- a/compendium_v2/migrations/env.py
+++ b/compendium_v2/migrations/env.py
@@ -1,10 +1,9 @@
import logging
+from logging.config import fileConfig
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
+from flask import current_app
from alembic import context
-from compendium_v2.db import metadata_obj
# this is the Alembic Config object, which provides
# access to the values within the .ini file in use.
@@ -12,13 +11,34 @@ config = context.config
# Interpret the config file for Python logging.
# This line sets up loggers basically.
-logging.basicConfig(level=logging.INFO)
+if config.config_file_name is not None:
+ fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+
+def get_engine():
+ try:
+ # this works with Flask-SQLAlchemy<3 and Alchemical
+ return current_app.extensions['migrate'].db.get_engine()
+ except TypeError:
+ # this works with Flask-SQLAlchemy>=3
+ return current_app.extensions['migrate'].db.engine
+
+
+def get_engine_url():
+ try:
+ return get_engine().url.render_as_string(hide_password=False).replace(
+ '%', '%%')
+ except AttributeError:
+ return str(get_engine().url).replace('%', '%%')
+
# add your model's MetaData object here
# for 'autogenerate' support
# from myapp import mymodel
# target_metadata = mymodel.Base.metadata
-target_metadata = metadata_obj
+config.set_main_option('sqlalchemy.url', get_engine_url())
+target_db = current_app.extensions['migrate'].db
# other values from the config, defined by the needs of env.py,
# can be acquired:
@@ -26,6 +46,12 @@ target_metadata = metadata_obj
# ... etc.
+def get_metadata():
+ if hasattr(target_db, 'metadatas'):
+ return target_db.metadatas[None]
+ return target_db.metadata
+
+
def run_migrations_offline():
"""Run migrations in 'offline' mode.
@@ -40,10 +66,7 @@ def run_migrations_offline():
"""
url = config.get_main_option("sqlalchemy.url")
context.configure(
- url=url,
- target_metadata=target_metadata,
- literal_binds=True,
- dialect_opts={"paramstyle": "named"},
+ url=url, target_metadata=get_metadata(), literal_binds=True
)
with context.begin_transaction():
@@ -57,15 +80,25 @@ def run_migrations_online():
and associate a connection with the context.
"""
- connectable = engine_from_config(
- config.get_section(config.config_ini_section),
- prefix="sqlalchemy.",
- poolclass=pool.NullPool,
- )
+
+ # this callback is used to prevent an auto-migration from being generated
+ # when there are no changes to the schema
+ # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+ def process_revision_directives(context, revision, directives):
+ if getattr(config.cmd_opts, 'autogenerate', False):
+ script = directives[0]
+ if script.upgrade_ops.is_empty():
+ directives[:] = []
+ logger.info('No changes in schema detected.')
+
+ connectable = get_engine()
with connectable.connect() as connection:
context.configure(
- connection=connection, target_metadata=target_metadata
+ connection=connection,
+ target_metadata=get_metadata(),
+ process_revision_directives=process_revision_directives,
+ **current_app.extensions['migrate'].configure_args
)
with context.begin_transaction():
diff --git a/compendium_v2/migrations/migration_utils.py b/compendium_v2/migrations/migration_utils.py
deleted file mode 100644
index f25f03c922761f6c036125d2b06857729aeee828..0000000000000000000000000000000000000000
--- a/compendium_v2/migrations/migration_utils.py
+++ /dev/null
@@ -1,41 +0,0 @@
-import logging
-import os
-
-from alembic.config import Config
-from alembic import command
-
-logger = logging.getLogger(__name__)
-DEFAULT_MIGRATIONS_DIRECTORY = os.path.dirname(__file__)
-
-
-def upgrade(dsn, migrations_directory=DEFAULT_MIGRATIONS_DIRECTORY):
- """
- migrate db to head version
-
- cf. https://stackoverflow.com/a/43530495,
- https://stackoverflow.com/a/54402853
-
- :param dsn: dsn string, passed to alembic
- :param migrations_directory: full path to migrations directory
- (default is this directory)
- :return:
- """
- alembic_config = Config()
- alembic_config.set_main_option('script_location', migrations_directory)
- alembic_config.set_main_option('sqlalchemy.url', dsn)
- command.upgrade(alembic_config, 'head')
-
-
-def postgresql_dsn(db_username, db_password, db_hostname, db_name, port=5432):
- return (f'postgresql://{db_username}:{db_password}'
- f'@{db_hostname}:{port}/{db_name}')
-
-
-if __name__ == "__main__":
- logging.basicConfig(level=logging.DEBUG)
- upgrade(postgresql_dsn(
- db_username='compendium',
- db_password='compendium321',
- db_hostname='localhost',
- db_name='compendium',
- port=65000))
diff --git a/requirements.txt b/requirements.txt
index 98804e02708e010e91e5add5daafa792bc4e0428..f49a79607d14fd2eed998d4429390cc95acb18b5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,6 +3,7 @@ click~=8.1
jsonschema~=4.17
flask~=2.2
flask-cors~=3.0
+flask-migrate~=4.0
flask-sqlalchemy~=3.0
openpyxl~=3.1
psycopg2-binary~=2.9
diff --git a/setup.py b/setup.py
index 48a37f1b4ad2ecc95203d262b259d951529a265e..52acb8cb8ef2714e7f7b93352b260b4ce5b35974 100644
--- a/setup.py
+++ b/setup.py
@@ -15,6 +15,7 @@ setup(
'jsonschema~=4.17',
'flask~=2.2',
'flask-cors~=3.0',
+ 'flask-migrate~=4.0',
'flask-sqlalchemy~=3.0',
'openpyxl~=3.1',
'psycopg2-binary~=2.9',