integrate alembic to GeoNature

GeoNature database schema is not yet managed by alembic,
but packaged geonature modules can rely on alembic to manage their schema.
To do so, add in the setup.py:
    entry_point = {
        'gn_module': [
            'migrations = gn_module_sample.migrations:versions',
        ],
    },

backend/geonature/app.py

@@ -9,19 +9,38 @@
 from flask_cors import CORS
 from sqlalchemy import exc as sa_exc
 from flask_sqlalchemy import before_models_committed
+from pkg_resources import iter_entry_points
 
 from geonature.utils.config import config
-from geonature.utils.env import MAIL, DB, MA
+from geonature.utils.env import MAIL, DB, MA, migrate
 from geonature.utils.module import import_backend_enabled_modules
 
 
+@migrate.configure
+def configure_alembic(alembic_config):
+ """
+ This function add to the 'version_locations' parameter of the alembic config the
+ 'migrations' entry point value of the 'gn_module' group for all modules having such entry point.
+ Thus, alembic will find migrations of all installed geonature modules.
+ """
+ version_locations = alembic_config.get_main_option('version_locations', default='').split()
+ for entry_point in iter_entry_points('gn_module', 'migrations'):
+ # TODO: define enabled module in configuration (skip disabled module, raise error on missing module)
+ _, migrations = str(entry_point).split('=', 1)
+ version_locations += [ migrations.strip() ]
+ alembic_config.set_main_option('version_locations', ' '.join(version_locations))
+ return alembic_config
+
+
 def create_app(with_external_mods=True, with_flask_admin=True):
  app = Flask(__name__)
  app.config.update(config)
 
  # Bind app to DB
  DB.init_app(app)
 
+ migrate.init_app(app, DB)
+
  MAIL.init_app(app)
 
  # For deleting files on "delete" media

backend/geonature/migrations/README

@@ -0,0 +1 @@
+Generic single-database configuration.

backend/geonature/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

backend/geonature/migrations/env.py

@@ -0,0 +1,90 @@
+from __future__ import with_statement
+
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option(
+ 'sqlalchemy.url',
+ str(current_app.extensions['migrate'].db.engine.url).replace('%', '%%'))
+target_metadata = current_app.extensions['migrate'].db.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline():
+ """Run migrations in 'offline' mode.
+
+ This configures the context with just a URL
+ and not an Engine, though an Engine is acceptable
+ here as well. By skipping the Engine creation
+ we don't even need a DBAPI to be available.
+
+ Calls to context.execute() here emit the given string to the
+ script output.
+
+ """
+ url = config.get_main_option("sqlalchemy.url")
+ context.configure(
+ url=url, target_metadata=target_metadata, literal_binds=True
+ )
+
+ with context.begin_transaction():
+ context.run_migrations()
+
+
+def run_migrations_online():
+ """Run migrations in 'online' mode.
+
+ In this scenario we need to create an Engine
+ and associate a connection with the context.
+
+ """
+
+ # 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 = current_app.extensions['migrate'].db.engine
+
+ with connectable.connect() as connection:
+ context.configure(
+ connection=connection,
+ target_metadata=target_metadata,
+ process_revision_directives=process_revision_directives,
+ **current_app.extensions['migrate'].configure_args
+ )
+
+ with context.begin_transaction():
+ context.run_migrations()
+
+
+if context.is_offline_mode():
+ run_migrations_offline()
+else:
+ run_migrations_online()

backend/geonature/migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+ ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+ ${downgrades if downgrades else "pass"}

backend/geonature/utils/env.py

@@ -11,6 +11,7 @@
 from sqlalchemy.orm.exc import NoResultFound
 from flask_marshmallow import Marshmallow
 from flask_mail import Mail
+from flask_migrate import Migrate
 
 
 # Must be at top of this file. I don't know why (?)
@@ -31,6 +32,7 @@
 os.environ['FLASK_SQLALCHEMY_DB'] = 'geonature.utils.env.DB'
 DB = SQLAlchemy()
 MA = Marshmallow()
+migrate = Migrate()
 
 GN_MODULE_FILES = (
  "manifest.toml",

backend/requirements-common.txt

@@ -7,6 +7,7 @@ Flask-Admin==1.5.6
 flask-cors==3.0.3
 Flask-Mail==0.9.1
 flask-marshmallow==0.12.0
+flask-migrate==2.7.0
 flask-script==2.0.5
 flask-sqlalchemy==2.4.4
 Flask-WeasyPrint==0.6

backend/requirements.in

@@ -3,4 +3,5 @@ flask-sqlalchemy
 flask-cors
 flask-mail
 flask-marshmallow
+flask-migrate
 WTForms-SQLAlchemy