feat: adding alembic database migrations

.github/workflows/pr-open.yml

@@ -102,6 +102,25 @@ jobs:
           tag_fallback: latest
           triggers: ('${{ matrix.package }}/')
 
+  build-custom:
+    name: Build Custom
+    needs: [vars]
+    runs-on: ubuntu-22.04
+    permissions:
+      packages: write
+    timeout-minutes: 10
+    steps:
+      - uses: bcgov-nr/action-builder-ghcr@v2.0.0
+        with:
+          keep_versions: 10
+          package: migrations-alembic
+          tag: ${{ needs.vars.outputs.tag }}
+          tag_fallback: latest
+          triggers: ('backend/alembic/versions')
+          build_file: migrations/Dockerfile
+          build_context: .
+
+
   # https://github.com/bcgov-nr/action-deployer-openshift
   deploys:
     name: Deploys

.gitignore

@@ -121,3 +121,6 @@ test-report.xml
 # VSCode
 .vscode/
 junk.txt
+
+
+__pycache__/

backend/README.md

@@ -16,12 +16,22 @@
 - [Docker Compose](https://docs.docker.com/compose/install/)
 
 ### Local Development
-- Run the `docker-compose -f .\docker-compose.py.yml up` command to start the entire stack.
-- The database changes are applied automatically by flyway
+
+#### Local Dev with Docker
+
+- Run the `docker compose -f .\docker-compose.py.yml up` command to start the entire stack.
+- The database changes are applied automatically by alembic
 - The models are generated into `backend-py/src/v1/models/model.py` .
-- Devs are encouraged to see the `backend-py/src/v1/models/model.py` file and update the models in entities.py. The reason of manual process behind is the sqlacodegen is still lacking support for  SQLAlchemy 2.x.
 - The API is Documentation available at http://localhost:3003/docs
 
+#### Local Dev - poetry
+
+* create the env `cd backend; poetry install`
+* activate the env `source $(poetry env info --path)/bin/activate`
+* start uvicorn 
+
+```uvicorn src.main:app --host 0.0.0.0 --port 3000 --workers 1 --server-header --date-header --limit-concurrency 100 --reload --log-config ./logger.conf```
+
 ### Unit Testing
 - Run `docker-compose up -d backend-py-test` command to run the unit tests from the root directory.
 - The folder is volume mounted , so any changes to the code will be reflected in the container and run the unit tests again.

backend/alembic.ini

@@ -0,0 +1,110 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python-dateutil library that can be
+# installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to dateutil.tz.gettz()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the
+# "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+revision_environment = true
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+version_path_separator = os  # Use os.pathsep. Default configuration used for new projects.
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+#sqlalchemy.url = driver://user:pass@localhost/dbname
+#sqlalchemy.url = sqlite:///fam.db
+sqlalchemy.url = postgresql+psycopg2://$POSTGRES_USER:$POSTGRES_PASSWORD@$POSTGRES_HOST:$POSTGRES_PORT/$POSTGRES_DB
+#sqlalchemy.url = postgresql+psycopg2://postgres:postgres@localhost:5432/py
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = DEBUG 
+# WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = DEBUG 
+# WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = DEBUG
+handlers =
+qualname = alembic
+
+[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/alembic/README

@@ -0,0 +1,3 @@
+Generic single-database configuration.
+
+alembic revision --autogenerate -m "initial schema"

backend/alembic/env.py

@@ -0,0 +1,155 @@
+from logging.config import fileConfig
+
+from sqlalchemy import create_engine, pool
+from sqlalchemy.schema import CreateSchema
+
+
+# import app.config
+# import app.models.model
+# import src.core.config
+import src.v1.models.model
+import src.core.config as app_config
+
+from alembic import context
+from alembic.script import ScriptDirectory
+
+import logging
+
+config = context.config
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+
+# 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.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# override logging setup for debugging
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.DEBUG)
+LOGGER.debug("test test test")
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+target_metadata = None
+
+# 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 process_revision_directives(context, revision, directives):
+    """overriding the default generation of revision ids to use a 
+    sequential integer instead of a hex string.
+
+    :param context: _description_
+    :type context: _type_
+    :param revision: _description_
+    :type revision: _type_
+    :param directives: _description_
+    :type directives: _type_
+    """
+    # extract Migration
+    migration_script = directives[0]
+    # extract current head revision
+    head_revision = ScriptDirectory.from_config(context.config).get_current_head()
+
+    if head_revision is None:
+        # edge case with first migration
+        new_rev_id = 1
+    else:
+        # default branch with incrementation
+        last_rev_id = int(head_revision.lstrip("V"))
+        new_rev_id = last_rev_id + 1
+    # fill zeros up to 4 digits: 1 -> 0001
+    # migration_script.rev_id = '{0:04}'.format(new_rev_id)
+    migration_script.rev_id = f"V{new_rev_id}"
+
+
+def get_url():
+    url = None
+    x_param_url = context.get_x_argument(as_dictionary=True).get("url")
+    LOGGER.debug(f"x_param_url: {x_param_url}")
+    if x_param_url:
+        url = x_param_url
+        LOGGER.debug(f"url from -x: {url}")
+
+    if not url:
+        LOGGER.debug(f"app_config.Configuration.SQLALCHEMY_DATABASE_URI: {app_config.Configuration.SQLALCHEMY_DATABASE_URI}")
+        url = app_config.Configuration.SQLALCHEMY_DATABASE_URI.unicode_string()
+        LOGGER.debug(f"url from app config: {url}")
+    LOGGER.debug(f"captured the url string: {url}")
+    return url
+    # return "postgresql://postgres:default@localhost:5432/postgres"
+
+
+def run_migrations_offline() -> None:
+    """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.
+
+    """
+    LOGGER.debug("running migrations offline")
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        literal_binds=True,
+        target_metadata=src.v1.models.model.metadata,
+        version_table='alembic_version',
+        version_table_schema=app_config.Configuration.DEFAULT_SCHEMA,
+        process_revision_directives=process_revision_directives
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    url = get_url()
+    LOGGER.debug(f"using url: {url}")
+    connectable = create_engine(url)
+
+    with connectable.connect() as connection:
+
+        context.configure(
+            connection=connection,
+            target_metadata=src.v1.models.model.metadata,
+            version_table='alembic_version',
+            version_table_schema=app_config.Configuration.DEFAULT_SCHEMA,
+            process_revision_directives=process_revision_directives
+        )
+        schema_create = CreateSchema(app_config.Configuration.DEFAULT_SCHEMA, if_not_exists=True)
+        LOGGER.debug(f"schema_create: {schema_create}")
+        connection.execute(schema_create)
+        # create_schema_sql = 'CREATE SCHEMA IF NOT EXISTS {}'
+        # connection.execute(create_schema_sql)
+
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

backend/alembic/script.py.mako

@@ -0,0 +1,26 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}