Add Alembic for database migrations.

Author: cht42

.pre-commit-config.yaml

@@ -36,8 +36,3 @@ repos:
         entry: bandit backend
         language: python
         pass_filenames: false
-      - name: pydocstyle
-        id: pydoctsyle
-        entry: pydocstyle backend
-        language: python
-        pass_filenames: false

.pylintrc

@@ -15,7 +15,7 @@ extension-pkg-whitelist=
 fail-under=8.0
 
 # Files or directories to be skipped. They should be base names, not paths.
-ignore=CVS
+ignore=CVS,versions
 
 # Files or directories matching the regex patterns are skipped. The regex
 # matches against base names, not paths.

README.md

@@ -23,3 +23,22 @@ bash keycloak/init.sh
 In the output of the script you will find the client secret. Copy it and put it the `.env`.
 
 You can then access the keycloak console and login with the admin credentials: http://localhost:8080
+
+## Running database migrations using [Alembic](https://alembic.sqlalchemy.org).
+
+First, modify your models in the file `database/models.py`.
+Then run the following command to generate the migration:
+
+```bash
+docker-compose exec backend alembic revision --autogenerate -m "<Your message>"
+```
+
+> :warning: Check this [page](https://alembic.sqlalchemy.org/en/latest/autogenerate.html) to see what alembic detects for the Autogenerate
+
+Check the migration file in the `alembic/versions` folder. If you are happy with it, you can run the migration:
+
+```bash
+docker-compose exec backend alembic upgrade head
+```
+
+Your database is now up to date !

backend/alembic.ini

@@ -0,0 +1,89 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(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.
+# 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 = false
+
+# 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
+# version_locations = %(here)s/bar %(here)s/bat alembic/versions
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+sqlalchemy.url =
+
+
+[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 = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+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 @@
+Generic single-database configuration.

backend/alembic/env.py

@@ -0,0 +1,78 @@
+import os
+from logging.config import fileConfig
+
+from alembic.context import context
+from sqlalchemy import engine_from_config, pool
+
+from app.database.models import Base
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+config.set_main_option("sqlalchemy.url", os.environ.get("DATABASE_URL"))
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+
+target_metadata = Base.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,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    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.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(connection=connection, target_metadata=target_metadata)
+
+        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 +1,24 @@
+"""${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/alembic/versions/8fd03ac6d77d_create_target_and_picture.py

@@ -0,0 +1,50 @@
+"""Create target and picture
+
+Revision ID: 8fd03ac6d77d
+Revises:
+Create Date: 2021-05-08 20:05:59.130362
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "8fd03ac6d77d"
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "targets",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("first_name", sa.String(), nullable=True),
+        sa.Column("last_name", sa.String(), nullable=True),
+        sa.Column("age", sa.Integer(), nullable=True),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_targets_id"), "targets", ["id"], unique=False)
+    op.create_table(
+        "pictures",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("path", sa.String(), nullable=True),
+        sa.Column("target_id", sa.Integer(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["target_id"],
+            ["targets.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_pictures_id"), "pictures", ["id"], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_pictures_id"), table_name="pictures")
+    op.drop_table("pictures")
+    op.drop_index(op.f("ix_targets_id"), table_name="targets")
+    op.drop_table("targets")
+    # ### end Alembic commands ###

backend/app/database/session.py

@@ -5,13 +5,7 @@
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
 
-SQLALCHEMY_DATABASE_URL = (
-    "postgresql://"
-    + os.environ.get("POSTGRES_USER", "app")
-    + ":"
-    + os.environ.get("POSTGRES_PASSWORD", "password")
-    + "@postgres:5432/app"
-)
+SQLALCHEMY_DATABASE_URL = os.environ.get("DATABASE_URL")
 
 engine = create_engine(SQLALCHEMY_DATABASE_URL)
 SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)

backend/app/main.py

@@ -4,16 +4,13 @@
 from fastapi.responses import Response
 from simber import Logger
 
-from app.database import models
-from app.database.session import engine
 from app.router import auth, targets
 from app.service.keycloak import verify_token
 
 LOG_FORMAT = "{levelname} [{filename}:{lineno}]:"
 logger = Logger(__name__, log_path="/logs/api.log")
 logger.update_format(LOG_FORMAT)
 
-models.Base.metadata.create_all(bind=engine)
 
 app = FastAPI(docs_url="/api/docs", openapi_url="/api/openapi")
 

backend/app/router/auth.py

@@ -9,13 +9,6 @@
 
 @router.post("/token")
 async def login(form_data: OAuth2PasswordRequestForm = Depends()):
-    """Login user.
-
-    Args:
-        form_data: form with username and password values
-
-    Returns:
-        Access token and refresh token with their expiry times
-    """
+    """Login user."""
     token = await authenticate_user(form_data.username, form_data.password)
     return token

backend/entrypoint.sh

@@ -1,3 +1,4 @@
 #!/bin/sh
 
+alembic upgrade head
 python app/main.py

backend/requirements.txt

@@ -6,3 +6,4 @@ simber==0.2.1
 SQLAlchemy==1.4.14
 pydantic==1.8.1
 psycopg2==2.8.6
+alembic==1.6.2

docker-compose.yaml

@@ -22,13 +22,25 @@ services:
       - .env
     environment:
       PYTHONPATH: .
+      DATABASE_URL: postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_USER}
     volumes:
       - ./backend:/app
       - ./logs/backend:/logs
     depends_on:
       - postgres
       - keycloak
 
+  frontend:
+    container_name: frontend
+    build:
+      context: frontend
+      dockerfile: Dockerfile
+    volumes:
+      - ./frontend/app:/app
+    environment:
+      NODE_ENV: development
+      CHOKIDAR_USEPOLLING: "true"
+
   postgres:
     container_name: postgres
     image: postgres