feat(backend): add alembic for db migrations

.gitignore

@@ -1,17 +1,13 @@
-# Backend config file
-/config.py
-
-# Local environments
+# Locally installed environments
 /.venv/
 /node_modules/
 
 # Local development database
 /.postgres/
-/.omnidb/
 
 # Cache files and directories
-*.pyc
-__pycache__/
+**/*.pyc
+**/__pycache__/
 /.parcel-cache/
 
 # Bundled files

README.md

@@ -36,3 +36,11 @@ Access to vitals data is available through the [Withings API](https://developer.
 
 A detailed [API integration guide](https://developer.withings.com/developer-guide/v3/integration-guide/public-health-data-api/public-health-data-api-overview/),
 as well as an [API reference guide](https://developer.withings.com/api-reference) are available online.
+
+# Development
+
+Run [alembic](https://alembic.sqlalchemy.org/en/latest/) migrations inside the container like so:
+
+```bash
+sudo docker exec -w /app/backend/database -it backend alembic upgrade head
+```

backend/database/alembic.ini

@@ -0,0 +1,110 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = migrations
+
+# 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 = 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 migrations/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:migrations/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.
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+sqlalchemy.url = driver://user:pass@localhost/dbname
+
+
+[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/database/migrations/env.py

@@ -0,0 +1,80 @@
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+from alembic import context
+
+from backend.database.engine import _pg_dsn as pg_connection_str
+
+# 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', pg_connection_str)
+
+# 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)
+
+# 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 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.
+
+    """
+    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() -> None:
+    """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/database/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() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

backend/database/migrations/versions/335e07a98bc8_create_user_tables.py

@@ -0,0 +1,50 @@
+"""create user tables
+
+Revision ID: 335e07a98bc8
+Revises: 
+Create Date: 2023-05-12 19:59:22.188464
+
+"""
+from alembic import op
+from sqlalchemy import Column, ForeignKey, Integer, String, DateTime, Date, Enum, CheckConstraint
+from sqlalchemy.sql.functions import now
+
+from backend.models.users import Gender
+
+
+# revision identifiers, used by Alembic.
+revision = '335e07a98bc8'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        'users',
+        Column('id', Integer, primary_key=True, autoincrement=True, index=True),
+        Column('email', String, unique=True, nullable=False),
+        Column('password', String, nullable=False),
+        Column('created', DateTime(timezone=True), nullable=False, server_default=now()),
+        Column('updated', DateTime(timezone=True), nullable=False, server_default=now(), onupdate=now()),
+        Column('first_name', String, nullable=False),
+        Column('last_name', String, nullable=False),
+    )
+
+    op.create_table(
+        'administrators',
+        Column('user_id', Integer, ForeignKey('users.id', ondelete="CASCADE"), primary_key=True,)
+    )
+
+    op.create_table(
+        'patients',
+        Column('user_id', Integer, ForeignKey('users.id', ondelete="CASCADE"), primary_key=True),
+        Column('date_of_birth', Date, nullable=False),
+        Column('gender', Enum(Gender), nullable=False),
+    )
+
+
+def downgrade() -> None:
+    op.drop_table('users')
+    op.drop_table('administrators')
+    op.drop_table('patients')

requirements.txt

@@ -1,9 +1,12 @@
+alembic==1.10.4
 anyio==3.6.2
 click==8.1.3
 fastapi==0.95.1
 greenlet==2.0.2
 h11==0.14.0
 idna==3.4
+Mako==1.2.4
+MarkupSafe==2.1.2
 psycopg2-binary==2.9.6
 pydantic==1.10.7
 sniffio==1.3.0