diff --git a/.gitignore b/.gitignore index 60b5d08..5b42d46 100644 --- a/.gitignore +++ b/.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 diff --git a/README.md b/README.md index 72e7a02..b812d5a 100644 --- a/README.md +++ b/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 +``` diff --git a/backend/database/alembic.ini b/backend/database/alembic.ini new file mode 100644 index 0000000..778a46d --- /dev/null +++ b/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 diff --git a/backend/database/migrations/env.py b/backend/database/migrations/env.py new file mode 100644 index 0000000..fd9cb5c --- /dev/null +++ b/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() diff --git a/backend/database/migrations/script.py.mako b/backend/database/migrations/script.py.mako new file mode 100644 index 0000000..55df286 --- /dev/null +++ b/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"} diff --git a/backend/database/migrations/versions/335e07a98bc8_create_user_tables.py b/backend/database/migrations/versions/335e07a98bc8_create_user_tables.py new file mode 100644 index 0000000..54a3148 --- /dev/null +++ b/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') diff --git a/requirements.txt b/requirements.txt index a7bf1e8..25e846a 100644 --- a/requirements.txt +++ b/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