Use alembic for database table creation (#298)

---------

Co-authored-by: Stef Piatek <[email protected]>

cli/src/pixl_cli/main.py

@@ -341,6 +341,7 @@ class APIConfig:
     -------
     base_url()
         Return the base url for the API
+
     """
 
     def __init__(self, kwargs: dict) -> None:

docker-compose.yml

@@ -268,6 +268,7 @@ services:
       orthanc-raw:
         condition: service_healthy
     healthcheck:
+      test: curl -f http://0.0.0.0:8000/heart-beat
       interval: 10s
       timeout: 30s
       retries: 5
@@ -279,6 +280,12 @@ services:
       ORTHANC_RAW_PASSWORD: ${ORTHANC_RAW_PASSWORD}
       ORTHANC_RAW_AE_TITLE: ${ORTHANC_RAW_AE_TITLE}
       VNAQR_MODALITY: ${VNAQR_MODALITY}
+      SKIP_ALEMBIC: ${SKIP_ALEMBIC}
+      PIXL_DB_HOST: ${PIXL_DB_HOST}
+      PIXL_DB_PORT: ${PIXL_DB_PORT}
+      PIXL_DB_NAME: ${PIXL_DB_NAME}
+      PIXL_DB_USER: ${PIXL_DB_USER}
+      PIXL_DB_PASSWORD: ${PIXL_DB_PASSWORD}
       PIXL_DICOM_TRANSFER_TIMEOUT: ${PIXL_DICOM_TRANSFER_TIMEOUT}
       PIXL_QUERY_TIMEOUT: ${PIXL_QUERY_TIMEOUT}
     ports:

docker/imaging-api/Dockerfile

@@ -38,6 +38,4 @@ RUN --mount=type=cache,target=/root/.cache \
     pip install core/ . && \
     if [ "$TEST" = "true" ]; then pip install core/ .[test]; fi
 
-HEALTHCHECK CMD /usr/bin/curl -f http://0.0.0.0:8000/heart-beat || exit 1
-
-ENTRYPOINT ["uvicorn", "pixl_imaging.main:app", "--host", "0.0.0.0", "--port", "8000"]
+ENTRYPOINT ["/app/scripts/migrate_and_run.sh"]

docker/postgres/Dockerfile

@@ -23,20 +23,4 @@ RUN sed -i '/en_GB.UTF-8/s/^# //g' /etc/locale.gen && locale-gen
 
 COPY --chmod=0755 ./postgres/postgres.conf /etc/postgresql/postgresql.conf
 
-COPY --chmod=0777 ./postgres/pixl-db_init.sh /docker-entrypoint-initdb.d/pixl-db_init.sh
-
-COPY --chmod=0777 ./postgres/create_pixl_tbls.py /pixl/create_pixl_tbls.py
-
-# Install requirements before copying modules
-COPY ./pixl_core/pyproject.toml /pixl/pixl_core/pyproject.toml
-RUN --mount=type=cache,target=/root/.cache \
-    python3 -m venv /pixl/venv \
-        && cd /pixl/venv/bin \
-        && ./pip install /pixl/pixl_core/
-
-WORKDIR /pixl/venv/bin
-
-COPY ./pixl_core/ /pixl/pixl_core
-
-RUN --mount=type=cache,target=/root/.cache \
-    ./pip install /pixl/pixl_core/
+COPY --chmod=0777 ./postgres/pixl-db_init.sh /docker-entrypoint-initdb.d/pixl-db_init.sh

pixl_imaging/README.md

@@ -24,3 +24,14 @@ pip install -e ../pixl_core/ .
 ## Usage
 
 Usage should be from the CLI driver, which interacts with the endpoint.
+
+
+## Configuration and database interaction
+
+The database tables are updated using alembic, see the [alembic](alembic) dir for more details.
+
+The `SKIP_ALEMBIC` environmental variable is used to control whether migrations are applied to the database.
+
+- Tests that don't use the database use `SKIP_ALEMBIC=true`, but otherwise you probably want to run this.
+- If you wanted to test out new migrations from a test/dev deployment on the GAE with data in,
+  then you can redeploy just the `imaging-api` container while keeping the `postgres` container up. 

pixl_imaging/alembic/README.md

@@ -0,0 +1,31 @@
+# Alembic configuration
+
+We've followed the  [alembic tutorial](https://alembic.sqlalchemy.org/en/latest/tutorial.html),
+there's a good explainer there of each of the files and directories. 
+
+## Running migrations in production
+
+This is automatically done when the pixl-imaging container is started, 
+as the entry point is [migrate_and_run.sh](../scripts/migrate_and_run.sh).
+
+## Creating a new migration after editing the database model
+
+For convenience, the [autogenerate-migration.sh](autogenerate-migration.sh) has been made.
+
+Which you can run giving a name for the migration like this:
+
+```shell
+cd alembic
+./autogenerate-migration.sh "<Description of changes to models>"
+```
+
+- This creates a postgres container
+- Runs the existing migrations
+- Checks for differences between the SQLAlchemy [models](../../pixl_core/src/core/db/models.py) 
+  and creates a new migration in [versions](versions)
+- Takes down the postgres container
+
+There's a couple of manual steps:
+
+- Check the changes autogenerated and update to match your intention
+- Commit the changes and review in a pull request as normal

pixl_imaging/alembic/alembic.ini

@@ -0,0 +1,116 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = .
+
+# 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>=3.9 or backports.zoneinfo library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# 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.
+# 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.
+
+# 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
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = --fix 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

postgres/create_pixl_tbls.py → pixl_imaging/alembic/autogenerate-migration.sh

@@ -1,3 +1,4 @@
+#!/bin/bash
 #  Copyright (c) University College London Hospitals NHS Foundation Trust
 #
 #  Licensed under the Apache License, Version 2.0 (the "License");
@@ -11,25 +12,26 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
+set -euxo pipefail
+cd "$(dirname "${BASH_SOURCE[0]}")" && pwd
 
-"""Create PIXL tables"""
-import os
+if [ $# -ne 1 ]
+  then
+    echo "Add a name for the migration in quotes"
+    exit 1
+fi
 
-from core.db.models import Base
-from sqlalchemy import URL, create_engine
-from sqlalchemy.sql.ddl import CreateSchema
+export PIXL_DB_HOST=localhost
 
-url = URL.create(
-    drivername="postgresql+psycopg2",
-    username=os.environ["POSTGRES_USER"],
-    password=os.environ["POSTGRES_PASSWORD"],
-    database=os.environ["POSTGRES_DB"],
-)
+# create postgres
+(cd ../.. && \
+  docker compose --env-file test/.env -p migration-test up  --wait -d --build postgres)
 
-engine = create_engine(url, echo=True, echo_pool="debug")
+# run current migrations
+alembic upgrade head
 
-with engine.connect() as connection:
-    connection.execute(CreateSchema("pipeline", if_not_exists=True))
-    connection.commit()
+# generate new migrations
+alembic revision --autogenerate -m "$1"
 
-Base.metadata.create_all(engine)
+# take containers down
+(cd ../.. && docker compose --env-file test/.env -p migration-test down --volumes )

pixl_imaging/alembic/env.py

@@ -0,0 +1,120 @@
+#  Copyright (c) University College London Hospitals NHS Foundation Trust
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+"""Alembic configuration"""
+from logging.config import fileConfig
+
+from decouple import Config, RepositoryEnv
+from sqlalchemy import URL, create_engine
+
+from alembic import context
+
+env_config = Config(RepositoryEnv("migrations.env"))
+
+# 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)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+from core.db import models
+
+target_metadata = models.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 include_name(name: str, type_: str, parent_names: str) -> bool:  # noqa: ARG001
+    """Filtering of allowed table names"""
+    if type_ == "schema":
+        return name in [target_metadata.schema]
+    return True
+
+
+def get_pixl_db_url() -> URL:
+    """Create PIXL database URL for connection."""
+    return URL.create(
+        drivername="postgresql+psycopg2",
+        host=env_config("PIXL_DB_HOST"),
+        port=env_config("PIXL_DB_PORT", int),
+        username=env_config("PIXL_DB_USER"),
+        password=env_config("PIXL_DB_PASSWORD"),
+        database=env_config("PIXL_DB_NAME"),
+    )
+
+
+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 = get_pixl_db_url()
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+        include_schemas=True,
+        include_name=include_name,
+        version_table_schema=target_metadata.schema,
+    )
+
+    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_pixl_db_url()
+    connectable = create_engine(url)
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            include_schemas=True,
+            include_name=include_name,
+            version_table_schema=target_metadata.schema,
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()