Use alembic for database table creation

alembic.ini

@@ -0,0 +1,116 @@
+# 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>=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

alembic/README

@@ -0,0 +1 @@
+Generic single-database configuration.

alembic/env.py

@@ -0,0 +1,99 @@
+#  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"""
+import os
+from logging.config import fileConfig
+
+from sqlalchemy import URL, create_engine
+
+from alembic import context
+
+# 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 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 = URL.create(
+        drivername="postgresql+psycopg2",
+        username=os.environ["POSTGRES_USER"],
+        password=os.environ["POSTGRES_PASSWORD"],
+        database=os.environ["POSTGRES_DB"],
+    )
+    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.
+
+    """
+    url = URL.create(
+        drivername="postgresql+psycopg2",
+        username=os.environ["POSTGRES_USER"],
+        password=os.environ["POSTGRES_PASSWORD"],
+        database=os.environ["POSTGRES_DB"],
+    )
+    connectable = create_engine(url)
+
+    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()

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"}

alembic/versions/bcaef54e2bfe_.py

@@ -0,0 +1,62 @@
+#  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.
+"""
+Initial setup
+
+Revision ID: bcaef54e2bfe
+Revises:
+Create Date: 2024-02-12 14:43:36.716242
+
+"""
+from collections.abc import Sequence
+from typing import Union
+
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "bcaef54e2bfe"
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.execute("create schema pipeline")
+    op.create_table(
+        "extract",
+        sa.Column("extract_id", sa.Integer(), nullable=False),
+        sa.Column("slug", sa.String(), nullable=True),
+        sa.PrimaryKeyConstraint("extract_id"),
+        schema="pipeline",
+    )
+    op.create_table(
+        "image",
+        sa.Column("image_id", sa.Integer(), nullable=False),
+        sa.Column("accession_number", sa.String(), nullable=False),
+        sa.Column("study_date", sa.Date(), nullable=False),
+        sa.Column("mrn", sa.String(), nullable=False),
+        sa.Column("hashed_identifier", sa.String(), nullable=True),
+        sa.Column("exported_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("extract_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(["extract_id"], ["pipeline.extract.extract_id"]),
+        sa.PrimaryKeyConstraint("image_id"),
+        schema="pipeline",
+    )
+
+
+def downgrade() -> None:
+    op.drop_table("image")
+    op.drop_table("extract")

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/postgres/Dockerfile

@@ -25,7 +25,8 @@ 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
+COPY alembic /pixl/alembic
+COPY alembic.ini /pixl/alembic.ini
 
 # Install requirements before copying modules
 COPY ./pixl_core/pyproject.toml /pixl/pixl_core/pyproject.toml

pixl_core/pyproject.toml

@@ -23,6 +23,7 @@ dependencies = [
     "sqlalchemy==2.0.24",
     "psycopg2-binary==2.9.9",
     "pandas==1.5.1",
+    "alembic==1.13.1",
     "pyarrow==14.0.1",
 ]
 

postgres/pixl-db_init.sh

@@ -25,4 +25,5 @@ psql -U "${POSTGRES_USER}" --dbname "${POSTGRES_DB}" -c "$ehr_create_command"
 
 source /pixl/venv/bin/activate
 
-python3 /pixl/create_pixl_tbls.py
+cd /pixl
+alembic upgrade head

ruff.toml

@@ -50,3 +50,5 @@ exclude=["scripts"]
 [extend-per-file-ignores]
 "**/tests/*" = ["PLR2004"] #  Magic value used in comparison
 "hasher/tests/*" = ["ARG001"] #  unused function argument
+"env.py" = ["INP001", "E402", "ERA001"]
+"alembic/versions/*" = ["D103", "INP001"]