Merge pull request #118 from kjsanger/feature/porch-2.0.0

Add npg_porch 2.0.0 server

docker/porch/Dockerfile

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+
+ARG BASE_IMAGE=python:3.10-slim
+FROM $BASE_IMAGE as builder
+
+ENV DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    build-essential \
+    gcc \
+    git \
+    libsqlite3-dev \
+    unattended-upgrades && \
+    unattended-upgrade -v
+
+WORKDIR /app
+
+COPY ./scripts/*.sh /app/docker/scripts/
+
+COPY ./logging.json /app/docker/logging.json
+
+ARG PORCH_VERSION=2.0.0
+
+# The last 2 lines are a workaround for porch's pip install not copying the scripts
+RUN python -m venv /app && \
+    . /app/bin/activate && \
+    pip install --no-cache-dir --upgrade pip && \
+    git clone --branch "v${PORCH_VERSION}" --single-branch https://github.com/wtsi-npg/npg_porch.git /tmp/npg_porch && \
+    cd /tmp/npg_porch && \
+    pip install --no-cache-dir . && \
+    mkdir /app/scripts && \
+    cp ./scripts/*.py /app/scripts/ 
+
+FROM $BASE_IMAGE
+
+ARG DEBIAN_FRONTEND
+
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -q -y --no-install-recommends \
+    curl \
+    libsqlite3-0 \
+    postgresql \
+    sudo \
+    tini \
+    locales && \
+    locale-gen en_GB en_GB.UTF-8 && \
+    localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8
+
+RUN apt-get install -q -y --no-install-recommends \
+    unattended-upgrades && \
+    unattended-upgrade -v && \
+    apt-get remove -q -y unattended-upgrades && \
+    apt-get autoremove -q -y && \
+    apt-get clean -q -y && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV LANG=en_GB.UTF-8 \
+    LANGUAGE=en_GB \
+    LC_ALL=en_GB.UTF-8 \
+    TZ="Etc/UTC"
+
+ARG APP_USER=appuser
+ARG APP_UID=1000
+ARG APP_GID=$APP_UID
+
+WORKDIR /app
+
+RUN groupadd --gid $APP_GID $APP_USER && \
+    useradd --uid $APP_UID --gid $APP_GID --shell /bin/bash --create-home $APP_USER
+
+COPY --from=builder --chown=$APP_USER:$APP_GID /app /app
+
+ARG DB_HOST=localhost
+ARG DB_PORT=5432
+ARG DB_SCHEMA=porch_dev
+ARG DB_NAME=porch_dev_db
+ARG DB_USER=porch_admin
+ARG DB_PASS=porch
+ARG URL_SLUG="$DB_USER:$DB_PASS@$DB_HOST:$DB_PORT/$DB_NAME"
+
+ENV DB_HOST=$DB_HOST \
+    DB_PORT=$DB_PORT \
+    DB_SCHEMA=$DB_SCHEMA \
+    DB_NAME=$DB_NAME \
+    DB_USER=$DB_USER \
+    DB_PASS=$DB_PASS \
+    DB_URL="postgresql+psycopg2://$URL_SLUG"
+
+RUN service postgresql start && \
+    /app/docker/scripts/create_database.sh && \
+    /app/docker/scripts/configure_database_service.sh && \
+    . /app/bin/activate && \
+    /app/scripts/deploy_schema.py && \
+    /app/docker/scripts/insert_admin_token.sh && \
+    service postgresql stop
+
+USER $APP_USER
+
+ARG PORT=8081
+
+ENV DB_URL="postgresql+asyncpg://$URL_SLUG" \
+    PORT=${PORT}
+
+EXPOSE ${PORT}
+
+HEALTHCHECK --interval=30s --timeout=30s --start-period=10s --retries=3 CMD curl -f http://localhost:${PORT} || exit 1
+
+ENTRYPOINT ["/usr/bin/tini", "--"]
+
+CMD ["/app/docker/scripts/entrypoint.sh"]

docker/porch/README.md

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+# NPG Porch Server
+
+**Not for use in production!**
+
+This is a Docker image hosting both a Porch server and its PostgreSQL database
+that works out of the box. To be used for running tests only.
+
+The application is populated with a hard-coded administrator user, password and
+administration token and is configured log to STDERR and STDOUT.
+
+## Using the container
+### Running
+
+To run the container (with the Porch port published to the host network):
+
+`docker run -d -name porch -p 8081:8081 wsinpg/python-3.10-npg-porch-[VERSION]:latest`
+
+where [VERSION] is the required npg_porch release e.g. 2.0.0
+
+### Connecting
+
+The Porch server is configured to use HTTP on port 8081 and an admin token of
+
+`00000000000000000000000000000000`
+
+has been set in the database. See the Dockerfile for the configuration of the
+backend database.

docker/porch/logging.json

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+{
+    "version": 1,
+    "formatters": {
+        "default": {
+            "()": "uvicorn.logging.DefaultFormatter",
+            "fmt": "%(levelprefix)s %(message)s",
+            "use_colors": null
+        },
+        "access": {
+            "()": "uvicorn.logging.AccessFormatter",
+            "fmt": "%(levelprefix)s %(client_addr)s - \"%(request_line)s\" %(status_code)s"
+        }
+    },
+    "handlers": {
+        "stderr": {
+            "formatter": "default",
+            "class": "logging.StreamHandler",
+            "stream": "ext://sys.stderr"
+        },
+        "stdout": {
+            "formatter": "default",
+            "class": "logging.StreamHandler",
+            "stream": "ext://sys.stdout"
+        },
+        "access": {
+            "formatter": "access",
+            "class": "logging.StreamHandler",
+            "stream": "ext://sys.stdout"
+        }
+    },
+    "loggers": {
+        "uvicorn": {
+            "handlers": ["access"],
+            "level": "INFO",
+            "propagate": false
+        },
+        "uvicorn.error": {
+            "handlers": ["stderr"],
+            "level": "DEBUG",
+            "propagate": false
+        },
+        "fastapi": {
+            "handlers": ["stderr"],
+            "level": "INFO"
+        }
+    },
+    "root": {
+        "handlers": ["stdout"],
+        "level": "DEBUG"
+    }
+}

docker/porch/scripts/configure_database_service.sh

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+#!/bin/bash
+
+set -eo pipefail
+set -x
+
+APP_USER=${APP_USER:? The APP_USER environment variable must be set}
+
+cat > "/etc/sudoers.d/$APP_USER" << EOF
+$APP_USER ALL= NOPASSWD: /usr/sbin/service postgresql start
+$APP_USER ALL= NOPASSWD: /usr/sbin/service postgresql restart
+$APP_USER ALL= NOPASSWD: /usr/sbin/service postgresql stop
+EOF

docker/porch/scripts/create_database.sh

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+#!/bin/bash
+
+set -eo pipefail
+set -x
+
+pg_isready --quiet || {
+ echo "PostgreSQL is not ready" >&2
+ exit 1
+}
+
+DB_SCHEMA=${DB_SCHEMA:? The DB_SCHEMA environment variable must be set}
+DB_NAME=${DB_NAME:? The DB_NAME environment variable must be set}
+DB_USER=${DB_USER:? The DB_USER environment variable must be set}
+DB_PASS=${DB_PASS:? The DB_PASS environment variable must be set}
+
+sudo -u postgres createuser -D -R -S ${DB_USER}
+sudo -u postgres createdb -O ${DB_USER} ${DB_NAME}
+
+sudo -u postgres psql -d ${DB_NAME} << EOF
+ALTER USER ${DB_USER} WITH PASSWORD '${DB_PASS}';
+
+CREATE SCHEMA ${DB_SCHEMA};
+
+SET search_path TO ${DB_SCHEMA}, public;
+
+GRANT ALL PRIVILEGES ON SCHEMA ${DB_SCHEMA} TO ${DB_USER};
+GRANT ALL PRIVILEGES ON ALL TABLES IN SCHEMA ${DB_SCHEMA} TO ${DB_USER};
+GRANT USAGE ON ALL SEQUENCES IN SCHEMA ${DB_SCHEMA} TO ${DB_USER};
+GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA ${DB_SCHEMA} TO ${DB_USER};
+EOF

docker/porch/scripts/entrypoint.sh

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+#!/bin/bash
+
+set -eo pipefail
+
+sudo service postgresql start
+
+pg_isready --quiet --timeout=30 || {
+ echo "PostgreSQL is not ready" >&2
+ exit 1
+}
+
+PORT=${PORT:? The PORT environment variable must be set}
+
+source /app/bin/activate
+
+exec uvicorn npg_porch.server:app --host 0.0.0.0 --port ${PORT} --reload --log-config /app/docker/logging.json

docker/porch/scripts/insert_admin_token.sh

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+#!/bin/bash
+
+set -eo pipefail
+set -x
+
+pg_isready --quiet || {
+ echo "PostgreSQL is not ready" >&2
+ exit 1
+}
+
+DB_SCHEMA=${DB_SCHEMA:? The DB_SCHEMA environment variable must be set}
+DB_NAME=${DB_NAME:? The DB_NAME environment variable must be set}
+
+ADMIN_TOKEN=${ADMIN_TOKEN:="00000000000000000000000000000000"}
+
+sudo -u postgres psql -d ${DB_NAME} << EOF
+INSERT INTO ${DB_SCHEMA}."token" (token, description, date_issued) VALUES ('${ADMIN_TOKEN}', 'Admin token', NOW());
+EOF