00-run-pulsar-dev.md

run-pulsar-dev.sh

This script was prepared for development work at the Galaxy Community Conference 2021 CoFest. It has been superseded by a Docker Compose-based project at:

https://github.com/natefoo/galaxy-pulsar-dev/

run-pulsar-dev.sh

#!/bin/bash
#
# Run Galaxy and Pulsar in Docker for development.
#
# Galaxy and Pulsar should be cloned at ./galaxy and ./pulsar, override with vars below. Necessary configs, as well as
# venvs for each, will be placed in ./config. These configs can be modified once created, if needed. Once created, they
# are not overwritten.
#
# To stop, run:
#   docker kill pulsar galaxy-job galaxy-web rabbitmq postgres
#
# To restart Galaxy or Pulsar, `docker kill` the relevant service(s) and rerun this script.
#
# These users may be useful:
#   - [email protected]: Galaxy Admin
#   - [email protected]: Runs all jobs locally
#   - [email protected]: Runs all jobs (except upload1) via Pulsar
#
# Galaxy's Pulsar lib, pulsar_galaxy_lib, will be built from the Pulsar clone and installed in to Galaxy's venv if the
# galaxy-job container is not already running.
set -euo pipefail

: ${SKIP_PULSAR_GALAXY_LIB:='false'}

: ${POSTGRES_IMAGE:='postgres:latest'}
: ${RABBITMQ_IMAGE:='rabbitmq:latest'}
: ${PULSAR_IMAGE:='python:3.8-buster'}
: ${GALAXY_IMAGE:='python:3.8-buster'}

: ${GALAXY_ROOT:="$(pwd)/galaxy"}
: ${PULSAR_ROOT:="$(pwd)/pulsar"}
: ${CONFIG_DIR:="$(pwd)/config"}

: ${RABBITMQ_USER:='guest'}
: ${RABBITMQ_PASS:='guest'}
: ${POSTGRES_USER:='galaxy'}
: ${POSTGRES_PASS:='galaxy'}

: ${UID:="$(id -u)"}
: ${GID:="$(id -g)"}


function log() {
    [ -t 0 ] && echo -e '\033[1;32m#' "$@" '\033[0m' 1>&2 || echo '#' "$@" 1>&2
}

function extract_lines() {
    local marker="$1"
    local begin=$(awk "/^__BEGIN_${marker}__/ {print NR + 1; exit 0; }" "$0")
    local end=$(awk "/^__END_${marker}__/ {print NR; exit 0; }" "$0")
    tail -n+${begin} "$0" | head -n $(($end - $begin))
}


if [ ! -d "$CONFIG_DIR" ]; then
    log "Creating config dir '${CONFIG_DIR}'"
    mkdir -p "$CONFIG_DIR"
fi


for cf in galaxy.yml job_conf.xml run-galaxy.sh run-pulsar.sh app.yml job_resource_params_conf.xml rule.py; do
    if [ ! -f "${CONFIG_DIR}/${cf}" ]; then
        log "Creating ${CONFIG_DIR}/${cf}"
        case "$cf" in
            galaxy.yml)
                extract_lines GALAXY_YML | sed -e "s/PGUSER/${POSTGRES_USER}/" -e "s/PGPASS/${POSTGRES_PASS}/" > "${CONFIG_DIR}/${cf}"
                ;;
            job_conf.xml)
                extract_lines JOB_CONF_XML > "${CONFIG_DIR}/${cf}"
                ;;
            run-galaxy.sh)
                extract_lines RUN_GALAXY_SH | sed -e "s/UID/${UID}/g" -e "s/GID/${GID}/g" > "${CONFIG_DIR}/${cf}"
                chmod +x "${CONFIG_DIR}/${cf}"
                ;;
            run-pulsar.sh)
                extract_lines RUN_PULSAR_SH | sed -e "s/UID/${UID}/g" -e "s/GID/${GID}/g" > "${CONFIG_DIR}/${cf}"
                chmod +x "${CONFIG_DIR}/${cf}"
                ;;
            app.yml)
                extract_lines APP_YML > "${CONFIG_DIR}/${cf}"
                ;;
            job_resource_params_conf.xml)
                extract_lines JOB_RESOURCE_PARAMS_CONF_XML > "${CONFIG_DIR}/${cf}"
                ;;
            rule.py)
                extract_lines DYNAMIC_RULE > "${CONFIG_DIR}/${cf}"
                ;;
        esac
    else
        log "${CONFIG_DIR}/${cf} already exists, remove to reinitialize"
    fi
done

if [ ! -d "${CONFIG_DIR}/venv-galaxy" ]; then
    # common_startup.sh doesn't upgrade pip or use python3's builtin venv, it probably should.
    log "Creating Galaxy .venv"
    docker run --rm -it --name galaxy-init -v "${CONFIG_DIR}:/galaxy" -w /galaxy --user "${UID}:${GID}" "$GALAXY_IMAGE" python3 -m venv .venv
    mv "${CONFIG_DIR}/.venv" "${CONFIG_DIR}/venv-galaxy"
    log "Upgrading pip"
    docker run --rm -it --name galaxy-init -v "${GALAXY_ROOT}:/galaxy" -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv" -w /galaxy --user "${UID}:${GID}" "$GALAXY_IMAGE" ./.venv/bin/pip install --upgrade pip setuptools wheel
    log "Running common_startup.sh"
    docker run --rm -it --name galaxy-init -v "${GALAXY_ROOT}:/galaxy" -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv" -v "${CONFIG_DIR}/galaxy.yml:/galaxy/config/galaxy.yml:ro" -v "${CONFIG_DIR}/job_conf.xml:/galaxy/config/job_conf.xml:ro" -e HOME=/tmp/galaxy -w /galaxy --user "${UID}:${GID}" "$GALAXY_IMAGE" bash ./scripts/common_startup.sh
else
    log "Skipping common_startup.sh, remove ${GALAXY_ROOT}/venv-galaxy to reinitialize"
fi

if [ ! -d "${CONFIG_DIR}/venv-pulsar" ]; then
    log "Creating Pulsar .venv"
    docker run --rm -it --name pulsar-init -v "${CONFIG_DIR}:/pulsar" -w /pulsar --user "${UID}:${GID}" "$PULSAR_IMAGE" python3 -m venv .venv
    mv "${CONFIG_DIR}/.venv" "${CONFIG_DIR}/venv-pulsar"
    log "Upgrading pip"
    docker run --rm -it --name pulsar-init -v "${PULSAR_ROOT}:/pulsar" -v "${CONFIG_DIR}/venv-pulsar:/pulsar/.venv" -w /pulsar --user "${UID}:${GID}" "$PULSAR_IMAGE" ./.venv/bin/pip install --upgrade pip setuptools wheel
    log "Installing devmode Pulsar install"
    docker run --rm -it --name pulsar-init -v "${PULSAR_ROOT}:/pulsar" -v "${CONFIG_DIR}/venv-pulsar:/pulsar/.venv" -w /pulsar --user "${UID}:${GID}" "$PULSAR_IMAGE" ./.venv/bin/pip install -e .
    log "Installing Pulsar additional dependencies"
    docker run --rm -it --name pulsar-init -v "${PULSAR_ROOT}:/pulsar" -v "${CONFIG_DIR}/venv-pulsar:/pulsar/.venv" -w /pulsar --user "${UID}:${GID}" "$PULSAR_IMAGE" ./.venv/bin/pip install kombu pycurl
fi


# Generate a fresh pulsar-galaxy-client and install it in Galaxy's venv

if ! $SKIP_PULSAR_GALAXY_LIB && [ -z "$(docker ps -q --filter name=galaxy-job)" ]; then
    log "Building minty fresh pulsar-galaxy-lib from ${PULSAR_ROOT}"
    rm -rf "${PULSAR_ROOT}/build" "${PULSAR_ROOT}/dist" "${PULSAR_ROOT}"/*.egg-info
    docker run --rm -it --name pulsar-galaxy-lib -v "${PULSAR_ROOT}:/pulsar" -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv" -w /pulsar --user "${UID}:${GID}" -e PULSAR_GALAXY_LIB=1 "$GALAXY_IMAGE" /galaxy/.venv/bin/python setup.py bdist_wheel
    whl=$(basename "${PULSAR_ROOT}/dist"/pulsar_galaxy_lib-*.whl)
    cp "${PULSAR_ROOT}/dist/${whl}" "${GALAXY_ROOT}"
    rm -rf "${PULSAR_ROOT}/build" "${PULSAR_ROOT}/dist" "${PULSAR_ROOT}"/*.egg-info

    log "Uninstalling pulsar-galaxy-lib from ${GALAXY_ROOT} venv"
    docker run --rm -it --name pulsar-galaxy-lib -v "${GALAXY_ROOT}:/galaxy" -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv" -w /galaxy --user "${UID}:${GID}" "$GALAXY_IMAGE" ./.venv/bin/pip uninstall -y pulsar-galaxy-lib

    log "Installing pulsar-galaxy-lib from ${PULSAR_ROOT} in ${GALAXY_ROOT} venv"
    docker run --rm -it --name pulsar-galaxy-lib -v "${GALAXY_ROOT}:/galaxy" -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv" -w /galaxy --user "${UID}:${GID}" "$GALAXY_IMAGE" ./.venv/bin/pip install "/galaxy/${whl}"

    log "Fixing devmode Pulsar after wheel build"
    docker run --rm -it --name pulsar-init -v "${PULSAR_ROOT}:/pulsar" -v "${CONFIG_DIR}/venv-pulsar:/pulsar/.venv" -w /pulsar --user "${UID}:${GID}" "$PULSAR_IMAGE" ./.venv/bin/pip install -e .
elif ! $SKIP_PULSAR_GALAXY_LIB; then
    log "Skipped rebuilding pulsar-galaxy-lib because 'galaxy-job' is running, kill that container to allow rebuilding"
else
    log 'Skipped rebuilding pulsar-galaxy-lib because $SKIP_PULSAR_GALAXY_LIB is true'
fi


# Run PostgreSQL

POSTGRES_ID="$(docker ps -q --filter name=postgres)"
if [ -z "$POSTGRES_ID" ]; then
    log "Starting PostgreSQL"
    docker run --rm -d --name postgres -e "POSTGRES_USER=$POSTGRES_USER" -e "POSTGRES_PASSWORD=$POSTGRES_PASS" "$POSTGRES_IMAGE"
else
    log "PostgreSQL already running in container id '$POSTGRES_ID'"
fi
POSTGRES_IP=$(docker inspect -f '{{ .NetworkSettings.IPAddress }}' postgres)
log "PostgreSQL IP is ${POSTGRES_IP}"
sed -i.old -e "s#PGHOST#${POSTGRES_IP}#" "${CONFIG_DIR}/galaxy.yml"


# Run RabbitMQ

RABBITMQ_ID="$(docker ps -q --filter name=rabbitmq)"
if [ -z "$RABBITMQ_ID" ]; then
    log "Starting RabbitMQ"
    docker run --rm -d --hostname rabbitmq --name rabbitmq "$RABBITMQ_IMAGE"
else
    log "RabbitMQ already running in container id '$RABBITMQ_ID'"
fi
RABBITMQ_IP=$(docker inspect -f '{{ .NetworkSettings.IPAddress }}' rabbitmq)
log "RabbitMQ IP is ${RABBITMQ_IP}"
sed -i.old -e "s#MQHOST#${RABBITMQ_IP}#" "${CONFIG_DIR}/job_conf.xml"
sed -i.old -e "s#MQHOST#${RABBITMQ_IP}#" "${CONFIG_DIR}/app.yml"


# Run Galaxy Web

rm -f "${GALAXY_ROOT}/docker-ip"

GALAXY_WEB_ID="$(docker ps -q --filter name=galaxy-web)"
if [ -z "$GALAXY_WEB_ID" ]; then
    # TODO: get output when it crashes
    log "Running Galaxy Web"
    #docker run --rm -it --name galaxy-web \
    docker run --rm -d --name galaxy-web \
        -p 8080:8080 \
        -v "${GALAXY_ROOT}:/galaxy" \
        -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv:ro" \
        -v "${CONFIG_DIR}/job_conf.xml:/tmp/job_conf.xml.sed-in:ro" \
        -v "${CONFIG_DIR}/job_resource_params_conf.xml:/galaxy/config/job_resource_params_conf.xml:ro" \
        -v "${CONFIG_DIR}/galaxy.yml:/galaxy/config/galaxy.yml:ro" \
        -v "${CONFIG_DIR}/run-galaxy.sh:/galaxy/run-galaxy.sh:ro" \
        -v "${CONFIG_DIR}/rule.py:/galaxy/lib/galaxy/jobs/rules/rule.py:ro" \
        -w /galaxy "$GALAXY_IMAGE" ./run-galaxy.sh web
else
    log "Galaxy Web already running in container id '$GALAXY_WEB_ID'"
fi

GALAXY_WEB_IP=$(docker inspect -f '{{ .NetworkSettings.IPAddress }}' galaxy-web)
log "Galaxy Web IP is ${GALAXY_WEB_IP}"
echo "$GALAXY_WEB_IP" > "${GALAXY_ROOT}/docker-ip"


# Run Galaxy Job

GALAXY_JOB_ID="$(docker ps -q --filter name=galaxy-job)"
if [ -z "$GALAXY_JOB_ID" ]; then
    log "Running Galaxy Job"
    docker run --rm -d --name galaxy-job \
        -v "${GALAXY_ROOT}:/galaxy" \
        -v "${CONFIG_DIR}/venv-galaxy:/galaxy/.venv:ro" \
        -v "${CONFIG_DIR}/job_conf.xml:/tmp/job_conf.xml.sed-in:ro" \
        -v "${CONFIG_DIR}/job_resource_params_conf.xml:/galaxy/config/job_resource_params_conf.xml:ro" \
        -v "${CONFIG_DIR}/galaxy.yml:/galaxy/config/galaxy.yml:ro" \
        -v "${CONFIG_DIR}/run-galaxy.sh:/galaxy/run-galaxy.sh:ro" \
        -v "${CONFIG_DIR}/rule.py:/galaxy/lib/galaxy/jobs/rules/rule.py:ro" \
        -w /galaxy "$GALAXY_IMAGE" ./run-galaxy.sh job
else
    log "Galaxy Job already running in container id '$GALAXY_JOB_ID'"
fi

GALAXY_JOB_IP=$(docker inspect -f '{{ .NetworkSettings.IPAddress }}' galaxy-job)
log "Galaxy Job IP is ${GALAXY_JOB_IP}"


# Run Pulsar

PULSAR_ID="$(docker ps -q --filter name=pulsar)"
if [ -z "$PULSAR_ID" ]; then
    log "Running Pulsar"
    #set -x; docker run --rm -it --name pulsar \
    docker run --rm -d --name pulsar \
        -v "${PULSAR_ROOT}:/pulsar" \
        -v "${CONFIG_DIR}/venv-pulsar:/pulsar/.venv:ro" \
        -v "${CONFIG_DIR}/app.yml:/pulsar/app.yml:ro" \
        -v "${CONFIG_DIR}/run-pulsar.sh:/pulsar/run-pulsar.sh:ro" \
        -w /pulsar "$PULSAR_IMAGE" ./run-pulsar.sh
else
    log "Pulsar already running in container id '$PULSAR_ID'"
fi

PULSAR_IP=$(docker inspect -f '{{ .NetworkSettings.IPAddress }}' pulsar)
log "Pulsar IP is ${PULSAR_IP}"

exit 0


__BEGIN_GALAXY_YML__
uwsgi:
  http: :8080
  buffer-size: 16384
  processes: 1
  threads: 4
  offload-threads: 2
  static-map: /static/style=static/style/blue
  static-map: /static=static
  static-map: /favicon.ico=static/favicon.ico
  master: true
  virtualenv: .venv
  pythonpath: lib
  module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
  thunder-lock: false
  die-on-term: true
  hook-master-start: unix_signal:2 gracefully_kill_them_all
  hook-master-start: unix_signal:15 gracefully_kill_them_all
  py-call-osafterfork: false
  enable-threads: true
galaxy:
  database_connection: postgresql://PGUSER:PGPASS@PGHOST/galaxy
  job_config_file: /tmp/job_conf.xml
  admin_users: [email protected]
  cleanup_job: never
__END_GALAXY_YML__
__BEGIN_JOB_CONF_XML__
<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <plugin id="pulsar_mq" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner" workers="4">
            <param id="amqp_url">amqp://guest:guest@MQHOST:5672//</param>
            <param id="galaxy_url">http://GXHOST:8080</param>
        </plugin>
    </plugins>
    <handlers assign_with="db-skip-locked"/>
    <destinations default="dynamic">
        <destination id="dynamic" runner="dynamic">
            <param id="function">rule</param>
        </destination>
        <destination id="local" runner="local"/>
        <destination id="pulsar_mq" runner="pulsar_mq" >
            <param id="jobs_directory">/tmp/pulsar/staging</param>
        </destination>
    </destinations>
    <resources default="default">
        <group id="default">force_dest</group>
    </resources>
</job_conf>
__END_JOB_CONF_XML__
__BEGIN_JOB_RESOURCE_PARAMS_CONF_XML__
<parameters>
    <param label="Force Destination" name="force_dest" type="select">
        <option value="local">local</option>
        <option value="pulsar_mq">pulsar_mq</option>
    </param>
</parameters>
__END_JOB_RESOURCE_PARAMS_CONF_XML__
__BEGIN_DYNAMIC_RULE__
import logging
log = logging.getLogger(__name__)

def rule(tool_id, user_email, resource_params):
    destination_id = 'pulsar_mq'
    if tool_id in ('upload1'):
        destination_id = 'local'
    elif user_email == '[email protected]':
        destination_id = 'local'
        log.debug(f'User {user_email} force mapped to {destination_id}')
    elif user_email == '[email protected]':
        destination_id = 'pulsar_mq'
        log.debug(f'User {user_email} force mapped to {destination_id}')
    override = resource_params.get('force_dest')
    if override:
        destination_id = override
        log.debug(f'Override dest selected: {destination_id}')
    else:
        log.debug(f'Default dest for tool selected: {destination_id}')
    return destination_id
__END_DYNAMIC_RULE__
__BEGIN_RUN_GALAXY_SH__
#!/bin/sh

groupadd -g GID galaxy
useradd -u UID -g GID -s /bin/bash -m -d /home/galaxy galaxy

while [ ! -f 'docker-ip' ];
do
    echo "Waiting for Galaxy Docker IP"
    sleep 1
done

DOCKER_IP=$(cat docker-ip)
echo "Galaxy Docker IP is ${DOCKER_IP}"

sed -e "s#GXHOST#${DOCKER_IP}#" /tmp/job_conf.xml.sed-in > /tmp/job_conf.xml

case $1 in
    web)
        su - galaxy -c '/bin/bash -c "cd /galaxy ; . ./.venv/bin/activate ; uwsgi --yaml config/galaxy.yml"'
        ;;
    job)
        su - galaxy -c '/bin/bash -c "cd /galaxy ; . ./.venv/bin/activate ; python3 ./scripts/galaxy-main --attach-to-pool=job-handlers"'
        ;;
esac
__END_RUN_GALAXY_SH__
__BEGIN_RUN_PULSAR_SH__
#!/bin/sh

groupadd -g GID pulsar
useradd -u UID -g GID -s /bin/bash -m -d /home/pulsar pulsar

su - pulsar -c '/bin/bash -c "cd /pulsar ; . ./.venv/bin/activate ; pulsar-main"'
__END_RUN_PULSAR_SH__
__BEGIN_APP_YML__
message_queue_url: amqp://guest:guest@MQHOST:5672//
persistence_directory: /tmp/pulsar/persistence
staging_directory: /tmp/pulsar/staging
dependency_resolution:
  resolvers:
    - prefix: /pulsar/_conda
      type: conda
      auto_init: true
      auto_install: true
__END_APP_YML__