docker-run-upload-analysis-files.sh

#!/bin/bash

set -e

PROJECT_NAME="$(<configuration/docker_image_project_name.txt)"
IMAGE_NAME=$PROJECT_NAME-upload-analysis-files

# Check that the correct number of arguments were provided.
if [[ $# -ne 9 ]]; then
    echo "Usage: ./docker-run-upload-analysis-files.sh
    <user> <pipeline-run-mode> <google-cloud-credentials-file-path> <pipeline-configuration-file-path> <run-id> <production-csv-path>
    <messages-csv-path> <individuals-csv-path> <automated-analysis-dir-path>"
    exit
fi

# Assign the program arguments to bash variables.
USER=$1
PIPELINE_RUN_MODE=$2
INPUT_GOOGLE_CLOUD_CREDENTIALS=$3
INPUT_PIPELINE_CONFIGURATION=$4
RUN_ID=$5
INPUT_PRODUCTION_CSV=$6
INPUT_MESSAGES_CSV=$7
INPUT_INDIVIDUALS_CSV=$8
AUTOMATED_ANALYSIS_DIR=$9


# Build an image for this pipeline stage.
docker build -t "$IMAGE_NAME" .

# Create a container from the image that was just built.
CMD="pipenv run python -u upload_analysis_files.py \
    \"$USER\" \"$PIPELINE_RUN_MODE\" /credentials/google-cloud-credentials.json /data/pipeline_configuration.json \"$RUN_ID\" \
    /data/production.csv /data/messages.csv /data/individuals.csv /data/automated-analysis
"
container="$(docker container create -w /app "$IMAGE_NAME" /bin/bash -c "$CMD")"
echo "Created container $container"
container_short_id=${container:0:7}

# Copy input data into the container
echo "Copying $INPUT_PIPELINE_CONFIGURATION -> $container_short_id:/data/pipeline_configuration.json"
docker cp "$INPUT_PIPELINE_CONFIGURATION" "$container:/data/pipeline_configuration.json"

echo "Copying $INPUT_GOOGLE_CLOUD_CREDENTIALS -> $container_short_id:/credentials/google-cloud-credentials.json"
docker cp "$INPUT_GOOGLE_CLOUD_CREDENTIALS" "$container:/credentials/google-cloud-credentials.json"

echo "Copying $INPUT_PRODUCTION_CSV -> $container_short_id:/data/production.csv"
docker cp "$INPUT_PRODUCTION_CSV" "$container:/data/production.csv"

if [[ $PIPELINE_RUN_MODE = "all-stages" ]]; then
    echo "Copying $INPUT_MESSAGES_CSV -> $container_short_id:/data/messages.csv"
    docker cp "$INPUT_MESSAGES_CSV" "$container:/data/messages.csv"

    echo "Copying $INPUT_INDIVIDUALS_CSV -> $container_short_id:/data/individuals.csv"
    docker cp "$INPUT_INDIVIDUALS_CSV" "$container:/data/individuals.csv"

    echo "Copying $AUTOMATED_ANALYSIS_DIR -> $container_short_id:/data/automated-analysis"
    docker cp "$AUTOMATED_ANALYSIS_DIR" "$container:/data/automated-analysis"
fi

# Run the container
echo "Starting container $container_short_id"
docker start -a -i "$container"

# Tear down the container, now that all expected output files have been copied out successfully
docker container rm "$container" >/dev/null