run_integration_test_standalone.sh

#!/bin/sh

start_time=$( date -u +'%FT%TZ' )

for cmd in s3cmd jq openssl
do
    if ! command -v "$cmd" >/dev/null 2>&1
    then
        printf '%s could not be found\n' "$cmd" >&2
        exit 1
    fi
done

infile=${1:-$(dirname "$0")/dummy_data.c4gh}
if [ ! -f "$infile" ]; then
    printf 'Unable to find regular file "%s"\n' "$infile" >&2
    exit 1
fi
infile=$( realpath "$infile" )

cd "$(dirname "$0")" || exit

if [ ! -f certs/client-key.pem ]; then
    echo 'Not found: certs/client-key.pem'
    echo 'Please run the "make_certs.sh" script'
    exit 1
fi >&2

# we need this certificate to be of 600 to work with db connection
chmod 600 certs/client-key.pem

SHA=$(openssl sha256 "$infile" | sed 's/.* //')
MD5=$(openssl md5    "$infile" | sed 's/.* //')

s3object=test/$(basename "$infile")
s3cmd -c s3cmd.conf put "$infile" "s3://inbox/$s3object"

encrypted_checksums=$( jq -c -n \
    --arg sha256 "$SHA" \
    --arg md5 "$MD5" \
    '$ARGS.named|to_entries|map(with_entries(select(.key=="key").key="type"))'
)

payload_string=$( jq -r -c -n \
    --arg operation upload \
    --arg user test \
    --arg filepath "$s3object" \
    --argjson encrypted_checksums "$encrypted_checksums" \
    '$ARGS.named|@base64'
)

properties=$( jq -c -n \
    --argjson delivery_mode 2 \
    --arg correlation_id 1 \
    --arg content_encoding UTF-8 \
    --arg content_type application/json \
    '$ARGS.named'
)

request_body=$( jq -c -n \
    --arg vhost test \
    --arg name sda \
    --argjson properties "$properties" \
    --arg routing_key inbox \
    --arg payload_encoding base64 \
    --arg payload "$payload_string" \
    '$ARGS.named'
)

# invoke ingestion for standalone (orchestrator)
curl -vvv --cacert certs/ca.pem --user test:test \
    --header 'Content-Type: application/json;charset=UTF-8' \
    --data-binary "$request_body" \
    'https://localhost:15672/api/exchanges/test/sda/publish'

tries=6
until datasetID=$(
    docker logs --since "$start_time" mapper 2>&1 |
    jq -r '
        select(.msg | startswith("Mapped file to dataset")).msg |
        capture("datasetid: (?<datasetid>[^,]+)").datasetid' |
    grep .
)
do
    tries=$((tries - 1))
    if [ "$tries" -eq 0 ]; then
        echo "Mapping failed"
        exit 1
    fi

    sleep 5
done

# check that the file's dataset appeared in the db.
if printf '%s\n' \
    'SELECT file_id FROM local_ega_ebi.file_dataset' \
    "WHERE dataset_id = :'id'" |
    docker run --rm --interactive \
    --name client \
    --network dev_utils_default \
    --volume "$PWD/certs:/certs" \
    --env PGSSLCERT=/certs/client.pem \
    --env PGSSLKEY=/certs/client-key.pem \
    --env PGSSLROOTCERT=/certs/ca.pem \
    neicnordic/pg-client:latest \
    postgresql://lega_out:lega_out@db:5432/lega -t \
        --variable=id="$datasetID" | grep .
then
    echo 'Success'
else
    echo 'Failure'
    exit 1
fi