remove curl transfer

data/templates/env_vars.txt

@@ -8,9 +8,5 @@ export NXF_EXECUTOR=local
 export NXF_WORK=$TMPDIR/work
 export NXF_HOME=$TMPDIR/home
 export CAPSULE_LOG=none
-# transfer.sh configuration
-export GLOBUS_BASE_URL={globus_base_url}
-export GLOBUS_GUEST_COLLECTION_ID={guest_collection_id}
-export JOB_MESSAGE='{message}'
 
 # ------------------------------------------------------------------------------

data/transfer/transfer.sh

-#!/usr/bin/env bash
-
-set -euxo pipefail
-
-# A simple way to download a set of files from an INTERVENE globus collection
-# using curl and HTTPS. Doesn't retry, resume, or do anything fancy.
-# All configuration is done with environment variables.
-# This script is kept here as a reference when deploying hattivatti to Puhti.
-
-check_environment_variables () {
-    # GLOBUS_BASE_URL https://docs.globus.org/globus-connect-server/v5/https-access-collections/#determining_the_collection_https_base_url
-    # GLOBUS_SECRET_TOKEN: globus sdk client token
-    # GLOBUS_GUEST_COLLECTION_ID: uuid, from message
-    # JOB_MESSAGE: a validated JSON message sent by the backend
-    env_vars=("GLOBUS_BASE_URL" "GLOBUS_SECRET_TOKEN" "GLOBUS_GUEST_COLLECTION_ID" "JOB_MESSAGE")
-    for var in "${env_vars[@]}"; do
-        echo "Checking environment variable $var"
-        # print indirect reference, only errors correctly with set -u
-        echo "${!var} OK"
-    done
-}
-
-grab_access_token () {
-    GLOBUS_ACCESS_TOKEN=$(curl -s -X POST -H "Authorization: Basic $GLOBUS_SECRET_TOKEN" \
-                               -d "scope=https://auth.globus.org/scopes/$GLOBUS_GUEST_COLLECTION_ID/https&grant_type=client_credentials" \
-                               https://auth.globus.org/v2/oauth2/token \
-                              | jq -r '.access_token')
-}
-
-download_files () {
-    GLOBUS_HEADER="\"Authorization: Bearer $GLOBUS_ACCESS_TOKEN\""
-
-    # step 1: extract a list of file names and extensions from the job message
-    # e.g. test.pgen
-    FILE_PATHS=$(mktemp)
-    jq -r '.pipeline_param.target_genomes[] | (.pgen, .pvar, .psam)' <(echo "$JOB_MESSAGE") > $FILE_PATHS
-    DIRECTORY=$(echo $JOB_MESSAGE | jq -r '.globus_details.dir_path_on_guest_collection + "/"')
-    CURL_CMD="curl -s -f -O -L -X GET \
-                        -H "$GLOBUS_HEADER" \
-                        --url "${GLOBUS_BASE_URL}/${DIRECTORY}/{PATH}" \
-                        -w "%{json}" >> transfer_log.json"
-    DOWNLOAD_PATH=$(mktemp)
-
-    # step 2: print a list of curl commands to a temporary file
-    xargs -I {PATH} echo $CURL_CMD < $FILE_PATHS > $DOWNLOAD_PATH
-
-    # step 3: run the curl commands to stage the files locally over HTTPS
-    source $DOWNLOAD_PATH
-}
-
-main () {
-    # clean up old transfer logs before starting downloads
-    rm -f transfer_log.json
-
-    check_environment_variables
-    grab_access_token
-    download_files
-
-    # clean up temporary files when exiting the script
-    # mktemp is quite secure so not really needed, just being tidy
-    trap 'rm -f $FILE_PATHS $DOWNLOAD_PATH' EXIT
-}
-
-main