diff --git a/src/api/workflows/vcf_gz.wdl b/src/api/workflows/vcf_gz.wdl index 83625fe..19d30cb 100644 --- a/src/api/workflows/vcf_gz.wdl +++ b/src/api/workflows/vcf_gz.wdl @@ -1,26 +1,20 @@ workflow vcf_gz { - String gohan_url - Array[File] vcf_gz_file_names # redundant - Array[String] original_vcf_gz_file_paths + String service_url + Array[File] vcf_gz_file_names String assembly_id String project_id String dataset_id - String service_url String filter_out_references - String temp_token - String temp_token_host + String secret__access_token - # scatter(file_name in vcf_gz_file_names) { - scatter(file_name in original_vcf_gz_file_paths) { + scatter(file_name in vcf_gz_file_names) { call vcf_gz_gohan { - input: gohan_url = gohan_url, + input: gohan_url = service_url, vcf_gz_file_name = file_name, assembly_id = assembly_id, dataset = dataset_id, filter_out_references = filter_out_references, - temp_token = temp_token, - temp_token_host = temp_token_host - + access_token = secret__access_token, } } } @@ -31,21 +25,18 @@ task vcf_gz_gohan { String assembly_id String dataset String filter_out_references - String temp_token - String temp_token_host + String access_token command { - echo "Using temporary-token : ${temp_token}" - QUERY="fileNames=${vcf_gz_file_name}&assemblyId=${assembly_id}&dataset=${dataset}&filterOutReferences=${filter_out_references}" # TODO: refactor # append temporary-token header if present - if [ "${temp_token}" == "" ] + if [ "${access_token}" == "" ] then RUN_RESPONSE=$(curl -vvv "${gohan_url}/private/variants/ingestion/run?$QUERY" -k | sed 's/"/\"/g') else - RUN_RESPONSE=$(curl -vvv -H "Host: ${temp_token_host}" -H "X-TT: ${temp_token}" "${gohan_url}/private/variants/ingestion/run?$QUERY" -k | sed 's/"/\"/g') + RUN_RESPONSE=$(curl -vvv -H "Authorization: ${access_token}" "${gohan_url}/private/variants/ingestion/run?$QUERY" -k | sed 's/"/\"/g') fi echo $RUN_RESPONSE @@ -67,11 +58,11 @@ task vcf_gz_gohan { # TODO: refactor # fetch run requests # append temporary-token header if present - if [ "${temp_token}" == "" ] + if [ "${access_token}" == "" ] then REQUESTS=$(curl -vvv "${gohan_url}/private/variants/ingestion/requests" -k) else - REQUESTS=$(curl -vvv -H "Host: ${temp_token_host}" -H "X-TT: ${temp_token}" "${gohan_url}/private/variants/ingestion/requests" -k) + REQUESTS=$(curl -vvv -H "Authorization: ${access_token}" "${gohan_url}/private/variants/ingestion/requests" -k) fi echo $REQUESTS