diff --git a/bin/copyBclDataToPrm.sh b/bin/copyBclDataToPrm.sh index e67852fe..8d4832d2 100755 --- a/bin/copyBclDataToPrm.sh +++ b/bin/copyBclDataToPrm.sh @@ -253,7 +253,7 @@ else --omit-dir-times \ --omit-link-times \ "${DATA_MANAGER}@${sourceServerFQDN}:${SEQ_DIR}/${filePrefix}" \ - "${PRM_ROOT_DIR}/rawdata/bcls/" + "${PRM_ROOT_DIR}/rawdata/bcls/" else log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Sequencer is busy producing data: skipping ${filePrefix}." continue @@ -267,7 +267,14 @@ else mv "${JOB_CONTROLE_FILE_BASE}."{started,failed} return else - log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Amount of files on tmp and prm is the same for ${filePrefix}. FINISHED" + log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Amount of files on tmp and prm is the same for ${filePrefix}." + log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "The data is available at ${PRM_ROOT_DIR}/rawdata/bcls/${filePrefix}/" + mountedCifsDevice="$(awk -v mountpoint="${PRM_ROOT_DIR}" '$2==mountpoint && $3=="cifs" {print $1}' /proc/mounts)" + if [[ -n "${mountedCifsDevice:-}" ]]; then + printf 'file:%s/rawdata/bcls/%s/\n' \ + "${mountedCifsDevice}" "${filePrefix}" \ + >> "${JOB_CONTROLE_FILE_BASE}.started" + fi mv "${JOB_CONTROLE_FILE_BASE}."{started,finished} fi diff --git a/bin/copyProjectDataToPrm.sh b/bin/copyProjectDataToPrm.sh index 8d7b9ec5..cc497b1b 100755 --- a/bin/copyProjectDataToPrm.sh +++ b/bin/copyProjectDataToPrm.sh @@ -540,21 +540,20 @@ else mv "${JOB_CONTROLE_FILE_BASE}."{started,failed} return fi - rm -f "${JOB_CONTROLE_FILE_BASE}.failed" - mv -v "${JOB_CONTROLE_FILE_BASE}."{started,finished} - log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Finished processing project ${project}." # # Add info for colleagues that will process the results. # This will appear in the messeages send by notifications.sh # - printf 'The data is available at %s.\n' "${PRM_ROOT_DIR}/projects/${project}/${run}/" \ - >> "${JOB_CONTROLE_FILE_BASE}.finished" + log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "The data is available at ${PRM_ROOT_DIR}/projects/${project}/${run}/." mountedCifsDevice="$(awk -v mountpoint="${PRM_ROOT_DIR}" '$2==mountpoint && $3=="cifs" {print $1}' /proc/mounts)" if [[ -n "${mountedCifsDevice:-}" ]]; then printf 'file:%s/projects/%s/%s/\n' \ "${mountedCifsDevice}" "${project}" "${run}" \ - >> "${JOB_CONTROLE_FILE_BASE}.finished" + >> "${JOB_CONTROLE_FILE_BASE}.started" fi + rm -f "${JOB_CONTROLE_FILE_BASE}.failed" + mv -v "${JOB_CONTROLE_FILE_BASE}."{started,finished} + log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Finished processing project ${project}." log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Found ${JOB_CONTROLE_FILE_BASE}.finished. Setting track & trace state to finished :)." dateFinished=$(date +%FT%T%z -r "${JOB_CONTROLE_FILE_BASE}.finished") printf '"%s"\n' "${dateFinished}" > "${JOB_CONTROLE_FILE_BASE}.trace_putFromFile_projects.csv" diff --git a/bin/copyRawDataToPrm.sh b/bin/copyRawDataToPrm.sh index e27c3065..41bd1f67 100755 --- a/bin/copyRawDataToPrm.sh +++ b/bin/copyRawDataToPrm.sh @@ -734,6 +734,17 @@ else log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${controlFileBase}/${runPrefix}.splitSamplesheetPerProject.finished present." rm -f "${JOB_CONTROLE_FILE_BASE}.failed" log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Finished processing ${filePrefix}." + # + # Add info for colleagues that will process the results. + # This will appear in the messeages send by notifications.sh + # + log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "The data is available at ${PRM_ROOT_DIR}/rawdata/." + mountedCifsDevice="$(awk -v mountpoint="${PRM_ROOT_DIR}" '$2==mountpoint && $3=="cifs" {print $1}' /proc/mounts)" + if [[ -n "${mountedCifsDevice:-}" ]]; then + printf 'file:%s/rawdata/\n' \ + "${mountedCifsDevice}" \ + >> "${JOB_CONTROLE_FILE_BASE}.started" + fi mv -v "${JOB_CONTROLE_FILE_BASE}."{started,finished} else log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${controlFileBase}/${runPrefix}.splitSamplesheetPerProject.finished absent -> splitSamplesheetPerProject failed."