Merge pull request #280 from pneerincx/updated_notifications

Updated logs for notifications.
molgenis · Aug 31, 2023 · 8b4c725 · 8b4c725
2 parents 62f5135 + 040700f
commit 8b4c725
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Showing 3 changed files with 25 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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."