From 2a21d5994ea5d2c9a48c275644e975308ac95d89 Mon Sep 17 00:00:00 2001
From: Vitor Trovisco <vmt25@cam.ac.uk>
Date: Fri, 22 Jul 2022 13:45:05 +0000
Subject: [PATCH] Update weekly_export.sh - remove time stamp from the archive
export json and other changes a) copying the original
canto_server_export_latest.json export file to within export-vm's archives
folder b) remove time stamp from the archive export json (keeping the date
stamp) c) simplification of the script d) better commenting
---
weekly_export.sh | 54 ++++++++++++++----------------------------------
1 file changed, 15 insertions(+), 39 deletions(-)
diff --git a/weekly_export.sh b/weekly_export.sh
index 96405b4..c94643b 100755
--- a/weekly_export.sh
+++ b/weekly_export.sh
@@ -11,7 +11,7 @@ LOGS="logs"
# Define log file
LOGFILE="${CANTOSPACE}/${LOGS}/canto_weekly_export.log"
-# Redirect all output to logfile
+# Redirect all Terminal/command line output to logfile
exec &>> "${LOGFILE}"
# Function to log messages with date stamp
@@ -22,7 +22,7 @@ function log () {
/bin/echo "${DATESTAMP}: ${1}"
}
-# Define export directory filepath
+# Define initial export directory filepath
EXPORT_DIR="${CANTOSPACE}/import_export"
#Define export filename
@@ -33,49 +33,25 @@ EXPORTVM_EXPORT_ARCHIVE="/data/export/archives/canto_export_json"
log "Starting"
+#Export of 'APPROVED' sessions from Canto into json file
+#this step also relabels those 'APPROVED' sessions as 'EXPORTED', so that they will not be exported again next time this is executed
if ./canto/script/canto_docker --non-interactive ./script/canto_export.pl canto-json --export-curator-names --export-approved > "${EXPORT_DIR}/${EXPORT_FILENAME}"; then
- log "Approved sessions exported into ${EXPORT_DIR} successful"
+ log "Approved sessions exported into ${EXPORT_DIR} successfully"
- if [[ -e "${EXPORT_DIR}/${EXPORT_FILENAME}" ]]; then
-
- # Create archive directory in canto-space if required
- ARCHIVE="${CANTOSPACE}/archive"
-
- if [[ ! -d "${ARCHIVE}" ]]; then
- log "Creating ${ARCHIVE}"
- mkdir "${ARCHIVE}"
- fi
-
- #Define date-time-stamped filename for archiving
- EXPORT_FILENAME_ARCHIVE="canto_server_export_$(date +"%Y-%m-%d-%T").json"
-
-
- function archiving()
- {
- local FILENAME=${1}
-
- log "Archiving ${EXPORT_FILENAME} to ${FILENAME}"
-
- cp "${EXPORT_DIR}/${EXPORT_FILENAME}" "${FILENAME}"
-
- }
+ #Define date-time-stamped filename for archiving
+ EXPORT_FILENAME_ARCHIVE="canto_server_export_$(date +"%Y-%m-%d").json"
- for FILE in "${ARCHIVE}/${EXPORT_FILENAME_ARCHIVE}" "${EXPORTVM_EXPORT_ARCHIVE}/${EXPORT_FILENAME_ARCHIVE}"; do
- archiving ${FILE}
- done
-
- log "Finished"
+ log "Archiving ${EXPORT_FILENAME} to "${ARCHIVE}/${EXPORT_FILENAME_ARCHIVE}""
+
+ #Copying the export file to within flybase-vm's archives, both as the generic 'canto_server_export_latest.json' file, which will be overwritten every week, as a date-stamped version
+ cp "${EXPORT_DIR}/${EXPORT_FILENAME}" "${ARCHIVE}/${EXPORT_FILENAME}"
+ cp "${EXPORT_DIR}/${EXPORT_FILENAME}" "${ARCHIVE}/${EXPORT_FILENAME_ARCHIVE}"
+
+ log "Finished"
- exit
+ exit
- else
-
- log "But ${EXPORT_DIR}/${EXPORT_FILENAME} cannot be found - cannot continue"
-
- log "Finished"
-
- exit
fi
else
--
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