Update weekly_routine.sh

1. replacing log references to "${JSONIMPORTFILE}" with "/import_export/import-fbrfs.json", so that the filename is explicit rather than a "." when the file is empty.

2. remove 'CURATEDPAPERLISTFILE' (./fbrf_input_list.tsv) and 'JSONIMPORTFILE' (/import_export/import-fbrfs.json) while archiving, so that the files cannot be re-used in a following epicycle.

weekly_routine.sh

@@ -284,12 +284,9 @@ if [[ ( -e "${CURATEDPAPERLISTFILE}" ) && ( -s "${CURATEDPAPERLISTFILE}" ) ]]; t
     # JWRN comment: again I suspect the sudo is superfluous so removed
     log "Importing ${JSONIMPORTFILE} into Canto"
     ./canto/script/canto_docker ./script/canto_add.pl --sessions-from-json "${JSONIMPORTFILE}" "ignore@flybase.org" 7227
-
-    # remove the fbrf_input_list.tsv file once done, so that the script doesn't try to add the same information again next time its run
-    #/bin/rm "${CURATEDPAPERLISTFILE}"
     
 else
-    log "Not loading ${JSONIMPORTFILE} into Canto. Either ${CURATEDPAPERLISTFILE} does not exist or is empty..."
+    log "Not loading ./import_export/import-fbrfs.json into Canto. Either ./fbrf_input_list.tsv does not exist or is empty..."
 fi
 
 if [[ -e "${CURATEDPAPERLISTFILE}" ]]; then
@@ -298,10 +295,11 @@ if [[ -e "${CURATEDPAPERLISTFILE}" ]]; then
     FBRFARCHIVE="fbrf_input_list_$(date +"%Y-%m-%d")"
 
     # Copy fbrf_input_list.tsv to archive
-    log "Copying ${CURATEDPAPERLISTFILE} to ${ARCHIVE}/${FBRFARCHIVE}"
+    log "Copying ./fbrf_input_list.tsv to ${ARCHIVE}/${FBRFARCHIVE}"
 
-    # Copy file to archive with correct name
+    # Archive file with correct name (and delete original)
     cp "${CURATEDPAPERLISTFILE}" "${ARCHIVE}/${FBRFARCHIVE}"
+    rm "${CURATEDPAPERLISTFILE}"
 
 fi
 
@@ -314,11 +312,11 @@ if [[ -e ".${JSONIMPORTFILE}" ]]; then
     JSONARCHIVE="import-fbrfs_json_$(date +"%Y-%m-%d")"
 
     # Copy /import_export/import-fbrfs.json to archive
-    log "Copying .${JSONIMPORTFILE} to ${ARCHIVE}/${JSONARCHIVE}"
+    log "Copying /import_export/import-fbrfs.json to ${ARCHIVE}/${JSONARCHIVE}"
 
-    # Copy file to archive with correct name 
+    # Archive file with correct name (and delete original)
     cp ".${JSONIMPORTFILE}" "${ARCHIVE}/${JSONARCHIVE}"
-
+    rm ".${JSONIMPORTFILE}"
 fi
 
 # Restart Canto post processing