Backup and Restore a Rosalution DB to and from LTS (#169)

* Updated the scripts to use the expected cgdslts remote source for rclone for the s3 bucket

* Update etc/database/restore-database-lts.sh

Co-authored-by: James Scherer <[email protected]>
Signed-off-by: Angelina Uno-Antonison <[email protected]>

---------

Signed-off-by: Angelina Uno-Antonison <[email protected]>
Co-authored-by: James Scherer <[email protected]>

.gitignore

@@ -68,4 +68,6 @@ media/
 
 # SSL/TLS Certificates
 **/.certificates/**
-*.pem
+*.pem
+
+etc/.rosalution-db-backups

etc/database/backup-database-lts.sh

@@ -0,0 +1,62 @@
+#! /bin/bash
+# ./backup-database-lts.sh <docker-container>
+usage() {
+  echo "usage: $0 <mongodb-archive>"
+  echo "  Backups a local MongoDB dump archive into UAB Long Term Storage remote"
+  echo "  source 'cgdslts'."
+  echo "  "
+  echo "  Visit https://docs.rc.uab.edu/data_management/transfer/rclone/#setting-up-an-s3-lts-remote"
+  echo "    for setup instructions for interacting with UAB LTS using rclone. Use 'cgdslts'"
+  echo "    instead of 'uablts' for the remote configured in the setup instructions."
+}
+
+fail=false
+
+if ! rclone --version &> /dev/null
+then
+    echo "Error: rclone could not be found."
+    fail=true
+fi
+
+if [[ $# -ne 1 ]]
+then
+    echo "Error: required input missing."
+    fail=true
+fi
+
+if $fail
+then
+    echo "Exiting script ..."
+    usage
+    exit 1
+fi
+
+TARGET_LOCAL_SOURCE_DATABASE_DUMP_FILEPATH=$1
+TARGET_S3_REMOTE="cgdslts"
+
+if [ ! -f "$TARGET_LOCAL_SOURCE_DATABASE_DUMP_FILEPATH" ]
+then
+    echo "Error: $TARGET_LOCAL_SOURCE_DATABASE_DUMP_FILEPATH does not exist"
+    usage
+    exit 1
+fi
+
+if ! rclone listremotes | grep -q "$TARGET_S3_REMOTE"
+then
+  echo "Missing expected '$TARGET_S3_REMOTE' rclone remote; aborting operation"
+  usage
+  exit 1
+fi
+
+if ! rclone lsf "$TARGET_S3_REMOTE:" | grep -q rosalution
+then
+  echo "Missing expected root path 'rosalution/' in bucket"
+  usage
+  exit 1
+fi
+
+
+destination_backup_path="$TARGET_S3_REMOTE:rosalution/db-backup/"
+rclone copy -P  "$TARGET_LOCAL_SOURCE_DATABASE_DUMP_FILEPATH" "$destination_backup_path"
+
+echo "Backup operation complete..."

etc/database/restore-database-lts.sh

@@ -0,0 +1,85 @@
+#! /bin/bash
+# ./restore-database-lts.sh <docker-container> clean
+usage() {
+  echo "usage: $0 <docker-container> clean(optional)"
+  echo "  Restores an archived 'rosalution_db' MongoDB Database for Rosalution, into the specified"
+  echo "  MongoDB docker container from the CGDS UAB Long Term Storage remote source 'cgdslts'."
+  echo "  "
+  echo "  Visit https://docs.rc.uab.edu/data_management/transfer/rclone/#setting-up-an-s3-lts-remote"
+  echo "    for setup instructions for interacting with UAB LTS using rclone. Use 'cgdslts'"
+  echo "    instead of 'uablts' for the remote configured in the setup instructions."
+}
+
+OPTIONAL_CLEAN=false
+
+fail=false
+
+if ! rclone --version &> /dev/null
+then
+    echo "Error: rclone could not be found."
+    fail=true
+fi
+
+if [[ $# -lt 1 ]]
+then
+    echo "Error: required input missing."
+    fail=true
+fi
+
+if [[ $# -ge 2 && "$2" == "clean" ]]
+then
+    OPTIONAL_CLEAN=true
+fi
+
+if $fail
+then
+    echo "Exiting script ..."
+    usage
+    exit 1
+fi
+
+DOCKER_CONTAINER=$1
+TARGET_S3_REMOTE="cgdslts"
+
+if ! rclone listremotes | grep -q "$TARGET_S3_REMOTE"
+then
+  echo "Missing expected '$TARGET_S3_REMOTE' rclone remote; aborting operation"
+  usage
+  exit 1
+fi
+
+if ! rclone lsf "$TARGET_S3_REMOTE:" | grep -q rosalution
+then
+  echo "Missing expected root path 'rosalution/' in bucket"
+  exit 1
+fi
+
+echo "Available Rosalution Backups"
+echo "------------------------------------------------------"
+rclone lsf cgdslts:rosalution/db-backup --files-only | sort
+echo "------------------------------------------------------"
+
+echo "Which backup would you like to restore?"
+read -r rosalution_db_backup
+
+backup_absolute_path="$TARGET_S3_REMOTE:rosalution/db-backup/$rosalution_db_backup"
+local_destination_directory=".rosalution-db-backups"
+local_relative_backup_path="$local_destination_directory/$rosalution_db_backup"
+if ! rclone lsf "$backup_absolute_path" | grep -q "$rosalution_db_backup"
+then
+  echo "Rosalution Backup '$backup_absolute_path' does not exist in CGDS' UAB LTS."
+fi
+
+mkdir -p .rosalution-db-backups
+
+rclone copy -P  "$backup_absolute_path" "$local_destination_directory"
+
+./restore-database.sh "$DOCKER_CONTAINER" "$local_relative_backup_path"
+
+if [ "$OPTIONAL_CLEAN" = true ]
+then
+  echo "Removing local backup copy..."
+  rm "$local_relative_backup_path"
+fi
+
+echo "Restore operation complete..."