Simply cloning a Fossil repository does not necessarily create a complete backup of the remote repository’s contents. With an existing clone, Fossil’s autosync feature isn’t enough to keep that clone fully up-to-date in a backup failover sense. This document explains what your clone may be missing and how to ensure that it is complete for cases where you wish to have a backup suitable for replacing it without data loss, should the need arise.

Sensitive Information

Fossil purposefully does not clone certain sensitive information unless you’re logged in with setup capability. As an example, a local clone may have a different user table than the remote, because only the Setup user is allowed to see the full version for privacy and security reasons.

Configuration Drift

Fossil allows the local configuration in certain areas to differ from that of the remote. With the exception of the prior item, you get a copy of these configuration areas on initial clone, but after that, some remote configuration changes don’t sync down automatically, such as the remote’s skin. You have to ask for updates to these configuration areas explicitly.

Private Branches

The very nature of Fossil’s private branch feature ensures that remote clones don’t get a copy of those branches. Normally this is exactly what you want, but in the case of making backups, you probably want these branches as well. One of the two backup methods below provides this.

Shunned Artifacts

Fossil purposefully doesn’t sync shunned artifacts. If you want your local clone to be a precise match to the remote, it needs to track changes to the shun table as well.

Unversioned Artifacts

Data in Fossil’s unversioned artifacts table doesn’t sync down by default unless you specifically ask for it. Like local configuration data, it doesn’t get pulled as part of a normal fossil sync, but unlike the config data, you don’t get unversioned files as part of the initial clone unless you ask for it by passing the --unversioned/-u flag.

Autosync Is Intransitive

If you’re using Fossil in a truly distributed mode, rather than the simple central-and-clones model that is more common, there may be no single source of truth in the network because Fossil’s autosync feature isn’t transitive.

That is, if you cloned from server A, and then you stand that up on a server B, then if I clone from you as repository C, changes to B autosync up to A, but not down to me on C until I do something locally that triggers autosync. The inverse is also true: if I commit something on C, it will autosync up to B, but A won’t get a copy until someone on B does something to trigger autosync there.

An easy way to run into this problem is to set up failover servers svr1 thru svr3.example.com, then set svr2 and svr3 up to sync with the first. If all of the users normally clone from svr1, their commits don’t get to svr2 and svr3 until something on one of the servers pushes or pulls the changes down to the next server in the sync chain.

Likewise, if svr1 falls over and all of the users re-point their local clones at svr2, then svr1 later reappears, svr1 is likely to remain a stale copy of the old version of the repository until someone causes it to sync with svr2 or svr3 to catch up again. And then if you originally designed the sync scheme to treat svr1 as the primary source of truth, those users still syncing with svr2 won’t have their commits pushed up to svr1 unless you’ve set up bidirectional sync, rather than have the two backup servers do pull only.

Solutions

The following script solves most of the above problems for the use case where you want a nearly-complete clone of the remote repository using nothing but the normal Fossil sync protocol. It requires that you be logged into the remote as a user with Setup capability.

#!/bin/sh
fossil sync --unversioned
fossil configuration pull all
fossil rebuild

The last step is needed to ensure that shunned artifacts on the remote are removed from the local clone. The second step includes fossil conf pull shun, so your repo won’t offer the shunned artifacts to others cloning from it, but the backup can’t be said to be “complete” if it contains information that the remote now lacks.

This method doesn’t get you a copy of the remote’s private branches, on purpose. It may also miss other info on the remote, such as SQL-level customizations that the sync protocol can’t see. (Some ticket system customization schemes do this.) You can solve such problems if you have access to the remote server, which allows you to get a SQL-level backup. This requires Fossil 2.12 or newer, which added the backup command, which takes care of locking and transaction isolation to allow backing up an in-use repository.

If you have SSH access to the remote server, something like this will work:

#!/bin/bash
bf=repo-$(date +%Y-%m-%d).fossil
ssh example.com "cd museum ; fossil backup -R repo.fossil backups/$bf" &&
    scp example.com:museum/backups/$bf ~/museum/backups

Encrypted Off-Site Backups

A useful refinement that you can apply to both methods above is encrypted off-site backups. You may wish to store backups of your repositories off-site on a service such as Dropbox, Google Drive, iCloud, or Microsoft OneDrive, where you don’t fully trust the service not to leak your information. This addition to the prior scripts will encrypt the resulting backup in such a way that the cloud copy is a useless blob of noise to anyone without the key:

pass="h8TixP6Mt6edJ3d6COaexiiFlvAM54auF2AjT7ZYYn"
gd="$HOME/Google Drive/Fossil Backups/$bf.xz.enc"
fossil sql -R ~/museum/backups/"$bf" .dump | xz -9 |
    openssl enc -e -aes-256-cbc -pbkdf2 -iter 52830 -pass pass:"$pass" -out "$gd"

If you’re adding this to the first script above, remove the “-R repo-name” bit so you get a dump of the repository backing the current working directory.

This requires OpenSSL 1.1 or higher. If you’re on 1.0 or older, you won’t have the -pbkdf2 and -iter options, and you may have to choose a different cipher algorithm; both changes are likely to weaken the encryption significantly, so you should install a newer version rather than work around the lack of these features. If you’re on macOS, which still ships 1.0 as of the time of this writing, Homebrew offers the current version of OpenSSL, but to avoid a conflict with the platform version it’s unlinked by default, so you have to give an explicit path to its “cellar” directory:

   /usr/local/Cellar/openssl\@1.1/1.1.1g/bin/openssl ...

Change the pass value to some other long random string, and change the iter value to something between 10000 and 100000. A good source for the first is here, and for the second, here.

Compressing the data before encrypting it removes redundancies that can make decryption easier, and it results in a smaller backup than you get with the previous script alone, at the expense of a lot of CPU time during the backup. You may wish to switch to a less space-efficient compression algorithm that takes less CPU power, such as lz4. Changing up the compression algorithm also provides some security-thru-obscurity, which is useless on its own, but it is a useful adjunct to strong encryption.

Restoring From An Encrypted Backup

The “restore” script for the above fragment is basically an inverse of it, but it’s worth showing it because there are some subtleties to take care of. If all variables defined in earlier scripts are available, then restoration is:

openssl enc -d -aes-256-cbc -pbkdf2 -iter 52830 -pass pass:"$pass" -in "$gd" |
    xz -d | sqlite3 ~/museum/restored-repo.fossil

We changed the -e to -d on the openssl command to get decryption, and we changed the -out to -in so it reads from the encrypted backup file and writes the result to stdout.

The decompression step is trivial.

The last change is tricky: we used fossil sql above to ensure that we’re using the same version of SQLite to write the encrypted backup DB as was used to maintain the repository, but unfortunately, we can’t get the built-in SQLite shell to write a backup into an empty database. Therefore, we have to either run the restoration against a possibly-different version of SQLite and hope there are no incompatibilities, or we have to go out of our way to build a matching version of sqlite3 before we can safely do the restoration.

Keep in mind that Fossil often acts as a dogfooding project for SQLite, making use of the latest features, so it is quite likely that a given random sqlite3 binary in your PATH may be unable to understand the dump file created by the backup script!