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# Server Maintenance and Backups
Updated: Apr 6, 2021
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Useful when presenting. --- ### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions - How do I maintain a Galaxy server? - What happens if I lose everything? --- ### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives - Learn about different maintenance steps - Learn what to back up and how to recover --- # Server Maintenance ??? - Server Maintenance --- ## Dataset Cleanup Can only delete (or purge) dataset when all 'associations' pointing at it have been marked `deleted`. | method | description | | ---- | ---- | | `scripts/cleanup_datasets/pgcleanup.py` | PostgreSQL-optimized fast cleanup script | | `scripts/cleanup_datasets/cleanup_datasets.py` | General cleanup script | | `gxadmin cleanup <days>` | calls pgcleanup | ??? - One of the important admimn tasks is to keep an eye on the storage consumption. - Every instance should have a data rention policy defined and shared with users. - Codebase contains scripts that can assist with cleaning up and reclaiming space. - The gxadmin tool can assist with invoking these scripts. --- class: reduce70 ## pgcleanup invocation ```console $ ./scripts/cleanup_datasets/pgcleanup.py --help usage: pgcleanup.py [-h] [-c CONFIG_FILE] [-d] [--dry-run] [--force-retry] [-o DAYS] [-U] [-s SEQUENCE] [-w WORK_MEM] [-l LOG_DIR] [ACTION [ACTION ...]] positional arguments: ACTION Action(s) to perform, chosen from: delete_datasets, delete_exported_histories, delete_inactive_users, delete_userless_histories, purge_datasets, purge_deleted_hdas, purge_deleted_histories, purge_deleted_users, purge_error_hdas, purge_hdas_of_purged_histories, purge_historyless_hdas, update_hda_purged_flag optional arguments: -h, --help show this help message and exit -c CONFIG_FILE, --config-file CONFIG_FILE, --config CONFIG_FILE Galaxy config file (defaults to $GALAXY_ROOT/config/galaxy.yml if that file exists or else to ./config/galaxy.ini if that exists). If this isn't set on the command line it can be set with the environment variable GALAXY_CONFIG_FILE. -d, --debug Enable debug logging (SQL queries) --dry-run Dry run (rollback all transactions) --force-retry Retry file removals (on applicable actions) -o DAYS, --older-than DAYS Only perform action(s) on objects that have not been updated since the specified number of days -U, --no-update-time Don't set update_time on updated objects -s SEQUENCE, --sequence SEQUENCE DEPRECATED: Comma-separated sequence of actions -w WORK_MEM, --work-mem WORK_MEM Set PostgreSQL work_mem for this connection -l LOG_DIR, --log-dir LOG_DIR Log file directory ``` ??? - Cleanup scripts provide various options for filtering on which datasets to take action. - Use the dry run option to verify what datasets you are about to affect. --- class: reduce70 ## pgcleanup actions | action | description | | ---- | ---- | | `delete_userless_histories` | <ul><li>Mark deleted all "anonymous" Histories (not owned by a registered user) that are older than the specified number of days.</li></ul> | | `delete_exported_histories` | <ul><li>Mark deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days.</li></ul> | | `purge_deleted_users` | <ul><li>Mark purged all users that are older than the specified number of days.</li><li>Mark purged all Histories whose user_ids are purged in this step.</li><li>Mark purged all HistoryDatasetAssociations whose history_ids are purged in this step.</li><li>Delete all UserGroupAssociations whose user_ids are purged in this step.</li><li>Delete all UserRoleAssociations whose user_ids are purged in this step EXCEPT FOR THE PRIVATE ROLE.</li><li>Delete all UserAddresses whose user_ids are purged in this step.</li></ul> | | `purge_deleted_histories` | <ul><li>Mark purged all Histories marked deleted that are older than the specified number of days.</li><li>Mark purged all HistoryDatasetAssociations in Histories marked purged in this step (if not already purged).</li></ul> | | `purge_deleted_hdas` | <ul><li>Mark purged all HistoryDatasetAssociations currently marked deleted that are older than the specified number of days.</li><li>Mark deleted all MetadataFiles whose hda_id is purged in this step.</li><li>Mark deleted all ImplicitlyConvertedDatasetAssociations whose hda_parent_id is purged in this step.</li><li>Mark purged all HistoryDatasetAssociations for which an ImplicitlyConvertedDatasetAssociation with matching hda_id is deleted in this step.</li></ul> | ??? - Some available actions are safer than others, for example "delete userless histories". - In Galaxy, when something is marked deleted, it still exists with a deleted flag. - Once purged the file is gone. --- class: reduce70 ## More pgcleanup actions | action | description | | ---- | ---- | | `purge_historyless_hdas` | <ul><li>Mark purged all HistoryDatasetAssociations whose history_id is null.</li></ul> | | `purge_error_hdas` | <ul><li>Mark purged all HistoryDatasetAssociations whose dataset_id is state = 'error' that are older than the specified number of days.</li></ul> | | `purge_hdas_of_purged_histories` | <ul><li>Mark purged all HistoryDatasetAssociations in histories that are purged and older than the specified number of days.</li></ul> | | `delete_datasets` | <ul><li>Mark deleted all Datasets whose associations are all marked as deleted (LDDA) or purged (HDA) that are older than the specified number of days.</li><li>JobExportHistoryArchives have no deleted column, so the datasets for these will simply be deleted after the specified number of days.</li></ul> | | `purge_datasets` | <ul><li>Mark purged all Datasets marked deleted that are older than the specified number of days.</li></ul> | ??? - Be wary about aggressive storage reclamation. It can aggravate users. - Well-defined and updated data retention policy brings benefits. --- # Additional cleaning scripts * `admin_cleanup_datasets.py` * Mark datasets as deleted that are older than specified cutoff. * Has email templated notification (can also be used to just send info without deleting). * Can be restricted to a tool. ??? - One of the included scripts can send templated email to the affected users. - Take advantage of this to give your users some time to backup their data before you reclaim the space. --- ## Other disk space cleanups - `tmpwatch` (`tmpreaper` on Debian-based distros) your job working directory - `cleanup_job` in `galaxy.yml` (defaults to `always` though) - `tmpwatch` your `new_file_path` - `/usr/bin/tmpwatch -v --mtime --dirmtime 7d /srv/galaxy/var/tmp` ??? - Galaxy generates intermediate data as part of the job execution. - These should be automatically cleaned up unless you change the cleanup_job flag in galaxy's configuration. --- # Backups ??? - Backups --- class: left ## What to backup **Must** be backed up: | item | path (from tutorials) | | ---- | ---- | | Database ([PITR][postgresql-pitr], enable in [galaxyproject.postgresql][ansible-postgresql]) | system dependent | | Installed shed tools | `/srv/galaxy/var/shed_tools` | | *Managed* (aka *mutable*) configs | `/srv/galaxy/var/config` | | Logs (if you like...) | `systemd-journald` | | Datasets (if you can...) | `/data` | If absolute reproducibility matters: | item | path (from tutorials) | | ---- | ---- | | Tool dependencies | `/srv/galaxy/var/dependencies` | | Data manager-installed reference data | `/srv/galaxy/var/tool-data` | ??? - Many parts of Galaxy are convenient to back up since they are straight folder hierarchies. - Use your system's recommended way to back up galaxy's database. - If you have local modifications to galaxy's code back up those as well. --- class: left ## What not to back up Restorable from Ansible Playbook: | item | path (from tutorials) | | ---- | ---- | | Galaxy | `/srv/galaxy/server` | | Virtualenv | `/srv/galaxy/venv` | | *Static* configs | `/srv/galaxy/config` | Recreatable at runtime: | item | path (from tutorials) | | ---- | ---- | | Anything in *managed/mutable data dir* not previously mentioned | `/srv/galaxy/var` | | Job working directories | `/srv/galaxy/jobs` | [postgresql-pitr]: https://www.postgresql.org/docs/current/continuous-archiving.html [ansible-postgresql]: https://github.com/galaxyproject/ansible-postgresql --- ## Restoring from backups If lost *database* or *managed/mutable configs*, then **restore these first** Then run playbook ??? - In case of an incident do not rush even when pressure is piling. - Careful planning of the restoration procedure will save you from hasty recovery attempts with errors. - Consider running a recovery drill pretending that e.g. your galaxy machine was wiped. --- ### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points - Use configuration management (e.g. Ansible) - Store configuration management in git - Back up the parts of Galaxy that can't be recreated --- ## Thank You! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
This material is licensed under the Creative Commons Attribution 4.0 International License