Server Maintenance: Cleanup, Backup, and Restoration

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# Server Maintenance: Cleanup, Backup, and Restoration

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  <a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a>
  
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  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
  
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  <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" />
    Simon Gladman</a>
  
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  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
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---

### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- How can I back up my Galaxy?

- What data should be included?

- How can I ensure jobs get cleaned up appropriately?

- 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

- Setup postgres backups

- Setup cleanups

- Learn what to back up and how to recover

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# 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 admin 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.

---
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## 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.

---
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## 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!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
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  <a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a>
  
  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
  
  <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" />
    Simon Gladman</a>
  
  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
  
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  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena">
    <img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-martenson">
    <img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo">
    <img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-nsoranzo">
    <img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann">
    <img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening">
    <img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70">
    <img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" />
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