Update Maintenance slides

topics/admin/tutorials/maintenance/slides.html

@@ -2,98 +2,163 @@
 layout: tutorial_slides
 logo: "GTN"
 
-title: "Server Maintenance"
+title: "Server Maintenance and Backups"
 zenodo_link: ""
 questions:
-  - How to maintain a Galaxy service?
+  - How do I maintain a Galaxy server?
+  - What happens if I lose everything?
 objectives:
   - Learn about different maintenance steps
-time_estimation: "1h"
+  - Learn what to back up and how to recover
+time_estimation: "30m"
 key_points:
-  - Remember to back Galaxy up
-  - Use Ansible
+  - Use configuration management (e.g. Ansible)
+  - Back up the parts of Galaxy that can't be recreated
 contributors:
   - natefoo
   - bgruening
   - slugger70
   - hexylena
 ---
+class: left
 
 # Runaway Storage
 
 Tips:
 - Set quotas
-- `tmpwatch` your job working directory
+- `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`
 - Set up dataset cleanup
 
 ---
 # Dataset Cleanup
 
-- `scripts/cleanup_datasets/pgcleanup.py`: PostgreSQL-optimized fast cleanup script
-- `scripts/cleanup_datasets/cleanup_datasets.py`: General cleanup script
-- `gxadmin cleanup 30`: calls pgcleanup
+| 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 |
 
 ---
-# Dataset Cleanup Lifecycle
+class: reduce70
 
-Mark deleted all "anonymous" histories not used within the last `$days` days:
+# pgcleanup invocation
 
 ```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s delete_userless_histories
+$ ./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
 ```
 
-Remove all history exports older than `$days` days:
+---
+class: reduce70
 
-```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s delete_exported_histories
-```
+# pgcleanup actions
 
-Mark purged HDAs in histories deleted `$days` or more days ago (not user-recoverable):
-
-```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s purge_deleted_histories
-```
+| 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> |
 
 ---
+class: reduce70
 
-# Dataset Cleanup Lifecycle
+# More pgcleanup actions
 
-Mark purged individual HDAs deleted `$days` or more days ago (not user-recoverable):
+| 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> |
 
-```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s purge_deleted_hdas
-```
+---
+class: left, reduce90
 
-Mark datasets with all purged HDAs last updated `$days` or more days ago deleted:
+# Backups
 
-```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s delete_datasets
-```
+Restorable from Ansible Playbook:
 
-Mark purged all datasets last updated `$days` or more days ago **and remove from disk**:
+| item | path (from tutorials) |
+| ---- | ---- |
+| Galaxy | `/srv/galaxy/server` |
+| Virtualenv | `/srv/galaxy/venv` |
+| *Static* configs | `/srv/galaxy/config` |
 
-```console
-python ./scripts/cleanup_datasets/pgcleanup.py \
-    -o $days -s purge_datasets
-```
+What to back 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` |
 
 ---
+class: left, reduce90
 
-# Backups
+# Backups (continued)
 
-What to back up:
-- Configs (done with Ansible)
-- Database
-- Installed shed tools and dependencies
-- Datasets (if you can...)
+What to back up if absolute reproducibility matters:
+
+| item | path (from tutorials) |
+| ---- | ---- |
+| Tool dependencies | `/srv/galaxy/var/dependencies` |
+| Data manager-installed reference data | `/srv/galaxy/var/tool-data` |
 
 What not to back up:
 
-- Anything in `database/` not mentioned above
-- Job working directories
+| item | path (from tutorials) |
+| ---- | ---- |
+| Anything in *managed/mutable data dir* not mentioned above | `/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