Galaxy Monitoring with gxadmin

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---

# Galaxy Monitoring with gxadmin

<div class="contributors-line">
		
	
<ul class="text-list">
			
			<li>
				
  <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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Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press `P` again to switch presenter notes off

Press `C` to create a new window where the same presentation will be displayed.
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Useful when presenting.

---

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

- What is gxadmin

- What can it do?

- How to write a query?

---

### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn gxadmin basics

- See some queries and learn how they help debug production issues

---

# Database Queries

Sometimes it's the best way to get the exact data you need

Can be very useful for:
- Debugging
- Reporting
- Analytics

But consider: [`gxadmin`](https://github.com/usegalaxy-eu/gxadmin) and sharing your SQL

???

- Admins often need to run database queries.
- Debugging the live application in production is difficult, but running queries is easy.
- Additionally running SQL queries is commonly used for debuggin and reporting and analytics.
- The community collects queries we commonly use in a program called gxadmin.

---
# Database Queries

"Can you send me the number of jobs per day/state from Main in September and October?"

```sql
SELECT
  date_trunc('month', j.create_time) AS month,
  j.state,
  COUNT(j.state) AS job_count
FROM job j
LEFT OUTER JOIN galaxy_user u
  ON j.user_id = u.id
WHERE u.email != 'monitor@bx.psu.edu'
GROUP BY month,
         j.state
HAVING date_trunc('month', j.create_time) >= '2016-09-01'
AND date_trunc('month', j.create_time) < '2016-11-01'
ORDER BY month, j.state;
```

???

- We often get requests like how many jobs were run in a time period, and did they finish successfully.
- So we write some SQL like this.
- As an admin, you'll want to understand SQL.

---
# Database Queries

```console
        month        |  state  | job_count
---------------------+---------+-----------
 2016-09-01 00:00:00 | deleted |     11369
 2016-09-01 00:00:00 | error   |     15375
 2016-09-01 00:00:00 | new     |      1179
 2016-09-01 00:00:00 | ok      |    165963
 2016-09-01 00:00:00 | paused  |       933
 2016-09-01 00:00:00 | waiting |         9
 2016-10-01 00:00:00 | deleted |     13190
 2016-10-01 00:00:00 | error   |     12539
 2016-10-01 00:00:00 | new     |      1183
 2016-10-01 00:00:00 | ok      |    167547
 2016-10-01 00:00:00 | paused  |       645
 2016-10-01 00:00:00 | queued  |        75
 2016-10-01 00:00:00 | running |        36
 2016-10-01 00:00:00 | waiting |        17
(14 rows)
```

???

- Here is the output of such a query.
- SQL is very powerful for extracting data and graphs for reporting.

---
# gxadmin

- It's unpleasant to write queries every time you need them.
- So the community collects SQL in `gxadmin`.
- It's a giant bash script full of SQL and some magic ✨
- [github.com/usegalaxy-eu/gxadmin](https://github.com/usegalaxy-eu/gxadmin)

???

- We often re-run the same queries.
- gxadmin makes it easier by storing the useful queries.
- everyone is welcome to contribute to it.

---
# Database Queries

"I need a list of current main toolshed users and a number of their repos"

```console
$ gxadmin query ts-repos
```

**OR**

```sql
SELECT
  u.username,
  COUNT(r.id) AS r_count
FROM galaxy_user u
JOIN repository r
  ON u.id = r.user_id
WHERE NOT r.deleted
GROUP BY u.id
ORDER BY r_count DESC
LIMIT 12;
```

???

- However, some of these queries we run over and over.
- And those we include in gxadmin.
- This way every admin has access to all of the interesting queries we run.
- And we don't get repetitive strain injury typing SQL.

---
# Database Queries

???

- Example output from the previous query.

---

# Database Queries

"What is the status of this job"

*Lots* of SQL or: `gxadmin report job-info <job-id>`

```console
# Galaxy Job 5132146

Property      | Value
------------- | -----
         Tool | toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7
        State | running
      Handler | handler_main_2
      Created | 2019-04-20 11:04:40.854975+02 (3 days 03:35:04.881599 ago)
Job Runner/ID | condor / 568537
        Owner | e08d6c893f5

## Destination Parameters

???

- Another extremely common query is: what is the status of this job?
- There is a gxadmin command which aggregates information about jobs.
- This can help you debug job failure to run issues.

---

# Database Queries

"Get me a list of recently registered users"

```console
$ gxadmin query latest-users
```

**OR**

```sql
SELECT
	id,
	create_time AT TIME ZONE 'UTC' as create_time,
	pg_size_pretty(disk_usage) as disk_usage,
	username,
	email,
	active
FROM galaxy_user
ORDER BY create_time desc
LIMIT 40
```

???

- Another common query, who has recently joined our server?
- This is an easy command to write, but it is also included in gxadmin.

---

# Database Queries

```console

id  |          create_time   | disk_usage |  username   |    email    |    groups    | active
------+------------------------+------------+-------------+-------------+--------------+--------
 5581 | 2019-04-23 14:53:58+02 |            | xxx         | xxx         |              | t
 5580 | 2019-04-23 11:25:03+02 | 1222 MB    | xxx         | xxx         |              | t
 5579 | 2019-04-23 10:40:30+02 | 841 MB     | xxx         | xxx         |              | t
 5578 | 2019-04-23 10:31:50+02 |            | xxx         | xxx         |              | t
 5577 | 2019-04-23 10:27:21+02 | 0 bytes    | xxx         | xxx         |              | t
 5576 | 2019-04-23 10:07:53+02 |            | xxx         | xxx         |              | t
 5575 | 2019-04-23 09:04:40+02 | 2011 MB    | xxx         | xxx         | training-gqa | t
 5574 | 2019-04-23 09:01:58+02 | 296 MB     | xxx         | xxx         |              | t
 5573 | 2019-04-23 08:58:42+02 | 605 MB     | xxx         | xxx         |              | t
 5572 | 2019-04-23 08:58:17+02 | 1762 MB    | xxx         | xxx         | training-gqa | t
 5571 | 2019-04-23 08:56:11+02 | 0 bytes    | xxx         | xxx         |              | f
 5570 | 2019-04-23 08:55:57+02 | 1759 MB    | xxx         | xxx         | training-gqa | t
 5569 | 2019-04-23 08:43:21+02 | 1621 MB    | xxx         | xxx         |              | t
 5568 | 2019-04-23 07:48:38+02 |            | xxx         | xxx         |              | t
 5567 | 2019-04-23 05:12:43+02 |            | xxx         | xxx         |              | t
```

???

- Example output of the previous query.
- With SQL you can choose just the columns or data that is relevant to you.
- This may not be so easily available in the interface.

---

# Tabular Output

Converting SQL query output to tabular and other formats

```SQL
COPY (...) to STDOUT with CSV DELIMITER E'\t'
```

**or**

```console
$ gxadmin query ...
$ gxadmin tsvquery ...
$ gxadmin csvquery ...
```

???

- However to reuse this data in other applications, the postgres format is not convenient.
- There is special syntax you can use to output CSV.
- gxadmin includes query variants to do this as well.

---

# Monitoring

Telegraf can consume Influx formatted output, which `gxadmin` can produce:

```console
$ gxadmin iquery queue
queue,tool_id=ncbi_blastx_wrapper/0.3.1,state=running count=76
queue,tool_id=rna_star/2.6.0b-2,state=queued count=36
queue,tool_id=rna_star/2.6.0b-2,state=running count=15
queue,tool_id=unicycler/0.4.7.0,state=running count=10
queue,tool_id=hisat2/2.1.0+galaxy4,state=running count=9
```

???

- For monitoring, many galaxy sites use Influx DB.
- gxadmin supports exporting influx compatible format.
- This makes it easy to add new data and graphs to your monitoring.

---
### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- gxadmin is a tool to run common database queries useful for Galaxy admins

- new queries are welcome and easy to contribute

---

## 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!

<div class="contributors-line">
		
<table class="contributions">
	
	<tr>
		<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>
		<td>
			
  <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>
  
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			
  <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" />
  </a>
  
  <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" />
  </a>
  
  <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" />
  </a>
  
  <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" />
  </a>
  
  <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" />
  </a>
  </td>
	</tr>

</table>

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