Galaxy Monitoring with gxadmin
Contributors
Nate Coraor
Björn Grüning
Simon Gladman
Helena RascheQuestions
What is gxadmin
What can it do?
How to write a query?
Objectives
Learn gxadmin basics
See some queries and learn how they help debug production issues
last_modification Published: Apr 26, 2019
last_modification Last Updated: Aug 8, 2024
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 and sharing your SQL
Speaker Notes
- 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?”
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;
Speaker Notes
- 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
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)
Speaker Notes
- 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
Speaker Notes
- 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”
$ gxadmin query ts-repos
OR
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;
Speaker Notes
- 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
username | r_count
------------------------------------------+---------
iuc | 571
devteam | 366
bgruening | 95
galaxyp | 87
jjohnson | 46
xuebing | 40
peterjc | 39
rnateam | 33
anton | 32
nml | 32
yhoogstrate | 31
iracooke | 30
(12 rows)
Speaker Notes
- 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>
# 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
Key | Value
--- | ---
description | `canu`
priority | `-128`
request_cpus | `20`
request_memory | `64G`
Speaker Notes
- 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”
$ gxadmin query latest-users
OR
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
Speaker Notes
- 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
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
Speaker Notes
- 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
COPY (...) to STDOUT with CSV DELIMITER E'\t'
or
$ gxadmin query ...
$ gxadmin tsvquery ...
$ gxadmin csvquery ...
Speaker Notes
- 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:
$ 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
Speaker Notes
- 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.
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 and all the contributors!
Tutorial Content is licensed under
Creative Commons Attribution 4.0 International License.