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Add option for displaying usernames or emails in query jobs-nonterminal #151

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Apr 2, 2024
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Add option for displaying usernames or emails in query jobs-nonterminal #151

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54 changes: 34 additions & 20 deletions parts/22-query.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -571,13 +571,13 @@ query_runtime-per-user() { ##? <email>: computation time of user (by email)
EOF
}

query_jobs-nonterminal() { ## [--states=new,queued,running] [--update-time] [--older-than=<interval>] [username|id|email]: Job info of nonterminal jobs separated by user
query_jobs-nonterminal() { ## [--states=new,queued,running] [--update-time] [--older-than=<interval>] [--show-user=id|email|username] [username|id|email]: Job info of nonterminal jobs separated by user
handle_help "$@" <<-EOF
You can request the user information by username, id, and user email

$ gxadmin query jobs-nonterminal helena-Rasche
id | tool_id | state | create_time | runner | ext_id | handler | user_id
---------+---------------------+---------+----------------------------+--------+--------+-----------------+---------
id | tool_id | state | create_time | runner | ext_id | handler | user
---------+---------------------+---------+----------------------------+--------+--------+-----------------+------
4760549 | featurecounts/1.6.3 | running | 2019-01-18 14:05:14.871711 | condor | 197549 | handler_main_7 | 599
4760552 | featurecounts/1.6.3 | running | 2019-01-18 14:05:16.205867 | condor | 197552 | handler_main_7 | 599
4760554 | featurecounts/1.6.3 | running | 2019-01-18 14:05:17.170157 | condor | 197580 | handler_main_8 | 599
Expand All @@ -591,16 +591,25 @@ query_jobs-nonterminal() { ## [--states=new,queued,running] [--update-time] [--o
You can also query all non-terminal jobs by all users

$ gxadmin query jobs-nonterminal | head
id | tool_id | state | create_time | runner | ext_id | handler | user_id
---------+---------------------+---------+----------------------------+--------+--------+-----------------+---------
4760549 | featurecounts/1.6.3 | running | 2019-01-18 14:05:14.871711 | condor | 197549 | handler_main_7 | 599
4760552 | featurecounts/1.6.3 | running | 2019-01-18 14:05:16.205867 | condor | 197552 | handler_main_7 | 599
4760554 | featurecounts/1.6.3 | running | 2019-01-18 14:05:17.170157 | condor | 197580 | handler_main_8 | 599
4760557 | featurecounts/1.6.3 | running | 2019-01-18 14:05:18.25044 | condor | 197545 | handler_main_10 | 599
4760573 | featurecounts/1.6.3 | running | 2019-01-18 14:05:47.20392 | condor | 197553 | handler_main_2 | 599
4760588 | featurecounts/1.6.3 | new | 2019-01-18 14:11:03.766558 | | | handler_main_9 | 11
4760589 | featurecounts/1.6.3 | new | 2019-01-18 14:11:05.895232 | | | handler_main_1 | 11
4760590 | featurecounts/1.6.3 | new | 2019-01-18 14:11:07.328533 | | | handler_main_2 | 11
id | tool_id | state | create_time | runner | ext_id | handler | user
---------+---------------------+---------+----------------------------+--------+--------+-----------------+------
4760549 | featurecounts/1.6.3 | running | 2019-01-18 14:05:14.871711 | condor | 197549 | handler_main_7 | 599
4760552 | featurecounts/1.6.3 | running | 2019-01-18 14:05:16.205867 | condor | 197552 | handler_main_7 | 599
4760554 | featurecounts/1.6.3 | running | 2019-01-18 14:05:17.170157 | condor | 197580 | handler_main_8 | 599
4760557 | featurecounts/1.6.3 | running | 2019-01-18 14:05:18.25044 | condor | 197545 | handler_main_10 | 599
4760573 | featurecounts/1.6.3 | running | 2019-01-18 14:05:47.20392 | condor | 197553 | handler_main_2 | 599
4760588 | featurecounts/1.6.3 | new | 2019-01-18 14:11:03.766558 | | | handler_main_9 | 11
4760589 | featurecounts/1.6.3 | new | 2019-01-18 14:11:05.895232 | | | handler_main_1 | 11
4760590 | featurecounts/1.6.3 | new | 2019-01-18 14:11:07.328533 | | | handler_main_2 | 11

You can display user emails or usernames rather than user ID using the --show-user option:

$ gxadmin query jobs-nonterminal --show-user=username
id | tool_id | state | create_time | runner | ext_id | handler | user
--------+----------------------+---------+---------------------+--------+--------+-----------+----------
897234 | hisat2/2.1.0+galaxy7 | running | 2021-05-25 04:13:19 | slurm | 987443 | handler_1 | zaphod
897798 | hisat2/2.1.0+galaxy7 | queued | 2021-05-25 08:20:12 | slurm | 988014 | handler_0 | ford
899127 | hisat2/2.1.0+galaxy7 | new | 2021-05-25 09:43:44 | slurm | 990129 | handler_2 | trillian

By default jobs in the states 'new', 'queued', and 'running' are considered non-terminal, but this can
be controlled by passing a comma-separated list to the '--states=' parameter. In addition, by default,
Expand All @@ -614,22 +623,27 @@ query_jobs-nonterminal() { ## [--states=new,queued,running] [--update-time] [--o
days:

$ gxadmin query jobs-nonterminal --states=queued,running --older-than='2 days' --update-time | head -5
id | tool_id | state | update_time | runner | ext_id | handler | user_id
--------+----------------------+---------+---------------------+--------------+--------+------------------+---------
335897 | trinity/2.9.1 | queued | 2021-03-10 10:44:09 | bridges | 335897 | main_w3_handler2 | 599
338554 | repeatmasker/4.0.9 | running | 2021-03-09 10:41:30 | jetstream_iu | 338554 | main_w4_handler2 | 11
338699 | hisat2/2.1.0+galaxy7 | queued | 2021-03-10 05:36:26 | jetstream_iu | 338699 | main_w3_handler2 | 42
id | tool_id | state | update_time | runner | ext_id | handler | user
--------+----------------------+---------+---------------------+--------------+--------+------------------+------
335897 | trinity/2.9.1 | queued | 2021-03-10 10:44:09 | bridges | 335897 | main_w3_handler2 | 599
338554 | repeatmasker/4.0.9 | running | 2021-03-09 10:41:30 | jetstream_iu | 338554 | main_w4_handler2 | 11
338699 | hisat2/2.1.0+galaxy7 | queued | 2021-03-10 05:36:26 | jetstream_iu | 338699 | main_w3_handler2 | 42
EOF

states='new,queued,running'
interval=
user_filter='true'
time_column='create_time'
user_column='job.user_id'

if (( $# > 0 )); then
for args in "$@"; do
if [[ "$args" = '--update-time' ]]; then
time_column='update_time'
elif [[ "$args" = '--show-user=email' ]]; then
user_column='galaxy_user.email'
elif [[ "$args" = '--show-user=username' ]]; then
user_column='galaxy_user.username'
elif [[ "${args:0:9}" = '--states=' ]]; then
states="${args:9}"
elif [[ "${args:0:13}" = '--older-than=' ]]; then
Expand All @@ -646,11 +660,11 @@ query_jobs-nonterminal() { ## [--states=new,queued,running] [--update-time] [--o
interval="AND job.$time_column < NOW() - interval '$interval'"
fi

user_id=$(gdpr_safe job.user_id user_id "anon")
user=$(gdpr_safe "$user_column" user "anon")

read -r -d '' QUERY <<-EOF
SELECT
job.id, job.tool_id, job.state, job.$time_column AT TIME ZONE 'UTC' AS $time_column, job.job_runner_name, job.job_runner_external_id, job.handler, $user_id
job.id, job.tool_id, job.state, job.$time_column AT TIME ZONE 'UTC' AS $time_column, job.job_runner_name, job.job_runner_external_id, job.handler, $user
FROM
job
LEFT OUTER JOIN
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