Merge pull request #151 from natefoo/jobs-nonterminal-user-display

Add option for displaying usernames or emails in query jobs-nonterminal
galaxyproject · Apr 2, 2024 · 0d93537 · 0d93537
2 parents 88b1922 + 5ddccdd
commit 0d93537
Showing 1 changed file with 34 additions and 20 deletions.
diff --git a/parts/22-query.sh b/parts/22-query.sh
@@ -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
@@ -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,
@@ -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
@@ -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