xnat download images error

[kwsn...@gmail.com]

When I'm trying to download Images from a large project through the xnat UI, I get the message  "XNAT has encountered an error with you reguest". When I dive into the logs, an error can be found in the sql.log:

2021-09-23 15:21:27,473 [https-jsse-nio-8443-exec-7] ERROR org.nrg.xft.db.PoolDBUtils - The following query took longer than 1000 ms to complete: 1177 ms (admin). This may not indicate an error but could indicate an inefficient query or a performance issue with the database:

In the code there is a timeout of 1000ms. Thats to short for my project with 6893 rows. 

The code thats behind this is in the PoolDBUtils.java file (see https://code.xnat.org/browse/~br=views/xdat/src/main/java/org/nrg/xft/db/PoolDBUtils.java?r=33f07efbe2758078678283868e55a7d4962b27ba#to935)

Does anybody know how to solve this or change it?

[Moore, Charlie]

Hello there,

That message isn't so much a timeout as it is a warning. That is, even if you trigger it, XNAT should still perform the query, so there's probably something else going on. Is there anything else in the logs?

Thanks,

Charlie

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Subject: [XNAT Discussion] xnat download images error

 

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[kwsn...@gmail.com]

In the turbine.log there is also an error, see the attached file. I hope you can help me.

Greetings,

Kornelis

Op donderdag 23 september 2021 om 16:19:25 UTC+2 schreef moore.c:

[Moore, Charlie]

Hi Kornelis,

That stack trace would appear to match the issue we have in our JIRA here: https://issues.xnat.org/browse/XNAT-6357 . Unfortunately, I'm not really aware of any way to resolve the issue. Hopefully someone else will have some ideas.

Thanks,

Charlie

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From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of kwsn...@gmail.com <kwsn...@gmail.com>

Sent: Monday, September 27, 2021 3:08 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] xnat download images error

 

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[kwsn...@gmail.com]

Hi Charlie,

That looks like the same error indeed. Perhaps someone from the development team can look at this and resolve it?

greetings

Kornelis

Op maandag 27 september 2021 om 16:21:56 UTC+2 schreef moore.c:

[Herrick, Rick]

Unfortunately there’s no way to resolve the issue short of a code change or change in the project (i.e. have fewer experiments in the project). The

 

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Rick Herrick

XNAT Architect/Developer

Computational Imaging Laboratory

Washington University School of Medicine

To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/eeb1fb99-959b-42be-a954-2b9d63f25f0an%40googlegroups.com.

[Herrick, Rick]

I did not mean to send that email that soon. My cat jumped on my wrist and I inadvertently hit the magic send key stroke 😊

 

Unfortunately, there’s no way to resolve the issue short of a code change or change in the project (i.e. have fewer experiments in the project). The method in which that’s happening really should be refactored anyway, because it does several operations more than necessary (e.g. repeatedly checking whether the user can access a particular XSI type within a project, when the answer is always the same for that XSI type and project combination). Even in cases where the code isn’t blowing up the database, it could run a lot more efficiently.

 

But that doesn’t help you right now. But like I said I have no ideas on how to work around this problem in the context of an existing XNAT deployment.

 

BTW, if you did mention it I can’t find it: what version of XNAT, PostgreSQL, etc., are you running?

[kwsn...@gmail.com]

Hi Rick,

The versions we are running are:

XNAT:1.8.2.2

PostgreSQL: 12.6

Linux: CentOS 7

Greetings

Kornelis

Op dinsdag 28 september 2021 om 20:26:40 UTC+2 schreef Rick Herrick: