LabKey Support Forum

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Maintenance Notice - Upgrade of LabKey.org for Wednesday, January 11th 2023 @ 8:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-01-11 15:39
LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 23.1

The site will be offline for approximately one hour.

Please save your work before this time.
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Chart / Graphical display of Cohorts that change during a study
(2 responses) rpiercy 2022-12-14 04:29
I have set up a visit based study with initially 3 Cohorts of participants. During the study 2 more separate Cohorts are generated from within one of the existing Cohorts to make 5 final cohorts. (i.e. some participants start in one cohort and then shift into two others, as their treatments change).

Setting this up with automatic cohort assignment with a dataset and visits seems straightforwards. However, when I try to view the data within any dataset graphically with time on the X axis and with participants grouped according to their cohort at any given time, it seems not to recognise that the cohorts change.

Is this actually possible to view graphically please (with correct cohort assignment at different times)?

I am using Labkey server 21.7.

Thank you.

Richard
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Scheduled Maintenance - LabKey TeamCity Build Server - Wednesday 12/14/2022 between 4-5 PM PST
(1 response) stuartm 2022-12-13 15:07

We will be performing maintenance on the LabKey TeamCity server on Wednesday 12/14/2022 between 4-5 PM PST. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

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Maintenance Notice - Upgrade of labkey.org for Monday, December 12th 2022 @ 9:00pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-12-12 14:21
LabKey.org will be offline this evening at 9:00pm Pacific Time for an upgrade to LabKey 22.12

The site will be offline for approximately one hour.

Please save your work before this time.
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Maintenance Notice - Upgrade of labkey.org for Thursday, November 10th 2022 @ 8:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-11-10 13:09
LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 22.11

The site will be offline for approximately one hour.

Please save your work before this time.
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Maintence Notice - Teamcity Build Server - Monday 11/7/2022 7-8A M PST
(1 response) stuartm 2022-11-07 06:41

We will be performing maintenance on the LabKey TeamCity server on Monday 11/07/2022 between 7-8 AM PST. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

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LabKey Update Recommended: Apache Batik Disclosed Vulnerabilities
hannahb 2022-11-03 10:54

Hello,

This is a recommendation to upgrade your LabKey Servers immediately - if you are a LabKey Cloud Customer, we will perform the upgrade and notify you of the short server downtime. For anyone managing their own LabKey Server, or for more details, read on.

Recently, the developers of Apache Batik announced two security vulnerabilities, https://nvd.nist.gov/vuln/detail/CVE-2022-41704 and https://nvd.nist.gov/vuln/detail/CVE-2022-42890

Batik is a library that LabKey Server uses to convert SVGs into PNGs and PDFs. We have assessed the vulnerability and determined that some versions of LabKey Server are impacted.

LabKey previously added a related mitigation, which is included in versions 22.7.3, 22.9.0, and 22.10.0 (and beyond). The mitigation addresses the vulnerability, even without the patch to Batik itself.

LabKey will include the latest version of Batik, 1.16, in the upcoming 22.7.8 and 22.11.0 releases. LabKey has also prepared version 22.3.10 to address 22.3.x deployments.

We recommend all LabKey users on versions older than 22.7.3 upgrade to one of the secured versions immediately. By the end of the day today, the LabKey team will push new secured builds to your support portal. We will also make these changes for all LabKey Cloud customers not already on secured versions which will involve a short server downtime. You will receive notice of this downtime.

Additionally, OpenSSL has disclosed two recent vulnerabilities in their 3.0.x versions. https://www.openssl.org/blog/blog/2022/11/01/email-address-overflows/

LabKey Server itself is NOT IMPACTED by this. However, other common software, including many recent Linux distributions, relies on OpenSSL so please be aware and patch as appropriate.

Please reach out if you have any questions or concerns for us.

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Maintenance Notice - Upgrade of labkey.org for Wednesday, October 12th 2022 @ 8:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-10-12 14:18
LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 22.10

The site will be offline for approximately one hour.

Please save your work before this time.
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Limit on number of sample derivatives created at a time in Sample Manager
(1 response) dahlstromew 2022-10-11 10:06

Is it possible to increase the number of sample derivatives a user can create at one time?
It seems we are limited to just 20 samples right now (see attached image).
Thanks

 Untitled.png 
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Maintence Notice - Teamcity Build Server - Wednesday 4 -5 PM PDT
stuartm 2022-10-04 11:09

We will be performing maintenance on the LabKey TeamCity build server on Wednesday 10/05/2022 between 4-5 PM PDT. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

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Maintenance Notice - Update of labkey.org for Wednesday, September 28th 2022 @ 6:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-09-28 11:52
LabKey.org will be offline this evening at 6:30pm Pacific Time for an update

The site will be offline for approximately 30 minutes.

Please save your work before this time.
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withCounter skipping over numbers
(2 responses) dahlstromew 2022-09-22 15:54

Hi,
We have a case where a user generated derivatives of a sample which has a "withCounter" modifier in the sample ID.
It is a simple modifier: LIB_${${MaterialInputs:first}_:withCounter(1,'00')}

In general, we only make one derivative for a sample, so the tail end of the sample ID would be _01.
However, a user generated a second set of derivative samples and they had _101 instead of _02 at the end.

The user assures me they didn't create and delete 99 derivatives....

I have not been able to reproduce this in our test environment, each derivative correctly counts up one digit at a time.
I also do not see any extra samples in the lineage trail.

What could cause this behavior?

Thanks
Eric

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Maintenance Notice - Update of labkey.org for Tuesday, September 20th 2022 @ 5pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-09-20 15:19
LabKey.org will be offline this evening at 5pm Pacific Time for an update

The site will be offline for approximately 15 minutes.

Please save your work before this time.
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Maintenance Notice - Upgrade of labkey.org for Tuesday, September 13th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-09-13 17:10
LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade

The site will be offline for approximately 30 minutes.

Please save your work before this time.
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Maintenance Notice - Upgrade of labkey.org for Friday, September 9th 2022 @ 8pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-09-09 12:22
LabKey.org will be offline this evening at 8pm Pacific Time for an upgrade to LabKey 22.9

The site will be offline for approximately one hour.

Please save your work before this time.
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Make a Visit an integer
(1 response) murff 2022-09-06 16:18

When setting up a new study if I pick visit, the users have the ability to enter decimal values for the visit. Ex (1.1000,1.2000, etc.)
How do I change that so the visit can only be an integer (1,2,3, etc).

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Download prolems community edition
(1 response) oliver cencic 2022-08-18 01:40

When I try to download the community edition of LabKey I get the following error message (independent of the web browser I use):
"The form was unable to submit. Please contact the site administrator."
The same problem appears btw when I try to send the contact form. So, maybe there is a general issue with your website.
Can someone help to solve the issue?

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Installation error of labkey on mac
(2 responses) justtopass 2022-08-14 14:19

Hi

I am trying to install labkey on mac but I get the below error when launching it. Would you please advise? Thanks

HTTP Status 404 – Not Found

Type Status Report

Message The requested resource [/labkey] is not available

Description The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.

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Freezer Rack Configurations
(2 responses) dahlstromew 2022-08-12 09:13

Hi,
Is it possible to configure rack partitions?
For example;
Shelf01-->Rack01-->Partition01-->Plates
Partition02-->Plates
Partition03-->Plates
etc..

I do not see any partition configure racks as a storage unit.

The reason I ask is that we have various racks with different numbers of partitions, and in our case, we store up to 25 plates per partition. If I just configure rack01-->plates, there could be more than 100 plates, which isn't very clean to look at in the freezer view.
Also, our partitions are divided by projects and researchers, so that would be lost in the freezer configuration.

Thanks

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A "pipeline-filewatcher" type job with pipeline task "Imports specimen using data file" reuses existing job record
(1 response) tstellin 2022-08-12 05:25

A month or so ago we updated our labkey jobs to use the new "pipeline-filewatcher" type job with pipeline task "Imports specimen using data file". Since doing this, we have observed a strange behavior: instead of creating a new Job record for a new "Imports specimen using data file" task, LabKey re-uses the most recent previously-existing job record. See attachment.

The attachment shows that the job was created on 2022-06-27 and last updated on 2022-08-12. When the task starts, it seems to re-use the old Job record. Every day, this record (with primary key rowId=98469) is re-used and modified to reflect that day's import. The job details page https://atlas.scharp.org/cpas/pipeline-status/HVTN/Tools and Reports/Specimen Management/details.view?rowId=98469 lists all previous runs in the log output (which I think will eventually make the page difficult to load).

Is this behavior expected? In the past, a new Job record (with a "created on" set to the timestamp the task started) would be created. We also see this behavior on our staging system (running v22.3.9).

 Screenshot 2022-08-12 051515.png 
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Maintenance Notice - Upgrade of labkey.org for Wednesday, August 10th 2022 @ 8pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-08-10 12:21
LabKey.org will be offline this evening at 8pm Pacific Time for an upgrade to LabKey 22.8

The site will be offline for approximately one hour.

Please save your work before this time.
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Artifactory Migration -- Completed
(1 response) ians 2022-07-19 16:46

On Friday, July 22, we will be moving our Artifactory server and, as a consequence, the domain will be updated from artifactory.labkey.com to labkey.jfrog.io. We are working to update to the new URL in all gradle and npm files that reference the old URL in develop as well as our release branches for 21.11, 22.3, and 22.7. If you are not building your own standalone modules that reference the old URL, you won’t need to do anything other than pull down the latest code for the release you are building from.

If you are building your own module or otherwise have references to artifactory.labkey.com, you will need to update these to labkey.jfrog.io. A simple find and replace of artifactory.labkey.com:443 and artifactory.labkey.com with labkey.jfrog.io should be all you need to do.

Our recommended update steps are below. As a precaution, we recommend clearing the npm cache and the all node_modules directories prior to building. Please run these commands from the root directory of your enlistment:

npm cache clear --force   #(Optional command -- only recommended if you are doing active React development)
gradlew cleanNodeModules
gradlew deployApp

The domain artifactory.labkey.com will remain for unauthenticated reading until 8/12. Please submit a ticket to your support portal or contact your Account Manager if you have any questions.

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Maintenance Notice - Upgrade of labkey.org for Friday, July 15th 2022 @ 10pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-07-15 10:57
LabKey.org will be offline this evening at 10pm Pacific Time for an upgrade to LabKey 22.7

The site will be offline for approximately one hour.

Please save your work before this time.
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Tomcat service is getting by itself after almost 24 hours
(1 response) yukti agrawal 2022-07-15 01:53

**Tomcat service one our prod server is getting killed by itself and hence labkey is giving 502 error after almost 24 hours everyday from last 3 days.
Labkey is running on EC2 instance on our server.

I have checked logs but couldn't find anything which causes the service to stop.**

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SQl WHERE statement trouble
(4 responses) katy wiseman 2022-06-14 09:57

Hi,

I'm trying to use a vey simple WHERE statement in my SQL query but I keep getting an error saying could not resolve column. You documentation seems to suggest what I'm trying to do is possible so I'm a bit lost.

I'm trying to do:
SELECT
*
FROM miseq_results

WHERE well = "A01"

and I get this error:
Query 'lists_temp_5991' has errors Edit Query
Error on line 5: Could not resolve column: A01 edit lists_temp_5991

and your documentation says that it should be possible to use where to filter on a value, rather than column=column:
Filter the results for certain values. Example:

SELECT *
FROM "Physical Exam"
WHERE YEAR(Date) = 2010 

Could someone help me with where I'm going wrong please?

Katy

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Maintenance Notice - Upgrade of labkey.org for Thursday, June 9th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-06-09 16:46

LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.6 along with additional maintenance tasks.

The site will be offline for approximately two hours.

Please save your work before this time.

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Scheduled Maintenance - teamcity.labkey.org Friday 6/3/2022 7 AM PDT
stuartm 2022-06-02 15:46

We will be performing maintenance on the LabKey TeamCity server on Friday 06/03/2022 between 7 - 8 AM PDT. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

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How to specify full path to project folder ?
(1 response) ambarish nag 2022-05-31 21:52

Hi,
I am looking at the code example for creating a list domain in https://github.com/LabKey/labkey-api-python/blob/develop/samples/domain_example.py
If I want to add a subfolder to the project folder name, e.g.
project_name ="Study/Study1" then the code crashes with the error: labkey.exceptions.ServerContextError: '"403: You don't have permission to create a new domain"'
How can this problem be fixed ?
Thanks in advance.

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Maintenance Notice - Upgrade of labkey.org for Thursday, May 12th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-05-12 13:50
LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.5

The site will be offline for approximately one hour.

Please save your work before this time.
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Scheduled Maintenance - teamcity.labkey.org Thursday 5/5/2022 4-5PM PDT
stuartm 2022-05-04 10:30

We will be performing maintenance on the LabKey TeamCity server on Thursday 05/05/2022 between 4 PM - 5 PM PST. This maintenance only affects developers. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

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Artifactory Configuration Change
(1 response) Susan Hert 2022-05-02 13:12

On Thursday, May 5 at 8:00 Pacific time, we will be updating our Artifactory configuration such that our libs-release, plugins-release, and libs-snapshot repositories will no longer proxy for certain third-party maven repositories, including MavenCentral and https://plugins.gradle.org. You will likely not have to make any changes as a result of this reconfiguration since we have updated our build.gradle files in the develop branch as well as all currently supported release versions to declare the required external repositories separately. However, if you maintain your own build.gradle file that includes a repositories {} configuration, you may need to add

    mavenCentral() 

at the top of that configuration block or add a separate

       maven { url: “https://some.repository.url” }

declaration in order to properly resolve external artifacts.

If you have questions or problems as a result of this, please let us know.

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Current user
(1 response) lubomir pavliska 2022-04-27 13:03

Hello.

How can I get the name of current user (current logged) in R Report? I need it for identification rows in excel file exported from R report.
I tried it via
res=GET("http://vav.fno.cz/login-whoAmI.api")
prettify(rawToChar(res$content))

but no working, empty content.

Thanks

Lubomir

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Java Vulnerability - Java upgrade recommended
hannahb 2022-04-22 15:09

We were recently made aware of a potential Java vulnerability affecting ECDSA (Elliptic Curve Digital Signature Algorithm) signatures. For more details, see https://nvd.nist.gov/vuln/detail/CVE-2022-21449
This vulnerability affects deployments that use ECDSA, however, we strongly recommend that every deployment immediately upgrade to the latest Java release, 17.0.3+7.

As always, please reach out if you have any questions or concerns for us.

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LabKey version 19.3.7
(1 response) Gina M Scott 2022-04-19 11:32

We are facing the log4j issue and cyber is asking us to upgrade Tomcat -
Can someone tell me if Tomcat 9.0.31 will work without issues for LabKey verison 19.3.7.

thank you
Gina

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Maintenance Notice - Upgrade of labkey.org for Wednesday, April 13th 2022 @ 9pm Pacific Time
(1 response) Jon (LabKey DevOps) 2022-04-13 10:50
LabKey.org will be offline this evening at 9pm Pacific Time for an upgrade to LabKey 22.4

The site will be offline for approximately one hour.

Please save your work before this time.
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Problems with uploading files
(4 responses) Bika 2022-04-06 22:16

Dear Labkey

I have installed a Labkey Server v19.1 or v21.3. When I upload a file in the files interface. I get the following error:“Couldn't create file on server. This may be a server configuration problem. Contact the site administrator.” Please help me to solve this problem.

Deployment Environment for Labkey v19.1:
Windows Server 2008 R2 SP1
PostgreSQL Version 9.52
Java Runtime Version12.0.2.10
Apache Tomcat Version 9.0.37

Deployment Environment for Labkey v21.3:
Windows Server 2012 R2
PostgreSQL Version 13.1
Java Runtime Version 15.0.1.9
Apache Tomcat Version 9.0.40

Best Regards
Bika

 1.png 
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Spring MVC security vulnerability - LabKey upgrade required
hannahb 2022-03-31 18:23

Yesterday, the developers of Spring MVC announced a security vulnerability, CVE-2022-22965. Spring is a popular open source library used by LabKey Server. We have assessed the vulnerability. While LabKey Server is fortunately not subject to the most commonly reported exploit variant, a customized attack against LabKey Server might succeed.

In the interest of providing hotfixes as quickly as possible, LabKey has applied the Spring development team’s recommended remediation for software that cannot immediately adopt the latest Spring MVC releases (5.3.18 or 5.2.20). We will upgrade to Spring 5.3.x in a future release, but have tested that the current hotfix eliminates the security concern.

By the end of the day today, the LabKey team will push new hotfixed builds to all Premium Edition Clients' support portal. We will also make these changes for all LabKey Cloud customers today which will involve a short server downtime. Community Edition clients should download the latest binaries and perform an upgrade.

In order to minimize the impact of this vulnerability, all administrators must upgrade their installations immediately.

As always, please reach out if you have any questions or concerns for us.

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Maintenance Notice - Update of labkey.org for Monday, March 29th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-03-29 19:55
An upgrade of labkey.org will occur this evening at 9pm PST.

The site is expected to be down for no more than 30 minutes.

Please save your work before this time.

We apologize for any inconvenience this may cause.
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Maintenance Notice - Minor Update of labkey.org for Friday, March 18th 2022 @ 8pm PST
(1 response) Jon (LabKey DevOps) 2022-03-18 16:03
A minor update to labkey.org will occur this evening on Friday, March 18th 2022 @ 8pm PST.

The server should be offline for no more than 30 minutes.

Please save your work before this time.
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Maintenance Notice - Upgrade of labkey.org to LabKey 22.3 for Thursday, March 10th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-03-10 12:12
LabKey.org will be offline this evening at 9pm PST for an upgrade to LabKey 22.3

The site will be offline for approximately one hour.

Please save your work before this time.
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Maintenance Notice: artifactory.labkey.com access will be limited for Friday, March 4th 2022 @ 4pm PST
(1 response) Jon (LabKey DevOps) 2022-03-04 10:38
Special work is required for the artifactory.labkey.com server this early evening at 4pm PST.

During this time, the TeamCity queue will be paused and the artifactory.labkey.com server will be intermittently available.

The expected outage window will last no later than 5pm PST.

We apologize for an inconvenience this may cause.
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Help with specimen import error: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit
tstellin 2022-03-01 05:15

On 2022-02-28 and 2022-02-22, our labkey server failed to import specimen data with an error we haven't seen before (stacktrace below). Are there any details on this error someone can provide? Is there a known way to address it?

...
28 Feb 2022 23:22:47,298 INFO : Updating vial rows 8040001 through 8050000.
28 Feb 2022 23:22:49,078 INFO : Updating processing locations on the specimen table...
28 Feb 2022 23:23:28,338 INFO : Complete.
28 Feb 2022 23:23:28,342 INFO : Updating first processed by initials on the specimen table...
28 Feb 2022 23:24:07,391 INFO : Complete.
28 Feb 2022 23:24:07,393 INFO : Updating vial availability...
28 Feb 2022 23:24:07,402 INFO : Marking vials unavailable based on Custom Query: study.UnavailableAccordingToLdms
28 Feb 2022 23:29:30,743 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/primary_types.tsv
28 Feb 2022 23:29:30,760 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/specimens.tsv
28 Feb 2022 23:29:30,764 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/column_translations.tsv
28 Feb 2022 23:29:30,769 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/additives.tsv
28 Feb 2022 23:29:30,772 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/labware_sample_types.tsv
28 Feb 2022 23:29:30,776 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/derivatives.tsv
28 Feb 2022 23:29:30,780 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615/labs.tsv
28 Feb 2022 23:29:30,787 INFO : Deleting /services/data/hvtn/Specimen Management/specimens/220228212006615
28 Feb 2022 23:29:30,835 INFO : Failed to complete task 'org.labkey.api.specimen.pipeline.StudyImportSpecimenTask'
28 Feb 2022 23:29:30,836 ERROR: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit
org.labkey.api.pipeline.PipelineJobException: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit
at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.doImport(AbstractSpecimenTask.java:162)
at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.run(AbstractSpecimenTask.java:67)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:304)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
at java.base/java.lang.Thread.run(Thread.java:831)
Caused by: java.lang.RuntimeException: Cache timeout for SchemaTableInfos for labkey, exceeding 300000ms limit
at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:130)
at org.labkey.api.cache.BlockingCache.get(BlockingCache.java:91)
at org.labkey.api.data.SchemaTableInfoCache.get(SchemaTableInfoCache.java:49)
at org.labkey.api.data.DbScope.getTable(DbScope.java:1148)
at org.labkey.api.data.DbSchema.getTable(DbSchema.java:426)
at org.labkey.experiment.api.property.StorageProvisionerImpl.getSchemaTableInfo(StorageProvisionerImpl.java:604)
at org.labkey.experiment.api.property.StorageProvisionerImpl.createTableInfoImpl(StorageProvisionerImpl.java:580)
at org.labkey.api.exp.api.StorageProvisioner.createTableInfo(StorageProvisioner.java:71)
at org.labkey.api.specimen.model.SpecimenTablesProvider.createTableInfo(SpecimenTablesProvider.java:201)
at org.labkey.api.specimen.model.SpecimenTablesProvider.createTableInfo(SpecimenTablesProvider.java:125)
at org.labkey.api.specimen.SpecimenSchema.getTableInfoSpecimen(SpecimenSchema.java:145)
at org.labkey.api.specimen.SpecimenSchema.getTableInfoSpecimen(SpecimenSchema.java:138)
at org.labkey.study.query.SpecimenDetailTable.getSpecimenAndVialFromSQL(SpecimenDetailTable.java:404)
at org.labkey.study.query.SpecimenDetailTable.getFromSQL(SpecimenDetailTable.java:374)
at org.labkey.api.data.AbstractTableInfo.getFromSQL(AbstractTableInfo.java:313)
at org.labkey.query.sql.QueryTable._getSql(QueryTable.java:363)
at org.labkey.query.sql.QueryTable.getFromSql(QueryTable.java:267)
at org.labkey.query.sql.QTable.appendSql(QTable.java:85)
at org.labkey.query.sql.QuerySelect._getSql(QuerySelect.java:1524)
at org.labkey.query.sql.QuerySelect.getSql(QuerySelect.java:1468)
at org.labkey.query.sql.QuerySelect$2.getFromSQL(QuerySelect.java:1296)
at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:2624)
at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:2440)
at org.labkey.api.data.Table.getSelectSQL(Table.java:1055)
at org.labkey.api.specimen.importer.RequestabilityManager$CustomQueryRule.getFilterSQL(RequestabilityManager.java:564)
at org.labkey.api.specimen.importer.RequestabilityManager$RequestableRule.updateRequestability(RequestabilityManager.java:408)
at org.labkey.api.specimen.importer.RequestabilityManager.updateRequestability(RequestabilityManager.java:828)
at org.labkey.api.specimen.importer.RequestabilityManager.updateRequestability(RequestabilityManager.java:845)
at org.labkey.api.specimen.importer.SpecimenImporter.updateCalculatedSpecimenData(SpecimenImporter.java:1083)
at org.labkey.api.specimen.importer.SpecimenImporter.process(SpecimenImporter.java:390)
at org.labkey.api.specimen.importer.SpecimenImporter.process(SpecimenImporter.java:306)
at org.labkey.api.specimen.pipeline.AbstractSpecimenTask.doImport(AbstractSpecimenTask.java:132)
... 9 more

view message
Maintenance Notice: artifactory.labkey.com upgrade for Monday, February 28th 2022 @ 7am PST
(1 response) Jon (LabKey DevOps) 2022-02-24 17:03
An upgrade of https://artifactory.labkey.com will occur on Monday, Feb 28th 2022 @ 7am PST

The estimated downtime will be approximately one hour. The TeamCity queue will be paused during this time.

Please plan accordingly.
view message
Scheduled Maintenance - LabKey TeamCity Server - Monday 2/28/2022 4PM-5PM PST
stuartm 2022-02-24 15:22

We will be performing maintenance on the LabKey TeamCity server on Monday 02/28/2022 between 4 PM - 5 PM PST. This maintenance only affects developers. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

view message
Maintenance Notice: artifactory.labkey.com upgrade for Friday, February 18th 2022 @ 7am PST
(1 response) Jon (LabKey DevOps) 2022-02-17 16:27
Hello Everyone,

An upgrade of https://artifactory.labkey.com will occur for Friday, February 18th @ 7am PST.

The estimated outage time is approximately one hour. Please plan accordingly.

Regards,

Jon
view message
Configuring PGAdmin4 to access the labkey database
(1 response) timcooper 2022-02-15 00:58

I'm attempting to add my local LabKey server to PGAdmin4. The server is running and accessible at:

http://localhost:8080/labkey

I followed the setup detailed here:

https://www.labkey.org/Documentation/wiki-page.view?name=installComponents

However, I am receiving an error:

Unable to connect to server: connection to server at "localhost" (127.0.0.1), port 8080 failed: expected authentication requrest from server, but received H

My PGAdmin settings are as follows:

Host name/address: localhost
Port: 8080
Maintenance database: labkey
Username: labkey (used to setup tomcat - I've also tried the username I initially created when first accessing the labkey server at http://localhost:8080/labkey)
Password: the database password associated with 'labkey'

What am I doing wrong?

Thanks!

view message
Maintenance Notice - Update of labkey.org for Friday, February 11th 2022 @ 5:30pm PST
(1 response) Jon (LabKey DevOps) 2022-02-11 17:02
An update to labkey.org will occur at 5:30pm PST.

The site should be down for approximately 30 minutes.

Please save your work before this time.

We apologize for any inconvenience.
view message
Maintenance Notice - Upgrade of labkey.org to LabKey 22.2 for Thursday, February 10th 2022 @ 9pm PST
(1 response) Jon (LabKey DevOps) 2022-02-10 17:01
LabKey.org will be offline this evening at 9pm PST for an upgrade to LabKey 22.2

The site will be offline for approximately one hour.

Please save your work before this time.
view message
Conditional formatting for duplicate values
(1 response) katy wiseman 2022-02-08 09:11

Hi,

I'm trying to set some conditional formatting to show when the same entry is in a column more than once. Is there way to do this with the conditional format criteria for a given field?

Thanks,

Katy

view message
Recommended Linux OS
(2 responses) tvaisar 2022-01-25 12:45

Hi Labkey team,
with the recent EOL of CentOS 8 (Dec 31,2021), I was wondering what is the recommended Linux operating system for Labkey Server?
a) if we were to upgrade current installation
b) if we were starting from scratch

Thanks a lot,

Tomas

view message
Maintance Notice - Teamcity Server 01/24/2022 4:30PM - 5:00PM PDT
(1 response) stuartm 2022-01-24 16:03

We have scheduled a short maintenance window tonight at 4:30 PM PDT to install updates to Teamcity.

We will pause the Teamcity queue, apply the updates and restart. We expect the downtime to be less than 30 minutes.

view message
Query validation fails and API getSchema
(4 responses) christian opitz 2022-01-20 07:56

Following the upgrade to 21.11.4 (thanks to log4j), I am not able to retrieve a table called RunRepresentativeDataState for the targetedms schema via the Rlabkey package. getSchema throws the following Error: Status code = 404, Error message = Could not find the query

Funnily enough the table is contained in the data frame returned by getQueries. However, one cannot use getQueryDetails with this particular as expected.

Running the query validation within Labkey confirms this error with: targetedms.RunRepresentativeDataState: Query not found: RunRepresentativeDataState

Is there any remedy to this?

Thank you very much.

view message
Maintenance Notice - Upgrade of labkey.org to LabKey 22.1 for Thursday, January 13th 2022 @ 7pm PST
(1 response) Jon (LabKey DevOps) 2022-01-13 12:32
LabKey.org will be offline this evening at 7pm PST for an upgrade to LabKey 22.1

The site will be offline for approximately one hour.

Please save your work before this time.
view message
Issue with web sockets
(3 responses) bront 2022-01-05 13:24

hi,

We are working on setting up 21.11.3-4-nci on Ubuntu 18.04 and are having some problems with web sockets. We're getting 404 errors.

Our LabKey installation resides on a separate server behind an Apache reverse proxy. The only allowed connection is TLS over port 8443.

Here is our current Apache setup:

RewriteEngine on
RewriteCond ${HTTP:Upgrade} websocket [NC]
RewriteCond ${HTTP:Connection} upgrade [NC]
RewriteRule /(.*) wss://172.19.20.190:8443/$1 [P,L]

ProxyPass / https://172.19.20.190:8443/
ProxyPassReverse / https://172.19.20.190:8443/

Any help or examples would be greatly appreciated.

Thanks,

bront

view message
JSON as Lists column data type
(3 responses) kotlenik 2021-12-27 10:05

Hi guys,
I am exploring LabKey Server (dockerized community version 21.10.0, PostgreSQL as database)
for some features needed by my client, among others - custom JSON data for each entity recorded in list.
I was able to find TEXT column data type as an option to record custom JSON content for record in list,
practically as string.
Keeping in mind that these are options to use JSON specific functions within PostgresSQL,
https://www.labkey.org/Documentation/wiki-page.view?name=labkeysql#postgresJson
could you guide me towards material, or give me advice about alternative and more appropriate
ways to record and query back JSON in list records - through a more specific column data type, or
some other way?
Cheers and thanks,
Adam

view message
Upgrading Old Version of Labkey
(2 responses) dslater 2021-12-17 13:09

With the log4j vulnerability out, we were going to upgrade our version of Labkey but its been a few years since we have. We are currently on version 16.3. It looks like from https://www.labkey.org/Documentation/wiki-page.view?name=upgradeSupportPolicy, I have to do a bunch of intermediate upgrades. I need to get version 19.1 but the previous release page at https://www.labkey.org/Documentation/wiki-page.view?name=prevReleases does not have it. How am I able to get 19.1?

view message
High priority- Log4J security announcement
(8 responses) hannahb 2021-12-10 13:55

Yesterday, researchers announced a critical vulnerability (CVE-2021-44228) in Log4J, a popular Java logging library that LabKey Server versions 20.11 and later use.

All LabKey Server administrators must take action to protect their installations immediately, especially installations that are open on the public Internet. We are making these changes for all hosted customers today which will involve a short server downtime. You will receive notice of this downtime shortly.

Right now, administrators must add a system property (-Dlog4j2.formatMsgNoLookups=true) so that Java will disable the part of Log4J with the vulnerability. The exact mechanism for setting this property depends on how Tomcat is installed and launched.

For Linux installations, locate the JAVA_OPTS or CATALINA_OPTS environment variables for your Tomcat installation. These settings are typically located under the /etc/init.d/tomcat startup file, the /etc/systemd/system/tomcat.service startup file, the /etc/default/tomcat file, or the CATALINA_HOME/bin/setenv.sh script. Once the JAVA_OPTS or CATALINA_OPTS line is located, add -Dlog4j2.formatMsgNoLookups=true to the end of the line and restart Tomcat.

For Windows installations running Tomcat as a service, typically admins should use the “tomcat9w.exe” utility to adjust the settings. The following doc page shows how to adjust these kinds of settings in a variety of environments.

https://www.labkey.org/Documentation/wiki-page.view?name=configWebappMemory

If you are setting the system property, you can confirm that it was picked up after restarting Tomcat. Go to the Admin Console->System Properties and confirm that the “log4j2.formatMsgNoLookups” property is shown with the value “true”.

https://www.labkey.org/Documentation/wiki-page.view?name=siteManagement#diagnostics

Early next week we will release a patched version of LabKey Server that incorporates Log4J 2.15.0 that eliminates the need for the system property going forward. We will post this version to support portals as soon as it is available.

Please reach out via your support portal with questions and requests for help in making these changes.

For more details on the Log4J vulnerability itself, see https://github.com/advisories/GHSA-jfh8-c2jp-5v3q

view message
Cannot select 'Use SASL authentication'
(4 responses) mkuscuog 2021-12-10 12:32

Hello,

I am not able to check Use SASL authentication in Configure LDAP Configuration popup on Authentication page. It is always unchecked when I open the configuration popup back after successful Apply.

Is there anything I am missing here? I don't remember having this issue in the old UI (long time back)

Thanks,
Mehmet.

 Screen Shot 2021-12-10 at 12.28.06 PM.png 
view message
Maintenance Notice - Upgrade of labkey.org to LabKey 21.12 for Thursday, Dec 9th 2021 @ 10pm PST
(1 response) Jon (LabKey DevOps) 2021-12-09 16:57
LabKey.org will be offline this evening at 10pm PST for an upgrade to LabKey 21.12

The site will be offline for approximately one hour.

Please save your work before this time.
view message
KeyError CSRF
(1 response) rakesh yadav 2021-11-23 12:01

Hello Team,

We are trying to query the LabKey using python API but unfortunately not receiving a response but the status code is 200.

This was the response when we passed 'disable_csrf=True', while passing 'disable_csrf=False' we are getting the error "Key Error = CSRF"

Can you please look into the issue and help me where we are going wrong.

Thanks and Regards

 Screenshot 2021-11-23 at 8.52.07 PM.png  Screenshot 2021-11-23 at 8.56.29 PM.png 
view message
Maintenance Notice - Upgrade of labkey.org to LabKey 21.11 for Thursday, Nov 11th 2021 @ 9pm PST
Jon (LabKey DevOps) 2021-11-11 13:43
Hello everyone,

LabKey.org will be down this evening (Thursday, Nov 11th) for an upgrade to LabKey 21.11 starting at 9pm PST.

The server will be offline for approximately one hour.

Please save your work before this time.

LabKey Support
view message
Maintance Notice - Teamcity Server 10/28/2021 5PM - 6PM PDT
stuartm 2021-10-27 09:59

We will be performing maintenance on the LabKey TeamCity server on Thursday 10/28/2021 between 5 PM - 6 PM PDT. This maintenance only affects developers. During this maintenance window the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. Any existing builds running on TeamCity agents will continue and not be interrupted.

We apologize for any inconvenience this may cause.

view message
Maximum length for a "Subject identifier"
johann pellet 2021-10-21 09:05

Hi,

I am trying to import some data in a dataset and I have for one entry this error:
ParticipantID value 'XXX_test13_LongAmp_100-extend_1pg' is too long, maximum length is 32 characters.

Howether, in the Dataset Definition, the type for a ParticipantID is text and the maximum text lenght is set to 4000 characters.
Do we have any lenght restriction for a subject identifier? If yes, could we increase the maximum length?

Thanks.

Regards,
Johann

view message
Retiring SVN server (svn.mgt.labkey.host) on November 1, 2021
(1 response) jeckels 2021-10-18 10:12

For LabKey Server version 20.11 (about one year ago), we completely migrated all code and configuration from out Subversion server into a variety of GitHub repositories. We retained full history on these files, so that you can see all of the edits made from the beginning of the project.

https://www.labkey.org/Premium/announcements-thread.view?rowId=20912

As we are no longer actively producing builds for older releases, we will be archiving the SVN server, svn.mgt.labkey.host, on or around November 1. While we will retain the ability to spin it up, we do not anticipate needing it again.

If you are using 20.11 or later, you shouldn't be affected at all. If you are using 20.7 or earlier and actively pulling code from Subversion, you'll be unable to do this anymore. Please reach out if you anticipate any problems.

Thanks,
Josh

view message
Maintenance Notice - Upgrade of labkey.org to LabKey 21.10 for Wednesday, Oct 13th 2021 @ 9pm PST
Jon (LabKey DevOps) 2021-10-13 15:10
Hello everyone,

LabKey.org will be down this evening (Wednesday, Oct 13th) for an upgrade to LabKey 21.10 starting at 9pm PST.

The server will be offline for approximately one hour.

Please save your work before this time.

LabKey Support
view message
NAb new study folder missing specimen tab
(4 responses) ehands 2021-10-05 09:38

Hi there,

I am trying to create a new protocol study for HVTN Nab Montefiori lab, and when creating a 'Study' sub-folder in the Montefiori Approved Runs folder, I am no longer seeing the option to select 'Repository Type: Standard Specimen Repository'. As a result, when I go in afterwards to upload specimens to this study folder, there is no Specimen tab available to do this. Please let me know how this can be resolved,

Thanks,
Ellie

 image (16).png 
view message
Update to test binaries in develop
Trey 2021-09-29 17:08

We are making some updates to the LabKey 'testAutomation' repository. They may require some action for folks but, hopefully, shouldn't be too disruptive.

  1. We are removing test.properties from source control and replacing it with test.properties.template. The gradle plugin (or the test harness) will generate test.properties from the template if it is missing when running tests.
    This change is intended to clean up folks' changelists a bit, similar to when we made template files for numerous IntelliJ config files that are frequently edited by IntelliJ.
    Additionally, the template file has been reorganized and annotated to help folks to understand and use the various properties.

  2. We are removing the chromedriver and geckodriver binaries from source control. The versions that are checked in are quite old and it isn't great practice to commit binaries into source control anyway. Going forward, you will need to install them manually.

What do you need to do?

  1. Backup your test.properties file. Once the change is merged and you've synced, run './gradlew :server:testAutomation:initProperties' to generate a new test.properties from the template file. Then copy your properties to the generated file (or restore your backup, but it won't have all the nice new annotations).
  2. Install up-to-date versions of geckodriver/chromedriver. Add/update 'webdriver.gecko.driver'/'webdriver.chrome.driver' properties in 'test.properties' to point at the corresponding binary. (Note: You can also install them somewhere seen by your PATH and forgo the driver properties)

I expect to merge these changes on Friday to let folks prepare and to wait for a needed gradle plugin change.

view message
Maintenance Notice - artifactory.labkey.com upgrade to Artifactory 7.X for Sunday, August 29th 2021 @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-08-26 15:33
There will be an upgrade on artifactory.labkey.com to Artifactory 7.X for the last Sunday of this month (Sunday, August 29th) at 8am PST.

The estimated downtime will be for approximately 4 hours. During this time, the TeamCity build queue will be paused.
view message
Using Aliases for Sample Types
(1 response) ophira 2021-08-15 04:24

Hi,

We created several Sample Types in our Community Edition Labkey Server.
In one of our Sample Types, each row has its own Name which is determined by us during upload, say HA_###.
There is also the Alias field, where we can use to have a more meaningful name, which we can also change without changing the row's Primary Key.

A few questions about this:

  1. can multiple Aliases be assigned to a single row? on first glance it seems that only one Alias can be assigned to a single row. If this is impossible, we can of course concatenate different aliases to a single value ("alias1;alias2")
  2. are there any "special" traits to the Alias field? for example, I noticed that it's not unique, so two rows can have the same alias. I didn't find a lot on this topic in the Documentation, perhaps I missed something.

Thanks,
Ophir

view message
Changing Base Column Labels in a Study
(1 response) Ronny Kursawe 2021-08-12 00:51

We are using Labkey 17.3 and the import of study data with "Study Reload" via "Pipeline". Data are uploaded via WebDav into the pipeline folder.

If I got it correctly, the "datasets_metadata.xml" file allows to specify the names, labels and descriptions of columns. Besides that, there is an option to specify the "subjectColumnName" in the "study.xml" file.

After reloading the study, there is still a section of "Base Columns" (Please find a screenshot enclosed).

Is there an option to change the label and description of such columns? It seems that the settings of the "datasets_metadata.xml" do not work.

 basecolumns.PNG 
view message
edit on list deletes entries rather than updates them
(1 response) Thomas 2021-08-05 01:29

Hi,

I installed the latest labkey version 21.7.0 on windows 10 and have encountered a funny behaviour:
When I edit an entry of a list (pencil symbol) the row disappears from the list rather than being updated
I can add new rows to a list without problems, but edit = delete

Is this a problem with my setup? Has anyone else seen this?

Many thanks

view message
Project migration between servers-Incomplete
(1 response) WayneH 2021-06-30 07:19

Good morning,

we recently ran into an issue migrating a project between servers in our v18.2 community edition. We are preparing to migrate to a licensed current version but are really concerned about the problem we ran into.. On two different occasions one user's migration did not transfer over complete subfolder contents. I myself performed the same using the export/import tools and found that everything transferred over except for the file repository and the assay data (designs, batch/run data and tables). In my case I selected all of the options including files and all subfolder content.
The project is separated into three folders. One main folder and two subfolders within it. The assay data and file repository is in one of those subfolders. The assay data is in the top level folder although the designs/templates are in the subfolder where the file repository is located. I believe this is the structure we have.
Any thoughts on why we're having trouble migrating the project completely?

Thanks

Wayne

view message
Problem to Import FlowJo Workspace
(1 response) johann pellet 2021-06-11 07:59

Hi,

I have a problem with my dataset when I am trying to import a Flowjob Workspace in my Labkey server (LabKey Server 19.3.0).

11 Jun 2021 16:51:18,000 DEBUG: Analysis results contains 275 statistics, 76 graphs
11 Jun 2021 16:51:21,656 ERROR: FlowJo Workspace import failed
org.labkey.api.query.RuntimeValidationException: name: Value is too long for column 'name', a maximum length of 256 is allowed. Supplied value was 259 characters long.
    at org.labkey.api.data.Table.insert(Table.java:708)
    at org.labkey.flow.persist.FlowManager.ensureAttributeName(FlowManager.java:468)
    at org.labkey.flow.persist.FlowManager.ensureAttributeName(FlowManager.java:484)
    at org.labkey.flow.persist.FlowManager.ensureAttributeNameAndAliases(FlowManager.java:549)
    at org.labkey.flow.persist.FlowManager.ensureStatisticNameAndAliases(FlowManager.java:508)
    at org.labkey.flow.persist.AttributeSetHelper.ensureStatisticNames(AttributeSetHelper.java:109)
    at org.labkey.flow.persist.AttributeSetHelper.prepareForSave(AttributeSetHelper.java:89)
    at org.labkey.flow.script.WorkspaceJob.extractAnalysis(WorkspaceJob.java:371)
    at org.labkey.flow.script.WorkspaceJob.createExperimentRun(WorkspaceJob.java:170)
    at org.labkey.flow.script.WorkspaceJob.createExperimentRun(WorkspaceJob.java:148)
    at org.labkey.flow.script.AbstractExternalAnalysisJob.doRun(AbstractExternalAnalysisJob.java:233)
    at org.labkey.flow.script.WorkspaceJob.doRun(WorkspaceJob.java:138)
    at org.labkey.flow.script.FlowJob.run(FlowJob.java:76)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:304)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
    at java.base/java.lang.Thread.run(Thread.java:831)
Caused by: name: Value is too long for column 'name', a maximum length of 256 is allowed. Supplied value was 259 characters long.
    at org.labkey.api.query.RuntimeValidationException.<init>(RuntimeValidationException.java:36)
    ... 19 more
11 Jun 2021 16:51:21,693 INFO : Job completed at 2021-06- 16:51
11 Jun 2021 16:51:21,693 INFO : Elapsed time 40.326s```

The 'name' is too long to be inserted in the database (as I undestand).  Could you please tell me what name refers to this value.

Thank you.

Regards,
Johann
view message
Maintenance Notice - artifactory.labkey.com update for Thursday, June 10th 2021 @ 8am PDT
(1 response) Jon (LabKey DevOps) 2021-06-08 15:53

The artifactory.labkey.com server will be taken offline for maintenance on Thursday, June 10th 2021 @ 8am PDT for approximately 30 minutes max.

During this time, the site will be unavailable and the TeamCity build queue will be paused.

We apologize for any inconvenience this may cause.

view message
Maintenance Notice: Artifactory outage for Friday, June 4th 2021 @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-06-03 14:42

The artifactory.labkey.com server will be taking offline for maintenance on Friday, June 4th 2021 @ 8am PST for approximately 30 minutes max.

During this time, the site will be unavailable and the TeamCity build queue will be paused.

We apologize for any inconvenience this may cause.

view message
Labkey Community Edition Consulting
(1 response) ophira 2021-06-02 01:25

Hello,

We started using Labkey Community Edition. For now, we are trying to avoid the costs of Premium editions, at least until we are certain that this solution is right for our organization.

However, we would love to consult with more experienced people regarding some design and implementation topics.
For this purpose, we are looking for someone who offers consulting services.

Are there organizations/individuals outside of Labkey who offer such a service?

Thanks,
Ophir

view message
Maintenance Notice: Migration of artifactory.labkey.com for Sunday, May 30th @ 12pm PST
(1 response) Jon (LabKey DevOps) 2021-05-27 15:18

We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Sunday, May 30th @ 12pm PST

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately seven hours.

We apologize for any inconvenience this may cause.

view message
Creating a single survey that posts data to multiple lists
(1 response) caroline norris 2021-05-20 04:03

Is is possible to use the Survey feature to create a single survey that posts data to more than one list on submission?

There is no information on how to do this in the Survey documentation, so just wondering if it's possible to do so without any custom development on our part?

view message
R Reports - R markdown- knitr pandoc - The input must be a UTF-8 encoded text.
(2 responses) hilariagrieve 2021-05-19 08:19

Hi,
I have installed The last version of labkey Server in a new Server and I reload the study folder with some troubleshoots but finally I did it.
But, I have problems with R reports. I remember that I have the same problem with the old server and I solve It but I don't know how.
I was researching and tried a lot of things but I didn't make it.
The problem is with r markdown, knitr and the error is that the imput must be a UTF-8 encondec text, and The file script.Rmd is not encoded in UTF-8.
I tried to set the File : Save with Encoding UTF-8 in R studio like https://support.rstudio.com/hc/en-us/articles/200532197-Character-Encoding.

Here is the log file:

Error executing command
javax.script.ScriptException: javax.script.ScriptException: An error occurred when running the script 'script.R', exit code: 1).

processing file: script.Rmd

|
| | 0%
|
|.......... | 14%
ordinary text without R code

|
|.................... | 29%
label: labkey (with options)
List of 1
$ echo: logi FALSE

|
|.............................. | 43%
ordinary text without R code

|
|........................................ | 57%
label: setup (with options)
List of 7
$ echo : logi FALSE
$ cache : logi TRUE
$ results : chr "hide"
$ warning : logi FALSE
$ comment : logi FALSE
$ message : logi FALSE
$ comments: chr ""

Loading required package: httr
Loading required package: jsonlite
Executing: pandoc -t html -o "script.html" "script.Rmd"
[WARNING] Could not deduce format from file extension .Rmd
Defaulting to markdown
UTF-8 decoding error in script.Rmd at byte offset 995 (e9).
The input must be a UTF-8 encoded text.
Quitting from lines 24-32 (script.Rmd)
Error in (function (input, format, ext, exec, cfg) : conversion failed
Calls: render ... eval -> eval -> <Anonymous> -> mapply -> <Anonymous>
Adem�s: Warning messages:
1: In readLines(con, warn = FALSE) :
entrada inv�lida encontrada en la conexi�n de entrada 'script.Rmd'
2: In xfun::read_utf8(input) :
The file script.Rmd is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 15, 46, 53, 59, 61, 72, ...
3: In read_utf8(input[1]) :
The file script.Rmd is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 15, 46, 53, 59, 61, 72, ...

Ejecuci�n interrumpida

view message
Trouble Starting LabKey Server Community Edition
(4 responses) etr 2021-05-07 15:27

Hello,
I am trying to install the Labkey server but I am experiencing some difficulties.
Please keep in mind I am not a usual user of either windows or tomcat for that matter.
Running on Windows Server 2012 R2, openjdk 16, tomcat 9.0

Catalina- log says something like this:

07-May-2021 22:05:40.736 SEVERE [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Error deploying deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml]
        java.lang.IllegalStateException: Error starting child
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:720)
                at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
                at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706)
                at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:689)
                at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1881)
                at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
                at java.util.concurrent.FutureTask.run(Unknown Source)
                at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
                at java.util.concurrent.AbstractExecutorService.submit(Unknown Source)
                at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:582)
                at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:472)
                at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1660)
                at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:315)
                at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
                at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
                at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
                at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
                at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
                at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
                at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
                at java.lang.Thread.run(Unknown Source)
        Caused by: org.apache.catalina.LifecycleException: Error starting the loader
                at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:432)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5028)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
                ... 25 more
        Caused by: java.lang.UnsupportedClassVersionError: org/labkey/bootstrap/LabKeyBootstrapClassLoader has been compiled by a more recent version of the Java Runtime (class file version 58.0), this version of the Java Runtime only recognizes class file versions up to 52.0
                at java.lang.ClassLoader.defineClass1(Native Method)
                at java.lang.ClassLoader.defineClass(Unknown Source)
                at java.security.SecureClassLoader.defineClass(Unknown Source)
                at java.net.URLClassLoader.defineClass(Unknown Source)
                at java.net.URLClassLoader.access$100(Unknown Source)
                at java.net.URLClassLoader$1.run(Unknown Source)
                at java.net.URLClassLoader$1.run(Unknown Source)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.net.URLClassLoader.findClass(Unknown Source)
                at java.lang.ClassLoader.loadClass(Unknown Source)
                at java.lang.ClassLoader.loadClass(Unknown Source)
                at java.lang.Class.forName0(Native Method)
                at java.lang.Class.forName(Unknown Source)
                at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:536)
                at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:408)
                ... 29 more
07-May-2021 22:05:40.738 INFO [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of deployment descriptor [C:\labkey\apps\tomcat\conf\Catalina\localhost\labkey.xml] has finished in [10] ms

If anyone can provide some info please.

Thanks,
ET

view message
Maintenance Notice: Migration of artifactory.labkey.com for Thursday, April 29th @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-04-27 11:13

We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Thursday, April 29th at 8am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately two hours.

We apologize for any inconvenience this may cause.

view message
Updates to IntelliJ config files in develop
Susan Hert 2021-04-26 11:43

I have just merged PR #66 in the LabKey/server repository to bring in some changes to the IntelliJ configuration files and to add a couple of tasks for setting up IntelliJ to use the LabKey default configurations.  These changes should mean you have to adjust fewer IntelliJ configurations manually when starting with a new enlistment and have fewer files in your "Never Commit These" change list.  The changes work best with IntelliJ Version 2021.1 or later.  Older (but not ancient) versions work as well but require more manual adjustment.

To avoid conflicts between the configuration files that this change deleted and the ones that get modified by Intellij for your local installation, please do the following before pulling down these changes:

  • Shut down IntelliJ
  • Make a copy of your .idea directory (just in case)
  • Stash the current changes in the .idea directory using git stash push -- .idea/ from the root of your LabKey enlistment
  • git pull
  • ./gradlew ijConfigure
  • Open your existing project in IntelliJ

Then:

  • Open your project in IntelliJ
  • Do a Refresh in the Gradle window.
  • If you are not using IntelliJ version 2021.1 or later
    • Edit the LabKey Dev configuration to fix the module classpath so it uses labkey-server.server.modules.platform.api.main
    • Edit the LabKey Production configuration to fix the module classpath so it uses labkey-server.server.modules.platform.api.main

If you are developing with TypeScript:

  • Go to Preferences -> Appearance & Behavior -> Path Variables and set a value for NODE_PATH that will point to the node binary used by the build (e.g., C:\Development\labkeyHome\build.node\node-v12.16.0\bin\node, or, for Mac or Linux, use the symlink created by the build that is version-independent: /Users/develop/labkeyHome/.node/node/bin/node).
  • Go to Preferences -> Languages & Frameworks -> Typescript and verify the Node interpreter settings. The interpreter should be pointing to the node version that you set as the NODE_PATH variable. If not, or if you need to change this at some point, you can do that here.

For instructions on setting up a development environment from scratch, see this page.

If you have any problems that seem related to these changes, please let us know.

Susan

view message
How to create and append to a dataset using R labkey API?
(1 response) kristen dang 2021-04-23 10:42

Hello,
I am having several errors when trying to use the R labkey API to create and load a dataset. I am able to load this same file as a dataset using the GUI, but cannot seem to do it with the R API.

When creating the design, I get an error about reserved fields. In the GUI I resolve this by matching specific upload file column names with reserved field names. I don't know how to do this in R:

fields <- labkey.domain.inferFields(baseUrl=labkey.getBaseUrl(), folderPath=fp, df=inDF)
 dd <- labkey.domain.createDesign(name=batch$batch, fields=fields)
 k = which(dd$fields$name %in% c("ParticipantId", "visitCode", "sampleName"))
 dd$fields$isPrimaryKey[k] = TRUE

    eaLabkeyList = labkey.domain.create(baseUrl=labkey.getBaseUrl(), folderPath=fp, domainKind="StudyDatasetVisit", domainDesign=dd, options=list(categoryName="SequencingTest",demographics=FALSE,useTimeKeyField=FALSE,keyPropertyName="sampleName"))

Error:

HTTP request was unsuccessful. Status code = 500, Error message = java.lang.IllegalArgumentException: Property: ParticipantId is reserved or exists in the current domain.

Once I create this file in the web UI, I'm not able to append other data to it by upload since the column names don't match. Is there some documentation for how to take care of the key name matching so I can do this in R?

Thanks for any help.

view message
How to use createAndLoad for Lists or Datasets using R?
(1 response) kristen dang 2021-04-23 10:32

Hello,
In the R labkey package, I tried to use to use the labkey.domain.createAndLoad to create and load a list, but was unable to understand the error message. I'd like to be able to use this command for List and Dataset creation. Can you please suggest how I should address the issue with "strictFieldValidation?" I included my command and the response below.

labkey.domain.createAndLoad(baseUrl = labkey.getBaseUrl(),folderPath=fp,name="sequencing_vendor_QC_metrics", df=combined, domainKind="VarList")

Error in handleError(response, haltOnError) : 
HTTP request was unsuccessful. Status code = 500, Error message = Unrecognized field "strictFieldValidation" (class org.labkey.list.model.ListDomainKindProperties), not marked as ignorable (22 known properties: "entireListTitleTemplate", "discussionSetting", "keyName", "name", "entireListIndexSetting", "titleColumn", "eachItemBodyTemplate", "fileAttachmentIndex", "allowDelete", "listId", "eachItemBodySetting", "lastIndexed", "description", "allowExport", "eachItemTitleTemplate", "domainId", "entireListIndex", "allowUpload", "keyType", "entireListBodySetting", "entireListBodyTemplate", "eachItemIndex"])

view message
How to make a link in a List to a file in the Files tab using R API?
(1 response) kristen dang 2021-04-22 17:54

Hello,
I have several Lists that include a column listing relevant files which are also loaded in the Files tab. I would like to add a link to the List that points to the file in the Files tab. There is an extensive page on how to do this with the GUI, but I am not sure how to do it with the R labkey package. Can this be done with R?

view message
Maintenance Notice: Migration of artifactory.labkey.com for Monday, April 26th @ 8am PST
(1 response) Jon (LabKey DevOps) 2021-04-22 13:20
We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Monday, April 26th at 8am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately two hours.

We apologize for any inconvenience this may cause.
view message
RLabkey: Permissions when inserting/updating rows
(1 response) christian opitz 2021-04-13 00:55

I am trying to update/insert rows using the provided R library. Trying with .netrc, explicitly setting admin user/password via labkey.setDefaults() or only using the API key generated as admin results in:

Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 403, Error message = User does not have permission to perform this operation.

Everything (API key, credentials) are tight to the administrator. I can however retrieve the data using getRows() or selectRows().

The target of the operation is a targetedmslist table that was imported via Skyline.

Any help is appreciated.

Thank you.

view message
Maintenance Notice: Migration of artifactory.labkey.com for Monday, April 5th @ 11am PST
(1 response) Jon (LabKey DevOps) 2021-04-02 14:54
We will be working to migrating the current artifactory.labkey.com instance to a new server starting on Monday, April 5th at 11am PST.

During this time, all TeamCity jobs will be paused and Artifactory will be unavailable during the migration.

The estimated downtime is approximately one hour.

We apologize for any inconvenience this may cause.
view message
Problem while using the "Import and Export a XAR File" tutorial
(4 responses) ophira 2021-03-22 09:50

Hello,

I am trying to understand the Experiment module using the documentation by following these instructions:
https://www.labkey.org/Documentation/wiki-page.view?name=xarSamples

I got stuck here:

  • Download either XarTutorial.zip or XarTutorial.tar.gz and extract to your computer.
  • Select the Pipeline tab, and click Setup.
  • Click Set a pipeline override.
  • Enter the path to the directory where you extracted the files.
  • Click Save.

On step “Select the Pipeline tab, and click Setup.”, I didn’t find any “Setup” and “Set a pipeline override” anywhere.
Should this feature work in the Trial version? In the CE version?

My trial server:
https://oa1.trial.labkey.host/home/project-begin.view?

Tried the above on the "Example Project" as well as a newly created project named "proj4experiment".

Thanks,
Ophir

view message
Custom Postgres Method in Labkey Query
(2 responses) sleisle 2021-03-17 16:08

Hello Labkey,

I'm attempting to use a custom postgres method to join two tables in a file-based module query, but when running the query, it errors out stating "Method not found". I saw a similar forum post from 2013 that talked about this being unsupported, but seeing how old the post was I figured I should check if it has been updated. Is there any way to call a custom method, or is it unsupported?

Thanks!

view message
Editor permission without deleting permission.
(4 responses) Chichero 2021-03-15 11:22

Dear LabKey team,

Is there a way to allow a user to insert and update data in a dataset and a sample set without allowing for deleting this data?

Could you propose a workaround if it is not possible?

Thank you,
Natalia

view message
Upgrade Labkey
(1 response) hilariagrieve 2021-03-04 03:13

Hi, I have installed the 17.2 version of Labkey Server Community Edition. I designed and implemented a LIMS for the Forensic Genetics Laboratory. I want to upgrade to 20.11 version but I read that is not recomended to upgrade from 17.2 to 20.3 directly. Can you send me the old versions to upgrade step by step the versions of labkey? I tried to installed a new instance of labkey and import the study folder but the assay data is not imported correctly. Thanks you very much. Hilaria Grieve

view message
Module Upgrade : Error: Unable to initialize search index.
(1 response) hilariagrieve 2021-03-03 06:17

ALL SITE ERRORS returns me this log file. Can you help me?

ERROR LuceneSearchServiceImpl 2021-03-03 09:24:27,258 Module Upgrade : Error: Unable to initialize search index. Search will be disabled and new documents will not be indexed for searching until this is corrected and the server is restarted.
java.nio.file.NoSuchFileException: C:\Program Files\Apache Software Foundation\Tomcat 8.5\temp\labkey_full_text_index_4zf_Lucene50_0.tip
at sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:79)
at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:97)
at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:102)
at sun.nio.fs.WindowsFileSystemProvider.newFileChannel(WindowsFileSystemProvider.java:115)
at java.nio.channels.FileChannel.open(FileChannel.java:287)
at java.nio.channels.FileChannel.open(FileChannel.java:335)
at org.apache.lucene.store.MMapDirectory.openInput(MMapDirectory.java:238)
at org.apache.lucene.codecs.blocktree.BlockTreeTermsReader.<init>(BlockTreeTermsReader.java:176)
at org.apache.lucene.codecs.lucene50.Lucene50PostingsFormat.fieldsProducer(Lucene50PostingsFormat.java:445)
at org.apache.lucene.codecs.perfield.PerFieldPostingsFormat$FieldsReader.<init>(PerFieldPostingsFormat.java:292)
at org.apache.lucene.codecs.perfield.PerFieldPostingsFormat.fieldsProducer(PerFieldPostingsFormat.java:372)
at org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:109)
at org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:74)
at org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:145)
at org.apache.lucene.index.ReadersAndUpdates.getReadOnlyClone(ReadersAndUpdates.java:197)
at org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:103)
at org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:473)
at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:103)
at org.apache.lucene.search.SearcherManager.<init>(SearcherManager.java:108)
at org.apache.lucene.search.SearcherManager.<init>(SearcherManager.java:76)
at org.labkey.search.model.WritableIndexManagerImpl.<init>(WritableIndexManagerImpl.java:106)
at org.labkey.search.model.WritableIndexManagerImpl.get(WritableIndexManagerImpl.java:86)
at org.labkey.search.model.LuceneSearchServiceImpl.initializeIndex(LuceneSearchServiceImpl.java:232)
at org.labkey.search.model.LuceneSearchServiceImpl.start(LuceneSearchServiceImpl.java:327)
at org.labkey.search.SearchModule.startBackgroundThreads(SearchModule.java:190)
at org.labkey.api.module.ModuleLoader.attemptStartBackgroundThreads(ModuleLoader.java:1309)
at org.labkey.api.module.ModuleLoader.initiateModuleStartup(ModuleLoader.java:1286)
at org.labkey.api.module.ModuleLoader.afterUpgrade(ModuleLoader.java:1451)
at org.labkey.api.module.ModuleLoader.lambda$startNonCoreUpgradeAndStartup$3(ModuleLoader.java:1433)
at java.lang.Thread.run(Thread.java:748)
ERROR StudyReload 2021-03-03 09:24:27,508 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:29:27,418 QuartzScheduler_Worker-2 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:34:27,422 QuartzScheduler_Worker-3 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:39:27,426 QuartzScheduler_Worker-5 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:44:27,415 QuartzScheduler_Worker-6 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:49:27,419 QuartzScheduler_Worker-7 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:54:27,423 QuartzScheduler_Worker-9 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 09:59:27,427 uartzScheduler_Worker-10 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:04:27,416 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:09:27,420 QuartzScheduler_Worker-3 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:14:27,424 QuartzScheduler_Worker-4 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:19:27,428 QuartzScheduler_Worker-5 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:24:27,417 QuartzScheduler_Worker-7 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:29:27,421 QuartzScheduler_Worker-8 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:34:27,425 QuartzScheduler_Worker-9 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:39:27,429 QuartzScheduler_Worker-1 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)
ERROR StudyReload 2021-03-03 10:44:27,418 QuartzScheduler_Worker-2 : Study reload failed in folder /LIMS SGFER
org.labkey.api.admin.ImportException: Could not find file studyload.txt in the pipeline root for Lims SGFER
at org.labkey.study.importer.StudyReload$ReloadTask.attemptReload(StudyReload.java:398)
at org.labkey.study.importer.StudyReload$ReloadTask.execute(StudyReload.java:284)
at org.quartz.core.JobRunShell.run(JobRunShell.java:213)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:557)

view message
Removing server/modules/build.gradle file
(1 response) Susan Hert 2021-02-05 11:44

In order to do away with some flawed logic related to applying the LabKey gradle plugins, I am planning to remove the server/modules/build.gradle file early next week in our develop branches, in time for LabKey Server version 21.3.0. If you are maintaining your own local modules, you may need to add or update your build.gradle files in order to apply the plugin that had been being applied from this file. See this page for more details.

After this file is removed, and we update to the 1.25.0 version of the LabKey Gradle plugins, if the Gradle plugin detects a module that has a module.properties file but does not have a module task, a warning like the following will be shown at the end of running the deployApp command:

The following projects have a 'module.properties' file but no 'module' task. These modules will not be included in the deployed server. You should apply either the 'org.labkey.build.fileModule' or 'org.labkey.build.module' plugin in each project's 'build.gradle' file.
        :server:modules:myModule
        :server:modules:otherModule

You can fix this by applying the appropriate plugin as suggested or by defining your own module task that creates the .module file needed for inclusion in your LabKey Server instance.

Also, if you previously had a build.gradle file that references configurations, tasks, etc. defined in the Gradle plugins, you may encounter errors during the configuration phase when running a Gradle task like the following.

FAILURE: Build failed with an exception.

* Where:
Build file '/path/to/Development/labkey/root/server/modules/myModule/build.gradle' line: 6

* What went wrong:
A problem occurred evaluating project ':server:modules:myModule'.
> Could not find method implementation() for arguments com.sun.mail:jakarta.mail:1.6.5 on object of type org.gradle.api.internal.artifacts.dsl.dependencies.DefaultDependencyHandler.

This is fixed in the same way, by applying the plugin that had been being applied in server/modules/build.gradle.

If you have questions or encounter problems, please let us know.

Susan

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Rlabkey webdav access failing with 401 unauthorized
(3 responses) Marcel de Leeuw 2021-01-31 06:31

Hello,

We are unsuccessful acessing files on the labkey server through Rlabkey. Selectrows in a folder succeeds, bu then acessing files through webdav in the same folder for the same user (API key) fails with error code 401 (unauthorized). Aslo, webdav through the browser works fine. What needs to be configured for webdav through Rlabkey?

baseurl <- "http://bifx.mrmhealth.com:8080/labkey"
folderpath <- "/MRM Health/M002/Pre-clinical/E-00065 Rat"
setwd("~/labkey/M002/Pre-clinical")

library(Rlabkey)

labkey.mgx <- labkey.selectRows(
  baseUrl = baseurl,
  folderPath=folderpath, 
  schemaName="assay.General.Whole metagenome", 
  queryName="Runs", 
  viewName="", 
  colNameOpt="rname")
datafile <- gsub(".+@files/(.+)", "\\1", labkey.mgx$realtiveabundances)

labkey.webdav.get(
  baseUrl=baseurl,
  folderPath=folderpath,
  remoteFilePath=datafile,
  localFilePath="rat.mgx.tsv",
  overwrite=T)

Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 401, Error message = /_webdav/MRM Health/M002/Pre-clinical/E-00065 Rat/@files/assaydata/ca-mrm-bacteria-filtered-ra_2020_12_04_20_04.tsv

Thanks and regards

view message
Troubleshotting Reloading Study in a new server with a new version of Labkey Server
(2 responses) hilariagrieve 2021-01-26 08:03

Hi!
I have problems reloading the Study in a new version of Labkey Server in another Server.
I have instaled in one server Labkey v17 with a Study Proyect data.
Now we have e new server, and I installed the new version of labkey v20.7. I tried to creat the same Study Proyect exporting the Study Proyect from the old server and importing this export in the new server.
Everything was fine untill the pipeline got an error.

This is the log file:
26 ene. 2021 11:55:33,943 INFO : Starting to run task 'org.labkey.study.importer.StudyImportInitialTask' at location 'webserver'
26 ene. 2021 11:55:36,082 INFO : Reloading study from LIMS SGFER_2021-01-26_10-44-53.folder.zip
26 ene. 2021 11:55:36,222 INFO : Loading top-level study properties (label, start/end date, description, etc.)
26 ene. 2021 11:55:40,028 INFO : Done importing top-level study properties (label, start/end date, description, etc.)
26 ene. 2021 11:55:49,286 INFO : Loading QC states
26 ene. 2021 11:55:50,341 INFO : Done importing QC states
26 ene. 2021 11:55:50,349 INFO : Loading treatment data tables
26 ene. 2021 11:55:51,090 INFO : Done importing treatment data tables
26 ene. 2021 11:55:51,138 INFO : Loading assay schedule tables
26 ene. 2021 11:55:51,620 INFO : Done importing assay schedule tables
26 ene. 2021 11:55:51,780 INFO : Loading datasets manifest from datasets_manifest.xml
26 ene. 2021 11:55:51,900 INFO : Loading dataset schema from datasets_metadata.xml
26 ene. 2021 11:55:56,663 INFO : Successfully completed task 'org.labkey.study.importer.StudyImportInitialTask'
26 ene. 2021 11:55:56,910 INFO : Starting to run task 'org.labkey.study.pipeline.StudyImportDatasetTask' at location 'webserver'
26 ene. 2021 11:55:57,055 INFO : Start batch Lims SGFER.dataset
26 ene. 2021 11:55:57,079 INFO : Causas: Starting delete
26 ene. 2021 11:55:57,098 INFO : Causas: Deleted 5075 rows
26 ene. 2021 11:55:57,130 INFO : Causas: Starting import from dataset5001,tsv
26 ene. 2021 11:56:14,049 DEBUG: commit complete
26 ene. 2021 11:56:14,084 INFO : Causas: Successfully imported 5091 rows from dataset5001,tsv
26 ene. 2021 11:56:14,126 INFO : Secuenciacion ABI: Starting delete
26 ene. 2021 11:56:14,128 INFO : Secuenciacion ABI: Deleted 0 rows
26 ene. 2021 11:56:14,147 INFO : Secuenciacion ABI: Starting import from dataset5003,tsv
26 ene. 2021 11:56:15,202 ERROR: dataset5003,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,339 INFO : Extracción de ADN: Starting delete
26 ene. 2021 11:56:15,341 INFO : Extracción de ADN: Deleted 0 rows
26 ene. 2021 11:56:15,344 INFO : Extracción de ADN: Starting import from dataset5004,tsv
26 ene. 2021 11:56:15,716 ERROR: dataset5004,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,737 INFO : Cuantificación Fluorimétrica: Starting delete
26 ene. 2021 11:56:15,739 INFO : Cuantificación Fluorimétrica: Deleted 0 rows
26 ene. 2021 11:56:15,741 INFO : Cuantificación Fluorimétrica: Starting import from dataset5005,tsv
26 ene. 2021 11:56:15,899 ERROR: dataset5005,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:15,921 INFO : Cuantificación Real Time: Starting delete
26 ene. 2021 11:56:15,923 INFO : Cuantificación Real Time: Deleted 0 rows
26 ene. 2021 11:56:15,926 INFO : Cuantificación Real Time: Starting import from dataset5006,tsv
26 ene. 2021 11:56:16,017 ERROR: dataset5006,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:16,039 INFO : Amplificación por PCR: Starting delete
26 ene. 2021 11:56:16,041 INFO : Amplificación por PCR: Deleted 0 rows
26 ene. 2021 11:56:16,044 INFO : Amplificación por PCR: Starting import from dataset5007,tsv
26 ene. 2021 11:56:16,538 ERROR: dataset5007,tsv -- Two columns mapped to target column: CausasId
26 ene. 2021 11:56:16,545 INFO : Finish batch Lims SGFER.dataset
26 ene. 2021 11:56:16,549 INFO : Updating participant visits
26 ene. 2021 11:56:16,566 INFO : Updating participants
26 ene. 2021 11:56:16,749 INFO : Updating participant visit table
26 ene. 2021 11:56:16,750 INFO : Updating visit table
26 ene. 2021 11:56:16,752 INFO : Updating cohorts
26 ene. 2021 11:56:16,754 INFO : Clearing participant visit caches
26 ene. 2021 11:56:16,757 INFO : Finished updating participants
26 ene. 2021 11:56:16,807 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyImportDatasetTask'

I attached a dataset file example that got that error, and this have 2 columns names that mapped to target column CausasId, "CaudasId" and "ParticipantId".

Please, can you help me to resolve this problem?
Everything is reloaded in the new study but the datasets data.
Thank you very much!
Hilaria

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GUI not fully loading
mitch blocher 2021-01-25 13:37

Ive noticed that occasionally The GUI will not display certain information such as scripts, Pop up boxed etc. I have ensured popups and JavaScript were enabled in my chrome browser, and cookies and Cache were deleted. All labkey servers worked fine except for one. The solution I found was to reset all settings in my chrome browser, however the specific culprit causing the issue was not found.

view message
Scheduled Maintenance: artifactory.labkey.com Friday January 22, 2021 @ 7 AM PDT
(1 response) Jon (LabKey DevOps) 2021-01-20 13:01
We will be performing scheduled maintenance on LabKey's artifactory server ( https://artifactory.labkey.com/ ) on Friday January 22, 2021 @ 7 AM PDT.

The expected downtime should be approximately 60-90 minutes.

This will affect build artifacts during this maintenance period.

While Artifactory is unavailable, you should use the --offline flag for gradle when building.

We are performing this maintenance to install the latest security patches for Artifactory and its underlying operating system.
view message
migration from standard server to docker and authentication
(1 response) ramez saour 2021-01-18 04:06

I have migrated labkey and tomcat7 config from standard host to docker image tomcat8 and same config as labkey, however, since moved to docker I cant authenticate to labkey portal. is there way to use local account (admin) or configure ldap connection inside docker?

I have also
<Resource name="ldap/ConfigFactory" auth="Container"
type="org.labkey.premium.ldap.LdapConnectionConfigFactory"
factory="org.labkey.premium.ldap.LdapConnectionConfigFactory"
host="10.5.0.9"
port="389"
principal="CN=zSvcADBindRDLK,OU=ServiceAccounts,OU=GEL,DC=corp,DC=gel,DC=ac"
credentials="***********"
/>

view message
XML counter columns
(1 response) katy wiseman 2021-01-14 01:43

Hi,

I'm trying to get an XML counter column to work as described here at the bottom of the page:
https://www.labkey.org/Documentation/Archive/20.7/wiki-page.view?name=sampleIDs

However it's not working. I've created the sample type as it's shown in the example and pasted the XML code into the XML metadata but it's not generating an automatic 'SampleInLot' number for each new 'Lot' in the table.

This is the XML metadata suggested:

<tables xmlns="http://labkey.org/data/xml">
<table tableName="MySampType" tableDbType="NOT_IN_DB">
<javaCustomizer class="org.labkey.experiment.api.CountOfUniqueValueTableCustomizer">
<properties>
<property name="counterName">
SampleCounter
</property>
<property name="counterType">
org.labkey.api.data.UniqueValueCounterDefinition
</property>
<!-- one or more pairedColumns used to derive the unique value -->
<property name="pairedColumn">
lot
</property>
<!-- one or more attachedColumns where the incrementing counter value is placed -->
<property name="attachedColumn">
sampleInLot
</property>
</properties>
</javaCustomizer>
</table>
</tables>

Does anyone have any thoughts about how to get this to work? Or any other alternatives?

Thanks,

Katy

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