LabKey Support Forum

Welcome to the LabKey Support Forum. This forum is for questions regarding LabKey Server general usage, installation, or development.

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Showing: limited to 100 messages
Beta version for LK 23.11
(1 response) elovan 2023-10-03 11:24

Hello,

Will there be a beta version of LK 23.11 that will be released prior to 11/16/2023. We are going to bypass LK 23.7 and move right into LK 23.11.

Thank you,

Emily Lovan

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Teamcity CI/CD Emergency Maintenance today 9/19/2023 at Noon PDT
stuartm 2023-09-19 10:10

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at Noon PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

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Out of heap memory after upgrade from v23.3.2 to v23.7.0
(1 response) Will H. 2023-08-28 18:12

I have a cronjob that makes queries and then performs row deletions on lists using the LabKey API (via the python package). The queries are simple but can return a large number of rows. The deletions are batched to 900 rows per API call. This workflow has been running fine for a while.

Last week I upgraded from LabKey v23.3.2 to v23.7.0 and immediately started getting out of memory errors when performing the row deletions.

ERROR ExceptionUtil            2023-08-27T01:52:59,521     http-nio-8080-exec-2 : Unhandled exception: Java heap space
java.lang.OutOfMemoryError: Java heap space
	at java.util.Arrays.copyOf(Arrays.java:3537) ~[?:?]
	at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:228) ~[?:?]
	at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:582) ~[?:?]
	at java.lang.StringBuilder.append(StringBuilder.java:179) ~[?:?]
	at org.labkey.list.model.ListManager$2.exec(ListManager.java:844) ~[list-23.7.0.jar:?]
	at org.labkey.list.model.ListManager$2.exec(ListManager.java:840) ~[list-23.7.0.jar:?]
	at org.labkey.api.data.TableSelector.lambda$forEachResults$1(TableSelector.java:278) ~[api-23.7.0.jar:?]
	at org.labkey.api.data.TableSelector$$Lambda$1265/0x00007fc3d0e3c130.handle(Unknown Source) ~[?:?]
	at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleResultSet(SqlExecutingSelector.java:457) ~[api-23.7.0.jar:?]
	at org.labkey.api.data.TableSelector.forEachResults(TableSelector.java:273) ~[api-23.7.0.jar:?]
	at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:839) ~[list-23.7.0.jar:?]
	at org.labkey.list.model.ListManager.lambda$deleteItemIndex$6(ListManager.java:592) ~[list-23.7.0.jar:?]
	at org.labkey.list.model.ListManager$$Lambda$1837/0x00007fc3d11bee58.run(Unknown Source) ~[?:?]
	at org.labkey.api.data.DbScope$CommitTaskOption.run(DbScope.java:2010) ~[api-23.7.0.jar:?]
	at org.labkey.api.data.DbScope$TransactionImpl.commit(DbScope.java:2327) ~[api-23.7.0.jar:?]
	at org.labkey.query.controllers.QueryController$BaseSaveRowsAction.executeJson(QueryController.java:4473) ~[query-23.7.0.jar:?]
	at org.labkey.query.controllers.QueryController$DeleteRowsAction.execute(QueryController.java:4622) ~[query-23.7.0.jar:?]
	at org.labkey.query.controllers.QueryController$DeleteRowsAction.execute(QueryController.java:4614) ~[query-23.7.0.jar:?]
	at org.labkey.api.action.BaseApiAction.handlePost(BaseApiAction.java:238) ~[api-23.7.0.jar:?]
	at org.labkey.api.action.BaseApiAction.handleRequest(BaseApiAction.java:128) ~[api-23.7.0.jar:?]
	at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:195) ~[api-23.7.0.jar:?]
	at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:512) ~[api-23.7.0.jar:?]
	at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1128) ~[api-23.7.0.jar:?]
	at org.labkey.api.view.ViewServlet._service(ViewServlet.java:240) ~[api-23.7.0.jar:?]
	at org.labkey.api.view.ViewServlet.service(ViewServlet.java:159) ~[api-23.7.0.jar:?]
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:623) ~[servlet-api.jar:4.0.FR]
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209) ~[catalina.jar:9.0.79]
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) ~[catalina.jar:9.0.79]
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) ~[tomcat-websocket.jar:9.0.79]
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178) ~[catalina.jar:9.0.79]
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153) ~[catalina.jar:9.0.79]
	at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:43) ~[api-23.7.0.jar:?]

I am running with 16GB of heap:

-Xms16G -Xmx16G -XX:-HeapDumpOnOutOfMemoryError

And the overall load on the system is quite low.

When investigating I looked at /admin-memTracker.view and was surprised to see ~30 instances of "SearchService:index". But I haven't looked at this page before, so perhaps that is normal.

Some other system details:
Servlet Container Apache Tomcat/9.0.79
Java Runtime Vendor Eclipse Adoptium
Java Runtime Name OpenJDK Runtime Environment
Java Runtime Version 17.0.8+7
Database Product Name PostgreSQL
Database Product Version 15.3

Is anyone else running into out of memory issues after moving to v23.7.0?

Thanks,
-Will

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Python API - Connection with _netrc failing?
(3 responses) connor henderson 2023-08-22 08:41

I'm trying to create a Python script that connects to my LabKey server, however, I'm not getting past authentication when I provide either a username/password or an API key. I've tried moving the _netrc file to the C:/Users/user_account/ path to no avail. I'm not quite sure where I'm going wrong as everything seems to match the documentation.

Python Code

# LabKey Settings
container_path = "Test_Lab"
context_path = "labkey"
labkey_server = "mylabkeyserver.ca"
api_key = 'apikey|8ba5866e0f50c2b9...'

# Debug: print paths and _netrc contents
print(f"{'$HOME path:':20s}", os.environ['HOME'])
print(f"{'$HOME dir:':20s}", os.listdir(os.environ['HOME']))
print(f"{'_netrc contents:':20s}", open(os.environ['HOME'] + "\\_netrc").read())

# Create the connection to the LabKey API
labkey_api = APIWrapper(labkey_server, container_path, context_path, use_ssl = False, api_key = api_key)

# Connect and try to get available roles
print("\nGetting user")
result = labkey_api.security.get_roles()
print(result)

Results

$HOME path:          C:\development\labkey\common
$HOME dir:           ['_netrc']
_netrc contents:     machine	mylabkeyserver.ca	login	apikey	password	apikey|8ba5866e0f50c2b9...

Getting user
---------------------------------------------------------------------------
TimeoutError                              Traceback (most recent call last)
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LabKey TeamCity Server Maintenance Thursday 8/10/2023 between 7-8 AM PDT
stuartm 2023-08-09 17:38

We will be performing maintenance on the LabKey TeamCity server on Thursday 8/10/2023 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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Capacity of "Lists"?
(2 responses) stravsmi 2023-06-22 23:27

Hi,

we are developing a solution based on LabKey Community and have different options for how to implement some functionality.

Is there a practical limitation to how large a "List", with per-row indexing, can get?
Is it feasible to have a "List" with many millions of rows, and to query it in reports?

view message
LabKey TeamCity Emergency Maintenance Monday June 12th 2023
stuartm 2023-06-12 07:56

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at 8 AM PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

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Maintenance Notice - Upgrade of LabKey.org for Thursday, May 11th 2023 @ 9:00pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-05-11 14:15
LabKey.org will be offline this evening at 9:00pm Pacific Time for an upgrade to LabKey 23.5

The site will be offline for approximately one hour.

Please save your work before this time.
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Assay Data not getting fetched in API
(2 responses) sadanand ranbhor 2023-05-08 02:44

Hi Team,
I have created an assay project folder structure screen shot attached.I am trying too invoke http://<hostname>/labkey/Custom Project 2/subfolder/assay-assayList.api GET API and I get following error
{
"exception": "Method Not Allowed: GET",
"success": false
}

Is there any issue with the API URL which I have formed ?Please let me know.

 Assay Project.png 
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Sample Managerment
(1 response) sadanand ranbhor 2023-05-08 01:20

Hello, I am working on labkey community version. I am looking for labkey Sample lifecycle implementation as the documentations/videos but I don't see the relevant menus in my system.Can you please suggest what could be going wrong? Is this feature only available with Professional edition.Please let me know

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Maintenance Notice - Update of LabKey.org for Wednesday, April 19th 2023 @ 7:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-04-19 11:25
LabKey.org will be offline this evening at 7:30pm Pacific Time for a minor maintenance update.

The site will be offline for no more than 15 minutes.

Please save your work before this time.
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Maintenance Notice - Upgrade of LabKey.org for Monday, April 17th 2023 @ 8:00pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-04-17 15:48
LabKey.org will be offline this evening at 8:00pm Pacific Time for a maintenance upgrade.

The site will be offline for no more than 30 minutes.

Please save your work before this time.
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Insert pdf as a printout in wiki
(1 response) chelsea st germain 2023-04-14 15:29

How do you insert a pdf or image into the wiki page? I've tried the following with no luck:

This doesn't work at all, this image file is just added as an attachment:

<img src=""final graph_LT_P_10.jpg">

This also doesn't work, and throws an error about an illegal element:

<!-- update web address for where pdf file is store in "data" element-->
<p><object style="min-height: 100vh; width: 100%;" width="320" height="240" data='/labkey/_webdav/FCIC/FCIC%20Task%20Work/T.08.00%20Cross-Cutting%20Analysis/Case%20Studies/HT-P-11_02/%40files/HT-P-11_02_CaseStudyBrief.pdf' /></object></p>

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Error when editing style "There was a problem while saving: Illegal element"
(1 response) chelsea st germain 2023-04-14 15:19

I have been trying to add some style elements to my wiki web parts and the text itself works fine, but I try to throw in any style element and it throws an error saying "There was a problem while saving: Illegal element". I checked the html code on another site and the HTML code works fine elsewhere, so I dont' know why I'm getting the error.

Example code below:

<style>
.aligncenter {
text-align: center;
}
</style>

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Maintenance Notice - Upgrade of LabKey.org for Thursday, April 13th 2023 @ 9:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-04-13 14:58
LabKey.org will be offline this evening at 9:30pm Pacific Time for an upgrade to LabKey 23.4

The site will be offline for approximately one hour.

Please save your work before this time.
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Getting duplicate key error after upgrade
(6 responses) Aaron Sword 2023-04-05 10:44

Hello,

I am new to Labkey so if I get something wrong or you need more info just let me know. I have upgraded our dev environment to the latest version (23.3.2-5) and now I am getting this error: ERROR: duplicate key value violates unique constraint "uq_modulename". Can anyone tell me what I have done to my server and if there is a way to fix it? Any info is greatly appreciated.

Thanks

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ViewName selection on survey lookup option
(1 response) jenica abrudan 2023-04-05 07:09

I have multiple survey fields where i need to select a lookup value from a list. Since the value sets a slightly different i am using viewName as in (https://www.labkey.org/Documentation/wiki-page.view?name=questionMetadata#viewName) but while this works for the first field - all subsequent fields have the same viewName applied even if the other fields have different viewName defined on the lookup.
Can different survey fields on the same survey use different viewName for subselecting values from the same lookup list ?

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LabKey Upgrade Recommended: Security Update
Keith 2023-03-30 11:23

LabKey is releasing hotfixes that address an important security vulnerability. It affects all LabKey products and was detected by our engineering team. The following maintenance releases include the security update:

  • 23.3.2
  • 22.11.9
  • 22.7.9
  • 22.3.11
  • 21.11.11

It is imperative that system administrators upgrade their LabKey Server instances immediately to remain secure. An updated and secured version of LabKey Server has been made available. We apologize for the inconvenience and thank you for patching your installations.

Please note that this update also includes other valuable but non-critical security improvements.

At this time, we are not releasing additional details as we do not want to make this vulnerability public for exploitation. We have no indications that anyone outside of LabKey is aware of the detected vulnerability.

We take security related issues very seriously, please reach out via the support forum if you have questions.

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Maintenance Notice - Upgrade of LabKey.org for Thursday, March 9th 2023 @ 9:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-03-09 18:47
LabKey.org will be offline this evening at 9:30pm Pacific Time for an upgrade to LabKey 23.3

The site will be offline for approximately one hour.

Please save your work before this time.
view message
How to login to community edition set up
(9 responses) sadanand ranbhor 2023-03-08 21:28
I have set up local LabKey community edition. How to l get access to login first time?
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Sample naming pattern - yearlySampleCount
(2 responses) katy wiseman 2023-02-21 08:20

Hi,

I'm trying to use the yearlySampleCount in my sample naming pattern but even in a new folder with nothing else in it it's not starting at 1. I entered ${yearlySampleCount} as my name expression and my first test sample was given a name of 17886. The next one was give 17887. I made a new project folder and made a new sample type with ${yearlySampleCount} as the naming expression and my first sample was given 17888. It looks like the scope is maybe extending across folders, but the documentation says it's only "All Sample Types / Data Classes in the current folder".

Is this how it's meant to be working or am I doing something very wrong?

Thanks,

Katy

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Maintenance Notice - Upgrade of LabKey.org for Wednesday, February 15th 2023 @ 8:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-02-15 10:50
LabKey.org will be offline this evening at 8:30pm Pacific Time for a minor upgrade of LabKey 23.2

The site will 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 for Friday, February 10th 2023 @ 8:30pm Pacific Time
(1 response) Jon (LabKey DevOps) 2023-02-10 12:59
LabKey.org will be offline this evening at 8:30pm Pacific Time for an upgrade to LabKey 23.2

The site will be offline for approximately one hour.

Please save your work before this time.
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Validation for Participant IDs
(2 responses) schwarza 2023-02-10 09:27

Hello,

Is it possible to create a regex validator for Participant IDs?

If not, is there any other way to enforce constraints on Participant IDs at the time users enter data (e.g., require the IDs to be 10-digit numbers)?

Thank you!

Leah

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Maintenance Notice - LabKey TeamCity Build Server on Friday, February 3rd 2023
(1 response) Trey 2023-02-01 13:20

We will be performing maintenance on the LabKey TeamCity server on Friday 2/3/2023 starting at 8 AM PST. During this maintenance the TeamCity Build Queue will be paused and no new builds will be started until the maintenance is completed. We are migrating to a multi-node, high availability configuration to improve performance and reliability.

The server will be offline periodically throughout the migration. We hope to have the maintenance complete and validated by 3PM.

We apologize for any inconvenience this may cause.

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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.
view message
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.

view message
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.
view message
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.

view message
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.
view message
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.
view message
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.
view message
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.
view message
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).

view message
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?

view message
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.

view message
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

view message
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´╝Ü“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

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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!

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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

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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 
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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.
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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 
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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
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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.

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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

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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

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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
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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 
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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.

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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.
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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

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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 
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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

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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

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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
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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.

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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.

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