Hello,

I collected MRM transitions on an Agilent QqQ, I used 2 scan segments. One scan segment was from 0-1.1mins, during this time solvent was sent to waste, then from 1.1 to end solvent was sent to MS for detection. When I upload the .d file into Skyline, it is only finding the 0-1.1 min time segment when there would be nothing. How do I get Skyline to find or read the other time segment where there is actually data?

I am using the latest community labkey server version to store/modify a database (a list as a table with multiple fields). My list has the default columns, including Modified. But, when I do a bulk upload to the list, the Modified column defaults to the upload date/time instead of the date I have entered into the uploaded spreadsheet. For example, if I upload this:

Name Modified
project1 9/20/24 10:13
project2 8/18/24 8:54
project3 8/16/24 15:50

I would actually get this:

Name Modified
project1 9/21/24 10:15
project2 9/21/24 10:15
project3 9/21/24 10:15

LabKey documentation defined Modified column behavior during bulk upload as "A date/time value that indicates when a record was last modified. If this time is not explicitly specified in the imported dataset, LabKey will set it to the date/time that the data file was last modified.". So why when I explicitly specify the date/time am I not getting it to show up in the list table?

For reference, an abridged version of my sheet is attached - it's in excel format and the Modified column has the specific format of "Date".

Hi all,

After a lull in the internal usage, we are getting around to upgrading our LabKey installation from 19.1.1-63156.2 to 23.11.11-11-13. We have successfully complied with the platform requirements:

Tomcat v9.0.17
JVM v17.0.6+9-LTS-190
Postgres 13.3 (Ubuntu 13.3-1.pgdg16.04+1)

Config files seem to be working properly, data has been upgraded and has data in it.. but when I try to initialize the new LabKey webapp, there is a database error:

org.labkey.api.util.ConfigurationException: core-0.000-22.000.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: type "uniqueidentifier" already exists
org.labkey.api.util.ExceptionUtil.renderErrorPage(ExceptionUtil.java:1036)
org.labkey.api.util.ExceptionUtil.handleException(ExceptionUtil.java:953)
org.labkey.api.util.ExceptionUtil.handleException(ExceptionUtil.java:681)
org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:91)
org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:120)

Site won't load and log files show that the system is trying to run (presumably) an upgrade script - which is where the page load is failing.

Any Ideas how to fix this? We did not do each of the intermediate upgrades from 19 to 23.. we DID upgrade previously from 17.3-55100.13 to 18.1-57017.17 and then to 19.1.1-63156.2. Not sure if that matters here or not.

Thanks!

Out of curiosity is there any way to enable version control for R reports in production labkey or some way we could have the reports source some files we can control in git? Right now we're considering copy/pasting R reports from the Labkey web ui into github and I was curious if there were a better way to do this we're missing?

Hi
I'm having a very weird issue when using the updateRows or insertRows functions in the RLabkey package. when a number is between 1E-5 and 9.999E-5 they get inserted as 0. when the number is E-4 or E-6 they go in fine. My script is running using the R scripting engine in LabKey and posting to a sample table. please see the attached file for data and error log examples.

Is there a catch for E-5 numbers somewhere in the Rlabkey package? If I edit the field manually in Labkey it will accept the correct E-5 number.

Thanks
Ellie

Hi,

I have a sample table in one of my project tables which is un-usably slow. It's only one sample table (other sample tables in the same folder are fine), and only in this project folder.

It has one lookup to a query. The query is running pretty quickly. Other sample tables have lookups to queries and are running fine.
However, when I try and either add a new row or edit a row the form hangs after I press submit. If I leave it for a while and then give up and press cancel the sample or change doesn't appear immediately. If I refresh the page after about 30 seconds, then the new row or change appears.

This is all that' in the XML metadata:
<tables xmlns="http://labkey.org/data/xml">
<table tableName="rna" tableDbType="NOT_IN_DB">
<columns>
</columns>
</table>
</tables>

I don't really know what else to check or how else to troubleshoot this. Any ideas?

Best,

Katy

I am trying to delete some data within a folder and a separate empty folder but I am getting the same error that the same error:

'Oops! An error has occurred. This IndexWriter is closed'

Happened multiple times for deleting both data entries and folders.

Hi,

I attempted to export a folder from PNNL Labkey and import it into a different Labkey instance. However, there is a discrepancy between the user IDs in PNNL Labkey and our Labkey. Many of our assays use the user ID as a column. I tried decompressing the zip file and manually replacing the PNNL user IDs with our user IDs. Despite not making any changes to the folder.xml file, I received an error stating, "The archive doesn't contain a folder.xml file." How can I resolve this issue?

Thanks.

Hello LabKey team,

I am trying to upgrade my LabKey instance from 23.11.11 to 24.3.10 community edition version. I am able to bring the web application but the backend database migration is having troubles.

anything I have to particularly miss here.

pg_restore: error: could not execute query: ERROR:  constraint "fk_surveys_surveydesignid" for relation "surveys" already exists
Command was: ALTER TABLE ONLY survey.surveys
    ADD CONSTRAINT fk_surveys_surveydesignid FOREIGN KEY (surveydesignid) REFERENCES survey.surveydesigns(rowid);

pg_restore: warning: errors ignored on restore: 859

thanks in advance!
Vipin

Hi there,

Am trying to import a load of data from CSV via the python API, but keep running into issues with primary key matching.
There is a way on the frontend to 'Import Lookup by Alternate Key' (see attached), I was wondering if there was some configurable option in the python API.

Thanks in advance,

Jack

Hi,

I have the units column turned on in my sample tables but someone has asked for a new measurement unit, block. I don't seem to be able to add to this table, am I missing something? Otherwise I will make my own list and lookup to that instead.

Best,
Katy

Is it possible to create permission group for projects and assign them to roles in projects and sub-folders?
Thanks and regards,
Eva

Am using the Python package to create some samples using the domain API.

Here is some example code:

from labkey.api_wrapper import APIWrapper

labkey_server = 'localhost:8443'
container_path = 'T Cell Cloning Samples/Sequencing'
contextPath = None
schema = 'samples'
table = 'tcc_sample_handover'
api = APIWrapper(labkey_server, container_path, contextPath)

definition = {
    "kind": "SampleSet",
    "domainDesign": {
        "name": "tcc_sample_handover",
        "description": "TCC Sample Handover",
        "fields": [
            {"name": "Name", "rangeURI": "string"},
            {"name": "hla_restriction", "rangeURI": "string"},
            {"name": "tcc_sample_id", "rangeURI": "string"},
            {"name": "tcc", "rangeURI": "string"},
            {"name": "antigen", "rangeURI": "string"},
            {"name": "peptide_sequence", "rangeURI": "string"},
            {"name": "donor", "rangeURI": "string"},
            {"name": "race_prep", "rangeURI": "boolean"},
            {"name": "post_sort_well", "rangeURI": "string"},
            {"name": "cell_per_well", "rangeURI": "string"},
            {"name": "date_frozen", "rangeURI": "dateTime"}
        ]
    }
}

result = api.domain.create(definition)
print(result)

I am unsure how I can add a naming pattern to the definition.
I've added an attachment for what the naming pattern looks like.
Here's a link to the labkey docs for naming patterns also:
https://www.labkey.org/Documentation/wiki-page.view?name=sampleIDs#:~:text=Each sample in a Sample,of the Sample Type definition.

I am attempting to upgrade from 23.11.11 to 24.3.4 on a container-based platform provided by my workplace. So, I have created a Dockerfile that containerizes the embedded LabKey LIMS distribution using the template provided in LabKey's github page. In doing so, I've completed all the instructions provided on the LabKey website for upgrading (migrating my web.xml and ROOT.xml (labkey.xml) configurations over to the application.properties file, moving the labkeyServer.jar into my image, creating the necessary new directories, etc.).

When I deploy my container, I get several errors during java execution of labkeyServer.jar (after the Labkey Server welcome message and Conditions Evaluation Report are printed). I will attach the log file here, but I believe the root cause of the crash is ModuleLoader. Some modules load just fine (API, Pipeline, Query, Experiment, Assay, Audit, etc.), but then I get several error messages during module loading from others (for example, see below).

Please tell me if this is a known issue and/or if I can get some assistance fixing my deployment. Thanks!

java.lang.NumberFormatException: For input string: "tcp://10.43.165.217:8080" ```

``` ERROR ModuleLoader             2024-06-17T16:30:38,986           Module Upgrade : Failure starting module: FileContent
java.lang.NullPointerException: Cannot invoke "org.labkey.api.message.settings.MessageConfigService.registerConfigType(org.labkey.api.message.settings.MessageConfigService$ConfigTypeProvider)" because the return value of "org.labkey.api.message.settings.MessageConfigService.get()" is null ```

``` ERROR ModuleLoader             2024-06-17T16:30:37,945           Module Upgrade : Failure starting module: Announcements
java.lang.NullPointerException: Cannot invoke "org.labkey.api.message.settings.MessageConfigService.registerConfigType(org.labkey.api.message.settings.MessageConfigService$ConfigTypeProvider)" because the return value of "org.labkey.api.message.settings.MessageConfigService.get()" is null ```

Hi,

I seem to be having an issues with the description field on a sample table. The description field is ticked in the table set up, and the display options are ticked in the advanced setting under edit metadata, but the field isn't showing up in the insert rows page. It is showing up in the grid view and the update rows page though.

We're on version 23.11.11 in our prod instance. We've been having some issues updating to the latest version (posts by GrumpyBadger). The fields do seem to be working in our dev instance which is 24.3.4 but I wanted to check I wasn't missing something whilst we get it updated.

Best,
Katy

I'm trying to upgrade our prod Labkey docker instance from 23.3.2 to 23.11.11.

The upgrade went ok on our dev instance but the upgrade fails every time when we try on prod, leaving things in a broken state so we have to roll back the database. I've done the database check via the UI and no issues are found.

The issue seems to be related to the Experiment module :

INFO  ModuleLoader             2024-05-28T14:04:00,532           Module Upgrade : Starting module 'Pipeline'
INFO  SpringModule             2024-05-28T14:04:00,533           Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml]
INFO  ModuleLoader             2024-05-28T14:04:00,875           Module Upgrade : Starting module 'plateWellViewer'
INFO  ModuleLoader             2024-05-28T14:04:00,876           Module Upgrade : Starting module 'prevalenceDashboard'
INFO  ModuleLoader             2024-05-28T14:04:00,877           Module Upgrade : Starting module 'Query'
172.17.0.1 - - [28/May/2024:14:04:01 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3357
WARN  RoleManager              2024-05-28T14:04:01,228           Module Upgrade : Could not resolve the role org.labkey.api.security.roles.TrustedAnalystRole! The role may no longer exist, or may not yet be registered.
INFO  ModuleLoader             2024-05-28T14:04:01,228           Module Upgrade : Starting module 'Experiment'
INFO  SpringModule             2024-05-28T14:04:01,229           Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml]
172.17.0.1 - - [28/May/2024:14:04:02 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3358
172.17.0.1 - - [28/May/2024:14:04:03 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3358
172.17.0.1 - - [28/May/2024:14:04:04 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3358
127.0.0.1 - - [28/May/2024:14:04:04 +0100] "GET /_/health HTTP/2.0" 200 15
172.17.0.1 - - [28/May/2024:14:04:05 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3358
172.17.0.1 - - [28/May/2024:14:04:06 +0100] "POST /admin-sql-getModuleStatus.view HTTP/1.1" 200 3358
FATAL ModuleLoader             2024-05-28T14:04:06,554           Module Upgrade : Startup failure, terminating
java.lang.NullPointerException: Cannot invoke "org.labkey.api.exp.property.ValidatorKind.getName()" because the return value of "org.labkey.api.exp.property.PropertyService.getValidatorKind(String)" is null
        at org.labkey.experiment.api.property.DomainImpl$PropertyChangeAuditInfo.lambda$renderValidators$0(DomainImpl.java:1107) ~[experiment-23.11.11.jar:?]
        at java.base/java.lang.Iterable.forEach(Unknown Source) ~[?:?]
        at java.base/java.util.Collections$UnmodifiableCollection.forEach(Unknown Source) ~[?:?]
        at org.labkey.experiment.api.property.DomainImpl$PropertyChangeAuditInfo.renderValidators(DomainImpl.java:1106) ~[experiment-23.11.11.jar:?]
        at org.labkey.experiment.api.property.DomainImpl.save(DomainImpl.java:718) ~[experiment-23.11.11.jar:?]
        at org.labkey.experiment.api.property.DomainImpl.save(DomainImpl.java:521) ~[experiment-23.11.11.jar:?]
        at org.labkey.experiment.api.property.DomainImpl.save(DomainImpl.java:369) ~[experiment-23.11.11.jar:?]
        at org.labkey.api.audit.AbstractAuditTypeProvider.ensureProperties(AbstractAuditTypeProvider.java:252) ~[api-23.11.11.jar:?]
        at org.labkey.api.audit.AbstractAuditTypeProvider.initializeProvider(AbstractAuditTypeProvider.java:149) ~[api-23.11.11.jar:?]
        at org.labkey.api.audit.AbstractAuditTypeProvider.<init>(AbstractAuditTypeProvider.java:109) ~[api-23.11.11.jar:?]
        at org.labkey.experiment.samples.SampleTimelineAuditProvider.<init>(SampleTimelineAuditProvider.java:58) ~[experiment-23.11.11.jar:?]
        at org.labkey.experiment.ExperimentModule.startupAfterSpringConfig(ExperimentModule.java:509) ~[experiment-23.11.11.jar:?]
        at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:122) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:229) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1668) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.ModuleLoader.initiateModuleStartup(ModuleLoader.java:1607) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.ModuleLoader.afterUpgrade(ModuleLoader.java:1824) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.ModuleLoader.lambda$startNonCoreUpgradeAndStartup$13(ModuleLoader.java:1803) ~[api-23.11.11.jar:?]
        at org.labkey.api.module.ModuleUpgrader.lambda$upgrade$0(ModuleUpgrader.java:111) ~[api-23.11.11.jar:?]
        at java.base/java.lang.Thread.run(Unknown Source) [?:?]
INFO  ContextListener          2024-05-28T14:04:06,587 gApplicationShutdownHook : Calling DefaultFileWatcher shutdownPre()
INFO  FileSystemWatcherImpl    2024-05-28T14:04:06,588       DefaultFileWatcher : FileSystemWatcherThread is terminating
INFO  ContextListener          2024-05-28T14:04:06,588 gApplicationShutdownHook : Calling PollingFileWatcher shutdownPre()
INFO  FileSystemWatcherImpl    2024-05-28T14:04:06,589       PollingFileWatcher : FileSystemWatcherThread is terminating

Anyone seen anything like this or have any advice?
(Full log attached)

Thanks,
Will

I have run into a problem with examining data in time-based plots (version 21.7). I can view individual participant data appropriately and even all individuals' data on the same plot, but as soon as I try to display the data (as means with error bars) summarised according to my allocated groups (via Chart Layout tab), the system freezes - just says "loading..." which never ends.

Is this a bug please?

Thank you.

Hey,

I've been trying (and successfully managed before) to set a lookup in a sample table to point to a query.

I've set my "group_id" column in my query as the key field:

   <column columnName="group_id">
    <isKeyField>true</isKeyField>
  </column>

And then gone to my sample table and made my lookup field and successfully chosen my query as the target table and pressed save.

However, it just hangs when I try and add a row and when I go back in to the table design it tells me that my query table doesn't exist:
Current Folder > samples > mixcr_output_paired_metadata_grouped . Error: Lookup target table does not exist.

I'm not sure where it's going wrong. Any ideas?

Best,

Katy

hello, recently updated to Labkey 24.3 also updated the Rlabkey package (version: 3.2.1) to work with new release.

I can pull data (apiKey|selectRows) into RStudio from labkey server without issue but writing to the server is where issues arise. Trying to insert rows (insertRows|importRows) from R Studio and getting the a 401 error. Have done this in previous releases of labkey (pre-tomcat embed) with no issue.

CONTENTS of ERROR:
Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 401, Error message = This request has an invalid security context. You may have signed in or signed out of this session. Try again by using the 'back' and 'refresh' button in your browser.

Hi LabKey,

I have a list that contains columns "Created By" and "Modified By", and I am trying to figure out how to access more of the data stored in those columns via your python API.

• On the website, those columns contain a user's Display Name as a clickable link, which goes to a little summary page of the user.
• When I use the "Export" button online to export the sheet to an excel workbook, the Created By and Modified By columns contain just the display names of users (no link or other data). I'm attaching a screenshot of the export button I'm referring to.
• When I use the code below to access the data via your python API, those columns are labelled "CreatedBy" and "ModifiedBy", and contain user ids.

my_results = api.query.select_rows(
    schema_name='lists',
    query_name='HVTN SDMC Lab/Assay Data Status Tracker',
    view_name='Full Export'
)

Is there a way to use access the Display Names associated with those user ids via the python API?

Thanks so much!

Beatrix

Hello LabKey support team,

I was running LabKey community edition version 21.11.4 and associated DB in postgres 14. Now I would like to migrate the instance to Version Number: 23.11.11 community edition.
I did the dump of the database and loaded it to the new database without issues but when I started the server, LabKey ended up with a couple of internal errors. Most of them are related to the foreign key mismatches. Is there a way to upgrade the schemas from previous versions? If you would like to have the complete error message I am happy to provide that as well. 
Regards,
Vipin

We are reaching out to inform LabKey Server users about a critical security update that was released on Monday, April 8. This update addresses several issues, including a vulnerability affecting LabKey Servers operating in Development mode.

Development mode provides enhanced logging and troubleshooting features to help identify and solve developer coding issues. While a Production server should never run in Development mode, some Staging, Test, and Development servers are configured to run in this manner. Follow these steps to check if a server is in Development or Production mode.

We recommend upgrading your LabKey Server instances to one of the updated releases (links below). If you have servers running in Development mode, this upgrade should happen immediately:

• 23.11.11
• 24.3.2

Similarly, for local development instances, it is recommended to pull the latest changes from LabKey’s Github repository to incorporate these critical updates.

LabKey TeamCity CI/CD server will be down for maintenance beginning at approximately 11am PDT. We expect the outage to last for approximately 1 hour.

Hello,

I am trying to pull data from the table "HVTN SDMC Lab/Assay Data Status Tracker" using the labkey python API. The table is located at:
https://atlas.scharp.org/cpas/list/HVTN/Tools and Reports/SCHARP LDO/Assay Tracker/grid.view?listId=24

I have version 3.0.0 of the labkey package installed, and I have tried various combinations of variables which throw different errors. For example:

labkey_server = "atlas.scharp.org"
project_name = "HVTN"  # Project folder name
context_path = "cpas"
api = APIWrapper(labkey_server, project_name, context_path, use_ssl=True)

schema = "lists"
table =  "HVTN SDMC Lab/Assay Data Status Tracker"
result = api.query.select_rows(schema, table)

returns the error QueryNotFoundError: "404: The specified query 'HVTN SDMC Lab/Assay Data Status Tracker' does not exist in schema 'lists'" (full traceback attached).

When viewing the page on my browser (I'm using Chrome), the header says:
Lists / HVTN SDMC Lab/Assay Data Status Tracker
HVTN SDMC Lab/Assay Data Status Tracker [folder image] Assay Tracker
(see attached screenshot).

So I have also tried

labkey_server = "atlas.scharp.org"
project_name = "Assay Tracker"  # Project folder name
context_path = "cpas"
api = APIWrapper(labkey_server, project_name, context_path, use_ssl=True)

schema = "lists"
table =  "HVTN SDMC Lab/Assay Data Status Tracker"
result = api.query.select_rows(schema, table)

But then I get QueryNotFoundError: '404: No such project: /Assay Tracker'.

Going through https://github.com/LabKey/labkey-api-python I couldn't find any utilities that would list projects or tables within a schema -- is there such a method available? I'm sorry I know this is more of a question about the structure of the database I'm trying to access, but I can't figure out how to figure out that structure and thus the appropriate method arguments. Can you advise?

Thank you so much!
Beatrix

LabKey TeamCity CI/CD server will be down for maintenance beginning at approximately 10:30am PDT. We expect the outage to last for approximately 2 hours.

LabKey TeamCity CI/CD server will be down for emergency maintenance beginning at 9am PDT. We expect the outage to last for approximately 30 mins. We apologize for the short notice.

Hi,

I'm trying to remove the name field from the deriving samples forms becasue my users will fill any available field and ruin my automated naming. I've worked out how to remove it from input forms through "edit metadata" and advanced setting, but I can't work out how/if I can remover it from here as well.

Any ideas?

This is LabKey community and we're on version 23.11.5 as of today!

Best,

Katy

Hi,

I've set up a series of tables in LabKey community where I am the site admin but other users are project and folder administrator. I am able to see the associated name of the user in the created by column however the other project/folder administrator is only able to see the key of the user (screenshot attached). Are there any permissions that I can give that aren't full system admin giving the ability to see the user names instead of the key?

I've tried giving her "See user and group details" permissions site wide but it didn't help.

Thanks,

Katy

Teamcity was down this morning from 7:45 AM to 8:30 AM PDT due to unscheduled critical software updates.

We prefer to schedule these types of updates when possible, however given the urgency of the required updates, we elected to perform the maintenance as soon as possible.

We apologize for any inconvenience this may have caused.

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Rlabkey_3.1.0

I got an error message (see below) using the executeSql function in Rlabkey.

test<-labkey.executeSql(
+     baseUrl="http://localhost:8080/labkey", 
+     folderPath = "/DEMO",
+     colNameOpt = "rname",
+     schemaName = "lists",
+     sql="SELECT * from Test")

Error in handleError(response, haltOnError) :
HTTP request was unsuccessful. Status code = 500, Error message = Error on line 1: Syntax error near 'U0VMRUNUJTIwKiUyMGZyb20lMjBUZXN...'

If I use the selectRows function I have the correct result:

> labkey.selectRows(
+     baseUrl="http://localhost:8080/labkey",
+     folderPath="/DEMO",
+     schemaName="lists",
+     queryName="Test")
  Patient ID GENDER Date
1       1022   Male      2016-08-08
2       1030   Male      2016-11-25
> 

I have checked all the logs and server configuration and I don't understand why the function executeSql does not work.

Thank you for your feedback.

Hi.
I have used Rlabkey to create lists and manipulate data on those lists. However, now I need to create assays.
labkey.create.domain() which I have used to create lists, accepts the folowing domain types and assays are not an option:

• "IntList": A list with an integer key field
• "VarList": A list with a string key field
• "StudyDatasetVisit": A dataset in a visit based study
• "StudyDatasetDate": A dataset in a date based study
• "IssueDefinition": An issue list domain
• "SampleSet": Sample set
• "DataClass": Data class

Can you please guide me through creating an assay using an R script?

Thank you.

I am trying to use make a custom entry form for a list similar to orderReagents form but use a value passed in the url to pre-poluate the form and i have tried to use LABKEY.ActionURL.getParameter(parameterName:param) but it doesn't seem to pick the param value from the URL . Is there a specific way to build the URL to pass the param value to a wiki page different then for a query ?

Hi. Our previous system administrator had configured Labkey using: Oracle JDK 1.8.0_181-b13, Apache Tomcat 8 and Labkey 18.2, postgresql 9.5.
Now I am sked to recreate the whole configuration, preferably with newer versions. I am on Ubuntu 22.04.3 LTS (Jammy) . I am using Labkey 23.7.4-7, Apache Tomcat 9 and OpenJDK17U and postgresql 15.5.
I followed the installation instructions and managed to successfully see the start up window for Labkey. at this point I am using an empty "labkey" database. I then proceeded to back up the previous database and files.
I backed up "Files" from /usr/local/labkey/files and put it in the same directory in the new configuration.
I furthermore, backed up and restored the old database in the empty "labkey" database.

However, now I get this error (I have attached screenshots of the whole log):

• HTTP Status 500 – Internal Server Error
• org.labkey.api.util.ConfigurationException: Error running scripts in module Core
• org.postgresql.util.PSQLException: ERROR: cannot drop view core.activeusers because other objects depend on it
  Detail: view core.contacts depends on view core.activeusers
  Hint: Use DROP ... CASCADE to drop the dependent objects too.
  Where: SQL statement "DROP VIEW core.activeusers"

can you please help me with that?

Hello there,

Please review the attached document and assist with the solution. thank you,

Zafar Olimov
zolimov@immunetolerance.org

Software Test Engineer II | Data Collaboration Team
Immune Tolerance Network | Benaroya Research Institute @ Virginia Mason
1201 Ninth Avenue | Seattle, WA 98101

Hello,

I want to try to generate deployable software from source code.
I have installed the development environment (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine). It includes:
1.Window Server 2019 Standard
2.jdk_x64_17.0.9_9
3.apache-tomcat-9.0.83
4.postgresql-15.5-1
5.Labkey server-23.12.RC0/platform-23.12.RC0
6.IntelliJ IDEA 2023.2.5 (Community Edition)
Version number: IC-232.10227.8, built on November 9, 2023
Runtime version: 17.0.9+7-b1000.46 amd64
Virtual Machine OpenJDK 64-bit server VM: JetBrains s.r.o.

My first build took a long time but failed. I followed the error message and build again with stacktrace and still got the error message as attached.

Thanks,
Bika

ETL status is stuck to 'running' and can't reset or truncate reset - it said the job is 'pending' and can't be reset. How do I get the ETL to re-run ?

I have just installed the latest Labkey version (LabKey23.11.1-2-community).

Everything is running fine so far. The only exception: when I apply changes under Site > Admin Console > Site Settings and click save, I get an error message (see below)

Can you give me advice on what is wrong?
KR, Oliver

Error Message: „Upps
Oops! An error has occurred.
Name is null
Please report this bug to LabKey Support by copying and pasting both your unique reference code and the full stack trace in the View Details section below.
Your unique reference code is: Z5C82Q

View Details:
java.lang.NullPointerException: Name is null
java.base/java.lang.Enum.valueOf(Enum.java:271)
org.labkey.api.util.UsageReportingLevel.valueOf(UsageReportingLevel.java:53)
org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1220)
org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1140)
org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:96)
org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:75)
org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:195)
org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:510)
org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1128)
org.labkey.api.view.ViewServlet._service(ViewServlet.java:240)
org.labkey.api.view.ViewServlet.service(ViewServlet.java:159)
javax.servlet.http.HttpServlet.service(HttpServlet.java:623)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:43)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1470)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:235)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:120)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168)
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:481)
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:670)
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:390)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:928)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1794)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.base/java.lang.Thread.run(Thread.java:840)

Hello,

I installed OpenJDK17U-jdk_x64_linux_hotspot_17.0.9_9 and apache-tomcat-9.0.82 and PostgreSQL-15 and LabKey23.3.12-15-community in ubuntu18.04.5. After installation running http ://localhost:8080/ works fine. HTTP Status 404 - Not Found appears when running http://localhost:8080/labkey. After diagnosing myself, I found that <CATALINA_HOME>/logs does not have labkey.log and labkey-errors.log.

Thanks,
Bika

What is the best way to truncate and re-populate a list using JavaScript. Can that be done without LABKEY.Query.executeSql ?

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

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.

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

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)

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.

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?

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.

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.

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

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>

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>

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

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 ?

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.

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

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

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.

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.

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.

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.

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

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.

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

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).

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?

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.

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

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).

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.

**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.**

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

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.

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.

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.

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.

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.

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

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.

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

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