**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.**

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.

Good afternoon,

I just wanted to know if there was a way to filter by row.. For example what we are trying to do is filter datasets to show rows that are not blank rather than applying a notnull filter to each field... But apply a global filter by row..

thanks.

Wayne H

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

Good morning,

We see in the javascript API reference methods for creating containers, user accounts and groups and adding members to the groups.. We are unclear on how we set permissions/security policy on the groups we create in order to define roles and permissions for users in the project. Can you point us in the right direction for this.. Our aim is to manage groups and users profiles and permissions programmatically.

Thanks,

WH

I imported some data to datasets via the assay module.. Wanting to produce a table describing the queries and fields in the schema but found that the datasetcolumns table in the study schema only shows fields created by the user not those created by the assay module.. Kinda odd..? Am I missing something? Don't want to ETL copy of data to another dataset for reporting..

Any thoughts?

Thanks,

Wayne

Hi,

We'd like to kick off a post-specimen import process that starts when labkey finishes a specimen import pipeline job. Does a feature like this exist in Labkey Server? I've looked through the UI and documentation, and didn't see anything, but wanted to double-check and make sure it doesn't exist.

Thanks!
-Tobin

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 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.

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.

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.

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.

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.

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.

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?

Hello

Our users have requested that we hide demographics data from all but a small set of admin users for our LabKey instance. To strike a balance between setting up this level of security and still being able to use datasets that refer back to the participantid in the Demographics table, we have created a separate AdminDemographics dataset to supplement the Demographics dataset. AdminDemographics contains PHI such as MRN, Names, Birth dates, etc and the Demographics dataset contains only the participant ID column. We keep these in sync with triggers.

We created the AdminDemographics dataset via:
CREATE TABLE LIKE studydataset.demographics INCLUDING ALL
We registered it with LabKey as a dataset with the additional key column field set to the _key column in the dataset, marked as system managed. When we rolled this out, however, LabKey had assigned the MRN column to this additional key and marked it as System Managed, see attached screenshot.

The impact of this was that MRN was not allowed to be set by users when adding new records, breaking the ability to add new patients to the system. We were able to correct this by manually resetting the additional key column back to none. I also noticed if I select the 'Demographic Data' check box the MRN is settable on insert.

My questions:

1. Why was MRN assigned to a system managed additional key column? Is 'MRN' some kind of reserved column name that gets auto assigned? The _key column exists distinct of the MRN column in the dataset.
2. Besides enforcing zero or 1 row per participant as described here, what impact does checking the 'Demographic Data' option have on the system? Apart from making MRN settable when adding new records we want to know what else is going on so we can test thoroughly.

EDIT: I attached csv files for the admindemographics entries in the study.dataset and exp.domaindescriptor tables in case that is helpful

Thanks!

Sev

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

Hello,

In case i am doing a survey design with a card layout. Is it possible to hide section based on an answer to a question in a different section?

Thank you in advance!

Hello support, our Labkey server is situated in France with CET time zone (Central Europe Time). We encounter a persistent CEST (Central Europe Summer Time) exception on date fields each time we try to import datasets in a Study type folder (time and participant are mandatory fields). Even the simple and structured excel files David Hansons uses for his demos produce the same error : “couldn’t convert date field, should be of type timestamp” while the field is already of type timestamp. The result is the same on both V18.3 and V20.3 (pre prod) Labkey installs. Please find attached, the Look and feel setting with the default date format to which I added a "z" to force the system date; the CEST error message, an example of an Excel file generating the exception. Only the “Demographics” file doesn't generate the error eventhough the date is in the same format. I assume there’s no such control on date field in demographics files. I deleted in Study the default CEST date format in case this caused the error but the result is the same. This very first step error prevents us to go further on our Labkey investigation tests.
Thanks in advance for your time.

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)

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've been following the documentation for setting up a developer machine (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine) but I ran into issues in the "Build LabKey" section.

When running the command "gradlew deployApp" the build fails immediately after the "Task :server:stageModules" starts. (stacktrace pasted below)

The only other inconsistency I found in the guide was in the "Configure the LabKey Project in IntelliJ" section when it asks to edit the configurations there is no modules named "api_main" or "org.labkey-api_main", so I continued with "api" instead.

Other configuration information:
apache-tomcat-9.0.30
jdk-13.0.2 (OpenJDK)
When running the gradlew command I see that it's using Gradle 6.0
SVN revision 65036

Stacktrace from error (using --stacktrace flag)

Task :server:stageModules FAILED

FAILURE: Build failed with an exception.

• What went wrong:
  Execution failed for task ':server:stageModules'.

Specify at least one source--a file or a resource collection.

• Try:
  Run with --info or --debug option to get more log output. Run with --scan to get full insights.

• Exception is:
  org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':server:stageModules'.
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.lambda$executeIfValid$1(ExecuteActionsTaskExecuter.java:187)
  at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:263)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:185)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:166)
  at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:109)
  at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
  at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:62)
  at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
  at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:56)
  at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)
  at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)
  at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)
  at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:416)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:406)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:102)
  at org.gradle.internal.operations.DelegatingBuildOperationExecutor.call(DelegatingBuildOperationExecutor.java:36)
  at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
  at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:41)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:374)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:361)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:354)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:340)
  at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.lambda$run$0(DefaultPlanExecutor.java:127)
  at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:191)
  at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:182)
  at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:124)
  at org.gradle.execution.plan.DefaultPlanExecutor.process(DefaultPlanExecutor.java:72)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph.executeWithServices(DefaultTaskExecutionGraph.java:191)
  at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph.execute(DefaultTaskExecutionGraph.java:168)
  at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:41)
  at org.gradle.execution.DefaultBuildWorkExecutor.execute(DefaultBuildWorkExecutor.java:40)
  at org.gradle.execution.DefaultBuildWorkExecutor.access$000(DefaultBuildWorkExecutor.java:24)
  at org.gradle.execution.DefaultBuildWorkExecutor$1.proceed(DefaultBuildWorkExecutor.java:48)
  at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:49)
  at org.gradle.execution.DefaultBuildWorkExecutor.execute(DefaultBuildWorkExecutor.java:40)
  at org.gradle.execution.DefaultBuildWorkExecutor.execute(DefaultBuildWorkExecutor.java:33)
  at org.gradle.execution.IncludedBuildLifecycleBuildWorkExecutor.execute(IncludedBuildLifecycleBuildWorkExecutor.java:36)
  at org.gradle.execution.DeprecateUndefinedBuildWorkExecutor.execute(DeprecateUndefinedBuildWorkExecutor.java:39)
  at org.gradle.execution.BuildOperationFiringBuildWorkerExecutor$ExecuteTasks.run(BuildOperationFiringBuildWorkerExecutor.java:56)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:402)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:394)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:92)
  at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
  at org.gradle.execution.BuildOperationFiringBuildWorkerExecutor.execute(BuildOperationFiringBuildWorkerExecutor.java:41)
  at org.gradle.initialization.DefaultGradleLauncher.runWork(DefaultGradleLauncher.java:241)
  at org.gradle.initialization.DefaultGradleLauncher.doClassicBuildStages(DefaultGradleLauncher.java:151)
  at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:130)
  at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:110)
  at org.gradle.internal.invocation.GradleBuildController$1.execute(GradleBuildController.java:60)
  at org.gradle.internal.invocation.GradleBuildController$1.execute(GradleBuildController.java:57)
  at org.gradle.internal.invocation.GradleBuildController$3.create(GradleBuildController.java:85)
  at org.gradle.internal.invocation.GradleBuildController$3.create(GradleBuildController.java:78)
  at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:189)
  at org.gradle.internal.work.StopShieldingWorkerLeaseService.withLocks(StopShieldingWorkerLeaseService.java:40)
  at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:78)
  at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:57)
  at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:31)
  at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
  at org.gradle.launcher.exec.BuildOutcomeReportingBuildActionRunner.run(BuildOutcomeReportingBuildActionRunner.java:63)
  at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
  at org.gradle.launcher.exec.BuildCompletionNotifyingBuildActionRunner.run(BuildCompletionNotifyingBuildActionRunner.java:39)
  at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$3.call(RunAsBuildOperationBuildActionRunner.java:51)
  at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$3.call(RunAsBuildOperationBuildActionRunner.java:45)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:416)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:406)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:102)
  at org.gradle.internal.operations.DelegatingBuildOperationExecutor.call(DelegatingBuildOperationExecutor.java:36)
  at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:45)
  at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:50)
  at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:47)
  at org.gradle.composite.internal.DefaultRootBuildState.run(DefaultRootBuildState.java:78)
  at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:47)
  at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:31)
  at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:42)
  at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:28)
  at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:78)
  at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:52)
  at org.gradle.tooling.internal.provider.SubscribableBuildActionExecuter.execute(SubscribableBuildActionExecuter.java:59)
  at org.gradle.tooling.internal.provider.SubscribableBuildActionExecuter.execute(SubscribableBuildActionExecuter.java:36)
  at org.gradle.tooling.internal.provider.SessionScopeBuildActionExecuter.execute(SessionScopeBuildActionExecuter.java:68)
  at org.gradle.tooling.internal.provider.SessionScopeBuildActionExecuter.execute(SessionScopeBuildActionExecuter.java:38)
  at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:37)
  at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:26)
  at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
  at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
  at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:60)
  at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:32)
  at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
  at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:41)
  at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:48)
  at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:32)
  at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:68)
  at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:39)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:27)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:35)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.create(ForwardClientInput.java:78)
  at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.create(ForwardClientInput.java:75)
  at org.gradle.util.Swapper.swap(Swapper.java:38)
  at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:75)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:63)
  at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:82)
  at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:37)
  at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
  at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:52)
  at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
  at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
  at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
  at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
  Caused by: : Specify at least one source--a file or a resource collection.
  at org.apache.tools.ant.taskdefs.Copy.validateAttributes(Copy.java:678)
  at org.apache.tools.ant.taskdefs.Copy.execute(Copy.java:450)
  at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
  at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:99)
  at org.gradle.api.internal.project.ant.BasicAntBuilder.nodeCompleted(BasicAntBuilder.java:80)
  at org.gradle.api.internal.project.ant.BasicAntBuilder.doInvokeMethod(BasicAntBuilder.java:107)
  at org.labkey.gradle.plugin.ServerDeploy$_addTasks_closure2$_closure23.doCall(ServerDeploy.groovy:85)
  at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:664)
  at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:637)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.run(ExecuteActionsTaskExecuter.java:539)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:402)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:394)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
  at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:92)
  at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:524)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:507)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.access$300(ExecuteActionsTaskExecuter.java:109)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.executeWithPreviousOutputFiles(ExecuteActionsTaskExecuter.java:258)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.execute(ExecuteActionsTaskExecuter.java:247)
  at org.gradle.internal.execution.steps.ExecuteStep.lambda$execute$1(ExecuteStep.java:33)
  at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:33)
  at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:26)
  at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:63)
  at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:35)
  at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:49)
  at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:34)
  at org.gradle.internal.execution.steps.CancelExecutionStep.execute(CancelExecutionStep.java:43)
  at org.gradle.internal.execution.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:73)
  at org.gradle.internal.execution.steps.TimeoutStep.execute(TimeoutStep.java:54)
  at org.gradle.internal.execution.steps.CatchExceptionStep.execute(CatchExceptionStep.java:34)
  at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:44)
  at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:54)
  at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:38)
  at org.gradle.internal.execution.steps.CacheStep.executeWithoutCache(CacheStep.java:153)
  at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:67)
  at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:41)
  at org.gradle.internal.execution.steps.BroadcastChangingOutputsStep.execute(BroadcastChangingOutputsStep.java:49)
  at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:44)
  at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:33)
  at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:38)
  at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:24)
  at org.gradle.internal.execution.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:92)
  at org.gradle.internal.execution.steps.SkipUpToDateStep.lambda$execute$0(SkipUpToDateStep.java:85)
  at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:55)
  at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:39)
  at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:76)
  at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:37)
  at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:36)
  at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:26)
  at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:94)
  at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:49)
  at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:79)
  at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:53)
  at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:74)
  at org.gradle.internal.execution.steps.SkipEmptyWorkStep.lambda$execute$2(SkipEmptyWorkStep.java:78)
  at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:78)
  at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:34)
  at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsStartedStep.execute(MarkSnapshottingInputsStartedStep.java:39)
  at org.gradle.internal.execution.steps.LoadExecutionStateStep.execute(LoadExecutionStateStep.java:40)
  at org.gradle.internal.execution.steps.LoadExecutionStateStep.execute(LoadExecutionStateStep.java:28)
  at org.gradle.internal.execution.impl.DefaultWorkExecutor.execute(DefaultWorkExecutor.java:33)
  at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:174)
  ... 125 more

• Get more help at https://help.gradle.org

Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0.
Use '--warning-mode all' to show the individual deprecation warnings.
See https://docs.gradle.org/6.0/userguide/command_line_interface.html#sec:command_line_warnings

BUILD FAILED in 2s
5 actionable tasks: 1 executed, 4 up-to-date

> 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.

After a manual upgrade to Labkey Server 20.3, when trying to access the admin console I receive the following error message:

An unexpected error occurred. If contacting support regarding this error, please refer to error code: VUNKPZ
java.lang.NoSuchFieldError: labkeyVersion

Any ideas what might went wrong?

Hi,

I would like to ask you if in the Audit Log, we can see what records/variables were added/updated/deleted?

I need to have this very fine granularity.

Thanks,
Marcia

Hello,

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

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

library(Rlabkey)

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

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

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

Thanks and regards

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

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

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

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

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

Error:

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

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

Thanks for any help.

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 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

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

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

Hello, I am trying to set up Labkey as our labs database. Some of the projects include expression matrix data but the assay format is not as I expected. If I understand correctly in the Samples Type the columns are the samples so it is not an annotation file for samples, and the Assay List is the expression matrix but in a list format and not a matrix. Is there a different way to do it? For now I uploaded the data to a subfolder defined as study, but the genes annotations can't be integrated with the data.
Thanks for any advice,
Karen

Hello,

I imported a new specimens archive and it said it was completed. However, the specimens are not populating in the Specimens Data tab. I noticed when I was importing the archive, there was not an option for "Replace" or "Merge" as the documentation suggested there would be. But I wasn't sure if that was because this was the first archive import for the study so therefore it's not necessary to replace or merge anything.

Is there an additional step after the import that needs to happen for the specimens to populate?

Thank you for your assistance!

LDAP Authentication for Linux - Community Version joseph mackey EDIT 2020-02-21 14:36
Status: Active

Hello,
I have installed Labkey 19.3 Community Version.
While I have a connection string that works from the test screen, I cannot configure it in the LDAP Auth Settings.
I have configured other applications for AD authentication and works when using the sAMAccountName and the full DN (so does the test)
Even when adding the configuration to the labkey.xml file, does not seem to make a difference.

Is there a way to enable verbose logging for LDAP auth attempts?
When adding DN to the LDAP principle template, is there a way to substitute sAMAccountName instead of email or UID?
When using My full DN I am able to log in with my email and AD password but i'm the only user able to login with AD credentials.
Build info:
OS RedHat Enterprise Linux 7.7
Product Name PostgreSQL
Product Version 12.1
JDBC Driver Name PostgreSQL JDBC Driver
JDBC Driver Version 42.2.8
Servlet Container Apache Tomcat/9.0.30
Java Runtime Vendor N/A
Java Runtime Name OpenJDK Runtime Environment
Java Runtime Version 13.0.2+8

chetc (LabKey Support) responded: 2020-03-06 10:55
Hello,

Yes there is. There is no need to enable anything since this is already happening. The labkey.log file should indicate a LDAP login failure and so should the AuditLog found in the admin console.

You should be able to sub for anything. The principal template is used to search through the LDAP global directory and reassociate one value for another.

You can find more information about LDAP Configuration on our Documentation site.
https://www.labkey.org/Documentation/wiki-page.view?name=configLdap

Thanks,
Chet

chetc (LabKey Support) responded: 2020-03-06 10:55
Hello,

We appreciate you utilizing our forums!

However this forum will become inactive very soon. To follow up on this question or to ask new question please use our new forum.

LabKey Support Forum - https://www.labkey.org/home/Support/LabKey Support Forum/project-begin.view?

Thanks,
Chet

Hello,

I get the following error when trying to run an R Report:

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

My script is the following:

knitr::opts_chunk$set(echo=FALSE, cache=FALSE, comment=FALSE, comments = "", warning=FALSE, eval = TRUE, encoding = "native.enc")
#knitr::opts_chunk$get();
knitr::pandoc('script.Rmd', format='html')

currentdir <- getwd()
assign("html_filename", paste(currentdir, "/script.html", sep=""))
assign("out_filename", paste("/nip/NRG_Samples/@files/Reports/GenotypingResults_CNR1rs2023239_DRD3rs6280/Report_GenotypingResults_CNR1rs2023239_DRD3rs6280_", format(Sys.time(), "%Y-%m-%d_%H:%M:%S"), ".html", sep=""))

#list.files(path = ".", pattern = NULL, all.files = FALSE,
#           full.names = FALSE, recursive = FALSE,
#           ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)

file.copy(from = html_filename, to = out_filename)

system("rm script.* *.tsv")
#system("rm cache/*.*")
#list.files(path = ".", pattern = NULL, all.files = FALSE,
#           full.names = FALSE, recursive = FALSE,
#           ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)

<html>...</html>

I look forward to your suggestions.

Thanks,
Marcia

Hello

We would like to give users an informational message following a dataset row insert that meets certain criteria. We have trigger scripts setup to check the criteria but it seems the only way to provide messages to the user is via the errors object, which would cancel the insert.

Is there a way we can set a message after an insert into a dataset that wont result in the transaction being cancelled?

Thanks

Sev

This issue happens sometimes with different values, and I don't understand why this happens:

I have a custom table created via ETL. It has a column that references a lookup table.

When I put legitimate data into this column, I get the following error:

SqlExecutor.execute(); SQL []; ERROR: insert or update on table "samples_samplesnotreceived" violates foreign key constraint "fk_samsamnotrecdiagnosis1"
Detail: Key (diagnosis1)=(Hallucinogen Persisting Perception Disorder) is not present in table "diagnosis".; nested exception is org.postgresql.util.PSQLException: ERROR: insert or update on table "samples_samplesnotreceived" violates foreign key constraint "fk_samsamnotrecdiagnosis1"
Detail: Key (diagnosis1)=(Hallucinogen Persisting Perception Disorder) is not present in table "diagnosis".

"Hallucinogen Persisting Perception Disorder" is indeed in the "diagnosis" table but it is unable to recognize it.

Please let me know how to correct this.

Thanks,
Marcia

Hi,

I am uploading specimen archive to labkey where it has values for forzen_time specified in the tsv file. However, in the grid view labkey does not show the frozen_time column. Also the column is not visible when I modify the grid view and so I cannot include it. At the backend, the column is present in the database and has values added in it. Is this a bug?? or am I missing something?

Also, is it possible to add user-defined fields to the specimen event? I added (for example) a field "frozen_date" to the specimen event and it is reflected in the database but the grid view does not show me this new field.

At Admin > Site > Admin Console,

I'm trying to delete a custom module/schema.

I go to the screen that has the following and click "OK":

"
Are you sure you want to remove the "genotype_etl" module and delete all data in the "genotype_etl" schema? This operation may render the server unusable and cannot be undone!

Deleting modules on a running server could leave it in an unpredictable state; be sure to restart your server.
"

Unfortunately, it runs for a long time and times out. The module is not removed and the schema is not deleted.

Please let me know how to fix this.

Thanks,
Marcia

Hello,

I have created a table via module-etl.

Is there a way to force the table to not allow records to be deleted?

Thanks,
Marcia

Hello,

Is it possible to create queries whose values are editable?

Thanks,
Marcia

Hi,
think there is a bug in v.20.3.0, in the MS2runs view RunSummary - the modifications link shows html code rather than a pop-up with list of modifications. See attached screenshot.

Tomas

Later this month, we will be migrating from our long-standing Subversion server, hedgehog.fhcrc.org, to a brand new server.

For automated systems like TeamCity, our automated build and test system, we will be doing a phased migration. We will start synchronizing the new server with the existing server, in a read-only capacity, that lets systems pull from it.

A little later, we will make the new server the system of record, and flip the original server to be a read-only system until it is completely retired. We will be migrating all branches, and retain the full source code history.

Stay tuned for more information, including target dates and instructions for how to migrate any existing enlistments you may have locally. We expect this should be a fairly painless operation for developers.

Thanks,
Josh

Hello,

I have different users who use different parts of a project.

Now, there are around 6 data transformations.

I would like to refine this so that a certain individual will only see 1 data transform.

Is this possible?

Thanks,
Marcia

As the title says, I want to get a hierarchical list of all folders.

This is what I've tried:

// Taking a stab in the dark here with the 'core' schema and 'Containers' query. 
SelectRowsCommand cmd = new SelectRowsCommand("core", "Containers");

// null for root. I was hoping this would return something useful, but as far as I can tell, it doesn't. 
SelectRowsResponse resp = cmd.execute(cn, null);

Thanks.

I would like to trigger pipeline jobs on a 19.3 server via Java client API. Therefore, I included the labkey-client-api-1.0.1-SNAPSHOT-all.jar in the project and wrote this code:

String user = "username";
String password = "password";
BasicAuthCredentialsProvider cp = new BasicAuthCredentialsProvider(user,password);
Connection cn = new Connection("http://localhost:8080/",cp);
FileNotificationCommand cmd = new FileNotificationCommand();
FileNotificationResponse response = cmd.execute(cn, "dummy collaboration/dummy study");

The server response is a 405 with the message: "You must use the POST method when calling this action." The _httpClientContext property of the Connection object shows that a GET request has been send.

How can I configure to send a POST request?

As previously announced, in the upcoming 18.3 release of LabKey Server, the DataIntegration (ETL) module will be a premium feature to support LabKey continued investment in its development. To support this, effective with SVN trunk commit r60372, the module has been moved from LabKey’s SVN server into a private, LabKey-managed GitHub repository.

This will impact you if:

• You have a local development box
• You are pulling source code from the trunk in SVN, or will be pulling source code for 18.3 or subsequent releases
• And at least one of the following is true on your development machine:
  • You are writing ETL xml definitions in a module
  • You are running ETLs defined by any module
  • You are writing user defined ETLs in the application

If you will be affected by this change and have not already been contacted, or if you have any other questions or concerns, please contact your LabKey representative.

Thank you!

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

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

We plan on upgrading TeamCity to 2018.1 later this week.
In preparation, we may need to take it offline briefly over the next day or two. We will send out a warning an hour before any such outage. They should last no more than 15 minutes; in-progress builds will be unaffected and the server should pick up right where it left off once it comes back up.

The upgrade itself may take the better part of a day. This thread will be updated at least 24 hours before we start the upgrade process.

With r60757 in trunk, the schemas directory (<labkeyRoot>/schemas) has been moved into the api module (<labkeyRoot>/server/api/schemas). This consolidation makes for one less special part of the build, which should allow a bit of clean up in a later release of the gradle plugins.

To avoid having two jars for these XSDs if you are building from source, you will need to do some special cleaning. For those who prefer a ham-fisted approach, you can accomplish this with

   gradlew cleanBuild
   gradlew deployApp

and a little patience. (And if you're picking up this change along with the update of the Gradle Plugins version, which happened with r60731, you'll essentially be rebuilding everything anyway, so you might as well use this option.)

If you prefer a more delicate cleaning, you can do:

   rm -r build/modules/schemas/
   rm build/deploy/labkeyWebapp/WEB-INF/lib/schemas-18.3-SNAPSHOT-schemas.jar 
   gradlew deployApp

In either case, you'll want to follow this cleaning with a Gradle refresh in IntelliJ so it will pick up the new location of the XSDs in its build as well.

Thanks!

Susan

Hello,

Currently, when I have a new module, I end up restarting the whole LabKey application.

Is there a way for updating/adding modules without restarting the whole LabKey system?

Thanks,
Marcia

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

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

The estimated downtime is approximately seven hours.

We apologize for any inconvenience this may cause.

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

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

The Edit Dataset Properties for the Study folder allows one additional key column. How can we add more than one additional key column? I'm currently using Creating Multiple Dataset Definitions from a TSV File. Is it possible to specify additional keys in this definition file?

Hello,

How is this error created? How can I fix it?

An unexpected error occurred
ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist Position: 681

org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist
Position: 681
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:37)
at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:31)
at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:450)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:280)
at org.labkey.api.data.BaseSelector.getArrayList(BaseSelector.java:102)
at org.labkey.api.data.BaseSelector.getArrayList(BaseSelector.java:97)
at org.labkey.announcements.model.AnnouncementManager.getAnnouncements(AnnouncementManager.java:115)
at org.labkey.announcements.AnnouncementsController$AnnouncementWebPart$MessagesBean.<init>(AnnouncementsController.java:2316)
at org.labkey.announcements.AnnouncementsController$AnnouncementWebPart$MessagesBean.<init>(AnnouncementsController.java:2306)
at org.labkey.announcements.AnnouncementsController$AnnouncementWebPart.<init>(AnnouncementsController.java:2255)
at org.labkey.announcements.AnnouncementsController$AnnouncementWebPart.<init>(AnnouncementsController.java:2286)
at org.labkey.announcements.AnnouncementsController$AnnoucementWebPartFactory.getWebPartView(AnnouncementsController.java:2348)
at org.labkey.api.view.Portal.getWebPartViewSafe(Portal.java:1208)
at org.labkey.api.view.Portal.populatePortalView(Portal.java:995)
at org.labkey.api.view.Portal.populatePortalView(Portal.java:959)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:327)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:280)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:80)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:415)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1208)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:206)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:528)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1100)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:687)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1520)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1476)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist
Position: 681
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2453)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2153)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:286)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:432)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:358)
at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:171)
at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:119)
at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:82)
at org.apache.tomcat.dbcp.dbcp2.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:82)
at org.labkey.api.data.dialect.StatementWrapper.executeQuery(StatementWrapper.java:1157)
at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.executeQuery(SqlExecutingSelector.java:391)
at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.getResultSet(SqlExecutingSelector.java:331)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:261)
... 53 more
DialectSQL = SELECT *
FROM (
SELECT
Threads.RowId AS RowId,
Threads.EntityId AS EntityId,
Threads.CreatedBy AS CreatedBy,
Threads.Created AS Created,
Threads.ResponseCreatedBy AS ResponseCreatedBy,
Threads.ResponseCreated AS ResponseCreated,
Threads.AssignedTo AS AssignedTo,
Threads.Container AS Container,
Threads.Title AS Title,
Threads.Body AS Body,
Threads.RendererType AS RendererType,
Threads.Expires AS Expires,
Threads.Status AS Status,
Threads.LatestId AS LatestId,
Threads.discussionsrcidentifier AS discussionsrcidentifier,
Threads.discussionsrcurl AS discussionsrcurl,
Threads.ResponseCount AS ResponseCount,
Threads.Modified AS Modified,
Threads.LastIndexed AS LastIndexed
FROM comm."Threads" Threads ) x
WHERE (Container = ?)
ORDER BY Created DESC
LIMIT 101

...

Hello,

I created a custom Schema and corresponding custom tables.

How would I enable auditing of these tables? Is there some special commands in XML?

Thanks,
Marcia

Hello,

Currently we are using LabKey to connect to an external MSSQL data source. When the data source is connected, it gives the ability to view these tables via the built-in queries on the connected schema. However, I would like all of these views to be available for users of the project by default and not have to go in and manually create a Query Report based on each of the 100 or so queries.

Is there any way to insert these query report views into the labkey project programmatically?

Thanks,
Jonathan

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

Hello,

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

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

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

Thanks,
Ophir

Hello,

I created a custom schema and table in Labkey via ETL script.

Now, when I am at Labkey GUI and open this table, the option to "delete" is unavailable.

Please is there a way to allow for "delete".

Thanks,
Marcia

Dear LabKey,

We are running LabKey 18.2.
We have observed that it is not possible to set a boolean type field to default value "false" through the "Edit Design" menu.

To reproduce this bug:

• from a list click "Design"
• "Edit design"
• Select the "Boolean" type field and go the the "Advanced" tab
• In "Default Value" select "SET VALUE"
• Enable the checkbox for the boolean field and save
  As a result the default value for this boolean field will be set to "true", instead of "[none]", as expected.

But, if you want to have a default value "false", repeating the steps and setting it to "false" will not work, it will permanently stay to default value "true".

Thanks for your support,
Eva

On 12/2, you were inadvertently sent a message from LabKey Support with the subject "RE: Table view permissions." The default email setting for our support forum was set too broadly; we have corrected the problem. We sincerely apologize for the inconvenience.

With r58720 in trunk, the version of gradlePlugins has been updated to 1.3. As always, the full list of changes in this version are available in the README for the gradlePlugin repository. There are a couple of changes here that I wanted to call your attention to, one of which requires action from you for better success in building.

For the impatient, the summary is:

• The build process will now download and use particular versions of npm and node. To avoid conflicts with node module versions, you need to remove any existing node_modules directories in the LabKey modules' enlistment directories before doing a build with the 1.3 gradlePlugin version. (If using npm from the command line, you should also update your path to reference the downloaded versions.)
• Local builds will now fail if a conflict in version numbers is detected between two builds of a module (but you can change this behavior if you so desire).

Node and NPM

The build process will download the versions of npm and node that are specified by the properties npmVersion and nodeVersion, respectively, which are defined in the root-level gradle.properties file of the LabKey enlistment.

To avoid potential conflicts with node module versioning, you should remove any existing node_modules directories from your LabKey modules' directories before doing your first build with the 1.3 version. The 1.3 version of gradlePlugin provides a task, cleanNodeModules, that does just this. You can invoke this task at the root level of your enlistment and it will execute the task for all LabKey modules that have a package.json file. Alternatively, you can manually remove the node_module directory for each LabKey module that has one.

When running npm from the command line, you will want to be sure to use the version of npm that the gradle build uses. You can reference the versions for the core module in the <LABKEY_ROOT>/build/modules/core/.node/ directory.

On non-Windows platforms, the deployApp command creates symlinks for both node and npm in the directory .node at the root level of your enlistment:

trunk$ ls -la .node/
total 0
drwxr-xr-x   4 developer  staff   128 Jun 14 14:11 .
drwxr-xr-x  38 developer  staff  1216 Jun 18 10:36 ..
lrwxr-xr-x   1 developer  staff    90 Jun 14 14:11 node -> /Users/developer/Development/labkey/trunk/build/modules/core/.node/node-v8.11.3-darwin-x64
lrwxr-xr-x   1 developer  staff    77 Jun 14 13:58 npm -> /Users/developer/Development/labkey/trunk/build/modules/core/.node/npm-v5.6.0

If on Windows, you can create the symbolic links in the <LABKEY_ROOT>/.node directory manually to point to the node and npm versions in the core module's .node directory, as shown above. You should then put <LABKEY_ROOT>/.node/node/bin and <LABKEY_ROOT>/.node/npm/bin in your path.

If not using npm on the command line, the symbolic links and path changes are not necessary. (Note that the <LABKEY_ROOT>/.node directory won't exist until you run a deployApp command after updating to version 1.3.)

Local Build Version Discrepancies

With the 1.3 version, a feature that was incubating in the last release has now come out of incubation with a slight behavior change. You may have noticed if you did a build after someone updated a version of an external dependency that you would get a warning message something like this about version conflicts that would be produced by the build.

WARNING: Artifact versioning problem(s) in directory /Users/developer/Development/labkey/trunk/build/modules/api/explodedModule/lib:
  Conflicting version of commons-compress jar file (1.14 in directory vs. 1.16.1 from build).
  Conflicting version of objenesis jar file (1.0 in directory vs. 2.6 from build).

Now your build will fail if such version conflicts are detected (because the build would not be in a good state if both versions were included). If you need to, you can change that behavior by setting a value for the versionConflictAction parameter, as described in the Version Conflicts in Local Builds documentation.

Hello,

Hello,

We will be performing scheduled maintenance on LabKey's artifactory server ( https://artifactory.labkey.com/ ) on Monday 12/10 between 7AM and 10 AM.

This will affect build artifacts during this maintenance period.

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

We are performing this maintenance to install the latest security patches for Artifactory and its underlying operating system.

When impersonating a reader for my tables, I'm able to see data within the table. However, users within a group under reader permissions are not able to see data in the tables. How do I resolve this?

It appears that some of the LABKEY.QueryWebPart.standardButtons no longer work on v18.1.

<div id="ExampleDiv" />
<script>
new LABKEY.QueryWebPart({
        renderTo: 'ExampleDiv',
        schemaName: 'core',
        queryName: 'users',
        containerPath: '/',
        buttonBar: {
            items:[
              LABKEY.QueryWebPart.standardButtons.insertNew,
              LABKEY.QueryWebPart.standardButtons.pageSize
            ]
        },
 });
<script/>

Results in a message at the top of the grid, "WARNING: button bar configuration contains reference to buttons that don't exist. Invalid original text: insert new, paging."

-Will

I ran a static Code Analyzer on the Labkey code and found the following issues that may need reviewing:

========================================================================================

1. The String equals method is called with argument org.labkey.api.util.Path, not a String. The equals method will always return false.

2 examples, please note the getPath() method returns a org.labkey.api.util.Path, not a String.

Example 1

org.labkey.api.webdav.AbstractWebdavResource
				.......
				.......
  	  			public boolean canRead(User user, boolean forRead)
    				{
        			if ("/".equals(getPath()))

=====================================================================================
Example 2

			org.labkey.api.webdav.WebFilesResolverImpl
				.......
				.......
				 public boolean canRead(User user, boolean forRead)
				 {
         			 if ("/".equals(getPath()))

~========================================================================================

2. The org.labkey.api.util.Path equals method is called and passes a String, the org.labkey.api.util.Path.equals method will return false when the input Object is not org.labkey.api.util.Path,

File: ./server/modules/platform/core/src/org/labkey/core/webdav/DavController.java

	      public void writeProperties(WebdavResource resource, Find type, List<String> propertiesVector)

			......
			......
			.......

   	          String displayName = resource.getPath().equals("/") ? "/" : resource.getName();

========================================================================================

 		       public void writeProperties(WebdavResource resource, Find type, List<String> propertiesVector) throws Exception
        		{
            		json.object();
            		json.key("id").value(resource.getPath());
            		String displayName = resource.getPath().equals("/") ? "/" : resource.getName();

========================================================================================
~

3. The HashMap.get(Object) call passes in object ColumnInfo which is not the key defined for the HashMap. The HashMap key is a String.

     Map<String, Integer> outputMap = DataIteratorUtil.createColumnAndPropertyMap(it);       // String is the key to this HashMap

        ColumnInfo containerColumn = table.getColumn("container");
 

        Integer indexContainer = outputMap.get(containerColumn);       // containerColumn is not a String

=====================================================================================

~
4. NullPointerExceptions

variable raf will get NullPointerException

class: org.labkey.core.webdav.DavbController$PutAction

WebdavStatus doMethod() throws DavException, IOException, RedirectException {

....
.....
....

           RandomAccessFile raf = null;
            OutputStream os = null;

            try
            {
                if (!exists)
                {
                    temp = getTemporary();
                   if (temp)
                        markTempFile(resource);
                    deleteFileOnFail = true;
                }

                File file = resource.getFile();
                boolean isBrowserDev = getUser().isTrustedBrowserDev();
                if (range != null)
                {
                    if (resource.getContentType().startsWith("text/html") && !isBrowserDev)
                        throw new DavException(WebdavStatus.SC_FORBIDDEN, "Partial writing of html files is not allowed");
                    if (null != AntiVirusService.get())
                        throw new DavException(WebdavStatus.SC_FORBIDDEN, "Partial writing not supported with virus scanner enabled");
                    if (range.start > raf.length() || (range.end - range.start) > Integer.MAX_VALUE)

=====================================================================================

variable context will get NullPointerException

org.labkey.api.reports.report.ScriptReportDescriptor

   public ReportDescriptorDocument getDescriptorDocument(ImportContext context)
    {
        // if we are doing folder export (or module file save), we don't want to double save the script property
        if (null != context)
            return getDescriptorDocument(context.getContainer(), context, true, Set.of(Prop.script.name()));
        else
            return getDescriptorDocument(context.getContainer(), context, true, Collections.emptySet());
    }

=====================================================================================

5. To honor if statement, remove Semicolon at:

if (BACKGROUND_WELL_GROUP.equals(group.getName()));

class: org.labkey.elispot.ElispotPlateTypeHandler

    {
        Map<String, Map<String, Double>> backgroundMap = new HashMap<>();
        WellGroup backgroundGroup = null;

        for (WellGroup group : plate.getWellGroups(WellGroup.Type.CONTROL))
        {
            if (BACKGROUND_WELL_GROUP.equals(group.getName()));
            {
                backgroundGroup = group;
                break;
            }
        }

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

LabKey uses Selenium to drive our functional UI test automation. The LabKey test team has been migrating our test code to Selenium 3 over the past few months. This will, among other things, allow our tests to run tests against more current releases of Firefox and protect us from incompatibilities with new versions of Java.

We've fixed most of the major issues we've encountered and are close to the home stretch. We have been performing the migration in a separate branch and we will merge our changes back to trunk on Tuesday, December 11.

This update is almost exclusively to test code and the following steps are necessary only if you currently run UI tests locally against trunk with Firefox 45. Selenium tests running under Chrome should continue to work, though there may be new failures due to minor performance variation in the newer version of Selenium. JavaScript test frameworks such as Jest should be unaffected.

After the merge

• Install a current version of Firefox if you don't have it. We've been validating with 62.0.2 on TeamCity. Geckodriver claims to support 57+ but we hit some pretty significant issues with versions as late as 60. We generally recommend using the latest ESR release but there will not be a reliable (for testing) ESR release until next July.
• Make sure server/test/test.properties is up-to-date
  • selenium.firefox.binary should point at a new version of Firefox instead of ESR 45
  • Make sure webtest.webdriver.logging=false. You'll get an unreasonable amount of logging if that isn't set
  • Run a test and make sure it works for you. Nothing in-depth, just make sure it works.

Please bear with us as we iron out the last few kinks over the next couple of weeks. Let us know immediately if you have any concerns or if you have any difficulty after the merge.

Hello,

I have an assay: assay.general.nrg_assay .

How do I reference this assay in the transformation scripts?

In the ETL structure, where do I put this scirpt?

Is it supposed to be ../queries/assay/general/nrg_assay.sql?

Thanks,
Marcia

• We are using Javascript + SQL
• We are trying to check for duplicates (with a algorithm since we have paired data). Then we want add the data if certain columns changed data for a give ID (ID Column, not unique column)
••• We do not want to update the rows, if the row data changes we want to create a new row.

Here are the questions:
1.). Is there a way to use drop/create temp tables and then remove these temp tables?
• Here are the operations I would typically use: CREATE, INSERT, DELETE, DROP, RANK which are all unavailable since they are not read only.
2.) Is there a way to direct insert rows from one table/list to another without first downloading the data?
3.) Is there a way to delete all rows of a table in Javascript quickly? It takes me 29 seconds to delete 3000 rows using the deleteRows() javascript API

Here is the current process:
1.) I am selecting all keys from the temp table (pre-made as a list) and downloading them the script as a data object using labkey.query.selectRows(): <1 seconds (also can have a problem with multiple users accessing the temp table at the same time)
2.) Deleting all rows using labkey.query.deleteRows()
3. ) Inserting the new data as a labkey.query.importData() JSON row object (~3000 rows x 14 columns, 328kb as a text file)
4.) SQL Operation to find duplicates (Based on stored queries/views)
5.) Get new/unique rows and download to javascript
6.) Insert new rows

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

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

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

Then:

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

If you are developing with TypeScript:

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

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

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

Susan

Hello,

I have a dataset/assay/list table.

There are multiple rows.

I would like to change the value for one of the columns for all of the rows.

I know that I can do this on a row-by-row basis using "edit".

However, is it possible to do this at the same time for multiple rows?

Thanks,
Marcia

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.

Hello,

I have an ETL Stored Procedure that gets data from an Assay.

Now, I would like that once this data has been copied to another table, that the data is erased in the Assay.

How do I do this in the Stored Procedure?

Thanks,
Marcia

Hi All,

For 20.11 we have finished migrating our source code to git. Prior releases will remain in SVN and continue to be maintained based upon our Release and Upgrade policy. Changes and updates to to the source code for 20.11 and beyond will only be performed in git. If you are building from SVN trunk source please migrate at your earliest convenience.

Migration instructions:

For this example these instructions the original enlistment is in ./trunk/:

1. Clone the new repo's develop branch to a sibling directory of your current enlistment
   git clone https://github.com/LabKey/server labkeyServer
2. Then reenlist or copy over the server/modules directory to the corresponding new location
   cp -r trunk/server/modules labkeyServer/server/
3. Reenlist or Copy over any additional enlistments (./remoteapi/*, ./server/testAutomation, etc.)
4. Copy over any other changes -- specifically ./settings.gradle, ./server/configs/pg.properties, ./server/configs/mssql.properties, etc.
   cp trunk/server/configs/pg.properties labkeyServer/server/configs/pg.properties
5. cd into the new directory
6. execute ./gradlew cleanNodeModules from the new enlistment's root --- our initial testers ran into some conflicts and errors within these directories
7. execute ./gradlew pickPg or ./gradlew pickMSSQL
8. The new enlistment should then build as normal.
9. (optional) If you are using IntelliJ, you will need to update the various project settings as you would for any new enlistment. Copying over the .idea directory can retain these, but it may also carryover some project specific settings that don't apply in the new location.

Ian

Hello,

I have created an ETL module based on your tutorials. It works fine.

However, how do I add a "Data Transforms" web part? Is there some sort of configuration that I must do before?

Thanks,
Marcia