Hi All

After our upgrade to 19.3 we get the following error, please assist:

An unexpected error occurred. If contacting support regarding this error, please refer to error code: YGSHYY

java.lang.NoSuchMethodError: org.labkey.api.settings.HeaderProperties: method 'void <init>()' not found

java.lang.NoSuchMethodError: org.labkey.api.settings.HeaderProperties: method 'void <init>()' not found
at org.labkey.jsp.compiled.org.labkey.core.view.template.bootstrap.header_jsp._jspService(header_jsp.java:127)
at org.labkey.api.view.JspView.renderView(JspView.java:174)
at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:372)
at org.labkey.api.view.HttpView.render(HttpView.java:134)
at org.labkey.api.view.HttpView.render(HttpView.java:119)
at org.labkey.api.view.HttpView.include(HttpView.java:518)
at org.labkey.api.view.HttpView.include(HttpView.java:494)
at org.labkey.jsp.compiled.org.labkey.core.view.template.bootstrap.pageTemplate_jsp._jspService(pageTemplate_jsp.java:159)
at org.labkey.api.view.JspView.renderView(JspView.java:174)
at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:372)
at org.labkey.api.view.HttpView.render(HttpView.java:134)
at org.labkey.api.view.HttpView.render(HttpView.java:119)
at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:619)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:499)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1299)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:688)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:367)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1639)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:830)

request attributes
LABKEY.OriginalURL = http://localhost:8080/labkey/study/Tutorials/Importable%20Demo%20Study/dataset.view?datasetId=5008&QCState=6%2C5%2C4%2C-1
LABKEY.StartTime = 1582871778453
LABKEY.action = dataset
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Study WebApplicationContext: startup date [Thu Feb 27 15:24:41 SAST 2020]; parent: Root WebApplicationContext
LABKEY.controller = study
LABKEY.Counter = 1
X-LABKEY-CSRF = e1ebbc72ca6c5417996b76b7e0eb4942
LABKEY.container = /Tutorials/Importable Demo Study
LABKEY.RequestURL = /labkey/study/Tutorials/Importable%20Demo%20Study/dataset.view?datasetId=5008&QCState=6%2C5%2C4%2C-1
LABKEY.OriginalURLHelper = /labkey/study/Tutorials/Importable%20Demo%20Study/dataset.view?datasetId=5008&QCState=6%2C5%2C4%2C-1

core schema database configuration
Server URL jdbc:postgresql://localhost/labkey
Product Name PostgreSQL
Product Version 11.2
Driver Name PostgreSQL JDBC Driver
Driver Version 42.2.8

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.

1. Is there a way to enable verbose logging for LDAP auth attempts?
2. 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

Hello!
I've installed the Labkey server in a dedicated server. I've followed all the installation steps, but when I try to access Labkey page, it displays HTTP Status 404 – Not Found
My operating system is Ubuntu 18.04.
Tomcat 9.0.30 successfully installed and running in path /opt/tomcat
Labkey files located at /usr/local/labkey/labkey
Labkey.xml located at /opt/tomcat/conf/Catalina/localhost/

Attached the labkey.xml content.

I've tried several things but it still not working.

Please help!

Regards,

Hi Folks,

We are upgrading our server's which has prompted an upgrade of LabKey.
I just grabbed the latest version of LabKey (19.3) community edition, and did a database dump from our server and imported into the new one, however I got the message that it is only supported to upgrade to 19.3 from minimum version 17.2. We are still on 16.1 (yes, it's been a while).

So before moving to the new server, my strategy would be to upgrade the existing infra, and then take the database dump and restore to the new server once that is up-to-date.

2 questions:

1. What is the recommended upgrade path? 16.1 -> 17.2 -> 19.3? Or
2. Where can I find the download links to previous versions? My recollection was there used to be a download archive page but I can't seem to find that now.

Cheers,
Trent

Hi,

I'm trying to run through an install of LabKey 19.2 on RHEL7.

The docs at https://www.labkey.org/Documentation/wiki-page.view?name=supported states LabKey 19.2 requires Java 12, and doesn't support Java 13.

They also have a detailed blog post on this topic at https://www.labkey.com/the-java-shake-up-what-it-means-to-labkey-and-you/

The Install docs at https://www.labkey.org/Documentation/wiki-page.view?name=installComponents state "Install the latest supported release of OpenJDK. " with a link to the Java section at https://www.labkey.org/Documentation/wiki-page.view?name=supported#java. That section talks about LabKey Server requiring OpenJDK 12, which if you follow the link on that page takes you to https://jdk.java.net/12/ which is apparently end of lifed now.

It looks like OpenJDK went from JDK 12 -> JDK 13 this month - on the 17th.

The blog post talks about 19.3 being due in Nov 2019 to track the JDK release cycing introducing support for JDK 13.

With the switch from JDK 12 -> JDK 13 having already happened, should we be installing current production LabKey on OpenJDK 12 since it's the only supported option for the latest LabKey?

I'd really much prefer to use RHEL's supported OpenJDK, but that maxes out at OpenJDK 11 which despite being supported by RedHat is not in the LabKey support matrix.

We are running a Linux RH7 installation of Labkey with a remote MS SQL 2016 database. Our database admin did install the groupConcatInstall.sql prior to the installation, but we still got the message in the Banner :" The GROUP_CONCAT aggregate function is not installed. ....". Our database confirmed the script is installed, is there a way to remove this message? I attached a screen shot of the message . Thank you

Hi Team ,

We have configured as per the vendor document and able to view http://<servername>:8080 , when we try to access http://<servername>:8080/labkey/

Error :
Configuration Error Detected at LabKey Server Startup
DataSources are not properly configured in labkey.xml.

There is a problem with your configuration. Please contact your organization's server administrator for assistance or visit the LabKey Support Portal to view additional support options.

org.labkey.api.util.ConfigurationException: DataSources are not properly configured in labkey.xml.
at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:990)
at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:347)
at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:249)

Regards
Jaiganesh Monie

We recently installed labkey on a linux RH7 server with a remote MS SQL Server 2016 database and during normal System Maintenance, the Database Maintenance task throws java.sql.SQLException: User does not have permission to perform this action. We would like to run the database maintenance task locally on the db server and would like to understand what tasks the Database maintenance is performing so we could duplicate that effort locally and disable the database maintenance task in System Maintenance schedule.

Hi i am having trouble starting up the labkey server : It is an old build (labkey 15) that is being restored to then do a proper upgrade,
any help is appreciated

500: Unexpected server error
A failure occurred during LabKey Server startup.

org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "keyvariable" of relation "propertydescriptor" does not exist
Position: 580
at org.springframework.jdbc.support.SQLStateSQLExceptionTranslator.translate(SQLStateSQLExceptionTranslator.java:111)
at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.translate(SQLErrorCodeSQLExceptionTranslator.java:322)
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.SqlExecutor.execute(SqlExecutor.java:102)
at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:71)
at org.labkey.api.data.Table.update(Table.java:792)
at org.labkey.api.data.Table.update(Table.java:664)
at org.labkey.api.exp.OntologyManager.updatePropertyDescriptor(OntologyManager.java:2286)
at org.labkey.api.audit.AbstractAuditTypeProvider.ensureProperties(AbstractAuditTypeProvider.java:192)
at org.labkey.api.audit.AbstractAuditTypeProvider.initializeProvider(AbstractAuditTypeProvider.java:135)
at org.labkey.api.audit.AbstractAuditTypeProvider.<init>(AbstractAuditTypeProvider.java:88)
at org.labkey.core.query.UserAuditProvider.<init>(UserAuditProvider.java:47)
at org.labkey.core.CoreModule.startupAfterSpringConfig(CoreModule.java:591)
at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:113)
at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:270)
at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1257)
at org.labkey.api.module.ModuleLoader.access$200(ModuleLoader.java:122)
at org.labkey.api.module.ModuleLoader$2.run(ModuleLoader.java:1220)
Caused by: org.postgresql.util.PSQLException: ERROR: column "keyvariable" of relation "propertydescriptor" does not exist
Position: 580
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2270)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1998)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:570)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:420)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:413)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
at org.labkey.api.data.dialect.StatementWrapper.execute(StatementWrapper.java:805)
at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:141)
at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:117)
at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:95)
... 14 more

I have installed tomcat and PostgreSQL database on the server and when i use url = http://<server name>:8080/ i am able to open apache default web page .

When i use url = http://<server name>:8080/labkey i am getting error : Http status 404

I am worried about the labkey.xml file , could you please correct me where i am missing configuring .

Hello,

I've went through the tutorial to install labkey community edition on my windows 10 laptop. I've installed all the required software, and confirmed that postgres and tomcat are working. I've built a demo website in tomcat to confirm that it's been installed correctly.

I'm just having trouble linking it all together. the labkey.xml file clearly isn't functioning right, as when i navigate to localhost:8080/labkey, i get a 404 error:

HTTP Status 404 – Not Found
Type: Status Report
Message: Not found
Description: The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.

Attached is a picture of my labkey.xml file. Currently, this file only resides in <CATALINA_HOME>/conf/Catalina/localhost/labkey.xml. Is this correct?
I'm really quite lost as to the issue. any help would be appreciated.

Thanks,
Noah

Hello,

I've installed lk 19.1 Community Edition on Windows. It was working perfectly, but when I tried to restore my labkey database using PostgreSQL 10.7, I lost my labkey credentials. Is there a way to recover my credentials?

Thank you

Hello,

I have a Labkey Community 19.1.1 installation running successfully with a remote SQL Server 2016 database using SQL Server Authentication.

The database administrators here much prefer the use of Windows Authentication for such databases. Is this possible?

Thank you.

Hello,

Recently upgraded this weekend to LK 19.1 and used the handy dandy manualUpgrade.sh script. However, now the index.html redirect line:

<meta http-equiv="Refresh" content="0; URL=./project/home/start.view">

fails since there is no project directory any longer... what am I missing?

Tomcat 9, Java 12, formerly running LK 18.3 (last week). No errors in the log files....

Thanks!

Hello,

We recently released LabKey Server 19.1.1, our first patch release for 19.1.x. This patch release fixes a problem with sample export/import and addresses other important issues. We strongly recommend upgrading all LabKey deployments to 19.1.1 or higher as soon as possible.

Premium Edition subscribers will find their 19.1.1 distribution on their server builds page. Community Edition users should visit the download page on www.labkey.com: http://www.labkey.com/forms/register-to-download-labkey-server

For more details on LabKey 19.1.x, see the release notes: https://www.labkey.org/Documentation/wiki-page.view?name=releaseNotes191

Regards,

LabKey Support

i have been getting this error the last couple of days when starting labkey on tomcat. Am running cent os 6.9 postgres 11 and tomcat 9. Somme assistance please

11-Apr-2019 16:14:56.773 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.17
11-Apr-2019 16:14:56.777 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Mar 13 2019 15:55:27 UTC
11-Apr-2019 16:14:56.777 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.17.0
11-Apr-2019 16:14:56.777 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
11-Apr-2019 16:14:56.777 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 2.6.32-696.30.1.el6.x86_64
11-Apr-2019 16:14:56.777 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
11-Apr-2019 16:14:56.778 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.201.b09-2.el6_10$
11-Apr-2019 16:14:56.778 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_201-b09
11-Apr-2019 16:14:56.778 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
11-Apr-2019 16:14:56.778 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
11-Apr-2019 16:14:56.779 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
11-Apr-2019 16:14:56.779 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf$
11-Apr-2019 16:14:56.779 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoade$
11-Apr-2019 16:14:56.779 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms4g
11-Apr-2019 16:14:56.780 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx4g
11-Apr-2019 16:14:56.780 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-HeapDumpOnOutOfMemoryError
11-Apr-2019 16:14:56.780 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
11-Apr-2019 16:14:56.781 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webre$
11-Apr-2019 16:14:56.781 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=$

I have an environment running 18.2 that is currently connected to MS SQL 2012 for the labkey application database, and my DBA team is asking me to switch to their shared 2016 environment. Their environment requires encrypted connections to the DB server.

My attempted connection xml:
<Resource name="jdbc/labkeyDataSource" auth="Container" type="javax.sql.DataSource" username="labkey" password="************" driverClassName="net.sourceforge.jtds.jdbc.Driver" url="jdbc:jtds:sqlserver://consqldev4.cc.emory.edu:1433/labkeydev" maxActive="20" maxIdle="10" accessToUnderlyingConnectionAllowed="true" validationQuery="SELECT 1" TrustServerCertificate="true" />

I am getting a failed connection error message:

org.labkey.api.util.ConfigurationException: DataSources are not properly configured in ROOT.xml.
Caused by: org.labkey.api.util.ConfigurationException: Can't connect to data source "labkeyDataSource".
Caused by: java.sql.SQLException: I/O Error: DB server closed connection.
Caused by: java.io.IOException: DB server closed connection.

The DB server is showing this error in its event viewer:

Encryption is required to connect to this server but the client library does not support encryption; the connection has been closed. Please upgrade your client library. [CLIENT: xx.xx.xx.xx]

I've seen a thread here on the forum where 2016, even though it isn't officially supported yet, is functional in a test environment. Link. I'm wondering how far I should go troubleshooting this if this is not yet supported.

Thanks for any information you might be able to give.

Hello All,

I have a new LabKey installation with server 19.1. The installation went smoothly and the admin user has been created. When I add the first user I get the following error:

500: Unexpected server error
javax/activation/DataHandler

Home Back
java.lang.NoClassDefFoundError: javax/activation/DataHandler
at org.labkey.api.util.MailHelper.createMultipartMessage(MailHelper.java:130)
at org.labkey.api.security.SecurityMessage.createMailMessage(SecurityMessage.java:53)
at org.labkey.api.security.SecurityManager.createMessage(SecurityManager.java:1049)
at org.labkey.api.security.SecurityManager.sendEmail(SecurityManager.java:1026)
at org.labkey.api.security.SecurityManager.sendRegistrationEmail(SecurityManager.java:2816)
at org.labkey.api.security.SecurityManager.addUser(SecurityManager.java:2743)
at org.labkey.core.security.SecurityController$AddUsersAction.handlePost(SecurityController.java:1342)
at org.labkey.core.security.SecurityController$AddUsersAction.handlePost(SecurityController.java:1277)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:91)
at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:70)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:176)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:487)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1265)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1220)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:200)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:668)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:834)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1415)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:835)
Caused by: java.lang.ClassNotFoundException: javax.activation.DataHandler
at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:436)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:588)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 50 more
request attributes
LABKEY.OriginalURL = http://localhost:8080/labkey/security-addUsers.view?
LABKEY.StartTime = 1553535942494
LABKEY.action = addUsers
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date [Mon Mar 25 17:40:53 UTC 2019]; parent: Root WebApplicationContext
LABKEY.controller = security
LABKEY.Counter = 0
org.labkey.api.util.ExceptionUtil$exception = java.lang.NoClassDefFoundError: javax/activation/DataHandler
X-LABKEY-CSRF = 69c367027f31cfb429044ddf64416823
LABKEY.container =
LABKEY.RequestURL = /labkey/security-addUsers.view?
LABKEY.OriginalURLHelper = /labkey/security-addUsers.view?

core schema database configuration
Server URL jdbc:postgresql://localhost:5432/labkey
Product Name PostgreSQL
Product Version 9.5.2
Driver Name PostgreSQL JDBC Driver
Driver Version 42.2.5

Any help is greatly appreciated.

Thanks,
Stefan

I have been stuck with this issue the last 16 hours I have tried following the responses but still getting the same errors. Am running centos and postgres11. n/b..am just taking up the installation from my partner who is not around in order to get the server running. Most of the installation was already configured so am just trying to complete the installation. Some assistance will be of beneficial use

In the section Create Folder Structure, I'm a bit confused as to what should be <labkey-home>.

I've created the directory /usr/local/labkey, and then I've added into that directory, apps, labkey, backups, src, src/labkey, so now
I have a total of 3 labkey directories. During the installation, there's no part that has me adding anything to /usr/local/labkey/labkey, or
/usr/local/labkey/src/labkey. I've added all the jars to tomcat-lib/, then is says to copy files to the labkey home directory, which I thought
was going to be /usr/local/labkey. But I also noticed that in the docs as a description for /usr/local/labkey/labkey, it says that that's the
actual install directory of the labkey server. I don't know what that means. Also is says in the description that /usr/local/labkey/src/labkey is the place where you store the downloaded binaries, yet there's no step that outlines anything related to either. So, for all the directories that need to be moved, example labkeywebapp, modules, and pipelines-lib, do these go under /usr/local/labkey, or /usr/local/labkey/labkey? And is /usr/local/labkey considered <labkey-home>, or is /usr/local/labkey/labkey considered <labkey-home>? Also, for Linux install, does anything go under /usr/local/labkey/src/labkey?

hi,

I am trying to download 18.3 Community Edition, but I there appears to be an error loading the Captcha.

https://www.labkey.com/products-services/labkey-server/download-community-edition/

"Error for site owner: Invalid Key Type"

Thanks,

bront

Hello,

I am trying to increase the memory from 1024 to 2048 for the Apache service as described here:

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

LabKey is running on Windows Server:
OS: Microsoft Standard Windows Server 2012 R2 Standard
Version: 6.3.9600 Build 9600

After increasing the memory to 2048, Apache fails to start. I have attached a screenshot of the error message. I couldn't find more detailed info in the system logs, but I am not a system admin.

When decrease the memory back to 1024, the Apache server starts.

Has anyone encountered this kind of problem?

Thanks,
Bill

I installed the labkey server, but I still do not get a create project folder under the home menu (I only get permalink page icon).

Hi

I am getting the same error as the previous poster but the files you mention are there and have the correct permissions

root@labkey:/opt/tomcat# ls -l /opt/tomcat/lib/
total 11916
-rw-r----- 1 tomcat tomcat   12966 Sep  4 22:14 annotations-api.jar
-rw-r----- 1 tomcat tomcat   54227 Sep  4 22:14 catalina-ant.jar
-rw-r----- 1 tomcat tomcat  120722 Sep  4 22:14 catalina-ha.jar
-rw-r----- 1 tomcat tomcat   77031 Sep  4 22:14 catalina-storeconfig.jar
-rw-r----- 1 tomcat tomcat  307887 Sep  4 22:14 catalina-tribes.jar
-rw-r----- 1 tomcat tomcat 1645873 Sep  4 22:14 catalina.jar
-rw-r----- 1 tomcat tomcat 2769774 Sep  4 22:14 ecj-4.7.3a.jar
-rw-r----- 1 tomcat tomcat   87515 Sep  4 22:14 el-api.jar
-rw-r----- 1 tomcat tomcat  167491 Sep  4 22:14 jasper-el.jar
-rw-r----- 1 tomcat tomcat  557126 Sep  4 22:14 jasper.jar
-rw-r----- 1 tomcat tomcat   27901 Sep  4 22:14 jaspic-api.jar
-rw-r----- 1 tomcat tomcat   63166 Sep  4 22:14 jsp-api.jar
-rw-r--r-- 1 tomcat tomcat  317816 Oct 24 10:30 jtds.jar
-rw-r--r-- 1 tomcat tomcat   44088 Oct 24 10:30 labkeyBootstrap.jar
-rw-r--r-- 1 tomcat tomcat  654100 Oct 24 10:30 mail.jar
-rw-r--r-- 1 tomcat tomcat 2036609 Oct 24 10:30 mysql.jar
-rw-r--r-- 1 tomcat tomcat  790405 Oct 24 10:30 postgresql.jar
-rw-r----- 1 tomcat tomcat  282576 Sep  4 22:14 servlet-api.jar
-rw-r----- 1 tomcat tomcat   11212 Sep  4 22:14 tomcat-api.jar
-rw-r----- 1 tomcat tomcat  842120 Sep  4 22:14 tomcat-coyote.jar
-rw-r----- 1 tomcat tomcat  307294 Sep  4 22:14 tomcat-dbcp.jar
-rw-r----- 1 tomcat tomcat   65344 Sep  4 22:14 tomcat-i18n-es.jar
-rw-r----- 1 tomcat tomcat   39274 Sep  4 22:14 tomcat-i18n-fr.jar
-rw-r----- 1 tomcat tomcat   42168 Sep  4 22:14 tomcat-i18n-ja.jar
-rw-r----- 1 tomcat tomcat   12166 Sep  4 22:14 tomcat-i18n-ru.jar
-rw-r----- 1 tomcat tomcat  148741 Sep  4 22:14 tomcat-jdbc.jar
-rw-r----- 1 tomcat tomcat   35811 Sep  4 22:14 tomcat-jni.jar
-rw-r----- 1 tomcat tomcat  208906 Sep  4 22:14 tomcat-util-scan.jar
-rw-r----- 1 tomcat tomcat  141069 Sep  4 22:14 tomcat-util.jar
-rw-r----- 1 tomcat tomcat  229653 Sep  4 22:14 tomcat-websocket.jar
-rw-r----- 1 tomcat tomcat   38022 Sep  4 22:14 websocket-api.jar

What other issues could cause this problem? Are there logs I can look at ?

Thanks

So I am following the instructions to configure LabKey on Linux found here: https://www.labkey.org/Documentation/wiki-page.view?name=configTomcat

Tomcat and postgres are up and running, and I have worked through to step 4, move the LabKey Server configuration file. When I got to this step, there was no /conf/Catalina/localhost/ directory in my install - I created one and then put the labkey.xml there.

I then continued through to step 11, Tomcat is running, and the landing page comes up. But when I go to /labkey, it throws a 404 not found error:
Type Status Report

Message /labkey

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

Is this a known issue? Is it unusual for the "/conf/Catalina/localhost" directory to not exist after an install? I could use any help debugging this.

Hi,

I am trying to manually install Labkey Server 18.1 on my computer (running a non-english version of Windows 7, 64-bit) on Chrome. I'm using tomcat (8.5.31) and postgres (9.5.13).

When I'm trying to run localhost:8080/labkey I get a following error:
Configuration Error Detected at LabKey Server Startup
DataSources are not properly configured in labkey.xml

Attached are labkey.xml and tomcat log.

Thank you for your support

Matt

If Labkey connects to a Postgres v10.3 database on Ubuntu 18.04 you get the following:

WARN  PostgreSqlDialectFactory 2018-05-07 00:56:54,603 18.example.com-startStop-1 : LabKey Server has not been tested against PostgreSQL version 10.3 (Ubuntu 10.3-1). PostgreSQL 9.6 is the recommended version.
INFO  DbScope                  2018-05-07 00:56:54,604 18.example.com-startStop-1 : Initializing DbScope with the following configuration:
    DataSource Name:          labkeyDataSource
    Server URL:               jdbc:postgresql://localhost/labkey
    Database Product Name:    PostgreSQL
    Database Product Version: 10.3 (Ubuntu 10.3-1)
    JDBC Driver Name:         PostgreSQL JDBC Driver
    JDBC Driver Version:      42.2.1
    SQL Dialect:              PostgreSql96Dialect

I'm guessing the extra "(Ubuntu 10.3-1)" appended to the version string is throwing off Labkey's version comparison.

-Will

Hi,

I am still runnning LabKey 15.2. If I understand the Upgrade matrix

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

correctly I would first need to upgrdade to 15.3. However, I cannot find a download link for 15.3

regards

Felix

With the help of the documentation at [https://www.labkey.org/Documentation/wiki-page.view?name=configLdap], I was able to get Labkey working with LDAP. However, Labkey's authentication GUI assumes a fairly simple LDAP configuration and it is currently allowing all our internal users and external customers to log in regardless. I would like to limit Labkey login to just the people we approve. For this purpose, I've set up an LDAP group called 'labkey'.

My current working Security Principal is uid=${uid},ou=Webusers,dc=bcgsc,dc=ca.

Our LDAP hierarchy looks as such:

Users are uid=${uid},ou=Webusers,dc=bcgsc,dc=ca

And the group is at cn=labkey,cn=Webgroups,ou=Groups,dc=bcgsc,dc=ca

Attached is the graphical representation of what I am working with.

How can I get this working with the following Context elements in labkey.xml?

<Environment name="ldapSearch_username" value="ldapAdmin@email.org" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_password" value="***" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_searchBase" value="dc=email,dc=org" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_lookupField" value="userPrincipalName" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_searchTemplate" value="(&amp;(objectClass=user)(userPrincipalName=${email}))" type="java.lang.String" override="false"/>

Using Test LDAP settings in Labkey continues to work no matter what I insert but I can't log in anymore if I start using these Context elements.