LabKey Support: LabKey Server Distribution and Support

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

Thu Feb 27 22:38:54 PST 2020

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

LDAP Authentication for Linux - Community Version

Fri Feb 21 14:36:12 PST 2020

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

HTTP Status 404 – Not Found

Wed Jan 29 09:40:48 PST 2020

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,

Upgrade path from 16.1

Tue Jan 14 15:51:56 PST 2020

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

OpenJDK 12, 13 and LabKey 19.2

Wed Sep 25 07:49:15 PDT 2019

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.

GROUP_CONCAT Banner Message - Remove it?

Thu Sep 05 07:49:36 PDT 2019

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

Unable to open weburl

Fri Aug 30 04:14:32 PDT 2019

Hi Team , We have configured as per the vendor document and able to view http://:8080 , when we try to access http://: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

MS SQL 2016 Server regular database maintenance task - description need

Thu Aug 29 12:10:28 PDT 2019

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.

Labkey error

Tue Aug 06 12:50:36 PDT 2019

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.(AbstractAuditTypeProvider.java:88) at org.labkey.core.query.UserAuditProvider.(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

installtion has been completed , need configuration setting help on labkey

Thu Aug 01 07:19:52 PDT 2019

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

Tomcat 404 when trying to open labkey.

Tue Jul 30 10:36:48 PDT 2019

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 /conf/Catalina/localhost/labkey.xml. Is this correct? I'm really quite lost as to the issue. any help would be appreciated. Thanks, Noah

Reset labkey credentials

Thu May 16 12:25:48 PDT 2019

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

SQL Server Windows Authentication

Tue Apr 23 11:14:19 PDT 2019

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.

Upgrade from 18.3 to 19.1 index.html issue

Mon Apr 15 09:55:54 PDT 2019

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

LabKey 19.1.1 updates

Thu Apr 11 09:27:34 PDT 2019

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

error starting child

Thu Apr 11 06:18:40 PDT 2019

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=$

Connecting to an encrypted MS SQL Server 2016 DB

Tue Apr 02 08:15:11 PDT 2019

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: 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](https://www.labkey.org/9e077ef4-b2ab-1029-961c-79704b7a2169/announcements-thread.view?entityId=35cbcc1e-3033-1034-9d77-84e20e6fce18&_docid=thread%3A35cbcc1e-3033-1034-9d77-84e20e6fce18). 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.

Adding first user causes 500: Unexpected server error

Mon Mar 25 11:06:33 PDT 2019

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

Configuration Error Detected at LabKey Server Startup

Wed Mar 13 05:10:42 PDT 2019

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

A little confused over the folder structure section of the installation doc for Linux

Wed Feb 13 11:13:52 PST 2019

In the section Create Folder Structure, I'm a bit confused as to what should be . 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 , or is /usr/local/labkey/labkey considered ? Also, for Linux install, does anything go under /usr/local/labkey/src/labkey?

Captcha Error

Mon Dec 03 12:47:54 PST 2018

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

LabKey Apache unable to start after increasing Tomcat memory

Fri Nov 16 10:25:32 PST 2018

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

no create project icon

Fri Nov 02 08:35:48 PDT 2018

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).

Tomcat 9 and Installation 404 (SOLVED)

Wed Oct 24 04:24:38 PDT 2018

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

Deploying on Linux server with Tomcat 8.5.35, getting 404 error

Mon Sep 17 10:22:53 PDT 2018

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.

Cannot connect to external DataSource after upgrade to LabKey 18.2

Thu Jul 26 02:03:06 PDT 2018

Dear LabKey support team, We have upgraded from LabKey 18.1 to 18.2 and the connection to the external data source we had running (a MySQL database), is not working anymore. I attach the log file for documentation of the error messages. First of all, the error was clearly stating that it is necessary to change a parameter value in the connection string: from "zeroDateTimeBehavior=convertToNull" to "zeroDateTimeBehavior=CONVERT_TO_NULL", which we did. But that did not solve the issue. We are running: jdk1.8.0_40 apache-tomcat-7.0.68 postgres 9.6 MySQL-server-community-5.1.33-0.rhel5 (for the external data source) Do you know how to restore the external data source connection? Thank you very much, Eva

Configuration Error Detected at LabKey Server Startup

Thu May 17 15:02:51 PDT 2018

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

Incorrect warning about Postgres 10.3 not supported by Labkey on Ubuntu 18.04

Mon May 07 01:02:25 PDT 2018

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

Download for Previous releases

Tue Apr 17 22:45:31 PDT 2018

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

LabKey17.3-56184.53-community broken

Fri Feb 02 01:11:35 PST 2018

Hi, The LabKey17.3-56184.53-community tar archive produces a non functional installation. The labkeywebapp folder is empty except for the WEB-INF folder.

How to get current LabKey's running version?

Wed Jan 10 12:46:28 PST 2018

Hi, Is there any way to obtain (via command line or GUI) current LabKey's running version? When accessing Admin Console -> Module Information -> Module Details version number indicated is 17.30 instead of 17.3 (see attached file) As it will be used in an IQ document we'd like to obtain the right value. Thanks,

Missing ant.jar when installing 17.3

Wed Dec 20 08:17:51 PST 2017

Hi, I'm installing a fresh server using provided installation file (LabKey17.3-55140.16-professional-bin.tar.gz), but when moving LabKey Server Libraries as indicated at https://www.labkey.org/Documentation/wiki-page.view?name=configTomcat there is no ant.jar into tomcat-lib (extracted from tgz provided file). Should I get ant.jar from somewhere else? Thanks,

Automatic Conversion/Searching Raw Files

Wed Dec 13 11:31:00 PST 2017

Hi All, Hope you are well. How does on 'tell' labkey server how to read RAW files? msConvert is installed in the pipeline root bin directory (C:\Labkey\bin where x!, etc. are). The server (installed on Windows) works fine with mzXML files, but when attempting to run on RAW clicking the X! search button doesn't actually do anything. To me - this suggests, the server doesn't actually think it can trigger a conversion. How does one let LabKey know it has msConvert and is perfectly qualified to do its own conversions? Note - we are NOT using the enterprise pipeline, so this is all being run on a single windows head computer. Thanks! ~ Parag M ~

upgrade problem with ms2-15.30-16.10.sql

Thu Oct 26 11:43:52 PDT 2017

Hi all, We have problem during the upgrade to 17.2. Please see below for the error. Please help. Thanks Toan INFO SqlScriptManager 2017-10-25 16:05:03,879 Module Upgrade : start running script : ms2-15.30-16.10.sql ERROR Table 2017-10-25 20:39:19,149 Module Upgrade : SQL Exception org.postgresql.util.PSQLException: ERROR: column "mascotfile" of relation "runs" already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2476) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2189) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:300) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:428) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:354) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:301) at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:287) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:264) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:260) at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:290) at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:290) at org.labkey.api.data.dialect.StatementWrapper.execute(StatementWrapper.java:1908) at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:156) at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:144) at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:122) at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:75) at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:70) at org.labkey.api.data.SqlScriptExecutor$Block.execute(SqlScriptExecutor.java:208) at org.labkey.api.data.SqlScriptExecutor.lambda$execute$0(SqlScriptExecutor.java:101) at java.util.ArrayList.forEach(ArrayList.java:1249) at org.labkey.api.data.SqlScriptExecutor.execute(SqlScriptExecutor.java:98) at org.labkey.api.data.dialect.SqlDialect.runSql(SqlDialect.java:588) at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:215) at org.labkey.api.data.SqlScriptRunner.runScripts(SqlScriptRunner.java:82) at org.labkey.api.module.DefaultModule.versionUpdate(DefaultModule.java:333) at org.labkey.api.module.ModuleUpgrader.upgrade(ModuleUpgrader.java:83) at org.labkey.api.module.ModuleUpgrader.lambda$upgrade$0(ModuleUpgrader.java:95) at java.lang.Thread.run(Thread.java:748) ERROR Table 2017-10-25 20:39:19,158 Module Upgrade : SQL [22230]

Additional LDAP configuration

Tue Aug 29 15:36:42 PDT 2017

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`? ``` ``` 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.

Fail to run labkey. [org.apache.catalina.LifecycleException: Failed to start component

Tue Aug 22 07:11:52 PDT 2017

Dear All, I have tried to install Labkey server but without any success. When i enter the adress localhost:8080/labkey i have this error in the tomcat manager. I use java 8, tomcat 8.5 on a debian stretch. If anyone can help i would be very grateful. I found the installation very complicated. THanks a lot, Bests, Thierry

how to visualized spectra with version 3.7

Tue Jun 27 06:53:23 PDT 2017

I have down load the 3.7 version of skyline software, but I have the message "spectrum information unavailable" It did work with previous 3.6 version. Thanks for help

Error - A failure occurred during LabKey Server startup.

Wed Jun 14 11:21:16 PDT 2017

I have been compiling TPP 5.0 on our Linux cluster (running also Labkey Server 16.3) having lot of problem. But an unexpected problem occurred when I found out that the Labkey Server stopped working - Below is the error I receive in web browser. Permissions on logs folder are for tomcat:tomcat drwxr-xr-x. 2 tomcat tomcat 36864 Jun 14 06:12 logs Thanks for any advice. Tomas 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.IllegalStateException: Error rolling labkey-errors.log file, likely a file permissions problem in CATALINA_HOME/logs at org.labkey.api.module.ModuleLoader.rollErrorLogFile(ModuleLoader.java:604) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:262) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:318) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:240) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4855) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5549) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1912) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

Data migration

Thu Apr 27 06:34:19 PDT 2017

Whats the best way to migrate data from v15.2 to 17.1 ?

HTTP 500 Bad SQL Grammar by SqlScriptRunner during module update on LabKey startup RHEL 7.3

Fri Apr 07 17:42:53 PDT 2017

Hello, I seem to have correctly installed LabKey17.1-49816.20-community-bin on Red Hat Linux 7.3, but when I go to the LabKey homepage after Tomcat startup, I get the following HTTP error: 500: Unexpected server error A failure occurred during LabKey Server startup. org.labkey.api.data.SqlScriptRunner$SqlScriptException: exp-15.10-15.20.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "keyvariable" does not exist at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:220) at org.labkey.api.data.SqlScriptRunner.runScripts(SqlScriptRunner.java:82) at org.labkey.api.module.DefaultModule.versionUpdate(DefaultModule.java:332) at org.labkey.api.module.ModuleUpgrader.upgrade(ModuleUpgrader.java:82) at org.labkey.api.module.ModuleUpgrader.lambda$upgrade$0(ModuleUpgrader.java:94) at java.lang.Thread.run(Thread.java:745) Caused by: org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "keyvariable" does not exist...... Any ideas on how to fix this? The Tomcat default homepage loads fine, and I can see in postgres that the labkey database has been built. A file with the relevant labkey.log and labkey-errors.log entries is attached. Thanks, Jim

Labkey Server Service stopped, can't able to start again

Wed Mar 29 05:07:01 PDT 2017

Dear All, I have installed Lebkey Server Community Edition, It was worked fine after installation. but now the services in services.msc has stopped automatically and i am not able to start those. It says, there are dependencies on other services but I checked all the dependent services(Those were running). Please help.

"Inactive" date ?

Tue Mar 28 13:42:12 PDT 2017

HI, I"m doing some analysis of our site users and am trying to make a view that shows the date a user was "deactivated" from the system. I can see when the account was "created", when the "Last Login" was ... but under "grid views" is there a way to see when someone's account was "deactivated" or "disabled"? Thanks! -- Nat Apologies if this belongs in the Community Forum ... please let me know if it does. thx.

Bulk email controls (SMTP)in LabKey

Fri Mar 10 11:49:15 PST 2017

Hi, We have run into an issue around sending bulk emails this week where the outbound queue of our SMTP server is *very* slow. Currently at almost 36 hrs after the original announcement was made from LabKey, there are about 1k emails still in outbound queue. The list is slowly shrinking ... So our user base of emails is now almost 9K in size, so not small anymore but not huge either. Our IT dept recommended we send out bulk emails in 1K batches (5 min apart), or put a 5 sec delay between individual emails ... oye, not getting into manual management of batch emails... I've pushed on them regarding whether there are controls/adjustibility on the SMTP server to automatically do this and I'm waiting to hear back. They also suggested I contact LabKey as to whether there is any outbound email functionality that is built into this product. I did search the support base prior to sending this but couldn't find anything related. Thoughts?? Nat Brace UW - Skyline

Example Workflow: LabKey and Illumina

Thu Mar 09 06:32:54 PST 2017

Hi. I want to set a genotyping dashboard. How I get the genotyping Module? I am interesting in Labkey and Illumina Workflow. Thanks

Telling Labkey to check a specific row (i.e. not the first row) for data headers

Tue Feb 21 11:40:40 PST 2017

I searched around, but couldn't find an answer to this exact question. We have a system that outputs excel files. The top of the file contains two columns of metadata, comprising six rows. There is a blank row directly below, and then on row 8, the data we wish to store begins. Row 8 contains the headers we want in our data domain, so our data fields have been designed to match these. However, when I upload a file, Labkey appears to check the first row for header information (which only contains two non-blank columns). Thus, the file does not upload successfully. Is there a way to tell Labkey to skip a few lines when searching for the headers? I saw on another post, someone suggested prepending the first seven lines with "#", but I am wondering if Labkey can be configured to ignore these automatically. Thanks, Simon

2 LabKeys sharing file storage?

Tue Feb 21 10:09:02 PST 2017

We are splitting one of our LabKey sites in two. One will be for customers and the other will be the internal lab use. They and their databases will be hosted on separate VMs, however we want them to share the same directory for file storage -- the same one they are using before the split. The idea is to allow us to reference the same data from both sites without duplicating storage. 1. Does anyone see a problem with this? 2. If we remove a project from one site would it delete the data files even if we wanted to continue to access them from the other site?

Upgrade Issue from LabKey 16.2 to 16.3

Mon Feb 13 14:46:10 PST 2017

Hi Cori. I am having problems with upgrading from 16.2 to 16.3 version. It returns me: 500: Unexpected server error A failure occurred during LabKey Server startup. org.labkey.api.data.SqlScriptRunner$SqlScriptException: study-16.20-16.30.sql : Can't invoke method updatePKAndContainer(ModuleContext moduleContext) on class org.labkey.study.StudyUpgradeCode at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:211) ... Caused by: org.postgresql.util.PSQLException: ERROR: no existe la columna «container» en la relación «c19d733_demographics» at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2453) I can't solve it. I wrote a post in labkey forums, but anyone answered me. Can you help me or contact me with someone who could help me? Thanks- Hilaria.

Text character limit for assy fields

Tue Jan 31 12:13:48 PST 2017

Hello all, We have an assay designed which has a field for gene ontology. This can get very long (above 4000 characters) and one of our users was wondering if there was a variable somewhere in the settings that would allow us to increase the maximum number of characters for Text fields. Assuming our database can handle such a change, is this something that could be done? Moreover, would this still allow us to use built-in assay types? Thanks!

New install, Home page editable when not signed in.

Wed Jan 11 15:59:25 PST 2017

I have just performed a new install of LabKey 16.3 on Windows Server 2012 R2. Everything looks good except that the home page is editable when i'm not signed in. The home folder permissions are set for "all site users" and "guests" as reader and nothing else. See attachments. I have another install where the home page is not editable and appears to have the same permissions set. That install is version 15.30. Is this a bug or is there a way to fix it? Rick.

How to configure LabKey server (linux) to run R scripts remotely on another server (linux)

Tue Jan 10 07:19:41 PST 2017

Hello LabKey We want to use labKey in an university research environment in epidemiology. We already have a computing server to run R and we want to add a new Labkey server to our environment. This tool seems strong but a bit hard to configure. In particular when you try to run R remotly. We would be delighted if you could help us find the appropriate documentation for this configuration. The documentation available on the website does not describe precisely this type of configuration and we have not found any information on your forum. We're trying to configure our LabKey server (linux) to run R scripts remotly on another server (linux) on the same VLAN but we get a java null pointer exception. We've follow this documentation : https://www.labkey.org/home/Documentation/wiki-page.view?name=LabKeyRserve#defaultremote but without success. When we try to modify this option : Sign in as an admin. Go to Admin > Site > Admin Console. Click Experimental Features. Under Rserve Reports, click Enable. We get a NullPointerException from java when we click on Views and Scripting Configuration : Do you know this error ? Or do you know where we can find information about this ? Many thanks. Kind regards Cordialement

Minimum permissions for Tomcat's conf directory

Wed Dec 21 10:23:35 PST 2016

On Linux, is it possible to run LabKey with Tomcat's conf directory as read-only? It is usually recommended to make this directory read-only (The user running Tomcat is the owner of this directory and its contents, with permissions 0400)? I've tried it out and was unable to reach LabKey's homepage and had to revert back to 0740, but I would still like to restrict how the configuration files are able to be accessed and changed by outside users. Thanks!

Support for Tomcat 8.5.x

Tue Dec 20 11:33:33 PST 2016

LabKey Server 16.3 now officially supports Tomcat 8.5.x, starting with the Tomcat 8.5.9 release. This Tomcat release includes a fix to an important issue that previously blocked our ability to approve use of the 8.5.x line. We expect to continue to support Tomcat 7.0.x and 8.0.x for the foreseeable future, although the Tomcat team now encourages use of 8.5.x. More details about the Tomcat issue fix at the following links: - http://www.mail-archive.com/search?l=dev@tomcat.apache.org&q=subject:%22Same+request+object+passed+to+two+threads%22&o=newest&f=1 - https://bz.apache.org/bugzilla/show_bug.cgi?id=60409 - http://mail-archives.apache.org/mod_mbox/tomcat-announce/201612.mbox/%3C76fe5f99-cc2c-4e48-b669-738f5dae7266%40apache.org%3E Feel free to test and use Tomcat 8.5.x and, as always, let us know if you encounter any issues with it. Adam

Error when trying to upgrade LabKey from 16.2 to 16.3

Tue Dec 20 02:06:45 PST 2016

Dear LabKey team, We've tried to upgrade LabKey from a 16.2 installation to 16, but we get this message in the labkey log files and labkey doesn't boot properly: ERROR ModuleLoader 2016-12-15 13:16:14,635 localhost-startStop-1 : Failure occurred during ModuleLoader init. java.lang.AbstractMethodError: Method org/labkey/illumina/IlluminaModule.getSchemaNames()Ljava/util/Collection; is abstract at org.labkey.illumina.IlluminaModule.getSchemaNames(IlluminaModule.java) at org.labkey.api.module.ModuleLoader.getModuleDataSourceNames(ModuleLoader.java:1622) at org.labkey.api.module.ModuleLoader.getAllModuleDataSourceNames(ModuleLoader.java:1613) at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:1008) at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:917) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:330) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:240) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4908) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5602) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1962) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) Do you have any hints about what could be the cause? Thanks a lot, Eva

First-time Setup redirects me to home, unable to complete administration set up, cannot log in

Thu Nov 24 11:55:12 PST 2016

Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in the top right, I am brought back to the homepage without being signed in. If I try to log in with bogus credentials, it does recognize that it couldn't find that user. Sometimes I get a page saying that maintenance mode is going on, and I am given a button for Adminstrator login. However, I am almost instantly redirected back to the homepage. My logs don't help much. I've included labkey.log, but my labkey-error.log is completely empty. PostgreSQL logs have a few interesting lines, I have attached it as well. EDIT: Investigating further, I also ran bin/configtest.sh from Tomcat's directory which uncovered some errors, although I don't see anything else using port 8080. System information: Apache Tomcat: 8.0.39 OS: Linux, Ubuntu 16.04 JVM: 1.8.0_112-b15 Oracle PostgreSQL: 9.5

A database connection is in an unexpected state.

Tue Nov 08 07:13:27 PST 2016

Hi, I'm trying to start Labkey 16.2 on tomcat 7, but I get the following error message: "A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool." I installed Labkey on Ubuntu 14.04 and the database is Postgress 9.5.5. How could I fix this error? Thanks, Romina.

Module has already been set - error

Tue Sep 20 17:27:00 PDT 2016

I am building a continuous integration environment for our labKey development team so that we can better QA and manage our releases. I have been able to successfully compile and push (copy) the web app to the staging server along with a restoring database from production. It seems that the web-server starts up correctly; however, upon first accessing the web-app, I receive the following error message. "Module has already been set" I added the entire stack-trace below I was wondering if anyone else had a similar experience and could point in the right direction. There is a second labkey installation on the same server, but it seems to be working without issue. Thanks, Jason ---- java.lang.IllegalStateException: Module has already been set. at org.labkey.api.view.BaseWebPartFactory.setModule(BaseWebPartFactory.java:177) at org.labkey.api.module.DefaultModule.getWebPartFactories(DefaultModule.java:414) at org.labkey.api.view.Portal.getPartsToAdd(Portal.java:1178) at org.labkey.api.view.Portal.addCustomizeDropdowns(Portal.java:905) at org.labkey.api.view.Portal.populatePortalView(Portal.java:1027) at org.labkey.api.view.Portal.populatePortalView(Portal.java:950) 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:178) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:409) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) 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:731) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:205) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:218) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:442) at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:623) at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) 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)

Upgrade version 15.2 to 16.1 (16.2)

Tue Sep 06 23:51:13 PDT 2016

Hi. I have tested Labkey server 16.1 and several tables (about 10 from 23 module lists) gives the message 500: Unexpected server error Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established before constructing. java.lang.IllegalStateException: Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established before constructing. at org.labkey.list.model.ListTable.(ListTable.java:105) … Similar or the same as Issue 26423. (solved in version 16.2)? So I have installed 16.2 version and all tables which had problem in 16.1 disappeared?! (… object not found) What happened? Can you help me please? In version 15.2 was all OK. All tables I created by default function in "Manage Lists - Create new lists”. I'm afraid to upgrade to the next version. Thanks lubomir pavliska Another cases and projects. Some project are OK. But in many cases is the same - error in primary key. I don't understand about it in version 15. was all OK and those projects come from 13. version.

Installing TPP on LabKey 16.2 Community Edition

Wed Aug 31 09:01:04 PDT 2016

I have been tasked with installing TPP (Trans Proteomic Pipeline) under Labkey 16.2 running on Windows Server 2012. The documentation on LabKey refers to TPP 4.6.3 but the current version is 4.8. The docs also point to the TPP source which is apparently not available. Can the TPP v4.8.0 .exe Installer version be used and if so, what process needs to be followed? Any help will be greatly appreciated. Thanks, Brian Main Leroy T. Canoles Cancer Research Center mainbp@evms.edu 757.446.5750

Labkey 16 trying to run upgrade script from 14.1

Wed Aug 24 13:25:30 PDT 2016

Hi, While trying to connect to the Labkey server, I am getting an unexpected server error with the attached messages. It looks like Labkey is trying to run a script (viability-14.20-14.20.sql) that upgrades from 14.10 to 14.20. Since I'm running Labkey 16, I'm not sure why it is trying to run the script. Please let me know how I can fix this. Thanks, Alex

How to make your own personalized installation package?

Sat Aug 13 03:00:47 PDT 2016

Hello,I installed only Labkey core and Filecontent and audit modules. Publishing package is installed there are many modules,Delete not every module is cumbersome. How to make your own personalized installation package? Thanks

LabKey in the cloud on a VM on Azure

Thu Aug 04 14:08:22 PDT 2016

Hello, I was wondering if anyone could guide me in the right direction to setting up a free instance of labkey on the cloud using a virtual machine in Azure. I have set up a VM machine on azure and they have provided me with a custom domain under their services. If I go to their domain name I get the error in my browser saying it took to long to respond and no connection is available to labkey. Now, what I am wondering is how can I setup the labkey services so that when I put the Azure domain into a browser I will be prompted with the login page of labkey. I am new to this so I have no clue how to set up it up- right now I can just connect through azures portal so I have direct access to the virtual machine with the lab key hosted on the computer/server. How do I setup the labkey server settings where accessing the domain directly would lead me to the login page of labkey? Or rather how do I configure a VM so that labkey will be accessible? Any help would be appreciated! Thanks

apache proxy and login-setPassword URL

Thu Jul 21 10:03:27 PDT 2016

I have the Labkey server running at http://servername:8080/labkey and have apache running in front of that to proxy https://servername/labkey to that address. That seems to work fine for the most part. The only issue I've run into with this is in the emails that are generated for when new users are generated. Those emails reference the http address with port 8080, which is not reachable from outside the server, like this: http://servername:8080/labkey/login-setPassword.view?verification=somestring&email=username%40domain.com I'd like that email invite to include an address like this: https://servername/labkey/login-setPassword.view?verification=somestring&email=username%40domain.com

Support for SQL Server 2016

Tue Jul 19 16:28:50 PDT 2016

Forgive me, this is a pretty elementary question. I am setting up a new BI server for a biobank, and am designing it now. We are a Microsoft shop, so the choice of DBMS is already made :) SQL Server 2016 has just been released by Microsoft, and is not mentioned as a supported release for current LabKey. We are going with it to get extra features not available in earlier releases. At the same time we are looking for alternatives to Microsoft's tools for information delivery because we have data we cannot store in Sharepoint, and I am thinking to take a close look at LabKey for this. How long might it be before Labkey will support SQL Server 2016? How risky is it to try and make them work together before it is officially supported? Are the risks just that things might not work, or are there data security implications?

500: CONFIGURATION ERROR

Wed Apr 20 10:57:03 PDT 2016

Hi, I installed every required component succesfully, But when I configure the application It returnes me an configuration error. I send you a .log file and a print. I checked that the database is running, and the database connection URL and user credentials in labkey.xml are ok. I installed, Tomcat 8.0.33, Postgres 9.5, and Java jdk1.8.0_77. Please, can you help me? Hilaria

Error during configuration

Tue Apr 05 04:03:01 PDT 2016

While doing the initial configuration in Site Settings once the Submit button was pressed, the labkey server returned error: Unhandled exception: 500: Unexpected server error java.lang.NullPointerException: Could not find domain for AppPropsEvent I am attaching the labkey.log file. My operating system is Debian GNU/Linux 8.3, Labkey version is 16.10, tomcat version Apache Tomcat/8.0.14 (Debian), Java JDK 1.8.0_74. Thank you!

Upgrade from 15.x to 16.1 Script formatting...

Wed Mar 23 09:16:37 PDT 2016

I am trying to upgrade LabKey Server using the manual-upgrade.sh script but I do not seem to get the correct format going to properly execute it. ===== manual-upgrade ===== ./manual-upgrade.sh -l dir /usr/local/labkey/ -d dir /usr/home/diego/Downloads/LabKey16.1-42836.12-community-bin/ -c dir /usr/local/apache-tomcat-8.0/conf/Catalina/ -u www --service /usr/local/etc/rc.d/tomcat8 --catalina /usr/local/apache-tomcat-8.0/bin/shutdown.sh /usr/local/apache-tomcat-8.0/bin/startup.sh ======== end ============= Thanks in advance! Diego

Windows Dev Env Setup

Wed Mar 16 09:15:49 PDT 2016

I'm trying to set up my development environment in Windows. I'm primarily working from the documentation at https://www.labkey.org/home/Documentation/wiki-page.view?name=build I'm documenting my progress here: https://gist.github.com/abalter/e7037098cf58b036a36c/edit I'm stuck on one particular issue. Right now I have JAVA_HOME=C:\Program Files\Java\jre1.8.0_74 When I start IntelliJ, I get 'tools.jar' seems to be not in IDEA classpath. Please ensure JAVA_HOME points to JDK rather than JRE. When I change to JAVA_HOME=C:\Program Files\Java\jdk1.8.0_74 and start IntelliJ, I get what is in the image. Suggestions?

Single Sign-On at the Project level or multipls CAS servers

Tue Mar 15 11:21:48 PDT 2016

Hello All, Each one of our Projects has it's own user base. Has anyone looked into providing Single Sign-on for users at the Project level? The current system only allows for one Single Sign-On server configuration. We would need to be able to point to multiple CAS servers. Any feedback is much appreciated. Thanks, Louie

time charts

Mon Mar 07 03:26:43 PST 2016

Hi I'm having troubles with creating time charts. I use the tutorial study/datasets HIV/CD4 . If I import the demo study and try to make a time chart with e.g the lab-data it says: No calculated interval values (i.e. Days, Months, etc.) for the selected 'Measure Date' and 'Interval Start Date' If I click view data then I can see there is empty fields in days/visits/visit day. This goes for any measure in any dataset I have tried I have clicked recalculate visits, is there anything else obvious I could try? If I check the Lab result data I can see the Day field. Best wishes Allan

Histogram as Quick Chart

Wed Mar 02 06:10:03 PST 2016

Hi I would like to implement histograms as quick charts, so that I can get a histogram showing the count of all groups in a categorical/text variable. It should be available for any data grid How can I go about doing that? Is it a module that implement these functions that I can change, or will I need to build it from the ground up? Best wishes Allan lind-Thomsen

LabKey Running R and Virtual Frame Buffer Server Config...

Thu Feb 25 14:35:33 PST 2016

Running: FreeBSD 10.2 (64bit) LabKey Server 15.3 (Latest Updates) Tomcat 8.0.28 tomcat user: www tomcat directory: /usr/local/apache-tomcat-8.0/ R-project: 3.2.2 VFB server: xorg-vfbserver-1.18.0.1 (pkg install) Have successfully installed R but I am having issues configuring the VFB server to work on LabKey Server. Followed the tutorial below, but it seems as though some steps might be different for FreeBSD... Please advise! https://www.labkey.org/home/Documentation/wiki-page.view?name=configVirtualFrame Configuration Test Output ========================= jpeg png tiff tcltk X11 aqua TRUE TRUE TRUE TRUE FALSE FALSE http/ftp sockets libxml fifo cledit iconv TRUE TRUE TRUE TRUE FALSE TRUE NLS profmem cairo ICU long.double libcurl TRUE TRUE TRUE TRUE TRUE FALSE > proc.time() user system elapsed 0.152 0.010 0.182 ===== END OUTPUT ===== Thanks in advance! Diego

LabKey Sample Study Installation Missing options...

Fri Feb 12 10:53:16 PST 2016

LabKey 15.3 is correctly running, now wanting to install ImportableDemoStudy.folder.zip, but noticed the instructions to the below tutorial do not match the options to what is available in my LabKey version. 1.) "Confirm that Inherit from Parent Folder is checked" do not seem to find that option anywhere... 2.) "On the New Study page, click Import Study" do not seem to find the "import study" option anywhere... 3.) Thanks in advance! Screenshot attached! LabKey Sample Study Article ============================ https://www.labkey.org/home/Documentation/wiki-page.view?name=setupDemoStudy

LabKey Server Not Starting on Tomcat Intiation...

Wed Feb 10 14:48:51 PST 2016

Have installed LabKey Server Community 15.3 on CentOS Linux release 7.2.1511 (Core) (PostgreSQL) 9.2.14. PostgreSQL and Tomcat are both running correctly. But LabKey Server does not load... Followed instructions from the following link: https://www.labkey.org/home/Documentation/wiki-page.view?name=config Have attached my catalina log file... What can be going wrong? Files in the wrong directory? Let me know if you all need more information. Thank you, Diego

Tomcat/WebDav bug fixed on LabKey 15.3 r42135.48

Mon Feb 01 16:12:50 PST 2016

An important bug has been fixed on LabKey 15.3 r42135.48 regarding WebDav and the recent updates to Tomcat, specifically Tomcat 8.0.30+ and Tomcat 7.0.67+ Due to unforeseen changes with Tomcat's handling of WebDav calls, some functions with the FileContent module (Files Web Part) would cause issues with creating new folders, generate Error 400 responses in the background, or even prevent LabKey from starting due to the WebDav controller failing during the initialization. All WebDav bugs have been identified and fixed, so if you have plans on upgrading Tomcat to one of the two versions listed above, please make sure you download our revised LabKey 15.3 build. Regards, Jon - LabKey Support

problem upgrading 15.2 to 15.3

Wed Jan 27 09:13:36 PST 2016

Hi I am trying to upgrade 15.2 to 15.3 in our devel instance. I have done some upgrades before without issues but now I am getting a weird error. This is my environment running in centos6: Core Database Configuration Server URL jdbc:postgresql://127.0.0.1/labkey Product Name PostgreSQL Product Version 9.2.8 JDBC Driver Name PostgreSQL Native Driver JDBC Driver Version PostgreSQL 9.4 JDBC4.1 (build 1201) JDBC Driver Location file:/opt/apache-tomcat-7.0.53/lib/postgresql.jar Runtime Information Mode Production Asserts disabled Servlet Container Apache Tomcat/7.0.53 Java Runtime 1.8.0_40 Java Home /opt/jdk1.8.0_40/jre Username labkey User Home Dir /home/labkey Webapp Dir /opt/LabKey15.2-39071.18-bin/labkeywebapp OS Linux Working Dir /home/labkey Server GUID 26b65700-c331-1031-a374-504196604ae0 Server Time 27/01/2016 17:40 but when doing the post-upgrade steps in the web interface I get this in the logs: https://gist.github.com/pescobar/11468150968f960f16ed I think the interesting lines are these ones: https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L196 https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L243 https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L334 https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L383 Trying to figure out what's going on I went to the admin console >> diagnostic >> database check >> do database check and then I get this error: Checking Container Column References... Checking PropertyDescriptor and DomainDescriptor consistency... ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /Shared/Demo Clinical Study Published ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Study ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Lab A ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Lab B ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /Shared/Demo Clinical Study Published When I try "click here to attempt recovery ." I get this error: 500: Unexpected server error SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "domainid" does not exist Position: 52 An this is the complete log when trying the recover https://gist.github.com/pescobar/d8ed83836a5bb2967d30 I have also notice that the postgres driver jar is "PostgreSQL 9.4 JDBC4.1 (build 1201)" but I am using postgres 9.2 installed fro the centos SCL repositories (https://wiki.centos.org/AdditionalResources/Repositories/SCL). I was thinking about upgrading postgres to 9.4 but in the labkey compatibility table I see that postgres 9.2 is supported so I am not sure if this could be the problem. does anyone knows which could be the issue? Thanks in advance for any help or suggestion. regards, Pablo.

Installation - NullPointerException

Thu Jan 21 14:26:59 PST 2016

Hi All, First time LabKey user. I am attempting to install LabKey on Linux with the following details: LabKey 15.3, Tomcat 8.0.30, JDK 1.8, Postgres 9.1.18 - all running on Debian 7. PG and Tomcat are working fine. Labkey installation is not, as it is throwing a server error - 500. Its able to run the SQL scripts and create few schemas, and populate the core schema (the log has a message of not supporting PSQL version 9.1.18, but this does not seem to be the issue, although I am planning an upgrade later). The Exception: INFO ModuleLoader 2016-01-20 16:55:55,521 localhost-startStop-1 : LabKey Server startup is complete, modules will be initialized after the first HTTP/HTTPS request INFO ViewServlet 2016-01-20 16:55:56,729 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-01-20 16:55:56,730 localhost-startStop-1 : WEBAPP: /usr/local/labkey/labkeywebapp/ INFO ViewServlet 2016-01-20 16:55:56,730 localhost-startStop-1 : PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ERROR DavController 2016-01-20 16:56:39,999 http-nio-8080-exec-2 : unexpected exception java.lang.NullPointerException at org.labkey.api.data.ContainerManager.toString(ContainerManager.java:1549) at org.labkey.api.data.ContainerManager._getFromCachePath(ContainerManager.java:1537) --- I have attempted to ease access to both the tomcat and the labkey directories, in case its an access issue, with no success. Any tips? Thanks.

HTTP Status 500 - Internal Server Error

Wed Jan 20 21:56:41 PST 2016

Longtime labkey user first time installation problem (well its been a while). Followed the linux instructions on the website (installing on Centos7) and when I start it up I get a 500 error. Versions all appear to be supported(javac 1.8.0_66, PostgreSQL 9.2.14, apache-tomcat-7.0.67). Tomcat appears to running just fine. Any suggestions would be great. Thanks -Rich

ETLs

Tue Jan 05 05:22:30 PST 2016

Hi I'm working with ETL's and have some questions. They spring from the fact that we have a collection of source tables on an external database server, which needs some basic cleaning/transforming before loading them into labkey. e.g. we need to change some',' and '.' to be able to convert a column to floating point. 1: If I use a stored procedure server to populate a source table. How do I make sure that the stored procedure is executed before loading the data into the destination? 2: Is it possible to use a stored procedure which return a table/select query as a source in the ETL step so that it is loaded directly into the destination? 3: Is there a better way to do the transform step than in stored procedures when using Labkey? 4: How does work? I couldn't find answers to these questions in the documentation, but if I have overlooked something please point me in the right direction. Best wishes Allan

Streamlined Server Upgrade/Startup Process in 16.1

Mon Jan 04 13:37:33 PST 2016

Greetings, Quick note just to let everyone know that LabKey Server's automatic upgrade process is becoming somewhat more automatic starting with the 16.1 release. Previously, the server would upgrade the core module at server startup, but would wait for an administrator login before upgrading other modules or initiating module startup. A trunk commit last week changed the server to initiate upgrade and startup of **all** modules at server startup time. Administrators can still log in to view upgrade/startup progress, but the server will no longer wait for a login. This change streamlines the startup process, simplifies upgrade code, and facilitates scripted upgrades of LabKey Server. We suspect most administrators won't notice a difference, but let us know if you have any questions or concerns about this change. Thanks, Adam

Problem with import of Labkey data into SAS

Mon Dec 21 05:09:46 PST 2015

Hi I'm trying to import a labkey list into SAS. I have installed the SAS and Java libraries and added them to the paths in the sasv9.cfg file I have created a _netrc file in my home directory (there is a copy attached with a changed password, but the password starts with a '-' which is kept), and I made an environmental variable named HOME pointing to my home directory. SAS code: %labkeySelectRows(dsn=mydata, baseUrl="http://rghorion001:8080/persimune", folderPath="/Persimune", schemaName="lists", queryName="mikrobiologi_pos_prover"); SAS error: ERROR: Could not instantiate class org/labkey/remoteapi/sas/SASSelectRowsResponse at line 27 column 69. ERROR: DATA STEP Component Object failure. Aborted during the EXECUTION phase. dec 21, 2015 1:24:21 PM org.labkey.remoteapi.Command _execute INFO: Requesting URL: http://rghorion001:8080/persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.queryName=mikrobiologi_pos_prover&schemaName=l ists&query.maxRows=1 org.labkey.remoteapi.CommandException: Unauthorized at org.labkey.remoteapi.Command.throwError(Command.java:355) at org.labkey.remoteapi.Command._execute(Command.java:321) at org.labkey.remoteapi.Command.execute(Command.java:202) at org.labkey.remoteapi.query.SelectRowsCommand.execute(SelectRowsCommand.java:61) at org.labkey.remoteapi.sas.SASBaseSelectCommand.execute(SASBaseSelectCommand.java:65) at org.labkey.remoteapi.sas.SASSelectRowsResponse.(SASSelectRowsResponse.java:54) at org.labkey.remoteapi.sas.SASSelectRowsResponse.(SASSelectRowsResponse.java:44) This indicates a login error, so I tried using Rlabkey to import the same list into R, which works, so there isn't an error in the _netrc file (unless SAS and R parse/interpret it differently). In the logfile, localhost_access_log I see: [21/Dec/2015:13:15:36 +0100] "GET /persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.showRows=all&query.queryName=mikrobiologi_pos_prover&schemaName=lists HTTP/1.1" 200 85737276 (for the R access) [21/Dec/2015:13:24:22 +0100] "GET /persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.queryName=mikrobiologi_pos_prover&schemaName=lists&query.maxRows=1 HTTP/1.1" 401 6444 (for SAS access) There doesn't seem to be anything in the other log-files. (labkey.log, labkey-errors.log) For good measure I restart SAS after each change. Furthermore, if I add the userName and password to the SAS-macro call, then it also works. My own conclusion is tha tit must på the SAS interpretation of the _netrc file that fails, but because it wotks with Rlabkey i'm not sure what kind of error it could be. Do you have any idea what might cause this? Best wishes Allan Lind-Thomsen Labkey ver. 15.3-41022.16 SAS Ver. 9.4 Labkey Server: windows 8 Client windows 7

Using custom perl/python/R script in LabKey only when importing files?

Thu Nov 26 12:44:40 PST 2015

Is it possible to add our own pipeline (perl/python/R scripts) elsewhere than when importing files? Is it possible to have them with the other analysis scripts/tools in the Sequence Analysis (DISCVR-Seq) module? I've spent some time reading about creating pipelines, but I can only find examples and description of pipelines used when importing files, not to work on files already uploaded/analysed.

auto-commit keeps LabKey 15.3 from starting

Wed Nov 25 19:26:40 PST 2015

I have setup LabKey several times (13.3, 14.1, 14.2, 14.3), and the 15.3 webapp is running, but this time I can't get past this JDBC error on first access. The labkey user has superuser access. I added the defaultAutoCommit line to try and resolve it, but no go. Any ideas? Thanks. Linux insilico 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Java 8 (installed apt-get PPA) Tomcat 7 (installed apt-get) PostgreSQL 9.3 (installed apt-get) LabKey 15.3 (download and fresh install to /usr/local/labkey) labkey.xml data source section: Configuration Error Detected at LabKey Server Startup A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool. This is a problem with your configuration. Please contact your local server administrator for assistance, or LabKey Software at support@labkey.com for operational assistance with correcting the configuration error. org.labkey.api.util.ConfigurationException: A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool. at org.labkey.api.data.DbScope._getConnection(DbScope.java:737) .

Upgrade to 15.3 failed.

Mon Nov 23 17:18:27 PST 2015

I'm attempting to upgrade to 15.3 on Windows. The installer gives me the following message: Postgres upgrade failed: 1. Unable to recover. However before that a message flashed up complaining about invalid characters in the install path. The message did not persist long enough for me to read it all :( Now it would appear that my install is broken and I have no idea how to fix it without reverting to a backup.

Failed to start labkey (first time) with exception, "java.lang.NullPointerException"

Thu Nov 19 08:54:36 PST 2015

Hello, I have tried to install Labkey on my Mac, but fail to initialise the Labkey app at, "localhost:8080/labkey". Error: """ ERROR ModuleLoader 2015-11-19 17:30:56,896 localhost-startStop-1 : Failure occurred during ModuleLoader init. java.lang.NullPointerException """ I followed the instructions on the website at, "https://www.labkey.org/home/Documentation/wiki-page.view?name=manualInstall". Versions: OS, OS X 10.10 Java, 1.8 PostgreSQL, 9.4.5 Tomcat, 8.0.28 Labkey, 15.1-3 Thank you for any help. Gratefully, Cameron

Mutant vs Control protein expression ratios

Wed Nov 18 15:20:36 PST 2015

Hi, I have been playing around with some ".mzXML" data obtained from "LTQ Orbitrap Velos" raw data on the LabKey server. I will like to find perturbed pathways based on the differential expressions of mutant/wild-type(control). Even though I have followed the tutorials in the LabKey documentation, I'm still not sure about the steps that are necessary to do this kind of analysis that I'm interested in. For example, I need to know which proteins are over/under- expressed in either mutant or the control. How can I use LabKey server to achieve this? Any help will be appreciated. Thanks

Change User Properties

Mon Nov 09 05:02:15 PST 2015

Hi According to the documentation there should be a "Change User Properties" link in the "Site Users" section, which don't seem to be there. It is however in the 'Admin Console', but when I click it I just get an empty page with a 'back' and a 'home' button. There is no errors in the log. Do you have any clue to what the problem might be? Does it require any setup to use? Best wishes Allan Lind-Thomsen

Login security

Mon Nov 09 04:44:48 PST 2015

Hi Is it possible to automatically block a user after a certain number of failed attempts? Best wishes Allan Lind-Thomsen

"A sequence database must be selected" error in search MS2 Data page

Sat Nov 07 04:01:49 PST 2015

Hi, I clicked on search to carry out X!TANDEM PEPTIDE SEARCH, but got the following error message: "A sequence database must be selected". I checked the Protein databse section of this page and only found dropdown link and a "none found" message. I noticed in the file section that there is no file in the "databases" folder even though I had already downloaded and imported the swissprot database as recommended in the documentation. Labkey version: apache-tomcat 7.0.62; Database Product Version: 9.4.4 Web browser: firefox OS: Windows7 I wonder why the protein database is not where it should be.

LabKey as primary credentials to authenticate to third party application

Wed Nov 04 18:38:47 PST 2015

Can we use labkey’s built-in authentication service (i.e. database authentication) to pass credentials to other software/sites? We want to integrate with other software, but do not want to have 2 credentialing systems. This seems to be point to an SSO integration but with LabKey as primary. We also do not want to use LDAP at this time. Would there be a capability or best practice to accomplish this from LabKey? Thanks!

cannot start Labkey Server on Linux

Thu Oct 29 10:47:02 PDT 2015

I tried to start the Labkey server (version 15.2) on Linux machine. I got the error messages please see the attached log file. Please help me! Thanks, Haibin

Skipping multiple question in surveys

Wed Oct 28 14:46:23 PDT 2015

Hello all, I'm a new user to LabKey and I will be using it mostly to collect survey data. I'm trying to do the following: Q1. Were you sick? Yes/No If yes, answer questions 2-5 If no, answer question 6 I'm able to use the skip logic on one question at a time, but wondering if it's possible to apply the skip logic to multiple questions as a group? Thanks! Patrick

Remote pipeline debugging

Mon Oct 26 08:22:06 PDT 2015

Hi, I'm setting up a remote pipeline server on a linux server (CentOS 6.5). The labkey webserver is a windows 2008 server. I've followed these instructions to set up the the remote pipeline server (https://www.labkey.org/wiki/home/Documentation/page.view?name=configureRemoteServer) and these instruction to have the labkey webserver to use the remote pipeline (https://www.labkey.org/wiki/home/Documentation/page.view?name=installConfigureEnterprisePipeline). Every time I try to send a job to the remote pipeline server from the labkey webserver, it still tries to run it locally from the Sequence Analysis module (DISCVR-Seq module). The message I get in the pipeline log has: "Starting to run task 'org.labkey.sequenceanalysis.pipeline.SequenceAlignmentTask' at location 'webserver'" and it can't find the tool I'm trying to run has it's not installed locally. I've added -DsequencePipelineEnabled=true in the Tomcat7w startup options and configured the remote and local pipelineConf.xml scripts. ActiveMQ is setup on the linux server (on the remote pipeline server) and seems to works. Is there something I missed and is there some documentation on labkey.org I should check to help me debug this?

Error received

Fri Oct 09 15:36:15 PDT 2015

org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is java.sql.SQLException: Invalid object name 'comm.Threads'. 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)

SQLServer 2008R2 deprecation warning

Thu Oct 08 11:12:51 PDT 2015

Hi everyone, We wanted to give everyone an update on our support for SQLServer 2008R2. We've long listed it as deprecated (since at least version 14.2), but we're shifting starting in 15.3 to actively encourage administrators to upgrade. In version 16.1, we will no longer support 2008R2. This is in line with our standard approach of dropping support for versions of third-party software that are no longer supported by their vendor. Microsoft's end-of-life for 2008R2 is complicated by the vast number of versions, but has been largely unsupported for a couple of years already: https://support.microsoft.com/en-us/lifecycle?c2=1044 We encourage everyone to plan ahead with their upgrade schedule. Thanks, Josh

failed upload of ProtProphet data

Thu Oct 01 05:47:38 PDT 2015

Hi, I am not sure what is wrong, but I tried to upload Comet search results from shotgun proteomics LCMS acquired on Thermo Fusion and the upload failed with the following in the log file (below). I was able to upload Comet search results and shotgun proteomics from Fusion before. I noticed that in reading the mzXML file it shows MS3: 0 and I am sure that is incorrect. Any suggestions? Thanks, Tomas 01 Oct 2015 05:23:34,566 INFO : Starting to load ProteinProphet file /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.prot.xml 01 Oct 2015 05:23:34,587 INFO : Resolved referenced PepXML file to /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.pep.xml 01 Oct 2015 05:23:34,588 INFO : Starting import from interact-150909_LRAPEGJW01.pep.xml 01 Oct 2015 05:23:34,595 INFO : Starting to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml 01 Oct 2015 05:23:34,627 DEBUG: 0.03 seconds to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml 01 Oct 2015 05:23:34,627 INFO : Starting to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718 01 Oct 2015 05:23:35,058 INFO : FASTA file "/data/dbase/Uniprot/uniprot.sptr.human.20150718" not imported, but another file, 'uniprot.sptr.human.20150718', has the same checksum 01 Oct 2015 05:23:35,062 DEBUG: 0.43 seconds to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718 01 Oct 2015 05:23:35,062 INFO : Starting to import peptide search results 01 Oct 2015 05:23:35,062 INFO : Importing MS/MS results is 0% complete 01 Oct 2015 05:23:35,063 INFO : Starting to parse /data/users/tvaisar/HDL/LRA/1509Shotgun/150909_LRAPEGJW01.mzXML to get scan counts 01 Oct 2015 05:23:38,125 INFO : Finished parsing to get scan counts. Total: 53396, MS1: 7724, MS2: 45672, MS3: 0, MS4:0 01 Oct 2015 05:23:38,144 ERROR: MS2 import failed java.lang.ArrayIndexOutOfBoundsException 01 Oct 2015 05:23:38,154 ERROR: ProteinProphet load failed java.lang.ArrayIndexOutOfBoundsException

Manual installation, CentOS 6.5, Postresql. Failed to start up

Fri Sep 25 19:34:38 PDT 2015

There seems to be a problem with my labkey.xml setup. The admin account 'yuw' for Postgresql was setup to be the same as the login account on my CentOS acct. Any clue? Thanks! Wen org.labkey.api.util.ConfigurationException: DataSources are not properly configured in labkey.xml. at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:887) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:318) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:230) at java.lang.Thread.run(Thread.java:745) Caused by: javax.naming.NameNotFoundException: Name [comp/env] is not bound in this Context. Unable to find [comp]. at org.apache.naming.NamingContext.lookup(NamingContext.java:819) at org.apache.naming.NamingContext.lookup(NamingContext.java:167) at org.apache.naming.SelectorContext.lookup(SelectorContext.java:156) at javax.naming.InitialContext.lookup(InitialContext.java:417) at org.labkey.api.module.ModuleLoader.ensureDatabase(ModuleLoader.java:902) at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:864)

MS SQL Server setup

Thu Sep 24 01:43:40 PDT 2015

Hi I'm still having problems with getting a running Labkey installation using MS SQL Server. The basic questions are: 1: What is the preferred process to install a Labkey server using MS SQL Server when you don't have full permission/control of the server and want to be certain that the labkey admin have all the necessary permissions (at the moment the labkay admin is owner of the database) ? 2: Can you describe what permissions are needed (besides from being owner of the database) in the database to successfully run labkey? 3: Must it be the labkey server that runs sp_updatestats or is it OK if we have the option 'Auto update statistics' enabled on the database? Background: environment: MS SQL Server 2012, tomcat 7,windows 8 server. Manual install of Labkey I'm not sysadmin so I don't have full control over the database, I have to ask our central IT department to do stuff, which takes 1-3 days depending on how busy they are. There are (at least) two issues: 1: GROUP_CONCAT Needs to be part of core schema, but the core schema cannot be made before the initial run of the server. I get an error if I try to create the core schema in advance and assign the GROUP_CONCAT functions to it before I start the server ("core schema already defined" exception). After moving GROUP_CONCAT back to dbo and remove the schema. I get another error "DROP ASSEMBLY failed because 'GroupConcat' is referenced by object 'GROUP_CONCAT_D'" but I was able to start labkey. Then it seemed to work but when I installed a module I was back to a previouos discussed "FastaAdmin already exist" exception. 2: sp_updatestats Need permission to run this stored procedure(in our system we don't have this pr default), this must be assigned before creating any database objects. Is it important who runs this procedure, as long as it is run? Will the following process work (using the labkey admin user): 1: create the database 2: Set permission to run sp_updatestats 3: start Labkey server and finish the basic installation process. 4: install GROUP_CONCAT 5: Move GROUP_CONCAT to core schema 6: Restart server Appreciate any comments and suggestions. Best wishes Allan

Import data from external schemas

Thu Sep 17 07:11:34 PDT 2015

Hi All Our data is almost exclusively stored in SQL databases, and data is comming continously into the tables. What is the preferred way to import these data into dataset/assays/lists to be able to work with them inside labkey? f.x. we have a table with basic information about the patient birthday, gender, enrollmen date etc, and with new patients being enrolled continously. What will be the best way to use this table as a basic demographic table in the study? I have looked at external schemas but it is not obvious for me how to do something like that in labkey. Best wishes Allan

Stopping Uniprot TrEMBL annotation upload

Wed Sep 16 13:03:47 PDT 2015

Hi, I adventurously started upload of the full Uniprot-TrEMBL annotation from uniprot_trembl.xml. It appears to be endless - has been running since Aug 23, and it is still adding new entries. Is there a way to abort/cancel this process? In retrospect subsetting the uniprot_trembl.xml to only relevant species would have been prudent, but at this point I am just trying to stop it. Perhaps incorrectly I tried to "Complete" the process in the Admin>Site>Pipeline, which marked it as Complete, yet the process is still running. Any advice? Thanks, Tomas

MS SQL Server problem

Wed Sep 16 05:10:24 PDT 2015

Hi All I'm having trouble with using MS SQL server 2012 (Build number: 11.0.3381.0) I made a manual install on Windows 8 (danish language): labkey 15.2 (build39349.20) Java 8 Tomcat 7.0 postgresql 9.4 And it worked. But with our setup it would be better to use MS SQL Server because we use that for everything else. I then changed the database to SQL Server and then I did get errors like: java.sql.SQLException: Parameter #20 has not been set. Does anybody knows about anything which might cause this? Any hints and thoughts will be appreciated. I have attached labkey.xml and labkey.log. Best wishes Allan Lind-Thomsen