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"11.1 API changes.pptx" attached to message "labkey PIVOT syntax?"

LabKey Server 11.1 What’s New for Developers Josh Eckels March 17, 2011 11.1 Feature List Improved look and feel GPAT data persistence in hard tables Server-side validation script enhancements JavaScript reports AJAX report designer Copy-to-study by reference Study data visualization File management UI enhancements Easier initial data import for GPAT Additional LabKey SQL syntax Agilent feature...

can't open scan

I'm trying to open a scan from an MS2 report. Instead of the scan image I get an image with the text: Could not find spectra for scan 814 in 219_1-10.mzXML All of the scans that I tried in this run give the same mmessage. I am able to open this mzXML file through the experiment browser. The log contains the two exceptions below. Has anyone seen this before? Thanks, Bill ERROR MSXMLParser...

"labkey.log" attached to message "Caused by: java.lang.IllegalStateException: Why am I in a transaction?"

INFO ModuleLoader 2015-07-17 11:53:02,719 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2015-07-17 11:53:05,172 localhost-startStop-1 : Attempting to create database "labkey" INFO DbScope 2015-07-17...

"labkey-errors.log" attached to message "Failed to start labkey (first time) with exception, "java.lang.NullPointerException""

ERROR ModuleLoader 2015-11-19 17:30:56,896 localhost-startStop-1 : Failure occurred during ModuleLoader init. java.lang.NullPointerException at java.io.File.<init>(File.java:277) at org.labkey.api.module.ModuleLoader.webappFilesExist(ModuleLoader.java:449) at org.labkey.api.module.ModuleLoader.verifyProductionModeResources(ModuleLoader.java:433) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:313)...

"labkey-errors.log" attached to message "cannot start Labkey Server on Linux"

ERROR ModuleLoader 2015-10-29 13:23:26,629 localhost-startStop-1 : Failure occurred during ModuleLoader init. java.lang.IllegalArgumentException: Could not find module 'experiment' on which module 'Nab' depends at org.labkey.api.module.ModuleDependencySorter.sortModulesByDependencies(ModuleDependencySorter.java:61) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:267)...

"cpas.install.log" attached to message "CPAS.XML Database setup"

at org.fhcrc.cpas.view.ViewContext.getACL(ViewContext.java:154) ... 70 more 21 Dec 2005 11:45:15,323 DEBUG ModuleLoader : ModuleLoader init 21 Dec 2005 11:45:15,647 DEBUG CoreModule : Ensuring databases are present 21 Dec 2005 11:45:15,756 DEBUG CoreModule : Attempting to create database cpas 21 Dec 2005 11:45:17,250 DEBUG CoreModule : Just created "cpasDataSource" database; attempting...

prophet parameter

Hi. It looks like the pipeline can't handle pepxml results where there are spectrum queries without search hits (sequest search). We wanted to keep all original search info through out the pipeline so the pipeline prophet min probability was set to 0. It errors at 'ERROR: MS2 import failed' and 'FATAL: XAR import FAILED' The peptide and protein prophet reports are generated but the job...

"server error.txt" attached to message "errors in LabKey flow analysis"

500: Unexpected server error Home Back Folder 'Mean(PE ' is not a valid statistic. [Show more details] org.labkey.flow.analysis.model.FlowException: 'Mean(PE ' is not a valid statistic. at org.labkey.flow.analysis.web.StatisticSpec.<init>(StatisticSpec.java:93) at org.labkey.flow.query.AttributeCache$StatisticCache.keyFromString(AttributeCache.java:202) at org.labkey.flow.query.AttributeCache$StatisticCache.keyFromString(AttributeCache.java:193)...

Upgrade version 15.2 to 16.1 (16.2)

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...

"TomCat_Setup.pdf" attached to message "DataSources are not properly configured in labkey.xml."

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

"labkey-errors.log" attached to message " Help Please"

ERROR ExceptionUtil 2014-12-24 12:27:46,558 localhost-startStop-1 : Exception detected and logged to mothership: java.lang.Exception: Null scale for "userid" in column "SqlScripts.createdby" in schema "core" at org.labkey.core.dialect.PostgreSql84Dialect$PostgreSQLColumnMetaDataReader.getDomainScale(PostgreSql84Dialect.java:1525) at org.labkey.core.dialect.PostgreSql84Dialect$PostgreSQLColumnMetaDataReader.getScale(PostgreSql84Dialect.java:1506)...

"cpas[1].log.1" attached to message "500: Unexpected server error"

03 Feb 2006 10:46:57,287 ERROR Global : Unhandled exception caught in Global.app: 500: Unexpected server error java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at org.fhcrc.cpas.util.BoundMap.get(BoundMap.java:89) at org.fhcrc.cpas.view.GroovyView.createModelBinding(GroovyView.java:475) at org.fhcrc.cpas.view.GroovyView.renderView(GroovyView.java:447) at org.fhcrc.cpas.view.WebPartView.render(WebPartView.java:123)...

"cpas.log.1" attached to message "500: Unexpected server error"

03 Feb 2006 10:46:57,287 ERROR Global : Unhandled exception caught in Global.app: 500: Unexpected server error java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at org.fhcrc.cpas.util.BoundMap.get(BoundMap.java:89) at org.fhcrc.cpas.view.GroovyView.createModelBinding(GroovyView.java:475) at org.fhcrc.cpas.view.GroovyView.renderView(GroovyView.java:447) at org.fhcrc.cpas.view.WebPartView.render(WebPartView.java:123)...

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

INFO ModuleLoader 2015-11-19 17:30:56,820 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR ModuleLoader 2015-11-19 17:30:56,896 localhost-startStop-1 : Failure occurred during ModuleLoader init. java.lang.NullPointerException ...

XTamden error

Hi, I got the following error when hitting the "X!Tandem peptide search" button. This is on Labkey/CPAS 8.1 and the xtandem (/tandem_2007-07-01_2) downloaded from the labkey website, and on a Debian Linux box. Any clues? -Aschwin --------- An unexpected error occurred [Show more details] java.lang.NullPointerException        at org.labkey.jsp.compiled.org.labkey.ms2.pipeline.search_jsp._jspService(search_jsp.java:187)...

RE: Issue #3666, "Sequest pipeline broken," has been updated

Hi, I’m trying to resolve the bug #3666 and to patch a new server install. To do this I need to move the newly compiled ms2 module to a labkey server that was installed with the installer. I think I had been able to do this before buy just moving the ms2.jar. Now it appears that ms2.module is the file to be moved but this doesn’t work either. I get the error below. I really do need to patch this...

"LabKey List Error" attached to message "Error when loading custom list field definitions?"

ERROR BaseRemoteService 2009-08-14 11:19:44,885 http-8080-Processor22 : GWT Service Error org.apache.commons.beanutils.ConversionException at org.labkey.api.data.ConvertHelper$_IntegerConverter.convert(ConvertHelper.java:457) at org.apache.commons.beanutils.ConvertUtilsBean.convert(ConvertUtilsBean.java:428) at org.apache.commons.beanutils.ConvertUtils.convert(ConvertUtils.java:217) ...

Query Metadata: Examples

This topic provides examples of metadataSql used to change the display and behavior of fields in tables and queries. Auditing Level Conditional Formatting Include Row Selection Checkboxes Hide a Field from Users Show/Hide Columns on Insert and/or Update Use a Format String for Display Use a Text Expression for Display Set a Display Width for a Column Display Columns in Specific Order...

"catalina.2024-01-02.log" attached to message "Build failed"

02-Jan-2024 14:50:12.244 messages [main] org.apache.catalina.startup.VersionLoggerListener.log Server.server version: Apache Tomcat/9.0.83 02-Jan-2024 14:50:12.257 messages [main] org.apache.catalina.startup.VersionLoggerListener.log Server Build: Nov 9 2023 20:57:42 UTC 02-Jan-2024 14:50:12.257 messages [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.83.0...

Physical Exam.xls

data Participant ID Date Height (cm) Weight (kg) Temperature (C) Systolic Blood Pressure xxx/ Diastolic Blood Pressure /xxx Pulse Respirations Clinician Signature/Date Pregnancy Form Language ARV? ARV Regimen Type 101344 2008-04-27 173.0000 68 37.0 117 83 61 101344 2008-05-25 175.0000 69 36.8 145 103 71 101344 2008-06-22 175.0000 71 38.2 166 101 68 101344 2008-08-17 173.0000 73 36.5 125 95 74...