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HIV Study Tutorial
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"cpas.log" attached to message "500: Unexpected server error"

09 Mar 2006 22:48:22,687 ERROR ViewServlet : error javax.servlet.ServletException: Servlet execution threw an exception at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:275) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)...

"cpas.webError.txt" attached to message "CPAS.XML Database setup"

500: Unexpected server error java.lang.reflect.InvocationTargetException [Show more details] 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...

"cpas_error.txt" attached to message "error to import experiment"

500: Unexpected server error String index out of range: -1 [Show more details] java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.substring(String.java:1768) at java.lang.String.substring(String.java:1735) at org.fhcrc.cpas.pipeline.PipelineService.getJobBackgroundInfo(PipelineService.java:243) at Experiment.ExperimentController.importXarFile(ExperimentController.java:2303)...

"error.htm" attached to message ""could not find column" error"

500: Unexpected server error   Could not find column Rank java.lang.AssertionError: Could not find column  Rank        at org.fhcrc.cpas.data.SchemaTableInfo.getColumns(SchemaTableInfo.java:374)        at org.fhcrc.cpas.data.SchemaTableInfo.getColumns(SchemaTableInfo.java:364)        at Demo.DemoController.getDataRegion(DemoController.java:177)        at Demo.DemoController.begin(DemoController.java:34)...

Dataset Properties

The properties of a dataset include how it is keyed, categorized, and shown or shared. Dataset Properties Page Action Buttons Edit Dataset Properties Data Row Uniqueness Additional Key Fields Using Time as an Additional Key Advanced Settings Edit Dataset Fields Dataset Properties Page Administrators can view and edit dataset properties either by clicking the name of a dataset...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

"500 Unexpected server error" attached to message "Unexpected server error String index out of range: -1"

500: Unexpected server error String index out of range: -1 [Show more details] java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.substring(Unknown Source) at java.lang.String.substring(Unknown Source) at org.fhcrc.cpas.pipeline.PipelineService.getJobBackgroundInfo(PipelineService.java:243) at Experiment.ExperimentController.importXarFile(ExperimentController.java:2303)...

Error when trying to upgrade LabKey from 16.2 to 16.3

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...

500 configuration error

When I opened the http://localhost.com:8080/labkey/ , it comes up like below. I am a new user in labkey but I am not good at computer, so is there anyone has this situation solved? 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,...

Reagents.tsv

Key Reagent 1 AD-mix 2 Acetyl chloride 3 Aluminium chloride 4 Armstrong's acid 5 Azobisisobutyronitrile 6 9-Borabicyclononane 7 Benzyl chloroformate 8 Benzyltrimethylammonium fluoride 9 1,8-Bis(dimethylamino)naphthalene 10 (Bis(trifluoroacetoxy)iodo)benzene 11 Bis(trimethylsilyl)acetamide 12 Bis(trimethylsilyl)amine 13 N-Bromosuccinimide 14 Burgess reagent 15 Tert-Butyl hydroperoxide 16 N-Butyllithium...

"ldaperrormsg" attached to message "LDAP authentication requires valid cerfication path"

simple bind failed: authldap.musc.edu:636 [Show more details] javax.naming.CommunicationException: simple bind failed: authldap.musc.edu:636 [Root exception is javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target] at...

You must have a DataSource named "labkeyDataSource" defined in labkey.xml.

Hi, I am trying ot install Labkey on SL7 (equivalent to CentOS7), using tomcat (7.0.54) and postgres (9.2.10) from the distributions repositories. I get a stack trace with the You must have a DataSource named "labkeyDataSource" defined in labkey.xml error, even though I have configured the dataSource. See attached labkey.xml The stack trace looks like this: org.labkey.api.util.ConfigurationException:...

CPAS MS2 problem

Hi everyone I successfully loaded 15 folders into CPAS , It was running really slow so I rebooted the machine, It starts up fine but when I click on MS2 to view my data it throws the following errors (below). I attached the cpas error logs. Any advice or thoughts anyone has would be muchly appreciated thanks -Rich An error has occurred: Servlet execution threw an exception javax.servlet.error.exception...

"labkey-errors.log" attached to message "Cannot connect to external DataSource after upgrade to LabKey 18.2"

ERROR DbScope 2018-07-26 10:08:18,596 localhost-startStop-1 : Cannot connect to DataSource "bc2statsDataSource" defined in labkey.xml. This DataSource will not be available during this server session. org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Could not create connection to database server. Attempted reconnect 3 times. Giving up.) ...

Compatibility with Tomcat 8?

I am attempting a new v15.1 server installation on MacOS X and when I try to use Tomcat 8 (8.0.23) it fails to start the labkey webapp: catalina.out:02-Jul-2015 10:03:16.729 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more Filters failed to start. Full details will be found in the appropriate container log file 02-Jul-2015 10:03:16.729 SEVERE [localhost-startStop-1]...

Sample Finder

This topic describes how to find samples in bulk using sample properties, attributes of their deriveSamples or associateSources, or in the Professional Edition, based on related assays. The Sample Finder helps you build a set of criteria to find samples of interest across all the Sample Types in your system. For example, you might want to find all samples of different types from a specific source...

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

Jul 17, 2015 11:49:07 AM org.apache.coyote.AbstractProtocol init INFO: Initializing ProtocolHandler ["http-bio-8080"] Jul 17, 2015 11:49:07 AM org.apache.catalina.startup.Catalina load INFO: Initialization processed in 832 ms Jul 17, 2015 11:49:07 AM org.apache.catalina.core.StandardService startInternal INFO: Starting service Catalina Jul 17, 2015 11:49:07 AM org.apache.catalina.core.StandardEngine...

CPAS.XML Database setup

I went with a Postgres 8.0 install, but I am now having problems with the cpas.xml setup. The error messages from my cpas.log and webpage (cpas.webError.txt) are attached. I am suspecting it's my Postgres and Tomcat setup: Tomcat 5.5.14 on port 8090 Postgres 8.0.5 My cpas.xml DB section: <Resource name="jdbc/cpasDataSource" auth="Container" type="javax.sql.DataSource" username="postgres" password=""...

"labkey_summary.log" attached to message "MS SQL Server problem"

INFO SqlScriptManager 2015-09-15 14:05:11,096 localhost-startStop-1 : start running script : group_concat_uninstall.sql INFO SqlScriptManager 2015-09-15 14:05:11,143 localhost-startStop-1 : finished running script : group_concat_uninstall.sql INFO SqlScriptManager 2015-09-15 14:05:11,174 localhost-startStop-1 : start running script : group_concat_install_1.00.23696.sql...

"Physical Exam works.xlsx" attached to message "Unable to import dates"

data ParticipantID Date SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Height Weight ARVRegimenType Pregnancy Language Signature 133428 2008-08-15 131 91 72 15 165 81.5 NVP-XR FALSE English TRUE 133428 2008-10-10 145 104 67 17 165 78.5 NVP-XR FALSE English TRUE 133428 2009-09-11 132 114 66 20 165 82.5 NVP-XR FALSE English TRUE 133428 2009-11-06 163 90 76 20 165 82.5 NVP-XR FALSE...