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HIV Study Tutorial
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"lastlog.txt" attached to message "Exporting Protein Prophet view fails"

DEBUG ViewServlet 2007-08-21 13:15:40,283 8080-Processor25 : >> POST /cpas/MS2/U54_A431/WholeCellLysate/Iressa_16h/HtvsL/exportProteinGroups.view?run=3600&MS2Peptides.sort=-PeptideProphet&grouping=proteinprophet&ProteinGroupsWithQuantitation.GroupProbability%7Egte=0.9 (roland.luethy@cshs.org;DEEAB2506347D8F34B83F0869507D2C7) DEBUG Table 2007-08-21 13:15:40,290 8080-Processor25 : SQL...

"070116_Tomcat_Error" attached to message "HTTP 500 - Internal server error The page cannot be displayed"

When 30 samples are selected. The page cannot be displayed There is a problem with the page you are trying to reach and it cannot be displayed. -------------------------------------------------------------------------------- Please try the following: Open the localhost:8080 home page, and then look for links to the information you want. Click the Refresh button, or try again later....

"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)...

Compare proteins error

Compare proteins gives an error. This is the message I am getting: 500: Unexpected server error [Show more details] java.lang.NullPointerException        at org.fhcrc.cpas.view.HomeTemplate.initDefaultMenu(HomeTemplate.java:103)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:68)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:61)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:49)...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

MS SQL server Javascript

hello, I have some javascript with SQL requests that work great on the postgres based labkey dev server. However when i place the same code into our production server on MS SQL the code will not execute the requested function. i have run sql queries that reference list and study data and they work fine. this particular code references list data alone. To help us answer this question can...

"startupFailure2.html" attached to message "localhost startup for CPAS"

An error has occurred: javax.servlet.ServletException: PL/pgSQL is not enabled in the "cpas" database because it is not enabled in your Template1 master database. Use PostgreSQL's 'createlang' command line utility to enable PL/pgSQL in the "cpas" database then restart Tomcat. org.apache.struts.action.EXCEPTION : java.lang.RuntimeException: javax.servlet.ServletException: PL/pgSQL is no...

"startupFailure.html" attached to message "localhost startup for CPAS"

An error has occurred: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. org.apache.struts.action.EXCEPTION : org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.        at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:122)...

Problems with Spectral Counts Compare in 9.2

I recently upgraded 9.2 and am having problems with using the Compare tool and Spectral Counts. I was previously running 9.1 with the the data in the older PostgreSQL 8.2 server and dumped and reimported my data into PostgreSQL 8.3 when i updated. I get the following error An unexpected error occurred java.lang.NullPointerException [Show more details] org.labkey.api.util.UnexpectedException:...

"propertydescriptor missing value.txt" attached to message "expXML property declaration import errors"

10 Jan 2006 13:45:07,916 DEBUG GroovyView : /Experiment/CustomProperties.gm 1: import java.util.*; import org.fhcrc.cpas.util.PageFlowUtil;import org.fhcrc.cpas.util.PageFlowUtil; ;out.print(""" 2: """);import org.fhcrc.cpas.exp.IdentifiableBase; ;out.print(""" 3: 4: 5: <table> 6: """);; for (name in customProperties.keySet()) 7: { ;out.print(""" 8: <tr> 9: <td class="ms-searchform">${toString(name)}<...

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

I see this error message right after installation. Can you please help me, where i need to check ? Thank you 500: Unexpected server error  A failure occurred during LabKey Server startup. java.lang.NullPointerException        at org.labkey.api.module.ModuleLoader.upgradeCoreModule(ModuleLoader.java:714)        at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:315)        at...

X!Tandem default settings

When i am trying to set X!Tandem default settings "Set Defualts" following error is shown: "Failure attempting to write defaults. Please try again." What does this error means? And why this error is occurring? CPAS ver 1.7 on Linux Debian Thanks Sudeep Hi Sudeep, The project default setting for X!Tandem search is written to <pipeline root>/default_input.xml and for Mascot search is written...

"PepcPipeline.log" attached to message "Runtime error when queueing pipelinejob"

12 Sep 2008 10:06:27,512 ERROR: Failed to set status to 'WAITING' for 'PepcPipeline.status'. com.thoughtworks.xstream.converters.reflection.ObjectAccessException: Could not get field class java.lang.reflect.Field.name : Can not set java.lang.String field org.apache.commons.logging.impl.Log4JLogger.name to org.apache.commons.logging.impl.Log4JLogger at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.visitSerializableFields(PureJavaReflectionProvider.java:111)...

"AID_fluoro2.xlsx" attached to page "FluoroSpot Assay"

PlateData Plate:JVL 10 IFN IL17 plate 4, Date:Monday, January 19, 2015, User: enzymatic, Path: R:\Users\MNPH\ELISpot register 3 JVL 10\Fluorospot IFN and IL17\Plate 4\JVL 10 IFN IL17 plate 4\JVL 10 IFN IL17 plate 4.plt Plate Data - Spots Number(in first image: FITC) 1 2 3 4 5 6 7 8 9 10 11 12 A 4 2 3 2 7 2 1 0 3 2 1 3 B 1246 1221 1187 1478 1462 1495 1462 1256 1651 1421 1377 1330 C 10 23...

"cpas.log" attached to message "error executing /_views/HomeTemplate.gm"

19 Jan 2006 15:00:05,481 DEBUG ModuleLoader : ModuleLoader init 19 Jan 2006 15:00:05,613 DEBUG CoreModule : Ensuring databases are present 19 Jan 2006 15:00:05,738 DEBUG CoreModule : Successful connection to cpasDataSource at jdbc:postgresql://localhost:5432/cpas 19 Jan 2006 15:00:05,810 INFO DbSchema : Loading DbSchema "core" from "PostgreSQL" at "jdbc:postgresql://localhost:5432...

Filter Data

You can filter data displayed in a grid to reduce the amount of data shown, or to exclude data that you do not wish to see. By default, these filters only apply for the current viewer and session, but filters may be saved as part of a grid view if desired. Filter Column Values Filter by Value Filtering Expressions Filter Value Variables Persistent Filters Faceted Filtering Understand...

"cpas.log" attached to message "sample-0.00-1.00.sql: Failed to load DbSchema "sample""

19 Jan 2006 15:00:05,481 DEBUG ModuleLoader : ModuleLoader init 19 Jan 2006 15:00:05,613 DEBUG CoreModule : Ensuring databases are present 19 Jan 2006 15:00:05,738 DEBUG CoreModule : Successful connection to cpasDataSource at jdbc:postgresql://localhost:5432/cpas 19 Jan 2006 15:00:05,810 INFO DbSchema : Loading DbSchema "core" from "PostgreSQL" at "jdbc:postgresql://localhost:5432...

CPAS Linux install failure after custom build

Hi, It seems I bumped into another problem. :-( Altough the debian build succeeded, I couldn't find a directory or file that resembled the cpas binary package that is distributed on the cpas website. As I wanted to follow the install instruction found from the cpas website. Therefore I looked through the ant targets and found dist_standard, dist_cpas and two others. Trying to run these resulted...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

25 Jan 2007 08:37:45,274 INFO : Mascot search for CAexample_mini.mzXML 25 Jan 2007 08:37:45,274 INFO : ======================================= 25 Jan 2007 08:37:45,326 INFO : MzXML2Search output 25 Jan 2007 08:37:45,326 INFO : ======================================= 25 Jan 2007 08:37:45,330 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 25 Jan 2007 08:37:45,385 INFO : 25 Jan 2007 08:37:45,386...

"FindPeptides mass accuracy.eml" attached to message "An unexpected error occurred"

Return-path: <support@labkey.org> Envelope-to: rune@philosof.dk Delivery-date: Wed, 04 Jun 2008 23:12:08 +0200 Received: from jarcon.fhcrc.org ([140.107.42.30]:60634 helo=smtp.fhcrc.org) by hosting.kollegienet.dk (envelope-from <support@labkey.org>) with esmtp (Exim 4.69) id 1K40H8-0001Gv-Ag for rune@philosof.dk; Wed, 04 Jun 2008 23:12:08 +0200 Received: from bushmaster (BUSHMASTER.FHCRC.ORG...