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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....

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)...

"labkey.log" attached to message "HTTP Status 500 - Internal Server Error"

INFO ModuleLoader 2016-01-13 16:18:47,610 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / ERROR DbScope 2016-01-13 16:18:48,567 localhost-startStop-1 : Connection to "labkeyDataSource" at jdbc:postgresql://localhost/labkey failed...

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)}<...

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...

Remote DataSource Access Error

Dear All, I was trying to add new Data resource of MySql remotely. I have mentioned the resource in Labkey.xml and saved it. but It shows the error. Please find configuration of Datasource and Screenshot of error  <Resource name="jdbc/mySqlDataSource" auth="Container"         type="javax.sql.DataSource"         username="root"         password=""         driverClassName="com.mysql.jdbc.Driver"...

"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)...

Critical Error when Upgrading to Labkey 15.2

Hi Folks, We are experiencing critical errors when attempting to upgrade Labkey server as follows. * Java 1.7.X --> 1.8.X * Labkey 14.4 --> 15.2 * PostgreSQL 8.4 --> 9.4 * Apache Tomcat 7.0.X Once the DB has been backed up, we are attempting to run the upgrade script on CentOS release 6.6 (Final) as follows ./manual-upgrade.sh -l /data/local/LabKey14.3-35337.10-bin -d /root/LabKey15.2-39071.18-bin...

"data_run2.xls" attached to page "Exploring Laboratory Data"

data ParticipantID VisitID Date WBC MCV HGB 101 7/10/08 4540 159 14.2 202 10/4/08 5442 224 11.4 303 7/20/08 4145 205 15.2 404 10/4/08 3202 187 14.1 505 7/10/08 5141 141 19.2 606 10/4/08 4220 152 15.3 101 11/18/08 10562 173 13.5 202 7/25/08 5210 146 17 303 3/10/09 7369 143 17.9 404 7/18/08 9156 95 18.1 505 3/31/09 10674 106 17.9 606 1/20/09 5233 107 16.1 101 1/20/09 8931...

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 "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...

"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...

Help Please

I am trying to install labkey server on: ubuntu 14, tomcat7, postgresql and I get the following error Can someone help me find why I get this error please? 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.RuntimeException: org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException:...

"Physical Exam doesnt work.xls" 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 16 165 67.5 NVP-XR English 133428 2008-10-10 145 104 67 19 165 83.5 NVP-XR English 133428 2009-09-11 132 114 66 12 165 89.5 NVP-XR English 133428 2009-11-06 163 90 76 14 165 71.5 NVP-XR English 133428 2009-12-04 164...