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HIV Study Tutorial
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"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...

"build message.txt" attached to message "Build failed"

PS C:\Labkey\LABKEY_HOME\server-23.12.RC0> .\gradlew deployApp -PdeployMode=prod --stacktrace Starting a Gradle Daemon, 1 incompatible and 2 stopped Daemons could not be reused, use --status for details > Task :server:modules:platform-23.12.RC0:assay:compileGwtAssayApplication Loading inherited module 'gwt.AssayApplication' Loading inherited module 'org.labkey.api.gwt.Internal' ...

Does LABKEY.ext.Store work with LabKey's parameterized queries?

If yes, could an example be provided? If no, why not and can such support be added? ;) Thanks. -Leo Hi Leo, Let me get this confirmed, but I think it does. Although the doc doesn't mention it here: https://www.labkey.org/download/clientapi_docs/javascript-api/symbols/LABKEY.ext.Store.html I am seeing config.parameters listed here: https://www.labkey.org/download/clientapi_docs...

"error_log.txt" attached to message "'java' is not recognized as an internal or external command"

13 Feb 2008 22:58:29,525 INFO : X! Tandem search for LO2_IP0102r_AX01_SG29to30.mzXML 13 Feb 2008 22:58:29,525 INFO : ======================================= 13 Feb 2008 22:58:29,572 INFO : tandem.exe output 13 Feb 2008 22:58:29,572 INFO : ======================================= 13 Feb 2008 22:58:29,572 INFO : running: tandem.exe input.xml 13 Feb 2008 22:58:29,587 INFO : 13 Feb 2008 22:58:29,587...

"QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf.log" attached to message "Mascot searching"

20 maj 2008 13:26:15,186 INFO : Mascot search for QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf 20 maj 2008 13:26:15,187 INFO : ======================================= 20 maj 2008 13:26:15,740 INFO : Check FASTA validity 20 maj 2008 13:26:15,775 INFO : ======================================= 20 maj 2008 13:26:15,848 INFO : 20 maj 2008 13:26:16,108 INFO : MzXML2Search output 20 maj 2008 13:26:16,108...

Problem with upgrade to 9.2

I followed the steps for a unix upgrade. After restarting tomcat, the /labkey page displays a "welcome" page but with boxed "?" marks where graphic elements should be. If I click "Sign In" I get a 500 error message: 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoClassDefFoundError: javax/script/ScriptEngineFactory        at java.lang.ClassLoader.defineClass1(Native...

"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...

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

01 Feb 2007 11:30:50,922 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 11:30:50,923 INFO : ======================================= 01 Feb 2007 11:30:50,996 INFO : MzXML2Search output 01 Feb 2007 11:30:50,996 INFO : ======================================= 01 Feb 2007 11:30:51,039 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 11:30:51,259 INFO : 01 Feb 2007 11:30:51,259...

Could not initialize class org.codehaus.groovy.ast.ClassHelper

I understand that you're planning to phase out the use of groovy, but for the moment using the 9.1 tarball I'm hitting this error in a freshly installed Labkey Server (on Ubuntu 8.04 on Amazon EC2). I'm kinda stumped, any ideas? The tomcat logs don't add anything (as in, grep on "groovy" and nothing comes up). Thanks, Brian ---------------- An unexpected error occurred Could not initialize...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-09492.tsv

ParticipantId sourcelsid date Day DataSets/Demographics/Gender oldcd4 Lymphocytes Hemoglobin DataSets/Demographics/Group DataSets/Demographics/TreatmentGroup CD4 119180 4/20/2008 0 f 239 1802 17 Group 1: Acute HIV-1 No ARV 120 119180 5/18/2008 28 f 266 1787 18 Group 1: Acute HIV-1 No ARV 133 119180 6/15/2008 56 f 224 1843 19 Group 1: Acute HIV-1 No ARV 112 119180 7/13/2008 84 f 163 1780 17 Group...

"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...

Configuration error deteced at LabKey Server Startup

Hello,   I am trying to install a local LabKey server on a machine running CentOS 6. I went through the installation steps, but am receiving this error when I go to open labkey in my browser. Also, I am only able to start up postgres when I am logged in as root; does this have something to do with the error? I am relatively new to Linux so please bear with me.   org.labkey.api.util.ConfigurationException:...

Module Upgrade : Error: Unable to initialize search index.

ALL SITE ERRORS returns me this log file. Can you help me? ERROR LuceneSearchServiceImpl 2021-03-03 09:24:27,258 Module Upgrade : Error: Unable to initialize search index. Search will be disabled and new documents will not be indexed for searching until this is corrected and the server is restarted. java.nio.file.NoSuchFileException: C:\Program Files\Apache Software Foundation\Tomcat...

"labkey_log.txt" attached to message "500 error trying to export a large query"

INFO DataSetDefinition 2011-09-27 09:46:44,914 TP-Processor11 : imported InfImmRec : 0.004s INFO DataSetDefinition 2011-09-27 09:46:55,738 TP-Processor1 : imported InfImmRec : 0.005s INFO DataSetDefinition 2011-09-27 09:48:00,614 TP-Processor1 : imported InfImmRec : 0.004s INFO DataSetDefinition 2011-09-27 09:48:21,426 TP-Processor5...

Creating New Modules

Hi guys, Wondering if I can get any guidance on coding my own module. I've compiled 1.4 from source code, tinkered with the demo module, and taken a look at the build scripts. As a first step, I copied the demo module into another directory in the modules folder and modified the build script: added <antcall target="myModule"/> to "build_module_classes" target 2. added   <target name="myModule"...

HIV Disease Progression - Demo Study-Lab Results-2019-04-11-0949.tsv

ParticipantId sourcelsid date Day DataSets/Demographics/Gender oldcd4 Lymphocytes Hemoglobin DataSets/Demographics/Group DataSets/Demographics/TreatmentGroup CD4 119180 4/20/2008 0 f 239 1802 17 Group 1: Acute HIV-1 No ARV 120 119180 5/18/2008 28 f 266 1787 18 Group 1: Acute HIV-1 No ARV 133 119180 6/15/2008 56 f 224 1843 19 Group 1: Acute HIV-1 No ARV 112 119180 7/13/2008 84 f 163 1780 17 Group...

possible bug: folderType XML file issue

I recently tried to create a folderType using an XML file. Making the file itself was fine, but there's a problem with how labkey handles the file: i created the XML file and started tomcat. i did not actually create a folder of this type yet. i then edited my XML file, forgot about it, and eventually restarted tomcat. labkey threw errors about already having a folderType of this name registered....

"running threads - after the annotation stop.txt" attached to message "Annotation of large protein databases"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) AWT-Windows (RUNNABLE) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]]...

"running threads - prior the annotation start.txt" attached to message "Annotation of large protein databases"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) AWT-Windows (RUNNABLE) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]]...

"_currently running threads.txt" attached to message "Annotation of large protein databases"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]] (TIMED_WAITING) DailyDigest...