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HIV Study Tutorial
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import Mascot pep.xml error

The attached file will not import. There are N-term protein modifications in this search. Are these supported? Thanks, Bill 26 Sep 2008 11:19:54,468 INFO : Trying to load data file file:/Z:/projects/UKPCF/cytoA_B/mascot/QTOF_PARAMS5/JJ-090606cytoAplusB-s1.mgf into the system 26 Sep 2008 11:19:54,484 INFO : No ExperimentDataHandler registered for data file file:/Z:/projects/UKPCF/cytoA_B/mascot...

"config_test.log" attached to message "First-time Setup redirects me to home, unable to complete administration set up, cannot log in"

INFO: Initializing ProtocolHandler ["http-nio-8080"] Nov 24, 2016 3:52:18 PM org.apache.coyote.AbstractProtocol init SEVERE: Failed to initialize end point associated with ProtocolHandler ["http-nio-8080"] java.net.BindException: Address already in use at sun.nio.ch.Net.bind0(Native Method) at sun.nio.ch.Net.bind(Net.java:433) at sun.nio.ch.Net.bind(Net.java:425) ...

"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)...

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...

test error:JDWP No transports

Sometimes if I stop the drt tests before they have finished I will get the following error when I start the next batch: FATAL ERROR in native method: JDWP No transports initialized, jvmtiError=JVMTI_ERROR_INTERNAL(113) ERROR: transport error 202: bind failed: Address already in use ["transport.c",L41] ERROR: JDWP Transport dt_socket failed to initialize, TRANSPORT_INIT(510) ["debugInit.c",L500]...

"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) ...

Step 2: Study Reports

In this step we will look at the variety of reports available in the online example. We will look at both built-in reports (automatically available in all study folders) and custom reports (created by the study researchers or data analysts). As you progress with the walkthrough, notice two things: First, all of these reports are 'live', that is, they represent the current state of the underlying...

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...

Panorama: Skyline Lists

Premium Feature — Available with a Panorama Premium Edition of LabKey Server or when using PanoramaWeb. Learn more or contact LabKey. Within Skyline, users can create lists which have one or more columns of different data types. This topic describes how to access these lists within Panorama. Skyline Lists When a Skyline Document import includes lists, you can access them by clicking the "lists"...

Java Error Message

I believe this is something I've seen occasionally before but now I just can't get past the error. The server is on a server with lots of other web services/servers but things were working just find and I've setup ports so that there is no confliction. Here is the error message we get and attached are all the log and config files I can think of that might help. Our LK server is DOWN. 500: Unexpected...

Server Error when starting

I am getting the following error when I start labkey after I have updated my postgres database from a backup of our lab's labkey server. Any help would be much appreciated. 500: Unexpected server error A failure occurred during LabKey Server startup. java.io.IOException: No such file or directory        at java.io.UnixFileSystem.createFileExclusively(Native Method)        at java.io.File.checkAndCreate(File.java:1704)...

Ontology Lookup

Premium Feature — Available in the Enterprise Edition of LabKey Server. Learn more or contact LabKey. Ontology Lookup Data Type Lookup Rules Usage Example Concept Picker for Insert/Update with Type-ahead Initialize Expected Vocabulary Ontology Lookup Data Type Once an ontology has been loaded and the module enabled in your folder, the fieldEditor will include an Ontology Lookup data...

Use of the Python API in Matlab and Converting Python Results to Matlab Objects

Matlab allows the capability to execute Python code and we have found that the use of the Python API from within Matlab can reach 20% better performance over using Matlab and the Web API. Although, converting results from Python objects to Matlab objects, specifically py.dict objects to structs using the struct() function, proves difficult due to the fact that the LabKey server will return Python...

"cpas_log.txt" attached to message "Search MS2 Data Failed"

06 Jan 2006 16:07:43,194 ERROR MS2PipelineProvider: Error writing default input file. java.io.FileNotFoundException: /h1/lyang/default_input.xml (Permission denied) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(FileOutputStream.java:179) at java.io.FileOutputStream.<init>(FileOutputStream.java:131) at java.io.FileWriter.<init>(FileWriter.java:73)...

"cpas.addUser.log" attached to message "Uploading MS2 Data"

21 Dec 2005 17:48:26,207 ERROR ViewServlet : error javax.servlet.ServletException: javax/activation/DataSource at org.apache.beehive.netui.pageflow.internal.DefaultExceptionsHandler.handleException(DefaultExceptionsHandler.java:188) at org.apache.beehive.netui.pageflow.FlowController.handleException(FlowController.java:258) at org.apache.beehive.netui.pageflow.FlowController.internalExecute(FlowController.java:442)...

drt GWT service failure

Every once in a while I get the exception below returned in the results of a FormSubmitCompleteEvent from a GWT FormHandler.onSubmitComplete(FormSubmitCompleteEvent event). It usually returns a url. I have to restart everything to make it go away. I haven't seen this outside of the drts. Any ideas? Thanks, Bill java.lang.NullPointerException at java.io.Reader.<init>(Reader.java:61) at java.io.InputStreamReader.<init>(InputStreamReader.java:55)...

"human_fasta_upload_failure.txt" attached to message "Error uploading human fasta file"

ERROR: duplicate key violates unique constraint "uq_proteinsequences_databaseid_lookupstring" [Show more details] org.postgresql.util.PSQLException: ERROR: duplicate key violates unique constraint "uq_proteinsequences_databaseid_lookupstring" at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297)...

Server Error

I am getting the following error when I start labkey and click any link, after I have updated my postgres database from a backup of our lab's labkey server. Any help would be much appreciated. 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoClassDefFoundError: com/google/common/base/Charsets        at org.labkey.ehr.etl.ETLRunnable.loadQueries(ETLRunnable.java:477)...