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HIV Study Tutorial
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job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

"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...

Limits on HTML in WIKI pages?

What are the limits on HTML in WIKI (and I assume, MESSAGE) pages? I tried to place an excel-converted spreadsheet on a wiki page. Initially it crashed the page display service and made the page very hard to delete. After removing external namespace references it displays properly on normal browsers (firefox, ie, safari) but loses all its formatting, color and fonts on the WIKI page. Well there...

"cpas.log" attached to message "CPAS.XML Database setup"

20 Dec 2005 16:50:51,091 DEBUG CoreModule : Connection to cpasDataSource at jdbc:postgresql://otrs.genophobe.org:8090/cpas failed with the following error: 20 Dec 2005 16:50:51,091 DEBUG CoreModule : Message: The connection attempt failed. SQLState: 08001 ErrorCode: 0 20 Dec 2005 16:50:51,091 DEBUG CoreModule : org.postgresql.util.PSQLException: The connection attempt failed. 20 Dec 2005...

"cpas_err" attached to message "ERROR: relation "core.users" does not exist"

500: Unexpected server error Home Back Folder ERROR: relation "core.users" does not exist [Show more details] org.postgresql.util.PSQLException: ERROR: relation "core.users" does not exist at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192)...

Sequest Fractions XAR import failed

Hi, We just did our first Sequest mudpit with 8.2 and are getting the failure below, I have attached the xar file. Thanks, Bill 01 Aug 2008 23:53:59,043 FATAL: Exception during import org.labkey.api.exp.XarFormatException: Could not find Parent protocol with LSID urn:lsid:uky.edu:Protocol.Folder-60:MS2.SequestAnalysis.Fractions:3     at org.labkey.api.exp.XarSource.getProtocol(XarSource.java:204)...

"ShowGraphError.doc" attached to message "Experiment graph error"

Error in generating graph: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) java.io.FileNotFoundException: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:106) at java.io.FileReader.(FileReader.java:55) at Experiment.ExperimentController$GraphView.renderView(ExperimentController.java:1512)...

"unix-ms2admin-exception.txt" attached to message "Error getting "Protein Annotations Loaded" status in showMS2Admin.view"

03 Feb 2006 17:22:38,295 ERROR GroovyView : error executing /_views/HomeTemplate.gm java.io.IOException: java.lang.ClassCastException: java.lang.Thread at MS2.MS2Controller$DisplayThreadStatusColumn.renderGridCellContents(MS2Controller.java:1286) at org.fhcrc.cpas.data.DisplayColumn.renderGridDataCell(DisplayColumn.java:261) at org.fhcrc.cpas.data.DataRegion.renderTableRow(DataRegion.java:663)...

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 ...

"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...

"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)...

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...

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...

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...

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=""...