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HIV Study Tutorial
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"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...

Help with javascript API's insertRows()

Hi, I'm developing a labkey 12.3 w/Ext4 file module that inserts rows into a table in a user-created schema (in a postgres db). The table contains multiple date columns whose dates are collected via a Ext form with datefield xtype widgets. Every time I try to insert I get this error: ERROR: column "date_used" is of type timestamp without time zone but expression is of type character varying...

"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.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)...

Error When Setting Up Developer Machine

I've been following the documentation for setting up a developer machine (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine) but I ran into issues in the "Build LabKey" section. When running the command "gradlew deployApp" the build fails immediately after the "Task :server:stageModules" starts. (stacktrace pasted below) The only other inconsistency I found in the guide was in...

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...

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...

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...

Labkey revision 29447 does not go through the upgrade stage

after a clean build I still get the following error: 500: Unexpected server error A failure occurred during LabKey Server startup. org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: constraint "fk_completiondates_employeeid" of relation "completiondates" does not exist        at org.sp...

"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...

Mascot results DO NOT LINK correctly in CPAS 1.7

Greetings to all. I have donwloaded and installed CPAS v1.7 on a workstation running WinXP-Pro with 2Gb Memory and Firefox 2.0. I'm now testing CPAS with Mascot running on a Linux server. The Mascot server is versions 2.1.03 I have configured the Mascot server and search parameters according to the online instructions. A number of steps appear to be working as it is shown in the attached log...

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=""...

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...

"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...

labkey.saveBatch fails when called from R transformation script

I have an assay with an R transformation script. This transformation script uses labkey.saveBatch() to create a new assay batch in a second assay before creating a batch in the original assay. (The first assay contains an FK to the second assay.) I've used a module with such a configuration on Labkey v15.1-v16.1. I recently upgraded to v16.3, skipping v16.2. Now my transformation script never...

Processsing Errors preclude access to valid search results

Occasionally CPAS files are flagged as Errors, apparently due to data failing to meet Peptide Prophet and/or Protein Prophet score requirements. However, examination of Mascot reports for the offending datasets reveal at least some valid and high scoring peptide assignments, not null or obviously flawed data. The fact that the models may not have sufficient information for quality scoring should...

problem generating graphs

(I think I just sent an empty message arggg) I am having problems generating graphs from a page that starts like this Flow Experiment Runs > 96 WellBatch0 - PanSurf1-4 > FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs' Run Name:    96 WellBatch0 - PanSurf1-4 Analysis Folder:    Flow Experiment Runs Well Name:    Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs and ends like this....

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 ...

"mvShared.log" attached to message "Accidently moved Shared Project"

INFO DbScope 2014-01-07 08:08:07,172 http-80-7 : Loading DbSchema "labkey.list" (Module) INFO DbScope 2014-01-07 08:08:07,174 http-80-7 : no schema metadata xml found for schema 'list' INFO DbScope 2014-01-07 08:08:07,179 http-80-7 : Loading DbSchema "labkey.list" (Module) INFO DbScope ...

AssertionFailedError when running DRT

I'm trying to run the Developer Regression Test (DRT) as documented here: https://www.labkey.org/wiki/home/Documentation/page.view?name=checkin I'm using 12.1, built from source, running on Windows 7. When I run "ant drt" in server/test/, I see the following: ... 14:56:31,011 =============== Completed BasicTest (1 of 5) ================= testSteps(org.labkey.test.tests.BasicTest) junit.framework.AssertionFailedError:...