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HIV Study Tutorial
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"labkeyerrorlog.txt" attached to message "Unable to create a new dataset/Managed Key"

ERROR Table 2012-12-19 16:08:43,735 http-8080-Processor20 : SQL Exception java.sql.SQLException: Conversion failed when converting the varchar value '.' to data type int. at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:368) at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2820) at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2258)...

First-time Setup redirects me to home, unable to complete administration set up, cannot log in

Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://<server-name>:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://<server-name>:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in...

conversion over network drive

Seem to be have some trouble with converting files over a network share (Works fine on local files). I pasted the tomcat log below. I have also attached the conversion configuration file. Any ideas have is muchly appreciated, have run out of ideas. Thanks -Rich 27 Feb 2008 07:19:39,923 ERROR ConvertSpectrum: Could not setup job to process M:\Richard_Green\raw\152066.RAW 27 Feb 2008 07:27:20,688...

more hard tables / studydata

one of our pages runs executeSql() study data. this statement: "SELECT DISTINCT s.Id FROM study.studydata s WHERE s.LSID IN ('urn:lsid:primate.wisc.edu:Study.Data-108:1047.2.0100922E7.r95061.34f573ec-17a0-102e-8c2a-9926f351b9ae')" throws this error: ERROR: UNION types text and integer cannot be matched Position: 1458 seems like it might be related to the other studyData bug i posted earlier?...

java error

if you have a query, and you go to a URL that tries to filter that query on a non-existent column the QWP says something to the effect of 'Ignoring filter/sort on columns 'age.AgeInYears', 'species' because they do not exist.' If you then try to change the view of this query you get the following java error. This is reproducible with several queries. Error below: An unexpected error occurred...

"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...

"submit_analysis_2015-03-24_16-08-37.log" attached to message "Submitting genotyping analysis to Galaxy fails"

24 Mar 2015 16:08:37,815 INFO : Creating analysis directory: analysis_6 24 Mar 2015 16:08:38,017 INFO : Verifying Galaxy configuration 24 Mar 2015 16:08:38,501 INFO : Writing reads file 24 Mar 2015 16:08:38,522 INFO : Writing properties file 24 Mar 2015 16:08:38,571 INFO : Writing FASTA file 24 Mar 2015 16:08:38,603 INFO : Sending files to Galaxy 24 Mar 2015 16:08:38,961 ERROR: Submitting genotyping...

"submit_analysis_2015-03-26_12-21-04.log" attached to message "Submitting genotyping analysis to Galaxy fails"

26 Mar 2015 12:21:04,351 INFO : Creating analysis directory: analysis_1 26 Mar 2015 12:21:04,418 INFO : Verifying Galaxy configuration 26 Mar 2015 12:21:04,547 INFO : Writing reads file 26 Mar 2015 12:21:04,560 INFO : Writing properties file 26 Mar 2015 12:21:04,578 INFO : Writing FASTA file 26 Mar 2015 12:21:04,592 INFO : Sending files to Galaxy 26 Mar 2015 12:21:06,800 ERROR: Submitting genotyping...

study_reload_source_2015-12-11_02-00-11.log

11 Dec 2015 02:00:11,737 INFO : Starting to run task 'org.labkey.study.pipeline.StudyReloadSourceTask' at location 'webserver' 11 Dec 2015 02:00:11,851 INFO : Starting REDCap export 11 Dec 2015 02:00:12,701 ERROR: An error occurred importing REDCap java.lang.RuntimeException: javax.net.ssl.SSLException: Unrecognized SSL message, plaintext connection? at org.labkey.redcap.ExportMetadataCommand.execute(ExportMetadataCommand.java:61)...

study_reload_source_2015-12-10_02-00-49.log

10 Dec 2015 02:00:51,050 INFO : Starting to run task 'org.labkey.study.pipeline.StudyReloadSourceTask' at location 'webserver' 10 Dec 2015 02:00:51,515 INFO : Starting REDCap export 10 Dec 2015 02:00:53,556 ERROR: An error occurred importing REDCap java.lang.RuntimeException: javax.net.ssl.SSLException: Unrecognized SSL message, plaintext connection? at org.labkey.redcap.ExportMetadataCommand.execute(ExportMetadataCommand.java:61)...

error message while uploading Flow Cytometry data

Getting an error message while uploading a package of .fcs files and flowjo workspace file. ' an error occured trying to load: java.lang.nullpointerexception (java.lang.nullpointerexception'. From the logs, the stack trace is: java.lang.NullPointerException     at org.labkey.pipeline.api.PipeRootImpl.findRootPath(PipeRootImpl.java:144)     at org.labkey.pipeline.api.PipeRootImpl.relativePath(PipeRootImpl.java:195)...

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...

Issue tracker email notification problem

We have been having notification problems from the Issue tracker. I've been able to reproduce the problem by impersonating a user and submitting an issue without assigning it to an individual. No error occurs on the initial submission but when the issue is updated and assigned, the following error appears in labkey-error.log. ERROR IssuesController 2009-10-30 10:16:40,568 http-8443-Processor13...

problem in Protein Prophet Query export in 9.10

A user in our lab was trying to export some xtandem data to excel using the protein prophet query function and received the error (below), I didn't find a problem with this with some other older data sets and it only produced an error exporting to xls not tsv. Comparing with just protein prophet (not query) also appears to have some problem with exporting. So far I have tried to restart the tomcat...

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...

Directory naming mistake (build system bug report)

Hi, I didn't see a way to create a new issue, but I found a tiny little problem that is easily fixed. When building the tarball I get the following error, which occurs both in version 2.0 and 1.7 --- Error ---- bin-tarball: BUILD FAILED /root/CPAS2.0-beta/release2.0/server/installer/build.xml:108: /root/CPAS2.0-beta/release2.0/build/labkeyWebApp/explodedWar not found. --- Error ----...

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...

usual SQL error with group_concat

I have a grouped SQL statement. The query has a field with the participantId and a field with a text description. I would like to group the query on Id and group_concat the description. This seems simple enough, but labkey is giving me this odd error saying " java.sql.Date cannot be cast to java.lang.String". I am having a hard time seeing where the date part is coming from. This is not the actual...

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)...