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HIV Study Tutorial
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"catalina.out" attached to message "Problem with upgrade to 9.2"

Aug 17, 2009 1:29:52 PM org.apache.coyote.http11.Http11BaseProtocol pause INFO: Pausing Coyote HTTP/1.1 on http-8080 Aug 17, 2009 1:29:52 PM org.apache.coyote.http11.Http11BaseProtocol pause INFO: Pausing Coyote HTTP/1.1 on http-8443 Aug 17, 2009 1:29:53 PM org.apache.catalina.core.StandardService stop INFO: Stopping service Catalina Aug 17, 2009 1:29:53 PM org.apache.coyote.http11.Http11BaseProtocol...

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)...

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"...

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...

Query Metadata: Examples

This topic provides examples of metadataSql used to change the display and behavior of fields in tables and queries. Auditing Level Conditional Formatting Include Row Selection Checkboxes Hide a Field from Users Show/Hide Columns on Insert and/or Update Use a Format String for Display Use a Text Expression for Display Set a Display Width for a Column Display Columns in Specific Order...

"errors.txt" attached to message "Labkey 16 trying to run upgrade script from 14.1"

500: Unexpected server error A failure occurred during LabKey Server startup. org.labkey.api.data.SqlScriptRunner$SqlScriptException: viability-14.10-14.20.sql : SqlExecutor.execute(); SQL []; Column names in each table must be unique. Column name 'runid' in table 'viability.results' is specified more than once.; nested exception is java.sql.SQLException: Column names in each table must be...

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...

API Timeout

I need to delete all the records from a list using the java API. Right now there are 221 records. If I manually go into labkey, show all the records, and delete them all, it works and takes more than 2 minutes (seems like a long time). When I try to do the same thing using the java API, I get a timeout error after 1 minute. The timeouts on our server are longer than that - it appears to be a client-side...

"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)...

"labkey_logs.txt" attached to message "How to configure LabKey server (linux) to run R scripts remotely on another server (linux)"

java.lang.NullPointerException at org.labkey.jsp.compiled.org.labkey.query.reports.view.configReportsAndScripts_jsp._jspService(configReportsAndScripts_jsp.java:150) at org.labkey.api.view.JspView.renderView(JspView.java:168) at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:370) at org.labkey.api.view.HttpView.render(HttpView.java:136) at org.labkey.api.view.HttpView.render(HttpView.java:121)...

"labkey-errors.log" attached to message "Mascot error in CPAS"

ERROR ExceptionUtil 2008-03-07 08:08:47,150 8080-Processor24 : Unhandled exception caught in Global.app: 500: Unexpected server error java.lang.NullPointerException at org.labkey.experiment.ExperimentController.flagWait(ExperimentController.java:2988) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)...

"after_jxl_jar" attached to message "Error Run 551:Not found on MS2 page"

HTTP Status 500 - -------------------------------------------------------------------------------- type Exception report message description The server encountered an internal error () that prevented it from fulfilling this request. exception javax.servlet.ServletException: 441 org.apache.beehive.netui.pageflow.PageFlowRequestProcessor.processInternal(PageFlowRequestProcessor.java:624)...

"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' ...

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...

LabKey17.3-56184.53-community broken

Hi, The LabKey17.3-56184.53-community tar archive produces a non functional installation. The labkeywebapp folder is empty except for the WEB-INF folder. Hi Joakim, This is actually expected since 17.2, the ownership of specific files were moved out of the labkeywebapp directory and are now being handled by the API module. What actually happens when you try to install LabKey? Are you getting...

"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)...

Linux CPAS server authenticating against AD?

Does anyone have experience getting a Linux CPAS server to authenticate against Microsoft AD? I've set up the LDAP parameters as follows: LDAP Servers: ldap://xxx.xx.xx.xx:636 LDAP Domain: nih.gov LDAP Principal Template: ${email}    Use SASL Authentication: No When I click on 'Test LDAP server', the browser window shows: 500: Unexpected server error 156.40.70.10:636; socket closed ...