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HIV Study Tutorial
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Trouble setting up cohorts

Hi I'm trying to set up automatic cohorts on a dataset I've just imported. I'm getting an error message rather than joy when I click 'update assignments 500: Unexpected server error ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column d.sequencenummin does not exist Hint: Perhaps you meant to reference the column "d.sequencenum". Position:...

Sample Naming Patterns

Each sample in a Sample Type must have a unique name/id. If your data does not already contain unique identifiers for each row, the system can generate them upon import using a Naming Pattern (previously referred to as a name expression) as part of the Sample Type definition. Overview and Basic Examples Naming Pattern Elements/Tokens Format Number Values Include Default Values Use String...

Step 5: Link Luminex Data to Study

Premium Feature — Available upon request with all Premium Editions of LabKey Server. Learn more or contact LabKey. Linking assay data into a study allows you to integrate it with other types of data from other sources. If you wish, you can skip this step and proceed to the next Luminex tutorial: advancedLuminexTutorial. In the steps below, we move selected, quality-controlled Luminex assay data...

upgrade problem with ms2-15.30-16.10.sql

Hi all,   We have problem during the upgrade to 17.2. Please see below for the error.   Please help. Thanks Toan INFO SqlScriptManager 2017-10-25 16:05:03,879 Module Upgrade : start running script : ms2-15.30-16.10.sql ERROR Table 2017-10-25 20:39:19,149 Module Upgrade : SQL Exception org.postgresql.util.PSQLException: ERROR: column "mascotfile"...

"Physical Exam doesnt work.xls" attached to message "Unable to import dates"

data ParticipantID Date SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Height Weight ARVRegimenType Pregnancy Language Signature 133428 2008-08-15 131 91 72 16 165 67.5 NVP-XR English 133428 2008-10-10 145 104 67 19 165 83.5 NVP-XR English 133428 2009-09-11 132 114 66 12 165 89.5 NVP-XR English 133428 2009-11-06 163 90 76 14 165 71.5 NVP-XR English 133428 2009-12-04 164...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

25 Jan 2007 08:37:45,274 INFO : Mascot search for CAexample_mini.mzXML 25 Jan 2007 08:37:45,274 INFO : ======================================= 25 Jan 2007 08:37:45,326 INFO : MzXML2Search output 25 Jan 2007 08:37:45,326 INFO : ======================================= 25 Jan 2007 08:37:45,330 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 25 Jan 2007 08:37:45,385 INFO : 25 Jan 2007 08:37:45,386...

ERROR: Query or table not found: study.Visit

Hi! I am using the platform like a LIMS and I adapted it to our Forensic Lab creating a Continuos Study Proyect. In Specimens eyelash, If I add the Vial Search Web Part, I have an error message that sais "Could not load records due to the following error: Error on line 1: Query or table not found: study.Visit" When I imported the Specimen Data, I had to set the visit_value like "1" because...

"Demographics.xls" attached to message "Import dataset with dateformat"

data ParticipantID Date StartDate Height Gender Country GroupAssignment Status_of_Infection Comments TreatmentGroup 101 2008-05-17 2008-05-17 72 m USA Group 1: Acute HIV-1 confirmed No ARV 202 2008-06-04 2008-06-04 64 f USA Group 1: Acute HIV-1 confirmed ARV 303 2008-07-30 2008-07-30 67 f USA Group 2: HIV-1 Negative 0 Latex allergy 404 2008-07-30 2008-07-30 70 f USA Group 1: Acute HIV-1 confirmed...

"labkey-errors.log" attached to message "FastaAdmin already exists"

ERROR Table 2015-09-09 10:17:29,918 Module Upgrade : SQL Exception java.sql.SQLException: There is already an object named 'ExpressionData' in the database. at net.sourceforge.jtds.jdbc.SQLDiagnostic.addDiagnostic(SQLDiagnostic.java:372) at net.sourceforge.jtds.jdbc.TdsCore.tdsErrorToken(TdsCore.java:2988) at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2421)...

"QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf.log" attached to message "Mascot searching"

20 maj 2008 13:26:15,186 INFO : Mascot search for QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf 20 maj 2008 13:26:15,187 INFO : ======================================= 20 maj 2008 13:26:15,740 INFO : Check FASTA validity 20 maj 2008 13:26:15,775 INFO : ======================================= 20 maj 2008 13:26:15,848 INFO : 20 maj 2008 13:26:16,108 INFO : MzXML2Search output 20 maj 2008 13:26:16,108...

Problem with upgrade to 9.2

I followed the steps for a unix upgrade. After restarting tomcat, the /labkey page displays a "welcome" page but with boxed "?" marks where graphic elements should be. If I click "Sign In" I get a 500 error message: 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoClassDefFoundError: javax/script/ScriptEngineFactory        at java.lang.ClassLoader.defineClass1(Native...

"Package_test_script.txt" attached to page "SND: APIs"

<button onClick="populateCategories()">Populate Categories</button> <button onClick="mySavePackage()">Save Package</button> <button onClick="populatePackageEvent()">Create Package Event</button> <button onClick="addPackageToProject()">Add Package to Project</button> <button onClick="myGetPackage()">Get Package</button> <button onClick="myDeletePackage()">Delete Package</button> <button onClick="myLookups()">Populate...

Building for production, gradle error: could not determine dependencies

Following this guide: https://www.labkey.org/Documentation/wiki-page.view?name=productionBuilds If I run a simple ./gradlew deployApp (optionally cleanBuild), then everything goes smoothly. Naturally I run into the following error on the web server:     Configuration Error Detected at LabKey Server Startup     This server does not appear to be compiled for production mode        org.labkey.api.util.ConfigurationException:...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

01 Feb 2007 11:30:50,922 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 11:30:50,923 INFO : ======================================= 01 Feb 2007 11:30:50,996 INFO : MzXML2Search output 01 Feb 2007 11:30:50,996 INFO : ======================================= 01 Feb 2007 11:30:51,039 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 11:30:51,259 INFO : 01 Feb 2007 11:30:51,259...

500: Unexpected server error when trying to delete folder.

I am trying to delete some folders in Labkey but I get this error: 500: Unexpected server error SqlExecutor.execute(); SQL []; ERROR: update or delete on table "material" violates foreign key constraint "fk_materialinput_material" on table "materialinput" Detail: Key (rowid)=(1522) is still referenced from table "materialinput".; nested exception is org.postgresql.util.PSQLException: ERROR:...

Configuration error deteced at LabKey Server Startup

Hello,   I am trying to install a local LabKey server on a machine running CentOS 6. I went through the installation steps, but am receiving this error when I go to open labkey in my browser. Also, I am only able to start up postgres when I am logged in as root; does this have something to do with the error? I am relatively new to Linux so please bear with me.   org.labkey.api.util.ConfigurationException:...

Creating New Modules

Hi guys, Wondering if I can get any guidance on coding my own module. I've compiled 1.4 from source code, tinkered with the demo module, and taken a look at the build scripts. As a first step, I copied the demo module into another directory in the modules folder and modified the build script: added <antcall target="myModule"/> to "build_module_classes" target 2. added   <target name="myModule"...

"getContainers-atlas-test.txt" attached to message "Strange behavior with LABKEY.Security.getContainers() function"

https://atlas-test.scharp.org/cpas/project/HVTN/Specimen%20Management/Lab%20Program/begin.view? https://atlas-test.scharp.org/cpas/project/HVTN/getContainers.view?_dc=1348616911600&container=%2FHVTN%2FSpecimen%20Management%2FLab%20Program%2F&includeSubfolders=false _dc=1348616911600 container=/HVTN/Specimen Management/Lab Program/ includeSubfolders=false { "sortOrder": 0, "children": [...

"180723_InsertRows Error Log.txt" attached to message "LImit to insertrows query"

WARN MapDataIterator 2018-07-23 10:55:18,110 http-bio-8443-exec-20 : Map already has column named 'ParticipantId' WARN MapDataIterator 2018-07-23 10:55:56,174 http-bio-8443-exec-6 : Map already has column named 'ParticipantId' WARN MapDataIterator 2018-07-23 10:56:39,133 http-bio-8443-exec-19 : Map already has column named 'ParticipantId' WARN MapDataIterator...

lin_384_well_metadata.xls

data SampleWellGroup PlateLocation SpecimenID ParticipantID VisitID Date SampleDescription Lot Number InitialDilution Factor Method Specimen 1 A3-A4 4E10 Antibody Lot 1 10 3 Concentration Specimen 2 B3-B4 2F5 Antibody Lot 1 10 3 Concentration Specimen 3 C3-C4 2G12 Antibody Lot 1 10 3 Concentration Specimen 4 D3-D4 sCD4 Antibody Lot 1 10 3 Concentration Specimen 5 E3-E4 HIVIG Antibody...