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HIV Study Tutorial
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dataset001.tsv

patient_document date participant_id study_id testfield2 testfield1 participantId meds given_birth eat first_name email specify_mood height aerobics address comments telephone_1 sex last_name weight drink date_enrolled dob gym age bmi Consent.docx Wed Jun 16 02:02:01 PDT 2021 PT-101 Malcolm Malcolm SpaceCowboy@gmail.com 53 187 Thursday,Tuesday 101 Serenity Ship, Out-of-sight, NoWhere, 18533...

JOIN Queries

This topic covers using JOIN in LabKey SQL to bring data together. All data is represented in tables, or queries. A list or dataset or user defined query are all examples of queries. Queries are always defined in a specific folder (container) and schema, but can access information from other queries, schema, and folders using JOINs. JOIN Columns from Different Tables Handle Query/Table Names...

Example Workflow: Develop a Transformation Script

This topic describes the process for developing a transformation script to transform assay data. You can use transformation scripts to change both run data and run properties as needed. In this example, we use perl, but using any scripting language will follow these general steps. Script Engine Setup Add Script to Assay Design Download Template Files Define the Desired Transformation Write...

Import Visit Names / Aliases

When data is collected by different sites and organizations, it can be difficult to keep visit naming standards consistent. The datasets generated might use many different ways of referring to the same visit. For example, the following list of values might all refer to the same visit: "Month 1" "M1" "Day 30" "First Month" Instead of editing your datasets to force them to be consistent, you...

"2023.04.06_labkey_bad_SQL_grammar_error.txt" attached to message "Getting duplicate key error after upgrade"

HTTP Status 500 – Internal Server Error Type Exception Report Message compliance-0.000-22.000.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "ownerentityid" of relation "signedsnapshot" already exists Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception ...

Linking Data Records to Image Files

This topic explains how to link data grids to image files which reside either on the same LabKey Server, or somewhere else on the web. This feature can be used with any LabKey data table as an alternative to propertyFields. For assay designs, see the following topic: assayImage. Scenario biopsies5.png Suppose you have a dataset where each of row of data refers to some image or file. For example,...

How is Study Data Stored in LabKey Server?

This topic answers a few questions about how study data is stored inside the server: When you create a study dataset and import data to it, how is that data stored and managed in the system? How is data from different studies related? Is the data from different studies physically or logically separated? Topics Data Tables within Schema Import Process System Tables Visit Labels ...

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"...

"interact.log" attached to message "duplicate key violates unique constraint"

27 Oct 2006 10:12:05,687 INFO : Clearing out existing MS2 data for interact.xml 27 Oct 2006 10:12:07,218 INFO : Finished clearing out existing MS2 data for interact.xml 27 Oct 2006 10:12:08,421 INFO : Loading FASTA file 27 Oct 2006 10:12:10,828 INFO : FASTA file "c:/Inetpub/wwwroot/ISB/data/dbase/ipi-human.db" has already been loaded 27 Oct 2006 10:12:11,375 INFO : Loading MS/MS results is 0%...

"2023.04.06_labkey_cast_class_error.txt" attached to message "Getting duplicate key error after upgrade"

HTTP Status 500 – Internal Server Error Type Exception Report Message class java.lang.String cannot be cast to class [Ljava.lang.Object; (java.lang.String and [Ljava.lang.Object; are in module java.base of loader 'bootstrap') Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception org.labkey.api.util.ConfigurationException: class...

prophet parameter

Hi. It looks like the pipeline can't handle pepxml results where there are spectrum queries without search hits (sequest search). We wanted to keep all original search info through out the pipeline so the pipeline prophet min probability was set to 0. It errors at 'ERROR: MS2 import failed' and 'FATAL: XAR import FAILED' The peptide and protein prophet reports are generated but the job...

"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...

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...

"2023.04.05_labkey_uq_modulename_error.txt" attached to message "Getting duplicate key error after upgrade"

HTTP Status 500 – Internal Server Error Type Exception Report Message ERROR: duplicate key value violates unique constraint "uq_modulename" Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception org.labkey.api.util.ConfigurationException: ERROR: duplicate key value violates unique constraint "uq_modulename" Detail: Key (lower(name::text))=(helloworld)...

Error upgrading labkey dev server

Dear Support Team, When upgrading LabKey from 17.1 to 17.2 we got this error in the log files during the first boot: INFO ModuleLoader 2017-07-24 12:52:18,782 Module Upgrade : Starting module 'Genotyping' ERROR ModuleLoader 2017-07-24 12:52:18,784 Module Upgrade : Failure starting module: Genotyping java.lang.IncompatibleClassChangeError: Found...

"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...

"Physical Exam works.xlsx" 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 15 165 81.5 NVP-XR FALSE English TRUE 133428 2008-10-10 145 104 67 17 165 78.5 NVP-XR FALSE English TRUE 133428 2009-09-11 132 114 66 20 165 82.5 NVP-XR FALSE English TRUE 133428 2009-11-06 163 90 76 20 165 82.5 NVP-XR FALSE...

Rendering Output

Hi there, I'm writing a module that executes ad-hoc queries on various data sources. The queries execute and ResultSets arereturned along with all the metadata (I can see this from within the debugger), but I'm not sure how to render the output using the CPAS API's. Attempting to set up a GridView/DataRegion/renderInTemplate results in the error (see below) about how no table has been set...

"2023.04.07_full_startup.txt" attached to message "Getting duplicate key error after upgrade"

__ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2023-04-06T15:32:50,268 main : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://172.19.20.197:5432/labkey_development?sslmode=require...

MS@ load error

I'm running the Sequest Pipeline just to validate that it is completing the pipeline. So I ran one of the CPASDemo files against a handy database (I think Mouse-Human, not yeast), using default params (not ICAT). I didn't expect good results but I did expect it to complete. I'm getting the error below. I've attached the pep.xml. Thanks, Bill 22 Oct 2007 23:36:52,718 DEBUG: Done creating FASTA...