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HIV Study Tutorial
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"CellCulture_003.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-021 PT-102 05/17/19 1 99 Media B S-022 PT-102 05/18/19 2 198 Media B S-023 PT-102 05/19/19 3 345 Media B S-024 PT-102 05/20/19 4 485 Media B S-025 PT-102 05/21/19 5 664 Media B S-026 PT-102 05/22/19 6 982 Media B S-027 PT-102 05/23/19 7 1548 Media B S-028 PT-102 05/24/19 8 2393 Media B S-029 PT-102 05/25/19 9 2821 Media...

"PepcPipeline.log" attached to message "Runtime error when queueing pipelinejob"

12 Sep 2008 10:06:27,512 ERROR: Failed to set status to 'WAITING' for 'PepcPipeline.status'. com.thoughtworks.xstream.converters.reflection.ObjectAccessException: Could not get field class java.lang.reflect.Field.name : Can not set java.lang.String field org.apache.commons.logging.impl.Log4JLogger.name to org.apache.commons.logging.impl.Log4JLogger at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.visitSerializableFields(PureJavaReflectionProvider.java:111)...

Participant Aliases

A single study participant can be known by different names in different research contexts. One lab might refer to the subject using the name "LK002-234001", whereas another lab might use the name "Primate 44". It is often necessary (and even desirable) to let the different providers of data use their own names, rather than try to standardize them at the various sources. LabKey Server can align all...

Step 2: Import Lab Data

In this step we import two different, but related, data tables to the buildLW1 you just created: Plasma sample inventory: a spreadsheet that describes different vials of plasma. Assay result data: a spreadsheet that holds the experimental results of assaying the plasma. These tables are connected by the fact that the assay data describes properties of the plasma in the vials. We will capture...

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...

"cpas.log" attached to message "500: Unexpected server error"

11 Jan 2006 14:02:23,381 DEBUG ModuleLoader : ModuleLoader init 11 Jan 2006 14:02:23,568 DEBUG CoreModule : Ensuring databases are present 11 Jan 2006 14:02:23,578 ERROR ModuleLoader : Failure ocurred during ModuleLoader init. java.lang.NoClassDefFoundError: org/apache/tomcat/dbcp/dbcp/BasicDataSource at org.fhcrc.cpas.module.CoreModule.ensureDataBases(CoreModule.java:86) at org.fhcrc.cpas.module.ModuleLoader.doInit(ModuleLoader.java:145)...

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

ERROR DavCrawler 2015-04-29 01:01:12,397 DavCrawler : Unexpected error org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.tomcat.dbcp.dbcp.BasicDataSource@830d625 at org.labkey.api.data.DbScope._getConnection(DbScope.java:657) at org.labkey.api.data.DbScope.getConnection(DbScope.java:472) at org.labkey.api.data.JdbcCommand.getConnection(JdbcCommand.java:55)...

"labkey-errors.log" attached to message "Problem with upgrade to 9.2"

ERROR ModuleLoader 2009-08-17 13:39:17,755 http-8080-Processor23 : Failure starting module: Query java.lang.NoClassDefFoundError: javax/script/ScriptEngineFactory at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:675) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124) at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)...

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,...

PSQLException: This ResultSet is closed

hi, I am seeing a repeated error on our development machine. It's happening about every minute or so. ERROR Table 2014-12-16 10:21:58,540 DavCrawler : doFinally org.postgresql.util.PSQLException: This ResultSet is closed.     at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkClosed(AbstractJdbc2ResultSet.java:2852)     at org.postgresql.jdbc2.AbstractJdbc2ResultSet.getStatement(AbstractJdbc2ResultSet.java:623)...

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 ...

"labkey.log" attached to message "Problem with upgrade to 9.2"

INFO DbScope 2009-08-17 13:39:03,161 main : Initializing DbScope with the following configuration: Server URL: jdbc:postgresql://localhost/labkey Database Product Name: PostgreSQL Database Product Version: 8.3.7 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 8.3 JDBC3 with SSL (build...

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...

"cpas.install.log" attached to message "CPAS.XML Database setup"

at org.fhcrc.cpas.view.ViewContext.getACL(ViewContext.java:154) ... 70 more 21 Dec 2005 11:45:15,323 DEBUG ModuleLoader : ModuleLoader init 21 Dec 2005 11:45:15,647 DEBUG CoreModule : Ensuring databases are present 21 Dec 2005 11:45:15,756 DEBUG CoreModule : Attempting to create database cpas 21 Dec 2005 11:45:17,250 DEBUG CoreModule : Just created "cpasDataSource" database; attempting...

Isolation Level in Transaction

hi, I am in the midst of deploying a custom Java module onto a development/test server, and I am getting the following error when I try to browse the schema or create queries: "Cannot change transaction isolation level in the middle of a transaction." I noticed an issue report that seems to address this. https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=21294 I've...

"FileSet_FileUpload_Stacktrace.txt" attached to message "Error when trying to use FileSet"

ERROR DavController 2013-04-10 09:04:49,039 http-8080-2: unexpected exception java.lang.NullPointerException at org.labkey.api.util.FileUtil.getAbsoluteCaseSensitiveFile(FileUtil.java:738) at org.labkey.filecontent.FileContentServiceImpl.fireFileCreateEvent(FileContentServiceImpl.java:791) at org.labkey.core.webdav.DavController.fireFileCreatedEvent(DavController.java:2619)...

Error at startup after upgrading to the trunk version: 27583

500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoSuchMethodError: org.labkey.api.ehr.EHRService.registerSimpleFormType(Lorg/labkey/api/ehr/EHRService$FORM_TYPE;Lorg/labkey/api/module/Module;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V        at org.labkey.onprc_ehr.ONPRC_EHRModule.registerEHRResources(ONPRC_EHRModule.java:184)        at...