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HIV Study Tutorial
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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...

"cpas.log" attached to message "Protein prophet import fails"

22 May 2007 21:22:05,401 INFO : X! Tandem search for A431_TotExtract_SILAC_Frac37to48.mzXML 22 May 2007 21:22:05,404 INFO : ======================================= 22 May 2007 21:49:16,736 INFO : X! Tandem search for A431_TotExtract_SILAC_Frac37to48.mzXML 22 May 2007 21:49:16,752 INFO : ======================================= ************************** + PATH=/stf/scratch/cluster/cpas/bin:/stf/home...

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...

"labkey.log" attached to message "DB related problem"

ERROR ModuleLoader 2008-04-10 13:55:24,745 main : Failure ocurred during ModuleLoader init. javax.servlet.ServletException: /opt/labkeyhome/labkeywebapp/WEB-INF/server-config.wsdd (Permission denied) at org.labkey.api.module.ModuleLoader.extractModules(ModuleLoader.java:350) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:209) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:168)...

"labkey-errors.log" attached to message "DB related problem"

ERROR ModuleLoader 2008-04-10 14:25:04,469 main : Failure ocurred during ModuleLoader init. javax.servlet.ServletException: /opt/labkeyhome/labkeywebapp/WEB-INF/server-config.wsdd (Permission denied) at org.labkey.api.module.ModuleLoader.extractModules(ModuleLoader.java:350) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:209) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:168)...

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...

query result that doesnt make any sense

Both my laptop and our test server are cloned from a postgres backup from our production server. they were taken at slightly different times, so they're not quite identical, but they're close. I have a query that runs fine locally, but is returning a completely confusing reuslt on test-ehr. The query attempts to identify the amount of blood drawn in the last 30 days for an animal: SELECT b.id,...

"labkey-db-error-report.txt" attached to message "DB related problem"

ERROR DbSchema 2008-04-10 15:16:04,331 8180-Processor24 : Exception loading schema core java.lang.NullPointerException at org.labkey.api.module.ModuleLoader.getModuleForSchemaName(ModuleLoader.java:1193) at org.labkey.api.data.DbSchema.getModuleForSchemaName(DbSchema.java:182) at org.labkey.api.data.DbSchema.getXmlStreamIfChanged(DbSchema.java:170) at org.labkey.api.data.DbSchema._get(DbSchema.java:105)...

"pipe-processing.log" attached to message "Cluster: prot-pep.xml not found"

2007-10-18 18:23:28 LOG: Running X!Tandem for CAexample SCRIPT:PATH=/share/apps/cpas/bin/tandem:/share/apps/cpas/bin/:/usr/local/bin:${PATH} mkdir /tmp/CAexample.work/ || exit $? syncp.pl tandem.xml /home/massspec/cpas/pipeline/projects/bill/2007/08/test1/CAexample.mzXML /tmp/CAexample.work/ || exit $? pushd /tmp/CAexample.work/ || exit $? tandemPrepare.pl --i=CAexample.mzXML --f=/home/massspec...

"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,...

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-errors.log" attached to message "Configuration Error Detected at LabKey Server Startup"

ERROR DbScope 2018-05-12 18:40:25,091 localhost-startStop-1 : Connection to "labkeyDataSource" at jdbc:postgresql://localhost/labkey failed with the following error: ERROR DbScope 2018-05-12 18:40:25,092 localhost-startStop-1 : Message: Connection to localhost:5432 refused. Check that the hostname and port are correct and that the postmaster is accepting TCP...

"labkey_mysql_error.txt" attached to message "Cannot connect to external DataSource after upgrade to LabKey 18.2"

INFO DbScope 2018-08-07 11:50:03,662 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://127.0.0.1/labkey Database Product Name: PostgreSQL Database Product Version: 9.6.6 JDBC Driver Name: PostgreSQL JDBC Driver JDBC Driver Version:...

"labkey.log" attached to message "DB related problem"

ERROR ModuleLoader 2008-04-14 12:18:31,495 main : Failure ocurred during ModuleLoader init. java.lang.NoClassDefFoundError: org/apache/tomcat/dbcp/dbcp/BasicDataSource at org.labkey.api.module.ModuleLoader.ensureDataBases(ModuleLoader.java:634) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:234) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:168) at...

"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...

studydata details possible bug

studydata gives me this URL as a details link: http://localhost:8080/labkey/study/WNPRC/EHR/datasetDetailRedirect.view?datasetId=03f66142-8965-102d-bff3-493dbd27f43e&lsid=urn%3Alsid%3Aprimate.wisc.edu%3AStudy.Data-108%3A1008.2.0080626E7.r95061.f295e1e2-b8ba-102d-8c2a-9926f351b9ae I get the error: 'please enter a valid integer value'. do they mean an integer value for datasetId? perhaps this...