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HIV Study Tutorial
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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...

"localhost.2006-08-19.log" attached to message "Error Run 551:Not found on MS2 page"

Aug 19, 2006 8:03:07 PM org.apache.catalina.core.StandardHostValve custom SEVERE: Exception Processing ErrorPage[errorCode=500, location=/error.gm] java.lang.IllegalStateException: getOutputStream() has already been called for this response at org.apache.catalina.connector.Response.getWriter(Response.java:599) at org.apache.catalina.connector.ResponseFacade.getWriter(ResponseFacade.java:195)...

"labkey-different-hang.txt" attached to message "Server not starting"

/Library/Java/JavaVirtualMachines/jdk1.8.0_92.jdk/Contents/Home/bin/java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:62664,suspend=y,server=n -Dcatalina.base=./ -Dcatalina.home=./ -Djava.io.tmpdir=./temp -Ddevmode=false -Dsun.io.useCanonCaches=false -Xmx1G -XX:MaxPermSize=512M -classpath "./bin/bootstrap.jar:./bin/tomcat-juli.jar:/Applications/IntelliJ IDEA.app/Contents/lib/idea_rt.jar" -javaagent:...

"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...

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 ...

"cpas.log" attached to message "CPAS MS2 problem"

09 Mar 2006 22:48:22,687 ERROR ViewServlet : error javax.servlet.ServletException: Servlet execution threw an exception at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:275) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)...

"labkey-errors.log" attached to message "500: Unexpected server error A failure occurred during LabKey Server startup."

ERROR Table 2013-11-13 09:02:38,423 main : SQL Exception org.postgresql.util.PSQLException: ERROR: column reference "resourceid" is ambiguous Position: 224 at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2157) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1886) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)...

Fail to run labkey. Failed to start component [SOLVED]

Dear All, I have tried to install Labkey server but without any success. When i enter the adress localhost:8080/labkey i have this error in the tomcat manager. I use java 8, tomcat 8.5 on a debian stretch. If anyone can help i would be very grateful. I found the installation very complicated. THanks a lot, Bests, Thierry Hi Theirry, Can you send us the full catalina and labkey log...

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"...

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...

"labkey.log" attached to message "500: Unexpected server error A failure occurred during LabKey Server startup."

INFO DbScope 2013-11-13 09:02:07,073 main : Attempting to create database "labkey" INFO DbScope 2013-11-13 09:02:27,178 main : Database "labkey" created INFO DbScope 2013-11-13 09:02:27,336 main : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource...

"Inaccessible_dataset.docx" attached to message "Inaccessible Dataset"

500: Unexpected server error Column date already exists for table c10d88_ogtt  HOME BACK FOLDER  java.lang.IllegalArgumentException: Column date already exists for table c10d88_ogtt        at org.labkey.api.data.AbstractTableInfo.addColumn(AbstractTableInfo.java:463)        at org.labkey.api.exp.api.StorageProvisioner.createTableInfo(StorageProvisioner.java:617)        at org.labkey.study.model.DataSetDefinition.loadStorageTableInfo(DataSetDefinition.java:653)...

can't open scan

I'm trying to open a scan from an MS2 report. Instead of the scan image I get an image with the text: Could not find spectra for scan 814 in 219_1-10.mzXML All of the scans that I tried in this run give the same mmessage. I am able to open this mzXML file through the experiment browser. The log contains the two exceptions below. Has anyone seen this before? Thanks, Bill ERROR MSXMLParser...

"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...

Triggers - Keys

Hello, I am investigating the trigger modules. I am able to get the sample # 1 to work. My question is how do I make the keys start from another number instead of at 1. I have tried the following code, but it did not work: /* TESTING SEQUENCING */ CREATE SEQUENCE seq_test START 1000000;      CREATE TABLE testtriggers.Items (     ItemId int DEFAULT nextval('seq_test') NOT NULL,     ItemName...