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HIV Study Tutorial
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"CellCulture_004.xls" attached to page "Step 1: Assay Tutorial Setup"

Sheet1 SpecimenID ParticipantID Date CultureDay TotalCellCount Media S-031 PT-102 05/17/19 1 99 Media B S-032 PT-102 05/18/19 2 198 Media B S-033 PT-102 05/19/19 3 345 Media B S-034 PT-102 05/20/19 4 485 Media B S-035 PT-102 05/21/19 5 664 Media B S-036 PT-102 05/22/19 6 982 Media B S-037 PT-102 05/23/19 7 1548 Media B S-038 PT-102 05/24/19 8 2393 Media B S-039 PT-102 05/25/19 9 2821 Media...

"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...

"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)...

"cpas.log" attached to message "Manual Unix Install (500: Unexpected server error)"

17 Jan 2006 11:18:37,092 DEBUG ModuleLoader : ModuleLoader init 17 Jan 2006 11:18:37,198 DEBUG CoreModule : Ensuring databases are present 17 Jan 2006 11:18:37,204 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)...

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...

Error When Setting Up Developer Machine

I've been following the documentation for setting up a developer machine (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine) but I ran into issues in the "Build LabKey" section. When running the command "gradlew deployApp" the build fails immediately after the "Task :server:stageModules" starts. (stacktrace pasted below) The only other inconsistency I found in the guide was in...

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...

ReagentRequests.xls

data Name Email UserID Reagent Quantity Date Comments Fulfilled Abraham Lincoln lincoln@wa.gov 104 Diethylzinc 2 7/25/09 Leave nothing for tomorrow which can be done today. Abraham Lincoln lincoln@wa.gov 104 Diethylzinc 1 7/26/09 Things may come to those who wait, but only the things left by those who hustle. George Washington washington@wa.gov 653 Cyclohexenone 7 7/25/09 It is better to offer...

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,...

"vector_import.tsv" attached to page "Bulk Registration of Entities"

name description nucSeqId selectionMethods tstV-101 pACYC177 Vector Sequence NS-25 ["kanamycin", "ampicillin"] tstV-102 pET-24(+) Vector Sequence NS-26 ["kanamycin"] tstV-103 pLysS sequence NS-27 ["chloramphenicol"] tstV-104 pPCR-Script NS-28 ["ampicillin"] tstV-105 thoroughly made up NS-24 ["blasticidin", "bleomycin"]

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 ...

"Technicians.xls" attached to page "Step 1: Set Up List Tutorial"

data Name Department Badge Abraham Lincoln Executive 104 Albert Einstein Inventions 299 Benjamin Franklin Inventions 209 George Washington Executive 653 Homer Documentation 701 Margaret Thatcher Executive 776 Marie Curie Radiology 88 Ralph Waldo Emerson Documentation 1802 Theodore Roosevelt Executive 897 Thomas Edison Inventions 129 &L&D&Cdata&RPage &P/&N

"Technicians.xls" attached to page "Create Lists"

data Name Department Badge Abraham Lincoln Executive 104 Albert Einstein Inventions 299 Benjamin Franklin Inventions 209 George Washington Executive 653 Homer Documentation 701 Margaret Thatcher Executive 776 Marie Curie Radiology 88 Ralph Waldo Emerson Documentation 1802 Theodore Roosevelt Executive 897 Thomas Edison Inventions 129 &L&D&Cdata&RPage &P/&N

"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)...

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...

"cert_error.txt" attached to message "java api with self-signed certificate"

javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target at com.sun.net.ssl.internal.ssl.Alerts.getSSLException(Unknown Source) at com.sun.net.ssl.internal.ssl.SSLSocketImpl.fatal(Unknown Source) ...

Step 3: Add a URL Property

In this previous step, we used lookups to link our lists to each other. In this step, we explore two ways to use the URL property of list fields to create other links that might be useful to researchers using the data. Create Links to Filtered Results Create Links to Files Create Links to Filtered Results It can be handy to generate an active filtering link in a list (or any grid of data)....

merge

I'm trying to sync a branch to the trunk. The branch was created at r12993, right be fore the 10.1 branch. Build is failing because it cannot find org.labkey.data.xml.ActionLink. It appears that this package is created during the build; the package is there but not the class. Thanks, Bill Bill, the class in question is generated by Xbeans from pipelineOptions.xsd. The change that introduced...