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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...

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...

"ShowGraphError.doc" attached to message "Experiment graph error"

Error in generating graph: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) java.io.FileNotFoundException: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:106) at java.io.FileReader.(FileReader.java:55) at Experiment.ExperimentController$GraphView.renderView(ExperimentController.java:1512)...

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...

"build out msg.txt" attached to message "Why build Labkey but the ./build/deploy/modules is empty?"

egatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68) at net.sf.antcontrib.logic.IfTask.execute(IfTask.java:217) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native...

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...

"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)...

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,...

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...

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 "Installation - NullPointerException"

INFO ModuleLoader 2016-01-20 16:55:37,596 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-01-20 16:55:39,716 localhost-startStop-1 : Attempting to create database "labkey" INFO DbScope ...

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-errors.log.1" attached to message "upgrading labkey server to 16.3 version"

ERROR ExceptionUtil 2017-02-08 10:54:41,191 http-nio-443-exec-7 : Exception detected and logged to mothership org.labkey.query.sql.Query$QueryInternalException: Internal error while parsing "SELECT "Secuenciacion ABI".ParticipantID, Causas.CausasId, Causas.Palabra_Clave, Causas.Fecha_Asentamiento, Causas.Estado_Causa, Causas.N_Actuacion_Adm, Causas.N_Actuacion_Proc, Causas.Procedencia_Causa,...

"errors.txt" attached to message "Annotation of large protein databases"

......... error 1 ......... ERROR DavCrawler 2012-01-03 18:38:06,885 DavCrawler : Unexpected error java.lang.OutOfMemoryError: Java heap space at java.lang.Throwable.getStackTraceElement(Native Method) at java.lang.Throwable.getOurStackTrace(Throwable.java:591) at java.lang.Throwable.getStackTrace(Throwable.java:582) at java.lang.Thread.getStackTrace(Unknown...

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...

"xar export error.txt" attached to message "Error uploading xars created via "SimpleFractionationProtocolTemplate""

type Exception report message description The server encountered an internal error () that prevented it from fulfilling this request. exception org.apache.beehive.netui.pageflow.internal.UnhandledException: Failed to create a valid XML file Schema validation error: Expected element 'InputRefs@http://cpas.fhcrc.org/exp/xml' instead of 'ProtocolApplicationParameters@http://cpas.fhcrc.org...

"labkey-errors.log" attached to message "upgrading labkey server to 16.3 version"

ERROR ExceptionUtil 2017-02-08 12:46:56,341 http-nio-443-exec-10 : Exception detected and logged to mothership org.labkey.query.sql.Query$QueryInternalException: Internal error while parsing "SELECT "Secuenciacion ABI".ParticipantID, Causas.CausasId, Causas.Palabra_Clave, Causas.Fecha_Asentamiento, Causas.Estado_Causa, Causas.N_Actuacion_Adm, Causas.N_Actuacion_Proc, Causas.Procedencia_Causa,...