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HIV Study Tutorial
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"MFL05-021507-02000727_100906.log" attached to message "ERROR: XMLStreamException in next() com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_summary>; expected </parameter>."

17 Apr 2007 13:32:46,576 INFO : X! Tandem search for MFL05-021507-02000727_100906.mzXML 17 Apr 2007 13:32:46,584 INFO : ======================================= 17 Apr 2007 13:32:47,032 INFO : tandem.exe output 17 Apr 2007 13:32:47,034 INFO : ======================================= 17 Apr 2007 13:32:47,036 INFO : running: tandem.exe input.xml 17 Apr 2007 13:32:47,396 INFO : 17 Apr 2007 13:32:47,400...

"Assay UI.pptx" attached to message "Suggestions for Extensible Assays"

Interacting with Assay Data 1 Basic Ways to Interact: Experiment: cuts across all assay types Assay: by batch, run or sample 2 Assay View: Most of this already exists in labkey Should give user a grid of data from one assay by either batch, run or sample (like grid here: /assay/home/assayRuns.view) I believe much of this already is possible in text-assays, but we should be able to define the...

"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)...

HIV Disease Progression - Demo Study-Demographics-2019-04-13-1512.tsv

ParticipantId Date Cohort 101 2008-04-27 HIV-1 Positive

"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...

problem in Protein Prophet Query export in 9.10

A user in our lab was trying to export some xtandem data to excel using the protein prophet query function and received the error (below), I didn't find a problem with this with some other older data sets and it only produced an error exporting to xls not tsv. Comparing with just protein prophet (not query) also appears to have some problem with exporting. So far I have tried to restart the tomcat...

Integrating R view with Javascript

hi, I am trying to call a saved R view via LABKEY.QueryWebPart. The data grid appears, but I can't see the R view (a bar chart). The viewName matches the saved R view. I may be going wrong with the updateURL, but currently my R view requires no params to run (everything is hard coded) Should I perhaps be using LABKEY.WebPart() instead of QueryWebPart? q = new LABKEY.QueryWebPart({...

"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"]

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...

Loading GO annotations - java error

When I try and load the GO annotations I get this: Loading GO annotations failed with the following exception: java.lang.ArrayIndexOutOfBoundsException: 4        at org.labkey.ms2.protein.tools.GoLoader.loadSingleGoFile(GoLoader.java:213)        at org.labkey.ms2.protein.tools.GoLoader.loadGoFromGz(GoLoader.java:141)        at org.labkey.ms2.protein.tools.GoLoader.access$200(GoLoader.java:32)...

"PNNL_labkey_Bad_SQL_Grammar_error_on_new_install_RHEL_20170407.txt" attached to message "HTTP 500 Bad SQL Grammar by SqlScriptRunner during module update on LabKey startup RHEL 7.3"

Tomcat homepage at http://chembiolims.pnl.gov:8080 is correctly served: 130.20.181.90 - - [07/Apr/2017:13:07:06 -0700] "GET / HTTP/1.1" 200 11250 130.20.181.90 - - [07/Apr/2017:13:07:06 -0700] "GET /tomcat.css HTTP/1.1" 304 - 130.20.181.90 - - [07/Apr/2017:13:07:07 -0700] "GET /tomcat.png HTTP/1.1" 304 - 130.20.181.90 - - [07/Apr/2017:13:07:07 -0700] "GET /bg-nav.png HTTP/1.1" 304 - 130.20.181.90...

"PhysicalExam.xls" attached to page "R Report Builder"

data ParticipantID Date Height Weight Temperature Systolic Diastolic Pulse Respirations ARV? ARVRegimenType 101 2008-05-17 184.4000 86 36.0 129 76 64 17 101 2008-08-04 184.7000 84 37.0 133 79 67 18 101 2008-09-02 183.4000 83 37.0 133 85 68 15 101 2008-11-23 185.3000 80 36.7 135 85 70 14 101 2009-01-18 184.8000 79 36.8 142 90 75 17 101 2009-02-17 185.2000 79 37.3 129 87 79 13 101 2009-03-16...

"labkey-errors.log" attached to message "How to export a folder with linked schemas"

ERROR QueryServiceImpl 2015-08-26 09:59:28,279 http-bio-8080-exec-4 : Error creating linked schema test_linked_schema java.lang.NullPointerException at org.labkey.query.LinkedSchema$LinkedSchemaUserWrapper.<init>(LinkedSchema.java:452) at org.labkey.query.LinkedSchema.getSourceSchema(LinkedSchema.java:158) at org.labkey.query.LinkedSchema.get(LinkedSchema.java:103) at org.labkey.query.QueryServiceImpl.getLinkedSchema(QueryServiceImpl.java:1333)...

Trouble with Visit Days

If I specify a visit day that has a range of values, ie 100.0-110.0, it works fine with datasets and the Study Navigator view. However, the specimen inventory tables do not seem able to resolve the right visit day. So, when looking at vials, for visit day, I see <103.0> instead of "Season 1" (which is the label for the visit day). Not too big a deal, but the real problem is in the vial reports,...

Manage Storage Locations

Organizations managing multiple storage systems may find it helpful to organize them by Physical Location, particularly when they may be in different rooms, on different floors, or even in different buildings across a campus. You could keep track of locations of your storage by using the "Description" field in the Storage Definition, but those details are only available in some areas. By configuring...

java error

if you have a query, and you go to a URL that tries to filter that query on a non-existent column the QWP says something to the effect of 'Ignoring filter/sort on columns 'age.AgeInYears', 'species' because they do not exist.' If you then try to change the view of this query you get the following java error. This is reproducible with several queries. Error below: An unexpected error occurred...

"labkey-error-log.log" attached to message "Failing to upgrade LabKey"

__ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2018-01-05 10:25:40,934 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost/labkey Database Product Name: PostgreSQL Database...

Physical Exam.xls

data Participant ID Date Height (cm) Weight (kg) Temperature (C) Systolic Blood Pressure xxx/ Diastolic Blood Pressure /xxx Pulse Respirations Clinician Signature/Date Pregnancy Form Language ARV? ARV Regimen Type 101344 2008-04-27 173.0000 68 37.0 117 83 61 101344 2008-05-25 175.0000 69 36.8 145 103 71 101344 2008-06-22 175.0000 71 38.2 166 101 68 101344 2008-08-17 173.0000 73 36.5 125 95 74...

Step 2: Study Reports

In this step we will look at the variety of reports available in the online example. We will look at both built-in reports (automatically available in all study folders) and custom reports (created by the study researchers or data analysts). As you progress with the walkthrough, notice two things: First, all of these reports are 'live', that is, they represent the current state of the underlying...

"Physical Exam works.xlsx" attached to message "Unable to import dates"

data ParticipantID Date SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Height Weight ARVRegimenType Pregnancy Language Signature 133428 2008-08-15 131 91 72 15 165 81.5 NVP-XR FALSE English TRUE 133428 2008-10-10 145 104 67 17 165 78.5 NVP-XR FALSE English TRUE 133428 2009-09-11 132 114 66 20 165 82.5 NVP-XR FALSE English TRUE 133428 2009-11-06 163 90 76 20 165 82.5 NVP-XR FALSE...