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HIV Study Tutorial
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Reagents.tsv

Key Reagent 1 AD-mix 2 Acetyl chloride 3 Aluminium chloride 4 Armstrong's acid 5 Azobisisobutyronitrile 6 9-Borabicyclononane 7 Benzyl chloroformate 8 Benzyltrimethylammonium fluoride 9 1,8-Bis(dimethylamino)naphthalene 10 (Bis(trifluoroacetoxy)iodo)benzene 11 Bis(trimethylsilyl)acetamide 12 Bis(trimethylsilyl)amine 13 N-Bromosuccinimide 14 Burgess reagent 15 Tert-Butyl hydroperoxide 16 N-Butyllithium...

"error.log" attached to message "parse errors for deleteURL and importURL elements in table metadata XML"

org.labkey.api.query.QueryException: Illegal URL expression: at org.labkey.api.data.AbstractTableInfo.parseDetailsURL(AbstractTableInfo.java:731) at org.labkey.api.data.AbstractTableInfo.loadFromXML(AbstractTableInfo.java:801) at org.labkey.api.query.FilteredTable.loadFromXML(FilteredTable.java:115) at org.labkey.api.data.AbstractTableInfo.overlayMetadata(AbstractTableInfo.java:1019)...

exp.propertyvalidator" does not exist

I just did an update rebuild on the trunk, then went into the admin console>site settings to set the address of my Mascot server. When I clicked save it threw the exception below: Thanks, Bill 500: Unexpected server error ERROR: relation "exp.propertyvalidator" does not exist org.postgresql.util.PSQLException: ERROR: relation "exp.propertyvalidator" does not exist        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1608)...

TB Server Issue Tracker Crash

When I tried to change the name of the Areas field on the issue tracker it crashed the tracker. I am with the TB Systems Biology group. Thank you. https://tbsystemsbiology.org/issues/TB%20Systems%20Biology%20Intranet/Proposals/list.view?#details An unexpected error occurred Column (Admin Only) already exists. Show more details java.lang.IllegalArgumentException: Column (Admin Only) already...

Spectra Counts: Peptide sequence, ProteinProphet protein assignment, No peptide filter

We're getting an error when using the spectral counting feature. We just installed R so this is the first time it has been tried. The error message is below. The R console in the study module is working (without graphics). Thanks, Bill Spectra Counts: Peptide sequence, ProteinProphet protein assignment, No peptide filter An unexpected error occurred java.lang.NullPointerException ...

"labkey-errors.log" attached to message "Cannot connect to external DataSource after upgrade to LabKey 18.2"

ERROR DbScope 2018-07-26 10:08:18,596 localhost-startStop-1 : Cannot connect to DataSource "bc2statsDataSource" defined in labkey.xml. This DataSource will not be available during this server session. org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Could not create connection to database server. Attempted reconnect 3 times. Giving up.) ...

Sample Finder

This topic describes how to find samples in bulk using sample properties, attributes of their deriveSamples or associateSources, or in the Professional Edition, based on related assays. The Sample Finder helps you build a set of criteria to find samples of interest across all the Sample Types in your system. For example, you might want to find all samples of different types from a specific source...

"labkey.log" attached to message "Error while running trigger script"

INFO ScriptService$Console 2020-04-07 17:59:07,547 io-127.0.0.1-8080-exec-4 : ** evaluating: queries/study/BasicsCase.js INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Getting entries in BasicsCase, success: 33 rows returned. INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Selected rows BasicsCase: INFO ScriptService$Console...

one bad email failing whole email with LABKEY.Message

from within a validation script I am sending emails using LABKEY.Message. I'm trying to send it a lot of emails. one of them is failing for some reason (it's a valid labkey user, but it's possible the email itself isnt valid). below is the error. does it provide any information that says whether labkey is the source of the error or whether the SMTP server is rejecting it? if labkey is...

CPAS.XML Database setup

I went with a Postgres 8.0 install, but I am now having problems with the cpas.xml setup. The error messages from my cpas.log and webpage (cpas.webError.txt) are attached. I am suspecting it's my Postgres and Tomcat setup: Tomcat 5.5.14 on port 8090 Postgres 8.0.5 My cpas.xml DB section: <Resource name="jdbc/cpasDataSource" auth="Container" type="javax.sql.DataSource" username="postgres" password=""...

"running threads - prior the annotation stop.txt" attached to message "Annotation of large protein databases"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) AWT-Windows (RUNNABLE) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]]...

"running threads - after the annotation start.txt" attached to message "Annotation of large protein databases"

Currently Running Threads ajp-8009-Acceptor-0 (RUNNABLE) ajp-8009-Poller-0 (WAITING) ajp-8009-Poller-1 (WAITING) ajp-8009-Poller-2 (WAITING) ajp-8009-Poller-3 (WAITING) ajp-8009-Poller-4 (WAITING) ajp-8009-Poller-5 (WAITING) ajp-8009-Poller-6 (WAITING) ajp-8009-Poller-7 (WAITING) AWT-Windows (RUNNABLE) BreakpointThread (TIMED_WAITING) ContainerBackgroundProcessor[StandardEngine[Catalina]]...

R views in Protein Prophet query in CPAS 8.1

Howdy Folks, The implementation of R in 8.1 is amazing. Special thanks to Brian "Cpas" Connolly for the detailed Linux notes on your website (and for your help with the upgrade). The R views created through spectral counting query work great, however when we try to run them through the Protein Prophet query we receive the following error: An error occurred rendering this view, you may not...

parse rrors for deleteURL and importURL elements in table metadata XML

Even though deleteURL and importURL are in the xsd for the tableInfo schema:   https://www.labkey.org/download/schema-docs/xml-schemas/index.html?schemas/tableInfo_xsd/elements/deleteUrl.html   https://www.labkey.org/download/schema-docs/xml-schemas/index.html?schemas/tableInfo_xsd/elements/importUrl.html I'm getting parse errors when I try to add those to my list's metadata XML: <tables...

Error - Module has already been set; renderView exception

I am periodically encountering a "500: Unexpected server error - Module has already been set." There is the following error included in the log: ERROR WebPartView : renderView() exception in org.labkey.api.view.template.DialogTemplate while responding to /login/home/login.view? Unfortunately, this error means a restart is necessary to get things up and running again. Appears to be tied to the...

"log1.txt" attached to message "764 ERROR"

07 Jun 2006 19:13:35,805 INFO : X! Tandem search for u937_1.mzXML 07 Jun 2006 19:13:35,805 INFO : ======================================= 07 Jun 2006 19:17:03,792 INFO : tandem.exe output 07 Jun 2006 19:17:03,792 INFO : ======================================= 07 Jun 2006 19:17:03,792 INFO : running: tandem.exe input.xml 07 Jun 2006 19:17:03,821 INFO : 07 Jun 2006 19:17:03,822 INFO : X! TANDEM...

Filter Data

You can filter data displayed in a grid to reduce the amount of data shown, or to exclude data that you do not wish to see. By default, these filters only apply for the current viewer and session, but filters may be saved as part of a grid view if desired. Filter Column Values Filter by Value Filtering Expressions Filter Value Variables Persistent Filters Faceted Filtering Understand...

"Physical Exam doesnt work.xls" 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 16 165 67.5 NVP-XR English 133428 2008-10-10 145 104 67 19 165 83.5 NVP-XR English 133428 2009-09-11 132 114 66 12 165 89.5 NVP-XR English 133428 2009-11-06 163 90 76 14 165 71.5 NVP-XR English 133428 2009-12-04 164...

containerlinkstemp problem

Happy Holidays CPASers, I have been wrapping my head around this problem. We recently ran some sequest data using a new fasta file (attached). Peptide and protein prophet looked fine so then We uploaded the database and didnt specify a species and chose not to guess one. We ran update seqId. We then uploaded our data and under Grouping: None Descriptions are listed for only some of the IPIs,...

Error while Importing Existing Analysis Results

Hello I tried to import Existing CPAS Analysis Results from an other server. Unfortunately I am always running into a null pointer exception (see below). I tried to import a pep file and I have both, the pep and prot file available in the import folder. The source server is a windows, the server where I try the import is a linux, don't know if this is relevant. Additional question: How can...