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org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist Position: 681

org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "comm.Threads" does not exist   Position: 681        at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)        at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)...

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...

database upgrade

Hi, I was upgrading our labkey installation from version 10.1 to version 11.3 and got the following error: 500: Unexpected server error A failure occurred during LabKey Server startup. org.labkey.api.data.SqlScriptRunner$SqlScriptException: exp-10.20-10.30.sql : ERROR: cannot alter type of a column used by a view or rule   Detail: rule _RETURN on view cabig.experiment depends on column...

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...

Compare proteins error

Compare proteins gives an error. This is the message I am getting: 500: Unexpected server error [Show more details] java.lang.NullPointerException        at org.fhcrc.cpas.view.HomeTemplate.initDefaultMenu(HomeTemplate.java:103)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:68)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:61)        at org.fhcrc.cpas.view.HomeTemplate.<init>(HomeTemplate.java:49)...

problem generating graphs

(I think I just sent an empty message arggg) I am having problems generating graphs from a page that starts like this Flow Experiment Runs > 96 WellBatch0 - PanSurf1-4 > FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs' Run Name:    96 WellBatch0 - PanSurf1-4 Analysis Folder:    Flow Experiment Runs Well Name:    Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs and ends like this....

13.2 Dataset label versus name - Can't find ViewName

I'm doing some internal upgrade testing on 13.2 for our servers and I noticed that the labkey log file now produces warnings for doing a Query.selectRows API call where the queryName is the dataset label and not the dataset name: WARN DataSetQueryView 2013-10-15 17:15:13,599 TP-Processor5 : Dataset in schema'study' was referenced by label (Protocol Deviation), not name (protocolDeviation). When...

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...

"AID_fluoro2.xlsx" attached to page "FluoroSpot Assay"

PlateData Plate:JVL 10 IFN IL17 plate 4, Date:Monday, January 19, 2015, User: enzymatic, Path: R:\Users\MNPH\ELISpot register 3 JVL 10\Fluorospot IFN and IL17\Plate 4\JVL 10 IFN IL17 plate 4\JVL 10 IFN IL17 plate 4.plt Plate Data - Spots Number(in first image: FITC) 1 2 3 4 5 6 7 8 9 10 11 12 A 4 2 3 2 7 2 1 0 3 2 1 3 B 1246 1221 1187 1478 1462 1495 1462 1256 1651 1421 1377 1330 C 10 23...

We have identified a vulnerability

Received alert about 11.3 vulnerability issues. Downloaded and installed current ver (19003 download which is diff. than 18991 listed on screen). When labkey started the modules are now all 11.2. In addition the modules from existing project are all gone. I can add modules to new projects but have not checked useability. Finally would love for the vulnerability alert at the top of the page...

"localhost.2014-06-04.log" attached to message "Projects not showing; Admin Console working fine"

Jun 04, 2014 1:13:55 PM org.apache.catalina.core.ApplicationContext log INFO: ContextListener: contextInitialized() Jun 04, 2014 1:13:55 PM org.apache.catalina.core.ApplicationContext log INFO: SessionListener: contextInitialized() Jun 04, 2014 1:13:55 PM org.apache.catalina.core.ApplicationContext log INFO: ContextListener: attributeAdded('org.apache.jasper.compiler.TldLocationsCache', 'org.apache.jasper.compiler.TldLocationsCache@416fa1ee')...

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...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

25 Jan 2007 08:37:45,274 INFO : Mascot search for CAexample_mini.mzXML 25 Jan 2007 08:37:45,274 INFO : ======================================= 25 Jan 2007 08:37:45,326 INFO : MzXML2Search output 25 Jan 2007 08:37:45,326 INFO : ======================================= 25 Jan 2007 08:37:45,330 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 25 Jan 2007 08:37:45,385 INFO : 25 Jan 2007 08:37:45,386...

Additional LDAP configuration

With the help of the documentation at [https://www.labkey.org/Documentation/wiki-page.view?name=configLdap], I was able to get Labkey working with LDAP. However, Labkey's authentication GUI assumes a fairly simple LDAP configuration and it is currently allowing all our internal users and external customers to log in regardless. I would like to limit Labkey login to just the people we approve. For...

"QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf.log" attached to message "Mascot searching"

20 maj 2008 13:26:15,186 INFO : Mascot search for QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf 20 maj 2008 13:26:15,187 INFO : ======================================= 20 maj 2008 13:26:15,740 INFO : Check FASTA validity 20 maj 2008 13:26:15,775 INFO : ======================================= 20 maj 2008 13:26:15,848 INFO : 20 maj 2008 13:26:16,108 INFO : MzXML2Search output 20 maj 2008 13:26:16,108...

(1) Search of assay contant data (2) Hierarchy concept

(1) Search is not working for me.   https://www.labkey.org/wiki/home/Documentation/page.view?name=luceneSearch I used the above document to search to take out all assay runs and batches that contains a string “OTD*”. I checked all categories and scopes to make sure it will return the information but it wasn’t. Could you tell me why my search is not returning obvious data? (2) Hierarchy concept...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

01 Feb 2007 11:30:50,922 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 11:30:50,923 INFO : ======================================= 01 Feb 2007 11:30:50,996 INFO : MzXML2Search output 01 Feb 2007 11:30:50,996 INFO : ======================================= 01 Feb 2007 11:30:51,039 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 11:30:51,259 INFO : 01 Feb 2007 11:30:51,259...

500: Unexpected server error when trying to delete folder.

I am trying to delete some folders in Labkey but I get this error: 500: Unexpected server error SqlExecutor.execute(); SQL []; ERROR: update or delete on table "material" violates foreign key constraint "fk_materialinput_material" on table "materialinput" Detail: Key (rowid)=(1522) is still referenced from table "materialinput".; nested exception is org.postgresql.util.PSQLException: ERROR:...

"labkey-errors.log" attached to message "Compare view?"

ERROR ManagerBase 2007-12-20 15:24:09,279 Thread-1 : IOException while loading persisted sessions: java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream classdesc serialVersionUID = -4897634681326991901, local class serialVersionUID = 2752793104866219513 java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream...