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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...

"propertydescriptor missing value.txt" attached to message "expXML property declaration import errors"

10 Jan 2006 13:45:07,916 DEBUG GroovyView : /Experiment/CustomProperties.gm 1: import java.util.*; import org.fhcrc.cpas.util.PageFlowUtil;import org.fhcrc.cpas.util.PageFlowUtil; ;out.print(""" 2: """);import org.fhcrc.cpas.exp.IdentifiableBase; ;out.print(""" 3: 4: 5: <table> 6: """);; for (name in customProperties.keySet()) 7: { ;out.print(""" 8: <tr> 9: <td class="ms-searchform">${toString(name)}<...

"Error.txt" attached to message "Import Data - ERROR: functions cannot have more than 100 arguments;"

ERROR Table 2014-07-30 16:52:37,487 ajp-bio-8009-exec-16 : SQL Exception org.postgresql.util.PSQLException: ERROR: functions cannot have more than 100 arguments at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)...

"cpas.log" attached to message "sample-0.00-1.00.sql: Failed to load DbSchema "sample""

19 Jan 2006 15:00:05,481 DEBUG ModuleLoader : ModuleLoader init 19 Jan 2006 15:00:05,613 DEBUG CoreModule : Ensuring databases are present 19 Jan 2006 15:00:05,738 DEBUG CoreModule : Successful connection to cpasDataSource at jdbc:postgresql://localhost:5432/cpas 19 Jan 2006 15:00:05,810 INFO DbSchema : Loading DbSchema "core" from "PostgreSQL" at "jdbc:postgresql://localhost:5432...

"cpas.log" attached to message "error executing /_views/HomeTemplate.gm"

19 Jan 2006 15:00:05,481 DEBUG ModuleLoader : ModuleLoader init 19 Jan 2006 15:00:05,613 DEBUG CoreModule : Ensuring databases are present 19 Jan 2006 15:00:05,738 DEBUG CoreModule : Successful connection to cpasDataSource at jdbc:postgresql://localhost:5432/cpas 19 Jan 2006 15:00:05,810 INFO DbSchema : Loading DbSchema "core" from "PostgreSQL" at "jdbc:postgresql://localhost:5432...

"labkey-errors.log" attached to message "java.lang.VerifyError"

ERROR ExceptionUtil 2013-11-20 09:38:48,131 http-8080-1 : Exception detected and logged to mothership: java.lang.NoClassDefFoundError: org/labkey/api/study/assay/AbstractAssayView at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Class.java:2493) at java.lang.Class.getConstructors(Class.java:1517) at org.labkey....

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...

"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...

"labkey.log" attached to message "MS SQL Server problem"

INFO ModuleLoader 2015-09-15 13:33:36,894 localhost-startStop-1 : __ || | _ |_ |/ _ (� _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2015-09-15 13:33:39,144 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

"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...

Problem with upgrade to 9.2

I followed the steps for a unix upgrade. After restarting tomcat, the /labkey page displays a "welcome" page but with boxed "?" marks where graphic elements should be. If I click "Sign In" I get a 500 error message: 500: Unexpected server error A failure occurred during LabKey Server startup. java.lang.NoClassDefFoundError: javax/script/ScriptEngineFactory        at java.lang.ClassLoader.defineClass1(Native...

"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...

upload failed due to Unexpected '<' in attribute value

I had the following error message. I attached the log file. Would you explain what's wrong and how to upload xtandem result without restarting whole process again, please? I tried to upload search.xar.xml file, bud it did not work. 26 Jan 2007 05:35:16,878 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial...

"AID_fluoro5.xlsx" attached to page "FluoroSpot Assay"

PlateData Plate:48 h incubation reading 10282014 Cy5 FITC cy3, Date:Tuesday, October 28, 2014, User: enzymatic, Path: R:\Users\MNPH\Fluorospot\Fluorospot 2014\CTL IFN IL4\48 h incubation reading 10282014 Cy5 FITC cy3\48 h incubation reading 10282014 Cy5 FITC cy3\48 h incubation reading 10282014 Cy5 FITC cy3.plt Plate Data - Spots Number(in first image: FITC) 1 2 3 4 5 6 7 8 9 10 11 12 A...

"labkey-query-stats.tsv.2" attached to message "Can't access web server after installing on Windows machine: HTTP Status 404 - Requested Resource Not Available"

#Summary - unique queries: 58, elapsed time: 5s #HTTP Requests - query count: 0, query time (ms): 0, request count: 0 #Background Threads - query count: 167, query time (ms): 1,200 Count Total Avg Max Last SQL 13 16 1 16 2014-09-29 14:32 INSERT INTO core.sqlscripts (_ts, createdby, created, modifiedby, modified, modulename, filename) VALUES (?, ?, ?, ?, ?, ?, ?) 12 0 0 0 2014-09-29 14:32 SELECT...

Exception on Labkey SQL Parse - Can't edit query source

I have a query built in Labkey's SQL and it worked fine in a previous version of Labkey, however in 13.1 it throws an exception while trying to parse this query. See the attached screenshot. I am unable to edit the source, properties, or metadata as they all end up in a 500 Error: Unexpected Server error with the same NPE; Here are the details: org.labkey.query.sql.Query$QueryInternalException:...

"MFL25-101906-pl1011.log" attached to message "upload failed due to Unexpected '<' in attribute value"

25 Jan 2007 17:08:21,151 INFO : X! Tandem search for MFL25-101906-pl1011.mzXML 25 Jan 2007 17:08:21,159 INFO : ======================================= 25 Jan 2007 17:08:21,667 INFO : tandem.exe output 25 Jan 2007 17:08:21,668 INFO : ======================================= 25 Jan 2007 17:08:21,671 INFO : running: tandem.exe input.xml 25 Jan 2007 17:08:21,742 INFO : 25 Jan 2007 17:08:21,746 INFO :...

"cpas.log" attached to message "Example1.xar.xml"

20 Jan 2006 09:25:45,234 DEBUG ModuleLoader : ModuleLoader init 20 Jan 2006 09:25:45,590 DEBUG CoreModule : Ensuring databases are present 20 Jan 2006 09:25:45,686 DEBUG CoreModule : Attempting to create database cpas 20 Jan 2006 09:25:47,631 DEBUG CoreModule : Just created "cpasDataSource" database; attempting to run bootstrap script. 20 Jan 2006 09:25:47,679 INFO DbSchema :...

"data_run2.xls" attached to page "Exploring Laboratory Data"

data ParticipantID VisitID Date WBC MCV HGB 101 7/10/08 4540 159 14.2 202 10/4/08 5442 224 11.4 303 7/20/08 4145 205 15.2 404 10/4/08 3202 187 14.1 505 7/10/08 5141 141 19.2 606 10/4/08 4220 152 15.3 101 11/18/08 10562 173 13.5 202 7/25/08 5210 146 17 303 3/10/09 7369 143 17.9 404 7/18/08 9156 95 18.1 505 3/31/09 10674 106 17.9 606 1/20/09 5233 107 16.1 101 1/20/09 8931...

Error importing protein prophet prot.xml files

Hello: I get the following errors from time to time in importing protein prophet prot.xml files: It seems to be something to do with the xml itself - but I cannot find the place in the file it refers to. Anyone seen this or know how to find the referenced line in the xml file? I have attached the guilty prot.xml file. I am using version 11 of labkey and TPP v4.3 JETSTREAM rev 1, Build 201101131447...