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HIV Study Tutorial
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"labkey.log" attached to message "Can't include TargetStudy in query on custom assay Data table"

ERROR Table 2014-02-21 10:44:14,885 st: ajp-bio-8009-exec-10 : SQL Exception org.postgresql.util.PSQLException: ERROR: syntax error at or near "OUTER" Position: 1644 at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2157) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1886) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)...

Slow queries on assay results

I have a module-based assay that is currently in use with 2.5k runs and 399k data (result) rows stored. The .data table contains a FK molecule, to hplc.molecule, a small hard table with ~40 rows . If I run the following query from within Labkey: PARAMETERS (FOO INTEGER) SELECT DISTINCT molecule FROM assay.hplc.hplc01.data WHERE run = FOO; The expanded query that actually is sent to the database...

Could not initialize class org.codehaus.groovy.ast.ClassHelper

I understand that you're planning to phase out the use of groovy, but for the moment using the 9.1 tarball I'm hitting this error in a freshly installed Labkey Server (on Ubuntu 8.04 on Amazon EC2). I'm kinda stumped, any ideas? The tomcat logs don't add anything (as in, grep on "groovy" and nothing comes up). Thanks, Brian ---------------- An unexpected error occurred Could not initialize...

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 when upgrading from 17.2 to 17.3 with study.QCstate and moveQCStateToCore

Working on moving from 17.2 to 17.3. When I start the development server within IntelliJ, I run into the following errors: org.labkey.api.data.SqlScriptRunner$SqlScriptException: study-17.20-17.30.sql : Can't invoke method moveQCStateToCore(ModuleContext moduleContext) on class org.labkey.study.StudyUpgradeCode        at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:220)...

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)...

500: Unexpected server error when deleting folders

We are running LabKey 18.3 and have realized that project users (non site admin users), users with "Project Administrator" and "Folder Administrator" can not delete the folders (or sub-folders) which were created by themselves. That is the error message: 500: Unexpected server error java.lang.NullPointerException at org.labkey.pipeline.api.PipelineManager.purge(PipelineManager.java:240) at org.labkey.pipeline.PipelineModule.containerDeleted(PipelineModule.java:237)...

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

Hello, How is this error created? How can I fix it? An unexpected error occurred 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"...

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 ...

HTTP 500 - Internal server error The page cannot be displayed

We are doing 2-DE gels and will have up to 96 mass spec runs in a single experiment. The data is processed okay but the problem arises when trying to display the results. After processing runs and trying to display an Excel Spreadsheet it is possible to display up to 20 analyses, but when displaying 40 (I did not try to determine the threshold for failure) or more the response is: HTTP 500 Internal...

Assay run imports are successful, but no data rows are visible

I have an assay defined with multiple batches/runs uploaded that were previously uploaded successfully and a trigger script to populate additional columns. Recently I tried to re-import one of my runs after making some edits to my trigger script. The re-import was successful in that no errors are thrown and the new run shows up in my Assay Runs webpart, but when I clicked on the newly created run...

"SQL_Latin1_General_CP1_CI_AS.docx" attached to message "unexpected server error specimen import"

500: Unexpected server error SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [S1000]; error code [468]; Cannot resolve the collation conflict between "SQL_Latin1_General_CP1_CI_AS" and "Latin1_General_CI_AS" in the equal to operation.; nested exception is java.sql.SQLException: Cannot resolve the collation conflict between "SQL_Latin1_General_CP1_CI_AS" and "Latin1_General_CI_AS"...

"2023.04.06_labkey_bad_SQL_grammar_error.txt" attached to message "Getting duplicate key error after upgrade"

HTTP Status 500 – Internal Server Error Type Exception Report Message compliance-0.000-22.000.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "ownerentityid" of relation "signedsnapshot" already exists Description The server encountered an unexpected condition that prevented it from fulfilling the request. Exception ...

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

INFO SqlScriptManager 2015-09-15 14:05:11,096 localhost-startStop-1 : start running script : group_concat_uninstall.sql INFO SqlScriptManager 2015-09-15 14:05:11,143 localhost-startStop-1 : finished running script : group_concat_uninstall.sql INFO SqlScriptManager 2015-09-15 14:05:11,174 localhost-startStop-1 : start running script : group_concat_install_1.00.23696.sql...

List - Index out of Range Error

hi, I am running 17.2 on our development server, and though I can create lists I can't populate them with data. Whenever I try, I get an index out of range error. I am not sure what's causing this. Any suggestions would be welcome. Thanks, bront -- from labkey.log INFO ScriptService$Console 2017-08-10 16:19:35,306 ajp-nio-8009-exec-5 : RhinoEngine.createTopLevel: initialize...

"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,...

Importing dat file error: Too simple xml parsing

Hi, When trying to import a mascot dat file, I got the following error: ERROR: XMLStreamException in hasNext() com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_hit>; expected </gamma>.  at [row,col {unknown-source}]: [14607,18]     at com.ctc.wstx.sr.StreamScanner.constructWfcException(StreamScanner.java:605)     at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:461)...

MS SQL server Javascript

hello, I have some javascript with SQL requests that work great on the postgres based labkey dev server. However when i place the same code into our production server on MS SQL the code will not execute the requested function. i have run sql queries that reference list and study data and they work fine. this particular code references list data alone. To help us answer this question can...

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

ERROR DavCrawler 2013-08-27 11:45:37,737 DavCrawler : Unexpected error org.labkey.api.util.ConfigurationException: Can't create a database connection to org.apache.commons.dbcp.BasicDataSource@f4741c6 at org.labkey.api.data.DbScope._getConnection(DbScope.java:540) at org.labkey.api.data.DbScope.getConnection(DbScope.java:397) at org.labkey.api.data.JdbcCommand.getConnection(JdbcCommand.java:52)...

Problems with Spectral Counts Compare in 9.2

I recently upgraded 9.2 and am having problems with using the Compare tool and Spectral Counts. I was previously running 9.1 with the the data in the older PostgreSQL 8.2 server and dumped and reimported my data into PostgreSQL 8.3 when i updated. I get the following error An unexpected error occurred java.lang.NullPointerException [Show more details] org.labkey.api.util.UnexpectedException:...