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HIV Study Tutorial
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javax.servlet.ServletException: Filter execution threw an exception

I have tried two different systems now, one an upgrade to several successive upgraded versions of the LabKey code distributions, and one on a fresh system, and I get the same stack trace. It means nothing to me. Nothing in the logs gives me any hints. Ideas? Both systems are running Debian 7, Java 7 and Tomcat 7. type Exception report message Filter execution threw an exception description...

"Package_test_script.txt" attached to page "SND: APIs"

<button onClick="populateCategories()">Populate Categories</button> <button onClick="mySavePackage()">Save Package</button> <button onClick="populatePackageEvent()">Create Package Event</button> <button onClick="addPackageToProject()">Add Package to Project</button> <button onClick="myGetPackage()">Get Package</button> <button onClick="myDeletePackage()">Delete Package</button> <button onClick="myLookups()">Populate...

Java api: uploading files to a list

Hello, We are using an external tool to view and modify lists in labkey. We have lists with some columns of Attachment type (file type). How can we modify the rows of the lists from the external application using Java Api? The method UpdateRowsCommand only supports string type. We would like to upload files to certains rows in these lists of labkey. We are trying to use UpdateRowsCommand: ...

withCounter skipping over numbers

Hi, We have a case where a user generated derivatives of a sample which has a "withCounter" modifier in the sample ID. It is a simple modifier: LIB_${${MaterialInputs:first}_:withCounter(1,'00')} In general, we only make one derivative for a sample, so the tail end of the sample ID would be _01. However, a user generated a second set of derivative samples and they had _101 instead of _02 at the...

Postgresql exception while inserting into List in 12.3

Hi, We have a form that uses labkey's javascript API to insert form data into a labkey list. The form works fine in 12.2, but on our 12.3 staging server, we get this error back from the LABKEY.Query.insertRows() function: "ERROR: Functions cannot have more than 100 arguments." And in tomcat's error logs: ERROR Table 2012-12-03 10:40:46,167 http-8080-Processor17 :...

"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...

"no property content.txt" attached to message "expXML property declaration import errors"

12 Jan 2006 11:27:21,713 INFO : Experiment Import for Uploaded file: 1/12/2006 11:27:21 12 Jan 2006 11:27:21,713 INFO : ======================================= 12 Jan 2006 11:27:23,526 INFO : Loaded nested property 'Experiment.Contact' for parent LSID 'urn:lsid:genologics.com.7:Experiment:Project.72.129' 12 Jan 2006 11:27:23,530 INFO : Finished loading Experiment with LSID 'urn:lsid:genologics.com.7:Experiment:Project.72.129'...

Dataset Properties

The properties of a dataset include how it is keyed, categorized, and shown or shared. Dataset Properties Page Action Buttons Edit Dataset Properties Data Row Uniqueness Additional Key Fields Using Time as an Additional Key Advanced Settings Edit Dataset Fields Dataset Properties Page Administrators can view and edit dataset properties either by clicking the name of a dataset...

Error When Setting Up Developer Machine

I've been following the documentation for setting up a developer machine (https://www.labkey.org/Documentation/wiki-page.view?name=devMachine) but I ran into issues in the "Build LabKey" section. When running the command "gradlew deployApp" the build fails immediately after the "Task :server:stageModules" starts. (stacktrace pasted below) The only other inconsistency I found in the guide was in...

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...

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"...

"mvShared.log" attached to message "Accidently moved Shared Project"

INFO DbScope 2014-01-07 08:08:07,172 http-80-7 : Loading DbSchema "labkey.list" (Module) INFO DbScope 2014-01-07 08:08:07,174 http-80-7 : no schema metadata xml found for schema 'list' INFO DbScope 2014-01-07 08:08:07,179 http-80-7 : Loading DbSchema "labkey.list" (Module) INFO DbScope ...

SSL error

Dear All, I'm brand new to labkey and this list ... and already ran into problems ;-( We've a labkey server on-site and I'd like to connect to it using the java api. The problem is that it's an SSL connection, and the certificate seems expired. I can connect with a browser (though I've to accept an exception for the connection), but using the java API I get the following exception: Exception...

"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...

labkey.saveBatch fails when called from R transformation script

I have an assay with an R transformation script. This transformation script uses labkey.saveBatch() to create a new assay batch in a second assay before creating a batch in the original assay. (The first assay contains an FK to the second assay.) I've used a module with such a configuration on Labkey v15.1-v16.1. I recently upgraded to v16.3, skipping v16.2. Now my transformation script never...

ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "exp.ObjectPropertiesView" does not exist Position: 714

Hello, Another error... how can i solve this? An unexpected error occurred ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "exp.ObjectPropertiesView" does not exist Position: 714 org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation...

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...

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....

"search.log" attached to message "Xar XML file import problems after peptide database search"

28 三月 2006 15:06:42,288 INFO : MS2 analysis for 7MIX_STD_110802_1.mzXML 28 三月 2006 15:06:42,288 INFO : ======================================= 28 三月 2006 15:06:42,496 INFO : tandem.exe output 28 三月 2006 15:06:42,496 INFO : ======================================= 28 三月 2006 15:06:42,521 INFO : 28 三月 2006 15:06:42,521 INFO : X! TANDEM 2 (2005.02.01) 28 三月 2006 15:06:42,521 INFO : 28 三月 2006 15:06:43,460...

Labkey error

Hi i am having trouble starting up the labkey server : It is an old build (labkey 15) that is being restored to then do a proper upgrade, any help is appreciated 500: Unexpected server error A failure occurred during LabKey Server startup. org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column...