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HIV Study Tutorial
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"labkey-errors.log" attached to message "Mascot error in CPAS"

ERROR ExceptionUtil 2008-03-07 08:08:47,150 8080-Processor24 : Unhandled exception caught in Global.app: 500: Unexpected server error java.lang.NullPointerException at org.labkey.experiment.ExperimentController.flagWait(ExperimentController.java:2988) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)...

job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

"labkeyerror.txt" attached to message "Permissions for Copied to Study Assays"

java.lang.NullPointerException at org.labkey.api.query.LookupForeignKey.getPkColumn(LookupForeignKey.java:123) at org.labkey.api.study.assay.SpecimenForeignKey.createLookupColumn(SpecimenForeignKey.java:181) at org.labkey.api.data.AbstractTableInfo.getLookupColumn(AbstractTableInfo.java:765) at org.labkey.query.QueryServiceImpl.getColumn(QueryServiceImpl.java:752)...

11.1 upgrade and now can't copy-to-study

I'm trying to copy an assay to a study, the same assay I previously successfully copied. The only thing I can think of that's changed is that the system has been upgraded to 11.1. When I try to copy-to-study, I get the following: java.lang.NullPointerException        at org.labkey.api.exp.api.StorageProvisioner.createTableInfo(StorageProvisioner.java:460)        at org.labkey.study.model.DataSetDefinition.loadStorageTableInfo(DataSetDefinition.java:426)...

Labkey Server on development environment is not working

I have been following the instructions on the Labkey website https://www.labkey.org/Documentation/wiki-page.view?name=devMachine accurately to set up my development environment. I also might have to tell you the Build from gradlew worked to completion showing me no errors. But after deploying it into Tomcat, the Lab key server shows the below error when we browse to : http://localhost:8080/labkey...

error messages returned by saveRows.view

I submitted data to the server using saveRows.view, where some rows lacked participantIds and dates. The server should clearly reject these; however, instead of an intelligible error message being returned to the client, it threw a java error (below) and simply returned 'Internal Server Error'. It would be better if it returned something more descriptive. That logic is easy enough to throw in an...

Database Question

Hello, I have some javascript with embedded sql that when i run the query on a labkey installation running on postgres installation it works fine but on a labkey installation that is under MSSQL i get the error message: Conversion failed when converting the varchar value '%,' to data type int. Any recommendations as to what the difference may be between the two installations that would prevent...

"comet_error_log_file.txt" attached to message "Error: Failed to locate comet/tandem."

10 Oct 2018 23:37:05,289 INFO : Comet search for AG_MAP_Plasma_Bound_F1 10 Oct 2018 23:37:05,289 INFO : ======================================= 10 Oct 2018 23:37:05,305 INFO : AG_MAP_Plasma_Bound_F1.mzXML 10 Oct 2018 23:37:05,336 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 10 Oct 2018 23:37:05,336 INFO : Check FASTA validity 10 Oct...

dataset5004.tsv

ParticipantId date QCStateLabel Weight_kg Temp_C SystolicBloodPressure DiastolicBloodPressure Pulse Respirations Signature Pregnancy Language ARV ARVtype height_cm 101344 2008-04-27 00:00:00.0 68 37.0 117 83 61 173.0 101344 2008-05-25 00:00:00.0 69 36.8 145 103 71 175.0 101344 2008-06-22 00:00:00.0 71 38.2 166 101 68 175.0 101344 2008-08-17 00:00:00.0 73 36.5 125 95 74 ...

NullPointerException in Schema Browser and Check

Hello, I'm implementing a module in Java, and I'm having trouble getting the data to show in the Query Browser. If I click on the module name, I get a NullPointerException (The stack trace is below). I've tried to use the debugger, but I'm getting a transaction cancelled error when I try to figure out which assertation is causing the exception. I would guess that this is coming from reading...

NullPointerException error for a LabKey list

When I try to edit information on one of our lists, I get a 500: Unexpected Server Error. I tried to remake the list as well and I am still getting the same problem. Other lists under this module seem to be working properly. Here is the error message: java.lang.NullPointerException        at org.labkey.list.view.ListDefinitionForm.setName(ListDefinitionForm.java:137)        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native...

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 :...

500 server error and api issue

hello i have uploaded a rather large dataset and am currently getting the following message. any details could be helpful. 500: Unexpected server error org.labkey.experiment.api.ExpObjectImpl Home Back Folder java.lang.NoClassDefFoundError: org.labkey.experiment.api.ExpObjectImpl        at org.labkey.experiment.api.ExperimentServiceImpl.getExpProtocol(ExperimentServiceImpl.java:561)...

Linux CPAS server authenticating against AD?

Does anyone have experience getting a Linux CPAS server to authenticate against Microsoft AD? I've set up the LDAP parameters as follows: LDAP Servers: ldap://xxx.xx.xx.xx:636 LDAP Domain: nih.gov LDAP Principal Template: ${email}    Use SASL Authentication: No When I click on 'Test LDAP server', the browser window shows: 500: Unexpected server error 156.40.70.10:636; socket closed ...

ERROR: Failed to set status to 'WAITING' for '/path/to/.log

As of just recently we are unable to import previous sequest searches into cpas. These searches were uploaded before, but when someone tries to import them again they do not appear in the pipeline, this is also true when someone tries to move searches into a new subdirectory. No error appears on the pipeline screen. The only way to correct this so far is to recopy all the data into a new directory...

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...

Status Assessment.xls

data Participant ID Source Lsid Date Day Meets Criteria for Acute Agrees to Acute Schedule Agrees to Provide Partner Info Partner #1 ID Partner #2 ID Cohort 249318596 2008-08-04 79 true true true 249320489 1 249318596 2008-11-23 190 true true true 249320489 1 249318596 2008-09-02 108 true true true 249320489 1 249318596 2009-04-17 335 true true true 249320489 1 249318596 2009-01-18...

can a group_concat column have a URL?

we have a SQL statement that includes a column generated using group_concat(). in general, labkey allows you to assign a URL for a given column. when i tried to do this for the group_concat column, i got this error: An unexpected error occurred java.lang.AssertionError        at org.labkey.api.data.MultiValuedRenderContext.next(MultiValuedRenderContext.java:76)        at org.labkey.api.data.MultiValuedDisplayColumn.renderGridCellContents(MultiValuedDisplayColumn.java:51)...

Error deleting lists

Hello: I am unable to delete lists that I create. I get this: java.lang.NullPointerException        at org.labkey.search.model.LuceneSearchServiceImpl.deleteDocument(LuceneSearchServiceImpl.java:753)        at org.labkey.search.model.AbstractSearchService.deleteResource(AbstractSearchService.java:450)        at org.labkey.list.model.ListDefinitionImpl.delete(ListDefinitionImpl.java:318)        at...

"cpas.install.log" attached to message "CPAS.XML Database setup"

at org.fhcrc.cpas.view.ViewContext.getACL(ViewContext.java:154) ... 70 more 21 Dec 2005 11:45:15,323 DEBUG ModuleLoader : ModuleLoader init 21 Dec 2005 11:45:15,647 DEBUG CoreModule : Ensuring databases are present 21 Dec 2005 11:45:15,756 DEBUG CoreModule : Attempting to create database cpas 21 Dec 2005 11:45:17,250 DEBUG CoreModule : Just created "cpasDataSource" database; attempting...