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Deploying on Linux server with Tomcat 8.5.35, getting 404 error
(1 response) gstarbuck 2018-09-17 10:22

So I am following the instructions to configure LabKey on Linux found here: https://www.labkey.org/Documentation/wiki-page.view?name=configTomcat

Tomcat and postgres are up and running, and I have worked through to step 4, move the LabKey Server configuration file. When I got to this step, there was no /conf/Catalina/localhost/ directory in my install - I created one and then put the labkey.xml there.

I then continued through to step 11, Tomcat is running, and the landing page comes up. But when I go to /labkey, it throws a 404 not found error:
Type Status Report

Message /labkey

Description The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.

Is this a known issue? Is it unusual for the "/conf/Catalina/localhost" directory to not exist after an install? I could use any help debugging this.

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Cannot connect to external DataSource after upgrade to LabKey 18.2
(3 responses) eva pujadas 2018-07-26 02:03
Dear LabKey support team,

We have upgraded from LabKey 18.1 to 18.2 and the connection to the external data source we had running (a MySQL database), is not working anymore.
I attach the log file for documentation of the error messages.

First of all, the error was clearly stating that it is necessary to change a parameter value in the connection string: from "zeroDateTimeBehavior=convertToNull" to "zeroDateTimeBehavior=CONVERT_TO_NULL", which we did. But that did not solve the issue.

We are running:
jdk1.8.0_40
apache-tomcat-7.0.68
postgres 9.6
MySQL-server-community-5.1.33-0.rhel5 (for the external data source)

Do you know how to restore the external data source connection?

Thank you very much,
Eva
 labkey-errors.log 
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Configuration Error Detected at LabKey Server Startup
(1 response) MP 2018-05-17 15:02

Hi,

I am trying to manually install Labkey Server 18.1 on my computer (running a non-english version of Windows 7, 64-bit) on Chrome. I'm using tomcat (8.5.31) and postgres (9.5.13).

When I'm trying to run localhost:8080/labkey I get a following error:
Configuration Error Detected at LabKey Server Startup
DataSources are not properly configured in labkey.xml

Attached are labkey.xml and tomcat log.

Thank you for your support

Matt

 labkey-errors.log  labkey.xml 
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Incorrect warning about Postgres 10.3 not supported by Labkey on Ubuntu 18.04
(4 responses) Will Holtz 2018-05-07 01:02

If Labkey connects to a Postgres v10.3 database on Ubuntu 18.04 you get the following:

WARN  PostgreSqlDialectFactory 2018-05-07 00:56:54,603 18.example.com-startStop-1 : LabKey Server has not been tested against PostgreSQL version 10.3 (Ubuntu 10.3-1). PostgreSQL 9.6 is the recommended version.
INFO  DbScope                  2018-05-07 00:56:54,604 18.example.com-startStop-1 : Initializing DbScope with the following configuration:
    DataSource Name:          labkeyDataSource
    Server URL:               jdbc:postgresql://localhost/labkey
    Database Product Name:    PostgreSQL
    Database Product Version: 10.3 (Ubuntu 10.3-1)
    JDBC Driver Name:         PostgreSQL JDBC Driver
    JDBC Driver Version:      42.2.1
    SQL Dialect:              PostgreSql96Dialect

I'm guessing the extra "(Ubuntu 10.3-1)" appended to the version string is throwing off Labkey's version comparison.

-Will

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Download for Previous releases
(1 response) felix rauscher 2018-04-17 22:45

Hi,

I am still runnning LabKey 15.2. If I understand the Upgrade matrix

https://www.labkey.org/Documentation/wiki-page.view?name=upgradeSupportPolicy

correctly I would first need to upgrdade to 15.3. However, I cannot find a download link for 15.3

regards

Felix

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LabKey17.3-56184.53-community broken
(9 responses) Joakim Bygdell 2018-02-02 01:11
Hi,
The LabKey17.3-56184.53-community tar archive produces a non functional installation.
The labkeywebapp folder is empty except for the WEB-INF folder.
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How to get current LabKey's running version?
(7 responses) rangarita 2018-01-10 12:46
Hi, Is there any way to obtain (via command line or GUI) current LabKey's running version? When accessing Admin Console -> Module Information -> Module Details version number indicated is 17.30 instead of 17.3 (see attached file) As it will be used in an IQ document we'd like to obtain the right value. Thanks,
 screen01.png 
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Missing ant.jar when installing 17.3
(1 response) rangarita 2017-12-20 08:17
Hi,

  I'm installing a fresh server using provided installation file (LabKey17.3-55140.16-professional-bin.tar.gz), but when moving LabKey Server Libraries as indicated at https://www.labkey.org/Documentation/wiki-page.view?name=configTomcat there is no ant.jar into tomcat-lib (extracted from tgz provided file).
  Should I get ant.jar from somewhere else?

  Thanks,
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Automatic Conversion/Searching Raw Files
(2 responses) paragm 2017-12-13 11:31
Hi All,

Hope you are well. How does on 'tell' labkey server how to read RAW files? msConvert is installed in the pipeline root bin directory (C:\Labkey\bin where x!, etc. are). The server (installed on Windows) works fine with mzXML files, but when attempting to run on RAW clicking the X! search button doesn't actually do anything. To me - this suggests, the server doesn't actually think it can trigger a conversion. How does one let LabKey know it has msConvert and is perfectly qualified to do its own conversions?

Note - we are NOT using the enterprise pipeline, so this is all being run on a single windows head computer.

Thanks!
~ Parag M ~
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upgrade problem with ms2-15.30-16.10.sql
(7 responses) toan nguyen 2017-10-26 11:43
Hi all,

  We have problem during the upgrade to 17.2. Please see below for the error.
  Please help.

Thanks
Toan

INFO SqlScriptManager 2017-10-25 16:05:03,879 Module Upgrade : start running script : ms2-15.30-16.10.sql
ERROR Table 2017-10-25 20:39:19,149 Module Upgrade : SQL Exception
org.postgresql.util.PSQLException: ERROR: column "mascotfile" of relation "runs" already exists
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2476)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2189)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:300)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:428)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:354)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:301)
        at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:287)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:264)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:260)
        at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:290)
        at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:290)
        at org.labkey.api.data.dialect.StatementWrapper.execute(StatementWrapper.java:1908)
        at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:156)
        at org.labkey.api.data.SqlExecutor$NormalStatementExecutor.execute(SqlExecutor.java:144)
        at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:122)
        at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:75)
        at org.labkey.api.data.SqlExecutor.execute(SqlExecutor.java:70)
        at org.labkey.api.data.SqlScriptExecutor$Block.execute(SqlScriptExecutor.java:208)
        at org.labkey.api.data.SqlScriptExecutor.lambda$execute$0(SqlScriptExecutor.java:101)
        at java.util.ArrayList.forEach(ArrayList.java:1249)
        at org.labkey.api.data.SqlScriptExecutor.execute(SqlScriptExecutor.java:98)
        at org.labkey.api.data.dialect.SqlDialect.runSql(SqlDialect.java:588)
        at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:215)
        at org.labkey.api.data.SqlScriptRunner.runScripts(SqlScriptRunner.java:82)
        at org.labkey.api.module.DefaultModule.versionUpdate(DefaultModule.java:333)
        at org.labkey.api.module.ModuleUpgrader.upgrade(ModuleUpgrader.java:83)
        at org.labkey.api.module.ModuleUpgrader.lambda$upgrade$0(ModuleUpgrader.java:95)
        at java.lang.Thread.run(Thread.java:748)
ERROR Table 2017-10-25 20:39:19,158 Module Upgrade : SQL [22230]
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Additional LDAP configuration
(19 responses) hwong 2017-08-29 15:36

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 this purpose, I've set up an LDAP group called 'labkey'.

My current working Security Principal is uid=${uid},ou=Webusers,dc=bcgsc,dc=ca.

Our LDAP hierarchy looks as such:

Users are uid=${uid},ou=Webusers,dc=bcgsc,dc=ca

And the group is at cn=labkey,cn=Webgroups,ou=Groups,dc=bcgsc,dc=ca

Attached is the graphical representation of what I am working with.

How can I get this working with the following Context elements in labkey.xml?

<Environment name="ldapSearch_username" value="ldapAdmin@email.org" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_password" value="***" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_searchBase" value="dc=email,dc=org" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_lookupField" value="userPrincipalName" type="java.lang.String" override="false"/>
<Environment name="ldapSearch_searchTemplate" value="(&amp;(objectClass=user)(userPrincipalName=${email}))" type="java.lang.String" override="false"/>

Using Test LDAP settings in Labkey continues to work no matter what I insert but I can't log in anymore if I start using these Context elements.

 phpLDAPadmin_(1.2.0.5)_-_-_Google_Chrome_2017-08-14_15-11-16.png 
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Fail to run labkey. [org.apache.catalina.LifecycleException: Failed to start component
(6 responses) thierry 2017-08-22 07:11
Dear All,
I have tried to install Labkey server but without any success.
When i enter the adress localhost:8080/labkey i have this error in the tomcat manager.
I use java 8, tomcat 8.5 on a debian stretch.
If anyone can help i would be very grateful. I found the installation very complicated.

THanks a lot,

Bests,

Thierry
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how to visualized spectra with version 3.7
(1 response) philippe leroux 2017-06-27 06:53
I have down load the 3.7 version of skyline software, but I have the message "spectrum information unavailable"
It did work with previous 3.6 version.
Thanks for help
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Error - A failure occurred during LabKey Server startup.
(8 responses) tvaisar 2017-06-14 11:21
I have been compiling TPP 5.0 on our Linux cluster (running also Labkey Server 16.3) having lot of problem. But an unexpected problem occurred when I found out that the Labkey Server stopped working -
Below is the error I receive in web browser.
Permissions on logs folder are for tomcat:tomcat

drwxr-xr-x. 2 tomcat tomcat 36864 Jun 14 06:12 logs

Thanks for any advice.

Tomas

500: Unexpected server error
A failure occurred during LabKey Server startup.

java.lang.IllegalStateException: Error rolling labkey-errors.log file, likely a file permissions problem in CATALINA_HOME/logs
       at org.labkey.api.module.ModuleLoader.rollErrorLogFile(ModuleLoader.java:604)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:262)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:318)
       at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:240)
       at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
       at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
       at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
       at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4855)
       at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5549)
       at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
       at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
       at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
       at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
       at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
       at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1912)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
       at java.util.concurrent.FutureTask.run(FutureTask.java:266)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at java.lang.Thread.run(Thread.java:745)
view message
Data migration
(1 response) Sam 2017-04-27 06:34
Whats the best way to migrate data from v15.2 to 17.1 ?
view message
HTTP 500 Bad SQL Grammar by SqlScriptRunner during module update on LabKey startup RHEL 7.3
(6 responses) Jim Collett 2017-04-07 17:42
Hello,

I seem to have correctly installed LabKey17.1-49816.20-community-bin on Red Hat Linux 7.3, but when I go to the LabKey homepage after Tomcat startup, I get the following HTTP error:

500: Unexpected server error

A failure occurred during LabKey Server startup.

org.labkey.api.data.SqlScriptRunner$SqlScriptException: exp-15.10-15.20.sql : SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "keyvariable" does not exist
       at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:220)
       at org.labkey.api.data.SqlScriptRunner.runScripts(SqlScriptRunner.java:82)
       at org.labkey.api.module.DefaultModule.versionUpdate(DefaultModule.java:332)
       at org.labkey.api.module.ModuleUpgrader.upgrade(ModuleUpgrader.java:82)
       at org.labkey.api.module.ModuleUpgrader.lambda$upgrade$0(ModuleUpgrader.java:94)
       at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.jdbc.BadSqlGrammarException: SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "keyvariable" does not exist......

Any ideas on how to fix this? The Tomcat default homepage loads fine, and I can see in postgres that the labkey database has been built. A file with the relevant labkey.log and labkey-errors.log entries is attached.
Thanks,
Jim
 PNNL_labkey_Bad_SQL_Grammar_error_on_new_install_RHEL_20170407.txt 
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Labkey Server Service stopped, can't able to start again
(5 responses) atul sharma 2017-03-29 05:07
Dear All,

I have installed Lebkey Server Community Edition, It was worked fine after installation.
but now the services in services.msc has stopped automatically and i am not able to start those.

It says, there are dependencies on other services but I checked all the dependent services(Those were running).


Please help.
view message
"Inactive" date ?
(1 response) Nat 2017-03-28 13:42
HI,
I"m doing some analysis of our site users and am trying to make a view that shows the date a user was "deactivated" from the system. I can see when the account was "created", when the "Last Login" was ... but under "grid views" is there a way to see when someone's account was "deactivated" or "disabled"?

Thanks!

-- Nat

Apologies if this belongs in the Community Forum ... please let me know if it does. thx.
view message
Bulk email controls (SMTP)in LabKey
(4 responses) Nat 2017-03-10 11:49
Hi,
We have run into an issue around sending bulk emails this week where the outbound queue of our SMTP server is *very* slow. Currently at almost 36 hrs after the original announcement was made from LabKey, there are about 1k emails still in outbound queue. The list is slowly shrinking ...

So our user base of emails is now almost 9K in size, so not small anymore but not huge either. Our IT dept recommended we send out bulk emails in 1K batches (5 min apart), or put a 5 sec delay between individual emails ... oye, not getting into manual management of batch emails...

I've pushed on them regarding whether there are controls/adjustibility on the SMTP server to automatically do this and I'm waiting to hear back. They also suggested I contact LabKey as to whether there is any outbound email functionality that is built into this product.

I did search the support base prior to sending this but couldn't find anything related.

Thoughts??

Nat Brace
UW - Skyline
view message
Example Workflow: LabKey and Illumina
(1 response) hilariagrieve 2017-03-09 06:32
Hi. I want to set a genotyping dashboard. How I get the genotyping Module?
I am interesting in Labkey and Illumina Workflow.
Thanks
view message
Telling Labkey to check a specific row (i.e. not the first row) for data headers
(3 responses) simon buckner 2017-02-21 11:40
I searched around, but couldn't find an answer to this exact question.

We have a system that outputs excel files. The top of the file contains two columns of metadata, comprising six rows. There is a blank row directly below, and then on row 8, the data we wish to store begins.

Row 8 contains the headers we want in our data domain, so our data fields have been designed to match these. However, when I upload a file, Labkey appears to check the first row for header information (which only contains two non-blank columns). Thus, the file does not upload successfully.

Is there a way to tell Labkey to skip a few lines when searching for the headers? I saw on another post, someone suggested prepending the first seven lines with "#", but I am wondering if Labkey can be configured to ignore these automatically.

Thanks,

Simon
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2 LabKeys sharing file storage?
(2 responses) fcf 2017-02-21 10:09
We are splitting one of our LabKey sites in two. One will be for customers and the other will be the internal lab use. They and their databases will be hosted on separate VMs, however we want them to share the same directory for file storage -- the same one they are using before the split. The idea is to allow us to reference the same data from both sites without duplicating storage.
 1. Does anyone see a problem with this?
 2. If we remove a project from one site would it delete the data files even if we wanted to continue to access them from the other site?
view message
Upgrade Issue from LabKey 16.2 to 16.3
(2 responses) hilariagrieve 2017-02-13 14:46
Hi Cori. I am having problems with upgrading from 16.2 to 16.3 version.
It returns me:

500: Unexpected server error
A failure occurred during LabKey Server startup.
org.labkey.api.data.SqlScriptRunner$SqlScriptException: study-16.20-16.30.sql : Can't invoke method updatePKAndContainer(ModuleContext moduleContext) on class org.labkey.study.StudyUpgradeCode
       at org.labkey.api.data.SqlScriptManager.runScript(SqlScriptManager.java:211)
...
Caused by: org.postgresql.util.PSQLException: ERROR: no existe la columna «container» en la relación «c19d733_demographics»
       at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2453)

I can't solve it. I wrote a post in labkey forums, but anyone answered me.
Can you help me or contact me with someone who could help me?

Thanks-
Hilaria.
view message
Text character limit for assy fields
(4 responses) jmikk 2017-01-31 12:13
Hello all,

We have an assay designed which has a field for gene ontology. This can get very long (above 4000 characters) and one of our users was wondering if there was a variable somewhere in the settings that would allow us to increase the maximum number of characters for Text fields. Assuming our database can handle such a change, is this something that could be done? Moreover, would this still allow us to use built-in assay types?

Thanks!
view message
New install, Home page editable when not signed in.
(2 responses) rick.watts 2017-01-11 15:59
I have just performed a new install of LabKey 16.3 on Windows Server 2012 R2. Everything looks good except that the home page is editable when i'm not signed in. The home folder permissions are set for "all site users" and "guests" as reader and nothing else. See attachments. I have another install where the home page is not editable and appears to have the same permissions set. That install is version 15.30.

Is this a bug or is there a way to fix it?

Rick.
 LabKeyHomePage.png  LabKeyPermissions.png 
view message
How to configure LabKey server (linux) to run R scripts remotely on another server (linux)
(4 responses) jasonl 2017-01-10 07:19
Hello LabKey

We want to use labKey in an university research environment in epidemiology.
We already have a computing server to run R and we want to add a new Labkey server to our environment. This tool seems strong but a bit hard to configure. In particular when you try to run R remotly.

We would be delighted if you could help us find the appropriate documentation for this configuration. The documentation available on the website does not describe precisely this type of configuration and we have not found any information on your forum.

We're trying to configure our LabKey server (linux) to run R scripts remotly on another server (linux) on the same VLAN but we get a java null pointer exception.

We've follow this documentation : https://www.labkey.org/home/Documentation/wiki-page.view?name=LabKeyRserve#defaultremote but without success.

When we try to modify this option :

Sign in as an admin.
Go to Admin > Site > Admin Console.
Click Experimental Features.
Under Rserve Reports, click Enable.

We get a NullPointerException from java when we click on Views and Scripting Configuration :

Do you know this error ? Or do you know where we can find information about this ?

Many thanks.

Kind regards
Cordialement
 labkey_logs.txt 
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Minimum permissions for Tomcat's conf directory
(3 responses) jmikk 2016-12-21 10:23
On Linux, is it possible to run LabKey with Tomcat's conf directory as read-only? It is usually recommended to make this directory read-only (The user running Tomcat is the owner of this directory and its contents, with permissions 0400)? I've tried it out and was unable to reach LabKey's homepage and had to revert back to 0740, but I would still like to restrict how the configuration files are able to be accessed and changed by outside users.

Thanks!
view message
Support for Tomcat 8.5.x
adam 2016-12-20 11:33
LabKey Server 16.3 now officially supports Tomcat 8.5.x, starting with the Tomcat 8.5.9 release. This Tomcat release includes a fix to an important issue that previously blocked our ability to approve use of the 8.5.x line. We expect to continue to support Tomcat 7.0.x and 8.0.x for the foreseeable future, although the Tomcat team now encourages use of 8.5.x.

More details about the Tomcat issue fix at the following links:

Feel free to test and use Tomcat 8.5.x and, as always, let us know if you encounter any issues with it.

Adam

view message
Error when trying to upgrade LabKey from 16.2 to 16.3
(4 responses) eva pujadas 2016-12-20 02:06
Dear LabKey team,
We've tried to upgrade LabKey from a 16.2 installation to 16, but we get this message in the labkey log files and labkey doesn't boot properly:

ERROR ModuleLoader 2016-12-15 13:16:14,635
localhost-startStop-1 : Failure occurred during ModuleLoader init.
java.lang.AbstractMethodError: Method
org/labkey/illumina/IlluminaModule.getSchemaNames()Ljava/util/Collection;
is abstract
at org.labkey.illumina.IlluminaModule.getSchemaNames(IlluminaModule.java)
at
org.labkey.api.module.ModuleLoader.getModuleDataSourceNames(ModuleLoader.java:1622)
at
org.labkey.api.module.ModuleLoader.getAllModuleDataSourceNames(ModuleLoader.java:1613)
at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:1008)
at
org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:917)
at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:330)
at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:240)
at
org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
at
org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
at
org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
at
org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4908)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5602)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at
org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
at
org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1962)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

Do you have any hints about what could be the cause?
Thanks a lot,
Eva
view message
First-time Setup redirects me to home, unable to complete administration set up, cannot log in
(8 responses) jmikk 2016-11-24 11:55
Hello all, I set up LabKey for the first time on a new server. Everything seemed fine at first, I could go to http://<server-name>:8080/labkey and start setting up an e-mail and password for the administrator. Then, when I continued to the next step I was immediately brought to the homepage ((http://<server-name>:8080/labkey/home/project-begin.view?). When I try to sign in from the Sign-In link in the top right, I am brought back to the homepage without being signed in. If I try to log in with bogus credentials, it does recognize that it couldn't find that user. Sometimes I get a page saying that maintenance mode is going on, and I am given a button for Adminstrator login. However, I am almost instantly redirected back to the homepage.

My logs don't help much. I've included labkey.log, but my labkey-error.log is completely empty. PostgreSQL logs have a few interesting lines, I have attached it as well.

EDIT: Investigating further, I also ran bin/configtest.sh from Tomcat's directory which uncovered some errors, although I don't see anything else using port 8080.


System information:
Apache Tomcat: 8.0.39
OS: Linux, Ubuntu 16.04
JVM: 1.8.0_112-b15 Oracle
PostgreSQL: 9.5
 labkey.log  postgres.log  config_test.log 
view message
A database connection is in an unexpected state.
(3 responses) Romina 2016-11-08 07:13
Hi, I'm trying to start Labkey 16.2 on tomcat 7, but I get the following error message:

"A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool."

I installed Labkey on Ubuntu 14.04 and the database is Postgress 9.5.5.

How could I fix this error?

Thanks,
Romina.
view message
Module has already been set - error
(3 responses) Jason Feingold 2016-09-20 17:27
I am building a continuous integration environment for our labKey development team so that we can better QA and manage our releases.

I have been able to successfully compile and push (copy) the web app to the staging server along with a restoring database from production. It seems that the web-server starts up correctly; however, upon first accessing the web-app, I receive the following error message.

"Module has already been set" I added the entire stack-trace below


I was wondering if anyone else had a similar experience and could point in the right direction.

There is a second labkey installation on the same server, but it seems to be working without issue.

Thanks,
Jason

----
java.lang.IllegalStateException: Module has already been set.
       at org.labkey.api.view.BaseWebPartFactory.setModule(BaseWebPartFactory.java:177)
       at org.labkey.api.module.DefaultModule.getWebPartFactories(DefaultModule.java:414)
       at org.labkey.api.view.Portal.getPartsToAdd(Portal.java:1178)
       at org.labkey.api.view.Portal.addCustomizeDropdowns(Portal.java:905)
       at org.labkey.api.view.Portal.populatePortalView(Portal.java:1027)
       at org.labkey.api.view.Portal.populatePortalView(Portal.java:950)
       at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:327)
       at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:280)
       at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:80)
       at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:178)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:409)
       at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281)
       at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:205)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:218)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:442)
       at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:623)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
       at java.lang.Thread.run(Thread.java:745)
view message
Upgrade version 15.2 to 16.1 (16.2)
(2 responses) info 2016-09-06 23:51
Hi.
I have tested Labkey server 16.1 and several tables (about 10 from 23 module lists) gives the message
 
500: Unexpected server error
 
Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
 
java.lang.IllegalStateException: Biostanice1.Index (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
      at org.labkey.list.model.ListTable.<init>(ListTable.java:105)

 
Similar or the same as Issue 26423. (solved in version 16.2)?
So I have installed 16.2 version and all tables which had problem in 16.1 disappeared?! (… object not found) What happened? Can you help me please?
 
In version 15.2 was all OK. All tables I created by default function in "Manage Lists - Create new lists”. I'm afraid to upgrade to the next version.
 
Thanks
lubomir pavliska

Another cases and projects.
Some project are OK. But in many cases is the same - error in primary key. I don't understand about it in version 15. was all OK and those projects come from 13. version.
 ListsErrors.log  EveryListsInProjects.png  Queries.png  Browser.png 
view message
Installing TPP on LabKey 16.2 Community Edition
(3 responses) mainbp 2016-08-31 09:01
I have been tasked with installing TPP (Trans Proteomic Pipeline) under Labkey 16.2 running on Windows Server 2012. The documentation on LabKey refers to TPP 4.6.3 but the current version is 4.8. The docs also point to the TPP source which is apparently not available. Can the TPP v4.8.0 .exe Installer version be used and if so, what process needs to be followed? Any help will be greatly appreciated.

Thanks,

Brian Main
Leroy T. Canoles Cancer Research Center
mainbp@evms.edu
757.446.5750
view message
Labkey 16 trying to run upgrade script from 14.1
(1 response) abello 2016-08-24 13:25
Hi,

While trying to connect to the Labkey server, I am getting an unexpected server error with the attached messages. It looks like Labkey is trying to run a script (viability-14.20-14.20.sql) that upgrades from 14.10 to 14.20. Since I'm running Labkey 16, I'm not sure why it is trying to run the script. Please let me know how I can fix this.

Thanks,

Alex
 errors.txt 
view message
How to make your own personalized installation package?
(5 responses) wit2wit 2016-08-13 03:00
Hello,I installed only Labkey core and Filecontent and audit modules. Publishing package is installed there are many modules,Delete not every module is cumbersome. How to make your own personalized installation package?

Thanks
view message
LabKey in the cloud on a VM on Azure
(1 response) lucasbran 2016-08-04 14:08
Hello, I was wondering if anyone could guide me in the right direction to setting up a free instance of labkey on the cloud using a virtual machine in Azure. I have set up a VM machine on azure and they have provided me with a custom domain under their services. If I go to their domain name I get the error in my browser saying it took to long to respond and no connection is available to labkey.

Now, what I am wondering is how can I setup the labkey services so that when I put the Azure domain into a browser I will be prompted with the login page of labkey. I am new to this so I have no clue how to set up it up- right now I can just connect through azures portal so I have direct access to the virtual machine with the lab key hosted on the computer/server. How do I setup the labkey server settings where accessing the domain directly would lead me to the login page of labkey? Or rather how do I configure a VM so that labkey will be accessible? Any help would be appreciated!

Thanks
view message
apache proxy and login-setPassword URL
(2 responses) shieldsr 2016-07-21 10:03
I have the Labkey server running at http://servername:8080/labkey and have apache running in front of that to proxy https://servername/labkey to that address. That seems to work fine for the most part.

The only issue I've run into with this is in the emails that are generated for when new users are generated. Those emails reference the http address with port 8080, which is not reachable from outside the server, like this:
http://servername:8080/labkey/login-setPassword.view?verification=somestring&email=username%40domain.com

I'd like that email invite to include an address like this:
https://servername/labkey/login-setPassword.view?verification=somestring&email=username%40domain.com
view message
Support for SQL Server 2016
(1 response) adam robinson 2016-07-19 16:28
Forgive me, this is a pretty elementary question.

I am setting up a new BI server for a biobank, and am designing it now. We are a Microsoft shop, so the choice of DBMS is already made :)

SQL Server 2016 has just been released by Microsoft, and is not mentioned as a supported release for current LabKey. We are going with it to get extra features not available in earlier releases.

At the same time we are looking for alternatives to Microsoft's tools for information delivery because we have data we cannot store in Sharepoint, and I am thinking to take a close look at LabKey for this.

How long might it be before Labkey will support SQL Server 2016? How risky is it to try and make them work together before it is officially supported? Are the risks just that things might not work, or are there data security implications?
view message
500: CONFIGURATION ERROR
(4 responses) hilariagrieve 2016-04-20 10:57
Hi, I installed every required component succesfully,
But when I configure the application It returnes me an configuration error. I send you a .log file and a print.
I checked that the database is running, and the database connection URL and user credentials in labkey.xml are ok.

I installed, Tomcat 8.0.33, Postgres 9.5, and Java jdk1.8.0_77.

Please, can you help me?

Hilaria
 error.png  postgres.png  labkey-errors (4).log  labkey (6).xml 
view message
Error during configuration
(5 responses) andrej studen 2016-04-05 04:03
While doing the initial configuration in Site Settings once the Submit button was pressed, the labkey server returned error:

Unhandled exception: 500: Unexpected server error
java.lang.NullPointerException: Could not find domain for AppPropsEvent

I am attaching the labkey.log file.

My operating system is Debian GNU/Linux 8.3, Labkey version is 16.10, tomcat version Apache Tomcat/8.0.14 (Debian), Java JDK 1.8.0_74.

Thank you!
 labkey.log 
view message
Upgrade from 15.x to 16.1 Script formatting...
(1 response) diego 2016-03-23 09:16
I am trying to upgrade LabKey Server using the manual-upgrade.sh script but I do not seem to get the correct format going to properly execute it.

===== manual-upgrade =====

./manual-upgrade.sh -l dir /usr/local/labkey/ -d dir /usr/home/diego/Downloads/LabKey16.1-42836.12-community-bin/ -c dir /usr/local/apache-tomcat-8.0/conf/Catalina/ -u www --service /usr/local/etc/rc.d/tomcat8 --catalina /usr/local/apache-tomcat-8.0/bin/shutdown.sh /usr/local/apache-tomcat-8.0/bin/startup.sh

======== end =============

Thanks in advance!
Diego
view message
Windows Dev Env Setup
(2 responses) balter 2016-03-16 09:15
I'm trying to set up my development environment in Windows. I'm primarily working from the documentation at

https://www.labkey.org/home/Documentation/wiki-page.view?name=build

I'm documenting my progress here: https://gist.github.com/abalter/e7037098cf58b036a36c/edit

I'm stuck on one particular issue. Right now I have

    JAVA_HOME=C:\Program Files\Java\jre1.8.0_74

When I start IntelliJ, I get

    'tools.jar' seems to be not in IDEA classpath.
    Please ensure JAVA_HOME points to JDK rather than JRE.

When I change to

    JAVA_HOME=C:\Program Files\Java\jdk1.8.0_74

and start IntelliJ, I get what is in the image.

Suggestions?
 IntelliJ Idea.PNG 
view message
Single Sign-On at the Project level or multipls CAS servers
(1 response) louie ona 2016-03-15 11:21
Hello All,

Each one of our Projects has it's own user base. Has anyone looked into providing Single Sign-on for users at the Project level? The current system only allows for one Single Sign-On server configuration. We would need to be able to point to multiple CAS servers.

Any feedback is much appreciated.

Thanks,

Louie
view message
time charts
(10 responses) Lind-Thomsen 2016-03-07 03:26
Hi
I'm having troubles with creating time charts.

I use the tutorial study/datasets HIV/CD4 .
If I import the demo study and try to make a time chart with e.g the lab-data it says:
No calculated interval values (i.e. Days, Months, etc.) for the selected 'Measure Date' and 'Interval Start Date'

If I click view data then I can see there is empty fields in days/visits/visit day.

This goes for any measure in any dataset I have tried

I have clicked recalculate visits, is there anything else obvious I could try?
If I check the Lab result data I can see the Day field.

Best wishes
Allan
view message
Histogram as Quick Chart
(1 response) Lind-Thomsen 2016-03-02 06:10
Hi

I would like to implement histograms as quick charts, so that I can get a histogram showing the count of all groups in a categorical/text variable. It should be available for any data grid

How can I go about doing that?
Is it a module that implement these functions that I can change, or will I need to build it from the ground up?

Best wishes
Allan lind-Thomsen
view message
LabKey Running R and Virtual Frame Buffer Server Config...
(9 responses) diego 2016-02-25 14:35
Running:
FreeBSD 10.2 (64bit)
LabKey Server 15.3 (Latest Updates)
Tomcat 8.0.28
tomcat user: www
tomcat directory: /usr/local/apache-tomcat-8.0/
R-project: 3.2.2
VFB server: xorg-vfbserver-1.18.0.1 (pkg install)


Have successfully installed R but I am having issues configuring the VFB server to work on LabKey Server. Followed the tutorial below, but it seems as though some steps might be different for FreeBSD... Please advise!


https://www.labkey.org/home/Documentation/wiki-page.view?name=configVirtualFrame

Configuration Test Output
=========================
jpeg png tiff tcltk X11 aqua
       TRUE TRUE TRUE TRUE FALSE FALSE
   http/ftp sockets libxml fifo cledit iconv
       TRUE TRUE TRUE TRUE FALSE TRUE
        NLS profmem cairo ICU long.double libcurl
       TRUE TRUE TRUE TRUE TRUE FALSE
> proc.time()
   user system elapsed
  0.152 0.010 0.182

===== END OUTPUT =====

Thanks in advance!
Diego
view message
LabKey Sample Study Installation Missing options...
(11 responses) diego 2016-02-12 10:53
LabKey 15.3 is correctly running, now wanting to install ImportableDemoStudy.folder.zip, but noticed the instructions to the below tutorial do not match the options to what is available in my LabKey version.

1.) "Confirm that Inherit from Parent Folder is checked" do not seem to find that option anywhere...
2.) "On the New Study page, click Import Study" do not seem to find the "import study" option anywhere...
3.) Thanks in advance! Screenshot attached!



LabKey Sample Study Article
============================
https://www.labkey.org/home/Documentation/wiki-page.view?name=setupDemoStudy
 Screenshot at 2016-02-11 20:05:49.png 
view message
LabKey Server Not Starting on Tomcat Intiation...
(26 responses) diego 2016-02-10 14:48
Have installed LabKey Server Community 15.3 on CentOS Linux release 7.2.1511 (Core) (PostgreSQL) 9.2.14.

PostgreSQL and Tomcat are both running correctly. But LabKey Server does not load...

Followed instructions from the following link: https://www.labkey.org/home/Documentation/wiki-page.view?name=config

Have attached my catalina log file... What can be going wrong? Files in the wrong directory?

Let me know if you all need more information.

Thank you,
Diego
 catalina_021012.log 
view message
Tomcat/WebDav bug fixed on LabKey 15.3 r42135.48
Jon (LabKey Support) 2016-02-01 16:12
An important bug has been fixed on LabKey 15.3 r42135.48 regarding WebDav and the recent updates to Tomcat, specifically Tomcat 8.0.30+ and Tomcat 7.0.67+

Due to unforeseen changes with Tomcat's handling of WebDav calls, some functions with the FileContent module (Files Web Part) would cause issues with creating new folders, generate Error 400 responses in the background, or even prevent LabKey from starting due to the WebDav controller failing during the initialization.

All WebDav bugs have been identified and fixed, so if you have plans on upgrading Tomcat to one of the two versions listed above, please make sure you download our revised LabKey 15.3 build.

Regards,

Jon - LabKey Support
view message
problem upgrading 15.2 to 15.3
(14 responses) pablo escobarlopez 2016-01-27 09:13
Hi

I am trying to upgrade 15.2 to 15.3 in our devel instance. I have done some upgrades before without issues but now I am getting a weird error. This is my environment running in centos6:

Core Database Configuration
Server URL jdbc:postgresql://127.0.0.1/labkey
Product Name PostgreSQL
Product Version 9.2.8
JDBC Driver Name PostgreSQL Native Driver
JDBC Driver Version PostgreSQL 9.4 JDBC4.1 (build 1201)
JDBC Driver Location file:/opt/apache-tomcat-7.0.53/lib/postgresql.jar

Runtime Information
Mode Production
Asserts disabled
Servlet Container Apache Tomcat/7.0.53
Java Runtime 1.8.0_40
Java Home /opt/jdk1.8.0_40/jre
Username labkey
User Home Dir /home/labkey
Webapp Dir /opt/LabKey15.2-39071.18-bin/labkeywebapp
OS Linux
Working Dir /home/labkey
Server GUID 26b65700-c331-1031-a374-504196604ae0
Server Time 27/01/2016 17:40

but when doing the post-upgrade steps in the web interface I get this in the logs:
https://gist.github.com/pescobar/11468150968f960f16ed

I think the interesting lines are these ones:
https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L196
https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L243
https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L334
https://gist.github.com/pescobar/11468150968f960f16ed#file-gistfile1-txt-L383

Trying to figure out what's going on I went to the admin console >> diagnostic >> database check >> do database check and then I get this error:

Checking Container Column References...

Checking PropertyDescriptor and DomainDescriptor consistency...
   ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /Shared/Demo Clinical Study Published
   ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Study
   ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Lab A
   ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /home/Security Tutorial/Lab B
   ERROR: Inconsistent project ids found for exp.domaindescriptor in folder /Shared/Demo Clinical Study Published

When I try "click here to attempt recovery ." I get this error:

500: Unexpected server error
SqlExecutor.execute(); bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: column "domainid" does not exist Position: 52

An this is the complete log when trying the recover
https://gist.github.com/pescobar/d8ed83836a5bb2967d30

I have also notice that the postgres driver jar is "PostgreSQL 9.4 JDBC4.1 (build 1201)" but I am using postgres 9.2 installed fro the centos SCL repositories (https://wiki.centos.org/AdditionalResources/Repositories/SCL). I was thinking about upgrading postgres to 9.4 but in the labkey compatibility table I see that postgres 9.2 is supported so I am not sure if this could be the problem.

does anyone knows which could be the issue?

Thanks in advance for any help or suggestion.

regards,
Pablo.
view message
Installation - NullPointerException
(9 responses) informaticsforlife 2016-01-21 14:26
Hi All,

First time LabKey user. I am attempting to install LabKey on Linux with the following details:
LabKey 15.3, Tomcat 8.0.30, JDK 1.8, Postgres 9.1.18 - all running on Debian 7.
PG and Tomcat are working fine. Labkey installation is not, as it is throwing a server error - 500. Its able to run the SQL scripts and create few schemas, and populate the core schema (the log has a message of not supporting PSQL version 9.1.18, but this does not seem to be the issue, although I am planning an upgrade later). The Exception:

INFO ModuleLoader 2016-01-20 16:55:55,521 localhost-startStop-1 :
LabKey Server startup is complete, modules will be initialized after the first HTTP/HTTPS request
INFO ViewServlet 2016-01-20 16:55:56,729 localhost-startStop-1 :
ViewServlet initialized
INFO ViewServlet 2016-01-20 16:55:56,730 localhost-startStop-1 :
WEBAPP: /usr/local/labkey/labkeywebapp/
INFO ViewServlet 2016-01-20 16:55:56,730 localhost-startStop-1 :
PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ERROR DavController 2016-01-20 16:56:39,999 http-nio-8080-exec-2 :
unexpected exception java.lang.NullPointerException

    at org.labkey.api.data.ContainerManager.toString(ContainerManager.java:1549)
    at org.labkey.api.data.ContainerManager._getFromCachePath(ContainerManager.java:1537)
---

I have attempted to ease access to both the tomcat and the labkey directories, in case its an access issue, with no success.
Any tips? Thanks.
view message
HTTP Status 500 - Internal Server Error
(4 responses) greener 2016-01-20 21:56
Longtime labkey user first time installation problem (well its been a while). Followed the linux instructions on the website (installing on Centos7) and when I start it up I get a 500 error. Versions all appear to be supported(javac 1.8.0_66, PostgreSQL 9.2.14, apache-tomcat-7.0.67). Tomcat appears to running just fine. Any suggestions would be great.
Thanks
-Rich
 labkey.log  labkey.xml  localhost_access_log.2016-01-20.txt  server.xml 
view message
ETLs
(2 responses) Lind-Thomsen 2016-01-05 05:22
Hi

I'm working with ETL's and have some questions. They spring from the fact that we have a collection of source tables on an external database server, which needs some basic cleaning/transforming before loading them into labkey. e.g. we need to change some',' and '.' to be able to convert a column to floating point.

1: If I use a stored procedure server to populate a source table. How do I make sure that the stored procedure is executed before loading the data into the destination?

2: Is it possible to use a stored procedure which return a table/select query as a source in the ETL step so that it is loaded directly into the destination?

3: Is there a better way to do the transform step than in stored procedures when using Labkey?

4: How does <incrementalFilter> work?

I couldn't find answers to these questions in the documentation, but if I have overlooked something please point me in the right direction.

Best wishes
Allan
view message
Streamlined Server Upgrade/Startup Process in 16.1
adam 2016-01-04 13:37
Greetings,

Quick note just to let everyone know that LabKey Server's automatic upgrade process is becoming somewhat more automatic starting with the 16.1 release. Previously, the server would upgrade the core module at server startup, but would wait for an administrator login before upgrading other modules or initiating module startup. A trunk commit last week changed the server to initiate upgrade and startup of all modules at server startup time. Administrators can still log in to view upgrade/startup progress, but the server will no longer wait for a login.

This change streamlines the startup process, simplifies upgrade code, and facilitates scripted upgrades of LabKey Server. We suspect most administrators won't notice a difference, but let us know if you have any questions or concerns about this change.

Thanks, Adam

view message
Problem with import of Labkey data into SAS
(14 responses) Lind-Thomsen 2015-12-21 05:09
Hi

I'm trying to import a labkey list into SAS.

I have installed the SAS and Java libraries and added them to the paths in the sasv9.cfg file

I have created a _netrc file in my home directory (there is a copy attached with a changed password, but the password starts with a '-' which is kept), and I made an environmental variable named HOME pointing to my home directory.

SAS code:
%labkeySelectRows(dsn=mydata,
        baseUrl="http://rghorion001:8080/persimune",
        folderPath="/Persimune",
        schemaName="lists",
        queryName="mikrobiologi_pos_prover");

SAS error:
ERROR: Could not instantiate class org/labkey/remoteapi/sas/SASSelectRowsResponse at line 27 column 69.
ERROR: DATA STEP Component Object failure. Aborted during the EXECUTION phase.
dec 21, 2015 1:24:21 PM org.labkey.remoteapi.Command _execute
INFO: Requesting URL:
http://rghorion001:8080/persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.queryName=mikrobiologi_pos_prover&schemaName=l
ists&query.maxRows=1
org.labkey.remoteapi.CommandException: Unauthorized
     at org.labkey.remoteapi.Command.throwError(Command.java:355)
     at org.labkey.remoteapi.Command._execute(Command.java:321)
     at org.labkey.remoteapi.Command.execute(Command.java:202)
     at org.labkey.remoteapi.query.SelectRowsCommand.execute(SelectRowsCommand.java:61)
     at org.labkey.remoteapi.sas.SASBaseSelectCommand.execute(SASBaseSelectCommand.java:65)
     at org.labkey.remoteapi.sas.SASSelectRowsResponse.<init>(SASSelectRowsResponse.java:54)
     at org.labkey.remoteapi.sas.SASSelectRowsResponse.<init>(SASSelectRowsResponse.java:44)

This indicates a login error, so I tried using Rlabkey to import the same list into R,
which works, so there isn't an error in the _netrc file (unless SAS and R parse/interpret it differently).

In the logfile, localhost_access_log I see:
[21/Dec/2015:13:15:36 +0100] "GET /persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.showRows=all&query.queryName=mikrobiologi_pos_prover&schemaName=lists HTTP/1.1" 200 85737276 (for the R access)
[21/Dec/2015:13:24:22 +0100] "GET /persimune/query/Persimune/selectRows.api?apiVersion=9.1&query.queryName=mikrobiologi_pos_prover&schemaName=lists&query.maxRows=1 HTTP/1.1" 401 6444 (for SAS access)

There doesn't seem to be anything in the other log-files. (labkey.log, labkey-errors.log)

For good measure I restart SAS after each change.

Furthermore, if I add the userName and password to the SAS-macro call, then it also works.

My own conclusion is tha tit must på the SAS interpretation of the _netrc file that fails, but because it wotks with Rlabkey i'm not sure what kind of error it could be. Do you have any idea what might cause this?

Best wishes
Allan Lind-Thomsen

Labkey ver. 15.3-41022.16
SAS Ver. 9.4
Labkey Server: windows 8
Client windows 7
 _netrc.copy 
view message
Using custom perl/python/R script in LabKey only when importing files?
(6 responses) martin lague 2015-11-26 12:44
Is it possible to add our own pipeline (perl/python/R scripts) elsewhere than when importing files? Is it possible to have them with the other analysis scripts/tools in the Sequence Analysis (DISCVR-Seq) module?

I've spent some time reading about creating pipelines, but I can only find examples and description of pipelines used when importing files, not to work on files already uploaded/analysed.
view message
auto-commit keeps LabKey 15.3 from starting
(7 responses) bill c white 2015-11-25 19:26
I have setup LabKey several times (13.3, 14.1, 14.2, 14.3), and the 15.3 webapp is running, but this time I can't get past this JDBC error on first access. The labkey user has superuser access. I added the defaultAutoCommit line to try and resolve it, but no go. Any ideas? Thanks.

Linux insilico 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Java 8 (installed apt-get PPA)
Tomcat 7 (installed apt-get)
PostgreSQL 9.3 (installed apt-get)
LabKey 15.3 (download and fresh install to /usr/local/labkey)

labkey.xml data source section:

   <Resource name="jdbc/labkeyDataSource" auth="Container"
        type="javax.sql.DataSource"
        defaultAutoCommit="true"
        username="labkey"
        password="l@bk3y"
        driverClassName="org.postgresql.Driver"
        url="jdbc:postgresql://localhost/labkey"
        maxActive="20"
        maxIdle="10"
        accessToUnderlyingConnectionAllowed="true"
        validationQuery="SELECT 1"
        />

Configuration Error Detected at LabKey Server Startup

A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool.

This is a problem with your configuration. Please contact your local server administrator for assistance, or LabKey Software at support@labkey.com for operational assistance with correcting the configuration error.

org.labkey.api.util.ConfigurationException: A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool.
       at org.labkey.api.data.DbScope._getConnection(DbScope.java:737)
.
view message
Upgrade to 15.3 failed.
(5 responses) rick.watts 2015-11-23 17:18
I'm attempting to upgrade to 15.3 on Windows. The installer gives me the following message: Postgres upgrade failed: 1. Unable to recover. However before that a message flashed up complaining about invalid characters in the install path. The message did not persist long enough for me to read it all :(

Now it would appear that my install is broken and I have no idea how to fix it without reverting to a backup.
view message
Failed to start labkey (first time) with exception, "java.lang.NullPointerException"
(2 responses) cameron macpherson 2015-11-19 08:54
Hello,

I have tried to install Labkey on my Mac, but fail to initialise the Labkey app at, "localhost:8080/labkey".

Error:
"""
ERROR ModuleLoader 2015-11-19 17:30:56,896 localhost-startStop-1 : Failure occurred during ModuleLoader init.
java.lang.NullPointerException
"""

I followed the instructions on the website at, "https://www.labkey.org/home/Documentation/wiki-page.view?name=manualInstall".

Versions:
OS, OS X 10.10
Java, 1.8
PostgreSQL, 9.4.5
Tomcat, 8.0.28
Labkey, 15.1-3

Thank you for any help.

Gratefully,

Cameron
 labkey.log  labkey-errors.log 
view message
Mutant vs Control protein expression ratios
(1 response) oo254 2015-11-18 15:20
Hi,

I have been playing around with some ".mzXML" data obtained from "LTQ Orbitrap Velos" raw data on the LabKey server. I will like to find perturbed pathways based on the differential expressions of mutant/wild-type(control). Even though I have followed the tutorials in the LabKey documentation, I'm still not sure about the steps that are necessary to do this kind of analysis that I'm interested in. For example, I need to know which proteins are over/under- expressed in either mutant or the control. How can I use LabKey server to achieve this? Any help will be appreciated. Thanks
view message
Change User Properties
(4 responses) Lind-Thomsen 2015-11-09 05:02
Hi

According to the documentation there should be a "Change User Properties" link in the "Site Users" section, which don't seem to be there. It is however in the 'Admin Console', but when I click it I just get an empty page with a 'back' and a 'home' button.
There is no errors in the log. Do you have any clue to what the problem might be? Does it require any setup to use?

Best wishes
Allan Lind-Thomsen
view message
Login security
(2 responses) Lind-Thomsen 2015-11-09 04:44
Hi

Is it possible to automatically block a user after a certain number of failed attempts?

Best wishes
Allan Lind-Thomsen
view message
"A sequence database must be selected" error in search MS2 Data page
(1 response) oo254 2015-11-07 04:01
Hi,

I clicked on search to carry out X!TANDEM PEPTIDE SEARCH, but got the following error message: "A sequence database must be selected". I checked the Protein databse section of this page and only found <root> dropdown link and a "none found" message.

I noticed in the file section that there is no file in the "databases" folder even though I had already downloaded and imported the swissprot database as recommended in the documentation.

Labkey version: apache-tomcat 7.0.62; Database Product Version: 9.4.4

Web browser: firefox

OS: Windows7

I wonder why the protein database is not where it should be.
view message
LabKey as primary credentials to authenticate to third party application
(2 responses) sfuertez 2015-11-04 18:38
Can we use labkey’s built-in authentication service (i.e. database authentication) to pass credentials to other software/sites? We want to integrate with other software, but do not want to have 2 credentialing systems.
This seems to be point to an SSO integration but with LabKey as primary. We also do not want to use LDAP at this time. Would there be a capability or best practice to accomplish this from LabKey?

Thanks!
view message
cannot start Labkey Server on Linux
(7 responses) ytm4 2015-10-29 10:47
I tried to start the Labkey server (version 15.2) on Linux machine. I got the error messages please see the attached log file.

Please help me!

Thanks,

Haibin
 labkey-errors.log 
view message
Skipping multiple question in surveys
(4 responses) patrickbkeating1 2015-10-28 14:46
Hello all,

I'm a new user to LabKey and I will be using it mostly to collect survey data.

I'm trying to do the following:

Q1. Were you sick? Yes/No

If yes, answer questions 2-5
If no, answer question 6

I'm able to use the skip logic on one question at a time, but wondering if it's possible to apply the skip logic to multiple questions as a group?
Thanks!
Patrick
view message
Remote pipeline debugging
(16 responses) martin lague 2015-10-26 08:22
Hi,
I'm setting up a remote pipeline server on a linux server (CentOS 6.5). The labkey webserver is a windows 2008 server. I've followed these instructions to set up the the remote pipeline server (https://www.labkey.org/wiki/home/Documentation/page.view?name=configureRemoteServer) and these instruction to have the labkey webserver to use the remote pipeline (https://www.labkey.org/wiki/home/Documentation/page.view?name=installConfigureEnterprisePipeline).

Every time I try to send a job to the remote pipeline server from the labkey webserver, it still tries to run it locally from the Sequence Analysis module (DISCVR-Seq module). The message I get in the pipeline log has: "Starting to run task 'org.labkey.sequenceanalysis.pipeline.SequenceAlignmentTask' at location 'webserver'" and it can't find the tool I'm trying to run has it's not installed locally.

I've added -DsequencePipelineEnabled=true in the Tomcat7w startup options and configured the remote and local pipelineConf.xml scripts. ActiveMQ is setup on the linux server (on the remote pipeline server) and seems to works.

Is there something I missed and is there some documentation on labkey.org I should check to help me debug this?
view message
Error received
(1 response) Lind-Thomsen 2015-10-09 15:36
org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is java.sql.SQLException: Invalid object name 'comm.Threads'.
    at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231)
    at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:37)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:31)
view message
SQLServer 2008R2 deprecation warning
jeckels 2015-10-08 11:12
Hi everyone,

We wanted to give everyone an update on our support for SQLServer 2008R2. We've long listed it as deprecated (since at least version 14.2), but we're shifting starting in 15.3 to actively encourage administrators to upgrade. In version 16.1, we will no longer support 2008R2.

This is in line with our standard approach of dropping support for versions of third-party software that are no longer supported by their vendor. Microsoft's end-of-life for 2008R2 is complicated by the vast number of versions, but has been largely unsupported for a couple of years already:

https://support.microsoft.com/en-us/lifecycle?c2=1044

We encourage everyone to plan ahead with their upgrade schedule.

Thanks,
Josh
view message
failed upload of ProtProphet data
(8 responses) tvaisar 2015-10-01 05:47
Hi,

I am not sure what is wrong, but I tried to upload Comet search results from shotgun proteomics LCMS acquired on Thermo Fusion and the upload failed with the following in the log file (below).
I was able to upload Comet search results and shotgun proteomics from Fusion before.
I noticed that in reading the mzXML file it shows MS3: 0 and I am sure that is incorrect.
Any suggestions?

Thanks,

Tomas
 
01 Oct 2015 05:23:34,566 INFO : Starting to load ProteinProphet file /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.prot.xml

01 Oct 2015 05:23:34,587 INFO : Resolved referenced PepXML file to /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,588 INFO : Starting import from interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,595 INFO : Starting to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 DEBUG: 0.03 seconds to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 INFO : Starting to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,058 INFO : FASTA file "/data/dbase/Uniprot/uniprot.sptr.human.20150718" not imported, but another file, 'uniprot.sptr.human.20150718', has the same checksum

01 Oct 2015 05:23:35,062 DEBUG: 0.43 seconds to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,062 INFO : Starting to import peptide search results

01 Oct 2015 05:23:35,062 INFO : Importing MS/MS results is 0% complete

01 Oct 2015 05:23:35,063 INFO : Starting to parse /data/users/tvaisar/HDL/LRA/1509Shotgun/150909_LRAPEGJW01.mzXML to get scan counts

01 Oct 2015 05:23:38,125 INFO : Finished parsing to get scan counts. Total: 53396, MS1: 7724, MS2: 45672, MS3: 0, MS4:0

01 Oct 2015 05:23:38,144 ERROR: MS2 import failed

java.lang.ArrayIndexOutOfBoundsException

01 Oct 2015 05:23:38,154 ERROR: ProteinProphet load failed

java.lang.ArrayIndexOutOfBoundsException
view message
Manual installation, CentOS 6.5, Postresql. Failed to start up
(9 responses) yuw 2015-09-25 19:34
There seems to be a problem with my labkey.xml setup. The admin account 'yuw' for Postgresql was setup to be the same as the login account on my CentOS acct.

Any clue?

Thanks!
Wen

<Resource name="jdbc/labkeyDataSource" auth="Container"
        type="javax.sql.DataSource"
        username="yuw"
        password="myPassword"
        driverClassName="org.postgresql.Driver"
        url="jdbc:postgresql://localhost/labkey"
        maxActive="20"
        maxIdle="10"
        accessToUnderlyingConnectionAllowed="true"
        validationQuery="SELECT 1"
        />


org.labkey.api.util.ConfigurationException: DataSources are not properly configured in labkey.xml.
       at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:887)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:318)
       at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:230)
       at java.lang.Thread.run(Thread.java:745)

Caused by: javax.naming.NameNotFoundException: Name [comp/env] is not bound in this Context. Unable to find [comp].
       at org.apache.naming.NamingContext.lookup(NamingContext.java:819)
       at org.apache.naming.NamingContext.lookup(NamingContext.java:167)
       at org.apache.naming.SelectorContext.lookup(SelectorContext.java:156)
       at javax.naming.InitialContext.lookup(InitialContext.java:417)
       at org.labkey.api.module.ModuleLoader.ensureDatabase(ModuleLoader.java:902)
       at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:864)
view message
MS SQL Server setup
(2 responses) Lind-Thomsen 2015-09-24 01:43
Hi
I'm still having problems with getting a running Labkey installation using MS SQL Server.

The basic questions are:
1: What is the preferred process to install a Labkey server using MS SQL Server when you don't have full permission/control of the server and want to be certain that the labkey admin have all the necessary permissions (at the moment the labkay admin is owner of the database) ?
2: Can you describe what permissions are needed (besides from being owner of the database) in the database to successfully run labkey?
3: Must it be the labkey server that runs sp_updatestats or is it OK if we have the option 'Auto update statistics' enabled on the database?

Background:
environment: MS SQL Server 2012, tomcat 7,windows 8 server. Manual install of Labkey

I'm not sysadmin so I don't have full control over the database, I have to ask our central IT department to do stuff, which takes 1-3 days depending on how busy they are.

There are (at least) two issues:

1: GROUP_CONCAT
Needs to be part of core schema, but the core schema cannot be made before the initial run of the server.
I get an error if I try to create the core schema in advance and assign the GROUP_CONCAT functions to it before I start the server ("core schema already defined" exception). After moving GROUP_CONCAT back to dbo and remove the schema. I get another error "DROP ASSEMBLY failed because 'GroupConcat' is referenced by object 'GROUP_CONCAT_D'" but I was able to start labkey. Then it seemed to work but when I installed a module I was back to a previouos discussed "FastaAdmin already exist" exception.

2: sp_updatestats
Need permission to run this stored procedure(in our system we don't have this pr default), this must be assigned before creating any database objects. Is it important who runs this procedure, as long as it is run?

Will the following process work (using the labkey admin user):
1: create the database
2: Set permission to run sp_updatestats
3: start Labkey server and finish the basic installation process.
4: install GROUP_CONCAT
5: Move GROUP_CONCAT to core schema
6: Restart server

Appreciate any comments and suggestions.

Best wishes

Allan
 labkey.log 
view message
Import data from external schemas
(1 response) Lind-Thomsen 2015-09-17 07:11
Hi All

Our data is almost exclusively stored in SQL databases, and data is comming continously into the tables.

What is the preferred way to import these data into dataset/assays/lists to be able to work with them inside labkey? f.x. we have a table with basic information about the patient birthday, gender, enrollmen date etc, and with new patients being enrolled continously. What will be the best way to use this table as a basic demographic table in the study?

I have looked at external schemas but it is not obvious for me how to do something like that in labkey.

Best wishes
Allan
view message
Stopping Uniprot TrEMBL annotation upload
(1 response) tvaisar 2015-09-16 13:03
Hi,

I adventurously started upload of the full Uniprot-TrEMBL annotation from uniprot_trembl.xml. It appears to be endless - has been running since Aug 23, and it is still adding new entries.
Is there a way to abort/cancel this process?
In retrospect subsetting the uniprot_trembl.xml to only relevant species would have been prudent, but at this point I am just trying to stop it.
Perhaps incorrectly I tried to "Complete" the process in the Admin>Site>Pipeline, which marked it as Complete, yet the process is still running.
Any advice?

Thanks,

Tomas
view message
MS SQL Server problem
(6 responses) Lind-Thomsen 2015-09-16 05:10
Hi All

I'm having trouble with using MS SQL server 2012 (Build number: 11.0.3381.0)

I made a manual install on Windows 8 (danish language):
labkey 15.2 (build39349.20)
Java 8
Tomcat 7.0
postgresql 9.4

And it worked. But with our setup it would be better to use MS SQL Server because we use that for everything else.

I then changed the database to SQL Server and then I did get errors like:
java.sql.SQLException: Parameter #20 has not been set.

Does anybody knows about anything which might cause this? Any hints and thoughts will be appreciated.

I have attached labkey.xml and labkey.log.

Best wishes
Allan Lind-Thomsen
 labkey.log  labkey.xml 
view message
Sequence Analysis | How to upload Human reference genome
(10 responses) che.l.martin 2015-09-11 17:03
Good Evening all,

Any one know how to setup the human reference genome in Sequence Analysis? I clicked the reference genome ..> more actions..> load from NCBI..> and entered the following info:

NCBI subfolder = /H_Sapien
Genome prefix = hs_ref
Genome name = GRCh38
Species = Human

But the download is empty,...Am I doing this correctly?

Che
view message
How to Build the GenotypeAssays module in my Labkey
(11 responses) che.l.martin 2015-09-10 09:46
Good Day All,

I am trying to add the GenotypeAssay module to my LabKey install but there are no clear build and install instructions for this module I . Has anyone done this on the Labkey Ubuntu install ??
view message
Unable to import dates
(11 responses) Lind-Thomsen 2015-09-09 06:29
Hi all

I'm just starting up learning labkey.

Following the tutorial on importing the 'Physical exam' dataset I can't get the dates right. (https://www.labkey.org/wiki/home/Documentation/page.view?name=simpleDataTablesTutorial1)

  • in the excel sheet the format is '15-08-2008'
  • it correctly guess the format as DateTime
  • in the preview it says '15-08-2008 00:00:00'
  • on importing it gives an error:
Date: Could not convert 'Fri Aug 15 00:00:00 CEST 2008' for field Date, should be TimeStamp
  • The underlying format in excel i a number (when converted to text)
If I convert to a TSV file it works ok. I think this error propagates into the rest of the tutorials where timepoints is used because they don't work as expected. Is there any settings that can cause/solve this?

I'm using labkey 15.2.

best wishes

Allan Lind-Thomsen

view message
FastaAdmin already exists
(12 responses) Lind-Thomsen 2015-09-09 01:51
Hi
I'm trying to do a manual update of labkey 14.3 to 15.2

When I restarted the tomcat, I logged in as admin and an update process started but ended with an error:
"There is already an object named 'FastaAdmin' in the database"

I then look through everything (didn't change anything) and restarted the server this time I got a similar error: There is already an object named 'ExpressionData' in the database. log file attached.

Any suggestions to what goes wrong?

Our setup:
tomcat 7.0.57 on windows 8 server
MS SQL database

Best wishes

Allan Lind-Thomsen
 labkey-errors.log 
view message
Trigger pipelines automatically
(1 response) eva pujadas 2015-08-14 09:09
Is there some way to trigger automatically pipelines (understood as sequences of tasks) when new files are dropped into the configured pipeline directory (e.g. in a pipeline override)?

From your documentation (https://www.labkey.org/wiki/home/Documentation/page.view?name=pipeline) it seems it is possible to automate some tasks like data upload. But when searching about the details in documentation and forums, we could not find how or if that is possible.

Thank your very much for your support,
Eva Pujadas
view message
Changing assay location from Project to Folder
(2 responses) cschoening 2015-08-10 04:47
Hello,

Our users have been creating many assays. The default setting for Assay Location when you create a new assay is Project (not Current Folder). So of course, the first dozen or so assays they set up used this default setting for the assay location. Now that we've started to organize things a bit further, we've set up folders underneath the project. When you add the Assay List web-part to any folder, the assay list shows all project assays. We sort of realized too late that we should not have used the default Project assay location, because we want the assay lists to only show the assays that belong to that particular folder. I haven't been able to find a way to go back and change this setting after the assay has been created. Is there something I'm missing, and if there is no way to change this through the application, how would be go about changing it through the backend database. Alternatively, we could even settle for a way to permanently filter the assay list so it only shows the assays for the current folder location.

We're running on Tomcat/PostgreSQL.

Thanks
Chris Schoening
Henry Jackson Foundation
view message
New Study/Dataset
(2 responses) pmedvedev 2015-08-05 12:19
Hello, new to the community so apologies if this has been answered in the past, but I couldn't find in documentation/forum.

We have a study/registry we've kept in an excel sheet and would like to transition into LabKey. At a high level all subjects are assigned an ID and have information collected at multiple events (separate label/column).

I tried "importing a dataset" but have gotten a number of errors. Is this the best way to setup a study from an excel sheet? This one seems to keep popping up: "Only one row is allowed for each Participant/Visit. Duplicates were found in the database or imported data".

Hope you can help,

Cheers,
view message
Author Role
(1 response) eva pujadas 2015-07-28 07:14
We are running LabKey 15.1, and we see in the Web interface, when setting permissions for a folder, the following Author Role description:
"Authors may read and add information in some cases, but may update and delete only information they added."

When trying such role using the impersonate function, it seems that Authors can create data and view all data (not only data belonging to the current user), but they are not able to update or delete the data created by themselves.
Also, that seems to apply only for lists, and not for datasets.
How does that correspond with the Author Role description? Are we understanding that incorrectly?

Is there a way to give a user permissions to edit/delete and to view only data created by him/herself, both in lists and datasets?

Thank you very much,
Eva Pujadas
view message
Dataset items with messages
(1 response) eva pujadas 2015-07-28 05:51
Is it possible to create messages (discussion threads) in datasets at the record level?

For lists, it is possible to allow one or multiple discussions per item (set in the list edit design).
But for datasets, we have only seen that at the end of the dataset view, there is a "DISCUSSION" link which allows submission of messages referring to the whole dataset. Is it in some way possible, to create those discussions for single records of a dataset, like it is possible in lists?

Something else:
It seems that visualization of messages in the details part of a list item does not work properly: once the discussion is hidden (or closed), hitting the "DISCUSSION" link does not allow showing it again.

Thank you very much for your great support,
Eva Pujadas
view message
pipeline override and write privileges on the folder
(7 responses) tvaisar 2015-07-23 07:01
Hi,
I have set a pipeline override for a project, but when I then go upload MS2 (or Panorama/Skyline) data a log file is not written (and upload to Panorama type folder within project fails) unless I give write privileges on the given folder on the linux box to "all" (i.e. drwxrwxrwx).
If I have the privileges set at our default drwxrwxr-x (with tomcat being member of the group which owns the folder) the log files cannot be written (Panorama Skyline file uploaded). I would have assumed that if tomcat is a member of the group which owns the folder that it should be allowed to write there and this should work.

Could you please advice how the privileges need to be set in order to get this work without giving write privileges to "all".

Thanks,

Tomas
view message
(1) Search of assay contant data (2) Hierarchy concept
(4 responses) mbrusnia 2015-07-22 16:35
(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
In our view, Batch can have multi runs.
However, after select a batch in view batches, it shows the run file. When I use “Import Data” under “view runs”,
It still creates a new batch and put the new imported file as one run associated with a new batch.
I can’t find a document how to tide multi runs to a given batch.
I also have used select batch -> import data -> "save and import another run"
The file has a new entry and the file name is also not overlap with any other run I have already uploaded.
However, I got the following error that was not making sense for me
500: Unexpected server error
The same file was uploaded twice - all files must be unique
rg.labkey.api.exp.ExperimentException: The same file was uploaded twice - all files must be unique
       at org.labkey.api.study.assay.AssayFileWriter.savePostedFiles(AssayFileWriter.java:192)
       at org.labkey.api.study.actions.AssayRunUploadForm.getAdditionalPostedFiles(AssayRunUploadForm.java:253)
       at org.labkey.api.study.actions.AssayRunUploadForm.getPropertyMapFromRequest(AssayRunUploadForm.java:130)
       at org.labkey.api.study.actions.AssayRunUploadForm.getRunProperties(AssayRunUploadForm.java:111)
       at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.validatePost(UploadWizardAction.java:682)
       at org.labkey.api.study.actions.UploadWizardAction$RunStepHandler.handleStep(UploadWizardAction.java:628)
       at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:169)
       at org.labkey.api.study.actions.UploadWizardAction.getView(UploadWizardAction.java:95)
       at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:80)
       at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:179)
       at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414)
       at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1032)
       at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1085)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:182)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
       at java.lang.Thread.run(Thread.java:745)

request attributes
LABKEY.OriginalURL = http://optides.fhcrc.org:8080/labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH
LABKEY.StartTime = 1437607929205
LABKEY.action = uploadWizard
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.labkey.api.module.SpringModule$1@5975c4f: display name [Study WebApplicationContext]; startup date [Mon May 04 04:53:43 PDT 2015]; parent: org.springframework.web.context.support.XmlWebApplicationContext@5762e5ed
LABKEY.controller = assay
LABKEY.Counter = 0
X-LABKEY-CSRF = 3fea1251744a79902feea5443850b61b
LABKEY.container = /Optides
LABKEY.RequestURL = /labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH
LABKEY.OriginalURLHelper = /labkey/assay/Optides/uploadWizard.view?rowId=22&uploadStep=BATCH

I would appreciate if you can help me how I can associate multi run to one batch file.
view message
Missing RedCap module?
(4 responses) juha kekalainen 2015-07-21 04:44
Hi,

I just installed latest LabKey v15.2 release to Windows 2012r2 and I seem to be missing RedCap module.

I tried to follow this guide, but I am not able to enable RedCap module:

https://www.labkey.org/wiki/home/Documentation/page.view?name=redCap

"Under Modules, place a checkmark next to REDCap." << there is no such checkmark.

I tried to search RedCap module at the C:\Program Files (x86)\LabKey Server\modules folder, but it is missing.

So, do I need to seperately install it or am I doing something wrong here? :)

Yours,
Juha
view message
Caused by: java.lang.IllegalStateException: Why am I in a transaction?
(2 responses) felix rauscher 2015-07-17 03:03
Hi,

I am trying to install labkey on a Ubuntu 14.04 linux. I am using the tomcat7 installation from the distribution. I am using postgres 9.4 installed via the postgres repositories.

The connection to the database is made, and the labkey database is created, but stays empty. In the browser I get the following exception:


org.labkey.api.util.ConfigurationException: Cannot connect to DataSource "labkeyDataSource" defined in labkey.xml. Server cannot start.
       at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:985)
       at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:890)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:318)
       at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:230)
       at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
       at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
       at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
       at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4809)
       at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5485)
       at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
       at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
       at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
       at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
       at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:670)
       at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
       at java.util.concurrent.FutureTask.run(FutureTask.java:266)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: Why am I in a transaction?
       at org.labkey.core.dialect.PostgreSql91Dialect.configureToDisableJdbcCaching(PostgreSql91Dialect.java:1604)
       at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.getResultSet(SqlExecutingSelector.java:316)
       at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:254)
       at org.labkey.api.data.BaseSelector.getObject(BaseSelector.java:163)
       at org.labkey.api.data.BaseSelector.getObject(BaseSelector.java:158)
       at org.labkey.core.dialect.PostgreSql91Dialect.determineSettings(PostgreSql91Dialect.java:813)
       at org.labkey.core.dialect.PostgreSql91Dialect.prepare(PostgreSql91Dialect.java:756)
       at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:973)
       ... 19 more


I attached the relevant log files.

Could you give me a hint on how to proceed?

Thanks

Felix
 catalina.out  labkey.log  labkey-errors.log 
view message
Sorting fails in MS2 module Compare
(6 responses) tvaisar 2015-07-16 06:58
Hi,

we have just installed a new instance of Labkey server 15.1 with postgres and start to feel out way around. Ran into issue when comparing multiple sets of proteomics data. Selecting few runs and comparing them (any comparison - ProteinProphet, Search Engine, etc. has the same issue) works fine, but when I try to sort on any column, the column returns with blank content - other columns for other samples are OK, but anything related to the samples which column was used to sort is blank. Going into Admin Console and looking at Errors - this is what I get.
Any suggestions?
Thanks,
Tomas Vaisar

ERROR Table 2015-07-16 06:30:24,302 t: http-bio-8080-exec-21 : SQL [19289]
    SELECT *
    FROM (
    SELECT
    InstanceCount AS InstanceCount,
    ctq$Proteins$.SeqId$BestName AS SeqId_fs_BestName,
    ctq$Proteins$.SeqId$BestGeneName AS SeqId_fs_BestGeneName,
    ctq$Proteins$.SeqId$FirstGENE_NAME AS SeqId_fs_FirstGENE_NAME,
    ctq$Proteins$.SeqId$FirstSWISS_PROT AS SeqId_fs_FirstSWISS_PROT,
    ctq$Proteins$.SeqId$FirstSWISS_PROT_ACCN AS SeqId_fs_FirstSWISS_PROT_ACCN,
    ctq$Proteins$.SeqId$FirstGEN_INFO AS SeqId_fs_FirstGEN_INFO,
    ctq$Proteins$.SeqId$SeqId AS SeqId_fs_SeqId,
    SortPattern AS SortPattern
    FROM (SELECT pvt.NormalizedId, pvt.ProteinCount, pvt.Proteins,
    MAX(pvt.CTAGG_MIN_ProteinGroupId) AS CTAGG_MIN_ProteinGroupId,
    MAX(pvt.CTAGG_COUNT_ProteinGroupId) AS CTAGG_COUNT_ProteinGroupId,
    (0) AS InstanceCount,
    (0) AS SortPattern
    FROM (
    SELECT aggf.NormalizedId, aggf.ProteinCount, aggf.Proteins,
    CTAGG_MIN_ProteinGroupId,
    CTAGG_COUNT_ProteinGroupId
    FROM (
    SELECT * FROM (
    SELECT
    grp.NormalizedId AS NormalizedId,
    grp.ProteinCount AS ProteinCount,
    grp.Proteins AS Proteins,
    grp.P763629254fs_ProteinProphetFileId_fs_Run AS P763629254fs_ProteinProphetFileId_fs_Run,
    grp.CTAGG_MIN_ProteinGroupId AS CTAGG_MIN_ProteinGroupId,
    grp.CTAGG_COUNT_ProteinGroupId AS CTAGG_COUNT_ProteinGroupId
    FROM (SELECT src.NormalizedId,
    src.ProteinCount,
    src.Proteins,
    src.P763629254fs_ProteinProphetFileId_fs_Run,
    MIN(src.ProteinGroupId) AS CTAGG_MIN_ProteinGroupId,
    COUNT(src.ProteinGroupId) AS CTAGG_COUNT_ProteinGroupId
    FROM (
    SELECT
    (SELECT COUNT (DISTINCT SeqId) FROM bogusTable n, ms2.proteingroupmemberships pgm WHERE n.ProteinGroupId = pgm.ProteinGroupId and n.NormalizedId = bogusTable.NormalizedId) AS ProteinCount,
    bogusTable.ProteinGroupId AS ProteinGroupId,
    bogusTable.NormalizedId AS NormalizedId,
    bogusTable.NormalizedId AS Proteins,
    bogusTable$ProteinGroupId_fs_ProteinProphetFileId$.run AS P763629254fs_ProteinProphetFileId_fs_Run
    FROM (SELECT * FROM (SELECT * FROM bogusTable) x
    WHERE ((ProteinGroupId IN (SELECT ProteinGroupId FROM (SELECT
    ProteinGroupMemberships.proteingroupid AS ProteinGroupId
    FROM ms2.proteingroupmemberships ProteinGroupMemberships ) x)))) bogusTable
    
        LEFT OUTER JOIN ms2.proteingroups bogusTable$ProteinGroupId$ ON (bogusTable.ProteinGroupId = bogusTable$ProteinGroupId$.rowid)
    
        LEFT OUTER JOIN ms2.proteinprophetfiles bogusTable$ProteinGroupId_fs_ProteinProphetFileId$ ON (bogusTable$ProteinGroupId$.proteinprophetfileid = bogusTable$ProteinGroupId_fs_ProteinProphetFileId$.rowid)
    ) AS src
    GROUP BY src.NormalizedId,
    src.ProteinCount,
    src.Proteins,
    src.P763629254fs_ProteinProphetFileId_fs_Run) grp
    ) AS agg
    ) AS aggf
    ) AS pvt
    GROUP BY pvt.NormalizedId, pvt.ProteinCount, pvt.Proteins) ctq
    
        LEFT OUTER JOIN
        (
            SELECT child.NormalizedId,
                array_to_string(array_agg(child$SeqId$.seqid), '{@~^') AS SeqId$SeqId,
                array_to_string(array_agg(child$SeqId$.protsequence), '{@~^') AS SeqId$ProtSequence,
                array_to_string(array_agg(child$SeqId$.hash), '{@~^') AS SeqId$Hash,
                array_to_string(array_agg(child$SeqId$.description), '{@~^') AS SeqId$Description,
                array_to_string(array_agg(child$SeqId$.sourceid), '{@~^') AS SeqId$SourceId,
                array_to_string(array_agg(child$SeqId$.sourceversion), '{@~^') AS SeqId$SourceVersion,
                array_to_string(array_agg(child$SeqId$.insertdate), '{@~^') AS SeqId$InsertDate,
                array_to_string(array_agg(child$SeqId$.changedate), '{@~^') AS SeqId$ChangeDate,
                array_to_string(array_agg(child$SeqId$.sourcechangedate), '{@~^') AS SeqId$SourceChangeDate,
                array_to_string(array_agg(child$SeqId$.sourceinsertdate), '{@~^') AS SeqId$SourceInsertDate,
                array_to_string(array_agg(child$SeqId$.orgid), '{@~^') AS SeqId$OrgId,
                array_to_string(array_agg(child$SeqId$.mass), '{@~^') AS SeqId$Mass,
                array_to_string(array_agg(child$SeqId$.bestname), '{@~^') AS SeqId$BestName,
                array_to_string(array_agg(child$SeqId$.bestgenename), '{@~^') AS SeqId$BestGeneName,
                array_to_string(array_agg(child$SeqId$.length), '{@~^') AS SeqId$Length,
                array_to_string(array_agg(child$SeqId$.deleted), '{@~^') AS SeqId$Deleted,
                array_to_string(array_agg(child$SeqId$.sourceid), '{@~^') AS SeqId$Source,
                array_to_string(array_agg(child$SeqId$.seqid), '{@~^') AS SeqId$CustomAnnotations,
                array_to_string(array_agg((SELECT MIN(Identifier) FROM prot.identifiers i, prot.identtypes it WHERE i.IdentTypeId = it.IdentTypeId AND it.Name = 'IPI' AND i.SeqId = child$SeqId$.SeqId)), '{@~^') AS SeqId$FirstIPI,
                array_to_string(array_agg((SELECT MIN(Identifier) FROM prot.identifiers i, prot.identtypes it WHERE i.IdentTypeId = it.IdentTypeId AND it.Name = 'GeneName' AND i.SeqId = child$SeqId$.SeqId)), '{@~^') AS SeqId$FirstGENE_NAME,
                array_to_string(array_agg((SELECT MIN(Identifier) FROM prot.identifiers i, prot.identtypes it WHERE i.IdentTypeId = it.IdentTypeId AND it.Name = 'SwissProt' AND i.SeqId = child$SeqId$.SeqId)), '{@~^') AS SeqId$FirstSWISS_PROT,
                array_to_string(array_agg((SELECT MIN(Identifier) FROM prot.identifiers i, prot.identtypes it WHERE i.IdentTypeId = it.IdentTypeId AND it.Name = 'SwissProtAccn' AND i.SeqId = child$SeqId$.SeqId)), '{@~^') AS SeqId$FirstSWISS_PROT_ACCN,
                array_to_string(array_agg((SELECT MIN(Identifier) FROM prot.identifiers i, prot.identtypes it WHERE i.IdentTypeId = it.IdentTypeId AND it.Name = 'GI' AND i.SeqId = child$SeqId$.SeqId)), '{@~^') AS SeqId$FirstGEN_INFO
            FROM (SELECT DISTINCT NormalizedId, SeqId FROM bogusTable n, ms2.proteingroupmemberships pgm WHERE n.ProteinGroupId = pgm.ProteinGroupId) child
        LEFT OUTER JOIN prot.sequences child$SeqId$ ON (child.SeqId = child$SeqId$.seqid)
            GROUP BY child.NormalizedId
        ) ctq$Proteins$ ON (ctq.Proteins = ctq$Proteins$.NormalizedId)) x
    
    ORDER BY InstanceCount DESC, SortPattern DESC
    LIMIT 5001

    org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:436)
    org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:268)
    org.labkey.api.data.SqlExecutingSelector.getResultSet(SqlExecutingSelector.java:121)
    org.labkey.api.data.TableSelector.getResults(TableSelector.java:274)
    org.labkey.api.data.TableSelector$1.call(TableSelector.java:289)
ERROR ExceptionUtil 2015-07-16 06:30:24,304 http-bio-8080-exec-21 : Exception detected and logged to mothership:
org.springframework.jdbc.BadSqlGrammarException: ExecutingSelector; bad SQL grammar []; nested exception is org.postgresql.util.PSQLException: ERROR: relation "bogustable" does not exist
  Position: 1871
    at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.translate(SQLErrorCodeSQLExceptionTranslator.java:276)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:37)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:31)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:441)
    at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:268)
    at org.labkey.api.data.SqlExecutingSelector.getResultSet(SqlExecutingSelector.java:121)
    at org.labkey.api.data.TableSelector.getResults(TableSelector.java:274)
    at org.labkey.api.data.TableSelector$1.call(TableSelector.java:289)
    at org.labkey.api.data.TableSelector$1.call(TableSelector.java:286)
    at org.labkey.api.data.AsyncQueryRequest$1.run(AsyncQueryRequest.java:109)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: relation "bogustable" does not exist
  Position: 1871
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2270)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1998)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:570)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:406)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:286)
    at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:208)
    at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:208)
    at org.labkey.api.data.dialect.StatementWrapper.executeQuery(StatementWrapper.java:916)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.executeQuery(SqlExecutingSelector.java:372)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.getResultSet(SqlExecutingSelector.java:322)
    at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:254)
    ... 6 more
view message
First subject not recognized
(1 response) domen finzgar 2015-07-10 06:49
Hello

I've been able to install a test labkey server on my home computer, everything works perfect except: When i import data from excel spreadsheet and link the subjectID column there is an odd problem. Labkey recognizes all subjects (sub01, sub02, ... sub50) however if i click on the first one (sub01) i get an error: Could not find Subject sub01

This error is only shown on every first record in the database, other subjects work great!

What could be the solution for this problem?

Thanks,

Domen
view message
Compatibility with Tomcat 8?
(2 responses) Alex Taylor 2015-07-02 12:41
I am attempting a new v15.1 server installation on MacOS X and when I try to use Tomcat 8 (8.0.23) it fails to start the labkey webapp: catalina.out:
02-Jul-2015 10:03:16.729 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal One or more Filters failed to start. Full details will be found in the appropriate container log file
02-Jul-2015 10:03:16.729 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.startInternal Context [/labkey] startup failed due to previous errors
labkey.log:
ERROR ModuleLoader             2015-07-02 10:03:16,726    localhost-startStop-1 : Failure occurred during ModuleLoader init.
java.lang.NullPointerException
        at java.io.File.<init>(File.java:277)
        at org.labkey.api.module.ModuleLoader.webappFilesExist(ModuleLoader.java:449)
        at org.labkey.api.module.ModuleLoader.verifyProductionModeResources(ModuleLoader.java:433)
        at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:313)
        at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:258)
        at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
        at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
        at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
        at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4574)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5193)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
        at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:586)
        at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1750)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
The version of Java is 1.8.0_25. The problem does not occur if I use a Tomcat 7 instance instead of the Tomcat 8. Digging in the Tomcat 8 source code for org.apache.catalina.core.StandardContext it appears that this may be due to sending Strings (specified in ModuleLoader's verifyProductionModeResources()) to getRealPath() that are not prepended with a '/' and hence result in it returning null:
4443    public String More ...getRealPath(String path) {
4444        // The WebResources API expects all paths to start with /. This is a
4445        // special case for consistency with earlier Tomcat versions.
4446        if ("".equals(path)) {
4447            path = "/";
4448        }
4449        if (resources != null) {
4450            try {
4451                return resources.getResource(path).getCanonicalPath();
4452            } catch (IllegalArgumentException iae) {
4453                // ServletContext.getRealPath() does not allow this to be thrown
4454            }
4455        }
4456        return null;
4457    }
Are there plans to add Tomcat 8 compatibility? Regards, Alex
view message
You must have a DataSource named "labkeyDataSource" defined in labkey.xml.
(6 responses) felix rauscher 2015-06-29 04:54
Hi,

I am trying ot install Labkey on SL7 (equivalent to CentOS7), using tomcat (7.0.54) and postgres (9.2.10) from the distributions repositories. I get a stack trace with the You must have a DataSource named "labkeyDataSource" defined in labkey.xml error, even though I have configured the dataSource. See attached labkey.xml

The stack trace looks like this:


org.labkey.api.util.ConfigurationException: DataSources are not properly configured in labkey.xml.
       at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:861)
       at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:344)
       at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:258)
       at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
       at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
       at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
       at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4809)
       at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5485)
       at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
       at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
       at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
       at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
       at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:672)
       at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1862)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
       at java.util.concurrent.FutureTask.run(FutureTask.java:266)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
       at java.lang.Thread.run(Thread.java:745)
Caused by: org.labkey.api.util.ConfigurationException: You must have a DataSource named "labkeyDataSource" defined in labkey.xml.
       at org.labkey.api.module.ModuleLoader.ensureDatabase(ModuleLoader.java:929)
       at org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:838)
       ... 18 more

Another question: How could I expand the stack-trace further?

Best Regards

Felix
 labkey.xml 
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LDAP auth with StartTLS
(3 responses) Will Holtz 2015-06-24 15:21
Is LDAP authentication on port 389 with StartTLS currently supported by Labkey? I would like to use such a configuration as ldaps:// is deprecated in favor of Start TLS [RFC2830], but my attempts are failing.

thanks,
-Will
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Manual Install fails with a LifecycleException
(3 responses) flavien jacques 2015-06-14 12:13
Hello everyone,

I'm struggling with a manual install on a Windows 7. I'm using Tomcat 7, Java version "1.8.0_45" and postgresql version "postgresql-9.4.4-1-windows-x64".

The deployment of Labkey is not happening because of this (catalina log):




INFOS: Déploiement du descripteur de configuration C:\Users\Flap\Downloads\apache-tomcat-7.0.62-windows-x64\apache-tomcat-7.0.62\conf\Catalina\localhost\labkey.xml
juin 14, 2015 9:04:16 PM org.apache.catalina.startup.SetContextPropertiesRule begin
AVERTISSEMENT: [SetContextPropertiesRule]{Context} Setting property 'debug' to '0' did not find a matching property.
juin 14, 2015 9:04:16 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
AVERTISSEMENT: [SetPropertiesRule]{Context/Loader} Setting property 'useSystemClassLoaderAsParent' to 'false' did not find a matching property.
juin 14, 2015 9:04:16 PM org.apache.catalina.loader.WebappLoader startInternal
GRAVE: LifecycleException
java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)
    at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:721)
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:582)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5393)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1912)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

juin 14, 2015 9:04:16 PM org.apache.catalina.core.ContainerBase addChildInternal
GRAVE: ContainerBase.addChild: start:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1912)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [WebappLoader[/labkey]]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5393)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 10 more
Caused by: org.apache.catalina.LifecycleException: start:
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:630)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    ... 12 more
Caused by: java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)
    at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:721)
    at org.apache.catalina.loader.WebappLoader.startInternal(WebappLoader.java:582)
    ... 13 more

juin 14, 2015 9:04:16 PM org.apache.catalina.startup.HostConfig deployDescriptor
GRAVE: Erreur lors du déploiement du descripteur de configuration C:\Users\Flap\Downloads\apache-tomcat-7.0.62-windows-x64\apache-tomcat-7.0.62\conf\Catalina\localhost\labkey.xml
java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/labkey]]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:904)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
    at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1912)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)




Am I missing something ? I've read several times the "How-to" and I can't figure where I'm making a mistake. I've attached the labkey.xml and relevant logs, any advices are more than appreciated !

Thanks,

Flavien
 labkey.xml  catalina.2015-06-14.log  tomcat7-stderr.2015-06-14.log 
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PostgreSQL 9.4.2, 9.3.7, 9.2.11, 9.1.16, and 9.0.20 released
(2 responses) avital 2015-05-26 11:18
Last week, PostgreSQL announced a critical fix for a potential data corruption problem [1]. The problem affects PostgreSQL Server versions; 9.3.x, 9.4.x. You can find more information in the PostgreSQL announcement [1].

We have reviewed the available information, and plan to upgrade all servers we manage in the coming week. We recommend all clients upgrade their servers during their next scheduled maintenance window.

If you have any questions, concerns or need any assistance in upgrading your PostgreSQL server, please do not hesitate to contact us.

[1] http://www.postgresql.org/about/news/1587/
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Project inaccessible in IE 8
(3 responses) bront 2015-05-26 06:48
hi,

I have a user who is stuck using IE 8 (8.0.7601.17514, to be exact) and cannot open his project folder. He indicates that the link is inactive and the project folder is depicted with a red X.

I cannot reproduce this error in any of the other modern browsers (including a current version of IE).

LabKey supports IE 8 (https://www.labkey.org/wiki/home/Documentation/page.view?name=supported), so I am wondering if there anything I can do (besides upgrade)?

Many thanks,

bront
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Known issue with Chrome v43 and menus
(1 response) jeckels 2015-05-22 09:20
Starting yesterday, we started noticing problems with some menus in LabKey Server with the latest update to Chrome, version 43. We're hopeful that a future Chrome update might resolve the issue, but are working on a patch to avoid the problem:

https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=23352

In the meantime, earlier versions of Chrome and all other browsers don't exhibit the problem.

Thanks,
Josh

Update: Sencha is aware of the issue and is working on a fix themselves, but encourages developers to work together to find workarounds as well.

https://www.sencha.com/forum/showthread.php?301116-Submenus-disappear-in-Chrome-43-beta&p=1100997
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Extending core tables
(1 response) Olivier 2015-05-08 02:30
Dear support team,

I'd like to extend one of the core tables with an additional field: e.g. I would like to add an additional field in the exp/Runs table - how can this be done?

Thanks,
Olivier
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Fail to access a local LabKey Server from internet
(1 response) you 2015-05-05 06:27
I set up LabKey Server 15.1 on a local Windows Server on port 8180. It works fine if I visit "localhost:8180/labkey" on that local machine.

But I cannot visit that server from internet "external_ip_address/8180", where the "external_ip_address" is the ip I got from "showip.com" on the local Windows Server.

I found that the port 8180 is closed from the view of the internet (seen from www.yougetsignal.com/tools/open-ports/), and when I run "netstat -n", I see:
"
Proto Local Address Foreign Address State
TCP 127.0.0.1:8180 127.0.0.1.63546 Established
TCP 127.0.0.1:8180 127.0.0.1.63547 Established
"

Any suggestion please?
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