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Installation - NullPointerException informaticsforlife  2016-01-21 14:26
Status: Closed
 
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.
 
 
Jon (LabKey DevOps) responded:  2016-01-21 16:48
Hi,

There is an issue we are having with certain versions of Tomcat, but I'd like to confirm this on your version.

Can you send us a copy of your LabKey.log file? It is located under the TOMCAT_HOME/logs/ directory.

Also, did you setup your server to run off of HTTPS or off of HTTP?

Regards,

Jon
 
informaticsforlife responded:  2016-01-22 07:33
Hi Jony,

Attached is the LabKey.log file. You will see the error repeated a few times, as I have attempted various solutions that included restarting Tomcat. I am using http, as I have not set Tomcat to use https.

I also have a separate question: Is all the data generated by the end user of the application stored in the PostGreSQL database? And if so, in which database schemas, and do you have any schema design level documentation.

Thanks a lot.
 
Jon (LabKey DevOps) responded:  2016-01-22 12:35
Hi,

Thanks for providing the log. So we did discover an issue where updated versions of Tomcat 8 (8.0.29+) and Tomcat 7 (7.0.67+) have had a change where they are handling webdav calls differently, causing things like this to break.

We have a fix that is currently going through testing and should be available for download soon once the testing is done on our downloads page here: https://www.labkey.com/download.php

Alternatively, if you need to get your version of LabKey running right now (download availability of the patched version of LabKey 15.3 should be available in a few days), we recommend downgrading to an earlier version of Tomcat (Tomcat 7.0.64 or earlier has consistently worked).

Regarding the other question about data generation: We do have an Audit Log report under Admin > Site > Admin Console that shows most things a user did along with any other actions the system may have done as well. This information is held in the Audit schema.

And in regard to schema design level documentation, can you clarify what you're looking to have or do?

Regards,

Jon
 
informaticsforlife responded:  2016-01-22 12:46
Hi Jon,

Thanks for looking into this. I guess I will wait for the fix, instead of downgrading Tomcat and then upgrading it at a later point in the future.

I have an integration process that may require me to derive data directly from the tables in your PostGreSQL schema(s), instead of going through the available APIs. I was wondering if there is any documentation on the schema(s) themselves that will help a new person figure out where to find the data stored by the user, like Assays and their parameters, ...etc
 
Jon (LabKey DevOps) responded:  2016-01-22 13:22
Hi,

I don't believe we have a sole schema document like what you're describing (I'm still checking through our docs). Everything like Assays, Studies, etc. are all individually documented in different sections of the help documentation on LabKey.org

Assays - https://www.labkey.org/home/Documentation/wiki-page.view?name=defineAssaySchema
Study - https://www.labkey.org/home/Documentation/wiki-page.view?name=studySerializationFormats
Using the Schema Browser to collect information - https://www.labkey.org/home/Documentation/wiki-page.view?name=querySchemaBrowser

Keep in mind that all of the tables in LabKey are pretty flexible, so many of the parameters can be dictated by you based on your personal needs.

Regards,

Jon
 
informaticsforlife responded:  2016-01-29 12:19
Hi,

If and when this issue is fixed in the next LabKey release, will there be an announcement about that somewhere, so one can proceed with installing the new version (or just the fix, if possible)?

Regards.
 
Jon (LabKey DevOps) responded:  2016-01-31 20:02
Hi,

Yes we will be making an announcement on our public forums. We should be releasing the fix sometime within this week based on what I've seen from our developers interactions. I will also update you via this specific post as well.

Thanks for your patience.

Regards,

Jon
 
Jon (LabKey DevOps) responded:  2016-02-01 16:39
Hello!

We've pushed out the revised build of LabKey 15.3 to our downloads page.

Feel free to download our revised build and install it on your server. It should install without any issue.

Regards,

Jon
 
informaticsforlife responded:  2016-02-02 11:30
Hi Jon,

Thanks for the quick response. I installed the new version and it works great!