Projects not showing; Admin Console working fine

Installation Forum (Inactive)
Projects not showing; Admin Console working fine robert.winkler  2014-06-04 14:29
Status: Closed
 
Hi, after a painful installation on Ubuntu 12.04 (tomcat 7), LabKey 14.1 starts up happily. The Admin Console works fine. I can create Projects as Admin, but whenever I go to http://localhost:8080/labkey/project/home/begin.view?, the following error comes up:
500: Unexpected server error
org.labkey.portal.ProjectController$ProjectUrlsImpl.getHidePortalPageURL(Lorg/labkey/api/data/Container;Ljava/lang/String;Lorg/labkey/api/view/ActionURL;)Lorg/labkey/api/view/ActionURL;
...
request attributes
LABKEY.StartTime = 1401916093656
LABKEY.container = /Test
LABKEY.action = begin
LABKEY.RequestURL = /labkey/project/Test/begin.view?
LABKEY.OriginalURLHelper = /labkey/project/Test/begin.view?
LABKEY.controller = project
X-LABKEY-CSRF = f405132fa5b689fbf738ff5cee43591c
LABKEY.Counter = 0
LABKEY.OriginalURL = http://localhost:8080/labkey/project/Test/begin.view?

core schema database configuration
Server URL    jdbc:postgresql://localhost/labkey
Product Name    PostgreSQL
Product Version    9.1.13
Driver Name    PostgreSQL Native Driver
Driver Version    PostgreSQL 9.3 JDBC4.1 (build 1100)

***Test is a project I created as Admin.***

root@rob-HP-Pavilion-TS-14-Notebook-PC:/opt/labkey# ls -al
total 52
drwxr-xr-x 7 tomcat7 root 4096 Jun 4 13:26 .
drwxr-xr-x 6 root root 4096 Jun 4 13:24 ..
drwxrwxr-x 2 tomcat7 root 4096 Jun 3 15:09 bin
drwxr-xr-x 7 tomcat7 tomcat7 4096 Jun 4 15:42 files
-rw-r--r-- 1 tomcat7 tomcat7 222 Jun 4 13:25 heapDumpRequest
-rw-r--r-- 1 root root 60 Jun 4 13:24 .labkeyInstalled
drwxrwxr-x 64 tomcat7 root 12288 Jun 4 13:32 labkeywebapp
drwxrwxr-x 30 tomcat7 root 4096 Jun 4 13:32 modules
drwxrwxr-x 2 tomcat7 root 4096 Jun 3 15:09 pipeline-lib
-rw-r--r-- 1 tomcat7 tomcat7 171 Jun 4 13:25 threadDumpRequest
-rw-r--r-- 1 tomcat7 root 11 Mär 22 03:45 VERSION
root@rob-HP-Pavilion-TS-14-Notebook-PC:/opt/labkey#

The owner of /opt/labkey and subdirectories is tomcat7.

Any hints?
 
 
jeckels responded:  2014-06-04 16:32
Hello,

There are some errors in your log files that indicate there may be a version mismatch between some of the files in your deployment.

How did you get the build of LabKey Server that you're running? Did you download it from labkey.com, build it from the source code, or some other approach?

If possible, try clearing the contents of the labkeywebapp and modules directories and re-copying the content from a 14.1 build, and then restarting Tomcat.

Thanks,
Josh
 
robert.winkler responded:  2014-06-05 08:00
Thanks for the rapid reply and for the important hint, Josh!

O.k., this is what I did, and which led to a working installation:

1) I slightly modified the Labkey installation python script for Ubuntu (attached), to accept tomcat7 and version 12.04.

2) I installed Labkey 12.2 => works and created a project "Test".

3) I stopped tomcat7 and updated the /usr/share/tomcat7/lib and /opt/labkey directory to version 14.1. Obviously important: I completely erased the /bin /modules /labkeywebapp and /pipeline-lib directory before copying the new ones. #chown tomcat7 -Rvf *

4) Tomcat7 start: LabKey seems to work fine!

The installation script helps a lot for the first installation on Ubuntu 12.04 LTS. It would be great, if someone could update it for Labkey 14.1 (Now only a few details are missing, I guess).

I could offer, to include LabKey on MASSyPup (http://www.lababi.bioprocess.org/index.php/lababi-software/78-massypup), a Linux Live DVD/USB for mass spectrometry data analysis. MASSyPup already runs the Trans Proteomic Pipeline (TPP). However, I think this would be not compatible with the LabKey license, is it?

Best regards, Robert
 
jeckels responded:  2014-06-05 13:13
Hi Robert,

I'm glad you have the server running normally. Thanks for the Python script.

LabKey Server is licensed as Apache 2.0, so you're free to redistribute it. I'm not sure what the rules are for MASSyPup distribution, but at least some of the other included tools, like ProteoWizard, are also Apache 2.0 licensed, so it would presumably be no problem.

Thanks,
Josh