The CombineArchive is a zip like format to bundle latest research files and annotate them with meta data. The CombineArchive WebInterface (WebCAT) is a web based user interface to create, modify, and share CombineArchives. No need for registration. No database. Just start using the web interface!
A public instance is running at https://cat.bio.informatik.uni-rostock.de/.
You will find detailed information on how to build and deploy the web application on the project page.
There is a Docker image available at binfalse/webcat. It is configured to automatically build the latest version of the application based on the Dockerfile included in this repository. In addition, we compile every version of the application in a tagged Docker image through maven.
Run a Docker container as:
docker run -it --rm -p 1234:8080 binfalse/webcat:latest
This will start the Tomcat web server and bind the host's port 1234 to the containers port 8080, which Tomcat listens at. It will permanently dump Tomcat's catalina output log.
As soon as the container is up and running you should be able to access the CombineArchive web interface at http://localhost:1234
The above command will destroy all archives and workspaces as soon as you stop/reboot the container.
It's however also possible to mount persistent storage into the container. Let's say you want to save everything at the host's /storage/for/webcat, then you can just mount that into the container using:
docker run --rm -it -p 1234:8080 -v /storage/for/webcat:/srv/CombineArchiveWeb binfalse/webcat:latest
After creating a COMBINE archive in WebCAT you'll find it on the host machine in /storage/for/webcat/WORKSPACE/ARCHIVE.
WebCAT's settings are configured using a tomcat-style context.xml. The context that is deployed by default is available from the git repository, you may use that as a template.
To change that configuration you can either mount a directory containing a file called ROOT.xml with an alternative configuration to the container's /usr/local/tomcat/conf/Catalina/localhost/ directory :
docker run --rm -it -p 1234:8080 -v /storage/dir/with/other/context:/usr/local/tomcat/conf/Catalina/localhost/ binfalse/webcat:latest
Or you create a new image based on this one, which overwrites the configuration with your context.xml.
A demo is currently hosted on our server. No need for registration! Just start to explore
The development is currently coordinated at our trac project management.
Some helpful resources can be found in the resources folder. It contains a default context configuration for tomcat, a default VHost configuration for the Apache WebServer and a folder called "nagios" containing a simple python3 script for nagios, to check if the webCAT instance is up and running. In case a stats secret is provided (and configured in the python script) it also checks for the maximum space quota.
We are always keen on getting feedback from our users. If you have any comments, requests for features, or experience any problems do not hesitate to leave a comment.
CombineArchiveWeb - a WebInterface to read/create/write/manipulate/... COMBINE archives
Copyright (C) 2014-2016:
- Martin Peters <[email protected]>
- Martin Scharm <[email protected]>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.