This is the BiVeS web application, a JAVA based web interface to the 
BiVeS itself consists of a number of modules:
- xmlutils is a library for advanced XML handling
- jCOMODI provides programmatic access to the COMODI ontology
- BiVeS-Core is the core library for comparison of computational models
- BiVeS-SBML is a module providing special strategies for models encoded in SBML
- BiVeS-CellML is a module providing special strategies for models encoded in CellML
- BiVeS ties all modules together and provides command line access
- BiVeS-WebApp is a web interface to access BiVeS through the network
- BiVeS-WebApp-Client provides a Java library for comparing models using the BiVeS-WebApp
We recommend building the application with Maven.
Along with the source code you will obtain a pom.xml that contains the configuration to build the web application with maven. Maven will download and manage all dependencies. Just call a
mvn package
to obtain a BiVeS-WebApp-*.war in the target directory. This war file can then be deployed to a JAVA compliant webserver, such as the Apache Tomcat.
If you prefer using and you need to download the dependencies yourself. Create a directory lib in the project directory to store dependent libraries. The following libraries are required:
- BiVeS (download a fat jar from http://bin.sems.uni-rostock.de/)
- json-simple (see https://code.google.com/p/json-simple/)
- javax.servlet-api (see e.g. http://repo1.maven.org/maven2/javax/servlet/javax.servlet-api/)
Then just call
ant dist
to obtain the war file that can be deployed to a JAVA compliant webserver, such as the Apache Tomcat.
Pre-compiled Java binaries can be found at http://bin.sems.uni-rostock.de/BiVeS-WebApp/
Since version 1.6.2 we provide a Docker image at the docker hub: binfalse/bives-webapp.
The image is based on an Apache Tomcat image and already has the BiVeS web application deployed as the default webapp of the Tomcat.
It will be automatically generated with every git-commit to this repository. In addition, we are generated a new version with every release of the BiVeS web application through maven..
Using Docker it is very easy and clean to run the web application. Just call
docker run -it --rm -p 1234:8080 binfalse/bives-webapp
and a Tomcat will start and bind to port 1234 of your machine.
Go ahead and open http://localhost:1234 to see if it's working! :)
You should, however, also mount a config file into the container at /usr/local/tomcat/conf/Catalina/localhost/ROOT.xml, which tells the visitors who's running the website (including a link to an imprint):
docker run -it --rm -p 1234:8080 -v /path/to/your.xml:/usr/local/tomcat/conf/Catalina/localhost/ROOT.xml binfalse/bives-webapp
An example config file can be found at src/main/docker/BiVeS-WebApp-DockerContext.xml.
Do not hesitate to contact us if you need assistance.
The BiVeS web application expects an HTTP POST request with a job encoded in JSON. To for example compare the two files at http://budhat.sems.uni-rostock.de/download?downloadModel=24 and http://budhat.sems.uni-rostock.de/download?downloadModel=25 asking for the HTML report you could launch the following curl call:
curl -d '{
"files":
[
"http://budhat.sems.uni-rostock.de/download?downloadModel=24",
"http://budhat.sems.uni-rostock.de/download?downloadModel=25"
],
"commands":
[
"reportHtml"
]
}' http://YOUR.BIVES.WEBAPP
Just replace http://YOUR.BIVES.WEBAPP with the URL to your installation of the BiVeS WebApp (or take our installation at http://bives.sems.uni-rostock.de).
You'll get more information about the usage and possible options/arguments by browsing to that installation with using your preferred web browser, see our installation for example.
There is a Java WebApp client for accessing the BiVeS WebApp from java based tools.
If you try to access / through an HTTP GET request BiVeS will return a 400 Bad Request status, signalling applications that something's missing and show a usage page in your web browser.
That's of course pretty difficult to monitoring for health..
Therefore we implemented /status that will return 200 OK and tell you the BiVeS version that it's running at the moment.
You could even evaluate it's content and check for the phrase running just fine :)
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.
To learn more about BiVeS have a look at the BiVeS project and our open-access scientific publication.
The GitHub pages of the SEMS project provide mode information on the BiVeS WebApp.
Artwork and text etc is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License
The code is licensed under an Apache 2.0 license:
Copyright martin scharm <https://binfalse.de/contact/>
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.