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  • Eamonn Maguire 11:27 am on August 29, 2013 Permalink | Reply
    Tags: , Installation guide,   

    Getting up and running with the BII Web Application 

    In true Star Wars fashion, we are bringing you the prequel to the last blog post discussing how to set up data file access from your JBoss installation. In this post we’ll discuss how to set up the BioInvestigation web application, from build to deployment.


    1. Getting Ready

    • First, you’ll need to have a Java installed.
    • Then you’ll need to download Maven, this is what automates the build process for the BII web application. A bit like Ant, but it adds dependency management, meaning no need for pesky lib directories. Why this version I hear you ask? Well for some silly reason, the Maven developers (as great as they are) thought that removing the ability to specify profiles in profiles.xml was a great idea. We don’t think it is. In Maven 3+ you can only specify profiles in the pom.xml file or in the settings.xml file under the .m2 directory on your system. So, use version 2.2.1. We’ll move on to configuring these profiles a little later.
    • Now you need Git which we’ll use to get the latest BII codebase from GitHub. If you haven’t heard of Git, you simply haven’t lived. Get out from underneath that SVN rock and join the Git revolution. It’s worth migrating just for the benefit of GitHub or some other funky equivalent (BitBucket or Launchpad).
    • Next, download JBoss 5.1.0 from http://sourceforge.net/projects/jboss/files/JBoss/JBoss-5.1.0.GA and move the JBoss directory to somewhere to your liking. For further examples, let’s say that’s /etc/jboss-5.1.0.GA/ for the rest of this post.
    • Finally, if you want to deploy properly, you’ll need a database. The BII works with Oracle, Postgres, MySQL or MariaDB. You can also run the application just for using the H2 database (we use this for testing). If your database of choice (apart from H2), you’ll need to create a database (we usually name it bioinvindex) and a user (it’s always a good idea to not just use root as the user) and grant that user all permissions to the database.


    2. Grabbing the code

    With everything in place, you need to ‘clone’ the BioInvIndex repository from GitHub. So navigate to a directory of your choosing, and via the command line type ‘git clone https://github.com/ISA-tools/BioInvIndex.git’. This will create a BioInvIndex directory for you with all the code inside.

    3. Configure your profiles

    I mentioned earlier about Maven and profiles. In the bioinvindex directory just created for you, you’ll see a profiles.xml file. Not to get too bogged down on details about what these profiles are for, I’ll give a brief explanation. The main pom.xml file (Project Object Model) for maven defines a number of dependencies, or libraries that are required for the application to run. Some of these dependencies are not always known in advance. For example, if I am running an application on MariaDB, why would I want to have Oracle and Postgres libraries in the final EAR (Enterprise Archive, the JBoss answer to WAR files in Tomcat)? The Profiles just allow us to automatically inject some properties in to the pom file on build depending on what the person building it wants to run. Some of these profiles also go towards creating the hibernate.properties file required by hibernate for connection to the database or in specifying to the application the whereabouts of the Lucene index (will talk more about that in a bit).

    So now, given you have some context, open profiles.xml up and you’ll find a number of individual ‘profile’ elements for the various database installations and a few for the Lucene index locations.

    First, find the profile matching your database and edit the username and password, database name (if not bioinvindex), URL and any version information, etc.

    Then, modify the index profiles (named index_local and index_deploy) that specify where the Lucene index for the BII web app will reside. The Lucene index is used to speed up the web application, massively reducing the number of database queries that are required. The majority of the web application front end is based on the contents of the Lucene index. Make sure that the application has read/write access to that location.


    4. Build!

    Run the command mvn clean package -Dmaven.test.skip=true -Pdeploy,<your_database_profile>,<your_index_profile>

    So, if I was deploying using mysql and using the index_deploy profiles, I would run

    mvn clean package -Dmaven.test.skip=true -Pdeploy,mysql,index_deploy

    Now watch the build succeed. When it completes, look in ear/target/ and you’ll see bii-x.y.ear where x and y are the major and minor versions respectively. The ear, or enterprise archive is what you’ll be deploying. Copy this file in to your JBoss directory, so given we’ve copied the JBoss installation files to /etc/jboss-5.1.0.GA/, we’d copy the ear to /etc/jboss-5.1.0.GA/server/default/deploy/

    5. Run the web application

    Finally, we want to actually run our application. The next step will rely solely on JBoss. navigate to /etc/jboss-5.1.0.GA/bin/ and you’ll see a number of scripts. The only one you need worry about is run.sh – to run JBoss using the default server (that’s where we copied the ear to), execute the following command – ./run.sh -c default -b & the last bit will bind the server to address, so it’ll be visible to the outside world and will run on port 8080 by default. You can change the port by following the guidance in this Stackoverflow post.


    Hopefully everything will start running, and the bii ear will be deployed and you’ll be able to see it at http://localhost:8080/bioinvindex. You will see errors in the startup log, but that’s because nothing exists in our database yet…there are no tables present at this point. We’ll create the database next.

    6. Set up the database

    For this, you’ll need the BII Manager. You can download this from http://isatab.sourceforge.net/tools.html. The latest version (1.6.1) is available here.

    Unzip it and you’ll have a BII-Data-Manager-x.y directory with some files in it. We’ll need to configure some things before we start:

    1. Firstly, the database connection information. Open up the hibernate.properties file under the config/ directory and copy in the same username, password, database URL, index location, etc. as you entered in the profiles.xml for the BII web application.
    2. Next, you may want to set up data-locations.xml. Data locations tell the manager tool where to copy data files and ISA-Tab files as well as the URL the web application will be able to access them from. More information on the set up of JBoss to point to these data directories is available in a previous blog post.

    Now, we’re ready to go. If you are using MySQL, H2, MariaDB or Postgres, you’ll be able to run the application by just double clicking isa_deps.jar or executing ./run.sh from the command line.

    If you are using Oracle, you will need to add the Oracle driver on the classpath. Edit the run.sh file to do this then when ready, from the command line, run ./run.sh.

    When the application starts, you’ll be presented with a log in screen. At this point, create a curator account. When this is done for the first time and the database has no schema available, the application will automatically create the schema via Hibernate (a fantastic tool). So you’ve nothing to do. Then, when that’s completed successfully (if it doesn’t check your hibernate.properties entries), you’ll be able to log in and load content.

    Finally, to make things a bit faster, open up your hibernate.properties file having used the data manager for the first time and delete the line


    This will stop the checking of the schema every time a connection is opened.

    That’s it! Let us know if we missed anything, and we’ll update this post.

    • Matthew Cserhati 11:01 pm on November 19, 2013 Permalink | Reply

      I was wondering how to make the web app public? Instead of being visible just on my local machine?

  • Eamonn Maguire 3:50 pm on August 23, 2013 Permalink | Reply
    Tags: , Data Files, , Static Content   

    Configuring Links to data files in the BII web app in JBoss 5.x 

    We have been getting asked a lot about general deployment within the ISA tools suite, particularly with respect to the web application, which can look a little complex. Here I’m going to describe one of the more perplexing tasks when setting up JBoss: how do I configure JBoss to serve up static content, i.e. my data files. I will also cover how to set up the URLs in data-locations.xml (for the BII Manager tool) to automatically place your files in this directory.

    Setting up JBoss to serve out files

    Probably the most annoying part of setting up JBoss is telling JBoss to serve out your data files from the web application. For instance, the BII data manager tool has sent the files to /tmp/data/bii/ on my file system and I want the URL http://localhost/data to point to that directory. There are a number of ways you can do this. You can use Apache or nginx to do this, you could change your data directory to be within the ROOT.war directory in your JBoss server directory, or you could do what I’m suggesting here and do everything through JBoss…which I think is a bit cleaner, and not so difficult when you know how.

    1. The first thing to do is modify the profile.xml file found under the server/default/config/bootstrap folder in your JBoss installation.


    In profile.xml, there is a bean named BootstrapProfileFactory, you need to modify this and add a value element to the java.net.URI list element. Here, I’ve added a path to my Downloads directory.


    2. Next, we need to set up a folder in my Downloads directory, which has to have a series of folders following the deploy pattern of  /server/<profile>/deploy/ – so now, the directory /Users/eamonnmaguire/Downloads/server/default/deploy/ should exist

    3. Within the deploy directory, create a data.war directory, and inside that create a WEB-INF directory. The name of the .war directory will dictate the URL, so data.war will correspond to http://localhost/data. In the WEB-INF directory, create an empty web.xml file. It’s contents will be <web-app></web-app> – Under the /Users/eamonnmaguire/Downloads/server/ I now have the following directory structure.


    4. Add your files

    Finally, within your data.war directory, add the files you want to display. Here I’ve added a PDF for simplicity.


    Start up JBoss running ./run.sh -c default and navigate your browser to http://localhost:8080/data/Diagnosis.pdf and I get this lovely page.


    That’s it!

    Now, to configure data-locations.xml. For out ISA-Tab for example, we simply set up the filesystem_path to be where, on our machine we want the files to be distributed. The web_url will be the URL we’ve just configured that has mapped data to that actual position in the file system.


    • Mutlu Dogruel 4:15 pm on August 23, 2013 Permalink | Reply

      Hi Eamonn, thanks for this useful information. A small correction: The directory in which you change profile.xml must be
      server/default/config/bootstrap/ instead of server/default/bootstrap/.

    • Matthew Cserhati 4:54 pm on November 20, 2013 Permalink | Reply

      How do you do this all on a Linux system?

      • Eamonn Maguire 4:56 pm on November 20, 2013 Permalink | Reply

        It’s much the same as on mac. The only thing that’s different is the file path.

        • Matthew Cserhati 4:57 pm on November 20, 2013 Permalink

          okay, so could you possibly give an example?

    • Eamonn Maguire 5:03 pm on November 20, 2013 Permalink | Reply

      Well, in the example, instead of /Users/eamonnmaguire/ you’d just have /home/csherati/data/server/default/deploy/data.war/

      The applicationURIs option would be /home/csherati/data/ instead of /Users/eamonnmaguire/Downloads/

      It’s essentially just a case of modifying the paths in this example. Linux and Mac are essentially the same under the hood.

    • Matthew Cserhati 5:53 pm on November 20, 2013 Permalink | Reply

      Hi Eaonn,
      Thanks, I tried, but it didn’t work. I tried putting a test.pdf file into /home/cserhati/data/server/default/deploy/data.war/ but I cannot see it. Is this the place, by the way, where I have to put all my isatab files?

    • Eamonn Maguire 6:03 pm on November 20, 2013 Permalink | Reply

      Which version of JBoss are you using? A few people have followed this guide now and it works.

      The ISATab files are placed in these directories automatically by the loader – the last step in the above post shows a fragment of the data-locations.xml file that resides in the BII Data Manager config directory – you edit that file to tell it where your data.war directory is.

      There is an alternative, which is straightforward if you use Apache for load balancing etc. in that you can use apache to handle the files, or something more suited to media such as nginx.

  • agbeltran 9:26 am on August 3, 2013 Permalink | Reply  

    OntoMaton at the International Conference on Biomedical Ontology (ICBO) 

    The 4th International Conference on Biomedical Ontology (ICBO 2013) took place in Montreal, Canada, on 8th and 9th July 2013. It was held jointly with the Canadian Semantic Web Symposium (CSWS 2013) and Data Integration in the Life Sciences (DILS 2013) in what was called the Semantic Trilogy 2013.

    The members of the core ISA team could not be present this time, but our collaborator and co-author Trish Whetzel was there to present OntoMaton in the Highlight Track entitled OntoMaton: Google spreadsheets meet NCBO BioPortal services. We take this opportunity to thank Trish for her presentation, which was very well received. We have had many new users from the Biomedical Ontology community since ICBO.

    The presentation was about our publication “OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets” available (open access) in Bioinformatics. 2013 February 15; 29(4): 525–527.

    OntoMaton is a script for Google Spreadsheets that relies on NCBO Bioportal Web Services to provide searching and tagging with ontology terms, using those ontologies registered in Bioportal. These functionality for ontology-based annotation of spreadsheets can be used collaboratively among distributed parties. Also, Google Spreadsheets provide version control.

    This is the link to the publication in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/29/4/525 and this is in PubMed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570217/.

    And the slides that Trish presented are here:

    If you are interested in OntoMaton, apart from the publication and slides, you can also see our previous blog postour YouTube video, some templates and the source code on Github.
    Thanks again Trish for presenting OntoMaton at ICBO!
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