Wednesday, November 5, 2008

OpenID Troubleshooting for openid4java

On deployment of the bioMoby Annotator, ran into some interesting problems with OpenID.

Firstly, for those of you who are trying to figure out why Yahoo is giving you the

"Warning: This website has not confirmed its identity with Yahoo! and might be fraudulent. Do not share any personal information with this website unless you are certain it is legitimate."

I recommend having a look at the Yahoo OpenID FAQs

I also recommend the following articles:

Why Yahoo! says your OpenID site's identity is not confirmed

If you're using Openid4java from sxip, try this:

If Yahoo is still giving you errors, consider their extra requirements:

Yahoo! will only support Relying Parties running on webservers with real hostnames (IP addresses are not supported) running on standard ports (Port 80 for HTTP and Port 443 for HTTPS).

This means localhost will not work and if it's running on say... port 8080, you'll need to figure out a way to forward from port 80 to port 8080

Your web app also needs to be available from the internet. You can test this by trying to access your website from another computer outside of your intranet.

So in the end: if your web address looks like http://localhost:8080/yourrealm/openid , it's not going to work. it needs to look similar to

If Yahoo is doing a discovery of your Yadis document on your REALM. ie. your index.html, make sure the header x-xrds-location is inserted into the head.

Again, if you're using Java Servlets and Apache Tomcat like I am, you'll need to do this using a Servlet Filter:

Instructions on Servlet Filter

Can't tell if it's in the header?
You can type curl -i in your command prompt to check

Another note:
If you're getting:
org.openid4java.message.MessageException: 769: Realm verification

try going into the init method for your openid consumer Servlet
and adding in manager.getRealmVerifier().setEnforceRpId(false); after this.manager = new ConsumerManager();

A good website to go to make sure that an openID 2.0 Provider does work with openid4java is

Sunday, August 31, 2008

Biomoby Web Service Display Page

WebServiceRetrieval.js requires:
jquery.pack.js - v1.2.3 or later
jquery.form.js -v2.12 or later

With regards to biomoby rifraf: Progress is made on the BioMoby Web Service Annotation Page. Finished making the javascript file (WebServiceRetrieval.js) to display a Web Service's descriptive information. Because the RDF graph for a Web Service can get pretty deep and because we want to pull out a lot of information, it slows down the query I've noticed and causes timeouts when accessing it remotely the way we're doing it. Had to break down the query into steps.

1) Query using a web service uri to get its immediate service description, organization description and operation uid
2) Query using the operation uid to get the operation task
3) Query using the operation uid to get the operation Input parameters
4) Query using the operation uid to get the operation Output parameters

Using ajax calls to submit a form containning the SPARQL queries, the script executes the Query 1 and pulls out the Operation uid. Query 2-4 use the operation uid and are all called at approximately the same time (as in they don't wait for one to complete before executing the other since they're all their own seperate ajax call)

Using the jquery form plugin to do the ajax calls which allows the script to work in all browsers: Firefox3, Safari, Opera and IE7.

Small catch: Need to talk to the guys who handle the Virtuoso server where I'm getting this Web Service description RDF as JSON from. Because ajax doesn't let you do cross domain requests for json (which we're doing) UNLESS you set datatype: jsonp.

When datatype is set to jsonp, jquery ajax sends an extra 'callback' parameter in the request to the server. This 'callback' parameter is usually has a value like eg. jsonp7120986. The server is suppose to take that and wrap it's response JSON in it like so:
jsonp7120986( {responseJSON} ) and set the response to text/plain.

If the server just sends back {responsJSON} without it being wrapped, it will cause an 'invalid label' error.

Our SPARQLEndpoint currently doesn't do this and I've been getting around it (so that I could keep coding) by making an intermediate java class which would wrap the JSON response in the callback. I'm sure the guys managing our SPARQL Endpoint will be able to help.

Now to make it look intuitive and beautiful...

Tuesday, August 26, 2008

Instructions for installing ED Wiki

Setting up Entity Describer wiki is up. Start with: InstructionsforED

Revisions necessary?


biomoby rifraf

At some point in the next few weeks we will be building/using a customized ED web page to conduct an experimental annotation jamboree on the biomoby web services.  We will be both measuring the differences in collected data between normal social tagging and semantic social tagging and providing a new layer of annotation for the biomoby framework.

The soon-to-be-created biomoby service annotation web page is an example of one application of the ED code (now available on Google code).   We hope that others will find many more uses for it over time.  When its ready, the little web page that could will

  1. Request a JSON representation of the RDF describing a biomoby web service from a new SPARQL endpoint containing the BioMoby service graph.  See here for an RDF/XML rendition of such a service description.
  2. Display the available information about the service in a reasonably intuitive and beautiful fashion.
  3. Allow the user to tag the service with either semantic tags (e.g. from the service ontology or elsewhere) or free text tags.
  4. Send the tagging information to the ED RDF repository.

The question of what exactly to collect and why is still a little vague however.  Why and how would tags, semantic or otherwise, be useful in the biomoby system?

Moby2.0 developer Luke McCarthy requested that the service tags focus on defining what might be reasonable semantic relationships (predicates) between the input and the output of the service.  An example might be for a a basic blast service, service input a) 'is homologous to' service output b).  

Any other suggestions regarding service semantics of interest warmly requested and appreciated.


Monday, August 25, 2008


ED is holding a code license: New BSD License
and a content license: Creative Commons 3.0 BY

The content license comes in BY and BY-SA

This license lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of licenses offered, in terms of what others can do with your works licensed under Attribution.

SA: This license lets others remix, tweak, and build upon your work even for commercial reasons, as long as they credit you and license their new creations under the identical terms. This license is often compared to open source software licenses. All new works based on yours will carry the same license, so any derivatives will also allow commercial use.

For all the licenses:


ED is now recording the aliases for a term. Aliases are being recorded as an rdfs:label attached to the topic (the guid of the term).

Google code

There's the site for ED on google code. The All the code for ED is containned within the surprise surprise 'ED' folder in the trunk. I've also created a new folder within the trunk that contains the javadocs which can be reached at:

which is linked to in the Entity describer google code project home page.

The IcaptureUtils project that the Entity describer uses, I made into a jar file and included it in ED's referenced libraries