[Biojava-l] AGAVE usage

[Patrick McConnell]

When developing web services, the general procedure is to return Java
objects in web service methods, and let the service engine build the WSDL
and serialize the XML.  For most applications (especially business
processes), this makes sense.  However, this does not translate to BioJava
perfectly since the data is extremely complex and BioJava has an internal
representation quite different from the XML.

So, we have two options (as I see it):
      (1) Build Java objects for each complexType.  This is fine, but alot
of work since we will have to map complexType -> Java class -> BioJava
class.
      (2) Go through the painstaking process of writing WSDL, and use the
Agave IO package.  This will be extremely painstaking because we will have
to interface with the SOAP level.

Does anyone have an opinion on this subject?  This is actually a design
decision that we should probably make across the board for BioJava web
service implementations.

I have done (1) for blast (with the exception of Java class -> BioJava
class), and it was pretty straight forward to implement.  I started to do
this for Agave, but I ran into some compatibility problems.  Among these
are:
      (1) At least one type extends string, which you cannot do in Java (it
is a final class).
      (2) The web services package I use does not (at this moment) support
choice.  So, I will have to find some workaround.  Does anyone know if this
is a limitation on other web service packages (I am using GLUE).

-Patrick





Brian King <kingb_98@yahoo.com>@biojava.org on 08/30/2002 12:29:48 AM

Please respond to brian.king@animorphics.net

Sent by:    biojava-l-admin@biojava.org


To:    MCCon012@mc.duke.edu
cc:    biojava-l@biojava.org

Subject:    [Biojava-l] AGAVE usage


Patrick,

Yes, I think the intention of having the FeatureSet at
the top level was to allow you to pass around
annotations without the associated sequence.  This can
be useful when you need to separate different
annotation types into different files.  If you are
validating using the XML Schema definition of AGAVE
(agave.xsd), XML Schema doesn't require a root
element, so you can have any globally scoped element
as the document root.  Most of the elements have
global scope, so a document with a single seq_feature
should be valid.

I'm working on a version of the AGAVE IO package that
spits out AGAVE 3, so I have a chance to reduce some
of the flakiness that was mentioned.

Brian


-------------------------------------------------
Looking at the schema, I believe that you can push
around annotations
without the sequence.

The root element, sciobj, can have zero or more of any
of the
following:
      bio_sequence
      contig
      FeatureSet
      chromosome.

So, I think what you are looking for is the
FeatureSet, which contains
an
annotations element, distinct from the bio_sequence
elements.

Please, an Agave expert correct me if I am wrong.

-Patrick




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