[MOBY-l] BioMoby Problems

[Jerzy Orlowski]

Hi

I am new to BioMoby and I am preparing a seminar aboutit in mt Institute.
However, I find my interaction with Biomoby quite painful in a few 
points. Maybe You can help me or You can benefit anyhow.

1. I got completely lost in the number of services.

I wanted try a simple example: make a blast file given an input protein.
I found it not that easy. I was unable to run anything i Remora. In 
taverna i failed to do anythig myself, but I found a working workflows:
http://www.ebi.ac.uk/Tools/webservices/tutorials/taverna
I don't know why it is so complicated

When I tried to make my own workflows in taverna, I was unable to put 
correct input in correct fields. The input types are not described, have 
no shown default values or examples. A "plain/text" field does not tell 
anything. The same problem I had in the jMoby dashboard.

2. Command line programs

The second thing I wanted to do is to write a simple command line 
program that connects to any service and parse he result.
I downloaded and compiled  jMoby. However, the examples from:

http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CmdLineClients.html 


Did not work

For

  <?xml version="1.0" encoding="UTF-8"?>
  <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
    <moby:mobyContent>
      <moby:mobyData moby:queryID="a1">
        <moby:Simple moby:articleName="">
          <moby:Object moby:namespace="DragonDB:Allele" moby:id="cho" />
        </moby:Simple>
      </moby:mobyData>
    </moby:mobyContent>
  </moby:MOBY>

I got error when searching for DragonDB

For

  <?xml version="1.0" encoding="UTF-8"?>
  <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
    <moby:mobyContent>
      <moby:mobyData moby:queryID="a1">
        <moby:Simple moby:articleName="">
          <moby:Object moby:namespace="NCBI_gi" moby:id="431260" />
        </moby:Simple>
      </moby:mobyData>
    </moby:mobyContent>
  </moby:MOBY>


I had no errors, but the resut contained only the:

<?xml version='1.0' encoding='UTF-8'?><moby:MOBY 
xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'><moby:mobyContent 
moby:authority='illuminae.com'><moby:serviceNotes>This data is provided 
by &lt;a HREF='http://seqhound.blueprint.org'&gt;SeqHound&lt;/a&gt;; 
&lt;a 
href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12401134&amp;dopt=Abstract'&gt;Michalickova 
K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.  
SeqHound: biological sequence and structure database as a platform 
forbioinformatics research. BMC Bioinformatics. 2002 Oct 
25;3(1):32&lt;/a&gt;</moby:serviceNotes>
       <moby:mobyData moby:queryID='a1'>

part


I also tried compiling some java code from:

http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/SimpleClient.html 


First, I had to set the classpath to moby-live/Java/build/classes (It 
took me a lot of time to find out where it is).
Then I got an error:

../test/HelloMOBY2.java:5: HelloMOBY2 is not abstract and does not 
override abstract method start(org.biomoby.client.MobyRequestEvent) in 
org.biomoby.client.MobyRequestEventHandler
public class HelloMOBY2 implements MobyRequestEventHandler{
      ^

When I created This method (doing nothing) i managed to compile the code 
wit javac, but I got error with java:

Exception in thread "main" java.lang.NoClassDefFoundError: 
org/apache/axis/AxisFault
       at HelloMOBY2.main(HelloMOBY2.java:8)

I got stucked

Best Regards

Jerzy Orlowski