[MOBY-l] BioMoby Problems

[Edward Kawas]

Hi Jerzy,

The XML was incorrect for one of the commandline examples. I have updated
the page to reflect what was wrong, but it may not be reflected in the
online documentation right away.

Basically, try running the command line client again but with

DragonDB:Allele replaced by DragonDB_Allele.

Also, have you taken a look at the page:
http://moby.ucalgary.ca/gbrowse_moby ? Might be good in giving you working
examples of how moby works.

The second command line example had an error in it as well. Again, it might
take a few hours to be reflected on line.

For the second example, the line:

articleName="" should read articleName="identifier".

For information on what the datatypes for services are, or under what
*namespace* the are can be used, examine the 'log' window in dashboard when
you select services or datatypes.

I am not sure about the answer to the last jmoby problem, so someone else
may have to help you on that one.

Let me know if I can help further.

Eddie

-----Original Message-----
From: moby-l-bounces at lists.open-bio.org
[mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: June-06-08 1:18 PM
To: moby-l at lists.open-bio.org
Subject: [MOBY-l] BioMoby Problems

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.h
tml 


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=PubM
ed&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.htm
l 


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








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