Dear Nikolaus,
I will update the CVS of
the CDK-Taverna project until Monday because I did some changes.
For me it looks like you
are using not the right cdk.jar version. But I am not sure. I will also update
the cdk.jar of this project.
I think that the changes
you did are not so important for this problem.
Normally you should be
able to use the cdk.jar and the cdk-taverna.jar within Taverna directly. You
just need to copy them. So you need not necessarily compile them again, you
only need to compile them again if you have done changes to the code.
If you need to work
directly with it, I could send you the two jars which should work. But they
will be on the CVS on Monday. (Or perhaps a bit earlier)
Best regards
Thomas
Von:
[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Im Auftrag von [EMAIL PROTECTED]
Gesendet: Freitag, 3. März 2006
13:45
An: [email protected]
Betreff: [Cdk-user] Problems with
cdk-taverna ...
Hi,
this is my second
try getting cdk-taverna to run.
After getting a bit
more into Java and CDK (I was a complete starter about 4 weeks ago), I got the
code from CVS and tried to follow the instructions in the readme file.
Here I had the
following problems which I hope I solved correctly:
After importing the
cdk-taverna project into eclipse:
1. Since I have no
CDK project in my eclipse I removed the cdk project from the required projects
(given that I have the cdk.jar included I thought this to be sensible)
2. Since I am
working with Taverna 1.3 I changed the required taverna-1.3.1.jar to my
taverna-1.3.jar
3. The following
files showed problems:
applications directory:
CDKTavernaTests.java => the boolean
values in lines 48 and 49 are Boolean objects but are later used as standard
boolean type ... chenged to simple boolean
TavernaTestData.java => in lines
190,191,194, and 199 the hashCode() function for the String is used. Since this
returns an int but the HashMap.put() functions expects an object, I changed this
to the String only
DetectHueckelAromaticityTest.java => in
line 61, I changed the return value from expectedDefaultReults[i] (which is
boolean) to Boolean object (with new Boolean(expectedDefaultReults[i]) )
cdk directory:
DetectHueckelAromaticity.java => in lines
76 and 81, I changed the true and false values in the
isAromaticBooleanList.add() functions to Boolean object by new Boolean()
writeCMLChemFileToFile.java => in line
48, did the same in matchedList.add()
After that, building
of the project worked perfectly.
I then generated the
jar (via ant clean jar) and copied it as well as the cdk.jar into the lib
directory and subsequently generated the apiconsumer.xml as described
I also checked that
all classes are in the taverna-cdk and they are.
When I now start
taverna eveything looks ok. I have cheminformatics things as local widgets as
well as additional functions such as parseSmiles. However, when I try a very
simple worklfow such as a string constant with a smiles and a parseSmiles
function I get errors that I would connect to taverna not finding functions
from cdk:
Using ParseSmiles:
>Caused by:
java.lang.NoSuchMethodError: org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules(Lorg/openscience/cdk/AtomContainer;)Lorg/openscience/cdk/SetOfMolecules;
>
at
org.openscience.cdk.tools.HydrogenAdder.addImplicitHydrogensToSatisfyValency(HydrogenAdder.java:280)
>
at org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:326)
>
at
org.openscience.cdk.applications.taverna.smiles.SmilesTools.parseSMILES(SmilesTools.java:46)
Using
readFromSmilesFile:
>Caused by:
java.lang.NoSuchMethodError: org.openscience.cdk.applications.taverna.CMLChemFile.getBuilder()Lorg/openscience/cdk/interfaces/IChemObjectBuilder;
>
at
org.openscience.cdk.applications.taverna.io.CDKIOReader.readFromSMILESFile(CDKIOReader.java:55)
Using
readFromMDLFile:
>Caused by:
java.lang.IncompatibleClassChangeError
>
at
org.openscience.cdk.applications.taverna.io.CDKIOReader.readFromMDLFile(CDKIOReader.java:93)
Can anybody help me
with this? I don't think it's the "corrections" I have done to the
code to get it compiled since these are not used in these simple workflows ...
Maybe it's just some
variable that needs to be set, but I have absolutely no idea which one :-()
Thanks a lot,
Nik
