Do you think that the problem is with
expander.io.converters.EnrichmentSolConverter.unmarshal()?
It is a method that was generated to support some DS changes in prev
versions.
Should I try to get rid of this converter?
I do not know if this helps but the code of the method is
public Object unmarshal(HierarchicalStreamReader reader,
UnmarshallingContext arg1) {
if (! reader.hasMoreChildren())
return null;
Class cType = arg1.getRequiredType();
reader.moveDown();
try
{
String nodeName = reader.getNodeName();
boolean prevVer = false;
float[][] rawPVals=null, relativeFreqs=null;
double minRawPVal=2;
if(nodeName.equals("rawPVals")){ //funcAnal prev
version{
prevVer = true;
rawPVals =
(float[][])arg1.convertAnother(arg1.currentObject(),
float[][].class);
}else
if(nodeName.equals("relativeFreqs")){//PromAnalSol prevVersion
prevVer = true;
relativeFreqs =
(float[][])arg1.convertAnother(arg1.currentObject(),
float[][].class);
}
if(!prevVer){//default converter can do the work
reader.moveUp();
Converter defaultConverter =
conLookup.lookupConverterForType(GeneralSolution.class);
Object res =
defaultConverter.unmarshal(reader, arg1);
return res;//defaultConverter.unmarshal(reader,
arg1);
}
Hashtable hitsHash=null, pwmLengthHash=null;
String seqsFilePath=null ;
reader.moveUp();
reader.moveDown();
String next = reader.getNodeName();
if(cType.equals(FuncAnalSol.class)){
minRawPVal =
Double.parseDouble(reader.getValue());
reader.moveUp();
reader.moveDown();
}
else//PromoterAnalSol
{
hitsHash =
(Hashtable)arg1.convertAnother(arg1.currentObject(),
Hashtable.class);
reader.moveUp();
reader.moveDown();
pwmLengthHash =
(Hashtable)arg1.convertAnother(arg1.currentObject(),
Hashtable.class);
reader.moveUp();
reader.moveDown();
seqsFilePath =
(String)arg1.convertAnother(arg1.currentObject(),
String.class);
reader.moveUp();
reader.moveDown();
}
next = reader.getNodeName();
String[] catNames =
(String[])arg1.convertAnother(arg1.currentObject(),
String[].class);
reader.moveUp();
reader.moveDown();
if(reader.getNodeName().equals("coverage")){
reader.moveUp();
reader.moveDown();
}
float[][] freqs =
(float[][])arg1.convertAnother(arg1.currentObject(),
float[][].class);
reader.moveUp();
reader.moveDown();
float[][] pVals =
(float[][])arg1.convertAnother(arg1.currentObject(),
float[][].class);
reader.moveUp();
reader.moveDown();
String[][][][] enrichmntGenes =
(String[][][][])arg1.convertAnother(arg1.currentObject(),
String[][][][].class);
reader.moveUp();
reader.moveDown();
reader.moveUp();
reader.moveDown();
double threshPVal =
Double.parseDouble(reader.getValue());
reader.moveUp();
reader.moveDown();
if(relativeFreqs == null)
relativeFreqs = freqs;
ArrayList<EnrichmentResult> enrichments =
generateEnrichmentsList(catNames/*,coverage*/, relativeFreqs,
pVals, rawPVals,enrichmntGenes,
threshPVal );
String baseSetsKey = reader.getValue();
reader.moveUp();
reader.moveDown();
String studyID = reader.getValue();
reader.moveUp();
reader.moveDown();
// double minPVal = Double.parseDouble(reader.getValue());
reader.moveUp();
reader.moveDown();
ArrayList opInfo = (ArrayList)
arg1.convertAnother(arg1.currentObject(),
ArrayList.class);
reader.moveUp();
reader.moveDown();
reader.moveUp();
reader.moveDown();
String solName = reader.getValue();
reader.moveUp();
reader.moveDown();
IOStorage opInput =
(IOStorage)arg1.convertAnother(arg1.currentObject(),
IOMgr.class);
reader.moveUp();
reader.moveDown();
String key = reader.getValue();
reader.moveUp();
EnrichmentSol res=null;
if(cType.equals(FuncAnalSol.class))
res = new FuncAnalSol(solName, opInfo,
opInput, catNames,enrichments,
baseSetsKey,studyID,baseSetsDetector);
else if(cType.equals(PromoterAnalSol.class)){
res = new PromoterAnalSol(solName, opInfo,
opInput,
catNames,enrichments, baseSetsKey,studyID,baseSetsDetector, hitsHash,
pwmLengthHash);
((PromoterAnalSol)res).setSeqsFilePath(seqsFilePath);
}
if(res!=null)
res.setKey(key);
return res;
}
catch(Exception e){
e.printStackTrace();
return null;
}
}
If this is not what you meant then which method are you referring to?
Thanks
Adi
Jörg Schaible-3 wrote:
>
> Hi Adi,
>
> adimaron wrote:
>
>>
>> Thanks for you reply.
>> The full stack was as follows:
>
> [snip]
>
>> Caused by: com.thoughtworks.xstream.mapper.CannotResolveClassException:
>> edu.tau.compbio.io.IOMgr-Constraints
>> at
>>
> com.thoughtworks.xstream.mapper.DefaultMapper.realClass(DefaultMapper.java:56)
>
> [snip]
>
> As already seen here:
>
>> Details: com.thoughtworks.xstream.converters.ConversionException: Could
>> not call edu.tau.compbio.util.OrderedHash.readObject() :
>> edu.tau.compbio.io.IOMgr-Constraints
>> ---- Debugging information ----
>> message : Could not call
>> edu.tau.compbio.util.OrderedHash.readObject()
>> cause-exception :
>> com.thoughtworks.xstream.mapper.CannotResolveClassException
>> cause-message : edu.tau.compbio.io.IOMgr-Constraints
>
> [snip]
>
>> The IOMgr is my class and it uses OrderedHash which is also my class.
>> Will it help if I put the code?
>
> It does not complain about "edu.tau.compbio.io.IOMgr", it complains about
> a
> type "edu.tau.compbio.io.IOMgr-Contraint". Seems to be an inner class.
>
>> When I tried adding the code from the compatibility link that you
>> suggested to support 1.1 objects
>> Which is initializing xstream as follows:
>>
>> XStream xstream = new XStream(new XppDriver(new
>> XStream11XmlFriendlyReplacer())) {
>> protected boolean useXStream11XmlFriendlyMapper() {
>> return true;
>> }
>> };
>>
>>
>> I got a whole different exception:
>> java.lang.IndexOutOfBoundsException: only START_TAG can have attributes
>> at org.xmlpull.mxp1.MXParser.getAttributeValue(MXParser.java:1005)
>> at
>> com.thoughtworks.xstream.io.xml.XppReader.getAttribute(XppReader.java:139)
>> at
>>
> com.thoughtworks.xstream.io.ReaderWrapper.getAttribute(ReaderWrapper.java:52)
>> at
>>
> com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.instantiateNewInstance(AbstractReflectionConverter.java:421)
>> at
>>
> com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:233)
>> at
>>
> expander.io.converters.EnrichmentSolConverter.unmarshal(EnrichmentSolConverter.java:72)
>
>
> What does this method? It seems to corrupt the state of the parser. To me
> it
> looks as if you run now in the next problem, but the type from above can
> be
> resolved now.
>
> [snip]
>
> - Jörg
>
>
> ---------------------------------------------------------------------
> To unsubscribe from this list, please visit:
>
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>
>
>
>
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