Details
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Bug
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Status: To Do
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Critical
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Resolution: Unresolved
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None
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None
Description
BioJava workers like "Read Gen Bank File" fails as they can't find org.biojava.bio.seq.SequenceIterator etc.
Are these still used, or can we remove them?
WARN 2013-10-10 16:10:27,190 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking Local service net.sourceforge.taverna.scuflworkers.biojava.SwissProtParserWorker for job DispatchJobEvent facade2:Workflow12:Read Swiss Prot File[]: Error evaluating the beanshell script net.sf.taverna.t2.activities.beanshell.BeanshellActivity$1@4798ee5e Sourced file: inline evaluation of: ``import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator . . . '' : Typed variable declaration : Class: SequenceIterator not found in namespace : at Line: 26 : in file: inline evaluation of: ``import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator . . . '' : SequenceIterator at bsh.BSHAmbiguousName.toClass(Unknown Source) at bsh.BSHType.getType(Unknown Source) at bsh.BSHTypedVariableDeclaration.eval(Unknown Source) at bsh.Interpreter.eval(Unknown Source) at bsh.Interpreter.eval(Unknown Source) at bsh.Interpreter.eval(Unknown Source) at net.sf.taverna.t2.activities.beanshell.BeanshellActivity$1.run(BeanshellActivity.java:171) at java.lang.Thread.run(Unknown Source)
Attachments
Issue Links
- is a clone of
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TAVERNA-170 Classloading for dependency activities is not working correctly
- To Do
- is related to
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TAVERNA-707 Update the User Manual - increase memory, installation, uninstallation etc. to reflect the state as of 2.5
- To Do