So I have been very successful in working iwth T2Flow files lately. But now
it has come to open and process T1 files.
*My code*:
currentDataflow = fileManager.openDataflow(new ScuflFileType(), file);
*Produces this error:*
net.sf.taverna.t2.workbench.file.exceptions.OpenException: Could not open
workflow C:\Documents and Settings\admin\My
Documents\Downloads\pathways_and_gene_annotations_for_qtl_phenotype_25510.xml
at
net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.openDataflowSilently(FileManagerImpl.java:478)
at
net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.performOpenDataflow(FileManagerImpl.java:415)
at
net.sf.taverna.t2.workbench.file.impl.OpenDataflowSwingWorker.doInBackground(OpenDataflowSwingWorker.java:51)
at
net.sf.taverna.t2.workbench.file.impl.OpenDataflowSwingWorker.doInBackground(OpenDataflowSwingWorker.java:32)
at org.jdesktop.swingworker.SwingWorker$1.call(SwingWorker.java:276)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(SwingWorker.java:315)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: net.sf.taverna.t2.workbench.file.exceptions.OpenException: Could
not translate Scufl file:
An error occurred whilst trying to find a T2 ActivityTranslator for a T1
processor [WSDLBasedProcessor:gene_descriptions]
at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflowStream(T1OpenHandler.java:170)
at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflowInMode(T1OpenHandler.java:121)
at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflow(T1OpenHandler.java:145)
at
net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.openDataflowSilently(FileManagerImpl.java:464)
... 10 more
Caused by: net.sf.taverna.t2.compatibility.WorkflowTranslationException: An
error occurred whilst trying to find a T2 ActivityTranslator for a T1
processor [WSDLBasedProcessor:gene_descriptions]
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.doTranslation(WorkflowModelTranslator.java:183)
at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflowStream(T1OpenHandler.java:168)
... 13 more
Caused by:
net.sf.taverna.t2.compatibility.activity.ActivityTranslatorNotFoundException:
Unable to find Activity Translator for:class
org.embl.ebi.escience.scuflworkers.wsdl.WSDLBasedProcessor
at
net.sf.taverna.t2.compatibility.activity.ActivityTranslatorFactory.getTranslator(ActivityTranslatorFactory.java:76)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createActivity(WorkflowModelTranslator.java:416)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessor(WorkflowModelTranslator.java:374)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessors(WorkflowModelTranslator.java:358)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.doTranslation(WorkflowModelTranslator.java:160)
... 14 more
------------------------------------------------------
Could someone provide a simple set of lines that correctly call the
translator? Im assuming that since this translates an entire T1 file into
file, I will be able to use all of the code I already wrote for the T2 file
with minor modifications.
Thanks again,
- John
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