Hi Pei, I checked ProductionPostSentenceAggregate_step1.xml <https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml?view=log> and there is not redundant descriptors. For the bug, how to go proceed to fix?
Also, are there other ways to launch smoking pipeline besides "takes-clinical-pipeline" project as document says. Thanks, Justin On Wed, Jul 22, 2015 at 4:48 PM, Chen, Pei <[email protected]> wrote: > Justin, > > There seems to be a bug or redundant descriptors. Check out: > > > https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ > > ProductionPostSentenceAggregate_step1.xml > <https://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml?view=log> > > > > > > *From:* Justin Zhang [mailto:[email protected]] > *Sent:* Wednesday, July 22, 2015 5:21 PM > *To:* [email protected] > *Subject:* Re: smoking status - TypeSystem.xml could not be found > > > > Thanks Pei for the response. > > > > I launched it from cakes-clinical-pipeline project, and added > "smoking-status" dependency. The older error is gone, and got the new > error. > > > > Caused by: org.apache.uima.resource.ResourceInitializationException: An > import could not be resolved. No .xml file with name > "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found in > the class path or data path. (Descriptor: > file:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml) > > at > org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178) > > > > I checked "TokenizerAnnotator.xml" file, it is in the following folder. > > > > eclipse_mars/workspace_eclipse_mars/ctakes > > ctakes justin$ ls ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml > > ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml > > > > From file ProductionPostSentenceAggregate_step1.xml, it has the relevant > lines. > > <delegateAnalysisEngine key="TokenizerAnnotator"> > > <import > name="org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"/> > > </delegateAnalysisEngine> > > > > Where is the folder I should check > "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" xml file? > > > > Thanks, > > > > Justin > > > > On Wed, Jul 22, 2015 at 3:28 PM, Chen, Pei <[email protected]> > wrote: > > It should be able automatically resolved by using the Type System name > rather than absolute path. > > How is the pipeline being launched? If you’re using eclipse and launching > it from the ctakes-clinical-pipeline project, be sure to include the > smoking-status in the pom.xml as a dependency [I don’t think smoking-status > was part of the main pipeline]? Or ensure that that project is included > during runtime? > > Disclaimer: I didn’t try this myself yet- but let me know if that works > for you. > > > > > > *From:* Braun, Florian A [mailto:[email protected]] > *Sent:* Wednesday, July 22, 2015 3:44 PM > *To:* [email protected] > *Subject:* RE: smoking status - TypeSystem.xml could not be found > > > > Wow, was just about to send an email on this. I am getting the exact same > error. > > > > I found the xml file under <ctakes-home>\ctakes-smoking-status\src\main\ > *resources*\org\apache\ctakes\smokingstatus\types\ > > > > Looks like it has an issue being under resources and not under the java? > > > > Any info would be appreciated. > > > > Florian > > > > *From:* Justin Zhang [mailto:[email protected] > <[email protected]>] > *Sent:* Wednesday, July 22, 2015 10:54 AM > *To:* [email protected] > *Subject:* smoking status - TypeSystem.xml could not be found > > > > When I ran smoking pipeline from Eclipse, encountered the following error. > > > > Caused by: org.apache.uima.util.InvalidXMLException: An import could not > be resolved. No .xml file with name > "org.apache.ctakes.smokingstatus.types.TypeSystem" was found in the class > path or data path. (Descriptor: > file:/Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml) > > > > Everything looks fine. > > > > The file is there physically. > > The importing part from ClassifiableEntriesAnnotator.xml file is > > <typeSystemDescription> > > <imports> > > <import > name="org.apache.ctakes.smokingstatus.types.TypeSystem"/> > > </imports> > > </typeSystemDescription> > > > > Could any one help me some clues? > > > > Thanks, > > > > > > -- > > Justin > > > > > > -- > > Justin > -- Justin
