Justin, I meant, what is the error: When you use /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes /ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml<http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml> Instead of: /Users/justin/App/eclipse_mars/workspace_eclipse_mars/ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/
From: Justin Zhang [mailto:[email protected]] Sent: Wednesday, July 22, 2015 6:19 PM To: [email protected] Subject: Re: smoking status - TypeSystem.xml could not be found Hi Pei, I checked ProductionPostSentenceAggregate_step1.xml<https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_ProductionPostSentenceAggregate-5Fstep1.xml-3Fview-3Dlog&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=NC8hDGtE8v99_f0CkYg4TWYDT5ga6tziR78hej5XtIM&e=> 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]<mailto:[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/<https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=bDdwEocxxNTXXMVCZCk59PcW0DhiE53FzSoLiOAQCwM&e=> ProductionPostSentenceAggregate_step1.xml<https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Dsmoking-2Dstatus_desc_analysis-5Fengine_ProductionPostSentenceAggregate-5Fstep1.xml-3Fview-3Dlog&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=CCqJyj0itS0tnsWZcPG9jszlf_CmaggbHiKtU2ajWHU&s=NC8hDGtE8v99_f0CkYg4TWYDT5ga6tziR78hej5XtIM&e=> From: Justin Zhang [mailto:[email protected]<mailto:[email protected]>] Sent: Wednesday, July 22, 2015 5:21 PM To: [email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>] Sent: Wednesday, July 22, 2015 3:44 PM To: [email protected]<mailto:[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]] Sent: Wednesday, July 22, 2015 10:54 AM To: [email protected]<mailto:[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
