Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 2A6AB200CC3 for ; Sat, 1 Jul 2017 05:03:04 +0200 (CEST) Received: by cust-asf.ponee.io (Postfix) id 28CF3160BF6; Sat, 1 Jul 2017 03:03:04 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id 47B6B160BEB for ; Sat, 1 Jul 2017 05:03:03 +0200 (CEST) Received: (qmail 56614 invoked by uid 500); 1 Jul 2017 03:03:02 -0000 Mailing-List: contact notifications-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list notifications@ctakes.apache.org Received: (qmail 56605 invoked by uid 99); 1 Jul 2017 03:03:02 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd1-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 01 Jul 2017 03:03:02 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd1-us-west.apache.org (ASF Mail Server at spamd1-us-west.apache.org) with ESMTP id 16FB9C10E1 for ; Sat, 1 Jul 2017 03:03:02 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd1-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: -99.211 X-Spam-Level: X-Spam-Status: No, score=-99.211 tagged_above=-999 required=6.31 tests=[KAM_ASCII_DIVIDERS=0.8, SPF_PASS=-0.001, T_RP_MATCHES_RCVD=-0.01, USER_IN_WHITELIST=-100] autolearn=disabled Received: from mx1-lw-us.apache.org ([10.40.0.8]) by localhost (spamd1-us-west.apache.org [10.40.0.7]) (amavisd-new, port 10024) with ESMTP id oRb7XzsQU8ZE for ; Sat, 1 Jul 2017 03:03:01 +0000 (UTC) Received: from mailrelay1-us-west.apache.org (mailrelay1-us-west.apache.org [209.188.14.139]) by mx1-lw-us.apache.org (ASF Mail Server at mx1-lw-us.apache.org) with ESMTP id D738C5F613 for ; Sat, 1 Jul 2017 03:03:00 +0000 (UTC) Received: from jira-lw-us.apache.org (unknown [207.244.88.139]) by mailrelay1-us-west.apache.org (ASF Mail Server at mailrelay1-us-west.apache.org) with ESMTP id 5BCC5E0663 for ; Sat, 1 Jul 2017 03:03:00 +0000 (UTC) Received: from jira-lw-us.apache.org (localhost [127.0.0.1]) by jira-lw-us.apache.org (ASF Mail Server at jira-lw-us.apache.org) with ESMTP id 1314F245DA for ; Sat, 1 Jul 2017 03:03:00 +0000 (UTC) Date: Sat, 1 Jul 2017 03:03:00 +0000 (UTC) From: "Jeff Headley (JIRA)" To: notifications@ctakes.apache.org Message-ID: In-Reply-To: References: Subject: [jira] [Comment Edited] (CTAKES-370) Include smoking status in clinical pipeline MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-JIRA-FingerPrint: 30527f35849b9dde25b450d4833f0394 archived-at: Sat, 01 Jul 2017 03:03:04 -0000 [ https://issues.apache.org/jira/browse/CTAKES-370?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16070968#comment-16070968 ] Jeff Headley edited comment on CTAKES-370 at 7/1/17 3:02 AM: ------------------------------------------------------------- I'm using version 3.2.2 and trying to do this in my application. It was previously working with the AggregatePlaintextFastUMLSProcessor. I tried using the one attached to this issue and made the import changes as mentioned in the description, but I am getting the below error: {code:java} org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed. (Descriptor: file:/D:/Software/project/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) . . Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:74) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 19 more Caused by: java.lang.IllegalArgumentException: URI is not hierarchical at java.io.File.(File.java:418) at org.apache.ctakes.core.resource.FileLocator.locateOnClasspath(FileLocator.java:182) at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:125) at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70) at org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:67) ... 20 more {code} The error happens in {{FileLocator}} at method {{private static File locateOnClasspath( final String relativePath )}} and the passed in parameter is: org/apache/ctakes/smokingstatus/data/KU/keywords.txt was (Author: jheadley): I'm using version 3.2.2 and trying to do this in my application. It was previously working with the AggregatePlaintextFastUMLSProcessor. I tried using the one attached to this issue and made the import changes as mentioned in the description, but I am getting the below error: {code:java} org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed. (Descriptor: file:/D:/Software/Epividian/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at com.epividian.ctakes.utils.CTAKESUtils.getAnalysisEngine(CTAKESUtils.java:143) at com.epividian.ctakes.processors.CommandLineProcessor.processLine(CommandLineProcessor.java:144) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580) at com.epividian.ctakes.processors.CommandLineProcessor.run(CommandLineProcessor.java:112) at com.epividian.ctakes.App.main(App.java:109) Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:74) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 19 more Caused by: java.lang.IllegalArgumentException: URI is not hierarchical at java.io.File.(File.java:418) at org.apache.ctakes.core.resource.FileLocator.locateOnClasspath(FileLocator.java:182) at org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:125) at org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70) at org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:67) ... 20 more {code} The error happens in {{FileLocator}} at method {{private static File locateOnClasspath( final String relativePath )}} and the passed in parameter is: org/apache/ctakes/smokingstatus/data/KU/keywords.txt > Include smoking status in clinical pipeline > ------------------------------------------- > > Key: CTAKES-370 > URL: https://issues.apache.org/jira/browse/CTAKES-370 > Project: cTAKES > Issue Type: Improvement > Components: ctakes-clinical-pipeline, ctakes-smoking-status > Affects Versions: 3.2.2 > Environment: Linux > Reporter: Tomasz Oliwa > Priority: Minor > Attachments: AggregatePlaintextFastUMLSProcessor.xml > > > The smoking status detection can be included in the clinical pipeline. > Attached is a AggregatePlaintextFastUMLSProcessor.xml that has the clinical pipeline + the smoking status detection integrated. > Currently cTAKES has smoking status resources that need to have > their imports adjusted for any smoking status detection to work. As a workaround, in: > ProductionPostSentenceAggregate_step1.xml > change: > > > to the absolute or relative path (depends on the installed system, on my machine it is) of these annotators: > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)