Return-Path: X-Original-To: apmail-incubator-ctakes-user-archive@minotaur.apache.org Delivered-To: apmail-incubator-ctakes-user-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 123D1D437 for ; Fri, 2 Nov 2012 18:42:43 +0000 (UTC) Received: (qmail 77939 invoked by uid 500); 2 Nov 2012 18:42:43 -0000 Delivered-To: apmail-incubator-ctakes-user-archive@incubator.apache.org Received: (qmail 77914 invoked by uid 500); 2 Nov 2012 18:42:43 -0000 Mailing-List: contact ctakes-user-help@incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: ctakes-user@incubator.apache.org Delivered-To: mailing list ctakes-user@incubator.apache.org Received: (qmail 77903 invoked by uid 99); 2 Nov 2012 18:42:43 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 02 Nov 2012 18:42:42 +0000 X-ASF-Spam-Status: No, hits=-0.0 required=5.0 tests=SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of Pei.Chen@childrens.harvard.edu designates 134.174.20.73 as permitted sender) Received: from [134.174.20.73] (HELO mailsmtp3.childrenshospital.org) (134.174.20.73) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 02 Nov 2012 18:42:36 +0000 Received: from pps.filterd (mailsmtp3 [127.0.0.1]) by mailsmtp3.childrenshospital.org (8.14.5/8.14.5) with SMTP id qA2Icbb7001793 for ; Fri, 2 Nov 2012 14:42:04 -0400 Received: from smtpndc2.chboston.org (smtpndc2.chboston.org [10.20.50.105]) by mailsmtp3.childrenshospital.org with ESMTP id 18ap2adng2-1 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Fri, 02 Nov 2012 14:42:04 -0400 Received: from pps.filterd (smtpndc2 [127.0.0.1]) by smtpndc2.chboston.org (8.14.5/8.14.5) with SMTP id qA2IfEp2015322 for ; Fri, 2 Nov 2012 14:42:03 -0400 Received: from chexhubcas3.chboston.org (internal-ndc-nat-v1260.tch.harvard.edu [10.20.50.4]) by smtpndc2.chboston.org with ESMTP id 17ay3g0a7q-1 (version=TLSv1/SSLv3 cipher=AES128-SHA bits=128 verify=NOT) for ; Fri, 02 Nov 2012 14:42:03 -0400 Received: from CHEXMBX1A.CHBOSTON.ORG ([fe80::3c05:8ca9:55a6:f320]) by CHEXHUBCAS3.CHBOSTON.ORG ([::1]) with mapi id 14.02.0309.002; Fri, 2 Nov 2012 14:42:03 -0400 From: "Chen, Pei" To: "ctakes-user@incubator.apache.org" Subject: RE: Can't find lookup dictionary from pear Thread-Topic: Can't find lookup dictionary from pear Thread-Index: Ac25J+97wjcCikv2SlCVgvfQMpmDNgAAMWTg Date: Fri, 2 Nov 2012 18:42:02 +0000 Message-ID: <924DE05C19409B438EB81DE683A942D9221695@CHEXMBX1A.CHBOSTON.ORG> References: In-Reply-To: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [10.7.2.184] Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.7.7855,1.0.431,0.0.0000 definitions=2012-11-02_05:2012-11-02,2012-11-02,1970-01-01 signatures=0 X-Proofpoint-Virus-Version: vendor=fsecure engine=2.50.10432:5.7.7855,1.0.431,0.0.0000 definitions=2012-11-02_05:2012-11-02,2012-11-02,1970-01-01 signatures=0 X-Virus-Checked: Checked by ClamAV on apache.org Hi Kline, I presume this is cTAKES version 2.5? Is the parent folder of "drugnerrrsources/lookup/g2_index" in the classpath= of your container (jboss?) ? My guess is that: 1) The resource is not in the classpath 2) The g2_index was lost during the creation of the pear and eventually int= o the war? i.e. does the new g2_index folder really exist in the target fol= der where the old classpath used to point? Note: You can also try an file absolute path to verify that indeed that is = a classpath issue. Hope that helps. Thanks, Pei From: Kline, Larry D [mailto:Larry.Kline@USONCOLOGY.COM]=20 Sent: Friday, November 02, 2012 2:30 PM To: ctakes-user@incubator.apache.org Subject: Can't find lookup dictionary from pear I am using the cTAKES DictionaryLookup pipeline to find drug mentions in do= cuments.=A0 When I run this from eclipse it works perfectly.=A0 But when I = run from a pear file that I generated it fails.=A0 It appears that it canno= t find the Lucene lookup dictionary folder that I created.=A0 This is the e= xception: =A0=A0=A0=A0=A0=A0 ... 16 more Caused by: java.io.FileNotFoundException: drugnerresources/lookup/g2_index =A0=A0=A0=A0=A0=A0 at edu.mayo.bmi.uima.core.resource.FileLocator.locateExp= licitly(FileLocator.java:74) [classes:] =A0=A0=A0=A0=A0=A0 at edu.mayo.bmi.uima.core.resource.FileLocator.locateFil= e(FileLocator.java:49) [classes:] =A0=A0=A0=A0=A0=A0 at edu.mayo.bmi.uima.core.resource.LuceneIndexReaderReso= urceImpl.load(LuceneIndexReaderResourceImpl.java:61) [classes:] =A0=A0=A0=A0=A0=A0 ... 52 more There's a large stack trace before this but this is the relevant part.=A0 I= t gets to this code (locateExplicitly()) only if a class loader get resourc= e call fails.=A0 That should probably have worked. In my DictionaryLookupAnnotator I have this: =A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0 RxnormIndex =A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 UseMemoryIndex =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Boolean =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 false =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 true =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 IndexDirectory =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 String =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 false =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 true =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0UseMemoryIndex =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 true =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 IndexDirectory =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 drugnerresource= s/lookup/g2_index =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0 edu.mayo.bmi.uima.core.resource.L= uceneIndexReaderResourceImpl =A0=A0=A0=A0=A0 =A0=A0=A0 You can see the definition of IndexDirectory is what it cannot find.=A0 The= location does exist at /resources/drugnerresources/lookup/g2= _index.=A0 I replaced g2_index with rxnorm_index, which is something that c= ame with the cTAKES distribution and that does not work either. When I build my pear file I include only the desc, resources, and metadata = folders from my project.=A0 The pear goes into the war directory and the wa= r is deployed to a jboss 7.1 server.=A0 I can see the pear being unpacked w= hen the war is deployed.=A0 Without the drug lookup all of this has worked = perfectly for months.=A0 But this is the first time I am trying to use the = cTAKES drug lookup. Thanks, Larry Kline The contents of this electronic mail message and any attachments are = confidential, possibly privileged and intended for the addressee(s) only.Only the addressee(s) may read, disseminate, retain or otherwise use this= message. If received in error, please immediately inform the sender and th= en delete this message without disclosing its contents to anyone.