Return-Path: X-Original-To: apmail-ctakes-dev-archive@www.apache.org Delivered-To: apmail-ctakes-dev-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 0395E18994 for ; Sat, 19 Sep 2015 12:00:48 +0000 (UTC) Received: (qmail 79077 invoked by uid 500); 19 Sep 2015 12:00:47 -0000 Delivered-To: apmail-ctakes-dev-archive@ctakes.apache.org Received: (qmail 79025 invoked by uid 500); 19 Sep 2015 12:00:47 -0000 Mailing-List: contact dev-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 dev@ctakes.apache.org Received: (qmail 79014 invoked by uid 99); 19 Sep 2015 12:00:47 -0000 Received: from Unknown (HELO spamd2-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 19 Sep 2015 12:00:47 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd2-us-west.apache.org (ASF Mail Server at spamd2-us-west.apache.org) with ESMTP id 254D61A2713 for ; Sat, 19 Sep 2015 12:00:47 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd2-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 4.001 X-Spam-Level: **** X-Spam-Status: No, score=4.001 tagged_above=-999 required=6.31 tests=[HTML_MESSAGE=3, KAM_LAZY_DOMAIN_SECURITY=1, URIBL_BLOCKED=0.001] autolearn=disabled Received: from mx1-eu-west.apache.org ([10.40.0.8]) by localhost (spamd2-us-west.apache.org [10.40.0.9]) (amavisd-new, port 10024) with ESMTP id I4q6RRKPha9m for ; Sat, 19 Sep 2015 12:00:34 +0000 (UTC) Received: from mail-qg0-f47.google.com (mail-qg0-f47.google.com [209.85.192.47]) by mx1-eu-west.apache.org (ASF Mail Server at mx1-eu-west.apache.org) with ESMTPS id A89852074B for ; Sat, 19 Sep 2015 12:00:33 +0000 (UTC) Received: by qgez77 with SMTP id z77so58414190qge.1 for ; Sat, 19 Sep 2015 05:00:32 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:content-type:mime-version:subject:from :in-reply-to:date:message-id:references:to; bh=HF4QNRM+K5t/dNyiI7Gn4GQNDKtWJc5XxzGkiGekFvI=; b=coyruZKwW6JlPTSOLOMAHPHlfuUb6nSAQRjVb34HB/nCifVxwJB1XgcnUEoZxaKa5b qH97w7i5UUBudcb2U7xnNk2cQq54+gnZwRRSyo67ufDQ9YVdMf9w52ZFAZNcJFQ8/SPP 5Ny1WhEURZIiZgYctWGbW5kL/8znh+L3sHGs+2pmCXenSN710bzz0c55Ed5IaL/BhLeU 4Y/r5tkKCiXafc2H1pCniVQKsroMFgbLO2iFbrUtQbkvZM1zXMQEAGnrizhVfqxObAHP qfR/rsoAfQ22JkOKPKA0Ni8YqW7tFBgM49+oR/GMe1NjqVtgUSKpY+noQXuwdDEVQh3y C8YQ== X-Gm-Message-State: ALoCoQkwP3bOnbVhRik9CqAKISoVXFVbDblAfyArcHCKh6nML3im2iFHSUBwe7b2gtoHEgvFuklF X-Received: by 10.140.238.214 with SMTP id j205mr12501435qhc.21.1442664032671; Sat, 19 Sep 2015 05:00:32 -0700 (PDT) Received: from [192.168.0.71] ([73.4.31.207]) by smtp.gmail.com with ESMTPSA id 203sm1630717qht.21.2015.09.19.05.00.31 (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); Sat, 19 Sep 2015 05:00:32 -0700 (PDT) Content-Type: multipart/signed; boundary="Apple-Mail=_00B2FFB1-B22E-48F4-81C6-BF181E3DB09A"; protocol="application/pgp-signature"; micalg=pgp-sha512 Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2102\)) Subject: Re: Creating a new annotator X-Pgp-Agent: GPGMail 2.5.1 From: britt fitch In-Reply-To: Date: Sat, 19 Sep 2015 08:00:30 -0400 Message-Id: <2D4C444A-8AF1-4A14-974A-BABE966B6198@wiredinformatics.com> References: To: "dev@ctakes.apache.org" , cbaechle@my.fau.edu X-Mailer: Apple Mail (2.2102) --Apple-Mail=_00B2FFB1-B22E-48F4-81C6-BF181E3DB09A Content-Type: multipart/alternative; boundary="Apple-Mail=_7BE96D79-7023-4186-8EE5-7440868E6BC8" --Apple-Mail=_7BE96D79-7023-4186-8EE5-7440868E6BC8 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Did you declare the new Age type in TypeSystem.xml? You may want to extend one of the existing types like EntityMention or = IdentifiedAnnotation. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com Britt.Fitch@wiredinformatics.com > On Sep 18, 2015, at 11:46 PM, Christopher Baechle = wrote: >=20 > I created a new annotator for finding socio-demographic information > from a clinical note. It works within eclipse, but fails when I run it > from the packaged distribution created from mvn install. >=20 > Caused by: org.apache.uima.cas.CASRuntimeException: JCas type > "org.apache.ctakes.sociodemo.Age" used in Java code, but was not > declared in the XML type descriptor. >=20 > Age is an Annotation. I didn't follow the normal convention of adding > it to org.apache.ctakes.typesystem and put it in my package > org.apache.ctakes.sociodemo. >=20 > I added my descriptor xml file to > AggregatePlaintextFastUMLSProcessor.xml. I think it might be a > classpath issue (the jvm unable to find my descriptor file). I added > the full absolute path to runctakesCVD.sh but it still persists. >=20 > Any suggestions? --Apple-Mail=_7BE96D79-7023-4186-8EE5-7440868E6BC8 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Did you declare the new Age type in TypeSystem.xml? 
You may want to extend one of the existing types like = EntityMention or IdentifiedAnnotation.

Cheers,

Britt

 
   
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com

On Sep 18, 2015, at 11:46 PM, Christopher Baechle <cbaechle@my.fau.edu>= wrote:

I = created a new annotator for finding socio-demographic information
from a clinical note. It works within eclipse, but fails when = I run it
from the packaged distribution created from mvn = install.

Caused by: = org.apache.uima.cas.CASRuntimeException: JCas type
"org.apache.ctakes.sociodemo.Age" used in Java code, =  but was not
declared in the XML type descriptor.

Age is an Annotation. I didn't follow the = normal convention of adding
it to = org.apache.ctakes.typesystem and put it in my package
org.apache.ctakes.sociodemo.

I = added my descriptor xml file to
AggregatePlaintextFastUMLSProcessor.xml. I think it might be = a
classpath issue (the jvm unable to find my descriptor = file). I added
the full absolute path to runctakesCVD.sh = but it still persists.

Any suggestions?

= --Apple-Mail=_7BE96D79-7023-4186-8EE5-7440868E6BC8-- --Apple-Mail=_00B2FFB1-B22E-48F4-81C6-BF181E3DB09A Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- Comment: GPGTools - https://gpgtools.org iQEcBAEBCgAGBQJV/U5eAAoJEN9mP6PnnMib3O4H/Re6jLYak6GvNoJKzvl3AeFJ A/onjhknm4kjP630vpOkgnAK7ngQsUsevKST3NNJbVP0igg6rcvHtGHcLk4NvtmY ceHHTZlgQXR8HNdlyM0xFow7t67ZQDgFsh5C267tIUD8r/I8CL8gMLafAT2pWegH Aq4dZmi8FLySp3xzAyJrT6sshcrM4PCKUfoVAJlTze+unSUbxA9moipRh5uLgLqc EgvtxbdWqpSisBELzjzgNzkTa/ILdXaA5LVYS+RXNov8KMISzkp+FyhoHVH8MPxx bVOVJwTEX0IPseOCGwwKGyJ2QNoBMUzoQieo58j27359P653tyzGxQdmRgFVobo= =ozmA -----END PGP SIGNATURE----- --Apple-Mail=_00B2FFB1-B22E-48F4-81C6-BF181E3DB09A--