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 A021A1843B for ; Wed, 10 Jun 2015 18:20:45 +0000 (UTC) Received: (qmail 76139 invoked by uid 500); 10 Jun 2015 18:20:45 -0000 Delivered-To: apmail-ctakes-dev-archive@ctakes.apache.org Received: (qmail 76086 invoked by uid 500); 10 Jun 2015 18:20:45 -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 Delivered-To: moderator for dev@ctakes.apache.org Received: (qmail 60037 invoked by uid 99); 10 Jun 2015 18:15:29 -0000 X-Virus-Scanned: Debian amavisd-new at spamd3-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 2.89 X-Spam-Level: ** X-Spam-Status: No, score=2.89 tagged_above=-999 required=6.31 tests=[DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, HTML_MESSAGE=3, SPF_PASS=-0.001, T_RP_MATCHES_RCVD=-0.01, URIBL_BLOCKED=0.001] autolearn=disabled Authentication-Results: spamd3-us-west.apache.org (amavisd-new); dkim=pass (1024-bit key) header.d=ucsd.edu DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=ucsd.edu; i=@ucsd.edu; q=dns/txt; s=041709-iport; t=1433960116; x=1465496116; h=reply-to:from:to:references:in-reply-to:subject:date: message-id:mime-version; bh=PATDuOTkFiHCYqmZFrUtBf8I19rjIB/t1+SV/kzlTZQ=; b=NacMhh6jcGXKf4RakbXvvXncWaLf5fbXAO+nkRCDGLDukRJk6s/4IcSX S4rL8g5b/ISU91AUG2EKgNbYTgzv/1/CBXUqpvzDiIy7iPe3Wg4PCziXD hsFSnzGADV7gCVPptZ+LAVFbyF2ucunrAlZyV2jcEmnaOWu2+uzA360Yo E=; X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: A2CcBADFfXhV/1EA74RcDoI3S1Rfgx66bQmBPhkBCIUxSgKBOjgUAQEBAQEBAYEKhCIBAQEBAwgCGQUFWQMCCREEAQEoAwICGS0JCAIEARILBYgeDa1whlSYUwGEeAEBAQEBAQEBAQEBAQEBAQEBAQEBARMEi0OFAgoBgi07EoEzBYtxbYQdgk+CHIFJYYZwgTCScINbJGJ8gVxeTwEBgkUBAQE X-IPAS-Result: A2CcBADFfXhV/1EA74RcDoI3S1Rfgx66bQmBPhkBCIUxSgKBOjgUAQEBAQEBAYEKhCIBAQEBAwgCGQUFWQMCCREEAQEoAwICGS0JCAIEARILBYgeDa1whlSYUwGEeAEBAQEBAQEBAQEBAQEBAQEBAQEBARMEi0OFAgoBgi07EoEzBYtxbYQdgk+CHIFJYYZwgTCScINbJGJ8gVxeTwEBgkUBAQE X-IronPort-AV: E=Sophos;i="5.13,588,1427785200"; d="out'?scan'208,217";a="366684065" Reply-To: From: "Tsung-Ting Kuo" To: "'Vijay Garla'" , References: <000601d0a302$0fc33da0$2f49b8e0$@ucsd.edu> <002801d0a39d$6682b760$33882620$@ucsd.edu> In-Reply-To: <002801d0a39d$6682b760$33882620$@ucsd.edu> Subject: RE: Question about YTEX Date: Wed, 10 Jun 2015 11:15:06 -0700 Organization: UCSD Message-ID: <003201d0a3a9$61254f60$236fee20$@ucsd.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0033_01D0A36E.B4CD7C40" X-Mailer: Microsoft Outlook 15.0 Thread-Index: AQFiaunqEegG+lHMH/Merg9/BuN/sQGLqkfnAaQPadqeaP6asA== Content-Language: en-us ------=_NextPart_000_0033_01D0A36E.B4CD7C40 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0034_01D0A36E.B4CD7C40" ------=_NextPart_001_0034_01D0A36E.B4CD7C40 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable BTW, my YTEX installation just completed, and the results is attached. = Does my YTEX installation create dictionary lookup table with all = concepts from the UMLS successfully? =20 Thanks very much! =20 Best regards, Tim =20 From: Tsung-Ting Kuo [mailto:tskuo@ucsd.edu]=20 Sent: Wednesday, June 10, 2015 9:49 AM To: 'Vijay Garla'; dev@ctakes.apache.org Subject: RE: Question about YTEX =20 Hi Vijay, =20 You are absolutely right =E2=80=93 after changing the permission of the = =E2=80=9Cresource=E2=80=9D directory, YTEX start installing without = problem! In the meanwhile, I have a quick question: since I have = installed the UMLS database and set the =E2=80=9Cumls.schema=E2=80=9D to = UMLS database name (I am using MySQL), how do I know whether YTEX = successfully creates a dictionary lookup table with all concepts from = the UMLS or not? =20 Thanks again! =20 Best regards, Tim =20 From: Vijay Garla [mailto:vijay.garla@yale.edu]=20 Sent: Tuesday, June 9, 2015 11:31 PM To: tskuo@ucsd.edu ; dev@ctakes.apache.org = =20 Cc: vijay.garla@yale.edu =20 Subject: Re: Question about YTEX =20 Hi Tsung-Ting, =20 I see the following error: =20 templateToConfig.extractTemplates: [echo] unpacking ytex templates from = /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar to = /usr/local/apache-ctakes-3.2.2/resources [unzip] Expanding: = /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar into = /usr/local/apache-ctakes-3.2.2/resources [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-rxnorm.template.xml [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-msh-csp-aod.template.xml [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-umls.template.xml [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/umls/mode= l/UMLS.hbm.template.xml [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionar= y/lookup/LookupDesc_stem_SNOMED.template.xml [unzip] Unable to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionar= y/lookup/LookupDesc_SNOMED.template.xml =20 I don't know why there was an issue extracting = ctakes-ytex-res-3.2.2.jar. Can you make sure that = /usr/local/apache-ctakes-3.2.2/resources exists and is writable? =20 -vj =20 On Wed, Jun 10, 2015 at 12:17 AM, Tsung-Ting Kuo > wrote: Hi Vijay Garla, =20 I am Tsung-Ting Kuo from UCSD, and I am interested in your YTEX project. = I tried to download it and setup based on the following page: =20 https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation = =20 =20 However, in the final step (step 7), I was not able to setup. The = attached =E2=80=9Csetup.out=E2=80=9D seems to show that the = =E2=80=9CUMLS.hbm.xml=E2=80=9D is missing. Could you kindly help to tell = me how to set it up? =20 Thanks very much! =20 Best regards, Tsung-Ting =20 =20 ------=_NextPart_001_0034_01D0A36E.B4CD7C40 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

BTW, my YTEX = installation just completed, and the results is attached. Does my YTEX = installation create dictionary = lookup table with all concepts from the UMLS = successfully?

 

Thanks very = much!

 

Best = regards,

Tim

 

From:<= /b> Tsung-Ting = Kuo [mailto:tskuo@ucsd.edu]
Sent: Wednesday, June 10, 2015 = 9:49 AM
To: 'Vijay Garla'; = dev@ctakes.apache.org
Subject: RE: Question about = YTEX

 

Hi = Vijay,

 

You are = absolutely right =E2=80=93 after changing the permission of the = =E2=80=9Cresource=E2=80=9D directory, YTEX start installing without = problem! In the meanwhile, I have a quick question: since I have = installed the UMLS database and set the =E2=80=9Cumls.schema=E2=80=9D to = UMLS database name (I am using MySQL), how do I know whether YTEX = successfully creates a dictionary lookup table with all concepts from = the UMLS or not?

 

Thanks = again!

 

Best = regards,

Tim

 

From:<= /b> Vijay Garla = [mailto:vijay.garla@yale.edu] =
Sent: Tuesday, June 9, 2015 11:31 PM
To: tskuo@ucsd.edu; dev@ctakes.apache.org
Cc:= vijay.garla@yale.edu
Subje= ct: Re: Question about YTEX

 

Hi = Tsung-Ting,

 

I see the following = error:

 

templateToConfig.extractTemplates:

    =  [echo] unpacking ytex templates from = /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar to = /usr/local/apache-ctakes-3.2.2/resources

=

    [unzip] Expanding: = /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar into = /usr/local/apache-ctakes-3.2.2/resources

=

    [unzip] Unable to = expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-rxnorm.template.xml

    [unzip] Unable to = expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-msh-csp-aod.template.xml

    [unzip] Unable to = expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGr= aph/sct-umls.template.xml

    [unzip] Unable to = expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/umls/mode= l/UMLS.hbm.template.xml

    [unzip] Unable to = expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionar= y/lookup/LookupDesc_stem_SNOMED.template.xml

<= div>

    [unzip] Unable = to expand to file = /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionar= y/lookup/LookupDesc_SNOMED.template.xml

<= p class=3DMsoNormal> 

I don't know why there was an issue = extracting ctakes-ytex-res-3.2.2.jar.  Can you make sure that =  /usr/local/apache-ctakes-3.2.2/resources exists and is = writable?

 

-vj

 

On Wed, Jun 10, 2015 at 12:17 AM, = Tsung-Ting Kuo <tskuo@ucsd.edu> = wrote:

Hi Vijay Garla,

 

I am Tsung-Ting Kuo from UCSD, and I am interested in your = YTEX project. I tried to download it and setup based on the following = page:

 

https://cwiki.apache.org/confluence/display/CTAKES/YTEX= +Installation

 

However, in the final step (step 7), I was not able to = setup. The attached =E2=80=9Csetup.out=E2=80=9D seems to show = that the =E2=80=9CUMLS.hbm.xml=E2=80=9D is missing. = Could you kindly help to tell me how to set it = up?

 

Thanks very much!

 

Best regards,

Tsung-Ting

 

<= p class=3DMsoNormal> 

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