Re: Accessing concepts for use of Preffered Terms [EXTERNAL]

Hi Thea and Johanne, I have a "easy button" recommendation at the end. Feel free to skip to that if you don't want to look at utility methods and just want to see some example code. > Here we try to access the CollectionMap allConceptsMap, which to our > understanding include all the concep

Re: JDK situation [EXTERNAL]

https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html From: Mullane, Sean *HS Sent: Wednesday, April 14, 2021 3:56 PM To: 'dev@ctakes.apache.org' Subject: JDK situation [EXTERNAL] * External Email - Caution * Since Oracle has change

Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]

Hi John, Just out of curiosity, if you have one method that works then why do you want to use a different method to do the same thing? I personally use the PIpelineBuilder as you have in your second example when I need to work with code - though that is extremely rare as piper files can handle

Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]

ive but correct me if I'm wrong. On Thu, Apr 22, 2021 at 1:58 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi John, > > Just out of curiosity, if you have one method that works then why do you > want to use a different method to do the same thing? > >

Re: svn or github [EXTERNAL]

Hi Javi, I too would like to get more developers and activity with source available on Github. Hopefully you can help us do it. One problem that we had in the past concerning use of Github is caused by large machine learning models in ctakes. Github has file size limits for repositories and

Re: svn or github [EXTERNAL]

Linkedin: es.linkedin.com/in/javiroman Big Data Blog: dataintensive.info On Tue, Apr 27, 2021 at 5:15 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Javi, > > I too would like to get more developers and activity with source available > on Github. Hopefully you

Re: svn or github [EXTERNAL]

and storing the blob in a location external to the git repository itself, in this case hosted by GitHub. This is just an idea. -- Javi Roman Twitter: @javiromanrh GitHub: github.com/javiroman Linkedin: es.linkedin.com/in/javiroman Big Data Blog: dataintensive.info On Tue, Apr 27, 2021 at

Re: rule-based lookup for custom lexicon [EXTERNAL]

To which ctakes component(s) are you referring? From: Greg Silverman Sent: Sunday, May 16, 2021 6:02 PM To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo Subject: rule-based lookup for custom lexicon [EXTERNAL] * External Email - Caution * I looked all

Re: rule-based lookup for custom lexicon [EXTERNAL]

s). When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything wrt to cTAKES specifics. Thanks! Greg-- On Tue, May 18, 2021 at 10:04 AM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > To which ctakes component(s) are you referring? > __

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

vid container: > > > > > https://urldefense.com/v3/__https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container__;!!NZvER7FxgEiBAiR_!7ZopTIhXKalQFx0xET_yET0agN2ZT8JWoa0UyqGSrXa4w-h_9-tRCEeiS4pr6s2Y-T4elV3bYac$ > > Tim > > > > _

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

vantages. I was thinking about creating some introductory examples for the combination and usage of UIMA Ruta and cTAKES. If you have a good use case, let me know. Best, (another) Peter Am 19.05.2021 um 14:30 schrieb Finan, Sean: > Hi all, > Correct. > > Tim is correct in the sens

Re: Java Question [EXTERNAL]

Hi John, >Can you help me with a few questions? - I will try. Others may offer alternate or additional information. > If I wanted to create a modified workflow without the entire source code, > could I create a jar file of the module I wanted to modify and then replace > that jar file in the U

Re: Java Question [EXTERNAL]

Hi John, I sent a reply directly to jrcaskey at medicine.wisc.edu Let me know if you don't get it. Sean

Discussion on Apache UIMA Ruta (Rule-based Text Annotation)

Hi all, I am happy to announce that Peter Klugl, creator of Apache UIMA Ruta, will participate in an informal discussion on Apache's UIMA Rule-based Text Annotator (Ruta). This Apache UIMA(tm) component consists of two major parts: An Analysis Engine, which interprets and executes the rule-b

Re: Discussion on Apache UIMA Ruta (Rule-based Text Annotation) [EXTERNAL]

, "Finan, Sean" wrote: Hi all, I am happy to announce that Peter Klugl, creator of Apache UIMA Ruta, will participate in an informal discussion on Apache's UIMA Rule-based Text Annotator (Ruta). This Apache UIMA(tm) component consists of two major parts: An A

Re: Discussion on Apache UIMA Ruta (Rule-based Text Annotation) [EXTERNAL] [SUSPICIOUS]

Ok, so much for keeping this private ... I should have been more specific about my email address. Michael - this was my fault, not yours. From: Finan, Sean Sent: Wednesday, May 26, 2021 7:59 AM To: dev@ctakes.apache.org Subject: Re: Discussion on Apache

Re: Discussion on Apache UIMA Ruta (Rule-based Text Annotation) [EXTERNAL] [SUSPICIOUS]

Sorry all, I should have said "If you are interested, send directly to my email address." I forgot that Apache automatically routes through the lists. Please send an email to: sean.fi...@tch.harvard.edu thanks, Sean ____ From: Finan, Sean Sent:

Re: Discussion on Apache UIMA Ruta (Rule-based Text Annotation) [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

BTW, I have created a new meeting and the invitation below is defunct. You still need to email me with your info to get an invitation. Sean From: Finan, Sean Sent: Wednesday, May 26, 2021 8:09 AM To: dev@ctakes.apache.org Subject: Re: Discussion on

Re: How to find IdentifiedAnnotationBuilder in build [EXTERNAL]

Hi John, It shouldn't be excluded from ctakes-core, but if you are looking at the binary distributable or maven central artifact for ctakes 4.0.0.1 then it will definitely be absent as it didn't exist in that version. It is only in the trunk version of ctakes currently under development. You

Re: Can you store cTAKES in an S3 bucket so you can use it with EMR for parallel processing? [EXTERNAL]

Hi John, I am not completely sure that I understand what you are asking, and I think that this is more of an s3 question than a ctakes question, but here are a couple of comments: > the cTAKES part of it relies on CTAKES_HOME being set - Is this requirement on your side? I never bother to set

Re: Can you store cTAKES in an S3 bucket so you can use it with EMR for parallel processing? [EXTERNAL]

sure if EFS will be available, which is why I'm trying to see if I can do it on S3. On Mon, Aug 2, 2021 at 11:41 AM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi John, > > I am not completely sure that I understand what you are asking, and I > think that t

Re: UIMA version 3 or later JCas required [EXTERNAL]

Without a little more information I cannot tell you exactly why you are getting that exact error. ctakes 4.0.0.1 was built with UIMA v2. Trying to use a newer version of uima and/or uimafit will (frequently) not work. Any declared dependency on ctakes, such as you have for core and clinical-

Re: An exception occured while executing the Java class. URI is not hierarchical [EXTERNAL]

Hi Benjamin, My first question is: what pipeline are you trying to run? My second question is: Do you really need to use LVG? Sean From: Benjamin hansen Sent: Wednesday, August 18, 2021 3:07 AM To: dev@ctakes.apache.org Subject: An exception occured whil

Re: Question about use of Time Annotators in 4.0.1 (trunk) [EXTERNAL]

Hi Peter, I use the piper files, and temporal sub piper TemporalSubPipe.piper in ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline contains the following: // Commands and parameters to create a default temporal processing sub-pipeline. This is not a full pipeline. //

Re: followup question [EXTERNAL]

Hi Peter, To your question: >there isn't yet much code that pulls these relations out in any user-friendly >way? the answer is mostly no. The relation-related code in ctakes is mostly for experimentation and not utilization. Annotations/Events and Relations are translated in a few places into

Re: followup question [EXTERNAL] [SUSPICIOUS]

e edges. Alternatively you could use Pair as the map key, but more than one relation type between two annotations would cause problems. Or an ugly Map>> in which the pairs are constantly added to the collection ... Sean ________ From: Finan, Sean Sent:

Re: empty preferredText [EXTERNAL]

I think that you are both correct. One or more preferred texts for a concept should be available if the user created a local copy of the umls that contains one a vocabulary that contains a preferred text. This is the first step in the process of creating a ctakes dictionary and takes place bef

Re: empty preferredText [EXTERNAL]

> let's hope for lots of those and good holidays for all. Peter On Tue, Dec 7, 2021 at 7:05 PM Finan, Sean wrote: > I think that you are both correct. > > One or more preferred texts for a concept should be available if the user > created a local copy of the umls that contains

Re: Performance of the cleartk history module [EXTERNAL]

Hi Peter, I have noticed this and just added a following engine that recognized text within event spans. It is a lazy solution, but it fit my needs and available time. Sean From: Peter Abramowitsch Sent: Monday, January 3, 2022 5:03 PM To: dev@ctakes.a

Re: Performance of the cleartk history module [EXTERNAL]

I see you made some source changes in that area and will check tomorrow. Peter On Mon, Jan 3, 2022 at 2:26 PM Finan, Sean wrote: > Hi Peter, > > I have noticed this and just added a following engine that recognized text > within event spans. It is a lazy

Re: Performance of the cleartk history module [EXTERNAL]

Email - Caution * Hi Sean Ok.. I was confused whether I was meant to find it in the sources. But while you're reading this, is there a brief way to describe the difference between the older:package org.apache.ctakes.assertion.medfacts.cleartk; and org.apache.ctakes.assertion.medfacts.cleartk.

Re: Performance of the cleartk history module [EXTERNAL]

so based on the sentence, I could look up and execute > > only the expressions that might match. This might cut the number of regex > > operations down to 5 or 10 and sometimes none at all.There were many > > other changes that related to negation detection, of course

Re: Question for Sean et al? [EXTERNAL]

Hi Peter, The fastest turnaround for you would probably be seen by modifying a local copy. According to this site the source is available: http://mastif.sourceforge.net/ Sean From: Peter Abramowitsch Sent: Thursday, February 10, 2022 2:12 PM To: dev@ct

Re: End of the road for UIMAv2 - please upgrade to UIMAv3 [EXTERNAL]

. Aug 2021, at 22:08, Finan, Sean wrote: > > If you absolutely require uima 3 for some reason then I don't think that I > can help you. You may want to ask the uima lists about mixing versions or > equivalent v2 solutions for your goals. Besides connecting pipes through remote s

Re: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline [EXTERNAL]

Hi Ankit, Did you add CuiListFileWriter to your pipeline? I don't think that it is in the default pipeline. As long as you are running the latest code it should be present. It is in ctakes-core org/apache/ctakes/core/cc/CuiListFileWriter.java It was added to ctakes on 02/14/2018. Sean __

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL]

Hi Richard, you bring up a valid concern. cTAKES Developers: The Apache Foundation has had an initiative to "move" all projects to GitHub for some time now. I don't know much about how this is done. If anybody out there has knowledge or experience that they can pass on, please share. Thank

Re: SmokingStatus & Side effects - piper file [EXTERNAL]

Hi Muhammad, Can you please copy & paste the contents of your piper file? Thanks, Sean From: Muhammad Ali Syed Sent: Thursday, June 2, 2022 2:30 PM To: dev@ctakes.apache.org Subject: SmokingStatus & Side effects - piper file [EXTERNAL] * External Email -

Re: SmokingStatus & Side effects - piper file [EXTERNAL]

: org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt //add SideEffectAnnotator sideEffectTable=sideEffectDic addLast util.log.FinishedLogger On Thu, Jun 2, 2022 at 2:39 PM Finan, Sean wrote: > Hi Muhammad, > > Can you please copy & paste the contents of you

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL]

kgzeq-X2pj1rNwzQNTpZkMZXDoYiZKdJp0n4tDY6q9IcsGRPGrA6KhvmouV_1y_txDVok-tGy3dVLaqefQlQ$ On Thu, Jun 2, 2022 at 5:52 PM Finan, Sean wrote: > Hi Richard, you bring up a valid concern. > > cTAKES Developers: > > The Apache Foundation has had an initiative to "move" all projects to > GitHub for some time now. > > I don't k

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

tion with the large file sizes in our repo. Tim On Thu, 2022-06-02 at 20:55 +, Finan, Sean wrote: * External Email - Caution * Thank you Gandhi and Richard. Unless somebody else beats me to it I will perform some research and see what approaches can be used and which might be best.

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

ling-git-lfs__;Iw!!NZvER7FxgEiBAiR_!rhJYtElNafdN8aZaA2ELRmZRsDeX81m0IVx2yab70SFpsojM4fuIKTHlfGjo-kKfHlz_WjVFM8RgPjuPiEhaTqoWLzBOtKgs$ Needs an LFS-aware host e.g. Bitbucket; I don't know what the Apache hosting setup is like. On Fri, Jun 3, 2022 at 9:31 AM Finan, Sean wrote: > Hi Tim, > > >we ran into issues i

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

s stuck in 2019 [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Hi all, > On 6. Jun 2022, at 16:09, Finan, Sean > wrote: > > Hi Kean, > > Thank you for the suggestion and the link. I am really glad that people are > interested in this guithub topic and taking

Re: Two Questions about OverlapJcasTermAnnotator [EXTERNAL]

Hi Peter, the "blood, urine"... in the example did work when I originally tested, but the default settings (window size, etc.) may have been changed since then. Everything in preftext is simple string literal. It is likely that certain things will not appear in raw text. The UMLS has some int

Re: Best practices for documenting NLP versions [EXTERNAL]

Hi all, This versioning topic had come up at least once before, so I thought that I'd give it a shot before it fell off my radar. I checked in some new stuff and rebuilt the snapshot, so you should be able to use one solution as of now. I couldn't find a great solution for compile-time alone v

Apache cTAKES is now on GitHub !

Hi all, I am pleased to announce that the cTAKES source code is now on GitHub at https://github.com/apache/ctakes [https://opengraph.githubassets.com/fcab5fb05ec83aeb556ec2e939a856d20cfb4d9684aa13253c82cc7370f1c9cd/apache/ctakes] GitHub - apache/ctakes: Apache ct

Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

l be the same as it was during the SVN days with designated contributors? Although I didn't receive any feedback, I might check in some improvements I made to the Negex module and to the ZoneAnnotator. These have been in production for a year now, so I'm pretty sure they're stable. Pe

Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

2022 at 7:49 PM Finan, Sean wrote: > Hi all, > > I am pleased to announce that the cTAKES source code is now on GitHub at > https://urldefense.com/v3/__https://github.com/apache/ctakes__;!!NZvER7FxgEiBAiR_!viVqLaCzQSb4zvpoyBsm2nLGuaXgzH7AX2s7CZsmYFCa1exu0w6KH9QGlTxxKQdsuv2Rgrmw-zT

Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

ore active :) Thanks On Fri, Dec 30, 2022 at 7:49 PM Finan, Sean wrote: > Hi all, > > I am pleased to announce that the cTAKES source code is now on GitHub at > https://urldefense.com/v3/__https://github.com/apache/ctakes__;!!NZvER7FxgEiBAiR_!viVqLaCzQSb4zvpoyBsm2nLGuaXgzH7AX2s

Re: [EXT]Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

r thoughts. On Tue, 3 Jan 2023 at 00:24, Finan, Sean wrote: > Hi all, > > I have poked around a tiny bit on other Apache GitHub repositories. It > looks like many (e.g. spark, Solr) also do not have enabled 'issues' > sections, while others do. In addition, most do not h

Re: [EXT]Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

it also helps to convert discussions to issues and vice versa. Please let us know your thoughts. On Tue, 3 Jan 2023 at 00:24, Finan, Sean wrote: > Hi all, > > I have poked around a tiny bit on other Apache GitHub repositories. It > looks like many (e.g. spark, Solr) also do not ha

Re: CUI Question [EXTERNAL]

Hi John, Each annotation gets a unique concept for every combination of possible codes, semantic types, etc. You have pasted a good example of when that happens: (abbreviated) < code="7092007" tui="T109"/> This is definitely a little confusing when the CUI for all 4 'unique' concepts is th

Re: CUI Question [EXTERNAL]

into is I’m trying to retrieve the file name via File noteFile = new File(ViewUriUtil.getURI(jCas).toString()); But this throws org.apache.uima.cas.CASRuntimeException: No sofaFS with name UriView found Thanks again, John From: Finan, Sean Date: Thursday, February 2, 2023 at 1:53 PM To:

Re: Issuing compiling from the main branch using github [EXTERNAL]

Hi Scott, Thanks for the report - especially the setup, failure message and commit details. Would you mind copying it into the GitHub issues area? https://github.com/apache/ctakes/issues I think that I know what happened ... The pom files for several modules used ${basedir} instead of the pr

Re: Issuing compiling from the main branch using github [EXTERNAL] [SUSPICIOUS]

I just checked in the revert on ctakes-ytex/scripts/data/build.xml Packaging works on my machine, but it had also worked for all previous tests so maybe there is still an issue. Sean From: Finan, Sean Sent: Friday, February 3, 2023 11:09 AM To: dev

Re: Issuing compiling from the main branch using github [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

the web projects, and if they do they usually want one, not both. With proper documentation (coming soon) this should not cause any confusion. Sean ____ From: Finan, Sean Sent: Friday, February 3, 2023 11:24 AM To: dev@ctakes.apache.org Subject: Re: Issuing compilin

Re: Crash course in cTakes [EXTERNAL]

Hi Rick, Thank you for the questions and for reminding us that the documentation is sparse, outdated and not very detailed. Everybody needs a prod now and then to get things done. I hope that we can get a solid README and Wiki going on GitHub, as well as an update to the primary website. It

Re: Crash course in cTakes [EXTERNAL]

to getting this application up and running. Until then, rik. On 2/3/23 15:57, Finan, Sean wrote: > Hi Rick, > > Thank you for the questions and for reminding us that the documentation is > sparse, outdated and not very detailed. Everybody needs a prod now and then > to get things done

Re: Which repo is the repo I should be reaping from? [EXTERNAL]

Gandhi is 100% correct. The github repository contains the latest code for ctakes. The svn repo referenced in the website is a now stale :^(. The svn repo does not contain anything that is not in the github version unless you count bugs. The ctakes.apache.org website downloads page should be

Re: Which repo is the repo I should be reaping from? [EXTERNAL]

vER7FxgEiBAiR_!p3HqewnKUv8GCDZuEyKMrrjHRHexsrkOJIZR1YN7oLB4fb01ZnWu1JYHyjkM6WKEW7g16hTDknGMdO56Loo0nAQWwNhKOzs$ It still assumes you want to use Git *with* Subversion. Thanks again everyone for all of this very helpful information, rik. On 2/7/23 11:19, Finan, Sean wrote: > Gandhi is 100% correct. > > The github repository c

It is Official! Steps toward a cTAKES 5.0 release.

Hi all, The cTAKES Project Management Committee has voted that it is time to officially begin the release process for cTAKES 5.0 It has been almost 6 years since version 4.0.0 was released, and with a worldwide user count estimated in the thousands, a new release will be extremely valuable. R

Re: dev Digest 20 Feb 2023 22:13:01 -0000 Issue 1432 [EXTERNAL]

2023 22:13:01 - Issue 1432 > > Topics (messages 6959 through 6959) > > It is Official! Steps toward a cTAKES 5.0 release. > 6959 by: Finan, Sean > > Administrivia: > > - > To post to the list

Re: It is Official! Steps toward a cTAKES 5.0 release. [EXTERNAL]

To: dev@ctakes.apache.org Subject: Re: It is Official! Steps toward a cTAKES 5.0 release. [EXTERNAL] * External Email - Caution * Hi Sean, I can volunteer for co-RM so that I can work under your guidance. Thanks. On Tue, 21 Feb 2023 at 03:43, Finan, Sean wrote: > Hi all, > > T

Re: It is Official! Steps toward a cTAKES 5.0 release. [EXTERNAL]

ctionality.Is there a comprehensive list? Probably it would be for each author to document their own additions, for accuracy and completeness. I will be doing that for sure. Peter On Wed, Feb 22, 2023 at 7:12 AM Finan, Sean wrote: > Hi Gandhi, > > Thank you very much for volunteering!

Re: It is Official! Steps toward a cTAKES 5.0 release.

here. Many thanks, Sean ________ From: Finan, Sean Sent: Monday, February 20, 2023 5:12 PM To: dev@ctakes.apache.org ; u...@ctakes.apache.org Subject: It is Official! Steps toward a cTAKES 5.0 release. [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi all, The cTAKES Project Management Committee

Re: cTAKES questions [EXTERNAL]

Hi John, Good questions. Unfortunately, I can't really say what is going on as it seems that a lot of the information is in your images - 1000 words and all that. Unfortunately, attachments and inserted images will not go through the dev@ email system. Please copy/paste some plain text in this

cTAKES build change, javac

Hi all, I am trying to make this understandable for all readers, so the statements that follow are simplified or abbreviated without tl/dr context. There have been recent improvements in the Apache build environments that require java 11. Those improvements make the java 8 build environments th

Re: cTAKES build change, javac [EXTERNAL] [SUSPICIOUS]

hackathon with modernization as a goal, please take charge of one and gain the credit! At the very least I will show. :^) Thanks all, Sean From: Finan, Sean Sent: Wednesday, May 17, 2023 10:47 PM To: dev@ctakes.apache.org Subject: cTAKES build change

Re: What's new in 5.0 && testing JDK 11 [EXTERNAL]

Hi Peter, In short (I have to run right now): I am really glad that your employer will give you time to work with ctakes! #1 The jdk 11 build compatibility was a necessity. It turned out that the Apache Jenkins system no longer has a version of maven built with java 8. They seem to also be b

Re: Building 2023AA Snomed RxNorm dictionary fails [EXTERNAL]

Hi Akram, The first thing that I'll mention is that there are a lot of updates to the ctakes Dictionary builder in the unreleased version 5.0, so I am going to talk about its use. https://github.com/apache/ctakes > 1. Combining SNOMED and RxNorm in Dictionary Creation: > I extracted data from

Re: Testing the 5.0 version [EXTERNAL]

Hi Peter, That is great news. I sometime soon I will take a gander at ctakes and see if I can identify areas of importance or concern to me and what I might do to test them. However, don't think of that as being a definitive list. All, please take advantage of Peter's offer and share items th

Re: Testing the 5.0 version [EXTERNAL]

web rest module from traditional spring framework to spring boot framework which can enable the end users to bootstrap the REST API easily and test the same which could improve the overall adoption rate without major complexity. On Thu, 10 Aug 2023 at 20:07, Finan, Sean wrote: > Hi Pe

Re: Starting to look at 5.0 repo and found this... [EXTERNAL]

Hi Pete, Thanks for testing! I haven't seen those compilation errors, but I think that changing the import statements to fit the project structure is the best thing to do. Just out of curiosity, are those imports in any particular module? Thanks, Sean From: Pe

Re: Compilation Errors and the context.tokenizer [EXTERNAL]

Hi guys, There is supposed to be another way to get around this that doesn't require changes to the maven setting.xml I checked in the fix back in January and it looks like the change is still present in the main branch. https://github.com/apache/ctakes/commit/ec37c5948a0abc6dcd278077911db2a651

Re: Compilation Errors and the context.tokenizer [EXTERNAL]

As for slf4j being on http:, I don't know that I ever saw that. If you check maven central it is actually https: https://repo1.maven.org/maven2/org/slf4j/ As referred to here: https://mvnrepository.com/artifact/org.slf4j/slf4j-api/2.0.5 I will do some more research on this tonight, though I we

Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL]

Hi Peter, My thoughts on this: > a newer version of Mastif than Ctakes is packaged with, and additional > modifications that I've made - Are you saying that you made a local/custom version of mastif that builds upon their latest (1.6?) version? Or do you just need to update the ctakes depende

Re: PREFTERMs not included in UMLS rare-word dictionary? [EXTERNAL]

Hi Kean, I can't think of a good reason for preferred text to not also be a lookup text. It sounds like you might have uncovered a flaw in the dictionary creator tool. Time for a rebuild with the 5.0 release ... Thanks for the report, Sean From: Kean Kaufmann

Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

much easier to do things like this in branches and only merge when it’s actually finished!) Thanks Tim From: Finan, Sean Date: Tuesday, December 5, 2023 at 10:59 AM To: dev@ctakes.apache.org Subject: Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL] [SUSPICIOUS] * External

Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

* To some extent I think (and hope!) it will be superseded by the PBJ code that will be in cTAKES 5.0.0 anyways. Tim From: Finan, Sean Date: Wednesday, December 20, 2023 at 3:43 PM To: dev@ctakes.apache.org Subject: Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL

Re: Build issues today [EXTERNAL]

Thank you for the heads-up. From: Jeffery Painter Sent: Tuesday, January 23, 2024 11:55 AM To: dev@ctakes.apache.org Subject: Build issues today [EXTERNAL] * External Email - Caution * Just a heads up, getting several build issues due to the fact that the 5.0.0

Re: Build issues today [EXTERNAL]

BAiR_!rLnzw0dsZI7qw5aqEdEC-KT8vlgYdrqKbYivutEU69f7S85vYrWwI1c3zq9t2IjAyDW-iO4YIewdSUyYJ6tZsaHpTg$ I am computing some large similarity matrices with the updated code today, and so far so good! Thanks, Jeff On 1/23/24 16:17, Finan, Sean wrote: > Thank you for the

Re: Build issues today [EXTERNAL]

today [EXTERNAL] * External Email - Caution * HI Sean, This seems to be the same issue which I discussed with you and Peter sometime last month that the fresh build and install is broken with version 5.0.0. It needs some tweaking to make it work. On Wed, 24 Jan 2024 at 02:47, Finan, Sean wrote: >

Re: Build issues today [EXTERNAL]

download it? On Wednesday, 24 January 2024 at 12:00:07 pm GMT-5, Finan, Sean wrote: Hi Gandhi, Jeff's problem is related to something that avoids the problem that you saw. You can get rid of your error if you switch the models to 5.0.0 instead of 5.0.0-SNAPSHOT (or 5.0.1-SNA

Re: Build issues today [EXTERNAL]

Hi Jeff, I updated the poms in 5.0.0-SNAPSHOT to use the correct models. There shouldn't be any problem building. Sean From: Jeffery Painter Sent: Tuesday, January 23, 2024 11:55 AM To: dev@ctakes.apache.org Subject: Build issues today [EXTERNAL] * External E

Re: Build issues today [EXTERNAL]

- is there a preferred way to reference cTakes in publications? - Jeffery On 1/26/24 12:29, Finan, Sean wrote: > Hi Jeff, > > I updated the poms in 5.0.0-SNAPSHOT to use the correct models. There > shouldn't be any problem building. > > Sean > __

Re: Build issues today [EXTERNAL]

to be working. I will cancel those PR's and update later today. Thanks, Jeff On 1/26/24 15:30, Finan, Sean wrote: > This is open for other responses, but I would probably use: > > > Savova, G. K. et al. Mayo clinical Text Analysis and Knowledge Extraction > System (cTAKES)

Re: Build issues today [EXTERNAL]

o setup and use) :-) - Jeff On 1/30/24 10:59, Finan, Sean wrote: > Hi Jeff, > > This looks pretty nice. Thank you for the reference - I gave it a skim but > will be more thorough in a second run through whenever I get the time. > > Sean >

Re: Custom dictionary no-"no" [was: Re: PREFTERMs not included in UMLS rare-word dictionary?] [EXTERNAL]

", "normal pressure glaucoma", ... Is this filtering expected? Is there a way for the user to control it? Thanks as always, Kean On Wed, Dec 6, 2023 at 5:22 PM Finan, Sean wrote: > Hi Kean, > > I can't think of a good reason for preferred text to not also be

Please test the Apache cTAKES 5.1.0 release candidate

Hi all, There is a candidate for version 5.1.0 of Apache cTAKES source code in a staging repository: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ The code is contained within the file: ctakes-5.1.0-source-release.zip

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

in its projecte, but it's not scooped up into the distribution. > I'm not sure where else to look.Can you fix it? > > Peter > > > On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean > wrote: > >> Hi all, >> >> There is a candidate for version 5

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > Java > > returned: 1 > > [ERROR] around Ant part ... > target="test.setup">... @ 5:70 in > > C:\Gandhi\Project\ctakes-5.1.0\ctak

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: >> > The >> > > fol

Fw: Please test the Apache cTAKES 5.1.0 release candidate

module jars to exist where they can be fetched, and as ctakes 5.1.0 will not be available through maven central before a release, the jars must be in your .m2 directory. From: Finan, Sean Sent: Friday, April 26, 2024 11:58 AM To: dev@ctakes.apache.org Subject

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

> a > > > >> > temporary mysqldb that is used to test that part of ytex. For me > > it > > > is > > > >> > working, but if you can find a way to run that surefire test in > the > > > >> > debugger, you can find

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

the master pom, and in the pom of ctakes-distribution, and the jar got built in its projecte, but it's not scooped up into the distribution. I'm not sure where else to look.Can you fix it? Peter On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean wrote: > Hi all, > > There is a can

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

.m2 folder you mean? Infact I was trying to build them on a machine which doesnt have any historic jars in the .m2 folder and thats why it was failing. And ytex issue still remains a mystery to me. If you have some time this week, we can connect to understand what exactly is the problem. On Thu, 2 Ma

Re: Mastif Zoner is there now [EXTERNAL]

Hi Peter, I am glad that mastif is now in the distrobution. Yes, testing the pre-release is a little rough, but once released everything is streamlined and -easy-. After the release there shouldn't be any of the funny business of cleaning, grabbing a tag, installing local jars, etc. Thanks a

Re: Remaining Maven errors visible in Eclipse [EXTERNAL]

Hi Peter, Thanks again for testing. I didn't have a problem with that ctakes.version in ytex-web, but I stuck a definition of it in just in case. It does the same thing as using parent.version, but just in case we ever change the parent I went with a definition of ctakes.version in the ytex-

Re: Resending without attachments., [EXTERNAL]

Hi all, I don't think that I have any of the original communications, but just picking up here: * From your dump, it looks as if the main concept dictionary is missing. If you just need the standard dictionary, you can use the information on this ctakes wiki page: https://github.com/apach

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean inst

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

se tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi,

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