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,

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

- Caution * Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org Subject: Re

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

ple - Token:Hello POS:NNP 15 May 2024 14:44:26 INFO ConfigParameterExample - Token:World POS:NNP Entity: Hello === Polarity: 0 Entity: World === Polarity: 0 Process finished with exit code 0 On Wed, May 1, 2024 at 3:55 PM Finan, Sean wrote: > Hi all, > > As you may have seen, the

Apache cTAKES 5.1.0 has been released

Hi all, I am pleased to announce that cTAKES 5.1.0 has been officially released. Zip files containing the source code and a binary build are in the Release area on our GitHub site: https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 cTAKES 5.1.0 jars are also accessible for maven depende

Re: Upgrade to JDK 17 Inquiry [EXTERNAL]

Hi Ryan, I have recently been working on upgrades to ctakes focused around vulnerability mitigation, so your question is very timely. The current version in the github master branch https://github.com/apache/ctakes , 6.0.0-SNAPSHOT, should build and run with java 17. I don't know of any plans

Re: [EXTERNAL] Upgrade to JDK 17 Inquiry

Hi John, Would you be able to share some of the changes that you needed to make for 21? Thanks, Sean From: Petersam, John Contractor Sent: Wednesday, July 3, 2024 3:45 PM To: dev@ctakes.apache.org Subject: RE: [EXTERNAL] Upgrade to JDK 17 Inquiry * External Ema

Re: [EXTERNAL] Upgrade to JDK 17 Inquiry

----Original Message- From: Finan, Sean Sent: Wednesday, July 03, 2024 3:57 PM To: dev@ctakes.apache.org Subject: Re: [EXTERNAL] Upgrade to JDK 17 Inquiry Hi John, Would you be able to share some of the changes that you needed to make for 21? Thanks, Sean F

Apache cTAKES, java jdk 17 and UIMA 3

Hi all, The ctakes version 6.0.0-SNAPSHOT in the main GitHub branch https://github.com/apache/ctakes has been upgraded to be compatible with java 17 and Uima 3. Please test your favorite workflows and let me know if you have any problems. I would like to get an -update- release out soon. This

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

Hi Richard, I have thought of that, and almost did as much. I think that main pom still has a bunch of slf4j dependencies commented out from my time in the sandbox. There are only some very minor reasons that I didn't, one being the ease of the transition. I have nothing against slf4j, and u

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

dress some of the mediums, > and now only have the subset of vulnerabilities left - 381. > > In the meantime, I am copying runnable jars & working scripts setting the > classpaths from other envs, to our dev env to get runnable code, and triage > the differences between our envs

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

Stated more succinctly than my babble! From: Richard Eckart de Castilho Sent: Friday, July 26, 2024 12:06 PM To: dev@ctakes.apache.org Subject: Re: SLF4J instead of Log4J at the API level? [EXTERNAL] * External Email - Caution * Hi, > On 26. Jul 2024, at 12:42

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

Hi Richard, Many, many thanks for doing this. I gave it a pass and don't see anything that looks like it might cause a problem. I will run some tests. My comments on your comments: - The lifecycle plugin in the root POM uses "version" instead of "versionRange" in the main branch - the PR fi

Re: Build cTAKES using GitHub action? [EXTERNAL]

> Btw. how about setting up a GitHub action for building cTAKES? I thought about that when we switched over from svn. I didn't do it myself because I am happy with Jenkins. It also seems like quite the beast to romp around in a GH action. I suppose that we could have build profiles that only

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

4J at the API level? [EXTERNAL] * External Email - Caution * Hi, > On 29. Jul 2024, at 12:02, Finan, Sean > wrote: > > - The main branch still uses ContextSingletonBeanFactoryLocator which is not > part of Spring anymore and thus the Eclipse has compiler errors > -- ​I can look for a

Re: Build cTAKES using GitHub action? [EXTERNAL]

GitHub action? [EXTERNAL] * External Email - Caution * > On 29. Jul 2024, at 12:14, Finan, Sean > wrote: > >> Btw. how about setting up a GitHub action for building cTAKES? > > I thought about that when we switched over from svn. I didn't do it myself > because I

Re: Error running Apache cTakes Pipeline [EXTERNAL]

Hi Ryan, As far as I know, none of the [xyz] code that you are referencing comes from ctakes. You probably need to find out where that code came from - hopefully your organization has a good relationship with the previous developer or there is a user in your organization who is familiar with t

Re: Error running Apache cTakes Pipeline [EXTERNAL]

ssing details that I will need to figure out, to ensure we can build new code, and then run this code. Yes - this xyzApp is a proprietary code module we wrote, and it is dependent on the other underlying out of the box cTake modules. Thanks, Ryan -Original Message----- From: Finan, Sean Sent

Re: [I] Exception: org.apache.uima.jcas.tcas.Annotation was not declared in the XML type descriptor (ctakes-ytex-uima) [ctakes] [EXTERNAL]

Hi Ravi, If you wish to unsubscribe, please send a message to dev-unsubscr...@ctakes.apache.org as outlined here: https://www.apache.org/foundation/mailinglists#request-addresses-for-unsubscribing Sean From: Ravi Tejwani Sent: Thursday, August 22, 2024 3:49 PM

Please test the cTAKES-6.0.0 candidate for release

Hi all, There is a candidate for version 6.0.0 of Apache cTAKES source code in a staging repository: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/6.0.0/ The code is contained within the file: ctakes-6.0.0-source-release.zip

Re: Please test the cTAKES-6.0.0 candidate for release

elease.zip Sean ____ From: Finan, Sean Sent: Tuesday, August 27, 2024 6:12 PM To: dev@ctakes.apache.org ; u...@ctakes.apache.org Subject: Please test the cTAKES-6.0.0 candidate for release Hi all, There is a candidate for version 6.0.0 of Apache cTAKES source code in

Fw: Please test the cTAKES-6.0.0 candidate for release

From: Finan, Sean Sent: Tuesday, August 27, 2024 6:12 PM To: dev@ctakes.apache.org ; u...@ctakes.apache.org Subject: Please test the cTAKES-6.0.0 candidate for release Hi all, There is a candidate for version 6.0.0 of Apache cTAKES source code in a staging repository: https

RE: cTAKES Dependency Parser / SRL updates

Excellent news, Thanks Pei (and Jinho) -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, April 05, 2013 1:04 PM To: dev@ctakes.apache.org Subject: RE: cTAKES Dependency Parser / SRL updates Thanks. This has been done in trunk now since r. 1465043

RE: files vs strings in collection reader

I don't think that File instantiation is more slow than the ae process, and Tim is talking about tens of thousands of files in the directory tree. The only filesystem call that should exist in any new File(..) is a normalize(..) or resolve(..) on the passed parameter(s), which should just be

RE: best practices

+1 for BP -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, June 14, 2013 2:59 PM To: dev@ctakes.apache.org Subject: RE: best practices +1 for a BP reference page. Note: I'll try and update the other projects for consistency's sake next week or so.

RE: to involve in your development group

Hi Sandeep, I just took a peek at the JavaOcr code, and it looks like they perform image filtering in the PixelImage class. This would probably cause a problem with dot matrix images as every corner of every dot would be removed as "noise", so dots that participate in curves on characters such

RE: dictionary questions

Hi Chase, I just ran a search in the bundled UMLS dictionary and the full term and cui does existfrom SnomedCT and NCI, with tui T007. The Dictionary Lookup that you are using filters out terms that don't have tui codes registered in the resources/org/apache/ctakes/dictionary/lookup/LookupDesc

RE: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor

This may sound strange, but SNOMED does not contain the term "CIN I". It contains the terms "CIN I - Cervical intraepitheal neoplasia 1" and "CIN I - mild dyskaryosis". -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, September 03, 2013 10:13 PM To: dev@ct

RE: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor

I don't know if this is exactly what you want, but you can use the hyperSql ( http://hsqldb.org/ ) database tool to perform searches on the umls dictionary used by cTakes. For instance " select * from UMLS_MS_2011AB where FWORD = 'CIN' " will provide all the available terms starting with CIN.

RE: cTAKES user interface

:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 9:52 AM To: dev@ctakes.apache.org Cc: Finan, Sean Subject: RE: cTAKES user interface Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy

RE: cTAKES user interface

mc.org 513-803-9032 -Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:15 AM To: Lingren, Todd; dev@ctakes.apache.org Subject: RE: cTAKES user interface > Sean Finan (I think is on this group) already wrote a command li

RE: cTAKES user interface

last hour. -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:20 AM To: Lingren, Todd; dev@ctakes.apache.org Subject: RE: cTAKES user interface > Sean Finan (I think is on this group) already wrote a command line CP

RE: Sundry; Problem Lists

I don't know if what I write below truly applies to the discussion, but here it is. >much of a problem list definition may already be contained to varying degrees > in existing cTakes databases. The UMLS does provide a problem list, but I haven't looked at it. http://www.nlm.nih.gov/research/umls

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