source for .jar's in resources folder

Hi, Is there any documentation about how the following resources (*.jar) are generated or come from: ./ctakes-temporal-res/src/main/resources/org/apache/ ctakes/temporal/ae/eventevent/model.jar ./ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/ contextualmodality/model.jar

Re: source for .jar's in resources folder [EXTERNAL]

takes, distributed > with and for it. They are machine learning models that have been developed > using expertly-written gold annotations on clinical documents. They are > updated with version releases just like code. > > Does that answer your question? > > > -----Original Message

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

will make the tests pass (having also UMLS credentials). Alex [1] - https://issues.apache.org/jira/browse/CTAKES-464 [2] - https://issues.apache.org/jira/browse/CTAKES-334 On Wed, Oct 4, 2017 at 8:15 AM, Alexandru Zbarcea <al...@apache.org> wrote: > Thanks Tim, > > I will let

Re: building cTAKES (discussion transferred from CTAKES-445

e official Jenkins would have to be a reference for the UMLS credentials. What do you think? Alex On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org> wrote: > Hi James, > > I have been working on stabilizing the build for 4.0.0, and I discovered > the followi

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

easons. > Since it's so related to the coref stuff I thought it should go > alongside the coreference module. But maybe it makes more sense as an > external project since it can't really function without externally > created resources -- what do you think? > Tim > > > On Su

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

ch I believe are the fake notes Dr. John Green wrote for us. I don't > know why they are rtf but they are nice, non-toy-length notes. > Tim > > ________ > From: Alexandru Zbarcea <al...@apache.org> > Sent: Tuesday, October 3, 2017 5:32 PM &

Re: building cTAKES (discussion transferred from CTAKES-445

Hi James, I have been working on stabilizing the build for 4.0.0, and I discovered the following: * CTAKES-445 (commited) * CTAKES-334 (patch provided - NOT committed by the community, but ready, tested) * UMLS credential UTest (work-in-progress) Exporting the ctakes_umlsuser, ctakes_umlspw

WSDL for isValidUMLSUser service

Does anybody has access to the WSDLs from: https://uts-ws.nlm.nih.gov/services/nwsSemanticNetwork I see that isValidUMLSUser service from https://uts-ws.nlm.nih.gov/ services/nwsSemanticNetwork is used without a stub being generated.

consistently usage of properties to manage dependency versions

Hi, I have reported another issue and provided patch: https://issues.apache.org/jira/browse/CTAKES-457 I hope it helps the release process and dependency management, making the project more consistent. Regards, Alexz diff --git ctakes-assertion/pom.xml ctakes-assertion/pom.xml index

Password shown in clear in logs

Hi, While trying to setup cTAKES in production to process a JMS queue of medical notes, I got flagged by one of our production rules: "Passwords in clear not allowed in logs" https://issues.apache.org/jira/browse/CTAKES-455 Patch provided, see attachment. It is a minor thing, and would help

Re: bitwise operator vs logical operator [EXTERNAL]

Thank you Tim, Alex On Sep 25, 2017 09:43, "Miller, Timothy" < timothy.mil...@childrens.harvard.edu> wrote: Thanks Alexz, I've committed the patch. Tim On Sun, 2017-09-24 at 21:57 -0400, Alexandru Zbarcea wrote: > Hi, > > I have reported and provided patch for: > ht

new module ctakes-scaleout is missing

Hi, Today, trying to build latest changes to ctakes, I noticed that a new dependency over ctakes-scaleout module has been introduced, but I couldn't find this module. [ERROR] [ERROR] Some problems were encountered while processing the POMs: [ERROR] Child module ctakes/ctakes-scaleout of

Re: Continuous Integration for cTAKES

Thank you James for your feedback, Alex On Thu, Sep 28, 2017 at 7:05 PM, James Masanz <masanz.ja...@gmail.com> wrote: > Thanks Alex, that's great! > > -- James > > On Thu, Sep 28, 2017 at 5:40 PM, Alexandru Zbarcea <al...@apache.org> > wrote: > > > Hi, &g

Continuous Integration for cTAKES

Hi, I have created a new Jira Issue[1] regarding CI/CD where I started to work on improvements of the current pipeline. I have helped Apache Infra in the past and I have enough karma to help this project with the right automation. I look forward to your feedback and advice, and maybe we can

Re: Continuous Integration for cTAKES

munity was looking for Jenkins integration (e.g. Jenkinsfile, javadocs, support for 3.x and 4.x etc)? Alex On Thu, Sep 28, 2017 at 7:43 PM, Alexandru Zbarcea <al...@apache.org> wrote: > Thank you James for your feedback, > > Alex > > On Thu, Sep 28, 2017 at 7:05 PM, James Masanz <ma

CTAKES-460: coreference Test should not be part of main

Hi, I have refactor a main class that should have been a UTest. https://issues.apache.org/jira/browse/CTAKES-460 This moves the test code from src/main to src/test and also added some refactoring. No impact. Can easily be merged. Alex

Re: CTAKES-460: coreference Test should not be part of main [EXTERNAL]

Mon, 2017-10-02 at 08:17 -0400, Alexandru Zbarcea wrote: > Hi, > > I have refactor a main class that should have been a UTest. > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.or > g_jira_browse_CTAKES- > 2D460=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx

[CTAKES-450] CDA Segment Annotator misses all headings after empty segment

Hi, I have provided another patch for CTAKES-450[1]. The fix provided in the original patch is correct. However, I tried to address also small issues and some refactoring, especially addressing the Unit Testing. If you think it requires more explanation, let me know. * extracted methods *

Re: new module ctakes-scaleout is missing [EXTERNAL]

anaged to check it in. That is what I get for having a dozen > unfinished side projects ... > > I have reverted the main pom back to its previous version. > > Sean > > -Original Message- > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > Sent: Wednesday, Septembe

Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

and identifying dates > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > Hi Gandhi, > > > > > > > > > > > > I don't recall you sending me that entire snippet of text. I think > &

Re: Quick question on continuously ingesting clinical documents [EXTERNAL]

Hi Matthew, Another approach would be to use Apache Camel with the File[1] component. Alex [1] - http://camel.apache.org/file2.html On Mon, Oct 9, 2017 at 12:09 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Matthew, > > I haven't done anything with Tim's Docker, so I don't

Re: Continuous Integration for cTAKES

at 9:49 PM, Alexandru Zbarcea <al...@apache.org> wrote: > Hi, > > I have created the following jobs: > >- cTAKES-trunk-Java-1.8 > > <https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/> >- cTAKES-trunk-Java-1.9 > &

Re: using ctakes in an app -

: Alexandru Zbarcea <zbarce...@gmail.com> Date: Fri, Sep 29, 2017 at 5:41 PM Subject: Re: Loading ctakes-temporal To: u...@ctakes.apache.org Hi Jonas, I think the following will help you (already proposed as PR to https://github.com/healthnlp/examples): https://github.com/azbarcea/ctakes- example

CTAKES-465 remove dependencies over deprecated Class-es

I have completed https://issues.apache.org/jira/browse/CTAKES-465 With this last patch, build is clean from all warnings related to deprecation. The way patches should be applied is in the order of how they were uploaded to Jira. For reference, one can also use

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

om/articles/closer-look-junit-categories > > Any thoughts on these approaches? > > I think that the regression test should be rewritten. It is pretty old > and doesn't actually test the default clinical pipeline as executed by bin/ > scripts anymore. > > Sean > > -Origi

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

;jenkins-" and/or $JENKINS_URL. > > https://wiki.jenkins.io/display/JENKINS/Building+a+software+project > > > Don't follow my lead ... we'll both get lost. > > Sean > > > -Original Message- > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > Sent: We

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

ere the class Metadata is used in > ConceptDaoTest. From a quick code search, Metadata is only used by the > class SourceMetadataUtil in core. SourceMetadataUtil is only used by two > classes, both in core. I think that the change in test status is actually > unrelated to th

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

> fix it again at that time. If some other party uses another system then > they can handle the problem as they see fit. > > All that said, you should feel free to tackle this in any manner that you > like. I am just offering some thoughts. > > Sean > > -Original Message--

Re: uimafit version and commit messages

ersion is 2.4.0. Was there a problem with 2.4.0? > > - Dave > > On Mon, Nov 27, 2017 at 6:08 PM, Alexandru Zbarcea <al...@apache.org> > wrote: > > > Hi Sean, > > > > I have noticed your commits for CTAKES-485 [2]. Kudos for the commit > > messages. I starte

Re: uimafit version and commit messages

Hi Richard and David, Thank you for your support and suggestions. As you correctly identified, upgrading UIMA to 2.4.0 has been made without issues ([1] or [2]). Sean, Tim, I look forward to your feedback related to latest commits. Let me know if you see something out of order. I also know that

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

t; need would need to compile/test with that profile every once in a while – > which I think kind of comes down to using something like @category and > profile “regression”, except with very different inferences. What do you > think about making another profile? Or am I just mudd

Re: cTAKES Jenkins build is successful. [EXTERNAL]

AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Alex, > Great work, > Cheers, > Sean > > -Original Message- > From: Alexandru Zbarcea [mailto:al...@apache.org] > Sent: Thursday, November 16, 2017 7:34 PM > To: Apache cTAKES Dev > Subject:

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi, The official Jenkins job (referenced in the pom.xml) is: https://builds.apache.org/job/ctakes-trunk/. As one may notice, the status is Unstable. I was working on the cTAKES-trunk-Java-1.8 Jenkins job [1] to try to fix the issues there. As such the tests failed can be found here [2]. So

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

---Original Message- > > From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] > > Sent: Saturday, November 18, 2017 8:13 AM > > To: dev@ctakes.apache.org > > Subject: Re: unknown dependencies [EXTERNAL] [SUSPICIOUS] > > > > Thanks Alex, looks like that wa

Re: cTAKES as REST service [EXTERNAL]

or 'ctakes-web-rest' so that the module can be used to build cTAKES as > > both traditional web app as well as expose it as an REST service. It's > just a thought from my side which we can discuss upon. > > > > Once the web-rest module is ready, I feel it will take cTAKES to a &g

Re: YTEX Assistance required RE: Test case failure [EXTERNAL]

Hi Gandhi, I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also encountered the issue few times, and is very inconsistent, without being able to track it down. It seems that ytexDates.iterator() is empty in certain conditions. I think is related to the order of executions and

Re: YTEX Assistance required RE: Test case failure [EXTERNAL]

to:gandhi.natara...@arisglobal.com] > Sent: Sunday, November 19, 2017 2:47 AM > To: dev@ctakes.apache.org > Subject: RE: YTEX Assistance required RE: Test case failure [EXTERNAL] > > Thanks for the info Alex. Will check and keep you posted. > > Regards, > Gandhi > &g

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

t: Re: unknown dependencies [EXTERNAL] [SUSPICIOUS] > > > > Thanks Alex, looks like that was probably a fat-fingered auto-import > > on my part. > > > > I like your idea, and I don't know the best way to to start either, > > but maybe one suggestion is to sta

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

ar files. > > Sean > > > -----Original Message- > From: Alexandru Zbarcea [mailto:al...@apache.org] > Sent: Monday, November 20, 2017 7:33 PM > To: Apache cTAKES Dev > Subject: Re: Contribute to ctakes: it is in your best interests! RE: > unknown dependencies

RE: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

t this information helps. The pamphlet section on models that Tim wrote is the best starting point. ML experts (which I am not) out there can contribute a lot more information, probably even a correction or two. Sean -----Original Message- From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] Sent

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

ng to use libraries like cleartk then there > > shouldn't be much of a problem. There are currently some initiatives > > trying to incorporate some deep learning frameworks. If anybody out > > there working on one is reading this then they can give you some > > information. > &g

Re: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

Hi Sean, Thank you for your feedback. I will go and commit then. I documented the execution of UMLS UTests on the Developer Install Guide [1] and yes, you're right, the priority would be to update and improve existing UTests and also to create new ones to catch up with code-coverage. As part of

cTAKES Jenkins build is successful.

Hi, The job: https://builds.apache.org/view/C/view/Apache%20cTAKES/job/ctakes-trunk-compiletest/ is successful. All tests pass. I think this is an important milestone. For quite some time we didn't have the build as successful :-) Alex

Re: svn commit: r1817150 - /ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java [EXTERNAL]

] - https://issues.apache.org/jira/browse/CTAKES-415 On Tue, Dec 5, 2017 at 2:26 PM, Alexandru Zbarcea <zbarce...@gmail.com> wrote: > Thank you James. Good catch. Will do that. I missed that when refactoring. > > Alex > > On Dec 5, 2017 1:09 PM, "James Masanz" <ma

RE: svn commit: r1817150 - /ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java [EXTERNAL]

Thank you Sean. I still try to fix the latest integration test DateAnnotatorTest. It is interesting that I cannot reproduce the issue. Let me know if any advice. Alex On Dec 5, 2017 08:32, "Finan, Sean" wrote: Hi Alex, I like the approach. Sean

Re: cTAKES as REST service [EXTERNAL]

Gandhi and Matthew, thank you for your hard work. I was working on upgrading libraries and fixing dependencies too. I would love to help with Spring dependency. For that reason, I have created issue: "upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472 [1]). Another great idea is the REST

limited access to Jira (issues) and Confluence (cwiki)

Hi, I have noticed that I have limited access to Jira [1] and Confluence [2]. I cannot assign issues to myself, nor modify wiki pages. I thought I need to wait until some permissions are propagated. However, I do not see any changes. Are there any conventions about how cTAKES community uses

Re: limited access to Jira (issues) and Confluence (cwiki)

rmissions assigned > separately from getting commit access to the svn repo. > > I just now gave you access to make changes to the cTAKES wiki and I've also > added you the list of Committers within JIRA for cTAKES. > > -- James > > On Mon, Oct 30, 2017 at 5:44 PM, Alexandru Z