ll
[2] - https://issues.apache.org/jira/browse/CTAKES-415
On Tue, Dec 5, 2017 at 2:26 PM, Alexandru Zbarcea
wrote:
> Thank you James. Good catch. Will do that. I missed that when refactoring.
>
> Alex
>
> On Dec 5, 2017 1:09 PM, "James Masanz" wrote:
>
>> Hi Alex,
Thank you James. Good catch. Will do that. I missed that when refactoring.
Alex
On Dec 5, 2017 1:09 PM, "James Masanz" wrote:
> Hi Alex,
>
> you might want to replace
> LOGGER.warn("couldn't drop table test_concepts. Maybe it doesn't even
> exists", e);
>
> with something that includes the tabl
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
-Original Message-
From: al...@apach
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 y
a problem with 2.4.0?
>
> - Dave
>
> On Mon, Nov 27, 2017 at 6:08 PM, Alexandru Zbarcea
> wrote:
>
> > Hi Sean,
> >
> > I have noticed your commits for CTAKES-485 [2]. Kudos for the commit
> > messages. I started to like the Jenkins integration [3], where in
Hi Sean,
I have noticed your commits for CTAKES-485 [2]. Kudos for the commit
messages. I started to like the Jenkins integration [3], where in the
changes section you can click on the change and takes you to the Jira
issue. Will also ease the release process to identify the features.
I have also
om other sources. Besides that, if those other
> > frameworks are willing 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
s. 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: Tuesday, November 21,
o these model.jar 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:
> unknow
>
> >
> >
> > -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]
endencies [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 start wi
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
s 'ctakes-web'
> > 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 m
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 h
Hi,
I notice that a miss-dependency has slipped in the code:
jdk.internal.org.objectweb.asm.commons.AnalyzerAdapter;
Now, that the Jenkins builds is successful, I think it is easier to
clean-up the code. I would like to be a common effort. I don't know the
best way to approach this.
Looking forw
8:04 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
> Sub
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
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 t
h 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 muddying the waters?
>
> Many thanks,
> Sea
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-
> From: Alexa
"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
://dzone.com/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
>
est. I can't see where 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 actu
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 trying
rately 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 Zbarcea
> wrote:
>
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 these
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 se
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
https://github.com/azbarcea/ctakes/
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 k
at 9:49 PM, Alexandru Zbarcea 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
>
> <https://builds.apa
: Alexandru Zbarcea
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-
examples/tree/fix-temporal-execution
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 wrote:
> Hi James,
>
> I have been working on stabilizing the build for 4.0.0, and I discovered
> the following:
> * CTAKES-445 (commit
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 makes
Really interesting indeed,
IBM Watson seems to have a Deep Learning component, too. I am curios about
an Apache cTAKES integration with Apache MXNet [1].
Alex
[1] - Apache MXNet: https://mxnet.incubator.apache.org/
On Thu, Oct 5, 2017 at 6:59 AM, Maite Meseure Hugues <
meseure.ma...@gmail.com>
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 wrote:
> Thanks Tim,
>
> I will let you know about the progress.
>
&
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
> Sent: Tuesday, October 3, 2017 5:32 PM
> To: Apache cT
to build a lucene index of all the sample notes in
> the ctakes-example module. I'll create a jira for it but probably won't be
> able to get to it right away.
> Tim
>
>
> From: Alexandru Zbarcea
> Sent: Monday, October 2, 20
; > > Cc: Miller, Timothy
> > >
> > > Subject: RE: Enabling drugner pipeline and identifying dates
> > >
> > > [EXTERNAL] [SUSPICIOUS]
> > >
> > >
> > >
> > > Hi Gandhi,
> > >
> > >
> > >
> >
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
>
>
m
On 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&d=DwIBaQ&c=qS4
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
Hi,
I was trying to do a UTest for the
org.apache.ctakes.coreference.data.PrintMimicMarkables (recently added),
but I couldn't find any of the existing resources that can be used for
this. Can anyone help me pointing to a resource (Lucene index) folder.
org.apache.ctakes.coreference.data.PrintMim
ty 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 wrote:
> Thank you James for your feedback,
>
> Alex
>
> On Thu, Sep 28, 2017 at 7:05 PM, James Masanz
> wrote:
>
>&
Thank you James for your feedback,
Alex
On Thu, Sep 28, 2017 at 7:05 PM, James Masanz
wrote:
> Thanks Alex, that's great!
>
> -- James
>
> On Thu, Sep 28, 2017 at 5:40 PM, Alexandru Zbarcea
> wrote:
>
> > Hi,
> >
> > I have created a new Jira Issue[
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 coll
rovement - a bunch of people from the community did a great job
> pulling ctakes up from dependency hell. There is always more to be done to
> keep it above ground, and 475 should help.
>
> Cheers,
> Sean
>
> -Original Message-
> From: Alexandru Zbarcea [mailto:z
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
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
* remove
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 ctakes/po
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 any
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 70112339..2f
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:
&g
Hi,
I have reported and provided patch for:
https://issues.apache.org/jira/browse/CTAKES-456
I hope it helps to improve readability at least.
Is there anything else related to the process of providing patches?
Regards,
Alexz
diff --git ctakes-coreference/src/main/java/org/apache/ctakes/corefere
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-
> From: Alexandru Zbarcea [mailto:zbarce...@
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
./c
Sean wrote:
> Hi Alexandru,
> I am just curious: what is your goal?
> Thanks,
> Sean
>
> -Original Message-
> From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
> Sent: Thursday, September 07, 2017 6:46 PM
> To: Apache cTAKES Dev
> Subject: WSDL for isValidU
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.
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