Re: Fw: Please test the Apache cTAKES 5.1.0 release candidate

Hi all, To get a clean environment, I started a new Windows Sandbox (on Windows 11), installed IntelliJ, and opened the downloaded ctakes sources as a project. Not sure if this was valid to try anymore - I tried to run HelloWorldAggregatePipeline.class directly. I haven't dug into this yet, but

Re: score attribute in UmlsConcept annotation

Hi Greg, It was created as a placeholder. None of the released engines that I know about use it. HTH, James On Tue, Oct 15, 2019, 7:48 PM Greg Silverman wrote: > I noticed this was always 0. Is this a place holder for future work? > > Thanks! > > Greg-- > > -- > Greg M. Silverman > Senior System

Re: ApacheCon europe, cTAKES

I'm also glad to hear you're going. I will not be there but looking forward to hearing about it. - James On Fri, Sep 13, 2019 at 11:48 AM gandhi rajan wrote: > Glad to hear that Sean. Wish you all the best and keep us posted. > > On Thursday, September 12, 2019, Finan, Sean < > sean.fi...@child

Re: cTAKES

Hi Kelly, It looks like you pasted an image, which doesn't always come through. Could you paste the text of the error messages, which facilitates search in the future (or upload the image to a public site and send us a link) On Mon, Oct 29, 2018, 1:03 PM Shields, Kelly J < kelly.shie...@highmarkh

Re: [Request for information] - how do I become a committer?

added you to the cTAKES wiki permissions On Fri, Oct 26, 2018 at 5:33 PM Rumpa Giri wrote: > Confluence userid = giri.rumpa2017 > > Thanks, > Rumpa > > On Fri, Oct 26, 2018 at 9:33 AM James Masanz > wrote: > > > Great to hear you are interested! W

Re: [Request for information] - how do I become a committer?

Great to hear you are interested! Welcome to the cTAKES community. Thanks for pointing out the broken link. Here's the newer name for that page: https://ctakes.apache.org/pmc-faqs.html If you send your apache confluence user ID, I can give you access to update the wiki pages for cTAKES. You can

Re: Family history identification in cTAKES

Hi Gandhi, The original annotator for discovering basic attributes of the original Named Entities used regular expressions to look for family history and was called NE Contexts when we were using XML descriptors for the annotators. See the part about Status annotator on this wiki page: https://cwi

Re: UMLS credentials don't seem to let me run UMLS process XML files

I suspect the UMLS team means that the ( https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser ) URL is not valid for a person to type into a browser. Without having seen their full email, that's the best I can surmise. When I look at the URL that they mentioned that has documentation ( https://uts.

Re: Custom Dictionary connected to mysql [EXTERNAL]

one advantage of having the database entries be lower-case is performance. since a dictionary in a database is typically significantly larger than a BSV file dictionary, it is advantageous to lower case the database dictionary entries just once. On Thu, Dec 21, 2017 at 4:17 PM, Chahal Arora wro

Re: identifying core semantic analysis engine of cTAKES

If you are using the Fast dictionary lookup component {1], and using the database that is available to download from sourceforge, then the TUI and CUI codes are coming from that database, which was created from the UMLS Metathesaurus. The flow of most components can be seen in the Component Use di

Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]

I haven't used CouchDB, but I like the idea of using another Apache project, and of having a nosql db option. Plus it looks like the JDBC connector on Github is also licensed under Apache License 2.0 On Mon, Dec 18, 2017 at 4:27 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Mat

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

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 table name variable, such as: LOGGER.warn(String.format("Couldn't drop table %s. Maybe it doesn't even exist.", sqlTableName), e); On Tue, Dec 5

Re: Regarding cTakes version upadtion

First, take a look at changes that might affect you, listed on the Wiki here: https://cwiki.apache.org/confluence/display/CTAKES/New+for+4.0#Newfor4.0-Changes I think in order to answer well, I'd need an explanation of how you are using cTAKES now - just as maven dependencies? Or do you install f

Re: Interpret context out of clinical note [EXTERNAL]

If I use Eclipse, at build time I also get the error method putAll(Map>) in the type Map> is not applicable for the arguments (Map) I haven't looked into why. A quick workaround is to add a cast to Map allCovering.putAll( (Map)JCasUtil.indexCovering( jCas, covered, covering ) ); On Wed, Nov

Re: cTAKES Jenkins build is successful.

I agree, it's a great milestone. thanks. James On Nov 16, 2017 6:34 PM, "Alexandru Zbarcea" wrote: > 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 qu

Re: Lab report [EXTERNAL]

Thanks Kean and Sean! -- James On Tue, Nov 14, 2017 at 7:09 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi all, > > I checked in Kean's code as LabValueFinder in ctakes-core. Use is fairly > straightforward - you can look at the annotator class or the unit test in > ctakes-regr

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

Unfortunately JIRA and the confluence wiki have permissions 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 P

RE: CAS Visual Debugger - [EXTERNAL]

Cool. Thanks On Oct 25, 2017 1:24 PM, "Finan, Sean" wrote: > Ok, there is a kludge ... > > 1. Start the CVD > 2. Go to File > load Type System > 3. Select your type system > 4. Exit > 5. Go to your home directory > 6. Look at the file named annotViewer.pref > There should be a line startin

Re: building cTAKES (discussion transferred from CTAKES-445 [EXTERNAL]

umlspw makes the whole build > > succeed. But having some credentials in the Jenkins job (official) > > doesn't make much sense. > > > > With all these patches, cTAKES would have a stable build, making it > > closer to be releasable from official Apache repository. &

Re: building cTAKES (discussion transferred from CTAKES-445 [EXTERNAL]

> > > > Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build > > succeed. But having some credentials in the Jenkins job (official) > > doesn't make much sense. > > > > With all these patches, cTAKES would have a stable build, making it > >

building cTAKES (discussion transferred from CTAKES-445

A question was asked within JIRA issue CTAKES-445 about building cTAKES that is more general than the topic of CTAKES-445, so I'm transferring that to this mailing list. It started with the following question how someone is able to provide complet

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

FWIW, I started taking a look at the patch. (It's in code that I'm not that familiar with, so a quick glance isn't sufficient for me.) I did a search in UMLS for m2 in the terminologies commonly used by cTAKES to see if adding m2 could result in marking something as a measurement when it's not - an

Re: Continuous Integration for cTAKES

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[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 hel

Re: Enabling drugner pipeline and identifying dates [EXTERNAL]

1) I would typically not use cTAKES for extracting patient names or sex. is there any database or metadata that you can get that information from? 2) Dates are found by the ContextDependentTokenizerAnnotator, which uses DateFSM.java in package org.apache.ctakes.core.fsm.machine. I believe drug ne

Re: Builds are now clean [was: Travis has one test failed [EXTERNAL]]

That's excellent! My preference would be for you to continue to submit attachments to JIRA issues. James On Sep 10, 2017 7:48 PM, "Hadrian Zbarcea" wrote: Hi all, I had issues with the tests as well. We need clean tests if we were to do any incremental refactoring. I added to patches to #334

Re: ctakes demo down [EXTERNAL]

Hi Dima, I would be surprised if the dictionary demo was gone for good since the temporal one is working, and they were both updated to 4.0 earlier this year, but can't say, since others maintain those servers. Not sure if you noticed further down that page, for support it suggests to submit a JI

Re: URI is not hierarchical

lvg from svn.code.sf.net/p/ctakesresources/code/trunk/ > ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/ and > put it in target/classes/org/apache/ctakes/. > > Thank you so much, you made my day today :) > > Dima > > > > > On Apr

Re: URI is not hierarchical

for linux/mac > but > > was not tested there. > > > > FYI #3, this was using your idea of not having ctakes-misc be under > ctakes. > > thanks for that tip! keeps things nicely separated - no need to update > > the parent pom at all. > > > > > >

Re: URI is not hierarchical

t;I couldn't > find it here or there or the other place ..." and then thrown a > FileNotFoundException. > > > > -Original Message- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Saturday, April 29, 2017 2:00 AM > To: dev@ctakes.apache.org &

Re: URI is not hierarchical

ested there. FYI #3, this was using your idea of not having ctakes-misc be under ctakes. thanks for that tip! keeps things nicely separated - no need to update the parent pom at all. On Sat, Apr 29, 2017 at 2:00 AM, James Masanz wrote: > Hi Dima, > > what revision of trunk are you u

Re: URI is not hierarchical

ory in trunk. It will build no matter where > it is on your system as long as you first do an ‘mvn clean compile’ in > trunk/ (without it, ctakes-misc/ will not build). > > Thanks again, James. > > Dima > > > > > On Apr 28, 2017, at 16:30, James Masanz wrote:

Re: URI is not hierarchical

l testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest): URI is not hierarchical On Fri, Apr 28, 2017 at 12:27 PM, James Masanz wrote: > > Going back to your original email, I notice cTAKES is referencing > lvg.properties > as being within a jar > > 14 Apr 2017 11:04:24 INFO LvgA

Improving Preparing a Release process and documentation

While creating 4.0 is still fresh in our minds, I encourage everyone to jot down any steps you did that weren't written anywhere, or lessons learned. Please either add to this [1] JIRA issue, or if you'd rather, just reply to this thread and I'll update the JIRA. A few things I have off the top o

Re: URI is not hierarchical

Going back to your original email, I notice cTAKES is referencing lvg.properties as being within a jar 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties =file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/ctakes- resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar

Re: ctakes 4.0.1 - Install experience

Looks like it's a left over from when we switched from using a local copy of LVG jar in a local lib directory to using a maven dependency several years ago. When I updated the artifactId and version of lvg for cTAKES 4.0, I didn't consider whether the explicit reference could be removed from that

Demos menu option on cTAKES homepage

Pei and others with access to update http://healthnlp.github.io/examples/ Following the Get Started -> Demo menu on http://ctakes.apache.org/ leads to a page with demos that aren't currently working. Will you have a chance to fix those soon or should the Demo menu be removed until they get fi

Re: 4.0.0 javadocs

mMDChztj3AZCzUOB4QA> now. Best, Murali On Mon, Apr 24, 2017 at 11:30 AM, James Masanz wrote: > Murali, > > Thanks all for getting the 4.0 build done/artifacts pushed. > > Can we get the javadocs pushed to > > http://ctakes.apache.org/apidocs/4.0.0/ > > thanks! > > -- James >

4.0.0 javadocs

Murali, Thanks all for getting the 4.0 build done/artifacts pushed. Can we get the javadocs pushed to http://ctakes.apache.org/apidocs/4.0.0/ thanks! -- James

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

o "HSQL Database Engine Standalone" and then setting the URL to > > point to my custom dictionary directory. It throws a SQLException that > says > > "wrong database file version". Is there some other step I'm missing? > > > > - Dave > >

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

in a vet dictionary fi you use the new > dictionary creator you can decide whether or not you want them to be > included. > > Sean > > -Original Message- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Saturday, April 22, 2017 11:32 PM > To: dev@ctak

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

Dave, It's an oversight that we didn't document that. Thanks for pointing that out! I'll update the documentation tomorrow and post again with proper details of the command to use. The short answer is that hsqldb jar includes a GUI. You use the 2.3.4 version of that jar, which is included with t

Re: [VOTE] Release Apache cTAKES 4.0.0 (rc3)

21, 2017 at 2:07 PM, Pei Chen wrote: > Hi James, > That sounds good. Looks like we should have enough +1 votes for rc3. > We can flip the artifacts to dist on Mon in case anyone wants to test > over the weekend? Do you want to update the links on the web site on > Mon? > &g

Re: [VOTE] Release Apache cTAKES 4.0.0 (rc3)

+1 for rc3 to be released as 4.0.0 Pei, Sean, and Murali, knowing that Tuesdays are good days for release announcements, do you see any problem with announcing the release on Tuesday the 25th if we end up with enough votes by end of Friday or even by the end of Saturday? If there is, I'd be willi

Re: suggestions to pick up complicated drug dosage?

Hi Arron, I don't believe there is any other cTAKES annotator that will do any better. I also don't know of any current work to improve that case. From what I remember offhand, the way dosages are picked up is based on first finding the drug name, and then finding a mention of dosage nearby. So ii

[VOTE] Re: Release Apache cTAKES 4.0.0 (rc2)

re-posting my latest but with [VOTE] added to the subject for anyone filtering on that. On Sat, Apr 15, 2017 at 10:02 PM, James Masanz wrote: > Hi everyone, > > - changing my vote to 0 for rc2. I'd prefer to have a new release > candidate ASAP but if we don't get one

Re: Release Apache cTAKES 4.0.0 (rc2)

4.0 as-is. I'd be happy to be release manager for a 4.0.1. -- James On Fri, Apr 14, 2017 at 8:04 PM, James Masanz wrote: > > -1 from me for rc2 because of various issues found > old dictionary lookup didn't work in an IDE unless you manually > download the latest

Re: Release Apache cTAKES 4.0.0 (rc2)

Sorry if I confused anyone, I was wrong about the net.sourceforge.ctakesresources maven artifacts. The 4.0.0 version of them have been there for a couple days (even the ones used by the original dictionary lookup). On Fri, Apr 14, 2017 at 8:04 PM, James Masanz wrote: > > -1 from me f

Re: Release Apache cTAKES 4.0.0 (rc2)

ggest we bundle all of the > fixes before creating another candidate? Are there other remaining > items to test? This just seems like basic functionality? > > On Fri, Apr 14, 2017 at 8:04 PM, James Masanz > wrote: > > -1 from me for rc2 because of various issues found >

Re: Release Apache cTAKES 4.0.0 (rc2)

-1 from me for rc2 because of various issues found old dictionary lookup didn't work in an IDE unless you manually download the latest zip - pom files needed updating (checked into trunk today) (more of the ctakesresources from sourceforge need to be put onto maven central for ctakes to work as

Re: cTAKES as a dependency

Prior to 4.0 there was a problem with some dependencies not being in maven - there were in local lib directory instead. Those dependencies were removed for 4.0 and there are no "system" dependencies in 4.0 I haven't tested it yet, but if you are using the fast dictionary lookup, setting up a maven

Re: testing release candidates Re: Release Apache cTAKES 4.0.0 (rc2) [SUSPICIOUS]

test? > > I will do the same. > > Thanks > Tim > > On Thu, 2017-04-13 at 12:24 -0400, James Masanz wrote: > > I agree. > > There are (or were) some places that have TBD. and the part about > > unzipping > > resources needs to be expanded to include

Re: testing release candidates Re: Release Apache cTAKES 4.0.0 (rc2) [SUSPICIOUS]

lly helpful. > > I want to test the cvd for standard dictionary lookup with the separate > resoureces. Am I meant to be testing documentation as well? As in, > something I can follow along and make sure it's correct? Or should I just > do it the way I know how to do it? >

testing release candidates Re: Release Apache cTAKES 4.0.0 (rc2)

Hi Everyone, We could use a google spreadsheet to end up with a sense of testing coverage and maybe reduce duplicate testing effort too. https://docs.google.com/spreadsheets/d/1FK-kEhwewLJaVCBgWsSAMhL2KNCD6L8AMfFM33oKR2Y/edit?usp=sharing And we can compare future releases to this one. I put a few

Re: Revert change to r.1768564

Sean can correct me if I'm wrong but as he explained it to me earlier today, he was thinking that the nightly jenkins build and developers who do builds on their own systems, both being more frequent than builds for announced releases, could default to not zipping the source, while the packageSourc

Re: Revert change to r.1768564

why don't we do that (right) after 4.0 is released. the build process will be fresh in people's minds and we can set it up and include it in the cTAKES release manager documentation so it is completely ready for 4.1. On Mon, Apr 10, 2017 at 12:32 PM, Finan, Sean < sean.fi...@childrens.harvard.edu>

Re: Revert change to r.1768564

Hi Murali, I checked into trunk changes that undid what had been done in r1768564. Do you think we'll be able to have a release candidate by tomorrow so we can give the community time to test it and announce the release on the 18th? Thanks! -- James On Mon, Apr 10, 2017 at 10:27 AM, Murali Minna

Re: Revert change to r.1768564

I'm working on it now On Mon, Apr 10, 2017 at 10:27 AM, Murali Minnah wrote: > Hello fellow cTAKERs > > Can someone please help revert this change? > > r.1768564 > ctakes-distribution/pom.xml > "Separated build into 2 profiles: packageBinary and packageSource > packageBinary is enabled by defaul

creating maven artifacts for dictionary resources

Does anyone have a cheat sheet for how to create the maven artifacts for the dictionary lookup resources we store on https://sourceforge.net/projects/ctakesresources I've created the zip for 4.0 with the dictionaries for the original dictionary lookup converted to be used with hsqldb 2.3.4, and ne

Re: SenseDisambiguatorAnnotator in ctakes 4.0?

fwiw, the only change to ytex I am making for 4.0 is what is necessary for updating hsqldb to 2.3.4 On Wed, Mar 29, 2017 at 10:02 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Lani, > > Great questions. As far as I know nobdy is changing what is in ytex for > this release. So

Re: Calling all ytex experts! Urgent!

terested in any hearing if you ran into any other issues On Fri, Mar 31, 2017 at 11:27 AM, James Masanz wrote: > Here's the error I'm seeing when I try mvn clean install -DskipTests=true > > java.sql.SQLSyntaxErrorException: incompatible data types in combination > > He

Re: Calling all ytex experts! Urgent!

Here's the error I'm seeing when I try mvn clean install -DskipTests=true java.sql.SQLSyntaxErrorException: incompatible data types in combination Here's the part of the log jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog [echo] execut

Re: The stable cTAKES tag to work with post the release 3.2.2?

Hi, 3.2.2 is the latest stable release. We are actively working on the next release - 4.0 - which we expect to be released in less than a month, with a release candidate planned for community testing by the end of this month. -- James On Thu, Mar 23, 2017 at 8:23 AM, Devikiran Ramadas wrote:

Re: Subscription

people can subscribe themselves by sending a plaintext (not html format) email to the appropriate *-subscr...@ctakes.apache.org email address(es) as described here: https://ctakes.apache.org/mailing-lists.html On Fri, Mar 17, 2017 at 6:14 AM, Hari, Sekhar wrote: > Hi there - > > Can you kindl

Re: Trouble with the DictionaryTool

great! look forward to having that in cTAKES (trunk) On Fri, Mar 17, 2017 at 12:01 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > yes > > -Original Message- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Friday, March 17, 20

Re: Trouble with the DictionaryTool

y do have an expanded version that I was going to check in this > weekend. I will back out your checkin as the new module is just named > "ctakes-gui", having more than the dictionary creator. > Sean > > -----Original Message- > From: James Masanz [mailto:masanz.ja...@gma

Re: Trouble with the DictionaryTool

I checked in the gui under trunk as ctakes-dictionary-gui FYI, I moved the data directory under resources It runs from source but haven't tested from a jar yet. Sean if you make changes, please make them to the trunk version. Thanks. On Thu, Mar 16, 2017 at 5:12 PM, Finan, Sean < sean.fi...@child

Re: [jira] [Commented] (CTAKES-420) Wiki wishlist

Thanks for the suggestions so far. All, if there are more, either comment on CTAKES-420 or reply to this thread. Thanks. On Thu, Mar 2, 2017 at 10:14 AM, Andrey Kurdyumov (JIRA) wrote: > > [ https://issues.apache.org/jira/browse/CTAKES-420?

Re: 2016AB UMLS (ctakessnorx)

previously OntologyConceptUtil was IdentifiedAnnotationUtil On Wed, Mar 8, 2017 at 11:12 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Martijn, > > The dictionary creator gui is in sandbox just like the command line tool, > but it is newer and easier to use. > > OntologyConcep

Re: Update to OpenNLP 1.7.1

; > not working for cTAKES? We could try to find a solution which works for > > > you without duplicating our effort. > > > > > > Jörn > > > > > > > > > On Wed, 2017-01-25 at 18:43 +, Finan, Sean wrote: > > > > Hi Jorn, > &g

wiki wishlist

In an earlier post I mentioned I was interested in moving away from Confluence for the cTAKES wiki, but the only new wikis Infra will create are Confluence ones. I suggest we use this thread + a JIRA item to compile a list of wiki changes people would like - formatting, content, anything to do wit

Re: (Re)introduce myself - James Masanz

ll be able ..." It seems that James is allowed to volunteer > to be an RM. I would also like to remind that 3 months ago I volunteered > to be Co-RM and would love to have James' help - not just because he has > previously been part of the release process, but also because he is o

(Re)introduce myself - James Masanz

Hi, I'm James Masanz -- if you've been on the dev list for more than a couple years, you might recognize my name from my previous contributions to cTAKES, which include having been a release manager. I've joined the Boston Children's Hospital NLP team. I will be devoting s

Re: headword field in identifiedannotations

I've forgotten most of what I knew about ConllDependencyNode - do you need headNode to have access to attributes specific to the ConllDependencyNode type or would a BaseToken suffice, to generalize the solution? If a ConllDependencyNode is what's needed, then what you proposed sounds good to me. -

[ANNOUNCE] Apache cTAKES 3.1.1 released

The Apache cTAKES team is pleased to announce the availability of the 3.1.1 release. For the complete release notes, please visit http://s.apache.org/ctakes-3.1.1-release-notes Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing

[ANNOUNCE] Apache cTAKES 3.1.0 released

The Apache cTAKES team is pleased to announce the availability of the 3.1.0 release. This release is our first release as a top level project. For the complete release notes, please visit http://s.apache.org/ctakes-3.1.0-release-notes Apache clinical Text Analysis and Knowledge Extraction System