VJ, Aside from the changes to the existing cTAKES code (sentence detector, etc.) [which we could leave out if it's still being debated], Do you think it's worth migrating the ytex code to trunk at this point? As you mentioned earlier, it's largely complementary. [I was just thinking of saving effort to maintain the separate branch and for simplicity for dev...]
--Pei > -----Original Message----- > From: vijay garla [mailto:[email protected]] > Sent: Wednesday, February 05, 2014 9:30 PM > To: [email protected]; [email protected]; > [email protected] > Subject: Re: YTEX cTAKES 3.1.1 ready > > Hi Vlad, > > I Updated the umls install guide; see > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1 > > I would prefer to add the docs in the ctakes confluence, but as far as I can > tell, I don't have write access there - can somebody give me write privileges > on the ctakes confluence site? > > There was a bug in the umls install; copy > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes- > ytex/scripts/data/build.xmlover > the corresponding file in your ctakes-3.1.2 install > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set. The > import is currently running on the UMLS 2013AA (I assume this will complete > without issues as long as the umls schema hasn't changed from 2012). > > what trial and error did you have to go through to build the distro? > > -vj > > > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <[email protected]> wrote: > > > Hi Vlad, > > > > sorry that the instructions aren't clear. > > > > re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot > > as usual (this is unchanged from 3.1.1). After that you still have to > > apply the lib and resources (these are things that cannot be > > distributed via apache). > > > > re 2) Yes, I need to update those docs. Hopefully will get to that at > > some point. However, I assume you already have a UMLS DB (also assume > > SQL Server). If you can't/don't want to use your existing umls DB, > > please tell me. The I'll priortize upgrading the doc on importing the > > umls tables (the scripts are there). > > > > best, > > > > VJ > > > > > > On Wed, Feb 5, 2014 at 4:44 PM, <[email protected]> wrote: > > > >> Hi VJ- > >> > >> so, with trial and error were able to make the distribution and now > >> have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive. > >> > >> Here's what's unclear. > >> > >> 1. Is now this the only (combined) thing that you need for ctakes > >> 3.1.1 + Ytex? > >> the current documentation (https://code.google.com/p/yte > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal > >> lation_cTAKES_3_1) > >> which most probably is outdated, talks about installing cTakes 3.1.1 > >> first and then applying 2 SNAPSHOT archives (downloadable) , lib and > >> resources. > >> This is a confusion point. > >> > >> 2. The directions to import UMLS subset are then outdated as well. > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to > >> import the RRF files for the UMLS subset and then just use the > >> resulting db. Thoughts? > >> > >> Thanks, > >> Vlad Valtchinov > >> Brigham Rad > >> > >> > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote: > >> > >>> Hi Vlad, > >>> > >>> > >> All of ytex has been moved into ctakes, it is currently in a branch ( > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't > >>> have to install ytex-0.8 - instead you will have to build and > >>> install from the ytex branch to create your own distribution. Steps 2 & 3 > are correct. > >>> > >>> Although it is a pain, if you have the jdk, maven, and svn, you can > >>> easily build your own distro: > >>> * open a command prompt > >>> * make sure jdk, maven, and svn are in your path > >>> * cd to some directory where you want to check stuff out (I like > >>> c:\temp) > >>> * run the following commands > >>> rmdir /s /q ctakes > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes > >>> cd ctakes mvn clean install -DskipTests > >>> > >>> And you will have the ctakes (with ytex) distro in > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.z > >>> ip > >>> > >>> What is the process for getting the ytex branch merged into trunk? > >>> As I mentioned, there are very few changes to other ctakes > >>> classes/types - this should be completely complementary and not > >>> affect any existing ctakes functionality. > >>> > >>> -vj > >>> > >>> > >>> > >>> > >>> > >>> > >>> On Thu, Jan 30, 2014 at 4:56 PM, <[email protected]> wrote: > >>> > >>>> Hi VJ-- > >>>> > >>>> this is great!! Thanks for all the hard work on it! > >>>> > >>>> We're starting to look into the new install. For now we're trying > >>>> the binaries out. > >>>> > >>>> There were these questions about the proper install steps: > >>>> > >>>> 1. Do we first install ytex-0.8 > >>>> 2. Then install the new cTakes 3.1.1 instance and also apply the > >>>> SNAPSHOT lib and resources zips 3. Work our way to install the UMLS > >>>> ontologies in the db > >>>> > >>>> Its is not entirely clear from the new document ( > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_ > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1) > >>>> if there's still need to install ytex-0.8, or YTEX has been > >>>> entirely merged into cTakes? > >>>> > >>>> If the last statement is correct, there are missing parts in i.e > >>>> the UMLS install steps that are linked from the new ctakes 3.1.1 > document. > >>>> > >>>> Thanks, > >>>> vlad > >>>> > >>>> > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote: > >>>>> > >>>>> Hello All, > >>>>> > >>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1. > >>>>> Most of the YTEX functionality has been ported and integrated > >>>>> with cTAKES, and I've tested with MySQL and MS SQL Server (oracle > tests pending). > >>>>> > >>>>> Most of the changes were made in new projects - very little > >>>>> existing cTAKES code has been modified. The only non-trivial > >>>>> changes are in > >>>>> /ctakes- > assertion/src/main/java/org/apache/ctakes/assertion/medfac > >>>>> ts/i2b2/api > >>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl & > >>>>> SingleDocumentProcessorCtakes to deal with newlines within > >>>>> sentences correctly. Can somebody take a look at the changes in the > ytex branch? > >>>>> > >>>>> I believe that the branch https://svn.apache.org/ > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes > >>>>> trunk, but would like other users to test it as well. Questions: > >>>>> > >>>>> * How can I distribute the ctakes binary distribution to ytex > >>>>> users before the merge? Can we make the branch build available > >>>>> somewhere? The binary distribution is too large to host on the > >>>>> ytex google code site (max > >>>>> 200 MB) > >>>>> * Non-ASF libraries - I have segregated these out into their own > >>>>> zip file that can be distributed via sourceforge. As a stopgap, I > >>>>> can upload this to the ytex google code site, but would prefer to > >>>>> upload to sourceforge. > >>>>> * UMLS Derivatives - Ditto for these - would like to move to > >>>>> sourceforge. > >>>>> * Documentation - How can I update the confluence docs? I would > >>>>> migrate the documentation from the google code website. > >>>>> > >>>>> Here the installation instructions (putting the wagon in front of > >>>>> the horse ...) > >>>>> > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1? > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1 > >>>>> > >>>>> Best, > >>>>> > >>>>> VJ > >>>>> > >>>>> > >>>>> -- > >>>> You received this message because you are subscribed to the Google > >>>> Groups "ytex-users" group. > >>>> To unsubscribe from this group and stop receiving emails from it, > >>>> send an email to [email protected]. > >>>> To post to this group, send email to [email protected]. > >>>> To view this discussion on the web visit > >>>> https://groups.google.com/d/ > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0% > >>>> 40googlegroups.com. > >>>> > >>>> For more options, visit https://groups.google.com/groups/opt_out. > >>>> > >>> > >>> -- > >> You received this message because you are subscribed to the Google > >> Groups "ytex-users" group. > >> To unsubscribe from this group and stop receiving emails from it, > >> send an email to [email protected]. > >> To post to this group, send email to [email protected]. > >> To view this discussion on the web visit > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd- > a273- > >> a3b1a7b36241%40googlegroups.com > >> . > >> > >> For more options, visit https://groups.google.com/groups/opt_out. > >> > > > >
