Hi Bhagwat, I have no idea why that isn't working. Ctakes-examples should have everything in its classpath.
Ok, try this instead: Update to the latest version of trunk. On the left or right you may see a "maven projects" tab. If you don’t you can activate it using the menubar: View > Tool Windows > Maven Projects. Expand the "Maven Projects" tab. You should see a list or tree with "profiles" at the top, followed by "Apache cTAKES" and then ctakes modules. Expand "profiles" and click the box next to runPiperGui. If you don't see "runPiperGui" then you don't really have the latest version of trunk. Expand "Apache ctakes" and double-click clean. When Clean has finished double-click "compile". You should see ctakes compile for a while and then a gui should pop up. This is the Piper File Submitter. Follow the instructions on the wiki, pointing to your piper file, etc. https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI Sean -----Original Message----- From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] Sent: Monday, November 20, 2017 7:12 AM To: dev@ctakes.apache.org Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Hello Sean, I have installed intellij IDE imported maven project and compiled it using cTAKES+4.0+Developer+Install+Guide. Then I have followed the steps you have given for running the piper file using IDE I set the following in Run Configuration Main class : org.apache.ctakes.core.pipeline.PiperFileRunner VM Options: -Xmx3G Working Directory: path/to/your/ctakes/ Use Classpath of module: ctakes-examples Arguments: -p Path/to/your/PiperFile.piper --user yourUmlUsername --pass yourUmlsPassword But I am getting this error : Could not find or load main class org.apache.ctakes.core.pipeline.PiperFileRunner Could you please provide some inputs on it. On 17 November 2017 at 22:04, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Bhagwat, > > It is a little late, but I just checked in a maven profile that will start > the piper file submitter gui. To use it: > > 1. update your local sandbox with trunk > 2. There should be a maven tab somewhere in eclipse ... > 3. On the maven tab, enable the profile "runPiperGui" > 4. run maven compile > > The compilation stage should start, and near the end the piper gui will > pop up. > > Sean > > -----Original Message----- > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > Sent: Friday, November 17, 2017 1:29 AM > To: dev@ctakes.apache.org > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > [SUSPICIOUS] [SUSPICIOUS] > > Hi Sean, > > I am using Eclipse Mars IDE. > Could you please tell me how to to set up an ide to run directly using the > source code. > > On 16 November 2017 at 20:23, Finan, Sean <Sean.Finan@childrens.harvard. > edu> > wrote: > > > Hi Bhagwat, > > > > I think that you are close, but that workflow won't pan out. > > > > If you want to run just like the ctakes release, run maven package, > > then go to the target/ directory in -distribution and unzip one of the > > created -bin files to another directory and then use that directory > > just like you would the ctakes release. Please note that you will > > need to copy the ctakes dictionary from your source into that > installation. > > > > If you are familiar with running from source that would be much easier. > > Are you using an IDE? It is very easy to set up an ide to run > > directly using the source code, which means that you don't have to > > both with the long package and copy process. > > > > > > Sean > > > > > > -----Original Message----- > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > > Sent: Thursday, November 16, 2017 4:17 AM > > To: dev@ctakes.apache.org > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > [SUSPICIOUS] [SUSPICIOUS] > > > > Hello Sean, > > > > Sorry to say but I haven't received any files, hope you are sending it > > on my personal email. > > Will it be possible to share it through dropbox or google drive? > > > > I have followed the steps provided on the link. > > After building ctakes-trunk, I have tried to run the piper file using > > ctake-distribution module where runpiper.bat file present, it means my > > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main). > > > > I ran the command > > > > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p > > D:\DefaultFastPipeline.piper --user USER --pass PASS > > > > it is giving following error: > > > > Error: Could not find or load main class org.apache.ctakes.core. > > pipeline.PiperFileRunner > > > > On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard. > > edu> > > wrote: > > > > > I just sent it 2 more times ... > > > > > > -----Original Message----- > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > > > Sent: Wednesday, November 15, 2017 11:20 AM > > > To: dev@ctakes.apache.org > > > Subject: RE: source code of user installation of cTakes. [EXTERNAL] > > > [SUSPICIOUS] [SUSPICIOUS] > > > > > > Hi Sean, > > > > > > Unfortunately I haven't received it in spam folder too. > > > > > > On Nov 15, 2017 7:47 PM, "Finan, Sean" > > > <sean.fi...@childrens.harvard.edu> > > > wrote: > > > > > > > Hi Bhagwat, > > > > > > > > I sent the email with the output zipped as it contains a > > > > javascript file and those are usually blocked as attachments. > > > > Check your spam folder and see if the server sent it there. > > > > > > > > You can find instructions on building ctakes trunk from code here: > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache. > > > > or > > > > g_ > > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14 > > > > JZ > > > > MS > > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX > > > > rN > > > > wY > > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr > > > > m0 > > > > O1 > > > > 1vwvOMhuk&e= > > > > cTAKES+4.0+Developer+Install+Guide > > > > > > > > After that just run your piper as you have been. > > > > > > > > Sean > > > > > > > > > > > > -----Original Message----- > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > > > > Sent: Wednesday, November 15, 2017 8:27 AM > > > > To: dev@ctakes.apache.org > > > > Subject: Re: source code of user installation of cTakes. > > > > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > > > > > > > Hi Sean, > > > > > > > > Thank you for looking at files, I have not yet received the output > > > > files though. > > > > > > > > For an additional information about my output files - I was trying > > > > to get the output using release cTakes-4.0.0 > > > > (apache-ctakes-4.0.0\bin\runPiperFile.bat). > > > > In this release(apache-ctakes-4.0.0\lib), I have copied > > > > ctakes-temporal.jar created from the source code in ctakes-trunk. > > > > With this I could remove the error from console but tlink is > > > > missing in output html. > > > > > > > > With the output file that you have generated could you please also > > > > provide the steps to get the output using the source code in trunk. > > > > > > > > > > > > On 15 November 2017 at 18:20, Finan, Sean > > <Sean.Finan@childrens.harvard. > > > > edu> > > > > wrote: > > > > > > > > > Hi Bhagwat, > > > > > > > > > > I got your output files, thanks. Tlinks are not present because > > > > > it comes from the ctakes 4.0.0 release, in which the html writer > > > > > was very primitive. It has come a long way since then, and the > > > > > version in trunk > > > > is > > > > > much more capable. I have emailed you the output files produced > > > > > by > > > > trunk. > > > > > You can decide whether or not to make the upgrade. > > > > > > > > > > Sean > > > > > > > > > > -----Original Message----- > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > > > > > Sent: Wednesday, November 15, 2017 6:49 AM > > > > > To: dev@ctakes.apache.org > > > > > Subject: Re: source code of user installation of cTakes. > > > > > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > > > > > > > > > Thank You Sean and Tim for such a useful information. > > > > > > > > > > Now I don't see any error logged on console after replacing > > > > > ctakes-temporal JAR file(Built from source code of trunk and > > > > > release > > > > 4.0.0 > > > > > as well). > > > > > > > > > > Unfortunately I could not generate TLINK statements in HTML file. > > > > > > > > > > Sean, as you mentioned I am sending my piper file, HTML file and > > > > > clinical note file to your personal email. > > > > > Could you please have a look at it, and provide your thoughts on > it. > > > > > > > > > > > > > > > > > > > > On 14 November 2017 at 19:16, Finan, Sean > > > <Sean.Finan@childrens.harvard. > > > > > edu> > > > > > wrote: > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > To build upon what Tim said, not all of the ctakes modules log > > > > > > in the same manor. Some of the more experimental annotators > > > > > > such as those in the temporal module log more 'debug' type > > > > > > events, while some of the standard modules kindly log 'progress' > > > > > > events, such as processing "start" and "finish". In addition, > > > > > > the loggers are typically named after the java class, and > > > > > > sometimes the classes are > > > oddly named. > > > > > > Instead of log messages from a "TimeAnnotator" you are seeing > > > > > > "BackwardsTimeAnnotator", which is appropriate. > > > > > > > > > > > > The apache email bounce will get rid of all attachments, so > > > > > > people on the lists will not be able to get attachments or > > embedded images. > > > > > > This can be frustrating, but it does add a bit of security for > > > > everybody > > > > > on the list. > > > > > > If you like you can email me your attachments directly - but > > > > > > piper files are plain text that you can just copy and paste > > > > > > into > > the email. > > > > > > If you are using test data (no phi) then you can send me a zip > > > > > > with the files in your html output directory and I will take a > > > > > > look > > > at them. > > > > > > > > > > > > Also, as Tim noted, capability and behavior of code in trunk > > > > > > are often very different from what you get from a release > version. > > > > > > Some things move very quickly in ctakes (and some very slowly). > > > > > > If you are willing to build the code then I always recommend > > > > > > using trunk - sometimes because I just plain forget what the > > > > > > previous release was > > > > > doing. > > > > > > > > > > > > Sean > > > > > > > > > > > > -----Original Message----- > > > > > > From: Miller, Timothy > > > > > > [mailto:timothy.mil...@childrens.harvard.edu] > > > > > > Sent: Tuesday, November 14, 2017 7:09 AM > > > > > > To: dev@ctakes.apache.org > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > That error comes from the tlink module, but **it should be > > > > > > possible to create tlinks even if you are getting it**. In > > > > > > fact, for stupid reasons (i.e. my stupidity) you will always > > > > > > see that error when running the tlink annotator. However, I do > > > > > > have a fix for the error, that may help the tlink module > > > > > > somewhat, checked in to trunk about 2 months ago. If you're > > > > > > working off of trunk already, please let me know, because then > > > > > > there is some mistake with my fix. If you're working off of a > > > > > > src release and willing to recompile, it should be a > > > > > reasonably small fix: > > > > > > > > > > > > > > > > > > Replace the existing time annotator model with this one: > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn. > > > > > > apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal-2Dres_ > > > > > > src_main_resources_org_apache_ctakes_temporal_ae_timeannotator > > > > > > _m > > > > > > od > > > > > > el.j > > > > > > ar- > > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop > > > > > > px eF U&r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=EPNtkyV_ > > > > > > yUzDNfVUlpTVzGIVBkZsqUVt-4tgYL9SM_8&e= > > > > > > > > > > > > > > > > > > and then update this java file: > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn. > > > > > > apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal_src_ > > > > > > main_java_org_apache_ctakes_temporal_ae_BackwardsTimeAnnotator > > > > > > .j > > > > > > av > > > > > > a- > > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio > > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s= > > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e= > > > > > > > > > > > > > > > > > > and recompile, and it should remove the error. > > > > > > > > > > > > > > > > > > Tim > > > > > > > > > > > > > > > > > > ________________________________ > > > > > > From: Bhagwat Posane <bhagwat.pos...@gmail.com> > > > > > > Sent: Tuesday, November 14, 2017 4:16 AM > > > > > > To: dev@ctakes.apache.org > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > Hello Sean, > > > > > > > > > > > > Ok, I understood it now, but in my output, the HTML file > > > > > > doesn't contain TimeAnnotator. below is the part of output: > > > > > > > > > > > > 14 Nov 2017 13:03:19 INFO ContextDependentTokenizerAnnotator > > > > > > - > > > > > > process(JCas) > > > > > > 14 Nov 2017 13:03:19 INFO POSTagger - process(JCas) > > > > > > 14 Nov 2017 13:03:19 INFO Chunker - process(JCas) > > > > > > 14 Nov 2017 13:03:20 INFO ChunkAdjuster - process(JCas) > > > > > > 14 Nov 2017 13:03:20 INFO ChunkAdjuster - process(JCas) > > > > > > 14 Nov 2017 13:03:22 INFO BackwardsTimeAnnotator - Starting > > > > > > processing > > > > > > 14 Nov 2017 13:03:22 INFO BackwardsTimeAnnotator - Finished > > > > > > processing > > > > > > 14 Nov 2017 13:03:22 INFO DocTimeRelAnnotator - Starting > > > > > > processing > > > > > > 14 Nov 2017 13:03:22 INFO DocTimeRelAnnotator - Finished > > > > > > processing > > > > > > 14 Nov 2017 13:03:22 INFO EventTimeRelationAnnotator - > > > > > > Starting processing Null value found in Feature(<Time-Class->, > > > > > > <NULL>) Null value found in Feature(<Time-Class->, <NULL>) > > > > > > Null value found in Feature(<Time-Class->, <NULL>) Null value > > > > > > found in Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) Null value found in > > > > > > Feature(<Time-Class->, <NULL>) > > > > > > 14 Nov 2017 13:03:23 INFO EventTimeRelationAnnotator - > > > > > > Finished processing > > > > > > 14 Nov 2017 13:03:23 INFO HtmlTextWriter - Starting > > > > > > processing > > > > > > 14 Nov 2017 13:03:23 INFO HtmlTextWriter - Finished > > > > > > processing > > > > > > > > > > > > I doubt, the blue colored output text is the culprit and > > > > > > causing TLINK not getting generated. To find the cause, I have > > > > > > checked multiple things with no success! > > > > > > However, event-time-relation is captured in xmi with no > > problem(P.S. > > > > > > Attached). > > > > > > For your reference my piper file is also attached. > > > > > > Could you please have a look at the outputs and guide me to > > > > > > find the root cause or please tell me if you are aware of this > behavior. > > > > > > > > > > > > On 13 November 2017 at 18:48, Finan, Sean > > > > <Sean.Finan@childrens.harvard. > > > > > > edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: > > > > > > Hi Bhagwat, > > > > > > > > > > > > The image that you've attached is not coming through, So I > > > > > > cannot see your html file. > > > > > > > > > > > > You should be able to click on any of the underlined terms in > > > > > > the document. When you click on one it will list attributes > > > > > > discovered in the run. For example, clicking on "4:00pm" may > > > > > > display on the right panel "CONTAINS x-ray". > > > > > > > > > > > > Sean > > > > > > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > > > > bhagwat.pos...@gmail.com>] > > > > > > Sent: Monday, November 13, 2017 3:25 AM > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > Hello Sean, > > > > > > > > > > > > Thank you for the inputs, I have successfully created HTML > output. > > > > > > My main aim is to understand context out of clinical note and > > > > > > I hope TLINK statements may help at some extent. > > > > > > I am interested TLINK tag output in HTML, Please correct me if > > > > > > my understanding is not upto the mark. > > > > > > > > > > > > But HTML file doesn't contain any TLINK tags, [Inline images > > > > > > 2] > > > > > > > > > > > > However I can see some tags(copied below) in xmi file which I > > > > > > suppose useful for TLINK tag generation. > > > > > > > > > > > > <relation:RelationArgument xmi:id="8553" id="0" argument="7466" > > > > > > role="Arg2"/> > > > > > > <relation:TemporalTextRelation xmi:id="8282" id="0" > > > category="ENDS-ON" > > > > > > discoveryTechnique="0" confidence="0.0" polarity="0" > > uncertainty="0" > > > > > > conditional="false" arg1="8272" arg2="8277"/> > > > > > > <relation:TemporalTextRelation xmi:id="8306" id="0" > > > category="CONTAINS" > > > > > > discoveryTechnique="0" confidence="0.0" polarity="0" > > uncertainty="0" > > > > > > conditional="false" arg1="8296" arg2="8301"/> > > > > > > > > > > > > > > > > > > I have used TemporalSubPipe.piper file commands to generate > > > > > > the > > > output. > > > > > > > > > > > > //////////////////////////////////////////////////////////// > > > > > > //////////////////////////////////////////////////////////// > > > > > > /////////////////// > > > > > > // Commands and parameters to create a default temporal > > > > > > processing sub-pipeline. This is not a full pipeline. > > > > > > > > > > > > // 'Generic' Events. Use addDescription and let the > > > > > > EventAnnotator set itself up with defaults. > > > > > > addDescription EventAnnotator > > > > > > > > > > > > // Times. There aren't default models, so set specifically > > > > > > add BackwardsTimeAnnotator classifierJarPath=/org/apache/ > > > > > > ctakes/temporal/ae/timeannotator/model.jar > > > > > > > > > > > > // DocTimeRel: the relation bin for Events to the Document > > > > > > Creation > > > > Time. > > > > > > add DocTimeRelAnnotator classifierJarPath=/org/apache/ > > > > > > ctakes/temporal/ae/doctimerel/model.jar > > > > > > > > > > > > // Event - Time binary relations. > > > > > > add EventTimeRelationAnnotator classifierJarPath=/org/apache/ > > > > > > ctakes/temporal/ae/eventtime/model.jar > > > > > > > > > > > > // Event - Event binary relations. > > > > > > add EventEventRelationAnnotator classifierJarPath=/org/apache/ > > > > > > ctakes/temporal/ae/eventevent/model.jar > > > > > > > > > > > > // Html output > > > > > > set OutputDirectory=D:\Bhagwat\HTMLoutput > > > > > > add pretty.html.HtmlTextWriter > > > > > > > > > > > > //XMI output > > > > > > writeXmis D:\Bhagwat\XMI > > > > > > //////////////////////////////////////////////////////////// > > > > > > //////////////////////////////////////////////////////////// > > > > > > /////////////////// > > > > > > > > > > > > Am I missing something? > > > > > > > > > > > > Could you please guide on this. > > > > > > > > > > > > > > > > > > > > > > > > On 10 November 2017 at 18:47, Finan, Sean > > > > <Sean.Finan@childrens.harvard. > > > > > > edu<mailto:sean.fi...@childrens.harvard.edu><mailto: > > > > > > sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@childrens.h > > > > > > ar > > > > > > va > > > > > > rd.e > > > > > > du>>> > > > > > > wrote: > > > > > > Hi Bhagwat, > > > > > > > > > > > > To get html output, you just need to add the html writer and > > > > > > set the output directory. > > > > > > > > > > > > Your #1 should do that. > > > > > > > > > > > > add pretty.html.HtmlTextWriter > > > > > > > > > > > > To set the output directory you can do one of the following: > > > > > > If running from command-line, set it with the -o {directory} > > option. > > > > > > Or edit the piper file: > > > > > > > > > > > > set OutputDirectory={directory} add pretty.html.HtmlTextWriter > > > > > > > > > > > > or on the same line as add (like your #2) > > > > > > > > > > > > add pretty.html.HtmlTextWriter OutputDirectory={directory} > > > > > > > > > > > > > > > > > > Hopefully at least one of those methods works for you. > > > > > > > > > > > > Sean > > > > > > > > > > > > -----Original Message----- > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > Sent: Friday, November 10, 2017 6:13 AM > > > > > > To: > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > Hello Sean, > > > > > > > > > > > > Thank you so much, the things you have given works well for > > > > > > me; I could generate the .xmi output file using reader > TextReader. > > > > > > And yes, the asterisk marked for "writeXmis" is to highlight > > > > > > for your understanding. > > > > > > > > > > > > The present challenge I am facing is - to parse XMI file and > > > > > > get the required data out of it(e.g. TemporalTextRelation in my > case). > > > > > > > > > > > > Is it possible to get the output in HTML format? > > > > > > > > > > > > I have tried to get the HTML output file using below command. > > > > > > > > > > > > 1) add pretty.html.HtmlTextWriter > > > > > > 2) add pretty.html.HtmlTextWriter D:\Bhagwat\output > > > > > > > > > > > > But it does not generate any output file > > > > > > > > > > > > Could you please provide some light on this. > > > > > > > > > > > > > > > > > > On 9 November 2017 at 20:43, Finan, Sean > > > > > > <sean.fi...@childrens.harvard.edu > > > > > > <mailto:sean.fi...@childrens.harvard.edu><mailto: > > > > > > sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@childrens.h > > > > > > ar > > > > > > va > > > > > > rd.e > > > > > > du > > > > > > >>> > > > > > > wrote: > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > I think that the problem may be reader specification. > > > > > > > readFiles accepts a root directory, not a single file. So > > > > > > > you should use "readFiles D:/Bhagwat" If there is more than > > > > > > > data in that directory then you should copy the data to a > > > > > > > different directory > > > and use that. > > > > > > > > > > > > > > readFiles uses the FileTreeReader class. I didn't have the > > > > > > > foresight to accept the possibility of a single file ... I > > > > > > > will do that now before I forget ... I will also add an > > > > > > > error message if the directory > > > > > > is empty. > > > > > > > > > > > > > > You can always use a different reader. I have never used > > > > > > > it, but I think that TextReader might do what you want. The > > > > > > > piper line would be reader TextReader > > > > > > > files=D:/Bhagwat/data.txt > > > > > > > > > > > > > > After that any of your specifications for writing xmi files > > > > > > > should > > > > > work. > > > > > > > One clarification: "writeXmis" does not have an asterisk. > > > > > > > You probably added one for my benefit. > > > > > > > > > > > > > > Sean > > > > > > > > > > > > > > -----Original Message----- > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > > Sent: Thursday, November 09, 2017 9:06 AM > > > > > > > To: > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > Hello Sean, > > > > > > > > > > > > > > Thank you very much for such a valuable inputs. With these, > > > > > > > I could dive a little deeper in it now. > > > > > > > > > > > > > > I have run the *DefaultFastPipeline.piper* file by adding > > > > > > > your given commands. > > > > > > > > > > > > > > To read clinical note as a input I have added this command > > > > > > > > > > > > > > readFiles D:/Bhagwat/data.txt > > > > > > > > > > > > > > > > > > > > > Execution of this piper file is successful on command line. > > > > > > > to get the output in file or directory, I have tried three > > > > > > > ways as below > > > > > > > > > > > > > > 1) addLast FileTreeXmiWriter > > > > > > > OutputDirectory=D:\Bhagwat\output // in piper > > > > > > > > file > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *2) writeXmis* D:/Bhagwat/output // in piper file > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 3) --xmiOut D:/Bhagwat/output // on command line > > > > > > > > > > > > > > > > > > > > > But it is not generating any output file. please suggest on > this. > > > > > > > > > > > > > > > > > > > > > On 8 November 2017 at 18:39, Finan, Sean > > > > > > > <sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@ > > > > > > childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu > > > <mailto: > > > > > > sean.fi...@childrens.harvard.edu>> > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > The ctakes-temporal module has the components needed to > > > > > > > > generate > > > > > > tlinks. > > > > > > > > Using trunk, the following can be added to the end of the > > > > > > > > default clinical pipeline piper file (or a copy): > > > > > > > > > > > > > > > > load TemporalSubPipe > > > > > > > > > > > > > > > > > > > > > > > > The TemporalSubPipe.piper file contains the following > > > > > > > > setup to create events, times, time relative to document > > > > > > > > writing > > > > > > > > (doctimerel) > > > > > > and tlinks: > > > > > > > > > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > /////////////////// > > > > > > > > // Commands and parameters to create a default temporal > > > > > > > > processing sub-pipeline. This is not a full pipeline. > > > > > > > > > > > > > > > > // 'Generic' Events. Use addDescription and let the > > > > > > > > EventAnnotator set itself up with defaults. > > > > > > > > addDescription EventAnnotator > > > > > > > > > > > > > > > > // Times. There aren't default models, so set > > > > > > > > specifically add BackwardsTimeAnnotator > > > > > > > > classifierJarPath=/org/apache/ > > > > > > > > ctakes/temporal/ae/timeannotator/model.jar > > > > > > > > > > > > > > > > // DocTimeRel: the relation bin for Events to the Document > > > > > > > > Creation > > > > > > Time. > > > > > > > > add DocTimeRelAnnotator classifierJarPath=/org/apache/ > > > > > > > > ctakes/temporal/ae/doctimerel/model.jar > > > > > > > > > > > > > > > > // Event - Time binary relations. > > > > > > > > add EventTimeRelationAnnotator > > > > > > > > classifierJarPath=/org/apache/ > > > > > > > > ctakes/temporal/ae/eventtime/model.jar > > > > > > > > > > > > > > > > // Event - Event binary relations. > > > > > > > > add EventEventRelationAnnotator > > > > > > > > classifierJarPath=/org/apache/ > > > > > > > > ctakes/temporal/ae/eventevent/model.jar > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > /////////////////// > > > > > > > > > > > > > > > > To see the code used for tlink detection, search ctakes > > > > > > > > for the EventTimeRelationAnnotator.java and > > > > > > > > EventEventRelationAnnotator.java classes. All piper "add" > > > > commands > > > > > are followed by a class name. > > > > > > > > > > > > > > > > I have a piper file that I use for testing a 'full' ctakes > > > > pipeline: > > > > > > > > > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > /////////////////// > > > > > > > > // Advanced Tokenization: Regex sectionization, BIO > > > > > > > > Sentence Detector (lumper), Paragraphs, Lists load > > > > > > > > AdvancedTokenizerPipeline > > > > > > > > > > > > > > > > // Always need these ... > > > > > > > > add ContextDependentTokenizerAnnotator > > > > > > > > add POSTagger > > > > > > > > > > > > > > > > // Chunkers > > > > > > > > load ChunkerSubPipe > > > > > > > > > > > > > > > > // Default fast dictionary lookup set minimumSpan=2 load > > > > > > > > DictionarySubPipe > > > > > > > > > > > > > > > > // Cleartk Entity Attributes (negation, uncertainty, etc.) > > > > > > > > load AttributeCleartkSubPipe > > > > > > > > > > > > > > > > // Entity Relations (degree/severity, anatomical location) > > > > > > > > load RelationSubPipe > > > > > > > > > > > > > > > > // Temporal (event, time, dtr, tlink) load TemporalSubPipe > > > > > > > > > > > > > > > > // Coreferences (e.g. patient = he) load CorefSubPipe > > > > > > > > > > > > > > > > // Html output > > > > > > > > add pretty.html.HtmlTextWriter > > > > > > > > > > > > > > > > // XMI output > > > > > > > > writeXmis > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > ////////////////////////////////////////////////////////// > > > > > > > > // > > > > > > > > /////////////////// > > > > > > > > > > > > > > > > > > > > > > > > Sean > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com > <mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM > > > > > > > > To: > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto > > > > > > > > :d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > > > Hi Sean and Tim, > > > > > > > > > > > > > > > > Could you please provide your valuable inputs for below > > > questions: > > > > > > > > > > > > > > > > I am interested in finding the context of clinical notes > > > > > > > > like if any procedure is happened or not. > > > > > > > > I think TLINKS values on web API maybe helpful to get the > > > > > > > > required result, not sure though. Please confirm > > > > > > > > > > > > > > > > I am not able to find the code to generate TLINKS, could > > > > > > > > you please help me locate the code. > > > > > > > > > > > > > > > > On 7 November 2017 at 16:18, Gandhi Rajan Natarajan < > > > > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@ar > > > > > > > > is > > > > > > > > gl > > > > > > > > obal > > > > > > > > .com > > > > > > ><mailto:gandhi.natara...@arisglobal.com<mailto:Gandhi.Nataraj > > > > > > >an > > > > > > >@ > > > > > > arisglobal.com>>> wrote: > > > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > > > Glad that you got it working. > > > > > > > > > > > > > > > > > > Regarding cTAKES functional questions below, I guess > > > > > > > > > Sean or Tim is the right person to give more info. > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com > > <mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM > > > > > > > > > To: > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mail > > > > > > > > > to > > > > > > > > > :d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > > > > > Thanks Gandhi, > > > > > > > > > > > > > > > > > > I have gone through both the links and able to get the > > results. > > > > > > > > > > > > > > > > > > I am interested in finding the context of clinical notes > > > > > > > > > like if any procedure is happened or not. > > > > > > > > > I think TLINKS values on web API maybe helpful to get > > > > > > > > > the required result, not sure though. Please confirm > > > > > > > > > > > > > > > > > > I am not able to find the code to generate TLINKS, could > > > > > > > > > you please help me locate the code. > > > > > > > > > > > > > > > > > > And also could anybody please guide me to find context > > > > > > > > > out of the note-sentence. > > > > > > > > > > > > > > > > > > On 3 November 2017 at 19:44, Gandhi Rajan Natarajan < > > > > > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@ > > > > > > arisglobal.com><mailto:gandhi.natara...@arisglobal.com<mailto: > > > > > > gandhi.natara...@arisglobal.com>>> wrote: > > > > > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > > > > > I'm not sure if it will help you. But I extended the > > > > > > > > > > code available in > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__g > > > > > > > > > > it > > > > > > > > > > hu > > > > > > > > > > b.co > > > > > > > > > > m_ > > > > > > > > > > he > > > > > > > > > > al > > > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d= > > > > > > > > > > Dw > > > > > > > > > > IB > > > > > > > > > > aQ&c > > > > > > > > > > =q > > > > > > > > > > S4 > > > > > > > > > > go > > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp > > > > > > > > > > yI > > > > > > > > > > is > > > > > > > > > > CYNY > > > > > > > > > > mQ > > > > > > > > > > CP > > > > > > > > > > 6r > > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw > > > > > > > > > > qn > > > > > > > > > > 6b OrBk &s =W yt > > > > > > > > > > apFSqEoy1Za7AzcNuuMLQutzXpWTHlzSVl2Gw7zU&e= > > > > > > > > > > to get the XML output and parsed the required mentions > > > > > > > > > > for me like Procedure, Disorder etc. > > > > > > > > > > > > > > > > > > > > You can look at the code here - > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__g > > > > > > > > > > it > > > > > > > > > > hu > > > > > > > > > > b.co > > > > > > > > > > m_ > > > > > > > > > > &d > > > > > > > > > > =D > > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > > > > > > > > > > fs > > > > > > > > > > 67 > > > > > > > > > > GvlG > > > > > > > > > > Zs > > > > > > > > > > tT > > > > > > > > > > py > > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS > > > > > > > > > > Of > > > > > > > > > > qj > > > > > > > > > > R05A > > > > > > > > > > QW Cn wq > > > > > > > > > > n6bOrBk&s=YNBbaimyz_GjWzdMxuIgONTtHRvZiaguYc0pCoNiYjA& > > > > > > > > > > e= gandhirajan/cTAKES/tree/master/cTakes-Rest-Service/ > > > > > > > > > > src/main/java/com/ctakes/nlp and see if it helps. Cheers. > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com > > > <mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM > > > > > > > > > > To: > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><ma > > > > > > > > > > il > > > > > > > > > > to > > > > > > > > > > :d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > > > > > > > Thank you Sean and Tim for your support. > > > > > > > > > > > > > > > > > > > > I have followed the links given by Sean and overview > > > > > > > > > > by Tim which is pretty helpful to get the better > > > > > > > > > > understanding of source > > > > > > code. > > > > > > > > > > > > > > > > > > > > I have run ctakes-example project that internally > > > > > > > > > > executes > > > > > > > > > > ClinicalPipelineFactory.getDefaultPipeline() method. > > > > > > > > > > This has given results like POS tag, Polarity, etc. > > > > > > > > > > Now, I am more interested in finding Procedure, > > > > > > > > > > Medication, Drug, > > > > > > > etc. > > > > > > > > > > Could you please point me to the code file or help > > > > > > > > > > with code snippet to capture above terms. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 30 October 2017 at 19:36, Finan, Sean > > > > > > > > > > <sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@ > > > > > > childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu > > > <mailto: > > > > > > sean.fi...@childrens.harvard.edu>> > > > > > > > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > > > > > > > If you are interested in the default clinical > > > > > > > > > > > pipeline, you can look at the wiki here: > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A_ > > > > > > > > > > > _c > > > > > > > > > > > wiki > > > . > > > > > > apache. > > > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p > > > > > > > > > > > op > > > > > > > > > > > lM > > > > > > > > > > > 69zy > > > > > > > > > > > _3 > > > > > > > > > > > xh > > > > > > > > > > > Kw > > > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > > > > > > > > > > > pK > > > > > > > > > > > Gd > > > > > > > > > > > 4f7d > > > > > > > > > > > 4g > > > > > > > > > > > Ta > > > > > > > > > > > o& > > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz > > > > > > > > > > > 5x > > > > > > > > > > > 7X > > > > > > > > > > > XCD3 > > > > > > > > > > > tr > > > > > > > > > > > fx > > > > > > > > > > > 4P > > > > > > > > > > > oJCYVmL-_RYlSoCOOPf-i_tMs&e= > > > > > > > > > > > Default+Clinical+Pipeline > > > > > > > > > > > For a visual representation of what Tim described. > > > > > > > > > > > > > > > > > > > > > > The AEs used for the ctakes 4.0 default clinical > > > > > > > > > > > pipeline are shown at the bottom of this wiki page: > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A_ > > > > > > > > > > > _c > > > > > > > > > > > wiki > > > . > > > > > > apache. > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC > > > > > > > > > > > op > > > > > > > > > > > px > > > > > > > > > > > eFU& > > > > > > > > > > > r= > > > > > > > > > > > fs > > > > > > > > > > > 67 > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA > > > > > > > > > > > dL > > > > > > > > > > > _T > > > > > > > > > > > aKVF > > > > > > > > > > > qO > > > > > > > > > > > nS > > > > > > > > > > > Of > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK > > > > > > > > > > > lf > > > > > > > > > > > 24 > > > > > > > > > > > gMo6 Gh Jw s& e= > > > > > > > > > > > confluence/display/CTAKES/Piper+Files > > > > > > > > > > > The Class names are shown, but not the packages. If > > > > > > > > > > > you have a decent IDE they should be easy to find - > > > > > > > > > > > for Intellij press CTRL-N and type the name of the > class. > > > > > > > > > > > > > > > > > > > > > > Another option is to use the Simple Pipeline > > > > > > > > > > > Fabricator gui to look at the available readers and > > > > > > > > > > > AEs and see what they do (and their required inputs). > > > > > > > > > > > Check the wiki > > > at: > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A_ > > > > > > > > > > > _c > > > > > > > > > > > wiki > > > . > > > > > > apache. > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC > > > > > > > > > > > op > > > > > > > > > > > px > > > > > > > > > > > eFU& > > > > > > > > > > > r= > > > > > > > > > > > fs > > > > > > > > > > > 67 > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA > > > > > > > > > > > dL > > > > > > > > > > > _T > > > > > > > > > > > aKVF > > > > > > > > > > > qO > > > > > > > > > > > nS > > > > > > > > > > > Of > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK > > > > > > > > > > > lf > > > > > > > > > > > 24 > > > > > > > > > > > gMo6 > > > > > > > > > > > Gh > > > > > > > > > > > Jw s& e= > > > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator > > > > > > > > > > > +G UI If you launch the gui and let it gather > > > > > > > > > > > information, you can look at the pipe bit names and > > > > > > > > > > > descriptions (reader, > > > AE). > > > > > > > > > > > If it interests you, click the "add" button (big > > > > > > > > > > > '+') and on the right you will see the path to the > > > > > > > > > > > source code for that bit of the pipeline. Not all > > > > > > > > > > > AEs > > > > > > > > > > are described ... > > > > > > > > > > > calling all community ... but I think that most are. > > > > > > > > > > > > > > > > > > > > > > Sean > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > > > From: Miller, Timothy > > > > > > > > > > > [mailto:timothy.mil...@childrens.harvard.edu<mailto: > > > > > > > > > > > T > > > > > > imothy.mil...@childrens.harvard.edu><mailto:Timothy. > > > > > > mil...@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h > > > > > > ar > > > > > > va > > > > > > rd.e > > > > > > du > > > > > > >>] > > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM > > > > > > > > > > > To: > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>< > > > > > > > > > > > ma > > > > > > > > > > > il > > > > > > > > > > > to:d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > > > Subject: Re: source code of user installation of > cTakes. > > > > > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > > > > > > > > > cTAKES is based on Apache UIMA, which is a > > > > > > > > > > > pipeline-building > > > > > > tool. > > > > > > > > > > > So the output you see in the CVD is the result of > > > > > > > > > > > many different pieces of the pipeline run in > > > > > > > > > > > succession, and they are each in different modules of > cTAKES. > > > > > > > > > > > ctakes-core has the most basic elements that will > > > > > > > > > > > run for every pipeline -- tokens, sentences, > > > > > > > etc. > > > > > > > > > > > ctakes-dictionary-lookup-fast is what maps text > > > > > > > > > > > spans to UMLS > > > > > > > > concepts. > > > > > > > > > > ctakes-assertion finds negation status. > > > > > > > > > > > ctakes-chunker creates syntactic chunks and > > > > > > > > > > > ctakes-pos-tagger finds part-of-speech tags for tokens. > > > > > > > > > > > There are many others but I think this covers the > > > > > > > > > > > basics. In general, if you see a type in the CVD > > > > > > > > > > > that you find interesting, your best bet is to grep > > > > > > > > > > > the code for that type and see where it is being > > > > > > > > > > > created (if you don't want to wait for an email > > > > > > > > > > from the list). > > > > > > > > > > > Pipeline components are known as "Analysis Engines" > > > > > > > > > > > (AEs) in UIMA lingo and as a result are often in a > > > > > > > > > > > package ending in > > > > > .ae. > > > > > > > > > > > Hope this helps you navigate the code! > > > > > > > > > > > Tim > > > > > > > > > > > > > > > > > > > > > > ________________________________________ > > > > > > > > > > > From: Bhagwat Posane <bhagwat.pos...@gmail.com<mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com > <mailto: > > > > bhagwat > > > > > . > > > > > > pos...@gmail.com>>> > > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM > > > > > > > > > > > To: > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>< > > > > > > > > > > > ma > > > > > > > > > > > il > > > > > > > > > > > to:d > > > > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > > > Subject: Re: source code of user installation of > cTakes. > > > > > > > > > > > [EXTERNAL] > > > > > > > > > > > > > > > > > > > > > > Thanks Gandhi, for the quick response. > > > > > > > > > > > > > > > > > > > > > > I have source code of cTAKES which is available > > > > > > > > > > > under > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A_ > > > > > > > > > > > _svn > > . > > > > > > > > > > > apache.org_repos_asf_ctakes_trunk&d=DwIBaQ&c=qS4goWB > > > > > > > > > > > T7 > > > > > > > > > > > po > > > > > > > > > > > plM6 > > > > > > > > > > > 9z > > > > > > > > > > > y_ > > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G > > > > > > > > > > > TK > > > > > > > > > > > - > > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR > > > > > > > > > > > _ > > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB > > > > > > > > > > > TC EN aERN 6B U3zisHhnM18Wo&e=. I see there are many > > > > > > > > > > > projects in it. > > > > > > > > > > > > > > > > > > > > > > I am checking user version using > > > > > > > > > > > \CTAKES_HOME\bin\runctakesCVD.bat, > > > > > > > > > > > this opens an UI. I could run analysis engine for a > > > > > > > > > > > clinical note according to the guidelines in the > > > user-install guide.. > > > > > > > > > > > It gives me descent result in the left pane of the UI. > > > > > > > > > > > Now I am looking for the source-code that gives this > > > > > > > > > > > result for a clinical note. Could you please point > > > > > > > > > > > me to the project, where can I see to it in the > > > > > > > > > > > ctakes-trunk or > > > so. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 30 October 2017 at 16:36, Gandhi Rajan Natarajan > > > > > > > > > > > < > > > > > > > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natara > > > > > > > > > > > ja > > > > > > > > > > > n@ > > > > > > arisglobal.com><mailto:gandhi.natara...@arisglobal.com<mailto: > > > > > > gandhi.natara...@arisglobal.com>>> wrote: > > > > > > > > > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > > > > > > > > > The source code of cTAKES is available under > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3 > > > > > > > > > > > > A_ > > > > > > > > > > > > _svn > > > . > > > > > > apache. > > > > > > > > > > > > or > > > > > > > > > > > > g_ > > > > > > > > > > > > re > > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi > > > > > > > > > > > > oC > > > > > > > > > > > > op > > > > > > > > > > > > pxeF > > > > > > > > > > > > U& > > > > > > > > > > > > r= > > > > > > > > > > > > He > > > > > > > > > > > > up > > > > > > > > > > > > -I > > > > > > > > > > > > bs > > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY > > > > > > > > > > > > x6 > > > > > > > > > > > > 67 > > > > > > > > > > > > 4h&m > > > > > > > > > > > > =E > > > > > > > > > > > > fs > > > > > > > > > > > > fu > > > > > > > > > > > > j3 > > > > > > > > > > > > 7p > > > > > > > > > > > > WN > > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs > > > > > > > > > > > > 6i > > > > > > > > > > > > ya > > > > > > > > > > > > qEJz > > > > > > > > > > > > 4R > > > > > > > > > > > > Pg > > > > > > > > > > > > Ch > > > > > > > > > > > > sB > > > > > > > > > > > > LY > > > > > > > > > > > > IC > > > > > > > > > > > > TCQHnrmw&e= > > > > > > > > > > > > asf/ctakes/trunk > > > > > > > > > > > > > > > > > > > > > > > > Regarding the resources to start off, cTAKES > > > > > > > > > > > > official site documentations should be fine. > > > > > > > > > > > > > > > > > > > > > > > > I also feel, mailing list is the one stop shop for > > > > > > > > > > > > all your other detailed queries. > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > > > > From: Bhagwat Posane > > > > > > > > > > > > [mailto:bhagwat.pos...@gmail.com > > > > > <mailto: > > > > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mail > > > > > > to > > > > > > :b > > > > > > hagw > > > > > > a > > > > > > t.pos...@gmail.com>>] > > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM > > > > > > > > > > > > To: > > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org > > > > > > ><mailto:dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > > > > Subject: source code of user installation of cTakes. > > > > > > > > > > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > > > > > > > I have seen the results of user installation of > > > > > > > > > > > > cTakes , the output is pretty interesting. > > > > > > > > > > > > > > > > > > > > > > > > Can anybody point to the source code of the same? > > > > > > > > > > > > > > > > > > > > > > > > I have just started exploring this project if > > > > > > > > > > > > anybody point me to good resources to understand > > > > > > > > > > > > it thoroughly that will be great > > > > > > > > > > help....!! > > > > > > > > > > > > > > > > > > > > > > > > I have downloaded the developer installation too. > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Bhagwat Posane > > > > > > > > > > > > This email and any files transmitted with it are > > > > > > > > > > > > confidential and intended solely for the use of > > > > > > > > > > > > the individual or entity to whom they are > > > > > > > > > > > addressed. > > > > > > > > > > > > If you are not the named addressee you should not > > > > > > > > > > > > disseminate, distribute or copy this e-mail. > > > > > > > > > > > > Please notify the sender or system manager by > > > > > > > > > > > > email immediately if you have received this e-mail > > > > > > > > > > > > by mistake and delete this e-mail from your > > > > > > > > > > > > system. If you are not the intended recipient you > > > > > > > > > > > > are notified that disclosing, copying, > > > > > > > > > > > > distributing or taking any action in reliance on > > > > > > > > > > > > the contents of this information is strictly > > > > > > > > prohibited and against the law. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > Thanks, > > > > > > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > Thanks, > > > > > > > > > > Bhagwat Posane > > > > > > > > > > This email and any files transmitted with it are > > > > > > > > > > confidential and intended solely for the use of the > > > > > > > > > > individual or entity to whom they are > > > > > > > > > addressed. > > > > > > > > > > If you are not the named addressee you should not > > > > > > > > > > disseminate, distribute or copy this e-mail. Please > > > > > > > > > > notify the sender or system manager by email > > > > > > > > > > immediately if you have received this e-mail by > > > > > > > > > > mistake and delete this e-mail from your system. If > > > > > > > > > > you are not the intended recipient you are notified > > > > > > > > > > that disclosing, copying, distributing or taking any > > > > > > > > > > action in reliance on the contents of this information > > > > > > > > > > is strictly > > > > > > prohibited and against the law. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Thanks, > > > > > > > > > Bhagwat Posane > > > > > > > > > This email and any files transmitted with it are > > > > > > > > > confidential and intended solely for the use of the > > > > > > > > > individual or entity to whom they are > > > > > > > > addressed. > > > > > > > > > If you are not the named addressee you should not > > > > > > > > > disseminate, distribute or copy this e-mail. Please > > > > > > > > > notify the sender or system manager by email immediately > > > > > > > > > if you have received this e-mail by mistake and delete > > > > > > > > > this e-mail from your system. If you are not the > > > > > > > > > intended recipient you are notified that disclosing, > > > > > > > > > copying, distributing or taking any action in reliance > > > > > > > > > on the contents of this information is strictly > > > > > prohibited and against the law. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > Thanks, > > > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Thanks, > > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Thanks, > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Thanks, > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Thanks, > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Thanks, > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > -- > > > > Thanks, > > > > Bhagwat Posane > > > > > > > > > > > > > > > -- > > Thanks, > > Bhagwat Posane > > > > > > -- > Thanks, > Bhagwat Posane > -- Thanks, Bhagwat Posane
