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
