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]
Sent: Friday, November 10, 2017 6:13 AM
To: 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>
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]
> Sent: Thursday, November 09, 2017 9:06 AM
> To: 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
> >
> 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]
> > Sent: Wednesday, November 08, 2017 2:41 AM
> > To: 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> 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]
> > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > To: 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> 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__github.com_
> > > > he
> > > > al
> > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=q
> > > > S4
> > > > go
> > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQ
> > > > CP
> > > > 6r
> > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&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__github.com_
> > > > &d
> > > > =D
> > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZs
> > > > tT
> > > > py
> > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQW
> > > > 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]
> > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > To: 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
> > > > >
> > > > 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__cwiki.apache.
> > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3
> > > > > xh
> > > > > Kw
> > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > > > Ta
> > > > > o&
> > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3tr
> > > > > 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__cwiki.apache.
> > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > fs
> > > > > 67
> > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqO
> > > > > nS
> > > > > Of
> > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6Gh
> > > > > 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__cwiki.apache.
> > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > fs
> > > > > 67
> > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqO
> > > > > nS
> > > > > Of
> > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6Gh
> > > > > Jw s& e=
> > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator+GUI
> > > > > 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]
> > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > To: 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>
> > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > To: 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=qS4goWBT7poplM69z
> > > > > y_
> > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_
> > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCENaERN6B
> > > > > 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> wrote:
> > > > >
> > > > > > Hi Bhagwat,
> > > > > >
> > > > > > The source code of cTAKES is available under
> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.
> > > > > > or
> > > > > > g_
> > > > > > re
> > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&
> > > > > > r=
> > > > > > He
> > > > > > up
> > > > > > -I
> > > > > > bs
> > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=E
> > > > > > fs
> > > > > > fu
> > > > > > j3
> > > > > > 7p
> > > > > > WN
> > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4R
> > > > > > 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]
> > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > To: 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
