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Posted to dev@ctakes.apache.org by Clayton Turner <ca...@g.cofc.edu> on 2014/07/30 17:11:48 UTC
Exporting YTEX Pipeline
Hi, I'm trying to export the data I get from running the pipeline through
the Collection Processing Engine.
I set up the pipeline where I have a directory where all the XML is output
to, but I am having issues at this point.
I've tried using the built in Exporter from the Data Mining section on this
page https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide but
those notes are out of date. Even altering directories to match the files
still gives me errors about not being able to find the ExporterImpl class.
The class version of this file only exists outside of the target directory
for the ctakes snapshot and attempting to use it still fails.
I then ventured to here:
https://code.google.com/p/ytex/source/browse/#svn%2Ftrunk%2Fworkspace%2Fexamples%2Ffracture
The files here match up to the data mining section from the previous link -
so I created my export.xml file and changed everything that needed to be
changed for my example (tried to even run bone fracture), but I cannot get
data exported, no matter what I do.
Is there a way to use some new(er) implementation of the
SparseDataExporterImpl class or is there an alternative for extracting data
for use with weka?
I've messaged about this in the past but I don't believe I was thorough
enough with my issues.
Thanks in advance,
Clayton
Re: Exporting YTEX Pipeline
Posted by vijay garla <vn...@gmail.com>.
Great that it worked! Note that the examples for fracture (bag of
words/bag of cuis) is just scratching the surface of feature
representations - there are a gazillion ways to export the document (bag of
words per section, include negation status, ...) Doing this via SQL makes
it super easy
Best,
VJ
On Wed, Jul 30, 2014 at 9:07 PM, Clayton Turner <ca...@g.cofc.edu>
wrote:
> Awesome!!
>
> It worked!
>
> The only things I had to change (since I'm on Windows) was flipping the
> slashes when necessary and removing the first slash when specifying the
> -Dlog4j.configuration=file:/...
>
> Thank you so much for putting up with my issues
>
> -Clayton
>
>
> On Wed, Jul 30, 2014 at 2:48 PM, vijay garla <vn...@gmail.com> wrote:
>
> > Can you try this:
> > copy
> >
> >
> https://code.google.com/p/ytex/source/browse/trunk/workspace/examples/fracture/cui/export.template.xml
> > to CTAKES_HOME\desc\ctakes-ytex\fracture\cui.xml
> > replace %DB_SCHEMA% with your database schema name (value of db.schema in
> > your ytex.properties file)
> >
> > Then from a command prompt, execute the following commands:
> > cd CTAKES_HOME
> > bin\setenv.bat
> > java -cp %CLASSPATH%
> > -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx256m
> > org.apache.ctakes.ytex.kernel.SparseDataExporterImpl -prop
> > desc\ctakes-ytex\fracture\cui.xml -type weka
> >
> > Tell me if you run into any issues.
> >
> > I will add this to the ctakes confluence doc.
> >
> > Best,
> >
> > VJ
> >
> >
> > On Wed, Jul 30, 2014 at 5:11 PM, Clayton Turner <ca...@g.cofc.edu>
> > wrote:
> >
> > > Hi, I'm trying to export the data I get from running the pipeline
> through
> > > the Collection Processing Engine.
> > >
> > > I set up the pipeline where I have a directory where all the XML is
> > output
> > > to, but I am having issues at this point.
> > >
> > > I've tried using the built in Exporter from the Data Mining section on
> > this
> > > page https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
> > but
> > > those notes are out of date. Even altering directories to match the
> files
> > > still gives me errors about not being able to find the ExporterImpl
> > class.
> > > The class version of this file only exists outside of the target
> > directory
> > > for the ctakes snapshot and attempting to use it still fails.
> > >
> > > I then ventured to here:
> > >
> > >
> >
> https://code.google.com/p/ytex/source/browse/#svn%2Ftrunk%2Fworkspace%2Fexamples%2Ffracture
> > >
> > > The files here match up to the data mining section from the previous
> > link -
> > > so I created my export.xml file and changed everything that needed to
> be
> > > changed for my example (tried to even run bone fracture), but I cannot
> > get
> > > data exported, no matter what I do.
> > >
> > > Is there a way to use some new(er) implementation of the
> > > SparseDataExporterImpl class or is there an alternative for extracting
> > data
> > > for use with weka?
> > >
> > > I've messaged about this in the past but I don't believe I was thorough
> > > enough with my issues.
> > >
> > > Thanks in advance,
> > > Clayton
> > >
> >
>
>
>
> --
> --
> Clayton Turner
> email: caturner3@g.cofc.edu
> phone: (843)-424-3784
> web: claytonturner.blogspot.com
>
> -------------------------------------------------------------------------------------------------
> “When scientifically investigating the natural world, the only thing worse
> than a blind believer is a seeing denier.”
> - Neil deGrasse Tyson
>
Re: Exporting YTEX Pipeline
Posted by Clayton Turner <ca...@g.cofc.edu>.
Awesome!!
It worked!
The only things I had to change (since I'm on Windows) was flipping the
slashes when necessary and removing the first slash when specifying the
-Dlog4j.configuration=file:/...
Thank you so much for putting up with my issues
-Clayton
On Wed, Jul 30, 2014 at 2:48 PM, vijay garla <vn...@gmail.com> wrote:
> Can you try this:
> copy
>
> https://code.google.com/p/ytex/source/browse/trunk/workspace/examples/fracture/cui/export.template.xml
> to CTAKES_HOME\desc\ctakes-ytex\fracture\cui.xml
> replace %DB_SCHEMA% with your database schema name (value of db.schema in
> your ytex.properties file)
>
> Then from a command prompt, execute the following commands:
> cd CTAKES_HOME
> bin\setenv.bat
> java -cp %CLASSPATH%
> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx256m
> org.apache.ctakes.ytex.kernel.SparseDataExporterImpl -prop
> desc\ctakes-ytex\fracture\cui.xml -type weka
>
> Tell me if you run into any issues.
>
> I will add this to the ctakes confluence doc.
>
> Best,
>
> VJ
>
>
> On Wed, Jul 30, 2014 at 5:11 PM, Clayton Turner <ca...@g.cofc.edu>
> wrote:
>
> > Hi, I'm trying to export the data I get from running the pipeline through
> > the Collection Processing Engine.
> >
> > I set up the pipeline where I have a directory where all the XML is
> output
> > to, but I am having issues at this point.
> >
> > I've tried using the built in Exporter from the Data Mining section on
> this
> > page https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
> but
> > those notes are out of date. Even altering directories to match the files
> > still gives me errors about not being able to find the ExporterImpl
> class.
> > The class version of this file only exists outside of the target
> directory
> > for the ctakes snapshot and attempting to use it still fails.
> >
> > I then ventured to here:
> >
> >
> https://code.google.com/p/ytex/source/browse/#svn%2Ftrunk%2Fworkspace%2Fexamples%2Ffracture
> >
> > The files here match up to the data mining section from the previous
> link -
> > so I created my export.xml file and changed everything that needed to be
> > changed for my example (tried to even run bone fracture), but I cannot
> get
> > data exported, no matter what I do.
> >
> > Is there a way to use some new(er) implementation of the
> > SparseDataExporterImpl class or is there an alternative for extracting
> data
> > for use with weka?
> >
> > I've messaged about this in the past but I don't believe I was thorough
> > enough with my issues.
> >
> > Thanks in advance,
> > Clayton
> >
>
--
--
Clayton Turner
email: caturner3@g.cofc.edu
phone: (843)-424-3784
web: claytonturner.blogspot.com
-------------------------------------------------------------------------------------------------
“When scientifically investigating the natural world, the only thing worse
than a blind believer is a seeing denier.”
- Neil deGrasse Tyson
Re: Exporting YTEX Pipeline
Posted by vijay garla <vn...@gmail.com>.
Can you try this:
copy
https://code.google.com/p/ytex/source/browse/trunk/workspace/examples/fracture/cui/export.template.xml
to CTAKES_HOME\desc\ctakes-ytex\fracture\cui.xml
replace %DB_SCHEMA% with your database schema name (value of db.schema in
your ytex.properties file)
Then from a command prompt, execute the following commands:
cd CTAKES_HOME
bin\setenv.bat
java -cp %CLASSPATH%
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx256m
org.apache.ctakes.ytex.kernel.SparseDataExporterImpl -prop
desc\ctakes-ytex\fracture\cui.xml -type weka
Tell me if you run into any issues.
I will add this to the ctakes confluence doc.
Best,
VJ
On Wed, Jul 30, 2014 at 5:11 PM, Clayton Turner <ca...@g.cofc.edu>
wrote:
> Hi, I'm trying to export the data I get from running the pipeline through
> the Collection Processing Engine.
>
> I set up the pipeline where I have a directory where all the XML is output
> to, but I am having issues at this point.
>
> I've tried using the built in Exporter from the Data Mining section on this
> page https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide but
> those notes are out of date. Even altering directories to match the files
> still gives me errors about not being able to find the ExporterImpl class.
> The class version of this file only exists outside of the target directory
> for the ctakes snapshot and attempting to use it still fails.
>
> I then ventured to here:
>
> https://code.google.com/p/ytex/source/browse/#svn%2Ftrunk%2Fworkspace%2Fexamples%2Ffracture
>
> The files here match up to the data mining section from the previous link -
> so I created my export.xml file and changed everything that needed to be
> changed for my example (tried to even run bone fracture), but I cannot get
> data exported, no matter what I do.
>
> Is there a way to use some new(er) implementation of the
> SparseDataExporterImpl class or is there an alternative for extracting data
> for use with weka?
>
> I've messaged about this in the past but I don't believe I was thorough
> enough with my issues.
>
> Thanks in advance,
> Clayton
>