I see, thanks Gandhi. Would you also be able to point me to some source
file examples of *reading* from XMIs (like how the ctakesCVD does to
populate the "Analysis Results" pane)? I tried tracing down from
the org.apache.uima.tools.cvd.CVD package, but could not find where these
things are happening.
For those also interested, the relevant snippet of code for generating XMIs
from JCASs is:
// assuming we already have a jcas object with extracted information
> ByteArrayOutputStream output = new ByteArrayOutputStream();
> XmiCasSerializer.serialize(jcas.getCas(), output);
> String outputStr = output.toString();
> Files.write(Paths.get("Result.xml"), outputStr.getBytes());
On Mon, Apr 9, 2018 at 11:48 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Reed,
>
>
>
> Just check the PipelineRunner class in the link - https://github.com/
> GoTeamEpsilon/ctakes-rest-service/blob/master/ctakes-
> web-rest/src/main/java/org/apache/ctakes/rest/service/
> CtakesRestController.java and see if it helps.
>
>
>
> *Regards,*
>
> *Gandhi*
>
>
>
> *From:* Reed Villanueva [mailto:villanuevar...@gmail.com]
> *Sent:* Tuesday, April 10, 2018 1:15 PM
> *To:* user@ctakes.apache.org
> *Subject:* How to get XMI output fie from java jcas?
>
>
>
> How can I get the output of a pipeline built in java as an XMI file
> similar to how piper files output extracted annotation information in form
> of XMI files? Eg. I have the code
>
>
>
> AggregateBuilder builder = *new *AggregateBuilder();
>
> builder.add( ClinicalPipelineFactory.*getDefaultPipeline*() );
>
> SimplePipeline.*runPipeline*( jcas, builder.createAggregateDescription()
> );
>
>
>
> But how do I get all of the annotation info in XMI form from the jcas
> after this (like what gets generated in outputDirectory when doing
>
> bin/*runClinicalPipeline * -i *inputDirectory* --xmiOut *outputDirectory*
> --user *umlsUsername* --pass *umlsPassword*
>
> )? Also, what class can be used to read existing XMI output files?
>
> Thank you.
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