RE: How to get XMI output fie from java jcas?

2018-04-10 Thread Gandhi Rajan Natarajan
HI Reed,

Iā€™m not very sure of CVD result analysis. But we do have an XML parser in 
cTAKES REST module to parse the output XML and generate JSON output of our 
desired format. Have a look at this link - 
https://github.com/GoTeamEpsilon/ctakes-rest-service/blob/master/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/XMLParser.java

Hope it helps.

Regards,
Gandhi

From: Reed Villanueva [mailto:villanuevar...@gmail.com]
Sent: Tuesday, April 10, 2018 3:45 PM
To: user@ctakes.apache.org
Subject: Re: How to get XMI output fie from java jcas?

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:ā€‹

// 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<mailto: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<mailto:villanuevar...@gmail.com>]
Sent: Tuesday, April 10, 2018 1:15 PM
To: user@ctakes.apache.org<mailto: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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Re: How to get XMI output fie from java jcas?

2018-04-10 Thread Reed Villanueva
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:ā€‹

// 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.
> 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.
>


RE: How to get XMI output fie from java jcas?

2018-04-10 Thread Gandhi Rajan Natarajan
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.
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.


How to get XMI output fie from java jcas?

2018-04-10 Thread Reed Villanueva
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.