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Posted to dev@ctakes.apache.org by John Doe <lu...@gmail.com> on 2021/04/22 17:09:08 UTC
Running cTAKES Default Clinical Pipeline from Code
Hello,
I'm having trouble running the default clinical pipeline from code. It
keeps giving me the error message that I have an invalid UMLS License.
However, I know my license is valid and I have managed to get the default
pipeline to run using the PiperFileReader with the same credentials.
This is the code that doesn't work that I would like to get working:
System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText("My text");
AnalysisEngineDescription aed =
ClinicalPipelineFactory.getDefaultPipeline();
SimplePipeline.runPipeline(jCas, aed);
This is the code that I managed to get to work. This just demonstrates to
me that it isn't really a credential issue.
PiperFileReader piperReader = new PiperFileReader();
PipelineBuilder builder = piperReader.getBuilder();
builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
piperReader.loadPipelineFile("path/to/default.piper");
builder.run("test text");
default.piper just loads the default pipeline:
load
./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
Does anyone know what the issue might be here?
Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi John,
You are not wrong.
You may want to take an approach similar to what is done in the ctakes-web-rest project.
In CtakesRestController, which can create one or more PipelineRunners to process text.
You can call runner.process( text ); as many times as you want and get results.
static private final class PipelineRunner {
private final AnalysisEngine _engine;
private final JCasPool _pool;
private PipelineRunner(final String piperPath) throws ServletException {
try {
PiperFileReader reader = new PiperFileReader(piperPath);
PipelineBuilder builder = reader.getBuilder();
AnalysisEngineDescription pipeline = builder.getAnalysisEngineDesc();
_engine = UIMAFramework.produceAnalysisEngine(pipeline);
_pool = new JCasPool(10, _engine);
} catch (Exception e) {
LOGGER.error("Error loading pipers");
throw new ServletException(e);
}
}
public MyResponseClass process(final String text) throws ServletException {
JCas jcas = null;
MyResponseClass myResponseObject = null;
if (text != null) {
try {
jcas = _pool.getJCas(-1);
jcas.setDocumentText(text);
_engine.process(jcas);
myReposonseObject = createMyResponseObject( jcas );
_pool.releaseJCas(jcas);
} catch (Exception e) {
LOGGER.error("Error processing Analysis engine");
throw new ServletException(e);
}
}
return myResponseObject;
}
}
Sean
________________________________________
From: John Doe <lu...@gmail.com>
Sent: Thursday, April 22, 2021 2:24 PM
To: dev@ctakes.apache.org
Subject: Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
* External Email - Caution *
Hi Sean,
I tried this piper builder approach below and it also didn't work.
PipelineBuilder pipelineBuilder = new PipelineBuilder();
pipelineBuilder.set(UmlsUserApprover.KEY_PARAM, "<my-key>");
AnalysisEngineDescription aed =
ClinicalPipelineFactory.getDefaultPipeline();
pipelineBuilder.addDescription(aed);
pipelineBuilder.run("text");
Mainly, I just want to understand what the issue is. But the reason it came
up is because I want to set up ctakes to work in real time. So I want
clients to be able to send in notes and have them get processed using the
default clinical pipeline on one of several nodes running ctakes. The
reason I don't want to use builder.run("text") is because it recreates the
jCas every time, which I don't think will scale well. I would rather each
node create the jCas once and call jCas.reset() after each note is done
getting processed rather than have it get instantiated again. I think
creating the jCas is expensive but correct me if I'm wrong.
On Thu, Apr 22, 2021 at 1:58 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi John,
>
> Just out of curiosity, if you have one method that works then why do you
> want to use a different method to do the same thing?
>
> I personally use the PIpelineBuilder as you have in your second example
> when I need to work with code - though that is extremely rare as piper
> files can handle everything that I normally want to do.
>
> If you want an example of how to build a pipeline using only code (no
> piper file) then check the ctakes-examples module, class
> ProcessDirBuilderRunner. It recreates the default clinical pipeline
> without dictionary lookup. Adding in the lookup is fairly simple:
>
> builder
> ...
> .set( UmlsUserApprover.KEY_PARAM, "my-umls-key" )
> .add( DefaultJCasTermAnnotator.class )
> ...
>
> or the single line
> .add( DefaultJCasTermAnnotator.class, Collections.emptyList(),
> UmlsUserApprover.KEY_PARAM, "my-umls-key" )
>
> The code above is just off the top of my head, so I apologize for any
> typos or slight misdirection. Hopefully it is enough to point a way for
> you.
>
> Sean
>
> ________________________________________
> From: John Doe <lu...@gmail.com>
> Sent: Thursday, April 22, 2021 1:09 PM
> To: dev@ctakes.apache.org
> Subject: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hello,
>
> I'm having trouble running the default clinical pipeline from code. It
> keeps giving me the error message that I have an invalid UMLS License.
> However, I know my license is valid and I have managed to get the default
> pipeline to run using the PiperFileReader with the same credentials.
>
> This is the code that doesn't work that I would like to get working:
>
> System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
> JCas jCas = JCasFactory.createJCas();
> jCas.setDocumentText("My text");
> AnalysisEngineDescription aed =
> ClinicalPipelineFactory.getDefaultPipeline();
> SimplePipeline.runPipeline(jCas, aed);
>
> This is the code that I managed to get to work. This just demonstrates to
> me that it isn't really a credential issue.
> PiperFileReader piperReader = new PiperFileReader();
> PipelineBuilder builder = piperReader.getBuilder();
> builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
> piperReader.loadPipelineFile("path/to/default.piper");
> builder.run("test text");
>
> default.piper just loads the default pipeline:
> load
> ./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
>
> Does anyone know what the issue might be here?
>
Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
Posted by John Doe <lu...@gmail.com>.
My work around is to create a pipeline wrapper class that has a run(JCas)
method and that seems to work fine. But I would still like to know what is
causing the issue. It is effectively doing this under the hood, which is
fine.
piperReader.loadPipelineFile("path/to/default.piper");
piperFileReader.getBuilder().set(UmlsUserApprover.KEY_PARAM, "<key>");
piperFileReader.getBuilder().build();
SimplePipeline.runPipeline(jCas,
piperFileReader.getBuilder().getAnalysisEngineDesc());
On Thu, Apr 22, 2021 at 2:24 PM John Doe <lu...@gmail.com> wrote:
> Hi Sean,
>
> I tried this piper builder approach below and it also didn't work.
>
> PipelineBuilder pipelineBuilder = new PipelineBuilder();
> pipelineBuilder.set(UmlsUserApprover.KEY_PARAM, "<my-key>");
> AnalysisEngineDescription aed =
> ClinicalPipelineFactory.getDefaultPipeline();
> pipelineBuilder.addDescription(aed);
> pipelineBuilder.run("text");
>
> Mainly, I just want to understand what the issue is. But the reason it
> came up is because I want to set up ctakes to work in real time. So I want
> clients to be able to send in notes and have them get processed using the
> default clinical pipeline on one of several nodes running ctakes. The
> reason I don't want to use builder.run("text") is because it recreates the
> jCas every time, which I don't think will scale well. I would rather each
> node create the jCas once and call jCas.reset() after each note is done
> getting processed rather than have it get instantiated again. I think
> creating the jCas is expensive but correct me if I'm wrong.
>
> On Thu, Apr 22, 2021 at 1:58 PM Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> Hi John,
>>
>> Just out of curiosity, if you have one method that works then why do you
>> want to use a different method to do the same thing?
>>
>> I personally use the PIpelineBuilder as you have in your second example
>> when I need to work with code - though that is extremely rare as piper
>> files can handle everything that I normally want to do.
>>
>> If you want an example of how to build a pipeline using only code (no
>> piper file) then check the ctakes-examples module, class
>> ProcessDirBuilderRunner. It recreates the default clinical pipeline
>> without dictionary lookup. Adding in the lookup is fairly simple:
>>
>> builder
>> ...
>> .set( UmlsUserApprover.KEY_PARAM, "my-umls-key" )
>> .add( DefaultJCasTermAnnotator.class )
>> ...
>>
>> or the single line
>> .add( DefaultJCasTermAnnotator.class, Collections.emptyList(),
>> UmlsUserApprover.KEY_PARAM, "my-umls-key" )
>>
>> The code above is just off the top of my head, so I apologize for any
>> typos or slight misdirection. Hopefully it is enough to point a way for
>> you.
>>
>> Sean
>>
>> ________________________________________
>> From: John Doe <lu...@gmail.com>
>> Sent: Thursday, April 22, 2021 1:09 PM
>> To: dev@ctakes.apache.org
>> Subject: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
>>
>> * External Email - Caution *
>>
>>
>> Hello,
>>
>> I'm having trouble running the default clinical pipeline from code. It
>> keeps giving me the error message that I have an invalid UMLS License.
>> However, I know my license is valid and I have managed to get the default
>> pipeline to run using the PiperFileReader with the same credentials.
>>
>> This is the code that doesn't work that I would like to get working:
>>
>> System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
>> JCas jCas = JCasFactory.createJCas();
>> jCas.setDocumentText("My text");
>> AnalysisEngineDescription aed =
>> ClinicalPipelineFactory.getDefaultPipeline();
>> SimplePipeline.runPipeline(jCas, aed);
>>
>> This is the code that I managed to get to work. This just demonstrates to
>> me that it isn't really a credential issue.
>> PiperFileReader piperReader = new PiperFileReader();
>> PipelineBuilder builder = piperReader.getBuilder();
>> builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
>> piperReader.loadPipelineFile("path/to/default.piper");
>> builder.run("test text");
>>
>> default.piper just loads the default pipeline:
>> load
>> ./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
>>
>> Does anyone know what the issue might be here?
>>
>
Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
Posted by John Doe <lu...@gmail.com>.
Hi Sean,
I tried this piper builder approach below and it also didn't work.
PipelineBuilder pipelineBuilder = new PipelineBuilder();
pipelineBuilder.set(UmlsUserApprover.KEY_PARAM, "<my-key>");
AnalysisEngineDescription aed =
ClinicalPipelineFactory.getDefaultPipeline();
pipelineBuilder.addDescription(aed);
pipelineBuilder.run("text");
Mainly, I just want to understand what the issue is. But the reason it came
up is because I want to set up ctakes to work in real time. So I want
clients to be able to send in notes and have them get processed using the
default clinical pipeline on one of several nodes running ctakes. The
reason I don't want to use builder.run("text") is because it recreates the
jCas every time, which I don't think will scale well. I would rather each
node create the jCas once and call jCas.reset() after each note is done
getting processed rather than have it get instantiated again. I think
creating the jCas is expensive but correct me if I'm wrong.
On Thu, Apr 22, 2021 at 1:58 PM Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi John,
>
> Just out of curiosity, if you have one method that works then why do you
> want to use a different method to do the same thing?
>
> I personally use the PIpelineBuilder as you have in your second example
> when I need to work with code - though that is extremely rare as piper
> files can handle everything that I normally want to do.
>
> If you want an example of how to build a pipeline using only code (no
> piper file) then check the ctakes-examples module, class
> ProcessDirBuilderRunner. It recreates the default clinical pipeline
> without dictionary lookup. Adding in the lookup is fairly simple:
>
> builder
> ...
> .set( UmlsUserApprover.KEY_PARAM, "my-umls-key" )
> .add( DefaultJCasTermAnnotator.class )
> ...
>
> or the single line
> .add( DefaultJCasTermAnnotator.class, Collections.emptyList(),
> UmlsUserApprover.KEY_PARAM, "my-umls-key" )
>
> The code above is just off the top of my head, so I apologize for any
> typos or slight misdirection. Hopefully it is enough to point a way for
> you.
>
> Sean
>
> ________________________________________
> From: John Doe <lu...@gmail.com>
> Sent: Thursday, April 22, 2021 1:09 PM
> To: dev@ctakes.apache.org
> Subject: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hello,
>
> I'm having trouble running the default clinical pipeline from code. It
> keeps giving me the error message that I have an invalid UMLS License.
> However, I know my license is valid and I have managed to get the default
> pipeline to run using the PiperFileReader with the same credentials.
>
> This is the code that doesn't work that I would like to get working:
>
> System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
> JCas jCas = JCasFactory.createJCas();
> jCas.setDocumentText("My text");
> AnalysisEngineDescription aed =
> ClinicalPipelineFactory.getDefaultPipeline();
> SimplePipeline.runPipeline(jCas, aed);
>
> This is the code that I managed to get to work. This just demonstrates to
> me that it isn't really a credential issue.
> PiperFileReader piperReader = new PiperFileReader();
> PipelineBuilder builder = piperReader.getBuilder();
> builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
> piperReader.loadPipelineFile("path/to/default.piper");
> builder.run("test text");
>
> default.piper just loads the default pipeline:
> load
> ./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
>
> Does anyone know what the issue might be here?
>
Re: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi John,
Just out of curiosity, if you have one method that works then why do you want to use a different method to do the same thing?
I personally use the PIpelineBuilder as you have in your second example when I need to work with code - though that is extremely rare as piper files can handle everything that I normally want to do.
If you want an example of how to build a pipeline using only code (no piper file) then check the ctakes-examples module, class ProcessDirBuilderRunner. It recreates the default clinical pipeline without dictionary lookup. Adding in the lookup is fairly simple:
builder
...
.set( UmlsUserApprover.KEY_PARAM, "my-umls-key" )
.add( DefaultJCasTermAnnotator.class )
...
or the single line
.add( DefaultJCasTermAnnotator.class, Collections.emptyList(), UmlsUserApprover.KEY_PARAM, "my-umls-key" )
The code above is just off the top of my head, so I apologize for any typos or slight misdirection. Hopefully it is enough to point a way for you.
Sean
________________________________________
From: John Doe <lu...@gmail.com>
Sent: Thursday, April 22, 2021 1:09 PM
To: dev@ctakes.apache.org
Subject: Running cTAKES Default Clinical Pipeline from Code [EXTERNAL]
* External Email - Caution *
Hello,
I'm having trouble running the default clinical pipeline from code. It
keeps giving me the error message that I have an invalid UMLS License.
However, I know my license is valid and I have managed to get the default
pipeline to run using the PiperFileReader with the same credentials.
This is the code that doesn't work that I would like to get working:
System.setProperty(UmlsUserApprover.KEY_PARAM, "my-umls-key");
JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText("My text");
AnalysisEngineDescription aed =
ClinicalPipelineFactory.getDefaultPipeline();
SimplePipeline.runPipeline(jCas, aed);
This is the code that I managed to get to work. This just demonstrates to
me that it isn't really a credential issue.
PiperFileReader piperReader = new PiperFileReader();
PipelineBuilder builder = piperReader.getBuilder();
builder.set( UmlsUserApprover.KEY_PARAM , "the-same-umls-key");
piperReader.loadPipelineFile("path/to/default.piper");
builder.run("test text");
default.piper just loads the default pipeline:
load
./resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
Does anyone know what the issue might be here?