Hi Sean,
I was able to make the custom dictionary XML work with "LookupXml" parameter.
But I face another issue in the rest implementation in this new approach using
PiperFileReader. If I use the following lines of code, for each post request
it makes a db connection once again and loads the annotator.
JCas jcas = JCasFactory.createJCas();
jcas.setDocumentText(analysisText);
SimplePipeline.runPipeline(jcas, pipeline);
This slows down the complete analysis and chokes the server. Is there an
approach to load the annotators only once like in earlier approach so that it
improves the performance?
Regards,
Gandhi
-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:[email protected]]
Sent: Wednesday, November 22, 2017 1:35 AM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Thanks for the detailed explanation Sean. We will have a look at the
PiperFileReader and try to implement the rest module in similar lines.
Will keep you posted. Thanks again.
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:[email protected]]
Sent: Wednesday, November 22, 2017 1:21 AM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to add that code. There is already a parameter named
"LookupXml" that can be used.
That being said, I just took a look at the code in github. To be honest, I
would not use the DemoServlet class. It uses a hardcoded pipeline, complete
with parameter values. Instead I would write a new one that utilizes the
PiperFileReader in core. If you do that then you can start up a demo with any
pipeline you want - there is no need to create new code for each different type
of pipeline - e.g. default clinical vs. temporal. You can set any custom
parameter values in the piper file.
This is the gist:
// Add a simple pre-defined existing pipeline from a file or resource
PiperFileReader reader = new PiperFileReader( PIPER_FILE_PATH );
// Get a description of the pipeline created from the file
PipelineBuilder builder = reader.getBuilder();
AnalysisEngineDescription pipeline = builder. getAnalysisEngineDesc();
// For each post, create a jcas object. Consider using a caspool instead.
JCas jcas = JCasFactory.createJCas();
// Set the posted text and run the pipeline
jcas.setDocumentText( TEXT );
SimplePipeline.runPipeline( jcas, pipeline );
There may be a better way to run than with the SimplePipeline, but the above
should suffice.
It would be cool if there was an option for response from the HtmlTextWriter,
but I don't know how quick and easy that would be to implement.
Sean
-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:[email protected]]
Sent: Tuesday, November 21, 2017 1:36 PM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sean and Sirisha,
Thanks a lot for the response.
I tried building and deploying the war from the following repo -
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4&s=kiJMuwmqMs4szLaIFtTi_lAJVc2h5KK5VYAkmN6wJmU&e=
On server start, it looks for sno_rx_16ab.xml. Not sure what configuration
exactly you are asking for.
Also as you said we are looking to set the parameter LookupXml dynamically in
AbstractJCasTermAnnotator.java file's initialize method as follows:
String _customDescriptorFilePath = System.getenv("CUSTOM_DESC_FILE_PATH");
if(_customDescriptorFilePath != null) { LOGGER.info( "Using custom
descriptor file path: " + _customDescriptorFilePath ); _descriptorFilePath =
_customDescriptorFilePath; }
Is this approach fine?
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:[email protected]]
Sent: Tuesday, November 21, 2017 9:32 PM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to have sno_rx_16ab* . I don't know exactly how you are
configured, but if you have another dictionary that you want to use instead of
the default sno_rx then you just need to create it and then point the custom
config .xml. This can be done a couple of ways, but basically set the
parameter LookupXml to point to your custom xml path. This needs to be done at
startup. Once ctakes is running (i.e. as a service) you cannot change the
dictionary.
This is briefly explained at the bottom of the wiki page:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-7baoaqCVXKSRgEv043CJiX_gElMEnuOa7GOCy80Gw4&s=3NuvXMGraH4F2tk5TDjgza9ie9kIyCuhbyeku-Xu3hI&e=
Sean
-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:[email protected]]
Sent: Tuesday, November 21, 2017 10:44 AM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sean,
When we try to deploy cTAKES as web application, it always looks for
sno_rx_16ab.xml by default on server start. So do you mean we should also have
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:[email protected]]
Sent: Tuesday, November 21, 2017 8:42 PM
To: [email protected]
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sandeep,
Adding a custom dictionary should never require code modification.
The dictionary creator gui will create a custom dictionary and its .xml
configuration file and place them in your ctakes resources/ directory. No code
changes necessary.
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K-fWZaRAkXxJHPoz7nhE5U4rhYmrwSrGwMqji82GLVc&s=DIMsU-EWm6kc1X-08Z2GlrsKmug3xQCnPgtDAXp3o1s&e=
If you search the ctakes devlist emails you should find some threads discussing
custom dictionaries and bsv files. (bar separated value, aka pipe-delimited).
For smaller custom dictionaries those can be created. The emails should
include information on creating the .xml dictionary configuration files.
Sean
-----Original Message-----
From: Sandeep Byatha Gururaja rao [mailto:[email protected]]
Sent: Tuesday, November 21, 2017 9:40 AM
To: [email protected]
Subject: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi,
Is there currently any way to use a custom dictionary descriptor file without
making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast
jar file.
Regards,
Sandeep
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