Queries on custom annotators

[Gandhi Rajan Natarajan]

Hi All,

We have wrote a custom annotation to identify the pharma company names, 
integrated it with cTAKES and it works fairly well with CVD. But when I tried 
integrating the same in my extended  web application that uses 
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo  as 
base, I face few issues.


1)      We have defined certain mandatory parameter for the annotator. The JAVA 
code and XML config for passing the parameters is as follows:

public static final String PARAM_JDBC_DRIVER = "JdbcDriver";
public static final String PARAM_JDBC_URL = "JdbcUrl";
public static final String PARAM_JDBC_USER = "JdbcUser";
public static final String PARAM_JDBC_PASS = "JdbcPass";
@ConfigurationParameter(name = PARAM_JDBC_DRIVER, mandatory = false, 
description = "JDBC Driver")
private String jdbcDriver;

@ConfigurationParameter(name = PARAM_JDBC_URL, mandatory = false, description = 
"JDBC URL")
private String jdbcUrl;

@ConfigurationParameter(name = PARAM_JDBC_USER, mandatory = false, description 
= "JDBC User")
private String jdbcUser ;

@ConfigurationParameter(name = PARAM_JDBC_PASS, mandatory = false, description 
= "JDBC Pass")
private String jdbcPass;



<configurationParameters>
<configurationParameter>
        <name>JdbcDriver</name>
        <description>JdbcDriver</description>
        <type>String</type>
        <multiValued>false</multiValued>
        <mandatory>false</mandatory>
      </configurationParameter>

<configurationParameter>
        <name>JdbcUrl</name>
        <description>JdbcUrl</description>
        <type>String</type>
        <multiValued>false</multiValued>
        <mandatory>false</mandatory>
      </configurationParameter>

<configurationParameter>
        <name>JdbcUser</name>
        <description>JdbcUser</description>
        <type>String</type>
        <multiValued>false</multiValued>
        <mandatory>false</mandatory>
      </configurationParameter>

<configurationParameter>
        <name>JdbcPass</name>
        <description>JdbcPass</description>
        <type>String</type>
        <multiValued>false</multiValued>
        <mandatory>false</mandatory>
      </configurationParameter>
</configurationParameters>

<configurationParameterSettings>
      <nameValuePair>
        <name>JdbcDriver</name>
        <value>
          <string>com.mysql.jdbc.Driver</string>
        </value>
      </nameValuePair>

      <nameValuePair>
        <name>JdbcUrl</name>
        <value>
          
<string>jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&amp;characterEncoding=utf8&amp;useSSL=false</string>
        </value>
      </nameValuePair>

      <nameValuePair>
        <name>JdbcUser</name>
        <value>
          <string>root</string>
        </value>
      </nameValuePair>

      <nameValuePair>
        <name>JdbcPass</name>
        <value>
          <string>admin123</string>
        </value>
      </nameValuePair>
</configurationParameterSettings>

If I change the mandate attribute from 'false' to 'true', while trying to use 
this annotator, I get an error stating that the mandatory parameter is not 
passed. I'm not sure what other configuration is required to make this work and 
pass mandatory values. Any help on this?


2)      Currently in the 'initialize' method of the annotator, I'm loading few 
metadata resources using the following code,


InputStream inputStream = annotCtx.getResourceAsStream(fileName);

But when this line is executed, it gives a following warning message in the 
console,

"13-Oct-2017 15:54:50.141 WARNING [localhost-startStop-1] 
org.apache.uima.impl.ChildUimaContext_impl.getResourceAsStream The unmanaged 
resource ORG.txt was accessed.This feature is deprecated, and support may be 
removed in future versions."

Could someone throw some light on how to resolve this warning and loaded the 
resource in a best way?

Regards,
Gandhi

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