Author: seanfinan
Date: Tue May 12 13:22:08 2015
New Revision: 1678940
URL: http://svn.apache.org/r1678940
Log:
CTAKES-359 : added additional check for <Result>true</Result> preceded by xml
declaration
Modified:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
Modified:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java?rev=1678940&r1=1678939&r2=1678940&view=diff
==============================================================================
---
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
(original)
+++
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
Tue May 12 13:22:08 2015
@@ -104,8 +104,8 @@ public enum UmlsUserApprover {
* @return true if the server at umlsaddr approves of the vendor, user,
password combination
*/
public boolean isValidUMLSUser( final String umlsUrl, final String vendor,
- final String user, final String pass
) {
- final String cacheCode = umlsUrl+vendor+user+pass;
+ final String user, final String pass ) {
+ final String cacheCode = umlsUrl + vendor + user + pass;
if ( _validUsers.contains( cacheCode ) ) {
return true;
}
@@ -136,7 +136,8 @@ public enum UmlsUserApprover {
if ( trimline.isEmpty() ) {
break;
}
- isValidUser = trimline.equalsIgnoreCase( "<Result>true</Result>" );
+ isValidUser = trimline.equalsIgnoreCase( "<Result>true</Result>" )
+ || trimline.equalsIgnoreCase( "<?xml version='1.0'
encoding='UTF-8'?><Result>true</Result>" );
}
writer.close();
reader.close();
Modified:
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java?rev=1678940&r1=1678939&r2=1678940&view=diff
==============================================================================
---
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
(original)
+++
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java
Tue May 12 13:22:08 2015
@@ -47,7 +47,7 @@ public class ThreadedUmlsDictionaryLooku
@Override
- public void initialize( final UimaContext aContext ) throws
ResourceInitializationException {
+ public void initialize( final UimaContext aContext ) throws
ResourceInitializationException {
super.initialize( aContext );
final String umlsAddress = EnvironmentVariable.getEnv( UMLSADDR_PARAM,
aContext );
final String umlsVendor = EnvironmentVariable.getEnv( UMLSVENDOR_PARAM,
aContext );
@@ -79,22 +79,24 @@ public class ThreadedUmlsDictionaryLooku
final URL url = new URL( umlsaddr );
final URLConnection connection = url.openConnection();
connection.setDoOutput( true );
- try(final OutputStreamWriter writer = new OutputStreamWriter(
connection.getOutputStream() );
- final BufferedReader reader = new BufferedReader( new
InputStreamReader( connection.getInputStream() ) )){
-
- writer.write( data );
- writer.flush();
- boolean result = false;
+ try ( final OutputStreamWriter writer = new OutputStreamWriter(
connection.getOutputStream() );
+ final BufferedReader reader = new BufferedReader( new
InputStreamReader( connection
+ .getInputStream() ) ) ) {
- String line;
- while ( (line = reader.readLine()) != null ) {
- final String trimline = line.trim();
- if ( trimline.isEmpty() ) {
- break;
- }
- result = trimline.equalsIgnoreCase( "<Result>true</Result>" );
- }
- return result;
+ writer.write( data );
+ writer.flush();
+ boolean result = false;
+
+ String line;
+ while ( (line = reader.readLine()) != null ) {
+ final String trimline = line.trim();
+ if ( trimline.isEmpty() ) {
+ break;
+ }
+ result = trimline.equalsIgnoreCase( "<Result>true</Result>" )
+ || trimline.equalsIgnoreCase( "<?xml version='1.0'
encoding='UTF-8'?><Result>true</Result>" );
+ }
+ return result;
}
} catch ( IOException ioE ) {
LOGGER.error( ioE.getMessage() );
Modified:
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?rev=1678940&r1=1678939&r2=1678940&view=diff
==============================================================================
---
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
(original)
+++
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
Tue May 12 13:22:08 2015
@@ -18,14 +18,6 @@
*/
package org.apache.ctakes.dictionary.lookup.ae;
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.resource.FileResourceImpl;
import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
@@ -33,128 +25,136 @@ import org.apache.ctakes.utils.env.Envir
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.factory.ExternalResourceFactory;
+import org.apache.uima.resource.ResourceInitializationException;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.net.URL;
+import java.net.URLConnection;
+import java.net.URLEncoder;
/**
* UIMA annotator that identified entities based on lookup.
- *
+ *
* @author Mayo Clinic
*/
-public class UmlsDictionaryLookupAnnotator extends DictionaryLookupAnnotator
-{
- /* Special implementation to pre bundle the UMLS SnowmedCT/RxNorm
dictionaries
- * Performs a check for user's UMLS licence at init time via their
RESTful API
- * User's will need to configure their UMLS username/password in their
config
- */
- public final static String UMLSADDR_PARAM = "ctakes.umlsaddr";
- public final static String UMLSVENDOR_PARAM = "ctakes.umlsvendor";
- public final static String UMLSUSER_PARAM = "ctakes.umlsuser";
- public final static String UMLSPW_PARAM = "ctakes.umlspw";
-
- private Logger iv_logger = Logger.getLogger(getClass().getName());
-
- private String UMLSAddr;
- private String UMLSVendor;
- private String UMLSUser;
- private String UMLSPW;
-
- @Override
- public void initialize(UimaContext aContext)
- throws ResourceInitializationException
- {
- super.initialize(aContext);
-
- try {
- UMLSAddr = EnvironmentVariable.getEnv(UMLSADDR_PARAM,
aContext);
- UMLSVendor =
EnvironmentVariable.getEnv(UMLSVENDOR_PARAM, aContext);
- UMLSUser = EnvironmentVariable.getEnv(UMLSUSER_PARAM,
aContext);
- UMLSPW = EnvironmentVariable.getEnv(UMLSPW_PARAM,
aContext);
-
- iv_logger.info("Using " + UMLSADDR_PARAM + ": " +
UMLSAddr + ": " + UMLSUser);
- if(!isValidUMLSUser(UMLSAddr, UMLSVendor, UMLSUser,
UMLSPW))
- {
- iv_logger.error("Error: Invalid UMLS License.
A UMLS License is required to use the UMLS dictionary lookup. \n" +
- "Error: You may request one at:
https://uts.nlm.nih.gov/license.html \n" +
- "Please verify your UMLS
license settings in the DictionaryLookupAnnotatorUMLS.xml configuration.");
- throw new Exception("Failed to initilize.
Invalid UMLS License");
- }
-
- } catch (Exception e) {
- throw new ResourceInitializationException(e);
- }
- }
-
- public static boolean isValidUMLSUser(String umlsaddr, String vendor,
String username, String password) throws Exception {
- String data = URLEncoder.encode("licenseCode", "UTF-8") + "="
- + URLEncoder.encode(vendor, "UTF-8");
- data += "&" + URLEncoder.encode("user", "UTF-8") + "="
- + URLEncoder.encode(username, "UTF-8");
- data += "&" + URLEncoder.encode("password", "UTF-8") + "="
- + URLEncoder.encode(password, "UTF-8");
- URL url = new URL(umlsaddr);
- URLConnection conn = url.openConnection();
- conn.setDoOutput(true);
- try(OutputStreamWriter wr = new
OutputStreamWriter(conn.getOutputStream())){
- wr.write(data);
- wr.flush();
- }
- try(BufferedReader rd = new BufferedReader(new
InputStreamReader(conn.getInputStream()))){
- boolean result = false;
- String line;
- while ((line = rd.readLine()) != null) {
- if(line.trim().length()>0)
- {
- result =
line.trim().equalsIgnoreCase("<Result>true</Result>");
- }
- }
- return result;
- }
- }
-
- public static AnalysisEngineDescription createAnnotatorDescription()
throws ResourceInitializationException{
- try {
- return
AnalysisEngineFactory.createEngineDescription(UmlsDictionaryLookupAnnotator.class,
- UMLSADDR_PARAM,
- "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser";,
- UMLSVENDOR_PARAM,
- "NLM-6515182895",
- "LookupDescriptor",
- ExternalResourceFactory.createExternalResourceDescription(
- FileResourceImpl.class,
-
FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml")),
- "DbConnection",
- ExternalResourceFactory.createExternalResourceDescription(
- JdbcConnectionResourceImpl.class,
- "",
- JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
- "org.hsqldb.jdbcDriver",
- JdbcConnectionResourceImpl.PARAM_URL,
- // Should be the following but it's WAY too slow
-
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
-
//"jdbc:hsqldb:file:target/unpacked/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
- "RxnormIndexReader",
- ExternalResourceFactory.createExternalResourceDescription(
- JdbcConnectionResourceImpl.class,
- "",
- JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
- "org.hsqldb.jdbcDriver",
- JdbcConnectionResourceImpl.PARAM_URL,
-
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls"),
- "OrangeBookIndexReader",
- ExternalResourceFactory.createExternalResourceDescription(
- JdbcConnectionResourceImpl.class,
- "",
- JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
- "org.hsqldb.jdbcDriver",
- JdbcConnectionResourceImpl.PARAM_URL,
-
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls")
- );
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- throw new ResourceInitializationException(e);
- }
-
- }
+public class UmlsDictionaryLookupAnnotator extends DictionaryLookupAnnotator {
+ /* Special implementation to pre bundle the UMLS SnowmedCT/RxNorm
dictionaries
+ * Performs a check for user's UMLS licence at init time via their RESTful
API
+ * User's will need to configure their UMLS username/password in their
config
+ */
+ public final static String UMLSADDR_PARAM = "ctakes.umlsaddr";
+ public final static String UMLSVENDOR_PARAM = "ctakes.umlsvendor";
+ public final static String UMLSUSER_PARAM = "ctakes.umlsuser";
+ public final static String UMLSPW_PARAM = "ctakes.umlspw";
+
+ private Logger iv_logger = Logger.getLogger( getClass().getName() );
+
+ private String UMLSAddr;
+ private String UMLSVendor;
+ private String UMLSUser;
+ private String UMLSPW;
+
+ @Override
+ public void initialize( UimaContext aContext )
+ throws ResourceInitializationException {
+ super.initialize( aContext );
+
+ try {
+ UMLSAddr = EnvironmentVariable.getEnv( UMLSADDR_PARAM, aContext );
+ UMLSVendor = EnvironmentVariable.getEnv( UMLSVENDOR_PARAM, aContext );
+ UMLSUser = EnvironmentVariable.getEnv( UMLSUSER_PARAM, aContext );
+ UMLSPW = EnvironmentVariable.getEnv( UMLSPW_PARAM, aContext );
+
+ iv_logger.info( "Using " + UMLSADDR_PARAM + ": " + UMLSAddr + ": " +
UMLSUser );
+ if ( !isValidUMLSUser( UMLSAddr, UMLSVendor, UMLSUser, UMLSPW ) ) {
+ iv_logger.error(
+ "Error: Invalid UMLS License. A UMLS License is required to
use the UMLS dictionary lookup. \n" +
+ "Error: You may request one at:
https://uts.nlm.nih.gov/license.html \n" +
+ "Please verify your UMLS license settings in the
DictionaryLookupAnnotatorUMLS.xml configuration." );
+ throw new Exception( "Failed to initilize. Invalid UMLS License"
);
+ }
+
+ } catch ( Exception e ) {
+ throw new ResourceInitializationException( e );
+ }
+ }
+
+ public static boolean isValidUMLSUser( String umlsaddr, String vendor,
String username, String password )
+ throws Exception {
+ String data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "="
+ + URLEncoder.encode( vendor, "UTF-8" );
+ data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "="
+ + URLEncoder.encode( username, "UTF-8" );
+ data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "="
+ + URLEncoder.encode( password, "UTF-8" );
+ URL url = new URL( umlsaddr );
+ URLConnection conn = url.openConnection();
+ conn.setDoOutput( true );
+ try ( OutputStreamWriter wr = new OutputStreamWriter(
conn.getOutputStream() ) ) {
+ wr.write( data );
+ wr.flush();
+ }
+ try ( BufferedReader rd = new BufferedReader( new InputStreamReader(
conn.getInputStream() ) ) ) {
+ boolean result = false;
+ String line;
+ while ( (line = rd.readLine()) != null ) {
+ if ( line.trim().length() > 0 ) {
+ result = line.trim().equalsIgnoreCase( "<Result>true</Result>" )
+ ||
+ line.trim().equalsIgnoreCase( "<?xml version='1.0'
encoding='UTF-8'?><Result>true</Result>" );
+ }
+ }
+ return result;
+ }
+ }
+
+ public static AnalysisEngineDescription createAnnotatorDescription() throws
ResourceInitializationException {
+ try {
+ return AnalysisEngineFactory.createEngineDescription(
UmlsDictionaryLookupAnnotator.class,
+ UMLSADDR_PARAM,
+ "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser";,
+ UMLSVENDOR_PARAM,
+ "NLM-6515182895",
+ "LookupDescriptor",
+ ExternalResourceFactory.createExternalResourceDescription(
+ FileResourceImpl.class,
+ FileLocator.locateFile(
"org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml" ) ),
+ "DbConnection",
+ ExternalResourceFactory.createExternalResourceDescription(
+ JdbcConnectionResourceImpl.class,
+ "",
+ JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
+ "org.hsqldb.jdbcDriver",
+ JdbcConnectionResourceImpl.PARAM_URL,
+ // Should be the following but it's WAY too slow
+
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls" ),
+
//"jdbc:hsqldb:file:target/unpacked/org/apache/ctakes/dictionary/lookup/umls2011ab/umls"),
+ "RxnormIndexReader",
+ ExternalResourceFactory.createExternalResourceDescription(
+ JdbcConnectionResourceImpl.class,
+ "",
+ JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
+ "org.hsqldb.jdbcDriver",
+ JdbcConnectionResourceImpl.PARAM_URL,
+
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls" ),
+ "OrangeBookIndexReader",
+ ExternalResourceFactory.createExternalResourceDescription(
+ JdbcConnectionResourceImpl.class,
+ "",
+ JdbcConnectionResourceImpl.PARAM_DRIVER_CLASS,
+ "org.hsqldb.jdbcDriver",
+ JdbcConnectionResourceImpl.PARAM_URL,
+
"jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls" )
+ );
+ } catch ( FileNotFoundException e ) {
+ e.printStackTrace();
+ throw new ResourceInitializationException( e );
+ }
+
+ }
}
