ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From seanfi...@apache.org
Subject svn commit: r1883545 - in /ctakes/trunk: ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
Date Tue, 17 Nov 2020 16:35:10 GMT
Author: seanfinan
Date: Tue Nov 17 16:35:10 2020
New Revision: 1883545

URL: http://svn.apache.org/viewvc?rev=1883545&view=rev
Log:
PipelineBuilder add run( jcas )
UmlsUserApprover point to new DotLogger package

Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
    ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java?rev=1883545&r1=1883544&r2=1883545&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java
Tue Nov 17 16:35:10 2020
@@ -433,8 +433,26 @@ final public class PipelineBuilder {
       }
       final JCas jcas = JCasFactory.createJCas();
       jcas.setDocumentText( text );
+      return run( jcas );
+   }
+
+   /**
+    * Run the pipeline on the given jcas.
+    * Use of this method is order-specific.
+    * This method will call {@link #build()} if the pipeline has not already been initialized.
+    *
+    * @param jCas ye olde ...
+    * @return this PipelineBuilder
+    * @throws IOException   if the pipeline could not be run
+    * @throws UIMAException if the pipeline could not be run
+    */
+   public PipelineBuilder run( final JCas jCas ) throws IOException, UIMAException {
+      if ( _readerDesc != null ) {
+         LOGGER.error( "Collection Reader specified, ignoring." );
+         return this;
+      }
       build();
-      SimplePipeline.runPipeline( jcas, _analysisEngineDesc );
+      SimplePipeline.runPipeline( jCas, _analysisEngineDesc );
       return this;
    }
 

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=1883545&r1=1883544&r2=1883545&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 Nov 17 16:35:10 2020
@@ -19,16 +19,17 @@
 package org.apache.ctakes.dictionary.lookup2.util;
 
 import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
-import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.core.util.log.DotLogger;
 import org.apache.ctakes.utils.env.EnvironmentVariable;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
 import java.net.HttpURLConnection;
 import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Properties;
@@ -71,10 +72,10 @@ public enum UmlsUserApprover {
 	static final private String CHANGE_ME = "CHANGE_ME";
 	// forget about copies of this URL sprinkled around the other libraries
 	static final private String UTS_APIKEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key";
-	
+
 
 	// cache of valid users
-	static private final Collection<String> _validUsers = new ArrayList<String>();
+	static private final Collection<String> _validUsers = new ArrayList<>();
 
 	/**
 	 * validate the UMLS license / user
@@ -95,27 +96,28 @@ public enum UmlsUserApprover {
 		
 		if (umlsApiKey == null) {
 			// emulate U&P style 
-			String user = getUser(uimaContext, properties);
-			if (user == null || !user.equals(API_KEY_LABEL)) {
-				LOGGER.error("USER AND PASSWORD MUST BE umls_api_key and your <umls_api_key>");
+			String user = getUser( uimaContext, properties );
+			if ( user == null || !user.equals( API_KEY_LABEL ) ) {
+				LOGGER.error( "USER AND PASSWORD MUST BE umls_api_key and your <umls_api_key>"
);
 				return false;
 			}
-			
-			String pass = getPassOrKey(uimaContext, properties);
-			if (pass == null || pass.indexOf("CHANGE") != -1 || pass.length() <= 24) {
-				LOGGER.error("Upgrade to a UMLS API KEY.  Password no longer accepted");
+
+			String pass = getPassOrKey( uimaContext, properties );
+			if ( pass == null || pass.contains( "CHANGE" ) || pass.length() <= 24 ) {
+				LOGGER.error( "Upgrade to a UMLS API KEY.  Password no longer accepted" );
 				return false;
 			}
-			return isValidUMLSUser(apiUrl, pass);
+			return isValidUMLSUser( apiUrl, pass );
 		}
 		return isValidUMLSUser(apiUrl, umlsApiKey);
 	}
 
 	/**
 	 * See if the user has simply supplied the API key using its own property name
-	 * @param properties
-	 * @param uimaContext 
-	 * @return
+	 *
+	 * @param properties  -
+	 * @param uimaContext -
+	 * @return -
 	 */
 	private String getSingleApiProp(final Properties properties, UimaContext uimaContext) {
 		String umlsApiKey = EnvironmentVariable.getEnv(API_KEY_PROP, uimaContext);
@@ -150,23 +152,24 @@ public enum UmlsUserApprover {
 	}
 
 	private String getPassOrKey(final UimaContext uimaContext,
-			final Properties properties) {
+			final Properties properties ) {
 		String where = "environment";
 		String pass = EnvironmentVariable.getEnv(
 				UmlsEnvironmentConfiguration.PASSWORD.toString(),
-				uimaContext);
-		if (pass == null || pass.equals(EnvironmentVariable.NOT_PRESENT) 
-				|| pass.indexOf("CHANGE") != -1) {
-			pass = EnvironmentVariable.getEnv(PASS_PARAM, uimaContext);
-			if (pass == null
-					|| pass.equals(EnvironmentVariable.NOT_PRESENT)
-					|| pass.indexOf("CHANGE") != -1) {
-				pass = properties.getProperty(PASS_PARAM);
+				uimaContext );
+		if ( pass == null || pass.equals( EnvironmentVariable.NOT_PRESENT )
+			  || pass.contains( "CHANGE" ) ) {
+			pass = EnvironmentVariable.getEnv( PASS_PARAM, uimaContext );
+			if ( pass == null
+				  || pass.equals( EnvironmentVariable.NOT_PRESENT )
+				  || pass.contains( "CHANGE" ) ) {
+				pass = properties.getProperty( PASS_PARAM );
 				where = "properties";
 			}
 		}
-		if (pass != null)
-			LOGGER.debug("ApiKey value found via: " + where);
+		if ( pass != null ) {
+			LOGGER.debug( "ApiKey value found via: " + where );
+		}
 		return pass;
 	}
 
@@ -177,11 +180,11 @@ public enum UmlsUserApprover {
 				UmlsEnvironmentConfiguration.USER.toString(), uimaContext);
 		if (user == null || user.equals(EnvironmentVariable.NOT_PRESENT)
 				|| user.equals(CHANGEME) || user.equals(CHANGE_ME)) {
-			user = EnvironmentVariable.getEnv(USER_PARAM, uimaContext);
-			if (user == null
-					|| user.equals(EnvironmentVariable.NOT_PRESENT)
-					|| user.indexOf("CHANGE") != -1) {
-				user = properties.getProperty(USER_PARAM);
+			user = EnvironmentVariable.getEnv( USER_PARAM, uimaContext );
+			if ( user == null
+				  || user.equals( EnvironmentVariable.NOT_PRESENT )
+				  || user.contains( "CHANGE" ) ) {
+				user = properties.getProperty( USER_PARAM );
 				where = "properties";
 			}
 		}
@@ -192,15 +195,15 @@ public enum UmlsUserApprover {
 
 	/**
 	 * New UTS authentication method
-	 * @param umlsUrl
-	 * @param umlsApiKey 
-	 * @return
+	 * @param umlsUrl -
+	 * @param umlsApiKey -
+	 * @return -
 	 */
 	private boolean isValidUMLSUser(String umlsUrl, String umlsApiKey) {
 		if (_validUsers.contains(umlsApiKey)) {
 			return true;
 		}
-		return doAuth(umlsUrl, umlsApiKey);
+		return doAuth(umlsUrl, umlsApiKey );
 	}
 
 	/**
@@ -213,17 +216,17 @@ public enum UmlsUserApprover {
 	 *            -
 	 * @param user     NOW needs to be the value "umls_api_key"
 	 *            -
-	 * @param pass	   THE API KEY
+	 * @param apikey      THE API KEY
 	 *            -
 	 * @return true if the server at umlsaddr approves of the vendor, user,
 	 *         password combination
 	 */
 	public boolean isValidUMLSUser(String umlsUrl, final String vendor,
-			final String user, final String apikey) {
+			final String user, final String apikey ) {
 
-		if (user == null || user.trim().isEmpty() || 
-				!user.equals(this.API_KEY_LABEL)) {
-			LOGGER.error("The user property must now be set to \'umls_api_key\' ");
+		if ( user == null || user.trim().isEmpty() ||
+			  !user.equals( API_KEY_LABEL ) ) {
+			LOGGER.error( "The user property must now be set to \'umls_api_key\' " );
 			logCheckUser();
 			return false;
 		}
@@ -272,17 +275,17 @@ public enum UmlsUserApprover {
 		return doAuth(umlsUrl, apikey);
 	}
 
-	private boolean doAuth(final String umlsUrl,  String apiKey) {
-		try (org.apache.ctakes.core.util.DotLogger dotter = new org.apache.ctakes.core.util.DotLogger())
{
+	private boolean doAuth( final String umlsUrl, String apiKey ) {
+		try ( DotLogger dotter = new DotLogger() ) {
 			apiKey = apiKey.trim();
-			LOGGER.info("Checking UMLS Account at " + umlsUrl + ":");
-			String data = "apikey="+apiKey;
-			final URL url = new URL(umlsUrl);
+			LOGGER.info( "Checking UMLS Account at " + umlsUrl + ":" );
+			String data = "apikey=" + apiKey;
+			final URL url = new URL( umlsUrl );
 			final HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-			connection.setRequestMethod("POST");
-			connection.setDoOutput(true);
+			connection.setRequestMethod( "POST" );
+			connection.setDoOutput( true );
 			final OutputStreamWriter writer = new OutputStreamWriter(
-					connection.getOutputStream());
+					connection.getOutputStream() );
 			writer.write(data);
 			writer.flush();
 			boolean isValidUser = false;



Mime
View raw message