Author: pabramowitsch
Date: Tue Nov 17 15:13:49 2020
New Revision: 1883540
URL: http://svn.apache.org/viewvc?rev=1883540&view=rev
Log:
Ctakes issue 545 UMLS Authentication
Added:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java
(with props)
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
- copied, changed from r1883539,
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java
Removed:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java
Added:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java?rev=1883540&view=auto
==============================================================================
---
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java
(added)
+++
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java
Tue Nov 17 15:13:49 2020
@@ -0,0 +1,55 @@
+package org.apache.ctakes.dictionary.lookup2.util;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+
+import org.apache.log4j.Logger;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+
+public class DummyAnnotator extends JCasAnnotator_ImplBase {
+
+ public static final String PARAM_SAVE_ANN = "PARAM_SAVE_ANN";
+ public static final String PARAM_PRINT_ANN = "PARAM_PRINT_ANN";
+
+ @Override
+ public void process(JCas jcas) throws AnalysisEngineProcessException {
+ // never run
+ }
+
+ @Override
+ public void initialize(UimaContext context)
+ throws ResourceInitializationException {
+ super.initialize(context);
+ }
+
+
+ public AnalysisEngineDescription createAnnotatorDescription()
+ throws ResourceInitializationException {
+ return AnalysisEngineFactory.createEngineDescription(
+ DummyAnnotator.class,
+ DummyAnnotator.PARAM_SAVE_ANN, true,
+ DummyAnnotator.PARAM_PRINT_ANN, true);
+ }
+}
Propchange:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/DummyAnnotator.java
------------------------------------------------------------------------------
svn:eol-style = native
Copied:
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
(from r1883539,
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java)
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java?p2=ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java&p1=ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java&r1=1883539&r2=1883540&rev=1883540&view=diff
==============================================================================
---
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTester.java
(original)
+++
ctakes/trunk/ctakes-dictionary-lookup-fast/src/test/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserTest.java
Tue Nov 17 15:13:49 2020
@@ -1,28 +1,127 @@
package org.apache.ctakes.dictionary.lookup2.util;
+import java.io.File;
+import java.util.Properties;
+import org.junit.Assert;
+import org.junit.Ignore;
import org.apache.ctakes.core.ae.UmlsEnvironmentConfiguration;
import org.apache.ctakes.utils.env.EnvironmentVariable;
+import org.apache.ctakes.utils.test.TestUtil;
import org.apache.log4j.Logger;
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
/**
- * @author SPF , chip-nlp
+ * @author SPF , chip-nlp, pabramowitsch
* @version %I%
* @since 8/24/2015
+ *
+ * To run this test suite, please substitute CHANGE_ME for your API Key
+ * then add the following to your environment
+ * umlsPass = <your api key>,
+ * or ctakes.umlspw = <your api key>
+ * ummlsUser = "umls_api_user",
+ * or ctakes.umlsuser="umls_api_user"
+ * Then Remove the @Ignore attribute below
+ * Then run.
+ *
*/
-final public class UmlsUserTester {
- static private final Logger LOGGER = Logger.getLogger( "UmlsUserTester" );
+@Ignore // needed for successful maven build/test when no API key is supplied
+final public class UmlsUserTest {
- private UmlsUserTester() {
+ static private final Logger LOGGER = Logger.getLogger( "UmlsUserTester" );
+ static UimaContext _uimaContext = null;
+
+ private final String apiKeyForTesting = "CHANGE_ME";
+
+ // reductio ad absurdem to get a UimaContext
+ static {
+ AnalysisEngine contextAE;
+ try {
+ DummyAnnotator da = new DummyAnnotator();
+ contextAE =
UIMAFramework.produceAnalysisEngine(da.createAnnotatorDescription());
+ _uimaContext = contextAE.getUimaContext();
+ } catch (ResourceInitializationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
-
- static public boolean canTestUmlsUser() {
- String user =
EnvironmentVariable.getEnv(UmlsEnvironmentConfiguration.USER.toString());
- if ( user == null || user.equals( EnvironmentVariable.NOT_PRESENT ) ) {
- return false;
- }
- String pass = EnvironmentVariable.getEnv(
UmlsEnvironmentConfiguration.PASSWORD.toString());
- return pass != null && !pass.equals( EnvironmentVariable.NOT_PRESENT );
+
+ @Test
+ public void testViaProps() {
+ Properties props = new Properties();
+ props.setProperty(UmlsUserApprover.USER_PARAM, "umls_api_key");
+ props.setProperty(UmlsUserApprover.PASS_PARAM, apiKeyForTesting);
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true, approver.isValidUMLSUser(_uimaContext,
props));
+ approver.resetUserCache();
}
-
+
+ @Test
+ public void testViaProps2() {
+ Properties props = new Properties();
+ props.setProperty(UmlsEnvironmentConfiguration.USER.toString(),
"umls_api_key");
+ props.setProperty(UmlsEnvironmentConfiguration.PASSWORD.toString(),
apiKeyForTesting);
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true, approver.isValidUMLSUser(_uimaContext,
props));
+ approver.resetUserCache();
+ }
+
+ @Test
+ public void testViaEnvironment() {
+ /**
+ * to pass this test please either pair of environment variables
+ * umlsUser, umlsPass
+ * ctakes.umlsuser
+ * ctakes.umlspass
+ */
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true, approver.isValidUMLSUser(_uimaContext,
System.getProperties()));
+ approver.resetUserCache();
+ }
+
+ @Test
+ public void testViaApiKeyasUser() {
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true,approver.isValidUMLSUser(
+ "","","umls_api_key", apiKeyForTesting));
+ approver.resetUserCache();
+ }
+
+ @Test
+ public void testOldApiParams() {
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertNotEquals(true,approver.isValidUMLSUser(
+ "","","mocuser","mockpwd"));
+ approver.resetUserCache();
+ }
+
+ @Test
+ public void testViaSingleProp() {
+ Properties props = new Properties();
+ props.setProperty(UmlsUserApprover.API_KEY_PROP, apiKeyForTesting);
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true, approver.isValidUMLSUser(_uimaContext,
props));
+ approver.resetUserCache();
+ }
+
+ /**
+ * for this test you will need to make sure any user/pass env vars have
been removed and instead
+ * export ctakes.umls_apikey="<Your Key>" or export
ctakes_umls_apikey="<Your Key>"
+ */
+ @Ignore
+ @Test
+ public void testViaSingleEnvar() {
+ Properties props = new Properties();
+ UmlsUserApprover approver = UmlsUserApprover.getInstance();
+ Assert.assertEquals(true, approver.isValidUMLSUser(_uimaContext,
props));
+ approver.resetUserCache();
+ }
+
}
