Java tutorial
/* * Copyright 2016 King's College London, Richard Jackson <richgjackson@gmail.com>. * * Licensed 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. */ package uk.ac.kcl.it; import org.apache.log4j.Logger; import org.junit.Test; import org.junit.runner.RunWith; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.ComponentScan; import org.springframework.core.env.Environment; import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.context.ActiveProfiles; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.TestExecutionListeners; import org.springframework.test.context.TestPropertySource; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import org.springframework.test.context.support.AnnotationConfigContextLoader; import uk.ac.kcl.mutators.Mutant; import uk.ac.kcl.rowmappers.DocumentRowMapper; import uk.ac.kcl.scheduling.SingleJobLauncher; import uk.ac.kcl.service.ElasticGazetteerService; import uk.ac.kcl.testexecutionlisteners.DeidTestExecutionListener; import javax.sql.DataSource; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.*; import java.util.regex.MatchResult; import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.stream.Collectors; import static org.junit.Assert.assertEquals; /** * * @author rich */ @RunWith(SpringJUnit4ClassRunner.class) @ComponentScan("uk.ac.kcl.it") @TestPropertySource({ "classpath:postgres_test.properties", "classpath:postgres_db.properties", // "classpath:sql_server_test.properties", // "classpath:sql_server_db.properties", "classpath:jms.properties", "classpath:noScheduling.properties", "classpath:gate.properties", "classpath:deidentification.properties", "classpath:elasticsearch.properties", "classpath:elasticgazetteer_test.properties", "classpath:jobAndStep.properties" }) @ContextConfiguration(classes = { SingleJobLauncher.class, PostGresTestUtils.class, SqlServerTestUtils.class, TestUtils.class }, loader = AnnotationConfigContextLoader.class) @TestExecutionListeners(listeners = DeidTestExecutionListener.class, mergeMode = TestExecutionListeners.MergeMode.MERGE_WITH_DEFAULTS) @ActiveProfiles({ "deid", "basic", "localPartitioning", "jdbc", "elasticsearch", "primaryKeyPartition", "postgres" }) //@ActiveProfiles({"deid","basic","localPartitioning","jdbc","elasticsearch","primaryKeyPartition","sqlserver"}) public class DeIdentificationPKPartitionWithoutScheduling { final static Logger logger = Logger.getLogger(DeIdentificationPKPartitionWithoutScheduling.class); @Autowired SingleJobLauncher jobLauncher; @Test @DirtiesContext public void deIdentificationTest() { jobLauncher.launchJob(); try { Thread.sleep(5000); } catch (InterruptedException e) { e.printStackTrace(); } assertEquals(106, testUtils.countOutputDocsInES()); assertEquals(106, dbmsTestUtils.countRowsInOutputTable()); } @Autowired @Qualifier("sourceDataSource") public DataSource sourceDataSource; @Autowired DocumentRowMapper documentRowMapper; @Autowired ElasticGazetteerService elasticGazetteerService; @Autowired TestUtils testUtils; @Autowired DbmsTestUtils dbmsTestUtils; @Autowired Environment env; @Value("#{'${mutatortype:0}'}") private int mutatortype; @Test public void deidentificationPerformanceTest() { dbmsTestUtils.createBasicInputTable(); dbmsTestUtils.createBasicOutputTable(); dbmsTestUtils.createDeIdInputTable(); List<Mutant> mutants = testUtils.insertTestDataForDeidentification(env.getProperty("tblIdentifiers"), env.getProperty("tblInputDocs"), mutatortype); int totalTruePositives = 0; int totalFalsePositives = 0; int totalFalseNegatives = 0; for (Mutant mutant : mutants) { Set<Pattern> mutatedPatterns = new HashSet<>(); mutant.setDeidentifiedString(elasticGazetteerService.deIdentifyString(mutant.getFinalText(), String.valueOf(mutant.getDocumentid()))); Set<String> set = new HashSet<>(mutant.getOutputTokens()); mutatedPatterns.addAll( set.stream().map(string -> Pattern.compile(Pattern.quote(string), Pattern.CASE_INSENSITIVE)) .collect(Collectors.toSet())); List<MatchResult> results = new ArrayList<>(); for (Pattern pattern : mutatedPatterns) { Matcher matcher = pattern.matcher(mutant.getFinalText()); while (matcher.find()) { results.add(matcher.toMatchResult()); } } int truePositives = getTruePositiveTokenCount(mutant); int falsePositives = getFalsePositiveTokenCount(mutant); int falseNegatives = getFalseNegativeTokenCount(mutant); System.out.println("Doc ID " + mutant.getDocumentid() + " has " + falseNegatives + " unmasked identifiers from a total of " + (falseNegatives + truePositives)); System.out.println("Doc ID " + mutant.getDocumentid() + " has " + falsePositives + " inaccurately masked tokens from a total of " + (falsePositives + truePositives)); System.out.println("TP: " + truePositives + " FP: " + falsePositives + " FN: " + falseNegatives); System.out.println("Doc ID precision " + calcPrecision(falsePositives, truePositives)); System.out.println("Doc ID recall " + calcRecall(falseNegatives, truePositives)); System.out.println(mutant.getDeidentifiedString()); System.out.println(mutant.getFinalText()); System.out.println(mutant.getInputTokens()); System.out.println(mutant.getOutputTokens()); System.out.println(); if (env.getProperty("elasticgazetteerTestOutput") != null) { try { try (BufferedWriter bw = new BufferedWriter( new FileWriter(new File(env.getProperty("elasticgazetteerTestOutput") + File.separator + mutant.getDocumentid())))) { bw.write("Doc ID " + mutant.getDocumentid() + " has " + falseNegatives + " unmasked identifiers from a total of " + (falseNegatives + truePositives)); bw.newLine(); bw.write("Doc ID " + mutant.getDocumentid() + " has " + falsePositives + " inaccurately masked tokens from a total of " + (falsePositives + truePositives)); bw.newLine(); bw.write("TP: " + truePositives + " FP: " + falsePositives + " FN: " + falseNegatives); bw.newLine(); bw.write("Doc ID precision " + calcPrecision(falsePositives, truePositives)); bw.newLine(); bw.write("Doc ID recall " + calcRecall(falseNegatives, truePositives)); bw.newLine(); bw.write(mutant.getDeidentifiedString()); bw.newLine(); bw.write(mutant.getFinalText()); bw.newLine(); bw.write(mutant.getInputTokens().toString()); bw.newLine(); bw.write(mutant.getOutputTokens().toString()); } } catch (IOException e) { e.printStackTrace(); } } totalTruePositives += truePositives; totalFalsePositives += falsePositives; totalFalseNegatives += falseNegatives; } System.out.println(); System.out.println(); System.out.println("THIS RUN TP: " + totalTruePositives + " FP: " + totalFalsePositives + " FN: " + totalFalseNegatives); System.out.println("Doc ID precision " + calcPrecision(totalFalsePositives, totalTruePositives)); System.out.println("Doc ID recall " + calcRecall(totalFalseNegatives, totalTruePositives)); if (env.getProperty("elasticgazetteerTestOutput") != null) { try { try (BufferedWriter bw = new BufferedWriter(new FileWriter( new File(env.getProperty("elasticgazetteerTestOutput") + File.separator + "summary")))) { bw.write("THIS RUN TP: " + totalTruePositives + " FP: " + totalFalsePositives + " FN: " + totalFalseNegatives); bw.newLine(); bw.write("Doc ID precision " + calcPrecision(totalFalsePositives, totalTruePositives)); bw.newLine(); bw.write("Doc ID recall " + calcRecall(totalFalseNegatives, totalTruePositives)); } } catch (IOException e) { e.printStackTrace(); } } } private int getFalsePositiveTokenCount(Mutant mutant) { int count = 0; Pattern mask = Pattern.compile("X+"); List<MatchResult> results = new ArrayList<>(); Matcher matcher = mask.matcher(mutant.getDeidentifiedString()); while (matcher.find()) { results.add(matcher.toMatchResult()); } for (MatchResult result : results) { StringTokenizer tokenizer = new StringTokenizer( mutant.getFinalText().substring(result.start(), result.end())); ArrayList<String> arHits = new ArrayList<>(); while (tokenizer.hasMoreTokens()) { arHits.add(tokenizer.nextToken()); } for (String hit : arHits) { boolean isAnIdentifier = false; for (String token : mutant.getOutputTokens()) { if (hit.matches(Pattern.quote(token))) { isAnIdentifier = true; } } if (!isAnIdentifier && !hit.equalsIgnoreCase("") && !hit.equalsIgnoreCase("-")) { count++; } } } return count; } private int getTruePositiveTokenCount(Mutant mutant) { int count = 0; Pattern mask = Pattern.compile("X+"); List<MatchResult> results = new ArrayList<>(); Matcher matcher = mask.matcher(mutant.getDeidentifiedString()); while (matcher.find()) { results.add(matcher.toMatchResult()); } for (MatchResult result : results) { StringTokenizer tokenizer = new StringTokenizer( mutant.getFinalText().substring(result.start(), result.end())); ArrayList<String> arHits = new ArrayList<>(); while (tokenizer.hasMoreTokens()) { arHits.add(tokenizer.nextToken()); } count = getHitCount(mutant, count, arHits); } return count; } private int getHitCount(Mutant mutant, int count, ArrayList<String> arHits) { for (String hit : arHits) { boolean hitFound = false; for (String token : mutant.getOutputTokens()) { if (hit.matches(Pattern.quote(token))) { hitFound = true; } } if (hitFound && !hit.equalsIgnoreCase("") && !hit.equalsIgnoreCase("-")) { count++; } } return count; } private int getFalseNegativeTokenCount(Mutant mutant) { int count = 0; StringTokenizer tokenizer = new StringTokenizer(mutant.getDeidentifiedString()); ArrayList<String> arHits = new ArrayList<>(); while (tokenizer.hasMoreTokens()) { arHits.add(tokenizer.nextToken()); } count = getHitCount(mutant, count, arHits); return count; } private double calcPrecision(int falsePositives, int truePositives) { return (((double) truePositives / ((double) falsePositives + (double) truePositives))) * 100.0; } private double calcRecall(int falseNegative, int truePositives) { return (((double) truePositives / ((double) falseNegative + (double) truePositives))) * 100.0; } }