Fix issue in merging data and json files

lukfor · Oct 25, 2023 · bfc5450 · bfc5450
1 parent a220ac7
commit bfc5450
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Showing 3 changed files with 19 additions and 7 deletions.
diff --git a/src/main/java/genepi/riskscore/io/OutputFile.java b/src/main/java/genepi/riskscore/io/OutputFile.java
@@ -2,7 +2,9 @@
 
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 public class OutputFile {
@@ -13,11 +15,18 @@ public class OutputFile {
 
 	private List<String> scores;
 
+	private Map<String, Integer> scoresIndex = new HashMap<String, Integer>();
+
 	public OutputFile(String filename) throws IOException {
 
 		OutputFileReader outputFile = new OutputFileReader(filename);
 
 		scores = outputFile.getScores();
+		int index = 0;
+		for (String score: scores) {
+			scoresIndex.put(score, index);
+			index++;
+		}
 
 		samples = new Vector<String>();
 		data = new Vector<double[]>();
@@ -45,15 +54,16 @@ public int getCountScores() {
 	public List<String> getScores() {
 		return scores;
 	}
-
+	
 	public double getValue(int score, int sample) {
 		return data.get(sample)[score];
 	}
 
-	public double[] getValuesByScore(int score) {
+	public double[] getValuesByScore(String score) {
+		int scoreIndex = scoresIndex.get(score);
 		double[] values = new double[samples.size()];
 		for (int i = 0; i < values.length; i++) {
-			values[i] = getValue(score, i);
+			values[i] = getValue(scoreIndex, i);
 		}
 		return values;
 	}

diff --git a/src/main/java/genepi/riskscore/io/ReportFile.java b/src/main/java/genepi/riskscore/io/ReportFile.java
@@ -87,7 +87,7 @@ public void mergeWithData(OutputFile data) {
 			// ignore empty scores
 			if (getSummaries().get(i).getVariantsUsed() > 0) {
 				if (data != null) {
-					getSummaries().get(i).setData(data.getValuesByScore(i));
+					getSummaries().get(i).setData(data.getValuesByScore(getSummaries().get(i).getName()));
 				}
 			}
 			getSummaries().get(i).updateStatistics();

diff --git a/src/test/java/genepi/riskscore/tasks/MergeScoreTaskTest.java b/src/test/java/genepi/riskscore/tasks/MergeScoreTaskTest.java
@@ -154,9 +154,11 @@ public void assertEqualsScoreFiles(String filename1, String filename2, double de
 		assertEquals(file1.getSamples().size(), file2.getSamples().size());
 		assertEquals(file1.getScores().size(), file2.getScores().size());
 		for (int i = 0; i < file1.getScores().size(); i++) {
-			assertEquals(file1.getScores().get(i), file2.getScores().get(i));
-			double[] values1 = file1.getValuesByScore(i);
-			double[] values2 = file2.getValuesByScore(i);
+			String name1 = file1.getScores().get(i);
+			String name2 = file2.getScores().get(i);
+			assertEquals(name1, name2);
+			double[] values1 = file1.getValuesByScore(name1);
+			double[] values2 = file2.getValuesByScore(name2);
 			assertEquals(values1.length, values2.length);
 			assertEquals(values1.length, file1.getSamples().size());
 			for (int j = 0; j < values1.length; j++) {