Fix test case

seppinho · Jan 18, 2021 · bf9348f · bf9348f · vercel · Jan 18, 2021
1 parent fd456ea
commit bf9348f
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Showing 2 changed files with 10 additions and 89 deletions.
diff --git a/src/main/java/genepi/mut/commands/ReportCommand.java b/src/main/java/genepi/mut/commands/ReportCommand.java
@@ -1,23 +1,8 @@
 package genepi.mut.commands;
 
 import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
 import java.util.concurrent.Callable;
-
-import genepi.mut.objects.ReportObject;
-import genepi.mut.objects.Sample;
-import genepi.mut.objects.Variant;
-import genepi.mut.util.MutationServerReader;
-import lukfor.reports.HtmlReport;
-import lukfor.tables.Table;
-import lukfor.tables.columns.IBuildValueFunction;
-import lukfor.tables.columns.types.StringColumn;
-import lukfor.tables.io.TableBuilder;
-import lukfor.tables.io.TableWriter;
-import lukfor.tables.rows.Row;
+import genepi.mut.tasks.ReportTask;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 
@@ -39,35 +24,10 @@ public Integer call() throws Exception {
 			return 1;
 		}
 
-		HtmlReport report = new HtmlReport("/report");
-		report.setSelfContained(true);
-		report.set("title", "mtDNA Server Report v2 (Beta)");
-
-		List<ReportObject> variants = new ArrayList<ReportObject>();
-		MutationServerReader reader = new MutationServerReader(input);
-		HashMap<String, Sample> samples = reader.parse();
-
-		for (Sample sample : samples.values()) {
-
-			for (ArrayList<Variant> a : sample.getVariants()) {
-
-				for(Variant variant : a) {
-				ReportObject reportObject = new ReportObject();
-				reportObject.setCoverage(variant.getCoverage());
-				reportObject.setId(sample.getId());
-				reportObject.setPos(variant.getPos());
-				reportObject.setFilter(variant.getFilter().name());
-				reportObject.setRef(variant.getRef());
-				reportObject.setVar(variant.getVariant());
-				variants.add(reportObject);
-
-				}
-			}
-		}
-
-		report.set("variants", variants);
-		report.generate(new File(output));
-
+		ReportTask task = new ReportTask();
+		task.setInput(input);
+		task.setOutput(output);
+		task.createReport();
 		return 0;
 	}
 

diff --git a/src/test/java/genepi/mut/steps/report/ReportGeneratorTest.java b/src/test/java/genepi/mut/steps/report/ReportGeneratorTest.java
@@ -1,23 +1,9 @@
 package genepi.mut.steps.report;
 
-import java.io.File;
-import java.io.FileReader;
-import java.lang.reflect.Type;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
 import org.junit.Test;
 
-import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
-
 import genepi.io.FileUtil;
-import genepi.mut.objects.ReportObject;
-import genepi.mut.objects.Sample;
-import genepi.mut.objects.Variant;
-import genepi.mut.util.MutationServerReader;
-import lukfor.reports.HtmlReport;
+import genepi.mut.tasks.ReportTask;
 
 public class ReportGeneratorTest {
 
@@ -27,35 +13,10 @@ public void testGenerate() throws Exception {
 		String input = "test-data/mtdna/report/1000g.txt";
 		String output = "test-data/mtdna/report/out.html";
 
-		HtmlReport report = new HtmlReport("/report");
-		report.setSelfContained(true);
-		report.set("title", "mtDNA Server Report v2 (Beta)");
-
-		List<ReportObject> objects = new ArrayList<ReportObject>();
-		MutationServerReader reader = new MutationServerReader(input);
-		HashMap<String, Sample> samples = reader.parse();
-
-		for (Sample sample : samples.values()) {
-
-			for (ArrayList<Variant> variants : sample.getVariants()) {
-
-				for (Variant variant : variants) {
-					ReportObject reportObject = new ReportObject();
-					reportObject.setCoverage(variant.getCoverage());
-					reportObject.setId(sample.getId());
-					reportObject.setPos(variant.getPos());
-					reportObject.setFilter(variant.getFilter().name());
-					reportObject.setRef(variant.getRef());
-					reportObject.setVar(variant.getVariant());
-					reportObject.setLevel(variant.getLevel());
-					reportObject.setType(variant.getType());
-					objects.add(reportObject);
-				}
-			}
-		}
-
-		report.set("variants", objects);
-		report.generate(new File(output));
+		ReportTask task = new ReportTask();
+		task.setInput(input);
+		task.setOutput(output);
+		task.createReport();
 
 		FileUtil.deleteFile(output);