From ca7beee0a495abb98ebf1d3c773246e801f5219c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 29 Jun 2017 16:49:13 +0200
Subject: [PATCH] skip invalid cell designer files
---
.../CellDesigner2SbgnmlConversionTest.java | 25 +++++++++++--------
1 file changed, 15 insertions(+), 10 deletions(-)
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
index 62d728acb6..e2a8401386 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
@@ -8,6 +8,7 @@ import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
+import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import org.junit.Test;
import org.junit.runner.RunWith;
@@ -22,9 +23,9 @@ import lcsb.mapviewer.model.map.model.Model;
@RunWith(Parameterized.class)
public class CellDesigner2SbgnmlConversionTest {
- Logger logger = Logger.getLogger(CellDesigner2SbgnmlConversionTest.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesigner2SbgnmlConversionTest.class.getName());
- private Path testPath;
+ private Path testPath;
public CellDesigner2SbgnmlConversionTest(Path testPath) {
this.testPath = testPath;
@@ -32,15 +33,19 @@ public class CellDesigner2SbgnmlConversionTest {
@Parameters(name = "{index} : {0}")
public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
+ Collection<Object[]> data = new ArrayList<>();
Files.walk(Paths.get("../converter-CellDesigner/testFiles")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- String tempPath = fPath.toString().substring(fPath.toString().indexOf("testFiles") + "testFiles".length() + 1);
- if (!tempPath.contains("_full")) {
- // String tName =
- // fPath.toString().substring(fPath.toString().indexOf("testFiles") +
- // "testFiles".length(), fPath.toString().indexOf(".xml"));
- data.add(new Object[] { fPath });
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")&& fPath.toString().indexOf("invalid")==-1) {
+ try {
+ String tempPath = fPath.toString().substring(fPath.toString().indexOf("testFiles") + "testFiles".length() + 1);
+ if (!tempPath.contains("_full")) {
+ String content = FileUtils.readFileToString(fPath.toFile());
+ if (content.indexOf("xmlns:celldesigner") >= 0) {
+ data.add(new Object[] { fPath });
+ }
+ }
+ } catch (Exception e) {
+ throw new RuntimeException();
}
}
});
--
GitLab