fixing access to local files. test better done via classpath

andreasprlic · andreasprlic · commit 208be50ff44a · 2014-08-23T09:11:47.000-07:00
diff --git a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankWriterTest.java
@@ -7,6 +7,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 
@@ -25,8 +26,10 @@ public class GenbankWriterTest extends TestCase{
 
 	@Test
 	public void testProcess() throws Exception {
-		File dnaFile = new File("src/test/resources/NM_000266.gb");
-		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( dnaFile );
+
+        InputStream inStream = GenbankWriterTest.class.getResourceAsStream("/NM_000266.gb");
+		//File dnaFile = new File("src/test/resources/NM_000266.gb");
+		LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( inStream );
 		ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
 		ArrayList<DNASequence> seqs = new ArrayList<DNASequence>();
 		for(DNASequence seq : dnaSequences.values()) {
diff --git a/biojava3-structure/src/test/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactoryTest.java b/biojava3-structure/src/test/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactoryTest.java
@@ -29,6 +29,7 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.InputStream;
 import java.util.List;
 
 import org.junit.Test;
@@ -40,21 +41,13 @@
  */
 public class RCSBLigandsFactoryTest {
 
-
-	private static final String TEST_DIR = "src/test/resources/";
-	
 	/**
-	 * Opens the file as a {@link FileInputStream}. Copied from ResourceList, which is not in biojava.
+	 * Opens the file as a {@link InputStream}.
 	 */
-	private FileInputStream openStream(String filename) {
-		File file = new File(TEST_DIR + filename);
-		FileInputStream fis;
-		try {
-			fis = new FileInputStream(file);
-		} catch (FileNotFoundException e) {
-			throw new RuntimeException(e);
-		}
-		return fis;
+	private InputStream openStream(String filename) {
+        InputStream is = this.getClass().getClassLoader().getResourceAsStream(filename);
+
+		return is;
 	}
 
 	/**
