Unverified Commit 69d60e74 authored by Kev's avatar Kev Committed by GitHub
Browse files

Merge pull request #234 from kpepper/artemis_unit_testing

Changed BamUtilsTest class to cope with connect exception.
parents 3b3a534e 858a6d9a
......@@ -25,6 +25,7 @@ import static org.junit.Assert.*;
import org.junit.Test;
import java.io.File;
import java.net.ConnectException;
import java.net.URL;
import htsjdk.samtools.BAMIndex;
......@@ -253,11 +254,19 @@ public class BamUtilsTest {
// Check getting the index file for a BAM file with an index for FTP
// Should create local copy.
//
File existingBamIndexFtpFile = BamUtils.getIndexFile("ftp://ftp.sanger.ac.uk/pub/project/pathogens/kp11/NV.bam");
assertNotNull(existingBamIndexFtpFile);
assertTrue(existingBamIndexFtpFile.exists());
assertTrue(existingBamIndexFtpFile.getName().endsWith(BAMIndex.BAMIndexSuffix));
assertTrue(existingBamIndexFtpFile.length()>0);
try
{
File existingBamIndexFtpFile = BamUtils.getIndexFile("ftp://ftp.sanger.ac.uk/pub/project/pathogens/kp11/NV.bam");
assertNotNull(existingBamIndexFtpFile);
assertTrue(existingBamIndexFtpFile.exists());
assertTrue(existingBamIndexFtpFile.getName().endsWith(BAMIndex.BAMIndexSuffix));
assertTrue(existingBamIndexFtpFile.length()>0);
}
catch (ConnectException e)
{
System.err.println("testGetIndexFileForFtpBam() : WARNING: Unable to run this test as cannot connect to Sanger FTP server");
e.printStackTrace();
}
}
@Test
......@@ -276,6 +285,11 @@ public class BamUtilsTest {
{
assertTrue(e.getMessage().contains("Failed to find an index file"));
}
catch (ConnectException e)
{
System.err.println("testCreateIndexFileForFtpCram() : WARNING: Unable to run this test as cannot connect to Sanger FTP server");
e.printStackTrace();
}
assertNull(createdCramIndexFtpFile);
......@@ -289,10 +303,18 @@ public class BamUtilsTest {
// Check getting the index file for a CRAM file with an index for FTP
// Should create local copy.
//
File existingCramIndexFtpFile = BamUtils.getIndexFile("ftp://ftp.sanger.ac.uk/pub/project/pathogens/kp11/NV.cram");
assertNotNull(existingCramIndexFtpFile);
assertTrue(existingCramIndexFtpFile.exists());
assertTrue(existingCramIndexFtpFile.getName().endsWith(CRAIIndex.CRAI_INDEX_SUFFIX));
assertTrue(existingCramIndexFtpFile.length()>0);
try
{
File existingCramIndexFtpFile = BamUtils.getIndexFile("ftp://ftp.sanger.ac.uk/pub/project/pathogens/kp11/NV.cram");
assertNotNull(existingCramIndexFtpFile);
assertTrue(existingCramIndexFtpFile.exists());
assertTrue(existingCramIndexFtpFile.getName().endsWith(CRAIIndex.CRAI_INDEX_SUFFIX));
assertTrue(existingCramIndexFtpFile.length()>0);
}
catch (ConnectException e)
{
System.err.println("testGetExistingIndexFileForFtpCram() : WARNING: Unable to run this test as cannot connect to Sanger FTP server");
e.printStackTrace();
}
}
}
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