/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* THE SOFTWARE.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.Globals;
import org.broad.igv.sam.Alignment;
import org.junit.BeforeClass;
import org.junit.Test;
import java.net.MalformedURLException;
import java.util.Iterator;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
/**
* @author Jim Robinson
* @date 1/10/12
*/
public class CGIAlignmentReaderTest {
@BeforeClass
public static void setup() {
Globals.setHeadless(true);
}
@Test
public void testURLs() throws MalformedURLException {
String testURL = "http://somehost/cramtools/cgi-bin/query.cgi?program=downsample_bam.pl&downsampled_coverage=10&file=input.sam/";
String queryPath = "query.cgi?";
String headerPath = "samHeader.cgi?";
String seqNamePath = "getSequenceNames.cgi?";
CGIAlignmentReader reader = new CGIAlignmentReader(testURL);
assertEquals(testURL, reader.getQueryURL());
assertEquals(testURL.replace(queryPath, headerPath), reader.getHeaderURL());
assertEquals(testURL .replace(queryPath, seqNamePath), reader.getSequenceNamesURL());
}
@Test
public void testURLsWithPort() throws MalformedURLException {
String testURL = "http://somehost:8080/cramtools/cgi-bin/query.cgi?program=downsample_bam.pl&downsampled_coverage=10&file=input.sam/";
String queryPath = "query.cgi?";
String headerPath = "samHeader.cgi?";
String seqNamePath = "getSequenceNames.cgi?";
CGIAlignmentReader reader = new CGIAlignmentReader(testURL);
assertEquals(testURL, reader.getQueryURL());
assertEquals(testURL.replace(queryPath, headerPath), reader.getHeaderURL());
assertEquals(testURL .replace(queryPath, seqNamePath), reader.getSequenceNamesURL());
}
// The following test is disabled until we can write our own CGI scripts to test against.
//@Test
// public void testQuery() throws Exception {
//
// String testURL = "http://somehost/query.cgi?file=input.sam";
//
// CGIAlignmentReader reader = new CGIAlignmentReader(testURL);
//
// // Assert that we get at least 1 record back.
// CloseableIterator<Alignment> iter = reader.iterator();
// assertTrue(iter.hasNext());
// iter.close();
//
//
// }
}