Unit test maintenance

igvteam · Aug 20, 2024 · 4a739bf · 4a739bf
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Showing 6 changed files with 10 additions and 72 deletions.
diff --git a/src/test/java/org/broad/igv/feature/genome/GenomeTest.java b/src/test/java/org/broad/igv/feature/genome/GenomeTest.java
@@ -53,45 +53,6 @@ public class GenomeTest extends AbstractHeadlessTest {
     @Rule
     public TestRule testTimeout = new Timeout((int) 60e3);
 
-    /**
-     * Test some aliases, both manually entered and automatic.
-     *
-     * @throws Exception
-     */
-    @Test
-    public void testAlias_01() throws Exception {
-        String genomeURL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome";
-        Genome genome = loadGenomeAssumeSuccess(genomeURL);
-
-        assertEquals("chrUn_gl000229", genome.getCanonicalChrName("GL000229.1"));
-        assertEquals("chr14", genome.getCanonicalChrName("14"));
-    }
-
-    @Test
-    public void testAlias_02() throws Exception {
-        // NCBI genome, test an auto-generated alias
-        String genomeURL = "https://igvdata.broadinstitute.org/genomes/NC_000964.genome";
-        Genome genome = loadGenomeAssumeSuccess(genomeURL);
-        assertEquals("gi|255767013|ref|NC_000964.3|", genome.getCanonicalChrName("NC_000964.3"));
-    }
-
-    /**
-     * Loads a genome
-     *
-     * @param genomeURL
-     * @return
-     */
-    private Genome loadGenomeAssumeSuccess(String genomeURL) {
-        Genome genome = null;
-        try {
-            genome = GenomeManager.getInstance().loadGenome(genomeURL);
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
-        Assume.assumeNotNull(genome);
-        return genome;
-    }
-
     @Test
     public void testGetNCBIName() throws Exception {
         String ncbiID = "gi|125745044|ref|NC_002229.3|";

diff --git a/src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java b/src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java
@@ -15,7 +15,7 @@ public class FastaBlockCompressedSequenceTest {
     @Test
     public void findBlockContaining() throws Exception {
 
-        String fasta = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.gz";
+        String fasta = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.gz";
 
         FastaBlockCompressedSequence seq = new FastaBlockCompressedSequence(fasta);
 
@@ -28,18 +28,18 @@ public void findBlockContaining() throws Exception {
     @Test
     public void compareSequences() throws Exception {
 
-        String sequencePath = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa";
-        String compressedSequencePath = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.gz";
+        String sequencePath = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa";
+        String compressedSequencePath = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.gz";
 
         Sequence fastaSequence = new FastaIndexedSequence(sequencePath);
         Sequence bgSequence = new FastaBlockCompressedSequence(compressedSequencePath);
 
-        int len1 = fastaSequence.getChromosomeLength("chr12");
         int len2 = bgSequence.getChromosomeLength("chr12");
+        int len1 = fastaSequence.getChromosomeLength("chr12");
         assertEquals(len1, len2);
 
+        byte[] seq2 = bgSequence.getSequence("chr12", 50000, 51000);
         byte[] seq1 = fastaSequence.getSequence("chr12", 50000, 51000);
-        byte[] seq2 = fastaSequence.getSequence("chr12", 50000, 51000);
 
         for (int i = 0; i < seq1.length; i++) {
             byte b1 = seq1[i];

diff --git a/src/test/java/org/broad/igv/feature/genome/load/JsonGenomeLoaderTest.java b/src/test/java/org/broad/igv/feature/genome/load/JsonGenomeLoaderTest.java
@@ -36,27 +36,3 @@ public void loadGenome() throws IOException {
     public void loadDescriptor() {
     }
 }
-
-
-/*
-{
-  "id": "hg38",
-  "name": "Human (GRCh38/hg38)",
-  "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
-  "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
-  "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",
-  "aliasURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",
-  "tracks": [
-    {
-      "name": "Refseq Genes",
-      "format": "refgene",
-      "url": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz",
-      "indexURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz.tbi",
-      "visibilityWindow": -1,
-      "removable": false,
-      "order": 1000000
-    }
-  ],
-  "chromosomeOrder": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"
-}
- */
diff --git a/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java b/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java
@@ -43,8 +43,8 @@
 
 public class IGVReferenceSourceTest {
 
-    public static final String FASTA_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa";
-    public static final String COMPRESSED_FASTA_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.gz";
+    public static final String FASTA_URL = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa";
+    public static final String COMPRESSED_FASTA_URL = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.gz";
     public static final String EXPECTED_REFERENCE_BASES = "AAACCCAGGGCAAAGAATCTGGCCCTA"; //bases at 22:27198875-271988902
 
     @Before

diff --git a/src/test/java/org/broad/igv/util/HttpUtilsTest.java b/src/test/java/org/broad/igv/util/HttpUtilsTest.java
@@ -66,6 +66,7 @@ public void testGetContentLength() throws IOException {
         HttpURLConnection conn = null;
         try {
             conn = (HttpURLConnection) (HttpUtils.createURL(broadURLString)).openConnection();
+            conn.setRequestProperty("User-Agent", "IGV");
             String contentLength = conn.getHeaderField("Content-length");
             assertEquals("52330665", contentLength);
 

diff --git a/src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java b/src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java
@@ -261,7 +261,7 @@ public void testRandomRead() throws IOException {
         assertEquals(length, bytesRead);
 
         byte[] buffer2 = new byte[length];
-        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(HttpUtils.createURL(BAM_URL_STRING)));
+        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new IGVSeekableHTTPStream(HttpUtils.createURL(BAM_URL_STRING)));
         bufferedStream.seek(startPosition);
         bytesRead = bufferedStream.read(buffer2, 0, length);
         assertEquals(length, bytesRead);
@@ -286,7 +286,7 @@ public void testEOF() throws IOException {
 
 
         byte[] buffer = new byte[length];
-        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(HttpUtils.createURL(BAM_URL_STRING)));
+        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new IGVSeekableHTTPStream(HttpUtils.createURL(BAM_URL_STRING)));
         bufferedStream.seek(startPosition);
         int bytesRead = bufferedStream.read(buffer, 0, length);
         assertEquals(remainder, bytesRead);