Description: ignoring build-time tests that require network access Author: Pierre Gruet Forwarded: not-needed Last-Update: 2020-09-01 --- a/src/test/java/org/broad/igv/feature/genome/GenomeTest.java +++ b/src/test/java/org/broad/igv/feature/genome/GenomeTest.java @@ -29,6 +29,7 @@ import org.broad.igv.feature.genome.fasta.FastaIndex; import org.broad.igv.util.TestUtils; import org.junit.Assume; +import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.TestRule; @@ -55,6 +56,7 @@ * Test some aliases, both manually entered and automatic. * @throws Exception */ + @Ignore("No network access") @Test public void testAlias_01() throws Exception { String genomeURL = "http://igv.broadinstitute.org/genomes/hg19.genome"; @@ -64,6 +66,7 @@ assertEquals("chr14", genome.getCanonicalChrName("14")); } + @Ignore("No network access") @Test public void testAlias_02() throws Exception { // NCBI genome, test an auto-generated alias --- a/src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java +++ b/src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java @@ -1,5 +1,6 @@ package org.broad.igv.feature.genome.fasta; +import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -10,6 +11,7 @@ public class FastaBlockCompressedSequenceTest { + @Ignore("No network access") @Test public void findBlockContaining() throws Exception { --- a/src/test/java/org/broad/igv/sam/AlignmentDataManagerTest.java +++ b/src/test/java/org/broad/igv/sam/AlignmentDataManagerTest.java @@ -115,6 +115,7 @@ + @Ignore("No network access") @Test public void testQuery() throws IOException { String testFile = "http://data.broadinstitute.org/igvdata/BodyMap/hg18/50bp/FCA/s_1_1_sequence.bam"; --- a/src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java +++ b/src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java @@ -42,6 +42,7 @@ import org.broad.igv.util.TestUtils; import org.junit.AfterClass; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import java.util.List; @@ -114,6 +115,7 @@ + @Ignore("No network access") @Test public void testRemoteCraiCram() throws Exception { @@ -151,4 +153,4 @@ return counter; } -} \ No newline at end of file +} --- a/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java +++ b/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java @@ -54,6 +54,7 @@ } + @Ignore("No network access") @Test public void testGetReferenceBases() throws Exception { @@ -72,6 +73,7 @@ } + @Ignore("No network access") @Test public void testGetReferenceBasesCompressed() throws Exception { --- a/src/test/java/org/broad/igv/sam/lite/BAMIndexTest.java +++ b/src/test/java/org/broad/igv/sam/lite/BAMIndexTest.java @@ -1,5 +1,6 @@ package org.broad.igv.sam.lite; +import org.junit.Ignore; import org.junit.Test; import java.util.List; @@ -10,6 +11,7 @@ * Created by jrobinso on 3/10/17. */ public class BAMIndexTest { + @Ignore("No network access") @Test public void chunksForRange() throws Exception { int refID = 14; @@ -29,6 +31,7 @@ } + @Ignore("No network access") @Test public void loadIndex() throws Exception { --- a/src/test/java/org/broad/igv/sam/reader/BAMHttpReaderTest.java +++ b/src/test/java/org/broad/igv/sam/reader/BAMHttpReaderTest.java @@ -42,6 +42,7 @@ import java.util.List; import java.util.stream.Collectors; +import org.junit.Ignore; import static org.junit.Assert.*; /** @@ -74,6 +75,7 @@ reader = null; } + @Ignore("No network access") @Test public void testGetHeader() throws IOException { SAMFileHeader header = reader.getFileHeader(); @@ -81,6 +83,7 @@ assertEquals("1.0", header.getVersion()); } + @Ignore("No network access") @Test public void testIterator() { CloseableIterator iter = reader.iterator(); @@ -101,6 +104,7 @@ } + @Ignore("No network access") @Test public void testQuery() throws Exception { checkNumber("Y", 10000000 - 1, 10004000, 4); --- a/src/test/java/org/broad/igv/tdf/TDFReaderTest.java +++ b/src/test/java/org/broad/igv/tdf/TDFReaderTest.java @@ -26,6 +26,7 @@ package org.broad.igv.tdf; import org.broad.igv.util.ResourceLocator; +import org.junit.Ignore; import org.junit.Test; import java.util.Set; @@ -41,6 +42,7 @@ */ public class TDFReaderTest { + @Ignore("No network access") @Test public void testReader() throws Exception { String url = "http://data.broadinstitute.org/igvdata/encode/hg18/broadHistone/SignalK562H3k4me3.tdf"; --- a/src/test/java/org/broad/igv/tdf/TDFRegressionTests.java +++ b/src/test/java/org/broad/igv/tdf/TDFRegressionTests.java @@ -36,6 +36,7 @@ import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.TestUtils; import org.junit.Assume; +import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.TestRule; @@ -61,6 +62,7 @@ /** * IGV-1417 and/or IGV-1421 - error reading a version 1 file (error thrown in header) */ + @Ignore("No network access") @Test public void test_IGV1417() { String tdfFile = "http://data.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.ewig.tdf"; @@ -68,6 +70,7 @@ assertEquals(1, reader.getVersion()); } + @Ignore("No network access") @Test public void test_v3() { String tdfFile = "http://data.broadinstitute.org/igvdata/test/tdf/NA12878.pilot2.454.bam.tdf"; @@ -92,6 +95,7 @@ // tstCHR_ALL(genPath, wigPath, tdf3Path, false, dm3posChromos, dm3emptyChromos); // } + @Ignore("No network access") @Test public void testChrAlldm3_v4() throws Exception{ String genPath = "http://igvdata.broadinstitute.org/genomes/dm3.genome"; --- a/src/test/java/org/broad/igv/tools/parsers/GCTtoIGVConverterTest.java +++ b/src/test/java/org/broad/igv/tools/parsers/GCTtoIGVConverterTest.java @@ -29,6 +29,7 @@ import org.broad.igv.tools.converters.GCTtoIGVConverter; import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.TestUtils; +import org.junit.Ignore; import org.junit.Test; import java.io.File; @@ -51,6 +52,7 @@ } + @Ignore("No network access") @Test public void testAffyMapping() throws IOException { String gctFile = TestUtils.DATA_DIR + "gct/affy_human.gct"; --- a/src/test/java/org/broad/igv/track/TrackLoaderTest.java +++ b/src/test/java/org/broad/igv/track/TrackLoaderTest.java @@ -36,6 +36,7 @@ import org.broad.igv.variant.VariantTrack; import htsjdk.tribble.Feature; import org.junit.Before; +import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.TestRule; @@ -258,6 +259,7 @@ tstFilesHeadless(filenamesTryIndex, true); } + @Ignore("No network access") @Test public void testFilesHeadlessNoIndex() throws Exception { tstFilesHeadless(filenamesNoIndex, false); --- a/src/test/java/org/broad/igv/util/HttpUtilsTest.java +++ b/src/test/java/org/broad/igv/util/HttpUtilsTest.java @@ -53,6 +53,7 @@ static String noRangeHeaderSupportString = "http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM714693&format=file&file=GSM714693%5Fhg19%5FwgEncodeGisDnaPetK562F1kAln%2Ebam"; + @Ignore("No network access") @Test public void testGetContentLength() throws IOException { // Open an input stream just to check permissions @@ -76,6 +77,7 @@ * * @throws Exception */ + @Ignore("No network access") @Test public void testBroadURL() throws Exception { assertTrue(HttpUtils.getInstance().useByteRange(HttpUtils.createURL(broadURLString))); @@ -88,6 +90,7 @@ * * @throws Exception */ + @Ignore("No network access") @Test public void testGenericURL() throws Exception { final URL url = HttpUtils.createURL(genericURLString); --- a/src/test/java/org/broad/igv/util/IGVHttpClientUtilsTest.java +++ b/src/test/java/org/broad/igv/util/IGVHttpClientUtilsTest.java @@ -49,6 +49,7 @@ private static String hg18URL = "http://data.broadinstitute.org/igvdata/test/hg18.unittest.genome"; private static int hg18bytes = 3617644; + @Ignore("No network access") @Test public void testGetContentLength() throws IOException { @@ -56,6 +57,7 @@ assertEquals(hg18bytes, HttpUtils.getInstance().getContentLength(HttpUtils.createURL(url))); } + @Ignore("No network access") @Test public void testExists() throws IOException { String url = hg18URL; --- a/src/test/java/org/broad/igv/util/ParsingUtilsTest.java +++ b/src/test/java/org/broad/igv/util/ParsingUtilsTest.java @@ -34,6 +34,7 @@ import org.broad.igv.track.TrackProperties; import org.broad.igv.track.WindowFunction; import org.junit.Before; +import org.junit.Ignore; import org.junit.Rule; import org.junit.Test; import org.junit.rules.TestRule; @@ -121,6 +122,7 @@ } } + @Ignore("No network access") @Test public void testGetLastModified_HTTP() throws Exception{ tstGetLastModified(HttpUtilsTest.broadURLString); --- a/src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java +++ b/src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java @@ -34,6 +34,7 @@ import org.broad.igv.util.HttpUtils; import org.broad.igv.util.TestUtils; import org.junit.Assume; +import org.junit.Ignore; import org.junit.Before; import org.junit.BeforeClass; import org.junit.Test; @@ -248,6 +249,7 @@ * * @throws IOException */ + @Ignore("No network access") @Test public void testRandomRead() throws IOException { @@ -276,6 +278,7 @@ * * @throws IOException */ + @Ignore("No network access") @Test public void testEOF() throws IOException { --- a/src/test/java/org/broad/igv/tools/IGVToolsTest.java +++ b/src/test/java/org/broad/igv/tools/IGVToolsTest.java @@ -209,6 +209,7 @@ } + @Ignore("No network access") @Test public void testTileGCT_01() throws IOException { String inputFile = TestUtils.DATA_DIR + "gct/OV.transcriptome__agilentg4502.data.txt"; @@ -217,6 +218,7 @@ igvTools.run(args); } + @Ignore("No network access") @Test public void testTileGCT_02() throws IOException { String inputFile = TestUtils.DATA_DIR + "gct/GBM.methylation__sampled.data.txt"; --- a/src/test/java/org/broad/igv/tools/converters/ExpressionFormatterTest.java +++ b/src/test/java/org/broad/igv/tools/converters/ExpressionFormatterTest.java @@ -30,6 +30,7 @@ import org.broad.igv.data.expression.ExpressionFileParser; import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.TestUtils; +import org.junit.Ignore; import org.junit.Test; import java.io.File; @@ -43,6 +44,7 @@ */ public class ExpressionFormatterTest extends AbstractHeadlessTest { + @Ignore("No network access") @Test public void testConvertGCT() throws Exception { //String inputPath = TestUtils.DATA_DIR + "gct/igv_test2.gct"; --- a/build_java11.gradle +++ b/build_java11.gradle @@ -134,6 +134,10 @@ test { inputs.property("moduleName", moduleName) + exclude '**/FeatureDatasetTest.class' + exclude '**/FastaIndexedSequenceTest.class' + exclude '**/FastaSequenceParserTest.class' + exclude '**/SeekableServiceStreamTest.class' doFirst { jvmArgs = [ '-Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize', --- a/src/test/java/org/broad/igv/tools/motiffinder/MotifFinderSourceTest.java +++ b/src/test/java/org/broad/igv/tools/motiffinder/MotifFinderSourceTest.java @@ -154,6 +154,7 @@ assertEquals("ACTG[M,A,C]ACTG.ACT[S,G,C]G", regex); } + @Ignore("No network access") @Test public void testExactSearch_EGFR() throws Exception{ String motif = "CTTCGGGGAGCAGCGATGCGACCCTCCGGGACGGCCGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAGGTAAGGGCGTGTCTCGCCGGCTCCCGCGCCGCCCCCGGATCGCGCCCCGGACCCCGCAGCCCGCCCAACCGCG"; @@ -162,6 +163,7 @@ tstSearchGenome_EGFR(motif, expStart, expStart + motif.length()); } + @Ignore("No network access") @Test public void testAmbiguousSearch_EGFR() throws Exception{ String motif = "CTTYKSVDAGCAGNGATGCRRCCCYCCGGGACGGCCGGGNCAGCGCKCCBGGCGCDGCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGRMWHGAAAGGNNVGGGCGTGTCTCGCCGGCTCCCGCGCCGCCCCCGGATCGCGCCCCGGACCCCGCAGCCCGCCCAACCGCG"; @@ -171,6 +173,7 @@ tstSearchGenome_EGFR(pattern, expStart, expStart + motif.length()); } + @Ignore("No network access") @Test public void testSearchNoResult() throws Exception{ tstSearchGenomeSingResult("GATCRYMKSWHBVDNGATCGATCGATCGATCGATCGATCGATCGATCGATC", Strand.POSITIVE, "chr7", @@ -181,6 +184,7 @@ * Test searching for a motif which has 2 overlapping hits * @throws Exception */ + @Ignore("No network access") @Test public void testSearchOverlapping() throws Exception{ String motif = "ATGCATGCATGC"; --- a/src/test/java/org/broad/igv/feature/AminoAcidManagerTest.java +++ b/src/test/java/org/broad/igv/feature/AminoAcidManagerTest.java @@ -31,6 +31,7 @@ import org.broad.igv.AbstractHeadlessTest; import org.broad.igv.feature.tribble.UCSCGeneTableCodec; +import org.junit.Ignore; import org.junit.Test; import java.util.HashMap; @@ -52,6 +53,7 @@ AminoAcidManager.resetToDefaultCodonTables(); } + @Ignore("No network access") @Test public void testFoo() { @@ -79,6 +81,7 @@ /** * Test getting the amino acids for the first exon on gene EGFR */ + @Ignore("No network access") @Test public void testStartEgfr() { String expectedSeq = "MRPSGTAGAALLALLAALCPASRALEEKKVC"; @@ -97,6 +100,7 @@ } + @Ignore("No network access") @Test public void testExon2EGFR() { // Note: frame == 1, phase == 2 @@ -115,6 +119,7 @@ } + @Ignore("No network access") @Test public void testExon3EGFR() { final int exonIndex = 2; @@ -143,6 +148,7 @@ /** * Test the last exon of a gene on the negative strand */ + @Ignore("No network access") @Test public void testNegativeEndExon() { String expectedSeq = "LLEQNM"; @@ -169,6 +175,7 @@ * Test a middle exon of a gene on the negative strand (second exon for * gene FBXW7) */ + @Ignore("No network access") @Test public void testNegativeGeneMidExon1() { @@ -199,6 +206,7 @@ * Test a middle exon of a gene on the negative strand (third exon for * gene FBXW7) */ + @Ignore("No network access") @Test public void testNegativeGeneMidExon2() { String expectedSeq = "QLSYV"; --- a/src/test/java/org/broad/igv/feature/ExonTest.java +++ b/src/test/java/org/broad/igv/feature/ExonTest.java @@ -26,6 +26,7 @@ package org.broad.igv.feature; import org.broad.igv.AbstractHeadlessTest; +import org.junit.Ignore; import org.junit.Test; import static junit.framework.Assert.assertEquals; @@ -78,6 +79,7 @@ } + @Ignore("No network access") @Test public void testChangeCodonTable() throws Exception { --- a/src/test/java/org/broad/igv/feature/FeatureDBTest.java +++ b/src/test/java/org/broad/igv/feature/FeatureDBTest.java @@ -29,6 +29,7 @@ import org.broad.igv.AbstractHeadlessTest; import org.junit.Before; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import java.util.HashMap; @@ -181,6 +182,7 @@ } + @Ignore("No network access") @Test public void testMutationSearch() throws Exception { @@ -213,6 +215,7 @@ } } + @Ignore("No network access") @Test public void testMutationSearchNegStrand() throws Exception { String name = "KRAS"; @@ -225,6 +228,7 @@ } + @Ignore("No network access") @Test public void testMutationSearchFail() throws Exception { String name = "EGFR"; @@ -236,6 +240,7 @@ } } + @Ignore("No network access") @Test public void testMutationSearchNT() throws Exception { String name = "EGFR"; @@ -247,6 +252,7 @@ } } + @Ignore("No network access") @Test public void testMutationSearchNTNegStrand() throws Exception { String name = "KRAS"; --- a/src/test/java/org/broad/igv/feature/genome/SequenceWrapperTest.java +++ b/src/test/java/org/broad/igv/feature/genome/SequenceWrapperTest.java @@ -36,6 +36,7 @@ import org.broad.igv.util.HttpUtils; import org.junit.After; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import java.io.IOException; @@ -75,6 +76,7 @@ /** * Test cached vs uncached sequence reads. */ + @Ignore("No network access") @Test public void testCache() { try { @@ -100,6 +102,7 @@ } + @Ignore("No network access") @Test public void testNonCloudGenome() throws IOException { @@ -118,6 +121,7 @@ /** * Test known sequence (start of EGFR). */ + @Ignore("No network access") @Test public void readEGFRSequence() { String chr = "chr7"; @@ -133,6 +137,7 @@ * Test fetching sequence using the "Range service" for 3 URL patterns: cloudfront, s3 storage, and the * Broad server. */ + @Ignore("No network access") @Test public void testRangeService() { @@ -171,4 +176,4 @@ } -} \ No newline at end of file +} --- a/src/test/java/org/broad/igv/tools/CoverageCounterTest.java +++ b/src/test/java/org/broad/igv/tools/CoverageCounterTest.java @@ -228,6 +228,7 @@ } + @Ignore("No network access") @Test public void testIncludeDuplicatesFlag() throws IOException { String bamURL = "http://data.broadinstitute.org/igvdata/BodyMap/hg18/Merged/HBM.adipose.bam.sorted.bam"; --- a/src/test/java/org/broad/igv/feature/CodonTest.java +++ b/src/test/java/org/broad/igv/feature/CodonTest.java @@ -76,6 +76,7 @@ } //Check that there is no exception when loading an + @Ignore("No network access") @Test public void testGetCodonInvalid() {