Class org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest

all > org.broadinstitute.hellbender.utils.io > IOUtilsUnitTest
94

tests
0

failures
3

ignored
0.543s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir - ignored
testCreateDirectory - ignored
testCreateFifoFile 0.006s passed
testCreateFifoFileThrows 0.002s passed
testCreateTempFileInDirectory 0.001s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0.003s passed
testExtractTarGzOverwrite 0.079s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.031s passed
testExtractTarGz[0](null) 0.061s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case217928093430464929796) 0.041s passed
testGenomicsDBPathParsing[0](null, null, null, false) 0s passed
testGenomicsDBPathParsing[10](gendb., null, null, false) 0s passed
testGenomicsDBPathParsing[11](gendb.dfdfdf://fdfdf, dfdfdf://fdfdf, gendb.dfdfdf://fdfdf, true) 0s passed
testGenomicsDBPathParsing[12](gendb://fdfdf, fdfdf, gendb:///gatkCloneMountPoint/fdfdf, true) 0s passed
testGenomicsDBPathParsing[13](gendb:///fdfd, /fdfd, gendb:///fdfd, true) 0s passed
testGenomicsDBPathParsing[14](gendb:///, /, gendb:///, true) 0s passed
testGenomicsDBPathParsing[15](gendb.hdfs://this-node:9000/dir, hdfs://this-node:9000/dir, gendb.hdfs://this-node:9000/dir, true) 0s passed
testGenomicsDBPathParsing[16](gendb.gs://my-bucket/dir, gs://my-bucket/dir, gendb.gs://my-bucket/dir, true) 0s passed
testGenomicsDBPathParsing[17](gendb.s3://my-bucket/dir, s3://my-bucket/dir, gendb.s3://my-bucket/dir, true) 0.001s passed
testGenomicsDBPathParsing[18](gendb-hdfs://this-node:9000/dir, null, null, false) 0s passed
testGenomicsDBPathParsing[19](gendb-gs://this-node:9000/dir, null, null, false) 0s passed
testGenomicsDBPathParsing[1](, null, null, false) 0s passed
testGenomicsDBPathParsing[2](dfdfdf://fdfdf, null, null, false) 0s passed
testGenomicsDBPathParsing[3](fdfdf, null, null, false) 0s passed
testGenomicsDBPathParsing[4](gendbdfdfdf://fdfdf, null, null, false) 0s passed
testGenomicsDBPathParsing[5](gendb-dfdfdf://fdfdf, null, null, false) 0s passed
testGenomicsDBPathParsing[6](gendb, null, null, false) 0s passed
testGenomicsDBPathParsing[7](gendbdfdf, null, null, false) 0s passed
testGenomicsDBPathParsing[8](agendb://dfdfd, null, null, false) 0.001s passed
testGenomicsDBPathParsing[9](gendb.://fdfdf, null, null, false) 0s passed
testGetAbsolutePathWithoutFileProtocol[0](relative/example.txt, /gatkCloneMountPoint/relative/example.txt) 0s passed
testGetAbsolutePathWithoutFileProtocol[1](/local/example.txt, /local/example.txt) 0s passed
testGetAbsolutePathWithoutFileProtocol[2](/local/file://example.txt, /local/file:/example.txt) 0s passed
testGetAbsolutePathWithoutFileProtocol[3](file:///local/example.txt, /local/example.txt) 0s passed
testGetAbsolutePathWithoutFileProtocol[4](gs://dir/example.txt, gs://dir/example.txt) 0.012s passed
testGetPathHandlesIntervals 0.006s passed
testIsHDF5File[0](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isValidHDF5.hdf5, true) 0.001s passed
testIsHDF5File[1](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils/isValidHDF5.ext, true) 0s passed
testIsHDF5File[2](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.tsv, false) 0.001s passed
testIsHDF5File[3](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.hdf, false) 0s passed
testIsHDF5File[4](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.hdf5, false) 0s passed
testIsHDF5File[5](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isEmpty.txt, false) 0s passed
testIsSpecialFile 0s passed
testReadNonExistentFileIntoByteArray 0s passed
testReadStreamIntoByteArrayInvalidBufferSize 0.001s passed
testRemoveExtension[0]() 0s passed
testRemoveExtension[1](/path/to) 0s passed
testRemoveExtension[2](gs://bucket/subdir) 0.001s passed
testReplaceExtension[0](file.old, file.new) 0s passed
testReplaceExtension[1](file.something.old, file.something.new) 0s passed
testReplaceExtension[2](src/test.something/file, src/test.something/file.new) 0s passed
testReplaceExtension[3](/.src.folder/some/thing/.secret/file.old, /.src.folder/some/thing/.secret/file.new) 0s passed
testSuccessfulCanReadFileCheck 0s passed
testSuccessfulCanReadFilesCheck 0.001s passed
testTempDir 0s passed
testTempPath[0](/tmp/local7162631692186075530) 0.001s passed
testTempPath[1](tmp) 0.004s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir17312648272200501407) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile17029480522115959566.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](null) - ignored
testUrlEncodeDecode[0](string, string) 0s passed
testUrlEncodeDecode[1](string., string.) 0s passed
testUrlEncodeDecode[2](string1, string1) 0s passed
testUrlEncodeDecode[3](string with space, string+with+space) 0s passed
testUrlEncodeDecode[4](string://, string%3A%2F%2F) 0s passed
testWriteTarGz 0.279s passed
testWriteTempResourceFromPath[0](large/testResourceFile.txt, null, this is a test resource file) 0.001s passed
testWriteTempResourceFromPath[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file) 0s passed
testWriteTempResource[0](large/testResourceFile.txt, null, this is a test resource file) 0.002s passed
testWriteTempResource[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file) 0s passed
testWriteThenReadFileIntoByteArray[0](0, 4096) 0s passed
testWriteThenReadFileIntoByteArray[10](10000, 4096) 0.001s passed
testWriteThenReadFileIntoByteArray[1](1, 4096) 0s passed
testWriteThenReadFileIntoByteArray[2](2000, 4096) 0s passed
testWriteThenReadFileIntoByteArray[3](4095, 4096) 0s passed
testWriteThenReadFileIntoByteArray[4](4096, 4096) 0.001s passed
testWriteThenReadFileIntoByteArray[5](4097, 4096) 0s passed
testWriteThenReadFileIntoByteArray[6](6000, 4096) 0s passed
testWriteThenReadFileIntoByteArray[7](8191, 4096) 0.001s passed
testWriteThenReadFileIntoByteArray[8](8192, 4096) 0s passed
testWriteThenReadFileIntoByteArray[9](8193, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[0](0, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[10](10000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[1](1, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[2](2000, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[3](4095, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[4](4096, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[5](4097, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[6](6000, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[7](8191, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096) 0.001s passed

Standard error

20:35:03.884 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile16737833296126581164/FIFOFILE
20:35:04.036 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/
20:35:04.036 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/
20:35:04.036 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/
20:35:04.037 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/
20:35:04.037 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/MANIFEST.txt
20:35:04.037 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/README.txt
20:35:04.038 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/hg19/
20:35:04.038 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/hg38/
20:35:04.038 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/hg38/
20:35:04.039 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/hg19/familial.config
20:35:04.039 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
20:35:04.040 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg19/
20:35:04.040 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg38/
20:35:04.041 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
20:35:04.041 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
20:35:04.060 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
20:35:04.060 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
20:35:04.073 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg19/
20:35:04.074 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg38/
20:35:04.074 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
20:35:04.075 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
20:35:04.076 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
20:35:04.076 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7005848834199374498/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config