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

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

tests

failures

ignored

0.523s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAppendPathToDir	-	ignored
testCreateDirectory	-	ignored
testCreateFifoFile	0.007s	passed
testCreateFifoFileThrows	0.002s	passed
testCreateTempFileInDirectory	0.001s	passed
testCreateTempFileWithContent	0.002s	passed
testDeleteDirOnExit	0s	passed
testDeleteRecursively	0.002s	passed
testExtractTarGzOverwrite	0.073s	passed
testExtractTarGzThrowsExceptionOnExistingOutput	0.030s	passed
testExtractTarGz[0](null)	0.059s	passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case27068990462924436144)	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)	0.001s	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)	0s	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)	0.001s	passed
testGenomicsDBPathParsing[7](gendbdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[8](agendb://dfdfd, null, null, false)	0s	passed
testGenomicsDBPathParsing[9](gendb.://fdfdf, null, null, false)	0s	passed
testGetAbsolutePathWithoutFileProtocol[0](relative/example.txt, /gatkCloneMountPoint/relative/example.txt)	0.001s	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)	0.013s	passed
testGetPathHandlesIntervals	0.005s	passed
testIsHDF5File[0](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isValidHDF5.hdf5, true)	0s	passed
testIsHDF5File[1](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils/isValidHDF5.ext, true)	0.001s	passed
testIsHDF5File[2](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.tsv, false)	0s	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)	0.001s	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)	0s	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/local13041481609146089760)	0s	passed
testTempPath[1](tmp)	0.003s	passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir16941643357749321991)	0s	passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile17199773606581822814.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	0.269s	passed
testWriteTempResourceFromPath[0](large/testResourceFile.txt, null, this is a test resource file)	0s	passed
testWriteTempResourceFromPath[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file)	0.001s	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)	0s	passed
testWriteThenReadFileIntoByteArray[1](1, 4096)	0.001s	passed
testWriteThenReadFileIntoByteArray[2](2000, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[3](4095, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[4](4096, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[5](4097, 4096)	0.001s	passed
testWriteThenReadFileIntoByteArray[6](6000, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[7](8191, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[8](8192, 4096)	0.001s	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

21:27:38.981 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile14188703827664200488/FIFOFILE
21:27:39.130 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/
21:27:39.131 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/
21:27:39.131 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/
21:27:39.131 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/
21:27:39.132 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/MANIFEST.txt
21:27:39.132 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/README.txt
21:27:39.133 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/hg19/
21:27:39.133 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/hg38/
21:27:39.133 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/hg38/
21:27:39.134 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/hg19/familial.config
21:27:39.134 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
21:27:39.135 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg19/
21:27:39.135 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg38/
21:27:39.135 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
21:27:39.136 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
21:27:39.153 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
21:27:39.153 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
21:27:39.163 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg19/
21:27:39.163 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg38/
21:27:39.163 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
21:27:39.164 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
21:27:39.164 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
21:27:39.165 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz11576588051955522790/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config