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

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

tests
0

failures
0

ignored
1.431s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.538s passed
testCreateDirectory 0.437s passed
testCreateFifoFile 0.009s passed
testCreateFifoFileThrows 0.003s passed
testCreateTempFileInDirectory 0s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.062s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.028s passed
testExtractTarGz[0](null) 0.048s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case262977317165160434) 0.031s 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:///home/runner/work/gatk/gatk/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) 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) 0s 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, /home/runner/work/gatk/gatk/relative/example.txt) 0s passed
testGetAbsolutePathWithoutFileProtocol[1](/local/example.txt, /local/example.txt) 0.001s 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) 0s passed
testGetPathHandlesIntervals 0.004s 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) 0s passed
testIsHDF5File[3](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.hdf, false) 0.001s 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 0.001s passed
testReadStreamIntoByteArrayInvalidBufferSize 0s 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 0s passed
testTempDir 0s passed
testTempPath[0](/tmp/local2612408545478905305) 0s passed
testTempPath[1](tmp) 0.003s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir5725577390877163207) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile14436331003451316465.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable6437158279684725619.file) 0s passed
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) 0.001s passed
testUrlEncodeDecode[4](string://, string%3A%2F%2F) 0s passed
testWriteTarGz 0.253s 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) 0.001s 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) 0.001s passed
testWriteThenReadStreamIntoByteArray[10](10000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[1](1, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[2](2000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[3](4095, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[4](4096, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[5](4097, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[6](6000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[7](8191, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096) 0s passed

Standard error

18:56:30.345 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
18:56:30.368 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:30.369 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:56:30.377 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:30.536 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:56:30.552 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:30.552 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:56:30.656 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
18:56:30.673 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:56:30.711 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage15966981498438279956/data/data1/current/BP-390105455-10.1.0.176-1747680990301/current, will proceed with Du for space computation calculation, 
18:56:30.711 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage15966981498438279956/data/data2/current/BP-390105455-10.1.0.176-1747680990301/current, will proceed with Du for space computation calculation, 
18:56:30.726 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
18:56:30.794 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
18:56:30.794 ERROR DataNode - Command processor encountered interrupt and exit.
18:56:30.794 WARN  DataNode - Ending block pool service for: Block pool BP-390105455-10.1.0.176-1747680990301 (Datanode Uuid b43dc6e7-16bb-4e1d-9d29-40ffb12292c0) service to localhost/127.0.0.1:38821
18:56:30.794 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
18:56:30.794 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
18:56:30.795 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
18:56:30.795 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
18:56:30.858 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
18:56:30.872 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:30.872 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:56:30.876 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:31.001 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:56:31.017 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
18:56:31.018 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
18:56:31.108 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
18:56:31.122 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
18:56:31.167 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage498468488186426575/data/data2/current/BP-1286506018-10.1.0.176-1747680990835/current, will proceed with Du for space computation calculation, 
18:56:31.167 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage498468488186426575/data/data1/current/BP-1286506018-10.1.0.176-1747680990835/current, will proceed with Du for space computation calculation, 
18:56:31.181 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
18:56:31.256 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile10876018461804175703/FIFOFILE
18:56:31.376 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/
18:56:31.377 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/
18:56:31.377 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/
18:56:31.377 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/
18:56:31.378 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/MANIFEST.txt
18:56:31.378 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/README.txt
18:56:31.379 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/hg19/
18:56:31.379 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/hg38/
18:56:31.379 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/hg38/
18:56:31.380 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/hg19/familial.config
18:56:31.380 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
18:56:31.381 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg19/
18:56:31.381 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg38/
18:56:31.381 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
18:56:31.381 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
18:56:31.395 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
18:56:31.396 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
18:56:31.404 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg19/
18:56:31.405 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg38/
18:56:31.405 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
18:56:31.405 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
18:56:31.406 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
18:56:31.406 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12991731062131283841/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config