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

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

tests
0

failures
0

ignored
1.597s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.793s passed
testCreateDirectory 0.426s passed
testCreateFifoFile 0.009s passed
testCreateFifoFileThrows 0.003s passed
testCreateTempFileInDirectory 0s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0.001s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.050s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.022s passed
testExtractTarGz[0](null) 0.041s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case218367659200059243697) 0.025s passed
testGenomicsDBPathParsing[0](null, null, null, false) 0.001s 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) 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) 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) 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 0s 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 0s passed
testTempDir 0s passed
testTempPath[0](/tmp/local16989977624078953237) 0s passed
testTempPath[1](tmp) 0.003s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir13603563763833872072) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile7815692338562916734.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable4348240442738555186.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) 0s passed
testUrlEncodeDecode[4](string://, string%3A%2F%2F) 0.001s passed
testWriteTarGz 0.201s 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) 0.002s passed
testWriteTempResource[0](large/testResourceFile.txt, null, this is a test resource file) 0.003s passed
testWriteTempResource[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file) 0.002s 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) 0s passed
testWriteThenReadFileIntoByteArray[9](8193, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[0](0, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[10](10000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[1](1, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[2](2000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[3](4095, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[4](4096, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[5](4097, 4096) 0.001s 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

17:47:25.138 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
17:47:25.150 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
17:47:25.151 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:47:25.154 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
17:47:25.282 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:47:25.293 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
17:47:25.293 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:47:25.369 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
17:47:25.387 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:47:25.734 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage6036370978444200958/data/data1/current/BP-1169206761-10.1.0.252-1761587245059/current, will proceed with Du for space computation calculation, 
17:47:25.734 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage6036370978444200958/data/data2/current/BP-1169206761-10.1.0.252-1761587245059/current, will proceed with Du for space computation calculation, 
17:47:25.745 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
17:47:25.816 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
17:47:25.816 ERROR DataNode - Command processor encountered interrupt and exit.
17:47:25.816 WARN  DataNode - Ending block pool service for: Block pool BP-1169206761-10.1.0.252-1761587245059 (Datanode Uuid c58c6f87-d59f-4bb4-b02a-cab1d08ef857) service to localhost/127.0.0.1:37803
17:47:25.816 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
17:47:25.816 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
17:47:25.817 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
17:47:25.817 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
17:47:25.897 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
17:47:25.909 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
17:47:25.909 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:47:25.914 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
17:47:26.034 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:47:26.045 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
17:47:26.046 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
17:47:26.119 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
17:47:26.132 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
17:47:26.210 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage12415932281804442861/data/data1/current/BP-1146855367-10.1.0.252-1761587245857/current, will proceed with Du for space computation calculation, 
17:47:26.210 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage12415932281804442861/data/data2/current/BP-1146855367-10.1.0.252-1761587245857/current, will proceed with Du for space computation calculation, 
17:47:26.221 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
17:47:26.265 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile1863517357061104591/FIFOFILE
17:47:26.365 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/
17:47:26.365 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/
17:47:26.365 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/
17:47:26.365 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/
17:47:26.366 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/MANIFEST.txt
17:47:26.366 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/README.txt
17:47:26.366 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/hg19/
17:47:26.367 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/hg38/
17:47:26.367 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/hg38/
17:47:26.367 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/hg19/familial.config
17:47:26.367 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
17:47:26.368 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg19/
17:47:26.368 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg38/
17:47:26.368 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
17:47:26.369 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
17:47:26.379 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
17:47:26.380 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
17:47:26.387 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg19/
17:47:26.387 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg38/
17:47:26.387 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
17:47:26.388 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
17:47:26.388 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
17:47:26.389 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz6452799019730520970/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config