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

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

tests
0

failures
0

ignored
1.439s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.507s passed
testCreateDirectory 0.478s passed
testCreateFifoFile 0.008s passed
testCreateFifoFileThrows 0.003s passed
testCreateTempFileInDirectory 0.001s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.058s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.026s passed
testExtractTarGz[0](null) 0.043s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case23435193296778240461) 0.035s 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) 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) 0.001s 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) 0.001s passed
testGetPathHandlesIntervals 0.004s 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 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/local10774504817674027800) 0.001s passed
testTempPath[1](tmp) 0.004s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir3735801166529531480) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile7032942824682731795.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable5019652939580904434.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) 0s passed
testWriteTarGz 0.260s 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) 0.001s 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) 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) 0s passed
testWriteThenReadStreamIntoByteArray[3](4095, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[4](4096, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[5](4097, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[6](6000, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[7](8191, 4096) 0.001s passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096) 0s passed

Standard error

19:58:15.718 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
19:58:15.738 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
19:58:15.738 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
19:58:15.744 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
19:58:15.891 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
19:58:15.905 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
19:58:15.906 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
19:58:15.998 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
19:58:16.017 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
19:58:16.053 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage4180805953901554952/data/data1/current/BP-296536791-10.1.0.127-1752609495686/current, will proceed with Du for space computation calculation, 
19:58:16.054 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage4180805953901554952/data/data2/current/BP-296536791-10.1.0.127-1752609495686/current, will proceed with Du for space computation calculation, 
19:58:16.072 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
19:58:16.141 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
19:58:16.141 ERROR DataNode - Command processor encountered interrupt and exit.
19:58:16.141 WARN  DataNode - Ending block pool service for: Block pool BP-296536791-10.1.0.127-1752609495686 (Datanode Uuid 2dc2e1b5-ec09-45c7-8ed2-9b1d8bda52a6) service to localhost/127.0.0.1:35185
19:58:16.141 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
19:58:16.142 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
19:58:16.142 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
19:58:16.142 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
19:58:16.216 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
19:58:16.231 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
19:58:16.232 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
19:58:16.240 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
19:58:16.375 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
19:58:16.392 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
19:58:16.393 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
19:58:16.492 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
19:58:16.510 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
19:58:16.550 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage3730641119899468576/data/data1/current/BP-1033221001-10.1.0.127-1752609496184/current, will proceed with Du for space computation calculation, 
19:58:16.550 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage3730641119899468576/data/data2/current/BP-1033221001-10.1.0.127-1752609496184/current, will proceed with Du for space computation calculation, 
19:58:16.564 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
19:58:16.643 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile12213045034338015314/FIFOFILE
19:58:16.760 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/
19:58:16.760 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/
19:58:16.760 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/
19:58:16.761 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/
19:58:16.761 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/MANIFEST.txt
19:58:16.761 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/README.txt
19:58:16.762 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/hg19/
19:58:16.762 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/hg38/
19:58:16.762 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/hg38/
19:58:16.762 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/hg19/familial.config
19:58:16.763 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
19:58:16.763 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg19/
19:58:16.763 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg38/
19:58:16.764 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
19:58:16.764 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
19:58:16.777 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
19:58:16.778 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
19:58:16.787 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg19/
19:58:16.787 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg38/
19:58:16.787 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
19:58:16.788 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
19:58:16.788 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
19:58:16.789 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2270153943485570955/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config