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

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

tests
0

failures
0

ignored
1.445s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.543s passed
testCreateDirectory 0.442s passed
testCreateFifoFile 0.008s passed
testCreateFifoFileThrows 0.003s passed
testCreateTempFileInDirectory 0s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.061s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.026s passed
testExtractTarGz[0](null) 0.045s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case24079175946654640186) 0.032s 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) 0.001s passed
testGetAbsolutePathWithoutFileProtocol[4](gs://dir/example.txt, gs://dir/example.txt) 0s passed
testGetPathHandlesIntervals 0.003s 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) 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 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 0.001s passed
testTempDir 0s passed
testTempPath[0](/tmp/local4961355493208860157) 0s passed
testTempPath[1](tmp) 0.003s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir4655056168144976655) 0.001s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile2303694002116386375.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable11804407399044617949.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 0.261s 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) 0.001s 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) 0s passed
testWriteThenReadFileIntoByteArray[6](6000, 4096) 0.001s 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) 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) 0s passed

Standard error

20:24:16.751 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
20:24:16.770 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
20:24:16.771 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:24:16.779 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
20:24:16.938 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:24:16.956 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
20:24:16.957 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:24:17.052 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
20:24:17.068 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:24:17.105 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage3969025958008449241/data/data1/current/BP-447011341-10.1.0.79-1739219056706/current, will proceed with Du for space computation calculation, 
20:24:17.105 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage3969025958008449241/data/data2/current/BP-447011341-10.1.0.79-1739219056706/current, will proceed with Du for space computation calculation, 
20:24:17.120 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
20:24:17.191 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:24:17.192 WARN  DataNode - Ending block pool service for: Block pool BP-447011341-10.1.0.79-1739219056706 (Datanode Uuid d2833925-160d-4e51-b272-f7e55e5da52d) service to localhost/127.0.0.1:44939
20:24:17.192 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:24:17.192 ERROR DataNode - Command processor encountered interrupt and exit.
20:24:17.192 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
20:24:17.193 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
20:24:17.194 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
20:24:17.259 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
20:24:17.272 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
20:24:17.275 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:24:17.279 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
20:24:17.409 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:24:17.422 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
20:24:17.423 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:24:17.512 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
20:24:17.526 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:24:17.565 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage16154086385634300955/data/data1/current/BP-905660417-10.1.0.79-1739219057235/current, will proceed with Du for space computation calculation, 
20:24:17.565 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage16154086385634300955/data/data2/current/BP-905660417-10.1.0.79-1739219057235/current, will proceed with Du for space computation calculation, 
20:24:17.579 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
20:24:17.661 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile2795282028636369478/FIFOFILE
20:24:17.779 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/
20:24:17.779 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/
20:24:17.779 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/
20:24:17.780 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/
20:24:17.780 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/MANIFEST.txt
20:24:17.780 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/README.txt
20:24:17.781 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/hg19/
20:24:17.781 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/hg38/
20:24:17.781 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/hg38/
20:24:17.782 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/hg19/familial.config
20:24:17.782 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
20:24:17.783 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg19/
20:24:17.783 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg38/
20:24:17.783 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
20:24:17.783 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
20:24:17.797 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
20:24:17.798 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
20:24:17.807 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg19/
20:24:17.807 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg38/
20:24:17.807 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
20:24:17.808 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
20:24:17.808 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
20:24:17.809 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz2772694714481407891/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config