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

94

tests

0

failures

0

ignored

2.203s

duration

100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.715s passed
testCreateDirectory 1.039s passed
testCreateFifoFile 0.009s passed
testCreateFifoFileThrows 0.004s passed
testCreateTempFileInDirectory 0s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.062s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.029s passed
testExtractTarGz[0](null) 0.048s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case22419341815395078160) 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) 0.001s 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) 0s 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]() 0.001s 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/local5981512668638001708) 0.001s passed
testTempPath[1](tmp) 0.003s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir363523694053887869) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile3477061560522904835.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable15028719572545634603.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 0.249s 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) 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) 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) 0.001s passed
testWriteThenReadFileIntoByteArray[4](4096, 4096) 0s 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) 0s passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096) 0s passed

Standard error

20:43:24.304 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
20:43:24.322 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
20:43:24.323 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:43:24.328 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
20:43:24.493 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:43:24.511 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
20:43:24.512 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:43:24.609 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
20:43:24.626 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:43:24.663 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2727989970351554970/data/data2/current/BP-1633327804-10.1.0.111-1752612204260/current, will proceed with Du for space computation calculation, 
20:43:24.663 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2727989970351554970/data/data1/current/BP-1633327804-10.1.0.111-1752612204260/current, will proceed with Du for space computation calculation, 
20:43:24.682 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
20:43:24.820 ERROR DataNode - Command processor encountered interrupt and exit.
20:43:24.820 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:43:24.820 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
20:43:24.820 WARN  DataNode - Ending block pool service for: Block pool BP-1633327804-10.1.0.111-1752612204260 (Datanode Uuid f38398f6-575b-4e81-a319-b496f58fc298) service to localhost/127.0.0.1:46223
20:43:24.821 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
20:43:24.821 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
20:43:24.822 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
20:43:25.572 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
20:43:25.586 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
20:43:25.586 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:43:25.591 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
20:43:25.724 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:43:25.737 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
20:43:25.738 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
20:43:25.830 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
20:43:25.843 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
20:43:25.881 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage9783424019782645664/data/data2/current/BP-87486855-10.1.0.111-1752612204957/current, will proceed with Du for space computation calculation, 
20:43:25.881 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage9783424019782645664/data/data1/current/BP-87486855-10.1.0.111-1752612204957/current, will proceed with Du for space computation calculation, 
20:43:25.895 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
20:43:25.979 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile15201385520265159146/FIFOFILE
20:43:26.102 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/
20:43:26.102 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/
20:43:26.102 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/
20:43:26.103 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/
20:43:26.103 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/MANIFEST.txt
20:43:26.103 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/README.txt
20:43:26.104 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/hg19/
20:43:26.104 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/hg38/
20:43:26.104 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/hg38/
20:43:26.104 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/hg19/familial.config
20:43:26.105 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
20:43:26.105 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg19/
20:43:26.105 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg38/
20:43:26.106 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
20:43:26.106 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
20:43:26.120 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
20:43:26.120 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
20:43:26.130 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg19/
20:43:26.130 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg38/
20:43:26.130 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
20:43:26.130 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
20:43:26.131 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
20:43:26.132 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz4167116491831090328/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config