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

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

tests
0

failures
0

ignored
1.542s

duration
100%

successful

Tests

Test Duration Result
testAppendPathToDir 0.579s passed
testCreateDirectory 0.476s passed
testCreateFifoFile 0.011s passed
testCreateFifoFileThrows 0.006s passed
testCreateTempFileInDirectory 0s passed
testCreateTempFileWithContent 0.001s passed
testDeleteDirOnExit 0s passed
testDeleteRecursively 0s passed
testExtractTarGzOverwrite 0.075s passed
testExtractTarGzThrowsExceptionOnExistingOutput 0.029s passed
testExtractTarGz[0](null) 0.048s passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case211652684761330175027) 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) 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) 0.001s 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) 0.001s 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) 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 0s 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/local8985726158216932713) 0s passed
testTempPath[1](tmp) 0.001s passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir8278197573349787595) 0s passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile7317456365993925167.file) 0s passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable17774795151997261532.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 0.267s 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) 0.001s 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) 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) 0.001s passed
testWriteThenReadStreamIntoByteArray[10](10000, 4096) 0.001s 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) 0.001s passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096) 0s passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096) 0s passed

Standard error

15:01:58.462 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
15:01:58.484 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
15:01:58.485 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:01:58.494 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
15:01:58.668 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:01:58.692 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
15:01:58.693 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:01:58.806 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
15:01:58.825 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:01:58.870 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage6513671309233587187/data/data1/current/BP-193253207-10.1.0.125-1772636518428/current, will proceed with Du for space computation calculation, 
15:01:58.870 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage6513671309233587187/data/data2/current/BP-193253207-10.1.0.125-1772636518428/current, will proceed with Du for space computation calculation, 
15:01:58.888 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
15:01:58.950 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
15:01:58.950 ERROR DataNode - Command processor encountered interrupt and exit.
15:01:58.950 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
15:01:58.950 WARN  DataNode - Ending block pool service for: Block pool BP-193253207-10.1.0.125-1772636518428 (Datanode Uuid 25c135e9-67dd-46ee-a7fb-93bc65caabd7) service to localhost/127.0.0.1:35325
15:01:58.950 WARN  IncrementalBlockReportManager - IncrementalBlockReportManager interrupted
15:01:58.951 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
15:01:58.951 WARN  CachingGetSpaceUsed - Thread Interrupted waiting to refresh disk information: sleep interrupted
15:01:59.029 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
15:01:59.047 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
15:01:59.047 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:01:59.052 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
15:01:59.190 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:01:59.208 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
15:01:59.209 WARN  HttpRequestLog - Jetty request log can only be enabled using Log4j
15:01:59.300 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
15:01:59.315 WARN  MetricsLoggerTask - Metrics logging will not be async since the logger is not log4j
15:01:59.356 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2885175401286514844/data/data1/current/BP-1651574216-10.1.0.125-1772636519002/current, will proceed with Du for space computation calculation, 
15:01:59.356 WARN  FsDatasetImpl - dfsUsed file missing in /tmp/minicluster_storage2885175401286514844/data/data2/current/BP-1651574216-10.1.0.125-1772636519002/current, will proceed with Du for space computation calculation, 
15:01:59.375 WARN  DirectoryScanner - dfs.datanode.directoryscan.throttle.limit.ms.per.sec set to value above 1000 ms/sec. Assuming default value of -1
15:01:59.454 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile524530790367659948/FIFOFILE
15:01:59.586 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/
15:01:59.587 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/
15:01:59.587 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/
15:01:59.587 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/
15:01:59.588 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/MANIFEST.txt
15:01:59.588 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/README.txt
15:01:59.589 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/hg19/
15:01:59.589 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/hg38/
15:01:59.589 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/hg38/
15:01:59.589 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/hg19/familial.config
15:01:59.590 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
15:01:59.591 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg19/
15:01:59.591 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg38/
15:01:59.592 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
15:01:59.592 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
15:01:59.610 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
15:01:59.611 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
15:01:59.620 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg19/
15:01:59.620 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg38/
15:01:59.620 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
15:01:59.621 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
15:01:59.621 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
15:01:59.622 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz12444148861523205659/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config