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