def test_simple(self): with drmaa.Session() as session: outputDirectoryLocation = getPath("tests/output") logDirectoryLocation = getPath("tests/output/log") specification = "-l h_vmem=2G -pe smp 1" jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None) jobManager.setCountSpecification(specification) inputLocation = "tests/data/manager/simple.fasta" outputLocation = getPath("tests/output/manager/temp.out") k = 7 organization = 0 job = jobManager.createCountJob(inputLocation, outputLocation, k, organization) args = [ CountKMers.INPUT_LONG, str(inputLocation), CountKMers.OUTPUT_LONG, str(outputLocation), CountKMers.KMER_LONG, str(k), CountKMers.ORGANIZATION_LONG, str(organization)] self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.o")) self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.e")) self.assertEquals(job.args[1:], args) self.assertEquals(job.nativeSpecification, specification)
def test_simple(self): specification = "-l h_vmem=16G -pe smp 8" with drmaa.Session() as session: jobManager = JobManagerDRMAA(getPath("tests/output/manager"), getPath("tests/output/manager/log"), session, None) self.assertEquals(jobManager.countSpecification, None) jobManager.setCountSpecification(specification) self.assertEquals(jobManager.countSpecification, specification)
def test_simple(self): with drmaa.Session() as session: outputDirectoryLocation = getPath("tests/output") logDirectoryLocation = getPath("tests/output/log") specification = "-l h_vmem=2G -pe smp 1" jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None) jobManager.setCountSpecification(specification) inputLocation = "tests/data/manager/simple.fasta" outputLocation = getPath("tests/output/manager/temp.out") k = 7 organization = 0 job = jobManager.createCountJob(inputLocation, outputLocation, k, organization) args = [ CountKMers.INPUT_LONG, str(inputLocation), CountKMers.OUTPUT_LONG, str(outputLocation), CountKMers.KMER_LONG, str(k), CountKMers.ORGANIZATION_LONG, str(organization) ] self.assertEquals( job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.o")) self.assertEquals( job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.e")) self.assertEquals(job.args[1:], args) self.assertEquals(job.nativeSpecification, specification)