def test_no_tag(self): with drmaa.Session() as session: outputDirectoryLocation = getPath("tests/output/manager") logDirectoryLocation = getPath("tests/output/manager/log") specification = "-l h_vmem=2G -pe smp 1" jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None) jobManager.setAggregateSpecification(specification) inclusionLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"] exclusionLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"] outputLocation = getPath("tests/output/manager/temp.out") tag = None job = jobManager.createAggregateJob(inclusionLocations, exclusionLocations, outputLocation, tag) args = [ AggregateKMers.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", AggregateKMers.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", AggregateKMers.OUTPUT_LONG, outputLocation, AggregateKMers.DELETE_LONG] self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-AggregateKMers1.o")) self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-AggregateKMers1.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.aggregateSpecification, None) jobManager.setAggregateSpecification(specification) self.assertEquals(jobManager.aggregateSpecification, specification)
def test_no_tag(self): with drmaa.Session() as session: outputDirectoryLocation = getPath("tests/output/manager") logDirectoryLocation = getPath("tests/output/manager/log") specification = "-l h_vmem=2G -pe smp 1" jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None) jobManager.setAggregateSpecification(specification) inclusionLocations = [ "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta" ] exclusionLocations = [ "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta" ] outputLocation = getPath("tests/output/manager/temp.out") tag = None job = jobManager.createAggregateJob(inclusionLocations, exclusionLocations, outputLocation, tag) args = [ AggregateKMers.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", AggregateKMers.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", AggregateKMers.OUTPUT_LONG, outputLocation, AggregateKMers.DELETE_LONG ] self.assertEquals( job.outputPath, ":" + os.path.join( logDirectoryLocation, "Neptune-AggregateKMers1.o")) self.assertEquals( job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-AggregateKMers1.e")) self.assertEquals(job.args[1:], args) self.assertEquals(job.nativeSpecification, specification)