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):
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)
