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_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)
