def test_simple(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.setDatabaseSpecification(specification)
inputLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
aggregatedLocation = getPath("tests/output/manager/aggregated.out")
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createDatabaseJob(inputLocations, aggregatedLocation, outputLocation)
args = [
"-dbtype", "nucl",
"-in", aggregatedLocation,
"-title", "DATABASE",
"-out", outputLocation]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CreateDatabase1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CreateDatabase1.e"))
self.assertEquals(job.args, 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.databaseSpecification, None)
jobManager.setDatabaseSpecification(specification)
self.assertEquals(jobManager.databaseSpecification, 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.databaseSpecification, None)
jobManager.setDatabaseSpecification(specification)
self.assertEquals(jobManager.databaseSpecification, specification)
def test_simple(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.setDatabaseSpecification(specification)
inputLocations = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
aggregatedLocation = getPath("tests/output/manager/aggregated.out")
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createDatabaseJob(inputLocations,
aggregatedLocation,
outputLocation)
args = [
"-dbtype", "nucl", "-in", aggregatedLocation, "-title",
"DATABASE", "-out", outputLocation
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-CreateDatabase1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(logDirectoryLocation,
"Neptune-CreateDatabase1.e"))
self.assertEquals(job.args, args)
self.assertEquals(job.nativeSpecification, specification)
