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.filterSpecification, None)
jobManager.setFilterSpecification(specification)
self.assertEquals(jobManager.filterSpecification, 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.filterSpecification, None)
jobManager.setFilterSpecification(specification)
self.assertEquals(jobManager.filterSpecification, 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.setFilterSpecification(specification)
inclusionDatabaseLocation = "tests/data/manager/FAKE_IN_DB.FAKE"
exclusionDatabaseLocation = "tests/data/manager/FAKE_EX_DB.FAKE"
inclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
exclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
inputLocation = "tests/data/manager/simple.fasta"
filteredOutputLocation = getPath("tests/output/manager/simple.filtered")
sortedOutputLocation = getPath("tests/output/manager/simple.sorted")
filterLength = 0.5
filterPercent = 0.5
seedSize = 11
job = jobManager.createFilterJob(inclusionDatabaseLocation, exclusionDatabaseLocation,
inclusion, exclusion, inputLocation, filteredOutputLocation, sortedOutputLocation,
filterLength, filterPercent, seedSize)
args = [
FilterSignatures.INCLUSION_DATABASE_LONG, str(inclusionDatabaseLocation),
FilterSignatures.EXCLUSION_DATABASE_LONG, str(exclusionDatabaseLocation),
FilterSignatures.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
FilterSignatures.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
FilterSignatures.INPUT_LONG, str(inputLocation),
FilterSignatures.FILTERED_OUTPUT_LONG, str(filteredOutputLocation),
FilterSignatures.SORTED_OUTPUT_LONG, str(sortedOutputLocation),
FilterSignatures.FILTER_LENGTH_LONG, str(filterLength),
FilterSignatures.FILTER_PERCENT_LONG, str(filterPercent),
FilterSignatures.SEED_SIZE_LONG, str(seedSize)]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-FilterSignatures1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-FilterSignatures1.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/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
specification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation,
logDirectoryLocation, session, None)
jobManager.setFilterSpecification(specification)
inclusionDatabaseLocation = "tests/data/manager/FAKE_IN_DB.FAKE"
exclusionDatabaseLocation = "tests/data/manager/FAKE_EX_DB.FAKE"
inclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
exclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
inputLocation = "tests/data/manager/simple.fasta"
filteredOutputLocation = getPath(
"tests/output/manager/simple.filtered")
sortedOutputLocation = getPath(
"tests/output/manager/simple.sorted")
filterLength = 0.5
filterPercent = 0.5
seedSize = 11
job = jobManager.createFilterJob(
inclusionDatabaseLocation, exclusionDatabaseLocation,
inclusion, exclusion, inputLocation, filteredOutputLocation,
sortedOutputLocation, filterLength, filterPercent, seedSize)
args = [
FilterSignatures.INCLUSION_DATABASE_LONG,
str(inclusionDatabaseLocation),
FilterSignatures.EXCLUSION_DATABASE_LONG,
str(exclusionDatabaseLocation),
FilterSignatures.INCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
FilterSignatures.EXCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
FilterSignatures.INPUT_LONG,
str(inputLocation), FilterSignatures.FILTERED_OUTPUT_LONG,
str(filteredOutputLocation),
FilterSignatures.SORTED_OUTPUT_LONG,
str(sortedOutputLocation), FilterSignatures.FILTER_LENGTH_LONG,
str(filterLength), FilterSignatures.FILTER_PERCENT_LONG,
str(filterPercent), FilterSignatures.SEED_SIZE_LONG,
str(seedSize)
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-FilterSignatures1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-FilterSignatures1.e"))
self.assertEquals(job.args[1:], args)
self.assertEquals(job.nativeSpecification, specification)
