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)