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.extractSpecification, None) jobManager.setExtractSpecification(specification) self.assertEquals(jobManager.extractSpecification, 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.setExtractSpecification(specification) referenceLocation = "tests/data/manager/simple.fasta" referenceSize = 12 rate = 0.01 inclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"] inhits = 2 exclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"] exhits = 2 gap = 3 size = 5 GC = 0.5 confidence = 0.95 aggregateLocation = "tests/data/manager/simple.kmers" outputLocation = getPath("tests/output/manager/temp.out") job = jobManager.createExtractJob(referenceLocation, referenceSize, rate, inclusion, inhits, exclusion, exhits, gap, size, GC, confidence, aggregateLocation, outputLocation) args = [ ExtractSignatures.REFERENCE_LONG, str(referenceLocation), ExtractSignatures.REFERENCE_SIZE_LONG, str(referenceSize), ExtractSignatures.RATE_LONG, str(rate), ExtractSignatures.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", ExtractSignatures.INHITS_LONG, str(inhits), ExtractSignatures.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", ExtractSignatures.EXHITS_LONG, str(exhits), ExtractSignatures.GAP_LONG, str(gap), ExtractSignatures.SIZE_LONG, str(size), ExtractSignatures.GC_LONG, str(GC), ExtractSignatures.CONFIDENCE_LONG, str(confidence), ExtractSignatures.KMERS_LONG, aggregateLocation, ExtractSignatures.OUTPUT_LONG, outputLocation] self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-ExtractSignatures1.o")) self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-ExtractSignatures1.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.setExtractSpecification(specification) referenceLocation = "tests/data/manager/simple.fasta" referenceSize = 12 rate = 0.01 inclusion = [ "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta" ] inhits = 2 exclusion = [ "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta" ] exhits = 2 gap = 3 size = 5 GC = 0.5 confidence = 0.95 aggregateLocation = "tests/data/manager/simple.kmers" outputLocation = getPath("tests/output/manager/temp.out") job = jobManager.createExtractJob(referenceLocation, referenceSize, rate, inclusion, inhits, exclusion, exhits, gap, size, GC, confidence, aggregateLocation, outputLocation) args = [ ExtractSignatures.REFERENCE_LONG, str(referenceLocation), ExtractSignatures.REFERENCE_SIZE_LONG, str(referenceSize), ExtractSignatures.RATE_LONG, str(rate), ExtractSignatures.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", ExtractSignatures.INHITS_LONG, str(inhits), ExtractSignatures.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta", ExtractSignatures.EXHITS_LONG, str(exhits), ExtractSignatures.GAP_LONG, str(gap), ExtractSignatures.SIZE_LONG, str(size), ExtractSignatures.GC_LONG, str(GC), ExtractSignatures.CONFIDENCE_LONG, str(confidence), ExtractSignatures.KMERS_LONG, aggregateLocation, ExtractSignatures.OUTPUT_LONG, outputLocation ] self.assertEquals( job.outputPath, ":" + os.path.join( logDirectoryLocation, "Neptune-ExtractSignatures1.o")) self.assertEquals( job.errorPath, ":" + os.path.join( logDirectoryLocation, "Neptune-ExtractSignatures1.e")) self.assertEquals(job.args[1:], args) self.assertEquals(job.nativeSpecification, specification)