def run(self):
#try:
# Create the analysis runner which runs the commands and saves the output
self.runner = AnalysisRunner(self.ana)
self.dbfactory.updateAnalysisStatus(self.ana,"RUNNING")
# Run the commands
self.runner.run()
self.dbfactory.current_status = "RUN_FINISHED"
self.dbfactory.saveAnalysis(self.ana)
# Post process the output including copying tmp files to final output directory
self.dbfactory.updateAnalysisStatus(self.ana,"PROCESSING_OUTPUT")
self.ana.postProcessOutput()
self.dbfactory.current_status = "PROCESSED_OUTPUT"
self.dbfactory.saveAnalysis(self.ana)
# Set the final status and save the analysis to the db
self.ana.current_status = "ANALYSIS_FINISHED"
self.dbfactory.saveAnalysis(self.ana)
def testRun(self):
self.ana = AnalysisFactory.createAnalysisFromModuleName("FastQC")
self.ana.setInputFiles(self.input_files, self.input_types)
self.assertTrue(len(self.input_files) == 1)
self.assertTrue(len(self.input_types) == 1)
cmds = self.ana.getCommands()
print cmds
self.assertTrue(len(cmds) == 1)
runner = AnalysisRunner(self.ana)
res = runner.run()
self.assertTrue(res)
self.ana.postProcessOutput()
output_str = self.ana.output_str
self.assertTrue(len(output_str) == 4)
def testRun(self):
self.ana = AnalysisFactory.createAnalysisFromModuleName(
"ParallelMpileup")
self.ana.setInputFiles(self.input_files, self.input_types)
self.ana.refgenome = self.refgenome
self.assertTrue(len(self.input_files) == 1)
self.assertTrue(len(self.input_types) == 1)
self.ana.init()
cmds = self.ana.getCommands()
print cmds
self.assertTrue(len(cmds) == 2)
runner = AnalysisRunner(self.ana)
res = runner.run()
self.assertTrue(res)
self.ana.postProcessOutput()
output_strings = self.ana.output_strings
print output_strings
for strobj in output_strings:
print strobj.output_string
self.assertTrue(len(output_strings) == 2)
def testRun(self):
anarun = AnalysisRunner(self.ana)
res = anarun.run()
self.assertTrue(res)
def testGetOutput(self):
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir'])
self.runner = AnalysisRunner(self.anaobj)
self.runner.run()
out = AnalysisUtils.getOutputStrings(self.runner.analysis)
self.assertTrue(len(out) > 0)
def testRun(self):
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir'])
self.runner = AnalysisRunner(self.anaobj)
self.runner.run()
tmpstr = AnalysisUtils.getOutputStrings(self.anaobj)
print tmpstr
self.assertTrue(len(AnalysisUtils.getOutputStrings(self.anaobj)) > 0)
def testGetOutput(self):
anarun = AnalysisRunner(self.ana)
res = anarun.run()
anarun.analysis.postProcessOutput()
out = anarun.analysis.output_files
print out
print anarun.analysis.summary_data
self.assertTrue(len(out) == 2)
class ObjectCreateCheck(unittest.TestCase
): # Class with unitttest.TestCase as arg -
def setUp(self):
self.inputs = ['/tmp']
self.anaobj = DirectoryListAnalysis()
def testSetInputFiles(self):
self.assertTrue(
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir']))
def testGetInput(self):
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir'])
tmpinputs = self.anaobj.input_files
self.assertEqual(len(tmpinputs), len(
self.inputs)) # Assertion that the test framework collates
def testRun(self):
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir'])
self.runner = AnalysisRunner(self.anaobj)
self.runner.run()
tmpstr = AnalysisUtils.getOutputStrings(self.anaobj)
print tmpstr
self.assertTrue(len(AnalysisUtils.getOutputStrings(self.anaobj)) > 0)
def testGetOutput(self):
AnalysisUtils.setInputFiles(self.anaobj, self.inputs, ['dir'])
self.runner = AnalysisRunner(self.anaobj)
self.runner.run()
out = AnalysisUtils.getOutputStrings(self.runner.analysis)
self.assertTrue(len(out) > 0)
def testCreateNewAnalysisRunner(
self): # Function gets called automatically
"""New instance should create successfully"""
anarun = AnalysisRunner(self.ana)
tmpinputs = AnalysisUtils.getInputFiles(anarun.analysis)
self.assertTrue(anarun)
def testRunMummer(self):
mummer = Mummer()
self.assertTrue(mummer)
self.assertTrue(AnalysisUtils.setInputFiles(mummer,self.input_files,['fasta','fasta']))
runner = AnalysisRunner(mummer)
self.assertTrue(runner.run())
self.assertTrue(len(mummer.output_strings) == 1)
self.assertTrue(mummer.output_strings[0].output_string.index('4: FINISHING DATA') > 0)
self.assertTrue(FileUtils.fileExists('../testout/mummer.delta'))
class AnalysisRunnerWrapper(object):
def __init__(self,args):
self.args = args;
self.dbobj = AnalysisDBFactory(settings.DBNAME)
logging.info("\n\nGot new analysis to run %30s\n\n" % args.analysis);
logging.info("%30s %15s is %20s" % (args.analysis,"analysis", args.analysis));
logging.info("%30s %15s is %20s" % (args.analysis,"input", args.input));
logging.info("%30s %15s is %20s" % (args.analysis,"input_type", args.input_type));
logging.info("%30s %15s is %20s" % (args.analysis,"outdir", args.outdir));
logging.info("%30s %15s is %20s" % (args.analysis,"param", args.param));
logging.info("%30s %15s is %20s" % (args.analysis,"runtype", args.runtype));
logging.info("%30s %15s is %20s" % (args.analysis,"queue", args.queue));
logging.info("%30s %15s is %20s" % (args.analysis,"cores", args.cores));
logging.info("%30s %15s is %20s" % (args.analysis,"mempercore",args.mempercore));
def fetchLaunchableJobIDs(self,numjobs,analysis):
self.dbfactory = AnalysisDBFactory(settings.DBNAME)
return self.dbfactory.fetchLaunchableJobIDs(numjobs,analysis)
def createAnalysisRunnerClassFromID(self,jobid):
self.dbfactory = AnalysisDBFactory(settings.DBNAME)
self.ana = self.dbfactory.fetchAnalysisByID(jobid)
logging.info("ANA FROM DB %s"%self.ana)
self.ana.status = "LOADED_FROM_DB"
self.dbfactory.saveAnalysis(self.ana)
def createAnalysisRunnerClass(self):
print self.args
self.dbfactory = AnalysisDBFactory(settings.DBNAME)
self.ana = AnalysisFactory.createAnalysisFromModuleName(self.args.analysis)
self.ana.setInputFiles (self.args.input,self.args.input_type)
self.ana.init()
self.ana.setParameters (self.args.param)
self.dbfactory.saveAnalysis(self.ana)
def run(self):
#try:
# Create the analysis runner which runs the commands and saves the output
self.runner = AnalysisRunner(self.ana)
self.dbfactory.updateAnalysisStatus(self.ana,"RUNNING")
# Run the commands
self.runner.run()
self.dbfactory.current_status = "RUN_FINISHED"
self.dbfactory.saveAnalysis(self.ana)
# Post process the output including copying tmp files to final output directory
self.dbfactory.updateAnalysisStatus(self.ana,"PROCESSING_OUTPUT")
self.ana.postProcessOutput()
self.dbfactory.current_status = "PROCESSED_OUTPUT"
self.dbfactory.saveAnalysis(self.ana)
# Set the final status and save the analysis to the db
self.ana.current_status = "ANALYSIS_FINISHED"
self.dbfactory.saveAnalysis(self.ana)