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 testCreateNewAnalysisRunner(
self): # Function gets called automatically
"""New instance should create successfully"""
anarun = AnalysisRunner(self.ana)
tmpinputs = AnalysisUtils.getInputFiles(anarun.analysis)
self.assertTrue(anarun)
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)
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'))