def test_command(self):
"""
Test the get_pipeline_script_command
"""
os.chdir(PATH)
buildout = BUILDOUT.copy()
accession = buildout['TestRun']
pipeline = BUILDOUT['pipeline'].copy()
options = OPTIONS.copy()
options['experiment_id'] = os.path.split(options['location'])[-1]
command = get_pipeline_script_command(accession, pipeline, options)
self.failUnless(command.split(' ') == SCRIPT, command.split(' '))
def test_cluster_given(self):
"""
Test the get_pipeline_script_command method with cluster
"""
os.chdir(PATH)
buildout = BUILDOUT.copy()
accession = buildout['TestRun']
pipeline = BUILDOUT['pipeline'].copy()
pipeline['CLUSTER'] = 'dummy'
options = OPTIONS.copy()
options['experiment_id'] = os.path.split(options['location'])[-1]
command = get_pipeline_script_command(accession, pipeline, options)
self.failUnless(" -cluster dummy " in command)
def test_more_options(self):
"""
Test the get_pipeline_script_command method with replicate and other
options.
"""
os.chdir(PATH)
buildout = BUILDOUT.copy()
accession = buildout['TestRun']
accession['replicate'] = '1'
pipeline = BUILDOUT['pipeline'].copy()
pipeline['HOST'] = 'dummyhost'
pipeline['PREPROCESS'] = 'dummypreprocess'
pipeline['PREPROCESS_TRIM_LENGTH'] = '1'
options = OPTIONS.copy()
options['experiment_id'] = os.path.split(options['location'])[-1]
options['description'] = 'dummydescription'
command = get_pipeline_script_command(accession, pipeline, options)
self.failUnless(" -bioreplicate 1 " in command)
self.failUnless(" -host dummyhost " in command)
self.failUnless(" -run_description 'dummydescription' " in command)
self.failUnless(" -preprocess 'dummypreprocess' " in command)
self.failUnless(" -preprocess_trim_length 1" in command)
