def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
RnaseqGlobals.set_conf_value('force',True)
RnaseqGlobals.set_conf_value('silent',True)
readset=Readset.load(RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset1.syml')[0]
self.pipeline=Pipeline(name='filter', readset=readset)
def make_run_objects(self, session):
#self=self.store_db()
try: verbose=os.environ['DEBUG']
except: debug=False
# create the pipeline_run object:
try:
label=RnaseqGlobals.conf_value('label') or self.readset.label
except AttributeError as ae:
raise UserError("No label defined. Please specify a label for the pipeline run, either in the readset or using the '--label' command line option")
pipeline_run=PipelineRun(status='standby',
input_file=', '.join(self.readset.reads_files),
user=RnaseqGlobals.conf_value('user'),
label=label,
working_dir=self.readset.working_dir)
self.pipeline_runs.append(pipeline_run)
# print "mro: self.pipeline_runs is %s" % ", ".join(str(x.id) for x in self.pipeline_runs)
# try: warn("pipeline.id is %s" % pipeline.id)
# except: warn("pipeline has no id")
self=session.merge(self)
session.commit()
if pipeline_run.id==None:
raise ProgrammerGoof("no id in %s" % pipeline_run)
self.context.pipeline_run_id=pipeline_run.id
RnaseqGlobals.set_conf_value('pipeline_run_id',pipeline_run.id)
# create step_run objects:
step_runs={}
for step in self.steps:
if step.is_prov_step: continue
step_run=StepRun(step_name=step.name, status='standby')
for output in step.output_list():
output=evoque_template(output, step, self.readset)
step_run.file_outputs.append(FileOutput(path=output))
if step.skip: # as set by self.set_steps_current()
if debug: print "step %s is current, skipping" % step.name
step_run.status='skipped'
step_run.success=True
pipeline_run.step_runs.append(step_run)
session.commit()
pipeline_run.step_runs.append(step_run) # maintains list in db as well
step_runs[step.name]=step_run
self.context.step_runs[step.name]=step_run
session.commit()
return (pipeline_run, step_runs)