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 setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
readset_file=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/paired1.syml'
self.readset=Readset.load(filename=readset_file)[0]
self.pipeline=Pipeline(name='test_newstep', readset=self.readset)
def setUp(self):
usage=""
RnaseqGlobals.initialize(usage)
self.db_file=os.path.join(RnaseqGlobals.conf_value('rnaseq','root_dir'),RnaseqGlobals.conf_value('testing','test_db'))
readset=Readset(name='readset', db_file=self.db_file).load()
self.readset=readset
if not readset.table_exists():
raise ProgrammerGoof("table %s doesn't exist" % readset.tablename())
def setUp(self):
usage="testing: "+__file__
RnaseqGlobals.initialize(usage)
self.db_file=os.path.join(RnaseqGlobals.conf_value('rnaseq','root_dir'),RnaseqGlobals.conf_value('testing','test_db'))
readset=Readset(name='readset', db_file=self.db_file).load()
self.readset=readset
#print "readset is %s" % readset
readset.execute(sql)
print "table %s created" % readset.tablename()
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
readset_file=os.path.join(RnaseqGlobals.root_dir(),'t','fixtures','readsets','readset1.syml')
self.readset=Readset.load(readset_file)[0]
self.pipeline=Pipeline(name='juan', readset=self.readset).load_steps()
session=RnaseqGlobals.get_session()
ps=session.query(Pipeline).all()
for p in ps:
session.delete(p)
session.commit()
def setUp(self):
usage=""
RnaseqGlobals.initialize(usage)
self.db_file=os.path.join(RnaseqGlobals.conf_value('rnaseq','root_dir'),RnaseqGlobals.conf_value('testing','test_db'))
readset=Readset(name='readset', db_file=self.db_file).load()
self.readset=readset
#print "readset is %s" % readset
sql="DROP TABLE IF EXISTS %s" % readset.tablename()
readset.execute(sql)
sql="CREATE TABLE %s (id INTEGER PRIMARY KEY AUTOINCREMENT, name VARCHAR[255], description TEXT)" % readset.tablename()
readset.execute(sql)
def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
templated.template_dir=RnaseqGlobals.root_dir()+"/t/fixtures/templates"
readset_file=RnaseqGlobals.root_dir()+"/t/fixtures/readsets/readset1.syml"
self.readset=Readset.load(readset_file)[0]
self.pipeline=Pipeline(name='juan', readset=self.readset).load_steps()
session=RnaseqGlobals.get_session()
# delete all pre-existing pipeline objects from the db:
plist=session.query(Pipeline)
for p in plist:
session.delete(p)
session.commit()
def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
templated.template_dir=RnaseqGlobals.root_dir()+'/t/fixtures/templates'
os.chdir(RnaseqGlobals.root_dir()+'/t/fixtures/readsets')
filename=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset_rel_glob.syml'
rlist=Readset.load(filename)
readset=rlist[0]
self.readset=readset
self.session=RnaseqGlobals.get_session()
rlist=self.session.query(Readset)
for rs in rlist:
self.session.delete(rs)
self.session.commit()
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
self.readset=Readset.load(RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset1.syml')[0]
def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
#templated.template_dir=RnaseqGlobals.root_dir()+"/../../fixtures/templates"
self.readset_dir=os.path.join(RnaseqGlobals.root_dir(),'t/fixtures/readsets')
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
