def test_create_project(self):
project_loader = ProjectLoader(dbsession)
project_loader.create_project('pytest project')
dbsession.commit()
last_project = dbsession.query(Project).order_by(
Project.id.desc()).first()
assert last_project.name == project_loader.project.name
project_loader.delete_project(project_loader.project.geid)
dbsession.commit()
deleted_project = dbsession.query(Project).filter(
Project.geid == project_loader.project.geid).first()
assert not deleted_project
def test_load_min(self):
loader = ProjectDataLoader(dbsession, self.project.geid,
'python/tests/pytest_min.xlsx')
assert not loader.xls.parse('Target').empty
assert not loader.xls.parse('Guide').empty
assert not loader.xls.parse('Amplicon').empty
assert not loader.xls.parse('Layout').empty
loader.load()
dbsession.commit()
target = dbsession.query(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Target.name == 'test_target').one()
assert target
guide = dbsession.query(Guide)\
.join(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Guide.name == 'test_guide')\
.one()
assert guide
amplicon = dbsession.query(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.one()
assert amplicon
primer = dbsession.query(Primer)\
.join(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.filter(Primer.sequence == 'AAAAA')\
.filter(Primer.strand == 'forward')\
.filter(Primer.start == 1)\
.filter(Primer.end == 10)\
.one()
assert primer
primer = dbsession.query(Primer)\
.join(Amplicon)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Amplicon.chromosome == 1)\
.filter(Amplicon.start == 1)\
.filter(Primer.sequence == 'CCCCC')\
.filter(Primer.strand == 'reverse')\
.filter(Primer.start == 101)\
.filter(Primer.end == 110)\
.one()
assert primer
def main():
log = logger.get_custom_logger(os.path.join(cfg['PROJECTS_FOLDER'], 'load_ref_data.log'))
try:
loader = RefLoader(dbsession)
loader.load_genomes()
dbsession.commit()
except Exception as e:
log.exception(e)
dbsession.rollback()
finally:
dbsession.close()
def test_load_mouse(self):
loader = ProjectDataLoader(dbsession, self.project.geid,
'python/tests/pytest_mouse.xlsx')
assert not loader.xls.parse('Target').empty
assert not loader.xls.parse('Guide').empty
assert not loader.xls.parse('Amplicon').empty
assert not loader.xls.parse('Layout').empty
loader.load()
dbsession.commit()
target = dbsession.query(Target)\
.join(Project)\
.filter(Project.geid == self.project.geid)\
.filter(Target.name == 'test_mouse_target').one()
assert target
assert target.genome.name == 'Mus_musculus'
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--geid",
dest="geid",
action="store",
help="Project GEP ID e.g. 'GEP00001'",
required=True)
options = parser.parse_args()
log = logger.get_custom_logger(
os.path.join(cfg['PROJECTS_FOLDER'], 'delete_project.log'))
try:
project = ProjectLoader(dbsession)
project.delete_project(options.geid)
dbsession.commit()
except Exception as e:
log.exception(e)
dbsession.rollback()
finally:
dbsession.close()
def teardown_method(self):
dbsession.delete(self.project)
dbsession.commit()
def setup_method(self):
project_loader = ProjectLoader(dbsession)
project_loader.create_project('pytest')
dbsession.commit()
self.project = project_loader.project