def test_metadata_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
self.args.changes = ['meep=boris', 'hilda=vrrp']
self.args.metadata = True
self.args.refpkg = pkg_path
update.action(self.args)
r._sync_from_disk()
self.assertEqual(r.metadata('meep'), 'boris')
self.assertEqual(r.metadata('hilda'), 'vrrp')
def test_metadata_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
self.args.changes = ['meep=boris', 'hilda=vrrp']
self.args.metadata = True
self.args.refpkg = pkg_path
update.action(self.args)
r._sync_from_disk()
self.assertEqual(r.metadata('meep'), 'boris')
self.assertEqual(r.metadata('hilda'), 'vrrp')
def test_metadata_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path)
class _Args(object):
refpkg=pkg_path
changes = ['meep=boris', 'hilda=vrrp']
metadata = True
update.action(_Args())
r._sync_from_disk()
self.assertEqual(r.metadata('meep'), 'boris')
self.assertEqual(r.metadata('hilda'), 'vrrp')
def test_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path)
test_file = config.data_path('bv_refdata.csv')
class _Args(object):
refpkg=pkg_path
changes = ['meep='+test_file, 'hilda='+test_file]
metadata = False
update.action(_Args())
r._sync_from_disk()
self.assertEqual(r.contents['files']['meep'], 'bv_refdata.csv')
self.assertEqual(r.contents['files']['hilda'], 'bv_refdata.csv1')
def test_update_stats_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
args = self.args
stats_path = os.path.join(config.datadir, 'phyml_aa_stats.txt')
args.refpkg = pkg_path
args.changes = ['tree_stats=' + stats_path]
args.frequency_type = 'empirical'
update.action(args)
r._sync_from_disk()
self.assertIn('tree_stats', r.contents['files'])
self.assertIn('phylo_model', r.contents['files'])
self.assertTrue(r.contents['files']['phylo_model'].endswith('.json'))
def test_update_stats_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
args = self.args
stats_path = os.path.join(config.datadir, 'phyml_aa_stats.txt')
args.refpkg = pkg_path
args.changes = ['tree_stats=' + stats_path]
args.frequency_type = 'empirical'
update.action(args)
r._sync_from_disk()
self.assertIn('tree_stats', r.contents['files'])
self.assertIn('phylo_model', r.contents['files'])
self.assertTrue(
r.contents['files']['phylo_model'].endswith('.json'))
def test_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
test_file = config.data_path('bv_refdata.csv')
self.args.refpkg = pkg_path
self.args.changes = ['meep=' + test_file, 'hilda=' + test_file]
update.action(self.args)
r._sync_from_disk()
self.assertEqual(r.contents['files']['meep'], 'bv_refdata.csv')
# Second file should have been assigned a non-clashing name
h = r.contents['files']['hilda']
self.assertNotEqual(h, 'bv_refdata.csv')
self.assertTrue(h.startswith('bv_refdata'))
self.assertTrue(h.endswith('.csv'))
self.assertTrue(os.path.exists(r.resource_path('hilda')))
def test_action(self):
with config.tempdir() as scratch:
pkg_path = os.path.join(scratch, 'test.refpkg')
r = refpkg.Refpkg(pkg_path, create=True)
test_file = config.data_path('bv_refdata.csv')
class _Args(object):
refpkg=pkg_path
changes = ['meep='+test_file, 'hilda='+test_file]
metadata = False
update.action(_Args())
r._sync_from_disk()
self.assertEqual(r.contents['files']['meep'], 'bv_refdata.csv')
# Second file should have been assigned a non-clashing name
h = r.contents['files']['hilda']
self.assertNotEqual(h, 'bv_refdata.csv')
self.assertTrue(h.startswith('bv_refdata'))
self.assertTrue(h.endswith('.csv'))
self.assertTrue(os.path.exists(r.resource_path('hilda')))
