def test_create(self):
with config.tempdir() as scratch:
class _Args(object):
clobber = True
locus = 'Nowhere'
description = 'A description'
author = 'Boris the Mad Baboon'
package_version = '0.3'
package_name = os.path.join(scratch, 'test.refpkg')
tree_stats = None
aln_fasta = None
aln_sto = None
phylo_model = None
seq_info = None
mask = None
profile = None
readme = None
tree = None
taxonomy = None
reroot = False
rppr = 'rppr'
create.action(_Args())
r = refpkg.Refpkg(_Args().package_name, create=False)
self.assertEqual(r.metadata('locus'), 'Nowhere')
self.assertEqual(r.metadata('description'), 'A description')
self.assertEqual(r.metadata('author'), 'Boris the Mad Baboon')
self.assertEqual(r.metadata('package_version'), '0.3')
self.assertEqual(r.metadata('format_version'), '1.1')
self.assertEqual(r.contents['rollback'], None)
args2 = _Args()
args2.package_name = os.path.join(scratch, 'test.refpkg')
args2.clobber = True
self.assertEqual(0, create.action(args2))
def _test_create_phylo_model(self, stats_path, stats_type=None,
frequency_type=None):
with config.tempdir() as scratch:
args = self._Args(scratch)
args.tree_stats = stats_path
args.stats_type = stats_type
args.frequency_type = frequency_type
create.action(args)
r = refpkg.Refpkg(args.package_name, create=False)
self.assertIn('phylo_model', r.contents['files'])
def _test_create_phylo_model(self, stats_path, stats_type=None,
frequency_type=None):
with config.tempdir() as scratch:
args = self._Args(scratch)
args.tree_stats = stats_path
args.stats_type = stats_type
args.frequency_type = frequency_type
create.action(args)
r = refpkg.Refpkg(args.package_name, create=False)
self.assertIn('phylo_model', r.contents['files'])
def test_create(self):
with config.tempdir() as scratch:
args = self._Args(scratch)
create.action(args)
r = refpkg.Refpkg(args.package_name, create=False)
self.assertEqual(r.metadata('locus'), 'Nowhere')
self.assertEqual(r.metadata('description'), 'A description')
self.assertEqual(r.metadata('author'), 'Boris the Mad Baboon')
self.assertEqual(r.metadata('package_version'), '0.3')
self.assertEqual(r.metadata('format_version'), '1.1')
self.assertEqual(r.contents['rollback'], None)
args2 = self._Args(scratch)
args2.package_name = os.path.join(scratch, 'test.refpkg')
args2.clobber = True
self.assertEqual(0, create.action(args2))
def test_create(self):
with config.tempdir() as scratch:
args = self._Args(scratch)
create.action(args)
r = refpkg.Refpkg(args.package_name, create=False)
self.assertEqual(r.metadata('locus'), 'Nowhere')
self.assertEqual(r.metadata('description'), 'A description')
self.assertEqual(r.metadata('author'), 'Boris the Mad Baboon')
self.assertEqual(r.metadata('package_version'), '0.3')
self.assertEqual(r.metadata('format_version'), '1.1')
self.assertEqual(r.contents['rollback'], None)
args2 = self._Args(scratch)
args2.package_name = os.path.join(scratch, 'test.refpkg')
args2.clobber = True
self.assertEqual(0, create.action(args2))
