def test_rollforward(self):
with config.tempdir() as scratch:
rpkg = os.path.join(scratch, 'tostrip.refpkg')
shutil.copytree(config.data_path('lactobacillus2-0.2.refpkg'),
rpkg)
r = refpkg.Refpkg(rpkg, create=False)
original_contents = copy.deepcopy(r.contents)
r.update_metadata('boris', 'hilda')
r.update_metadata('meep', 'natasha')
updated_contents = copy.deepcopy(r.contents)
r.rollback()
r.rollback()
class _Args(object):
refpkg = rpkg
def __init__(self, n):
self.n = n
self.assertEqual(rollforward.action(_Args(3)), 1)
r._sync_from_disk()
self.assertEqual(r.contents['metadata'],
original_contents['metadata'])
self.assertEqual(rollforward.action(_Args(2)), 0)
r._sync_from_disk()
self.assertEqual(r.contents['metadata'],
updated_contents['metadata'])
self.assertEqual(r.contents['rollforward'], None)
self.assertNotEqual(r.contents['rollback'], None)
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_rollforward(self):
with config.tempdir() as scratch:
rpkg = os.path.join(scratch, 'tostrip.refpkg')
shutil.copytree(config.data_path('lactobacillus2-0.2.refpkg'), rpkg)
r = refpkg.Refpkg(rpkg, create=False)
original_contents = copy.deepcopy(r.contents)
r.update_metadata('boris', 'hilda')
r.update_metadata('meep', 'natasha')
updated_contents = copy.deepcopy(r.contents)
r.rollback()
r.rollback()
class _Args(object):
refpkg = rpkg
def __init__(self, n):
self.n = n
self.assertEqual(rollforward.action(_Args(3)), 1)
r._sync_from_disk()
self.assertEqual(r.contents['metadata'], original_contents['metadata'])
self.assertEqual(rollforward.action(_Args(2)), 0)
r._sync_from_disk()
self.assertEqual(r.contents['metadata'], updated_contents['metadata'])
self.assertEqual(r.contents['rollforward'], None)
self.assertNotEqual(r.contents['rollback'], None)
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_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_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_strip(self):
with config.tempdir() as scratch:
rpkg = os.path.join(scratch, 'tostrip.refpkg')
shutil.copytree(config.data_path('lactobacillus2-0.2.refpkg'), rpkg)
r = refpkg.Refpkg(rpkg, create=False)
r.update_metadata('boris', 'hilda')
r.update_metadata('meep', 'natasha')
class _Args(object):
refpkg = rpkg
strip.action(_Args())
r._sync_from_disk()
self.assertEqual(r.contents['rollback'], None)
self.assertEqual(r.contents['rollforward'], None)
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_strip(self):
with config.tempdir() as scratch:
rpkg = os.path.join(scratch, 'tostrip.refpkg')
shutil.copytree(config.data_path('lactobacillus2-0.2.refpkg'),
rpkg)
r = refpkg.Refpkg(rpkg, create=False)
r.update_metadata('boris', 'hilda')
r.update_metadata('meep', 'natasha')
class _Args(object):
refpkg = rpkg
strip.action(_Args())
r._sync_from_disk()
self.assertEqual(r.contents['rollback'], None)
self.assertEqual(r.contents['rollforward'], None)
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')))
