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import utils
import os
import unittest
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.location
def _make_test_file(fname):
with open(fname, 'w') as fh:
fh.write('contents')
class Tests(unittest.TestCase):
def test_database_location(self):
"""Test DatabaseLocation"""
dl1 = ihm.location.DatabaseLocation('abc', version=1)
dl2 = ihm.location.DatabaseLocation('abc', version=1)
self.assertEqual(dl1, dl2)
dl3 = ihm.location.DatabaseLocation('abc', version=2)
self.assertNotEqual(dl1, dl3)
# details can change without affecting equality
dl4 = ihm.location.DatabaseLocation('abc', version=1,
details='foo')
self.assertEqual(dl1, dl4)
self.assertEqual(dl1.db_name, 'Other')
self.assertEqual(dl1.access_code, 'abc')
self.assertEqual(dl1.version, 1)
self.assertIsNone(dl1.details)
self.assertEqual(str(dl1), "<ihm.location.DatabaseLocation('abc')>")
def test_pdb_location(self):
"""Test PDBLocation"""
loc = ihm.location.PDBLocation('1abc', version='foo', details='bar')
self.assertEqual(loc.db_name, 'PDB')
self.assertEqual(loc.access_code, '1abc')
self.assertEqual(loc.version, 'foo')
self.assertEqual(loc.details, 'bar')
def test_pdb_dev_location(self):
"""Test PDBDevLocation"""
loc = ihm.location.PDBDevLocation(
'PDBDEV_00000029', version='foo', details='bar')
self.assertEqual(loc.db_name, 'PDB-Dev')
self.assertEqual(loc.access_code, 'PDBDEV_00000029')
self.assertEqual(loc.version, 'foo')
self.assertEqual(loc.details, 'bar')
def test_model_archive_location(self):
"""Test ModelArchiveLocation"""
loc = ihm.location.ModelArchiveLocation(
'ma-bak-cepc-0250', version='foo', details='bar')
self.assertEqual(loc.db_name, 'MODEL ARCHIVE')
self.assertEqual(loc.access_code, 'ma-bak-cepc-0250')
self.assertEqual(loc.version, 'foo')
self.assertEqual(loc.details, 'bar')
def test_bmrb_location(self):
"""Test BMRBLocation"""
loc = ihm.location.BMRBLocation('27600', version='foo', details='bar')
self.assertEqual(loc.db_name, 'BMRB')
self.assertEqual(loc.access_code, '27600')
self.assertEqual(loc.version, 'foo')
self.assertEqual(loc.details, 'bar')
def test_emdb_location(self):
"""Test EMDBLocation"""
loc = ihm.location.EMDBLocation('EMDB-123', version='foo',
details='bar')
self.assertEqual(loc.db_name, 'EMDB')
self.assertEqual(loc.access_code, 'EMDB-123')
self.assertEqual(loc.version, 'foo')
self.assertEqual(loc.details, 'bar')
def test_massive_location(self):
"""Test MassIVELocation class"""
d = ihm.location.MassIVELocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'MASSIVE')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_proxl_location(self):
"""Test ProXLLocation class"""
d = ihm.location.ProXLLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'ProXL')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_jpost_location(self):
"""Test JPOSTLocation class"""
d = ihm.location.JPOSTLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'jPOSTrepo')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_iprox_location(self):
"""Test IProXLocation class"""
d = ihm.location.IProXLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'iProX')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_alpha_fold_db_location(self):
"""Test AlphaFoldDBLocation class"""
d = ihm.location.AlphaFoldDBLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'AlphaFoldDB')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_proteome_xchange_location(self):
"""Test ProteomeXchangeLocation class"""
d = ihm.location.ProteomeXchangeLocation(
'abc', version=1, details='foo')
self.assertEqual(d.db_name, 'ProteomeXchange')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_bmr_big_location(self):
"""Test BMRbigLocation class"""
d = ihm.location.BMRbigLocation(
'abc', version=1, details='foo')
self.assertEqual(d.db_name, 'BMRbig')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_empiar_location(self):
"""Test EMPIARLocation class"""
d = ihm.location.EMPIARLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'EMPIAR')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_sasbdb_location(self):
"""Test SASBDBLocation class"""
d = ihm.location.SASBDBLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'SASBDB')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_pride_location(self):
"""Test PRIDELocation class"""
d = ihm.location.PRIDELocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'PRIDE')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_biogrid_location(self):
"""Test BioGRIDLocation class"""
d = ihm.location.BioGRIDLocation('abc', version=1, details='foo')
self.assertEqual(d.db_name, 'BioGRID')
self.assertEqual(d.access_code, 'abc')
self.assertEqual(d.version, 1)
self.assertEqual(d.details, 'foo')
def test_location(self):
"""Test Location base class"""
loc = ihm.location.Location(details='foo')
loc._allow_duplicates = True
self.assertEqual(loc._eq_vals(), id(loc))
# Locations should never compare equal to None
self.assertNotEqual(loc, None)
def test_file_location_local(self):
"""Test InputFileLocation with a local file"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory('.') as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
_make_test_file(fname)
loc = ihm.location.InputFileLocation(fname)
self.assertEqual(loc.path, os.path.abspath(fname))
self.assertIsNone(loc.repo)
self.assertEqual(loc.file_size, 8)
def test_file_location_local_not_exist(self):
"""Test InputFileLocation with a local file that doesn't exist"""
with utils.temporary_directory() as tmpdir:
fname = os.path.join(tmpdir, 'test.pdb')
self.assertRaises(
ValueError, ihm.location.InputFileLocation, fname)
def test_file_location_repo(self):
"""Test InputFileLocation with a file in a repository"""
r = ihm.location.Repository(doi='1.2.3.4')
loc = ihm.location.InputFileLocation('foo/bar', repo=r)
self.assertEqual(loc.path, 'foo/bar')
self.assertEqual(loc.repo, r)
self.assertIsNone(loc.file_size)
self.assertEqual(str(loc),
"<ihm.location.InputFileLocation('foo/bar')>")
self.assertEqual(str(r), "<ihm.location.Repository('1.2.3.4')>")
# locations should only compare equal if path and repo both match
loc2 = ihm.location.InputFileLocation('foo/bar', repo=r)
self.assertEqual(loc, loc2)
loc3 = ihm.location.InputFileLocation('otherpath', repo=r)
self.assertNotEqual(loc, loc3)
r2 = ihm.location.Repository(doi='5.6.7.8')
loc4 = ihm.location.InputFileLocation('foo/bar', repo=r2)
self.assertNotEqual(loc, loc4)
loc5 = ihm.location.InputFileLocation(None, repo=r)
self.assertNotEqual(loc, loc5)
loc6 = ihm.location.InputFileLocation(None, repo=r2)
self.assertNotEqual(loc, loc6)
def test_repository_equality(self):
"""Test Repository equality"""
r1 = ihm.location.Repository(doi='foo')
r2 = ihm.location.Repository(doi='foo')
r3 = ihm.location.Repository(doi='foo', url='bar')
r4 = ihm.location.Repository(doi='bar')
self.assertEqual(r1, r2)
self.assertEqual(hash(r1), hash(r2))
self.assertNotEqual(r1, r3)
self.assertNotEqual(r1, r4)
def test_repository(self):
"""Test Repository"""
# Make tmpdir under current directory, as it's not always possible to
# get a relative path from cwd to /tmp (e.g. on Windows where they may
# be on different drives)
with utils.temporary_directory(os.getcwd()) as tmpdir:
subdir = os.path.join(tmpdir, 'subdir')
subdir2 = os.path.join(tmpdir, 'subdir2')
os.mkdir(subdir)
_make_test_file(os.path.join(subdir, 'bar'))
s = ihm.location.Repository(doi='10.5281/zenodo.46266',
root=os.path.relpath(tmpdir),
url='foo', top_directory='baz')
self.assertEqual(s._root, tmpdir)
self.assertEqual(s.url, 'foo')
self.assertEqual(s.top_directory, 'baz')
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
self.assertIsNone(loc.repo)
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46266')
self.assertEqual(loc.path, os.path.join('subdir', 'bar'))
# Shouldn't touch locations that are already in repos
loc = ihm.location.InputFileLocation(repo='foo', path='bar')
self.assertEqual(loc.repo, 'foo')
ihm.location.Repository._update_in_repos(loc, [s])
self.assertEqual(loc.repo, 'foo')
# Shortest match should win
loc = ihm.location.InputFileLocation(
os.path.relpath(os.path.join(subdir, 'bar')))
s2 = ihm.location.Repository(doi='10.5281/zenodo.46280',
root=os.path.relpath(subdir),
url='foo', top_directory='baz')
# Repositories that aren't above the file shouldn't count
s3 = ihm.location.Repository(doi='10.5281/zenodo.56280',
root=os.path.relpath(subdir2),
url='foo', top_directory='baz')
ihm.location.Repository._update_in_repos(loc, [s2, s3, s])
self.assertEqual(loc.repo.doi, '10.5281/zenodo.46280')
self.assertEqual(loc.path, 'bar')
def test_repository_no_checkout(self):
"""Test Repository with no checkout"""
r = ihm.location.Repository(doi='10.5281/zenodo.46266')
f = ihm.location.InputFileLocation(repo=r, path='foo')
self.assertEqual(f.repo.doi, '10.5281/zenodo.46266')
self.assertEqual(f.path, 'foo')
self.assertEqual(str(f), "<ihm.location.InputFileLocation('foo')>")
def test_repository_get_full_path(self):
"""Test Repository._get_full_path"""
r = ihm.location.Repository(doi='10.5281/zenodo.46266',
top_directory='/foo')
self.assertEqual(r._get_full_path('bar'), '/foo%sbar' % os.sep)
def test_file_locations(self):
"""Test FileLocation derived classes"""
r = ihm.location.Repository(doi='10.5281/zenodo.46266')
loc = ihm.location.InputFileLocation(repo=r, path='foo')
self.assertEqual(loc.content_type, 'Input data or restraints')
loc = ihm.location.OutputFileLocation(repo=r, path='foo')
self.assertEqual(loc.content_type,
'Modeling or post-processing output')
loc = ihm.location.WorkflowFileLocation(repo=r, path='foo')
self.assertEqual(loc.content_type, 'Modeling workflow or script')
loc = ihm.location.VisualizationFileLocation(repo=r, path='foo')
self.assertEqual(loc.content_type, 'Visualization script')
if __name__ == '__main__':
unittest.main()
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