def test_convert(self):
path_core_1 = os.path.join(self.dir, 'core_1.xlsx')
path_core_2 = os.path.join(self.dir, 'core_2-*.csv')
path_core_3 = os.path.join(self.dir, 'core_3.xlsx')
path_seq_1 = os.path.join(self.dir, 'seq_1.fna')
path_seq_2 = os.path.join(self.dir, 'seq_2.fna')
path_seq_3 = os.path.join(self.dir, 'seq_3.fna')
io.Writer().run(path_core_1,
self.kb,
seq_path=path_seq_1,
data_repo_metadata=False)
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
kb = io.Reader().run(path_core_2,
seq_path=self.seq_path)[core.KnowledgeBase][0]
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, path_seq_2, shallow=False))
io.convert(path_core_2, path_seq_2, path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3,
seq_path=self.seq_path)[core.KnowledgeBase][0]
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, path_seq_3, shallow=False))
def _default(self):
args = self.app.pargs
io.convert(args.source_core,
args.source_seq,
args.dest_core,
args.dest_seq,
strict=args.strict)
def _default(self):
args = self.app.pargs
io.convert(args.source_core,
args.source_seq,
args.dest_core,
args.dest_seq,
taxon=args.taxon,
protected=(not args.unprotected))
def test_convert_sloppy(self):
path_core_1 = os.path.join(self.dir, 'core_1.xlsx')
path_core_2 = os.path.join(self.dir, 'core_2-*.csv')
path_core_3 = os.path.join(self.dir, 'core_3.xlsx')
path_seq_1 = os.path.join(self.dir, 'seq_1.fna')
path_seq_2 = os.path.join(self.dir, 'seq_2.fna')
path_seq_3 = os.path.join(self.dir, 'seq_3.fna')
io.Writer().run(path_core_1,
self.kb,
seq_path=path_seq_1,
data_repo_metadata=False)
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))
wb = wc_utils.workbook.io.read(path_core_1)
row = wb['!!KB'].pop(4)
wb['!!KB'].insert(5, row)
wc_utils.workbook.io.write(path_core_1, wb)
with self.assertRaisesRegex(ValueError, "cannot be loaded because"):
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
env = EnvironmentVarGuard()
env.set('CONFIG__DOT__wc_kb__DOT__io__DOT__strict', '0')
with env:
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
kb = io.Reader().run(path_core_2,
seq_path=self.seq_path)[core.KnowledgeBase][0]
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, path_seq_2, shallow=False))
io.convert(path_core_2, path_seq_2, path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3,
seq_path=self.seq_path)[core.KnowledgeBase][0]
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, path_seq_3, shallow=False))
def test_convert_sloppy(self):
path_core_1 = os.path.join(self.dir, 'core_1.xlsx')
path_core_2 = os.path.join(self.dir, 'core_2-*.csv')
path_core_3 = os.path.join(self.dir, 'core_3.xlsx')
path_seq_1 = os.path.join(self.dir, 'seq_1.fna')
path_seq_2 = os.path.join(self.dir, 'seq_2.fna')
path_seq_3 = os.path.join(self.dir, 'seq_3.fna')
io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))
wb = wc_utils.workbook.io.read(path_core_1)
row = wb['Knowledge base'].pop(0)
wb['Knowledge base'].insert(1, row)
wc_utils.workbook.io.write(path_core_1, wb)
with self.assertRaisesRegex(ValueError, "The columns of worksheet 'Knowledge base' must be defined in this order"):
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2, strict=False)
kb = io.Reader().run(path_core_2, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, path_seq_2, shallow=False))
io.convert(path_core_2, path_seq_2, path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, path_seq_3, shallow=False))