def test_read_csv(self):
'''
test the read wrapper of SBtab files
'''
with self.assertRaises(SBtab.SBtabError):
SBtab.read_csv('wrong_file_path', 'doc_name')
with self.assertRaises(SBtab.SBtabError):
SBtab.read_csv('wrong_file_path', 'doc_name', xlsx=True)
valid_table_types = misc.extract_supported_table_types()
for file_name in self.table_names:
if not file_name.startswith('_'):
sbtab = SBtab.read_csv('python/tests/tables/' + file_name,
'doc_name')
self.assertEqual(type(sbtab), SBtab.SBtabDocument)
for sbtab in self.sbtabs:
self.assertIsNotNone(sbtab._get_header_row())
self.assertIsNotNone(sbtab.table_type)
self.assertIn(sbtab.table_type, valid_table_types)
self.assertIsNotNone(sbtab.table_name)
self.assertEqual(sbtab.header_row[:7], '!!SBtab')
self.assertIsNotNone(sbtab.header_row.find("'"))
self.assertEqual(sbtab.header_row.find('"'), -1)
sbtab_xlsx = SBtab.read_csv('python/tests/tables/_transition.xlsx',
'doc_name',
xlsx=True)
self.assertEqual(type(sbtab_xlsx), SBtab.SBtabDocument)
with self.assertRaises(SBtab.SBtabError):
sbtab_xlsx = SBtab.read_csv('python/tests/tables/_transition.xlsx',
'doc_name')
def check_type_validity(self, ttype, definitions_file=None):
'''
Checks if the given table type is supported by default.
Parameters
----------
ttype: str
Table type to be tested.
Returns: Bool
Flag that indicates if the given table type is supported by default.
'''
try:
supported_types = misc.extract_supported_table_types(
definitions_file)
except:
raise SBtabError('The definition file could not be found to'\
' establish supported table types.')
if ttype in supported_types: return True
else:
raise SBtabError(
'The table type %s is not supported. Make sure to provide a definition file that contains this table type.'
% ttype)
#print('The table type %s is not supported.' % ttype)
return True
def test_extract_supported_table_types(self):
'''
PART 2 OF 3:
test (with examples) if the definitions file can be used to extract the supported table types
'''
table_types = misc.extract_supported_table_types()
self.assertIn('Reaction', table_types)
self.assertIn('Compound', table_types)
self.assertIn('Quantity', table_types)
def test_extract_supported_table_types(self):
'''
PART 2 OF 3:
test (with examples) if the definitions file can be used to extract the supported table types
'''
table_types = misc.extract_supported_table_types()
self.assertIn('Reaction', table_types)
self.assertIn('Compound', table_types)
self.assertIn('Quantity', table_types)
def test_check_type_validity(self):
'''
test if the table types are checked accurately
'''
valid_table_types = misc.extract_supported_table_types()
for t in valid_table_types:
self.assertTrue(self.docs[0].check_type_validity(t))
with self.assertRaises(SBtab.SBtabError):
self.docs[0].check_type_validity('Rubbish')
def test_check_type_validity(self):
'''
test if the table types are checked accurately
'''
valid_table_types = misc.extract_supported_table_types()
for t in valid_table_types:
self.assertTrue(self.docs[0].check_type_validity(t))
with self.assertRaises(SBtab.SBtabError):
self.docs[0].check_type_validity('Rubbish')
def test_find_descriptions(self):
'''
PART 3 OF 3:
test if the descriptions can be read from the definitions file and
the correct table types are inherent
'''
sbtab_def = misc.open_definitions_file()
table_types = misc.extract_supported_table_types()
for tt in table_types:
(col2description, col2link) = misc.find_descriptions(sbtab_def, tt)
self.assertNotEqual(col2description, {})
self.assertNotEqual(col2link, {})
for entry in col2link:
self.assertEqual(entry[0], '!')
self.assertTrue(col2link[entry] == 'True' or col2link[entry] == 'False')
def test_find_descriptions(self):
'''
PART 3 OF 3:
test if the descriptions can be read from the definitions file and
the correct table types are inherent
'''
sbtab_def = misc.open_definitions_file()
table_types = misc.extract_supported_table_types()
for tt in table_types:
(col2description, col2link) = misc.find_descriptions(sbtab_def, tt)
self.assertNotEqual(col2description, {})
self.assertNotEqual(col2link, {})
for entry in col2link:
self.assertEqual(entry[0], '!')
self.assertTrue(col2link[entry] == 'True'
or col2link[entry] == 'False')
def test_doc_row_attributes(self):
'''
test if doc row attributes are read correctly
'''
valid_table_types = misc.extract_supported_table_types()
for doc in self.docs:
self.assertIsNotNone(doc.doc_row)
self.assertIsNotNone(doc.date)
self.assertEqual(doc.doc_row[:8], '!!!SBtab')
self.assertIsNotNone(doc.doc_row.find("'"))
self.assertEqual(doc.doc_row.find('"'), -1)
self.assertNotIn(doc.doc_row, "''")
self.assertNotIn('^M', doc.doc_row)
self.assertNotIn('\n', doc.doc_row)
self.assertNotIn('\r', doc.doc_row)
self.assertIn('Date=', doc.doc_row)
def test_doc_row_attributes(self):
'''
test if doc row attributes are read correctly
'''
valid_table_types = misc.extract_supported_table_types()
for doc in self.docs:
self.assertIsNotNone(doc.doc_row)
self.assertIsNotNone(doc.date)
self.assertEqual(doc.doc_row[:8], '!!!SBtab')
self.assertIsNotNone(doc.doc_row.find("'"))
self.assertEqual(doc.doc_row.find('"'), -1)
self.assertNotIn(doc.doc_row,"''")
self.assertNotIn('^M',doc.doc_row)
self.assertNotIn('\n',doc.doc_row)
self.assertNotIn('\r',doc.doc_row)
self.assertIn('Date=', doc.doc_row)
def test_header_row(self):
'''
test if the SBtab has a valid header row
'''
valid_table_types = misc.extract_supported_table_types()
for sbtab in self.sbtabs:
self.assertIsNotNone(sbtab._get_header_row())
self.assertIsNotNone(sbtab.table_type)
self.assertIn(sbtab.table_type, valid_table_types)
self.assertIsNotNone(sbtab.table_name)
self.assertEqual(sbtab.header_row[:7], '!!SBtab')
self.assertIsNotNone(sbtab.header_row.find("'"))
self.assertEqual(sbtab.header_row.find('"'), -1)
self.assertNotIn(sbtab._get_header_row(), "''")
self.assertNotIn('^M', sbtab.header_row)
self.assertNotIn('\n', sbtab.header_row)
self.assertNotIn('\r', sbtab.header_row)
self.assertIn('TableType=', sbtab.header_row)
self.assertIn('TableID=', sbtab.header_row)
self.assertIn('Date=', sbtab.header_row)
def check_type_validity(self, ttype):
'''
Checks if the given table type is supported by default.
Parameters
----------
ttype: str
Table type to be tested.
Returns: Bool
Flag that indicates if the given table type is supported by default.
'''
try:
supported_types = misc.extract_supported_table_types()
except:
raise SBtabError('The definition file could not be found to'\
' establish supported table types.')
if ttype in supported_types: return True
else:
#raise SBtabError('The table type %s is not supported.' % ttype)
print('The table type %s is not supported.' % ttype)
return True
