def test___init__with_lines_and_starting_line_number(self):
l1 = text_line_parser('apple\nkiwi\npear\nmelon', starting_line_number = 5)
self.assertEqual( 4, len(l1) )
l2 = text_line_parser(l1)
self.assertEqual( 4, len(l2) )
self.assertEqual( ( 5, 'apple' ), l2[0] )
self.assertEqual( ( 6, 'kiwi' ), l2[1] )
self.assertEqual( ( 7, 'pear' ), l2[2] )
self.assertEqual( ( 8, 'melon' ), l2[3] )
def test___init__with_lines(self):
l1 = text_line_parser('apple\nkiwi\npear\nmelon')
self.assertEqual( 4, len(l1) )
l2 = text_line_parser(l1)
self.assertEqual( 4, len(l2) )
self.assertEqual( ( 1, 'apple' ), l2[0] )
self.assertEqual( ( 2, 'kiwi' ), l2[1] )
self.assertEqual( ( 3, 'pear' ), l2[2] )
self.assertEqual( ( 4, 'melon' ), l2[3] )
def test_add_line_numbers(self):
l = text_line_parser('foo\nbar\n')
l.add_line_numbers()
self.assertMultiLineEqual(
'''1|foo
2|bar
''',
str(l) )
l = text_line_parser('foo\nbar')
l.add_line_numbers()
self.assertMultiLineEqual(
'''1|foo
2|bar''',
str(l) )
def test_continuation(self):
text = r'''foo bar
kiwi \
apple
pear \
orange
almond \
peanut \
walnut \
rum
coke'''
l = text_line_parser(text)
l.merge_continuations()
l.add_line_numbers()
self.assertMultiLineEqual(
''' 1|foo bar
2|kiwi apple
3|
4|pear orange
5|
6|almond peanut walnut rum
7|
8|
9|
10|coke''',
str(l) )
def test_prepend_with_negative_index(self):
l = text_line_parser('1234\n5678')
l.prepend('_', index = -2)
self.assertMultiLineEqual(
'''12_34
56_78''',
str(l) )
def test_prepend_with_index(self):
l = text_line_parser('1234\n5678')
l.prepend('_', index = 1)
self.assertMultiLineEqual(
'''1_234
5_678''',
str(l) )
def test_cut_sections(self):
text = '''\
section:1
a
b
c
section:2
d
e
f
section:3
g
h
i
'''
l = text_line_parser(text)
sections = l.cut_sections(r'^section\:.*$', r'^\s*$', include_pattern = True)
self.assertEqual( 3, len(sections) )
self.assertEqual( ( 1, 'section:1' ), sections[0][0] )
self.assertEqual( ( 2, 'a' ), sections[0][1] )
self.assertEqual( ( 3, 'b' ), sections[0][2] )
self.assertEqual( ( 4, 'c' ), sections[0][3] )
self.assertEqual( ( 6, 'section:2' ), sections[1][0] )
self.assertEqual( ( 7, 'd' ), sections[1][1] )
self.assertEqual( ( 8, 'e' ), sections[1][2] )
self.assertEqual( ( 9, 'f' ), sections[1][3] )
self.assertEqual( ( 11, 'section:3' ), sections[2][0] )
self.assertEqual( ( 12, 'g' ), sections[2][1] )
self.assertEqual( ( 13, 'h' ), sections[2][2] )
self.assertEqual( ( 14, 'i' ), sections[2][3] )
def parse(clazz, text, filename='<unknown>'):
name = None
unixpath = None
pythonpath = None
requires = None
variables = []
for line in text_line_parser(text):
text = line.text_no_comments.strip()
if text:
key, sep, value = text.partition(':')
if sep != ':':
raise ValueError('Invalid config line \"%s\" at %s:%s' %
(line.text, filename, line.line_number))
key = key.strip()
value = value.strip()
if key == 'name':
name = value
elif key in ['unixpath']:
unixpath = [path.expanduser(p) for p in value.split(':')]
elif key in ['pythonpath']:
pythonpath = [path.expanduser(p) for p in value.split(':')]
elif key == 'requires':
requires = set(string_util.split_by_white_space(value))
elif key == 'variables':
variables = string_util.split_by_white_space(value)
else:
raise ValueError('Invalid config value \"%s\" at %s:%s' %
(line.text, filename, line.line_number))
return clazz(name, unixpath, pythonpath, requires, variables)
def test_replace_line_with_lines(self):
text = '''\
kiwi
apple
melon
cheese'''
l = text_line_parser(text)
self.assertEqual( [ 1, 2, 3, 4 ], l.line_numbers() )
l.replace_line_with_lines(2, string_list(['wine', 'pepper']))
self.assertMultiLineEqual( '''\
kiwi
wine
pepper
melon
cheese''', str(l) )
self.assertEqual( [ 1, 2, 3, 4, 5 ], l.line_numbers() )
return
text = '''\
kiwi
apple
melon
cheese'''
l = text_line_parser(text)
l.replace_line_with_lines(1, string_list(['wine', 'pepper']))
self.assertMultiLineEqual( '''\
wine
pepper
apple
pepper
melon
cheese''', str(l) )
text = '''\
kiwi
apple
melon
cheese'''
l = text_line_parser(text)
l.replace_line_with_lines(4, string_list(['wine', 'pepper']))
self.assertMultiLineEqual( '''\
kiwi
apple
pepper
melon
wine
pepper''', str(l) )
def test_prepend(self):
l = text_line_parser('foo\nbar\n')
l.prepend('ABC: ')
self.assertMultiLineEqual(
'''ABC: foo
ABC: bar
''',
str(l) )
def test___init__with_tuple_seq(self): lines = [ ( 1, 'apple' ), ( 2, 'kiwi' ), ( 3, 'pear' ), ( 4, 'melon' ) ] l = text_line_parser(lines) self.assertEqual( 4, len(l) ) self.assertEqual( ( 1, 'apple' ), l[0] ) self.assertEqual( ( 2, 'kiwi' ), l[1] ) self.assertEqual( ( 3, 'pear' ), l[2] ) self.assertEqual( ( 4, 'melon' ), l[3] )
def test_1_empty_line(self):
l = text_line_parser('\n')
self.assertEqual( 1, len(l) )
self.assertEqual( '', l[0].text )
self.assertMultiLineEqual(
'''
''',
str(l) )
def test_append(self):
l = text_line_parser('foo\nbar\n')
l.append(':ABC')
self.assertMultiLineEqual(
'''foo:ABC
bar:ABC
''',
str(l) )
def test_1_line_with_newline(self):
l = text_line_parser('foo\n')
self.assertEqual( 1, len(l) )
self.assertEqual( 'foo', l[0].text )
self.assertMultiLineEqual(
'''foo
''',
str(l) )
def test__fold_literals(self):
text = '''\
child1
child2
sub2a
sub2a1
sub2b
> this is a multi
line literal
that includes \'\'\'whatever\'\'\'
sub2c
foo
sub2d
>this is a another multi
#
line literal
sub2e
> this is yet another multi
#
line literal
foo
sub3d'''
from bes.text.text_line_parser import text_line_parser
parser = text_line_parser(text)
literals = P._fold_literals(parser)
expected = '''\
child1
child2
sub2a
sub2a1
sub2b
@@tree_text_literal:0@@
sub2c
foo
sub2d
@@tree_text_literal:1@@
sub2e
@@tree_text_literal:2@@
sub3d'''
self.assertMultiLineEqual(expected, str(parser))
self.assertEqual([
'@@tree_text_literal:0@@', '@@tree_text_literal:1@@',
'@@tree_text_literal:2@@'
], sorted(literals.keys()))
self.assertEqual(
"this is a multi\nline literal\nthat includes '''whatever'''\n",
literals['@@tree_text_literal:0@@'].text)
self.assertEqual("this is a another multi\n#\nline literal\n\n",
literals['@@tree_text_literal:1@@'].text)
self.assertEqual("this is yet another multi\n\n#\nline literal\nfoo",
literals['@@tree_text_literal:2@@'].text)
def test_strip(self): text = ''' apple kiwi orange ''' l = text_line_parser(text) l.strip() self.assertEqual( [ '', 'apple', 'kiwi', 'orange', '' ], l.to_string_list() )
def caca_dependencies(clazz, filename, python_exe):
'Return list of files filename depends on or None if snakefood is not found.'
rv = execute.execute('%s -v %s' % (python_exe, filename),
raise_error=False)
parser = text_line_parser(rv.stderr)
parser.remove_empties()
for line in parser:
f = clazz._IMPORT_PATTERN.findall(line.text)
if f:
print(f[0][2])
return None
def test_windows_line_break(self):
'Test that windows line breaks are interpreted and preserved correctly.'
text = '''kiwi\r\napple\r\nmelon\r\ncheese\r\n'''
l = text_line_parser(text)
self.assertEqual( [
( 1, 'kiwi' ),
( 2, 'apple' ),
( 3, 'melon' ),
( 4, 'cheese' ),
], l.lines )
self.assertMultiLineEqual( text, str(l) )
def test_expand_continuations_with_indent(self):
text = '''foo\\bar\\baz'''
l = text_line_parser(text)
self.assertEqual( [
( 1, 'foo\\bar\\baz' ),
], l.lines )
l.expand_continuations(indent = 2)
self.assertEqual( [
( 1, 'foo' ),
( 2, ' bar' ),
( 3, ' baz' ),
], l.lines )
def test_renumber(self):
text = '''\
kiwi
apple
melon
cheese'''
l = text_line_parser(text)
self.assertEqual( [ 1, 2, 3, 4 ], l.line_numbers() )
l.remove_line_number(2)
self.assertEqual( [ 1, 3, 4 ], l.line_numbers() )
l.renumber()
self.assertEqual( [ 1, 2, 3 ], l.line_numbers() )
def test_match_all(self):
text = '''apple
kiwi
orange
apricot
banana
watermelon'''
l = text_line_parser(text)
l.strip()
self.assertEqual( [ ( 1, 'apple' ), ( 4, 'apricot' ) ], l.match_all('^a.*$') )
self.assertEqual( [], l.match_all('^nothere.*$') )
self.assertEqual( [ ( 1, 'apple' ) ], l.match_all('^app.*$') )
def test_match_first(self):
text = '''
Health ID: 8573008129436468
Test Name Results Reference Range Lab
CHLORIDE 101 98-110 mmol/L
'''
l = text_line_parser(text)
patterns = [
r'^\s*Test\s+Name\s\s+Result\s\s+Flag\s\s+Reference\s+Range\s\s+Lab\s*$',
r'^\s*Test\s+Name\s\s+Results\s\s+Reference\s+Range\s\s+Lab\s*$',
]
self.assertEqual( 3, l.match_first(patterns).line.line_number )
def test_re_findall(self):
text = '''\
cheese = brie;
fruit = kiwi;
wine = barolo;
cheese = cheddar;
'''
l = text_line_parser(text)
pattern = r'cheese\s+=\s+(.*);'
self.assertEqual( [
( 0, ( 1, 'cheese = brie;' ), ['brie'] ),
( 3, ( 4, 'cheese = cheddar;' ), ['cheddar'] ),
], l.re_findall(r'cheese\s+=\s+(.*);') )
def test_find_by_line_number(self): text = '''apple kiwi orange apricot banana watermelon''' l = text_line_parser(text) l.strip() self.assertEqual( 0, l.find_by_line_number(1) ) self.assertEqual( 3, l.find_by_line_number(4) ) self.assertEqual( 5, l.find_by_line_number(6) ) self.assertEqual( -1, l.find_by_line_number(666) )
def test_replace_line_text(self):
text = '''\
kiwi
apple
melon
eggs'''
l = text_line_parser(text)
l.replace_line_text(3, 'whiskey')
self.assertMultiLineEqual( '''\
kiwi
apple
whiskey
eggs''', str(l) )
def test_append_line(self):
text = '''\
kiwi
apple
melon
eggs'''
l = text_line_parser(text)
l.append_line('wine')
self.assertMultiLineEqual( '''\
kiwi
apple
melon
eggs
wine''', str(l) )
def test_cut_lines(self):
text = '''
apple
kiwi
orange
apricot
banana
watermelon'''
l = text_line_parser(text)
l.remove_empties()
l.strip()
self.assertEqual( [ 'kiwi', 'orange', 'apricot' ], l.cut_lines('^ap.*$', '^ba.*$').to_string_list() )
self.assertEqual( [ 'banana', 'watermelon' ], l.cut_lines('^apr.*$', None).to_string_list() )
self.assertEqual( [ 'apple', 'kiwi' ], l.cut_lines(None, '^or.*$').to_string_list() )
def test_remove_empties(self):
text = '''
foo
bar
baz
'''
l = text_line_parser(text)
l.remove_empties()
self.assertEqual( [ 'foo', 'bar', 'baz' ], l.to_string_list(strip_text = True) )
def instructions(self, env):
buf = StringIO()
buf.write('#!/bin/bash\n')
buf.write('echo "----1----"\n')
buf.write('declare -px\n')
buf.write('echo "----2----"\n')
for f in self.files_abs:
buf.write('source \"%s\"\n' % (f))
buf.write('echo "----3----"\n')
buf.write('declare -px\n')
buf.write('echo "----4----"\n')
script = temp_file.make_temp_file(content=buf.getvalue(),
delete=not self._debug)
if self._debug:
sys.stdout.write('env_dir: script=%s\n' % (script))
sys.stdout.flush()
os.chmod(script, 0o755)
try:
rv = execute.execute(script, raise_error=True, shell=True, env=env)
finally:
if not self._debug:
file_util.remove(script)
parser = text_line_parser(rv.stdout)
if self._debug:
sys.stdout.write('env_dir: stdout=%s\n' % (rv.stdout))
sys.stdout.write('env_dir: stderr=%s\n' % (rv.stderr))
sys.stdout.flush()
if rv.stderr:
raise RuntimeError(rv.stderr)
env1 = self._parse_env_lines(parser.cut_lines('----1----',
'----2----'))
env2 = self._parse_env_lines(parser.cut_lines('----3----',
'----4----'))
delta = self._env_delta(env1, env2)
instructions = []
for key in delta.added:
instructions.append(instruction(key, env2[key], action.SET))
for key in delta.removed:
instructions.append(instruction(key, None, action.UNSET))
for key in delta.changed:
value1 = env1[key]
value2 = env2[key]
for inst in self._determine_change_instructions(
key, value1, value2):
instructions.append(inst)
return sorted(instructions, key=lambda x: (x.key, x.value))
def test_match_first_with_line_number(self):
text = '''\
apple1
kiwi
apple2
strawberry
banana
kiwi2
'''
l = text_line_parser(text)
self.assertEqual( 1, l.match_first([ '^apple.*$' ]).line.line_number )
self.assertEqual( 'apple1', l.match_first([ '^apple.*$' ]).line.text )
self.assertEqual( 3, l.match_first([ '^apple.*$' ], line_number = 2).line.line_number )
self.assertEqual( 'apple2', l.match_first([ '^apple.*$' ], line_number = 2).line.text )