def testModuleDerivationPass(self):
# missing exec in derived is okay
text = text0 + '''
base: R(base=1)
x: 2
$out: x
simulate(base):
x: R(1:5)
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['command'], 'base=1')
text = text0 + '''
base: R(base=1)
x: 2
$out: x
simulate(base): R(base=2)
x: R(1:5)
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['command'], 'base=2')
# Derive from one of compact modules
text = text0 + '''
normal, t: R(), R()
n: 1000
@normal:
y: 5
n: 6
$x: x
simulate(normal):
mu: 1
'''
res = DSC_Script(text)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('n', [6]), ('y', [5]), ('mu', [1])])
def testFilterPass(self):
text = text0 + '''
simulate, t: R(), R()
n: 100, 200, 300, 400, 500
k: 0, 1
@FILTER:
simulate: (n <= 300 and k = 0) or (n > 300 and k = 1)
t: n = 500
$x: x
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['input_filter'], '(_n <= 300 and _k == 0) or (_n > 300 and _k == 1)')
text = text0 + '''
simulate, t: R(), R()
n: 100, 200, 300, 400, 500
k: 0, 1
@FILTER: (n in [100,200,300] and k = 0)
$x: x
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['input_filter'], '(_n in (100,200,300) and _k == 0)')
text = text0 + '''
simulate, t: R(), R()
n: 100, 200, 300, 400, 500
k: 0, 1
@FILTER:
*: n in [100,200,300]
t: n = 300
$x: x
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['input_filter'], '(_n in (100,200,300))')
def testBasicSyntaxPass(self):
'''basic syntax parser success'''
# exec decoration
res = DSC_Script(text3)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
# alias for specific module, both syntax supported
res = DSC_Script(text6)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
self.assertEqual(list(res.modules['simulate'].plugin.alias_map.items()), [('x', 'x_1')])
res = DSC_Script(text7)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
self.assertEqual(list(res.modules['simulate'].plugin.alias_map.items()), [('x', 'x_1')])
res = DSC_Script(text8)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [1]), ('y', [2])])
self.assertEqual(list(res.modules['simulate'].plugin.alias_map.items()), [('x', 'x_1')])
# use global variable
res = DSC_Script(text11)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [2]), ('y', [2])])
res = DSC_Script(text12)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('x', [4,3,2,1]), ('y', [2])])
# alias partial list / dict
res = DSC_Script(text13)
self.assertEqual(list(res.modules['simulate'].plugin.dump()['container_variables'].items()), [('x', [None, 'xvar']), ('y', [None, 'yy'])])
# filter decorator
res = DSC_Script(text14)
self.assertEqual(res.modules['simulate'].dump()['input_filter'], '(_x < 3)')
def testQuotedKeywords(self):
text = text0 + '''
simulate: R()
K: TRUE, FALSE, NULL
$out: K
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['input']['K'], ['TRUE', 'FALSE', 'NULL'])
text = text0 + '''
simulate: Python()
K: 'TRUE', 'FALSE', 'NULL'
$out: K
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['input']['K'], ["'TRUE'", "'FALSE'", "'NULL'"])
def testConfOperatorPass(self):
text = text0 + '''
simulate: R()
$x: x
@CONF: work_dir = /tmp, exec_path = /tmp
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].path, ['/tmp'])
text = text0 + '''
simulate: R()
$x: x
@CONF: work_dir = /tmp, exec_path = (/tmp, ~/tmp), lib_path = ./, R_libs = (ashr@stephenslab/ashr (>=2.2.7), psych)
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].path, ['/tmp', '~/tmp'])
self.assertEqual(res.modules['simulate'].exe['header'], 'library(ashr)\nlibrary(psych)')
def testFileOperatorPass(self):
# file() operator
text = text0 + '''
simulate: R()
data: file(.txt)
$out: n
'''
res = DSC_Script(text)
self.assertEqual(res.modules['simulate'].dump()['plugin_status']['temp_file'], ['data <- paste0(${_output[0]:nr}, ".data.txt")'])
def testParenthesisOperatorPass(self):
# () operator
# FIXME: likely wrong here?
text = text0 + '''
simulate: R()
(n,p): (1,2), (5,6)
$x: x
'''
res = DSC_Script(text)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('n', [1, 5]), ('p', [2, 6])])
# R{} operator
text = text0 + '''
simulate: R()
(n,p): R{list(c(1,2), c(5,6))}
$x: x
'''
res = DSC_Script(text)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('n', [1, 5]), ('p', [2, 6])])
def testModuleVariablesPass(self):
# module input and output can have same name
text = text0 + '''
simulate: R()
n: $n
$n: n
'''
res = DSC_Script(text)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('n', ['$n'])])
self.assertEqual(res.modules['simulate'].dump()['output_variables'], {'n':'n'})
def testGroupedParametersPass(self):
# grouped parameters
text = text0 + '''
simulate: R()
(n,p): (1,2), (5,6)
a,b: (3,4)
t: 5
$x: x
'''
res = DSC_Script(text)
self.assertEqual(list(res.modules['simulate'].dump()['input'].items()), [('n', [1, 5]), ('p', [2, 6]), ('a', [3]), ('b', [4]), ('t', [5])])