def test_sections(self):
sy=superyaml(domain=os.getcwd())
d_sy=sy.load('sections.syml',{'these':'some other'})
self.assertEqual(d_sy['these'],'some other')
self.assertEqual(d_sy['this_color'],'red', 'this_color=red: got %s' % d_sy['this_color'])
self.assertEqual(type(d_sy['section1']['flintstones']), type([]), "got a list for section1->flintstones")
self.assertEqual(d_sy['section1']['flintstones'][0], 'fred', 'section1=fred: got %s' % d_sy['section1']['flintstones'][0])
def test_basic(self):
sy=superyaml(domain=os.getcwd())
d={'this':'that', 'these':'those'}
d_sy=sy.load('basic.syml',d)
self.assertEqual(d['this'],'that')
self.assertEqual(d['these'],'those')
def test_bowtie(self):
sy = superyaml(domain="/proj/hoodlab/share/vcassen/rna-seq/rnaseq/templates")
d_sy = sy.load("bowtie.syml", {})
warn(yaml.dump(d_sy))
d_sy = sy.load("bowtie.syml", d_sy)
warn(yaml.dump(d_sy))
self.assertEquals(d_sy["exe"], "bowtie", 'got d[exe]=%s, expected "bowtie"' % d_sy["exe"])
def test_composite(self):
sy=superyaml(domain='/proj/hoodlab/share/vcassen/rna-seq/rnaseq/templates')
readset=sy.load('readset.syml',{})
bowtie=sy.load('bowtie.syml',readset)
warn("bowtie 1",yaml.dump(bowtie))
self.assertEquals(bowtie['exe'],'bowtie','got d[exe]=%s, expected "bowtie"' % bowtie['exe'])
bowtie.update(readset)
bowtie=sy.load('bowtie.syml',bowtie)
warn("bowtie 2",yaml.dump(bowtie))
expected=("%(exe)s %(ewbt)s %(args)s" % hashslice(bowtie,'exe','ewbt','args')) + " ${input} ${output}"
warn("expected is %s" % expected)
self.assertEquals(bowtie['usage'], expected,
'got bowtie[usage]=%s, expected %s' % (bowtie['usage'], expected))
from superyaml import *
import yaml
sy=superyaml({'config_file': 'linear.yml',
})
sy.load()
print "sy.config is %s" % yaml.dump(sy.config)
from superyaml import *
import yaml
sy=superyaml({'config_file': 'cyclic.yml',
})
sy.load() # should throw an exception
print "sy is %s" % yaml.dump(sy)
def test_internal_substitution(self):
sy=superyaml(domain=os.getcwd())
d_sy=sy.load('internal_substitution.syml',{'these':'some other'})
self.assertEqual(d_sy['these'],'some other')
self.assertEqual(d_sy['this_color'],'red', 'this_color=red: got %s' % d_sy['this_color'])
def test_basic_substitution(self):
sy=superyaml(domain=os.getcwd())
d_sy=sy.load('basic_substitution.syml',{'these':'some other'})
self.assertEqual(d_sy['these'],'some other')
from superyaml import *
import yaml
sy=superyaml({'config_file': 'repeat.syml',
})
sy.load() # should throw an exception
print "sy.config is %s" % yaml.dump(sy.config)
from superyaml import *
import yaml
sy=superyaml({'config_file': 'simple.yml',
})
sy.load()
print "sy.config is %s" % yaml.dump(sy.config)