Exemple #1
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 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])
Exemple #2
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 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')
Exemple #3
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    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"])
Exemple #4
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    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)



Exemple #7
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 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'])
Exemple #8
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 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)