def create(outdir, tc):
grammar = tc.grammar
c = adpc.Config
os.chdir(c.workdir)
shutil.copy(os.path.join(c.grammars, grammar), c.workdir)
os.mkdir(grammar[:-4])
out = tc.unique_filename() + Suffix.mf + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.mf + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.fe,
[ grammar, '-p', c.fe_path, '--pure-prefix' ],
f1, f2)
if i != 0:
raise cg.CallError('Metafrontend failed'
+ testbox.look_into([f1, f2]))
out = tc.unique_filename() + Suffix.java + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.java + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.javac,
[ '-cp', c.classpath,
grammar[:-4] + os.path.sep + grammar[:-4] + '.java' ],
f1, f2)
if i != 0:
raise cg.CallError('Java Compiler failed'
+ testbox.look_into([f1, f2]))
def extract(filename, algebra):
pat_score = re.compile('^Optimal Score: ([-.0-9]+)')
pat_algebra = re.compile('^Algebra: ([A-Za-z0-9]+)')
pat_end = re.compile('^================================================================================')
pat_begin = re.compile('^============================== Suboptimal Output ===============================')
pat_cand = re.compile('^(.+) \(Score: ([-.0-9]+)\)')
d = cg.Data()
f = open(filename)
look = testbox.look_into([filename])
state = -1
length = -1
last_len = -1
for i in f:
if state == -1:
match = pat_algebra.search(i)
if match:
if algebra == 'count' and match.group(1) == algebra:
d.algebra = 'count'
state = 0
elif match.group(1) == 'count':
pass
elif algebra == '' or match.group(1) == algebra:
d.algebra = match.group(1)
state = 0
elif state == 0:
match = pat_score.search(i)
if match:
state = 1
d.setScore(match.group(1))
elif state == 1:
match = pat_begin.search(i)
if match:
state = 2
elif state == 2:
match = pat_end.search(i)
if match:
state = 3
break
match = pat_cand.search(i)
if match:
if length == -1:
length = last_len
elif StdTranslate.test_length and length != len(match.group(1)):
raise cg.TranslateError('Candidate structure deviates:\n'
+ ' ' + match.group(1) + ' (len: ' + str(len(match.group(1)))
+ ') vs. len: ' + str(length) + look)
d.addCandidate( (match.group(2), match.group(1)) )
last_len = len(match.group(1))
f.close()
if state == -1:
raise cg.TranslateError('Algebra ' + algebra + ' not found.' + look)
elif state != 3:
raise cg.TranslateError('Missing begin and/or end.' + look)
if len(d.candidates) == 0 and algebra != 'count':
raise cg.TranslateError('Empty candidate list for algebra ' + algebra
+ '.' + look)
f.close()
return d
def execute(outdir, progname, filename, tc, sys_fn = sysext.sys):
c = adpc.Config
os.chdir(c.workdir)
para = []
if tc.flavour == 'rna' or tc.flavour == 'window':
para += Call.default_opts_rna
else:
para += Call.default_opts
if hasattr(tc, 'parameter'):
para += tc.parameter.split()
out = tc.unique_filename() + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sys_fn(c.java,
[ '-cp', c.classpath,
progname + '.' + progname, "-f", os.path.join(c.input, filename)]
+ tc.default_parameter + para,
f1, f2)
if i != 0:
raise cg.CallError("error executing adp program (exit status: " + str(i) + ")"
+ testbox.look_into([f1, f2]))
def clean(outdir, tc):
c = adpc.Config
os.chdir(c.workdir)
out = tc.unique_filename() + Suffix.clean + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.clean + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.make, ["clean"], f1, f2)
if i != 0:
raise cg.CallError("make clean failed" + testbox.look_into([f1, f2]))
os.unlink(tc.grammar)
ls = os.listdir(c.workdir)
if not (ls == [] or ls == ['.svn'] or ls == ['.hg']):
raise cg.CallError("make clean doesn't clean everything"
+ testbox.look_into([c.workdir]))
def clean(outdir, tc):
grammar = tc.grammar
c = adpc.Config
os.chdir(c.workdir)
for i in os.listdir(grammar[:-4]):
os.unlink(grammar[:-4] + os.path.sep + i)
os.rmdir(grammar[:-4])
os.unlink(grammar)
ls = os.listdir(c.workdir)
if not (ls == [] or ls == ['.svn'] or ls == ['.hg']):
raise cg.CallError("not everything is clean" +
testbox.look_into([c.workdir]))
def extract(filename, algebra):
pat_score = re.compile('^Algebra: ([A-Za-z0-9]+), score: ([-.0-9]+)')
pat_end = re.compile(
'^================================================================='
)
pat_begin = re.compile(
'^-----------------------------------------------------------------'
)
pat_cand = re.compile('^[ \t]+([-0-9.]+) \| (.+)$')
d = cg.Data()
f = open(filename)
state = 0
for i in f:
if state == 0:
match = pat_score.search(i)
if match:
if algebra == 'count' and match.group(1) == algebra:
d.setScore(match.group(2))
d.algebra = 'count'
state = 2
elif match.group(1) == 'count':
pass
elif algebra == '' or match.group(1) == algebra:
state = 1
d.algebra = match.group(1)
d.setScore(match.group(2))
elif state == 1:
match = pat_begin.search(i)
if match:
state = 2
elif state == 2:
match = pat_end.search(i)
if match:
state = 3
break
match = pat_cand.search(i)
if match:
d.addCandidate(match.groups())
f.close()
look = testbox.look_into([filename])
if state == 0:
raise cg.TranslateError('Algebra ' + algebra + ' not found.' +
look)
elif state != 3:
raise cg.TranslateError('Missing begin and/or end.' + look)
if len(d.candidates) == 0 and algebra != 'count':
raise cg.TranslateError('Empty candidate list.' + look)
f.close()
return d
def design(self, dest):
os.chdir(self.config.cwd)
out = self.unique_filename() + Suffix.out
testbox.checkFilename(out)
err = self.unique_filename() + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(dest, out)
f2 = os.path.join(dest, err)
i = sysext.sys(self.config.hand,
self.hand_opts + [ os.path.join(self.config.state,
self.grammar + Suffix.i + Suffix.out) ],
f1, f2)
self.failIf(i != 0, "Couldn't generate hand output"
+ testbox.look_into([f1, f2]))
def serialize(self, out_dir):
c = self.config
os.chdir(c.grammars)
out = self.grammar + Suffix.i + Suffix.out
testbox.checkFilename(out)
err = self.grammar + Suffix.i + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(out_dir, out)
f2 = os.path.join(out_dir, err)
i = sysext.sys(c.adpcompile,
['-iuc', '-te', os.path.join(c.grammars, self.grammar) ], f1, f2)
self.failIf(i != 0, "Couldn't create serialized output."
+ testbox.look_into([f1, f2]))
return i
def _create_b(outdir, tc):
c = adpc.Config
out = tc.unique_filename() + Suffix.make + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.make + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.make, ["BINPATH=" + c.binpath,
"ADPCOMPILE=" + c.adpcompile,
"ADPC=" + c.adpc_bin + " " + c.binpath],
f1, f2)
if i != 0:
raise cg.CallError('making adp program failed' +
testbox.look_into([f1, f2]))
def _create_a(outdir, tc):
c = adpc.Config
os.chdir(c.workdir)
shutil.copy(os.path.join(c.grammars, tc.grammar), c.workdir)
out = tc.unique_filename() + Suffix.adp + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.adp + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.adpc_bin, [c.binpath, tc.grammar],
f1, f2)
if i != 0:
raise cg.CallError('generating c src from adp program failed'
+ testbox.look_into([f1, f2]))
def serialize(self, out_dir):
c = self.config
os.chdir(c.grammars)
out = self.grammar + Suffix.i + Suffix.out
testbox.checkFilename(out)
err = self.grammar + Suffix.i + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(out_dir, out)
f2 = os.path.join(out_dir, err)
i = sysext.sys(c.adpcompile,
['-iuc', '-te',
os.path.join(c.grammars, self.grammar)], f1, f2)
self.failIf(
i != 0,
"Couldn't create serialized output." + testbox.look_into([f1, f2]))
return i
def test(self):
filename_out = self.unique_filename() + Suffix.out
self.call(self.config.output)
a = self.unpickle()
f1 = self.config.state + os.path.sep + filename_out
# uncomment this to debug the Translators
#a = self.extract(f1)
f2 = os.path.join(self.config.output, filename_out)
b = self.extract(f2)
try:
a.compare(b)
except cg.DataError, (message):
self.fail(
'Different program output:\n' + str(message) +
testbox.look_into([f1, f2]) +
'\nor into the corresponding default language state-file\n')
def testSerialize(self):
"""serialized output from adpc"""
i = self.serialize(self.config.output)
suff = self.grammar + Suffix.i + Suffix.out
f1 = os.path.join(self.config.state, suff)
f2 = os.path.join(self.config.output, suff)
f = open(f1)
g = open(f2)
l1 = f.readline().split(';')
l2 = g.readline().split(';')
f.close()
g.close()
look = testbox.look_into([f1, f2])
self.failIf(len(l1) != len(l2),
"Length of serialized array is different" + look)
self.failIf(l1 != l2, "Serialized arrays are not equal" + look)
def extract(filename, algebra):
pat_score = re.compile('^Algebra: ([A-Za-z0-9]+), score: ([-.0-9]+)')
pat_end = re.compile('^=================================================================')
pat_begin = re.compile('^-----------------------------------------------------------------')
pat_cand = re.compile('^[ \t]+([-0-9.]+) \| (.+)$')
d = cg.Data()
f = open(filename)
state = 0
for i in f:
if state == 0:
match = pat_score.search(i)
if match:
if algebra == 'count' and match.group(1) == algebra:
d.setScore(match.group(2))
d.algebra = 'count'
state = 2
elif match.group(1) == 'count':
pass
elif algebra == '' or match.group(1) == algebra:
state = 1
d.algebra = match.group(1)
d.setScore(match.group(2))
elif state == 1:
match = pat_begin.search(i)
if match:
state = 2
elif state == 2:
match = pat_end.search(i)
if match:
state = 3
break
match = pat_cand.search(i)
if match:
d.addCandidate(match.groups())
f.close()
look = testbox.look_into([filename])
if state == 0:
raise cg.TranslateError('Algebra ' + algebra + ' not found.' + look)
elif state != 3:
raise cg.TranslateError('Missing begin and/or end.' + look)
if len(d.candidates) == 0 and algebra != 'count':
raise cg.TranslateError('Empty candidate list.' + look)
f.close()
return d
def testSerialize(self):
"""serialized output from adpc"""
i = self.serialize(self.config.output)
suff = self.grammar + Suffix.i + Suffix.out
f1 = os.path.join(self.config.state, suff)
f2 = os.path.join(self.config.output, suff)
f = open(f1)
g = open(f2)
l1 = f.readline().split(';')
l2 = g.readline().split(';')
f.close()
g.close()
look = testbox.look_into([f1, f2])
self.failIf(
len(l1) != len(l2),
"Length of serialized array is different" + look)
self.failIf(l1 != l2, "Serialized arrays are not equal" + look)
def extract(filename, algebra):
pat_bounds = re.compile('^([0-9]+) +([0-9]+)')
pat_cand = re.compile('^([.()\\[\\]]+) \(([-.0-9]+)\)')
f = open(filename)
look = testbox.look_into([filename])
d = cg.WindowData()
e = cg.Data()
bounds = None
for i in f:
match = pat_bounds.search(i)
if match:
e.optimal_score = Equal()
e.algebra = algebra
d.addWindow(bounds, e)
e = cg.Data()
g = match.groups()
bounds = (int(g[0]), int(g[1]))
length = len(i) - 1
else:
match = pat_cand.search(i)
if match:
g = match.groups()
if len(g[0]) != length:
raise cg.TranslateError(
'Length of candidate structure does not match in window '
+ str(bounds) + ':\n"' + ' ' + g[0] + ' (len: ' +
str(len(g[0])) + ') vs len: ' + str(length) + look)
e.addCandidate((g[1], g[0]))
else:
if len(i) - 1 != length:
raise cg.TranslateError(
'Length of sequence does not match in window ' +
str(bounds) + ':\n' + ' ' + i + ' (len: ' +
str(len(i) - 1) + ') vs. len: ' + str(length) +
look)
f.close()
e.optimal_score = Equal()
e.algebra = algebra
d.addWindow(bounds, e)
d.windows.pop(0)
return d
def extract(filename, algebra):
pat_bounds = re.compile('^([0-9]+) +([0-9]+)')
pat_cand = re.compile('^([.()\\[\\]]+) \(([-.0-9]+)\)')
f = open(filename)
look = testbox.look_into([filename])
d = cg.WindowData()
e = cg.Data()
bounds = None
for i in f:
match = pat_bounds.search(i)
if match:
e.optimal_score = Equal()
e.algebra = algebra
d.addWindow(bounds, e)
e = cg.Data()
g = match.groups()
bounds = (int(g[0]), int(g[1]))
length = len(i) - 1
else:
match = pat_cand.search(i)
if match:
g = match.groups()
if len(g[0]) != length:
raise cg.TranslateError('Length of candidate structure does not match in window ' + str(bounds) + ':\n"'
+ ' ' + g[0] + ' (len: ' + str(len(g[0])) + ') vs len: '
+ str(length) + look)
e.addCandidate((g[1], g[0]))
else:
if len(i) - 1 != length:
raise cg.TranslateError('Length of sequence does not match in window ' + str(bounds) + ':\n'
+ ' ' + i + ' (len: ' + str(len(i)-1) + ') vs. len: '
+ str(length) + look)
f.close()
e.optimal_score = Equal()
e.algebra = algebra
d.addWindow(bounds, e)
d.windows.pop(0)
return d
def execute(outdir, progname, filename, tc, sys_fn = sysext.sys):
c = adpc.Config
os.chdir(c.workdir)
if hasattr(tc, 'parameter'):
para = tc.parameter.split()
else:
para = []
out = tc.unique_filename() + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.err
testbox.checkFilename(err)
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sys_fn('./' + progname,
[ "-f", c.input + os.path.sep + filename] + para,
f1, f2)
if i != 0:
raise cg.CallError("error executing adp program (exit status: " + str(i) + ")"
+ testbox.look_into([f1, f2]))
def extract(filename, algebra):
pat_score = re.compile('^([A-Za-z0-9]+): ([-.0-9]+)')
pat_cand = re.compile('^([.()\\[\\]]+) \(([-.0-9]+)\)')
look = testbox.look_into([filename])
d = cg.Data()
f = open(filename)
state = 0
length = -1
last_len = -1
for i in f:
if state == 0:
match = pat_score.search(i)
if match:
state = 1
d.algebra = match.group(1)
d.setScore(match.group(2))
elif state == 1:
match = pat_cand.search(i)
if match:
if length == -1:
length = last_len
d.addCandidate((match.group(2), match.group(1)))
if length != -1 and length != len(match.group(1)):
raise cg.TranslateError(
'Candidate structure length deviates:\n' + ' ' +
match.group(1) + ' (len: ' +
str(len(match.group(1))) + ') vs. len: ' +
str(length) + look)
last_len = len(match.group(1))
f.close()
if state == 0:
raise cg.TranslateError('Found no algebra at all.' + look)
if len(d.candidates) == 0 and algebra != 'count':
raise cg.TranslateError('Empty candidate list.' + look)
f.close()
return d
def extract(filename, algebra):
pat_score = re.compile('^([A-Za-z0-9]+): ([-.0-9]+)')
pat_cand = re.compile('^([.()\\[\\]]+) \(([-.0-9]+)\)')
look = testbox.look_into([filename])
d = cg.Data()
f = open(filename)
state = 0
length = -1
last_len = -1
for i in f:
if state == 0:
match = pat_score.search(i)
if match:
state = 1
d.algebra = match.group(1)
d.setScore(match.group(2))
elif state == 1:
match = pat_cand.search(i)
if match:
if length == -1:
length = last_len
d.addCandidate( (match.group(2), match.group(1)) )
if length != -1 and length != len(match.group(1)):
raise cg.TranslateError('Candidate structure length deviates:\n'
+ ' ' + match.group(1) + ' (len: ' + str(len(match.group(1)))
+ ') vs. len: ' + str(length) + look)
last_len = len(match.group(1))
f.close()
if state == 0:
raise cg.TranslateError('Found no algebra at all.' + look)
if len(d.candidates) == 0 and algebra != 'count':
raise cg.TranslateError('Empty candidate list.' + look)
f.close()
return d
def create(outdir, tc):
grammar = tc.grammar
c = adpc.Config
Call._create_a(outdir, tc)
out = tc.unique_filename() + Suffix.make + 'tup.' + Suffix.out
testbox.checkFilename(out)
err = tc.unique_filename() + Suffix.make + 'tup.' + Suffix.err
f1 = os.path.join(outdir, out)
f2 = os.path.join(outdir, err)
i = sysext.sys(c.make, ["BINPATH=" + c.binpath,
"ADPCOMPILE=" + c.adpcompile,
"ADPC=" + c.adpc_bin + " " + c.binpath,
grammar[:-4] + '.c'], f1, f2)
if i != 0:
raise cg.CallError('making tupel step failed'
+ testbox.look_into([f1, f2]))
sed_file = grammar[:-4] + '_' + CallTuple.algebra + '.sed'
tmp = sed_file + '.tmp'
pat = re.compile('result_score')
pat_head = re.compile('int maxloop;\\\\')
shutil.move(sed_file, tmp)
f = open(tmp)
g = open(sed_file, 'w')
for i in f:
if pat.search(i):
j = pat.sub('result_score.tup1', i)
elif pat_head.match(i):
j = i
g.write('#undef is_suboptimal\\\n#define is_suboptimal(a, b, c) abs(a.tup1 - b) <= c\\\n')
else:
j = i
g.write(j)
f.close()
g.close()
os.unlink(tmp)
Call._create_b(outdir, tc)
def extract(filename, algebra):
pat_score = re.compile('^Optimal Score: ([-.0-9]+)')
pat_algebra = re.compile('^Algebra: ([A-Za-z0-9]+)')
pat_end = re.compile(
'^================================================================================'
)
pat_begin = re.compile(
'^============================== Suboptimal Output ==============================='
)
pat_cand = re.compile('^(.+) \(Score: ([-.0-9]+)\)')
pat_bounds = re.compile('^([0-9]+) +([0-9]+)')
f = open(filename)
look = testbox.look_into([filename])
d = cg.WindowData()
bounds = None
length = -1
state = -1
for i in f:
if state == -1:
match = pat_algebra.search(i)
if match:
if algebra == '' or algebra == match.group(1):
al = algebra
else:
raise cg.TranslateError(
'Wrong algebra in window mode: ' + algebra +
' vs. ' + match.group(1) + look)
state = 0
elif state == 0:
match = pat_score.search(i)
if match:
e = cg.Data()
e.algebra = al
e.optimal_score = float(match.group(1)) / 100
state = 1
continue
else:
match = pat_bounds.search(i)
if match:
bounds = (int(match.group(1)), int(match.group(2)))
if length < 0:
length = len(i) - 1
elif len(i) - 1 != length:
raise cg.TranslateError(
'Length of sequence/bounds differs in window ' +
str(bounds) + ':\n' + ' ' + i + ' (len: ' +
str(len(i) - 1) + ' vs. len: ' + str(length) + look)
elif state == 1:
match = pat_begin.search(i)
if match:
state = 2
else:
raise cg.TranslateError('Found no start in window ' +
str(bounds) + '.' + look)
elif state == 2:
match = pat_cand.search(i)
if match:
(cand, score) = match.groups()
if len(cand) != length:
raise cg.TranslateError(
'Length of candidate structures does not match in window '
+ str(bounds) + ':\n' + cand + ' (len: ' +
str(len(cand)) + ') vs. len: ' + str(length) +
look)
e.candidates.append((float(score) / 100, cand))
else:
match = pat_end.search(i)
d.addWindow(bounds, e)
if match:
state = 0
else:
raise cg.TranslateError(
'Found no end or candidate in window ' +
str(bounds) + '.' + look)
f.close()
if state != 0:
raise cg.TranslateError('Found no end at the end.' + look)
return d
def extract(filename, algebra):
pat_score = re.compile('^Optimal Score: ([-.0-9]+)')
pat_algebra = re.compile('^Algebra: ([A-Za-z0-9]+)')
pat_end = re.compile('^================================================================================')
pat_begin = re.compile('^============================== Suboptimal Output ===============================')
pat_cand = re.compile('^(.+) \(Score: ([-.0-9]+)\)')
pat_bounds = re.compile('^([0-9]+) +([0-9]+)')
f = open(filename)
look = testbox.look_into([filename])
d = cg.WindowData()
bounds = None
length = -1
state = -1
for i in f:
if state == -1:
match = pat_algebra.search(i)
if match:
if algebra == '' or algebra == match.group(1):
al = algebra
else:
raise cg.TranslateError('Wrong algebra in window mode: ' + algebra
+ ' vs. ' + match.group(1) + look)
state = 0
elif state == 0:
match = pat_score.search(i)
if match:
e = cg.Data()
e.algebra = al
e.optimal_score = float(match.group(1)) / 100
state = 1
continue
else:
match = pat_bounds.search(i)
if match:
bounds = ( int(match.group(1)), int(match.group(2)) )
if length < 0:
length = len(i) - 1
elif len(i) - 1 != length:
raise cg.TranslateError('Length of sequence/bounds differs in window '
+ str(bounds) + ':\n'
+ ' ' + i + ' (len: ' + str(len(i) - 1) + ' vs. len: '
+ str(length) + look)
elif state == 1:
match = pat_begin.search(i)
if match:
state = 2
else:
raise cg.TranslateError('Found no start in window '
+ str(bounds) + '.' + look)
elif state == 2:
match = pat_cand.search(i)
if match:
(cand, score) = match.groups()
if len(cand) != length:
raise cg.TranslateError('Length of candidate structures does not match in window '
+ str(bounds) + ':\n'
+ cand + ' (len: ' + str(len(cand)) + ') vs. len: '
+ str(length) + look)
e.candidates.append((float(score) / 100, cand))
else:
match = pat_end.search(i)
d.addWindow(bounds, e)
if match:
state = 0
else:
raise cg.TranslateError('Found no end or candidate in window '
+ str(bounds) + '.' + look)
f.close()
if state != 0:
raise cg.TranslateError('Found no end at the end.' + look)
return d
