def add_group(self,hcur,cur,k,v):
cur[k] = HDFgroup()
cur._add_group(k,cur[k])
cur._groups[k]._parent = cur
self.increment_level()
self.cur[self.ilevel] = cur._groups[k]
self.hcur[self.ilevel] = hcur[k]
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr,v in hcur.iteritems():
k=cur._escape_name(kr)
if valid_variable_name(k):
vtype = str(type(v))
if vtype in HDFreader.datasets:
self.add_dataset(cur,k,v)
elif vtype in HDFreader.groups:
self.add_group(hcur,cur,k,v)
#end if
else:
print 'hdfreader warning: attribute '+k+' is not a valid variable name and has been ignored'
#end if
#end for
return
def add_group(self, hcur, cur, k, v):
cur[k] = HDFgroup()
cur._add_group(k, cur[k])
cur._groups[k]._parent = cur
self.increment_level()
self.cur[self.ilevel] = cur._groups[k]
self.hcur[self.ilevel] = hcur[k]
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr, v in hcur.iteritems():
k = cur._escape_name(kr)
if valid_variable_name(k):
vtype = str(type(v))
if vtype in HDFreader.datasets:
self.add_dataset(cur, k, v)
elif vtype in HDFreader.groups:
self.add_group(hcur, cur, k, v)
#end if
else:
print 'hdfreader warning: attribute ' + k + ' is not a valid variable name and has been ignored'
#end if
#end for
return
def add_group(self, hcur, cur, k, v):
cur[k] = HDFgroup()
cur._add_group(k, cur[k])
cur._groups[k]._parent = cur
self.increment_level()
self.cur[self.ilevel] = cur._groups[k]
self.hcur[self.ilevel] = hcur[k]
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr, v in hcur.items():
k = cur._escape_name(kr)
if valid_variable_name(k):
if isinstance(v, h5py.Dataset):
self.add_dataset(cur, k, v)
elif isinstance(v, h5py.Group):
self.add_group(hcur, cur, k, v)
#end if
else:
self.warn('attribute ' + k +
' is not a valid variable name and has been ignored')
#end if
#end for
return
def __init__(self, fpath, verbose=False, view=False):
HDFglobals.view = view
if verbose:
print(' Initializing HDFreader')
#end if
self.fpath = fpath
if verbose:
print(' loading h5 file')
#end if
try:
self.hdf = h5py.File(fpath, 'r')
except IOError:
self._success = False
self.hdf = obj(obj=obj())
else:
self._success = True
#end if
if verbose:
print(' converting h5 file to dynamic object')
#end if
#convert the hdf 'dict' into a dynamic object
self.nlevels = 1
self.ilevel = 0
# Set the current hdf group
self.obj = HDFgroup()
self.cur = [self.obj]
self.hcur = [self.hdf]
if self._success:
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr, v in hcur.items():
k = cur._escape_name(kr)
if valid_variable_name(k):
if isinstance(v, h5py.Dataset):
self.add_dataset(cur, k, v)
elif isinstance(v, h5py.Group):
self.add_group(hcur, cur, k, v)
else:
self.error('encountered invalid type: ' + str(type(v)))
else:
self.warn(
'attribute ' + k +
' is not a valid variable name and has been ignored')
#end if
#end for
#end if
if verbose:
print(' end HDFreader Initialization')
#end if
return
def __init__(self,fpath,verbose=False,view=False):
HDFglobals.view = view
if verbose:
print ' Initializing HDFreader'
self.fpath=fpath
if verbose:
print ' loading h5 file'
try:
self.hdf = h5py.File(fpath,'r')
except IOError:
self._success = False
self.hdf = obj(obj=obj())
else:
self._success = True
#end if
if verbose:
print ' converting h5 file to dynamic object'
#convert the hdf 'dict' into a dynamic object
self.nlevels=1
self.ilevel=0
# Set the current hdf group
self.obj = HDFgroup()
self.cur=[self.obj]
self.hcur=[self.hdf]
if self._success:
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr,v in hcur.iteritems():
k=cur._escape_name(kr)
if valid_variable_name(k):
vtype = str(type(v))
if vtype in HDFreader.datasets:
self.add_dataset(cur,k,v)
elif vtype in HDFreader.groups:
self.add_group(hcur,cur,k,v)
else:
print 'hdfreader error: encountered invalid type: '+vtype
sys.exit()
#end if
else:
print 'hdfreader warning: attribute '+k+' is not a valid variable name and has been ignored'
#end if
#end for
#end if
if verbose:
print ' end HDFreader Initialization'
return
def __init__(self, fpath, verbose=False, view=False):
HDFglobals.view = view
if verbose:
print ' Initializing HDFreader'
self.fpath = fpath
if verbose:
print ' loading h5 file'
try:
self.hdf = h5py.File(fpath, 'r')
except IOError:
self._success = False
self.hdf = obj(obj=obj())
else:
self._success = True
#end if
if verbose:
print ' converting h5 file to dynamic object'
#convert the hdf 'dict' into a dynamic object
self.nlevels = 1
self.ilevel = 0
# Set the current hdf group
self.obj = HDFgroup()
self.cur = [self.obj]
self.hcur = [self.hdf]
if self._success:
cur = self.cur[self.ilevel]
hcur = self.hcur[self.ilevel]
for kr, v in hcur.iteritems():
k = cur._escape_name(kr)
if valid_variable_name(k):
vtype = str(type(v))
if vtype in HDFreader.datasets:
self.add_dataset(cur, k, v)
elif vtype in HDFreader.groups:
self.add_group(hcur, cur, k, v)
else:
print 'hdfreader error: encountered invalid type: ' + vtype
sys.exit()
#end if
else:
print 'hdfreader warning: attribute ' + k + ' is not a valid variable name and has been ignored'
#end if
#end for
#end if
if verbose:
print ' end HDFreader Initialization'
return
def found_element_start(self, ename, attributes):
cur = self.cur[self.ilevel]
if ename in self.element_aliases.keys():
if self.element_aliases[ename].find('attributes') != -1:
self.error('an alternative to exec is needed')
#exec('name = '+self.element_aliases[ename])
else:
name = self.element_aliases[ename]
#end if
else:
name = ename
#end if
#alter the name if it is a python keyword
name = cur._escape_name(name)
if self.contract_names:
name = name.lower().replace('-', '_')
#end if
if self.strip_prefix != None:
if name.startswith(self.strip_prefix):
name = name.split(self.strip_prefix)[1]
#end if
#end if
# joinable = in joins and no attributes
# if in elements and joinable: don't add
# else if not in elements and joinable: add unnumbered
# else if not in elements: add unnumbered
# else: add numbered, if number==1: rename first element
joinable = name in self.element_joins and len(list(
attributes.keys())) == 0
epattern = re.compile(name + '\d+')
in_elements = False
for k in cur._elements.keys():
if epattern.match(k) or k == name:
in_elements = True
#end if
#end for
#in_elements = name in cur._elements.keys()
if in_elements and joinable:
#check if there is a previous unjoinable element w/ same name
if len(cur._elements[name]._attributes) != 0:
#rename the prior element as a numbered one
nelements = cur._element_counts[name]
if nelements == 1:
#it should be the first one
newname = name + str(1)
cur[newname] = cur[name]
cur._add_element(newname, cur[newname])
del cur._elements[name]
del cur[name]
else:
self.error(
'prior unjoinable element is not the first\nthis should be impossible'
)
#end if
#add the joinable element as unnumbered
# later joinable elements will be joined to this one
cur[name] = XMLelement()
cur._add_element(name, cur[name])
#end if
elif not in_elements:
#add unnumbered
cur[name] = XMLelement()
cur._add_element(name, cur[name])
cur._element_counts[name] = 1
else:
#add in a numbered way
nelements = cur._element_counts[name]
if nelements == 1:
#rename the first element
newname = name + str(1)
cur[newname] = cur[name]
cur._add_element(newname, cur[newname])
del cur._elements[name]
del cur[name]
#end if
nelements += 1
newname = name + str(nelements)
cur[newname] = XMLelement()
cur._add_element(newname, cur[newname])
cur._element_counts[name] = nelements
name = newname
#end if
cur._elements[name]._parent = cur #mark change
self.increment_level()
self.cur[self.ilevel] = cur._elements[name]
cur = self.cur[self.ilevel]
for kraw, v in attributes.items():
if self.contract_names:
k = kraw.lower().replace('-', '_')
else:
k = kraw
#end if
if valid_variable_name(k):
kname = cur._escape_name(k)
cur[kname] = v
cur._add_xmlattribute(kname, cur[kname])
else:
if self.warn:
print('xmlreader warning: attribute ' + k +
' is not a valid variable name and has been ignored')
#end if
#end if
#end for
return
def found_element_start(self,ename,attributes):
#print self.pad,name,attributes
cur = self.cur[self.ilevel]
if ename in self.element_aliases.keys():
if self.element_aliases[ename].find('attributes')!=-1:
exec 'name = '+self.element_aliases[ename]
else:
name = self.element_aliases[ename]
#end if
else:
name=ename
#end if
#alter the name if it is a python keyword
name = cur._escape_name(name)
if self.contract_names:
name = name.lower().replace('-','_')
#end if
if self.strip_prefix!=None:
if name.startswith(self.strip_prefix):
name = name.split(self.strip_prefix)[1]
#end if
#end if
# joinable = in joins and no attributes
# if in elements and joinable: don't add
# else if not in elements and joinable: add unnumbered
# else if not in elements: add unnumbered
# else: add numbered, if number==1: rename first element
joinable = name in self.element_joins and len(attributes.keys())==0
epattern = re.compile(name+'\d+')
in_elements=False
for k in cur._elements.keys():
if epattern.match(k) or k==name:
in_elements=True
#end if
#end for
#in_elements = name in cur._elements.keys()
if in_elements and joinable:
#check if there is a previous unjoinable element w/ same name
if len(cur._elements[name]._attributes)!=0:
#rename the prior element as a numbered one
nelements=cur._element_counts[name]
if nelements==1:
#it should be the first one
newname = name+str(1)
cur[newname]=cur[name]
cur._add_element(newname,cur[newname])
del cur._elements[name]
del cur[name]
else:
print 'prior unjoinable element is not the first'
print ' this should be impossible, stopping'
sys.exit()
#end if
#add the joinable element as unnumbered
# later joinable elements will be joined to this one
cur[name] = XMLelement()
cur._add_element(name,cur[name])
#end if
elif not in_elements:
#add unnumbered
cur[name] = XMLelement()
cur._add_element(name,cur[name])
cur._element_counts[name]=1
else:
#add in a numbered way
nelements=cur._element_counts[name]
if nelements==1:
#rename the first element
newname = name+str(1)
cur[newname]=cur[name]
cur._add_element(newname,cur[newname])
del cur._elements[name]
del cur[name]
#end if
nelements+=1
newname = name + str(nelements)
cur[newname] = XMLelement()
cur._add_element(newname,cur[newname])
cur._element_counts[name]=nelements
name = newname
#end if
cur._elements[name]._parent = cur #mark change
self.increment_level()
self.cur[self.ilevel] = cur._elements[name]
cur = self.cur[self.ilevel]
for kraw,v in attributes.iteritems():
if self.contract_names:
k = kraw.lower().replace('-','_')
else:
k = kraw
#end if
if valid_variable_name(k):
kname = cur._escape_name(k)
cur[kname] = v
cur._add_xmlattribute(kname,cur[kname])
else:
if self.warn:
print 'xmlreader warning: attribute '+k+' is not a valid variable name and has been ignored'
#end if
#end if
#end for
return
def test_valid_variable_name():
from superstring import valid_variable_name
assert(valid_variable_name('valid_variable_name'))
assert(valid_variable_name('_valid_variable_name'))
assert(valid_variable_name('__valid_variable_name'))
assert(valid_variable_name('valid_variable_name__'))
assert(valid_variable_name('validVariableName'))
assert(not valid_variable_name('invalid variable name'))
assert(not valid_variable_name('invalid_variable-name'))
assert(not valid_variable_name('inval!d_variable_name'))
assert(not valid_variable_name('inv@lid_variable_name'))
assert(not valid_variable_name('in>alid_variable_name'))
assert(not valid_variable_name('invalid_variable_name '))
