def returnMap(self,outcomes,name):
"""
This method returns a map if the ET contains symbolic sequences.
This is needed since since RAVEN requires numeric values for sequences.
@ In, outcomes, list, list that contains all the sequences IDs provided in the ET
@ In, name, string, name of the ET
@ Out, etMap, dict, dictionary containing the map
"""
# check if outputMap contains string ID for at least one sequence
# if outputMap contains all numbers then keep the number ID
allFloat = True
for seq in outcomes:
try:
float(seq)
except ValueError:
allFloat = False
break
etMap = {}
if allFloat == False:
# create an integer map, and create an integer map file
root = ET.Element('map')
root.set('Tree', name)
for seq in outcomes:
etMap[seq] = outcomes.index(seq)
ET.SubElement(root, "sequence", ID=str(outcomes.index(seq))).text = str(seq)
fileID = name + '_mapping.xml'
updatedTreeMap = ET.ElementTree(root)
xmlU.prettify(updatedTreeMap)
updatedTreeMap.write(fileID)
else:
for seq in outcomes:
etMap[seq] = utils.floatConversion(seq)
return etMap
def printXML(self):
"""
Returns string representation of tree (in XML format).
@ In, None
@ Out, msg, string, string representation
"""
xml = inputTreeToXml(self, fromNode=True)
return xmlUtils.prettify(xml)
def writeFile(self):
"""
Writes the input file to disk.
@ In, None
@ Out, None
"""
#prettify tree
pretty = xmlUtils.prettify(self.tree)
#make sure file is written cleanly and anew
if self.isOpen(): self.close()
self.writelines(pretty,overwrite=True)
self.close()
def writeWorkflow(self, templates, destination, run=False):
""" todo """
# TODO use destination?
# write templates
inner, outer, cash = templates
outer_file = os.path.abspath(os.path.join(destination, 'outer.xml'))
inner_file = os.path.abspath(os.path.join(destination, 'inner.xml'))
cash_file = os.path.abspath(os.path.join(destination, 'cash.xml'))
print('HERON: writing files ...')
msg_format = ' ... wrote "{1:15s}" to "{0}/"'
with open(outer_file, 'w') as f:
f.write(xmlUtils.prettify(outer))
print(msg_format.format(*os.path.split(outer_file)))
with open(inner_file, 'w') as f:
f.write(xmlUtils.prettify(inner))
print(msg_format.format(*os.path.split(inner_file)))
with open(cash_file, 'w') as f:
f.write(xmlUtils.prettify(cash))
print(msg_format.format(*os.path.split(cash_file)))
# write library of info so it can be read in dispatch during inner run
data = (self.__case, self.__components, self.__sources)
lib_file = os.path.abspath(
os.path.join(destination, self.namingTemplates['lib file']))
with open(lib_file, 'wb') as lib:
pk.dump(data, lib)
print(msg_format.format(*os.path.split(lib_file)))
# copy "write_inner.py", which has the denoising and capacity fixing algorithms
conv_src = os.path.abspath(
os.path.join(self._template_path, 'write_inner.py'))
conv_file = os.path.abspath(os.path.join(destination,
'write_inner.py'))
shutil.copyfile(conv_src, conv_file)
print(msg_format.format(*os.path.split(conv_file)))
# run, if requested
if run:
self.runWorkflow(destination)
def writeFile(self, asString=False, **kwargs):
"""
Writes the input file to disk.
@ In, asString, bool, optional, if indicated then return string instead of writing
@ In, kwargs, dict, optional, additional arguments to pass to prettify
@ Out, pretty, str, optional, only returned if asString is True
"""
#prettify tree
pretty = xmlUtils.prettify(self.tree, **kwargs)
if asString:
return pretty
#make sure file is written cleanly and anew
if self.isOpen():
self.close()
self.writelines(pretty, overwrite=True)
self.close()
def writeFile(self):
"""
Writes the input file to disk. Because we store a list of dynamic nodes
instead of a full tree, requires some special treatment
@ In, None
@ Out, None
"""
if self.isOpen(): self.close()
#write the root node manually
self.writelines('<'+self.rootName+' type="Dynamic">\n',overwrite=True)
#write out each time step node
for node in self.pivotNodes:
pretty = xmlUtils.prettify(node,startingTabs=1,addRavenNewlines=False)
self.writelines(pretty)
self.writelines('</'+self.rootName+'>\n')
self.close()
def writeWorkflow(self, template, destination, run=False):
"""
Writes a template to file.
@ In, template, xml.etree.ElementTree.Element, file to write
@ In, destination, str, path and filename to write to
@ In, run, bool, optional, if True then run the workflow after writing? good idea?
@ Out, errors, int, 0 if successfully wrote [and run] and nonzero if there was a problem
"""
pretty = xmlUtils.prettify(template)
with open(destination, 'w') as f:
f.write(pretty)
if run:
errors = self.runWorkflow(destination)
else:
# 0 meaning successfully wrote file
errors = 0
return errors
def getNode(fname, nodepath):
"""
Searches file for particular node. Note that this takes the first matching node path in the file.
@ In, fname, string, name of file with XML tree to search
@ In, nodepath, string, "."-separated string with xml node name path, i.e., Simulation.RunInfo.Sequence
@ Out, getNode, ET.Element, prettified element
"""
#TODO add option to include parent nodes with ellipses
root = ET.parse(fname).getroot()
#format nodepath
nodepath = nodepath.replace('.', '/')
#check if root is desired node
if root.tag == nodepath:
node = root
docLevel = 0
else:
docLevel = len(nodepath.split('/'))
node = xmlUtils.findPathEllipsesParents(root, nodepath, docLevel)
if node is None:
raise IOError('Unable to find ' + nodepath + ' in ' + fname)
return xmlUtils.prettify(node, doc=True, docLevel=docLevel)
def saveDataToFile(self, source):
"""
Saves the given data as database to file.
@ In, source, DataObjects.DataObject, object to write to file
@ Out, None
"""
ds, meta = source.getData()
# we actually just tell the DataSet to write out as netCDF
path = self.get_fullpath()
# TODO set up to use dask for on-disk operations
# convert metadata into writeable
for key, xml in meta.items():
ds.attrs[key] = xmlUtils.prettify(xml.getRoot())
# get rid of "object" types
for var in ds:
if ds[var].dtype == np.dtype(object):
# is it a string?
if mathUtils.isAString(ds[var].values[0]):
ds[var] = ds[var].astype(str)
# is there existing data? Read it in and merge it, if so
# -> we've already wiped the file in initializeDatabase if it's in write mode
if os.path.isfile(path):
exists = xr.load_dataset(path)
if 'RAVEN_sample_ID' in exists:
floor = int(exists['RAVEN_sample_ID'].values[-1]) + 1
new = ds['RAVEN_sample_ID'].values + floor
ds = ds.assign_coords(RAVEN_sample_ID=new)
# NOTE order matters! This preserves the sampling order in which data was inserted
# into this database
ds = xr.concat((exists, ds), 'RAVEN_sample_ID')
# if this is open somewhere else, we can't write to it
# TODO is there a way to check if it's writable? I can't find one ...
try:
ds.to_netcdf(path, engine=self._format)
except PermissionError:
self.raiseAnError(
PermissionError,
f'NetCDF file "{path}" denied RAVEN permission to write! Is it open in another program?'
)
try:
os.remove(fName)
except OSError:
later.append(fName)
return later
#establish test XML
xmlString = '<root ratr="root_attrib"><child catr1="child attrib 1" catr2="child attrib 2"><cchild ccatr="cc_attrib">cchildtext</cchild></child></root>'
inFileName = 'testXMLInput.xml'
open(inFileName, 'w').write(xmlString)
xmlTree = ET.parse(inFileName)
toRemove = attemptFileClear(inFileName, toRemove)
# test prettify
pretty = utils.toString(xmlUtils.prettify(xmlTree))
prettyFileName = 'xml/testXMLPretty.xml'
open(prettyFileName, 'w').writelines(pretty)
gold = ''.join(
line.rstrip('\n\r') for line in open(
os.path.join(os.path.dirname(__file__), 'gold', prettyFileName), 'r'))
test = ''.join(line.rstrip('\n\r') for line in open(prettyFileName, 'r'))
if gold == test:
results['pass'] += 1
toRemove = attemptFileClear(prettyFileName, toRemove)
else:
print('ERROR: Test of "pretty" failed! See', prettyFileName,
'(below) vs gold/', prettyFileName)
print('( START', prettyFileName, ')')
for line in file(prettyFileName, 'r'):
print(line[:-1]) #omit newline
"""
try:
os.remove(fName)
except OSError:
later.append(fName)
return later
#establish test XML
xmlString = '<root ratr="root_attrib"><child catr1="child attrib 1" catr2="child attrib 2"><cchild ccatr="cc_attrib">cchildtext</cchild></child></root>'
inFileName = 'testXMLInput.xml'
open(inFileName,'w').write(xmlString)
xmlTree = ET.parse(inFileName)
toRemove = attemptFileClear(inFileName,toRemove)
# test prettify
pretty = xmlUtils.prettify(xmlTree)
prettyFileName = 'xml/testXMLPretty.xml'
open(prettyFileName,'w').writelines(pretty)
gold = ''.join(line.rstrip('\n\r') for line in open(os.path.join(os.path.dirname(__file__),'gold',prettyFileName),'r'))
test = ''.join(line.rstrip('\n\r') for line in open( prettyFileName ,'r'))
if gold==test:
results['pass']+=1
toRemove = attemptFileClear(prettyFileName,toRemove)
else:
print('ERROR: Test of "pretty" failed! See',prettyFileName,'(below) vs gold/',prettyFileName)
print('( START',prettyFileName,')')
for line in file(prettyFileName,'r'):
print(line[:-1]) #omit newline
print('( END',prettyFileName,')')
results['fail']+=1
