def testSimpleInitialization(self):
"""Test case - Simple initialization of a data category and data block
"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
#
fn = tempname(suffix='.cif')
attributeNameList = [
'aOne', 'aTwo', 'aThree', 'aFour', 'aFive', 'aSix', 'aSeven',
'aEight', 'aNine', 'aTen'
]
rowList = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]]
nameCat = 'myCategory'
#
#
curContainer = DataContainer("myblock")
aCat = DataCategory(nameCat, attributeNameList, rowList)
aCat.printIt()
curContainer.append(aCat)
curContainer.printIt()
#
myContainerList = []
myContainerList.append(curContainer)
ofh = open(fn, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myContainerList)
ofh.close()
myContainerList = []
ifh = open(fn, "r")
pRd = PdbxReader(ifh)
pRd.read(myContainerList)
ifh.close()
for container in myContainerList:
for objName in container.getObjNameList():
name, aList, rList = container.getObj(objName).get()
self.lfh.write("Recovered data category %s\n" % name)
self.lfh.write("Attribute list %r\n" %
repr(aList))
self.lfh.write("Row list %r\n" %
repr(rList))
except:
traceback.print_exc(file=self.lfh)
self.fail()
def __parser(self, tokenizer, containerList):
""" Parser for PDBx data files and dictionaries.
Input - tokenizer() reentrant method recognizing data item names (_category.attribute)
quoted strings (single, double and multi-line semi-colon delimited), and unquoted
strings.
containerList - list-type container for data and definition objects parsed from
from the input file.
Return:
containerList - is appended with data and definition objects -
"""
# Working container - data or definition
curContainer = None
#
# Working category container
categoryIndex = {}
curCategory = None
#
curRow = None
state = None
# Find the first reserved word and begin capturing data.
#
while True:
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
if curWord is None:
continue
reservedWord, state = self.__getState(curWord)
if reservedWord is not None:
break
while True:
#
# Set the current state -
#
# At this point in the processing cycle we are expecting a token containing
# either a '_category.attribute' or a reserved word.
#
if curCatName is not None:
state = "ST_KEY_VALUE_PAIR"
elif curWord is not None:
reservedWord, state = self.__getState(curWord)
else:
self.__syntaxError("Miscellaneous syntax error")
return
#
# Process _category.attribute value assignments
#
if state == "ST_KEY_VALUE_PAIR":
try:
curCategory = categoryIndex[curCatName]
except KeyError:
# A new category is encountered - create a container and add a row
curCategory = categoryIndex[curCatName] = DataCategory(
curCatName)
try:
curContainer.append(curCategory)
except AttributeError:
self.__syntaxError(
"Category cannot be added to data_ block")
return
curRow = []
curCategory.append(curRow)
else:
# Recover the existing row from the category
try:
curRow = curCategory[0]
except IndexError:
self.__syntaxError(
"Internal index error accessing category data")
return
# Check for duplicate attributes and add attribute to table.
if curAttName in curCategory.getAttributeList():
self.__syntaxError(
"Duplicate attribute encountered in category")
return
else:
curCategory.appendAttribute(curAttName)
# Get the data for this attribute from the next token
tCat, tAtt, curQuotedString, curWord = next(tokenizer)
if tCat is not None or (curQuotedString is None
and curWord is None):
self.__syntaxError("Missing data for item _%s.%s" %
(curCatName, curAttName))
if curWord is not None:
#
# Validation check token for misplaced reserved words -
#
reservedWord, state = self.__getState(curWord)
if reservedWord is not None:
self.__syntaxError("Unexpected reserved word: %s" %
(reservedWord))
curRow.append(curWord)
elif curQuotedString is not None:
curRow.append(curQuotedString)
else:
self.__syntaxError("Missing value in item-value pair")
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
continue
#
# Process a loop_ declaration and associated data -
#
elif state == "ST_TABLE":
# The category name in the next curCatName,curAttName pair
# defines the name of the category container.
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
if curCatName is None or curAttName is None:
self.__syntaxError("Unexpected token in loop_ declaration")
return
# Check for a previous category declaration.
if curCatName in categoryIndex:
self.__syntaxError(
"Duplicate category declaration in loop_")
return
curCategory = DataCategory(curCatName)
try:
curContainer.append(curCategory)
except AttributeError:
self.__syntaxError(
"loop_ declaration outside of data_ block or save_ frame"
)
return
curCategory.appendAttribute(curAttName)
# Read the rest of the loop_ declaration
while True:
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
if curCatName is None:
break
if curCatName != curCategory.getName():
self.__syntaxError(
"Changed category name in loop_ declaration")
return
curCategory.appendAttribute(curAttName)
# If the next token is a 'word', check it for any reserved words -
if curWord is not None:
reservedWord, state = self.__getState(curWord)
if reservedWord is not None:
if reservedWord == "stop":
return
else:
self.__syntaxError(
"Unexpected reserved word after loop declaration: %s"
% (reservedWord))
# Read the table of data for this loop_ -
while True:
curRow = []
curCategory.append(curRow)
for _ in curCategory.getAttributeList():
if curWord is not None:
curRow.append(curWord)
elif curQuotedString is not None:
curRow.append(curQuotedString)
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
# loop_ data processing ends if -
# A new _category.attribute is encountered
if curCatName is not None:
break
# A reserved word is encountered
if curWord is not None:
reservedWord, state = self.__getState(curWord)
if reservedWord is not None:
break
continue
elif state == "ST_DEFINITION":
# Ignore trailing unnamed saveframe delimiters e.g. 'save_'
sName = self.__getContainerName(curWord)
if (len(sName) > 0):
curContainer = DefinitionContainer(sName)
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
elif state == "ST_DATA_CONTAINER":
#
dName = self.__getContainerName(curWord)
if len(dName) == 0:
dName = "unidentified"
curContainer = DataContainer(dName)
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
elif state == "ST_STOP":
return
elif state == "ST_GLOBAL":
curContainer = DataContainer("blank-global")
curContainer.setGlobal()
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
elif state == "ST_UNKNOWN":
self.__syntaxError("Unrecogized syntax element: " +
str(curWord))
return
def testUpdateDataFile(self):
"""Test case - write data file"""
self.lfh.write(
"\nStarting %s %s\n"
% (self.__class__.__name__, sys._getframe().f_code.co_name)
)
try:
# Create a initial data file --
#
tmpf = tempname(suffix=".cif")
myDataList = []
ofh = open(tmpf, "w")
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
# Read and update the data -
#
myDataList = []
ifh = open(tmpf, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock = myDataList[0]
myBlock.printIt()
myCat = myBlock.getObj("pdbx_seqtool_mapping_ref")
myCat.printIt()
for iRow in range(0, myCat.getRowCount()):
myCat.setValue("some value", "ref_mon_id", iRow)
myCat.setValue(100, "ref_mon_num", iRow)
ofh = open(tempname(suffix=".cif"), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
except:
traceback.print_exc(file=sys.stderr)
self.fail()
def testWriteDataFile(self):
"""Test case - write data file"""
self.lfh.write(
"\nStarting %s %s\n"
% (self.__class__.__name__, sys._getframe().f_code.co_name)
)
try:
#
myDataList = []
ofh = open(tempname(suffix=".cif"), "w")
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
except:
traceback.print_exc(file=sys.stderr)
self.fail()
def testUpdateDataFile(self):
"""Test case - update data file
"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
# Create a initial data file --
#
myDataList = []
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append([9, 2, 3, 4, 5, 6, 7])
aCat.append([10, 2, 3, 4, 5, 6, 7])
aCat.append([11, 2, 3, 4, 5, 6, 7])
aCat.append([12, 2, 3, 4, 5, 6, 7])
#self.lfh.write("Assigned data category state-----------------\n")
#aCat.dumpIt(fh=self.lfh)
tmpf = tempname(suffix='.cif')
curContainer.append(aCat)
myDataList.append(curContainer)
ofh = open(tmpf, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
#
# Read and update the data -
#
myDataList = []
ifh = open(tmpf, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock = myDataList[0]
myBlock.printIt()
myCat = myBlock.getObj('pdbx_seqtool_mapping_ref')
myCat.printIt()
for iRow in range(0, myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id', iRow)
myCat.setValue(100, 'ref_mon_num', iRow)
ofh = open(tempname(suffix='.cif'), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
except:
traceback.print_exc(file=self.lfh)
self.fail()