def testEditAttributes(self):
"""Test case - get and extend atttribute names"""
try:
#
dcA = DataCategory("A", self.__attributeList, self.__rowListAsciiA)
self.assertEqual(0, dcA.getRowIndex())
self.assertEqual(None, dcA.getCurrentAttribute())
#
na = len(dcA.getAttributeList())
tL = dcA.getAttributeListWithOrder()
self.assertEqual(len(tL), na)
na = len(dcA.getAttributeList())
self.assertEqual(dcA.appendAttribute("ColNew"), na + 1)
row = dcA.getFullRow(0)
self.assertEqual(row[na], "?")
#
row = dcA.getFullRow(dcA.getRowCount() + 1)
for cV in row:
self.assertEqual(cV, "?")
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_cond_select_values(self, category_data):
dcM = DataCategory('A', category_data['attributeListMiss'],
category_data['rowListUnicodeMiss'])
atL = dcM.getAttributeList()
for ii, at in enumerate(atL[1:]):
assert len(
dcM.selectIndices(category_data['testRowUnicodeMiss'][ii],
at)) == dcM.getRowCount()
#
print("Window %r" % [tt for tt in window(atL)])
for atW in window(atL, size=1):
assert len(
dcM.selectValueListWhere(
atW, category_data['testRowUnicodeMiss'][-1],
category_data['attributeListMiss']
[-1])) == dcM.getRowCount()
for atW in window(atL, size=2):
assert len(
dcM.selectValueListWhere(
atW, category_data['testRowUnicodeMiss'][-1],
category_data['attributeListMiss']
[-1])) == dcM.getRowCount()
for atW in window(atL, size=3):
assert len(
dcM.selectValueListWhere(
atW, category_data['testRowUnicodeMiss'][-1],
category_data['attributeListMiss']
[-1])) == dcM.getRowCount()
for atW in window(atL, size=4):
assert len(
dcM.selectValueListWhere(
atW, category_data['testRowUnicodeMiss'][-1],
category_data['attributeListMiss']
[-1])) == dcM.getRowCount()
def test_compare_values(self, category_data):
dcU = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
dcM = DataCategory('A', category_data['attributeListMiss'],
category_data['rowListUnicodeMiss'])
na = dcU.getAttributeList()
assert len(na) >= 1
tupL = dcU.cmpAttributeValues(dcU)
for tup in tupL:
assert tup[1] == True
tupL = dcU.cmpAttributeValues(dcM)
for tup in tupL:
if tup[0] in ['colC', 'colD']:
assert tup[1] == False
else:
assert tup[1] == True
#
dcX = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
assert dcX.setValue(
u'134ĆćĈĉĊċČÄ�ÄŽÄ�Ä�Ä‘Ä’Ä“Ä Ä¡Ä¢Ä£Ä¤Ä¥Ä¦Ä§Ä¨xyz',
attributeName='colD',
rowIndex=dcX.getRowCount() - 2)
tupL = dcU.cmpAttributeValues(dcX)
for tup in tupL:
if tup[0] in ['colD']:
assert tup[1] == False
else:
assert tup[1] == True
def test_edit_extend(self, category_data):
dcA = DataCategory('A', category_data['attributeList'],
category_data['rowListAsciiA'])
na = len(dcA.getAttributeList())
assert dcA.appendAttributeExtendRows('colNew') == na + 1
row = dcA.getRow(dcA.getRowCount() - 1)
assert row[na] == "?"
def testCompareValues(self):
"""Test case - compare object values -"""
try:
dcU = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
dcM = DataCategory("A", self.__attributeListMiss,
self.__rowListUnicodeMiss)
na = dcU.getAttributeList()
self.assertGreaterEqual(len(na), 1)
tupL = dcU.cmpAttributeValues(dcU)
for tup in tupL:
self.assertEqual(tup[1], True)
tupL = dcU.cmpAttributeValues(dcM)
for tup in tupL:
if tup[0] in ["colC", "colD"]:
self.assertEqual(tup[1], False)
else:
self.assertEqual(tup[1], True)
#
dcX = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
self.assertTrue(
dcX.setValue(u"134ĆćĈĉĊċČčĎďĐđĒēĠġĢģĤĥĦħĨxyz",
attributeName="colD",
rowIndex=dcX.getRowCount() - 2))
tupL = dcU.cmpAttributeValues(dcX)
for tup in tupL:
if tup[0] in ["colD"]:
self.assertEqual(tup[1], False)
else:
self.assertEqual(tup[1], True)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testGetValues(self):
"""Test case - value getters"""
try:
dcU = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
aL = dcU.getAttributeList()
logger.debug("Row length %r", dcU.getRowCount())
for ii, v in enumerate(self.__testRowUnicode):
at = aL[ii + 1]
for j in range(0, dcU.getRowCount()):
logger.debug("ii %d j %d at %s val %r ", ii, j, at, v)
self.assertEqual(dcU.getValue(at, j), v)
self.assertEqual(dcU.getValueOrDefault(at, j, "mydefault"),
v)
#
# negative indices are interpreted in the python manner
self.assertEqual(dcU.getValueOrDefault("colOrd", -1, "default"), 9)
self.assertRaises(IndexError, dcU.getValue, "colOrd",
dcU.getRowCount() + 1)
self.assertRaises(ValueError, dcU.getValue, "badAtt", 0)
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_edit_attributes(self, category_data):
dcA = DataCategory('A', category_data['attributeList'],
category_data['rowListAsciiA'])
assert 0 == dcA.getRowIndex()
assert None == dcA.getCurrentAttribute()
#
na = len(dcA.getAttributeList())
tL = dcA.getAttributeListWithOrder()
assert len(tL) == na
na = len(dcA.getAttributeList())
assert dcA.appendAttribute("ColNew") == na + 1
row = dcA.getFullRow(0)
assert row[na] == "?"
#
row = dcA.getFullRow(dcA.getRowCount() + 1)
for c in row:
assert c == "?"
def testEditExtend(self):
"""Test case - category extension methods"""
try:
dcA = DataCategory("A", self.__attributeList, self.__rowListAsciiA)
na = len(dcA.getAttributeList())
self.assertEqual(dcA.appendAttributeExtendRows("colNew"), na + 1)
row = dcA.getRow(dcA.getRowCount() - 1)
self.assertEqual(row[na], "?")
#
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_compare_attributes(self, category_data):
dcU = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
dcM = DataCategory('A', category_data['attributeListMiss'],
category_data['rowListUnicodeMiss'])
na = len(dcU.getAttributeList())
t1, t2, t3 = dcU.cmpAttributeNames(dcU)
assert len(t1) == 0
assert len(t3) == 0
assert len(t2) == na
t1, t2, t3 = dcU.cmpAttributeNames(dcM)
assert len(t1) == 0
assert len(t3) == 3
assert len(t2) == na
def test_get_values(self, category_data):
dcU = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
aL = dcU.getAttributeList()
print("Row length %r " % dcU.getRowCount())
for ii, v in enumerate(category_data['testRowUnicode']):
at = aL[ii + 1]
for j in range(0, dcU.getRowCount()):
print("ii %d j %d at %s val %r " % (ii, j, at, v))
assert dcU.getValue(at, j) == v
assert dcU.getValueOrDefault(at, j, 'mydefault') == v
#
# negative indices are interpreted in the python manner
assert dcU.getValueOrDefault('colOrd', -1, 'default') == 9
with pytest.raises(IndexError):
dcU.getValueOrDefault('colOrd', dcU.getRowCount() + 1, 0)
with pytest.raises(ValueError):
dcU.getValueOrDefault('badAtt', 0, 0)
def testCompareAttributes(self):
"""Test case - compare object attributes -"""
try:
dcU = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
dcM = DataCategory("A", self.__attributeListMiss,
self.__rowListUnicodeMiss)
na = len(dcU.getAttributeList())
t1, t2, t3 = dcU.cmpAttributeNames(dcU)
self.assertEqual(len(t1), 0)
self.assertEqual(len(t3), 0)
self.assertEqual(len(t2), na)
t1, t2, t3 = dcU.cmpAttributeNames(dcM)
self.assertEqual(len(t1), 0)
self.assertEqual(len(t3), 3)
self.assertEqual(len(t2), na)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testCondSelectValues(self):
"""Test case - value selections -
"""
try:
dcM = DataCategory("A", self.__attributeListMiss,
self.__rowListUnicodeMiss)
# self.__testRowUnicodeMiss = [u'someData', 100222, None, '?', '.', u'abcdĆćĈĉĊċČčĎďĐđĒēĔĕĖėĘęĚěĜĝĞğĠġĢģĤĥĦħĨxyz', 234.2345]
# self.__attributeListMiss
atL = dcM.getAttributeList()
for ii, at in enumerate(atL[1:]):
self.assertEqual(
len(dcM.selectIndices(self.__testRowUnicodeMiss[ii], at)),
dcM.getRowCount())
#
logger.debug("Window %r", [tt for tt in window(atL)])
for atW in window(atL, size=1):
self.assertEqual(
len(
dcM.selectValueListWhere(
atW, self.__testRowUnicodeMiss[-1],
self.__attributeListMiss[-1])), dcM.getRowCount())
for atW in window(atL, size=2):
self.assertEqual(
len(
dcM.selectValueListWhere(
atW, self.__testRowUnicodeMiss[-1],
self.__attributeListMiss[-1])), dcM.getRowCount())
for atW in window(atL, size=3):
self.assertEqual(
len(
dcM.selectValueListWhere(
atW, self.__testRowUnicodeMiss[-1],
self.__attributeListMiss[-1])), dcM.getRowCount())
for atW in window(atL, size=4):
self.assertEqual(
len(
dcM.selectValueListWhere(
atW, self.__testRowUnicodeMiss[-1],
self.__attributeListMiss[-1])), dcM.getRowCount())
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def process_entry(file_in, file_out):
try:
cif_file = gemmi.cif.read(file_in) # pylint: disable=no-member
data_block = cif_file[0]
except Exception as e:
logger.error("Failed to read cif file in Gemmi")
logger.error(e)
return 1
logging.info("Finding Centre of Mass")
com = get_center_of_mass(data_block)
if not com:
return 1
try:
io = IoAdapterCore()
ccL = io.readFile(file_in)
except Exception as e:
logger.error("Failed to read cif file using IoAdapterCore %s", e)
return 1
if len(ccL) == 0:
logger.error("No data parsed from file")
return 1
# First block only
b0 = ccL[0]
obj = b0.getObj("struct")
# If category does not exist
if obj is None:
# Need entry.id
eid = "XXXX"
eobj = b0.getObj("entry")
if eobj:
if "id" in eobj.getAttributeList():
eid = eobj.getValue("id", 0)
obj = DataCategory("struct")
obj.appendAttribute("entry_id")
obj.setValue(eid, "entry_id", 0)
ccL[0].append(obj)
newdata = [["pdbx_center_of_mass_x", com.x],
["pdbx_center_of_mass_y", com.y],
["pdbx_center_of_mass_z", com.z]]
for [it, val] in newdata:
if it not in obj.getAttributeList():
obj.appendAttribute(it)
obj.setValue(str(val), it, 0)
try:
logging.info("Writing mmcif file: %s", file_out)
ret = io.writeFile(file_out, ccL)
if not ret:
logger.info("Writing failed error %s", ret)
return 1
except Exception as e:
logger.error("Failed to write ccif file in IoAdapater %s", e)
return 1
# existing_data = data_block.get_mmcif_category('_struct.')
# new_data = {
# **existing_data,
# 'pdbx_center_of_mass_x': [com.x],
# 'pdbx_center_of_mass_y': [com.y],
# 'pdbx_center_of_mass_z': [com.z]
# }
# logging.info("Writing mmcif file: %s", file_out)
# try:
# data_block.set_mmcif_category('_struct.', new_data)
# cif_file.write_file(file_out)
# except Exception as e:
# logger.error("Failed to write cif file in Gemmi")
# logger.error(e)
# return 1
return 0
def __parser(self,
tokenizer,
containerList,
categorySelectionD=None,
excludeFlag=False):
""" 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.
On return:
The input containerList is appended with data and definition objects -
"""
catSelectD = categorySelectionD if categorySelectionD is not None else {}
logger.debug("Exclude Flag %r Category selection %r", excludeFlag,
catSelectD)
# Working container - data or definition
curContainer = None
# the last container of type data -
previousDataContainer = 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)
#
# check if we have all of the selection
if not excludeFlag and self.__allSelected(
curContainer, catSelectD):
return
try:
if catSelectD:
if not excludeFlag and curCatName in catSelectD:
curContainer.append(curCategory)
elif excludeFlag and curCatName not in catSelectD:
curContainer.append(curCategory)
else:
logger.debug(
"Skipped unselected/excluded category %s",
curCatName)
else:
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]
curRow = curCategory.getRow(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, _, 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)
#
# check if we have all of the selection
if not excludeFlag and self.__allSelected(
curContainer, catSelectD):
return
try:
if catSelectD:
if not excludeFlag and curCatName in catSelectD:
curContainer.append(curCategory)
elif excludeFlag and curCatName not in catSelectD:
curContainer.append(curCategory)
else:
logger.debug(
"Skipped unselected/excluded category %s",
curCatName)
else:
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 sName:
curContainer = DefinitionContainer(sName)
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
else:
# reset current container to the last data contatiner
curContainer = previousDataContainer
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
elif state == "ST_DATA_CONTAINER":
#
dName = self.__getContainerName(curWord)
if not dName:
dName = "unidentified"
curContainer = DataContainer(dName)
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
previousDataContainer = curContainer
curCatName, curAttName, curQuotedString, curWord = next(
tokenizer)
elif state == "ST_STOP":
###
# curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
continue
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
