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 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 test_basic_ascii(self, category_data):
dcA = DataCategory('A', category_data['attributeList'],
category_data['rowListAsciiA'])
dcB = DataCategory('A', category_data['attributeList'],
category_data['rowListAsciiA'])
assert dcA == dcA
assert dcB == dcB
assert dcA == dcB
def test_basic_unicode(self, category_data):
dcA = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
dcB = DataCategory('A', category_data['attributeList'],
category_data['rowListUnicode'])
assert dcA == dcA
assert dcB == dcB
assert dcA == dcB
def testBasicAscii(self):
"""Test case - subcclass instantiation with ascii data"""
try:
dcA = DataCategory("A", self.__attributeList, self.__rowListAsciiA)
dcB = DataCategory("A", self.__attributeList, self.__rowListAsciiA)
self.assertEqual(dcA, dcA)
self.assertEqual(dcB, dcB)
self.assertEqual(dcA, dcB)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def invokeMethods(self, fh=sys.stdout):
_ = fh
mI = self.__dApi.getMethodIndex()
lenD = len(mI)
i = 0
for k, mRefL in mI.items():
for mRef in mRefL:
i += 1
mId = mRef.getId()
mType = mRef.getType()
categoryName = mRef.getCategoryName()
attributeName = mRef.getAttributeName()
#
logger.debug("\n")
logger.debug("++++++++++++++++++--------------------\n")
logger.debug(
"Invoking dictionary method on file object: %s (%d/%d)", k,
i, lenD)
logger.debug(" + Method id: %s", mId)
logger.debug(" + Type: %s", mType)
logger.debug(" + Category: %s", categoryName)
logger.debug(" + Attribute: %s", attributeName)
#
if mType == "datablock":
logger.debug("Invoke datablock method %s", mId)
# self.invokeDataBlockMethod(type,self.__dApi.getMethod(id))
# continue
#
for db in self.__dataContainerList:
if mType == "category":
if not db.exists(categoryName):
dc = DataCategory(categoryName)
db.append(dc)
dObj = db.getObj(categoryName)
dObj.invokeCategoryMethod(mType,
self.__dApi.getMethod(mId),
db)
elif mType == "attribute":
if not db.exists(categoryName):
dc = DataCategory(categoryName)
db.append(dc)
dObj = db.getObj(categoryName)
# logger.debug("invoke - %r %r %r %r" % (attributeName, type, self.__dApi.getMethod(id), db))
dObj.invokeAttributeMethod(attributeName, mType,
self.__dApi.getMethod(mId),
db)
elif mType == "datablock":
logger.debug("Invoke datablock method %s", mId)
db.invokeDataBlockMethod(mType,
self.__dApi.getMethod(mId),
db)
else:
pass
def _makeKeyItem(self, catName, attName, keyItemList, iDef):
itemName = CifName.itemName(catName, attName)
#
dc = DataCategory("definition")
dc.appendAttribute("id")
dc.appendAttribute("scope")
dc.appendAttribute("class")
dc.appendAttribute("update")
dc.append([itemName, "Item", "Single", "2013-08-22"])
iDef.append(dc)
#
dc = DataCategory("description")
dc.appendAttribute("text")
dc.append(['synthentic componsite key'])
iDef.append(dc)
#
dc = DataCategory("name")
dc.appendAttribute("category_id")
dc.appendAttribute("object_id")
dc.append([catName, attName])
iDef.append(dc)
tcontainer = 'Set'
purpose = 'Composite'
source = 'Derived'
contents = 'Name'
dimension = '[%d]' % len(keyItemList)
#
dc = DataCategory("type")
dc.appendAttribute("purpose")
dc.appendAttribute("source")
dc.appendAttribute("contents")
dc.appendAttribute("container")
dc.appendAttribute("dimension")
dc.append([purpose, source, contents, tcontainer, dimension])
iDef.append(dc)
dc = DataCategory("method")
dc.appendAttribute("purpose")
dc.appendAttribute("expression")
tmpl = '''
With row as %s
%s = [%s]
'''
mText = tmpl % (catName, itemName, ','.join(keyItemList))
dc.append(['Evaluation', mText])
iDef.append(dc)
def __makeKeyItem(self, catName, attName, keyItemList, iDef):
itemName = CifName.itemName(catName, attName)
#
dc = DataCategory("definition")
dc.appendAttribute("id")
dc.appendAttribute("scope")
dc.appendAttribute("class")
dc.appendAttribute("update")
dc.append([itemName, "Item", "Single", "2013-08-22"])
iDef.append(dc)
#
dc = DataCategory("description")
dc.appendAttribute("text")
dc.append(["synthentic componsite key"])
iDef.append(dc)
#
dc = DataCategory("name")
dc.appendAttribute("category_id")
dc.appendAttribute("object_id")
dc.append([catName, attName])
iDef.append(dc)
tcontainer = "Set"
purpose = "Composite"
source = "Derived"
contents = "Name"
dimension = "[%d]" % len(keyItemList)
#
dc = DataCategory("type")
dc.appendAttribute("purpose")
dc.appendAttribute("source")
dc.appendAttribute("contents")
dc.appendAttribute("container")
dc.appendAttribute("dimension")
dc.append([purpose, source, contents, tcontainer, dimension])
iDef.append(dc)
dc = DataCategory("method")
dc.appendAttribute("purpose")
dc.appendAttribute("expression")
tmpl = """
With row as %s
%s = [%s]
"""
mText = tmpl % (catName, itemName, ",".join(keyItemList))
dc.append(["Evaluation", mText])
iDef.append(dc)
def testBasicUnicode(self):
"""Test case - __eq__ and __ne__ methods w/ unicode"""
try:
dcA = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
dcB = DataCategory("A", self.__attributeList,
self.__rowListUnicode)
self.assertEqual(dcA, dcA)
self.assertEqual(dcB, dcB)
self.assertEqual(dcA, dcB)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testBasicAsciiDiff(self):
"""Test case - __eq__ and __ne__ methods"""
try:
dcA = DataCategory("A", self.__attributeList, self.__rowListAsciiA)
dcB = DataCategory("A", self.__attributeList, self.__rowListAsciiB)
self.assertEqual(dcA, dcA)
self.assertIs(dcA, dcA)
self.assertEqual(dcB, dcB)
self.assertNotEqual(dcA, dcB)
self.assertIsNot(dcA, dcB)
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 __buildCategoryDefinition(self, name, description, keyAttributeNames,
examples, contexts):
"""Construct an attribute definition from input attribute dictionary
containing metadata extracted from the XML schema, and from the
input schema name mapping dictionary.
Args:
name (str): category name
description (str): category description
keyAttributeNames (list): key attribute names
examples (list): category examples
contexts (list): category contexts
Returns:
Definition container (object):
"""
defC = DefinitionContainer(name)
#
dc = DataCategory(
"category",
attributeNameList=["id", "description", "mandatory_code"])
dc.append([name, description, "no"])
defC.append(dc)
#
dc = DataCategory("category_key", attributeNameList=["name"])
for keyAttributeName in keyAttributeNames:
keyItemName = CifName.itemName(name, keyAttributeName)
dc.append([keyItemName])
defC.append(dc)
dc = DataCategory("category_group", attributeNameList=["id"])
dc.append(["inclusive_group"])
dc.append(["validation_report_group"])
defC.append(dc)
# pdbx_category_context
dc = DataCategory("pdbx_category_context",
attributeNameList=["category_id", "type"])
for cType in contexts:
dc.append([name, cType])
defC.append(dc)
#
dc = DataCategory("category_examples",
attributeNameList=["detail", "case"])
for example in examples:
dc.append([".", example])
defC.append(dc)
return defC
def _createfile1(pathout):
my_data_list = []
cur_container = DataContainer("myblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(("1", "2", "3"))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute("absorpt_coefficient_mu")
acat.appendAttribute("entry_id")
acat.appendAttribute("method")
acat.appendAttribute("details")
acat.append(("?", "D_12345", "X-RAY DIFFRACTION", "some details"))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute("title")
acat.appendAttribute("pdbx_descriptor")
acat.append(("Start title", "Start Descriptor"))
cur_container.append(acat)
my_data_list.append(cur_container)
# Second block
cur_container = DataContainer("secondblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(("3", "2", "1"))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def _createfile1(pathout):
my_data_list = []
cur_container = DataContainer("myblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(('1', '2', '3'))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute('absorpt_coefficient_mu')
acat.appendAttribute('entry_id')
acat.appendAttribute('method')
acat.appendAttribute('details')
acat.append(('?', 'D_12345', 'X-RAY DIFFRACTION', 'some details'))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute('title')
acat.appendAttribute('pdbx_descriptor')
acat.append(('Start title', 'Start Descriptor'))
cur_container.append(acat)
my_data_list.append(cur_container)
# Second block
cur_container = DataContainer("secondblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(('3', '2', '1'))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def testReplaceValues(self):
"""Test case - replace values"""
try:
dcU = DataCategory("A", self.__attributeListMiss,
self.__rowListUnicodeMiss)
at = self.__attributeListMiss[3]
curV = self.__testRowUnicodeMiss[2]
self.assertEqual(dcU.replaceValue(curV, "newVal", at),
dcU.getRowCount())
at = self.__attributeListMiss[4]
curV = self.__testRowUnicodeMiss[3]
self.assertEqual(dcU.replaceValue(curV, "newVal", at),
dcU.getRowCount())
at = self.__attributeListMiss[5]
curV = self.__testRowUnicodeMiss[4]
self.assertEqual(dcU.replaceValue(curV, "newVal", at),
dcU.getRowCount())
at = self.__attributeListMiss[6]
curV = self.__testRowUnicodeMiss[5]
self.assertEqual(dcU.replaceValue(curV, "newVal", at),
dcU.getRowCount())
for ii in range(3, 7):
at = self.__attributeListMiss[ii]
self.assertEqual(dcU.replaceSubstring("newVal", "nextVal", at),
dcU.getRowCount())
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 AddCategory(self, categoryID, items):
"""Add Category"""
category = DataCategory(categoryID)
for item in items:
category.appendAttribute(item)
#
self.__container.append(category)
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 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_single_row(self, rw_data):
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.appendAttribute("details")
aCat.append([1, 2, 3, 4, 5, 6, 7, 'data_my_big_data_file'])
aCat.append([1, 2, 3, 4, 5, 6, 7, 'loop_my_big_data_loop'])
aCat.append([1, 2, 3, 4, 5, 6, 7, 'save_my_big_data_saveframe'])
aCat.append([1, 2, 3, 4, 5, 6, 7, '_category.item'])
curContainer.append(aCat)
bCat = curContainer.getObj("pdbx_seqtool_mapping_ref")
print("----attribute list %r\n" % bCat.getAttributeList())
row = bCat.getRow(0)
print("----ROW %r\n" % row)
with open(str(rw_data['pathOutputFile2']), "w") as ofh:
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
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 _createfile2(pathout):
my_data_list = []
cur_container = DataContainer("test")
acat = DataCategory("new")
acat.appendAttribute("item")
acat.append(('1',))
cur_container.append(acat)
acat = DataCategory("second_category")
acat.appendAttribute('row')
acat.appendAttribute('rowb')
acat.append(('1', '2'))
cur_container.append(acat)
acat = DataCategory("third")
acat.appendAttribute('id')
acat.appendAttribute('val')
acat.append(('1', 'a'))
acat.append(('2', 'b'))
acat.append(('3', 'c'))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute('method')
acat.appendAttribute('entry_id')
acat.append(('NEW', 'something'))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute('new')
acat.appendAttribute('pdbx_descriptor')
acat.append(('Something to add', 'Override descriptor'))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def _createfile2(pathout):
my_data_list = []
cur_container = DataContainer("test")
acat = DataCategory("new")
acat.appendAttribute("item")
acat.append(("1",))
cur_container.append(acat)
acat = DataCategory("second_category")
acat.appendAttribute("row")
acat.appendAttribute("rowb")
acat.append(("1", "2"))
cur_container.append(acat)
acat = DataCategory("third")
acat.appendAttribute("id")
acat.appendAttribute("val")
acat.append(("1", "a"))
acat.append(("2", "b"))
acat.append(("3", "c"))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute("method")
acat.appendAttribute("entry_id")
acat.append(("NEW", "something"))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute("new")
acat.appendAttribute("pdbx_descriptor")
acat.append(("Something to add", "Override descriptor"))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def test_edit_row_accessors(self, category_data):
dcA = DataCategory('A', category_data['attributeList'],
category_data['rowListAsciiA'])
with pytest.raises(IndexError):
dcA.getRow(dcA.getRowCount() + 1)
with pytest.raises(IndexError):
dcA.getRowAttributeDict(dcA.getRowCount() + 1)
with pytest.raises(IndexError):
dcA.getRowItemDict(dcA.getRowCount() + 1)
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 test_edit_remove_row(self, category_data):
dcA = DataCategory('A',
category_data['attributeList'],
category_data['rowListUnicode'],
raiseExceptions=True)
for jj in range(0, dcA.getRowCount()):
ii = dcA.getRowCount()
dcA.removeRow(0)
assert ii - 1 == dcA.getRowCount()
#
assert 0 == dcA.getRowCount()
def add_category(self, category_id, items):
"""
This method creates a data category object, adds all items to it and appends it to the container
:param category_id: a string; an mmcif category e.g. 'emd_admin'
:param items: a list of strings; each element in the list is an item of mmcif category as defined by category_id
:return: a list of strings; each element represents a value for the corresponding element in data_items
"""
category = DataCategory(category_id)
for item in items:
category.appendAttribute(item)
self.__container.append(category)
def testUpdateDataFile(self):
"""Test case - update data file
"""
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])
curContainer.append(aCat)
myDataList.append(curContainer)
ofh = open(self.__pathOutputFile1, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
#
# Read and update the data -
#
myDataList = []
ifh = open(self.__pathOutputFile1, "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)
with open(self.__pathOutputFile2, "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
#
self.assertEqual(len(myDataList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_set_values(self, category_data):
dcU = DataCategory('A', category_data['attributeListMiss'],
category_data['rowListUnicodeMiss'])
for i in range(0, dcU.getRowCount()):
dcU.setValue('newValue', attributeName='colM1', rowIndex=i)
assert dcU.setValue('newValue',
attributeName='colM1',
rowIndex=dcU.getRowCount() + 5)
with pytest.raises(ValueError):
dcU.setValue('newValue', 'colX', 0)
