def test_update_attribute(self, rw_data):
ifn = rw_data['pathBigPdbxDataFile']
ofn = rw_data['pathOutputFile2']
myContainerList = []
with open(str(ifn), "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myContainerList)
#
dsId = "D_000000"
atName = 'entry_id'
for container in myContainerList:
container.setName(dsId)
# remove category citation
container.remove('citation')
for objName in container.getObjNameList():
dcObj = container.getObj(objName)
if dcObj.hasAttribute(atName):
for iRow in range(0, dcObj.getRowCount()):
dcObj.setValue(dsId, attributeName=atName, rowIndex=iRow)
elif objName.lower() == 'entry':
dcObj.setValue(dsId, attributeName='id', rowIndex=0)
#
with open(str(ofn), "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.write(myContainerList)
assert len(myContainerList) == 1
def __writeFile(
self,
ofh,
containerList,
maxLineLength=900,
columnAlignFlag=True,
lastInOrder=None,
selectOrder=None,
useStopTokens=False,
formattingStep=None,
enforceAscii=False,
cnvCharRefs=False,
):
"""Internal method mapping arguments to PDBxWriter API."""
#
pdbxW = PdbxWriter(ofh)
pdbxW.setUseStopTokens(flag=useStopTokens)
pdbxW.setMaxLineLength(numChars=maxLineLength)
pdbxW.setAlignmentFlag(flag=columnAlignFlag)
pdbxW.setRowPartition(numParts=formattingStep)
pdbxW.setConvertCharRefs(flag=cnvCharRefs)
pdbxW.setSetEnforceAscii(enforceAscii)
pdbxW.write(containerList,
lastInOrder=lastInOrder,
selectOrder=selectOrder)
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 testSingleRowFile(self):
"""Test case - read /write single row and null row in data file"""
try:
#
myDataList = []
ifh = open(self.__pathTestFile, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
myBlock = myDataList[0]
myCat = myBlock.getObj("symmetry")
logger.debug("----attribute list %r", myCat.getAttributeList())
row = myCat.getRow(0)
logger.debug("----ROW %r", row)
#
# myCat.dumpIt()
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 strip(self, inpPath, outPath, stripList=[]):
""" Strip categories from inpPath and write to outPath
"""
try:
myDataList = []
with open(inpPath, "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
#
myBlock = myDataList[0]
myName = myBlock.getName()
newContainer = DataContainer(myName)
for objName in myBlock.getObjNameList():
myObj = myBlock.getObj(objName)
if myObj.getName() not in stripList:
newContainer.append(myObj)
#
with open(outPath, "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.setPreferSingleQuotes()
pWr.write([newContainer])
return True
except Exception as e:
logger.exception("Failing with %s" % str(e))
return False
def testWriteDataFile(self):
"""Test case - write data file"""
try:
#
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([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])
aCat.append([7, 6, 5, 4, 3, 2, 1])
# aCat.printIt()
curContainer.append(aCat)
# curContainer.printIt()
#
myDataList.append(curContainer)
with open(self.__pathOutputFile1, "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 testUpdateAttribute(self):
"""Test case - udpdate entry_id"""
ifn = self.__pathBigPdbxDataFile
ofn = self.__pathOutputFile2
try:
#
myContainerList = []
with open(ifn, "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myContainerList)
#
dsId = "D_000000"
atName = "entry_id"
for container in myContainerList:
container.setName(dsId)
# remove category citation
container.remove("citation")
for objName in container.getObjNameList():
dcObj = container.getObj(objName)
if dcObj.hasAttribute(atName):
for iRow in range(0, dcObj.getRowCount()):
dcObj.setValue(dsId, attributeName=atName, rowIndex=iRow)
elif objName.lower() == "entry":
dcObj.setValue(dsId, attributeName="id", rowIndex=0)
#
with open(ofn, "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.write(myContainerList)
self.assertEqual(len(myContainerList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def WriteCif(self, outputFilePath=None):
"""Write out cif file"""
if not outputFilePath:
return
#
ofh = open(outputFilePath, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(self.__dataList)
ofh.close()
def test_read_write_data_file_stop(self, rw_data):
myDataList = []
with open(str(rw_data['pathTestFileStop']), "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
with open(str(rw_data['pathOutputFile3']), "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.write(myDataList)
assert len(myDataList) == 1
def test_read_write_data_file(self, writer_paths):
myDataList = []
with open(str(writer_paths['pathPdbxDataFile']), "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
with open(str(writer_paths['pathOutputFile1']), "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.write(myDataList)
assert len(myDataList) == 1
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 testRowListInitialization(self):
"""Test case - Row list initialization of a data category and data block"""
try:
#
fn = self.__pathOutputFile4
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()
logger.debug("Recovered data category %s", name)
logger.debug("Attribute list %r", repr(aList))
logger.debug("Row list %r", repr(rList))
self.assertEqual(len(myContainerList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def write(self):
"""
Given a file name, a pdbx writer is used to write data stored in self.__dataList
:return written: a boolean; True when pdf writer is finished
"""
written = False
if self.filename:
ofh = open(self.filename, "w")
pdbx_writer = PdbxWriter(ofh)
pdbx_writer.write(self.__dataList)
ofh.close()
written = True
return written
def testReadWriteDataFileStop(self):
"""Test case - data file read write test with stop tokens"""
try:
myDataList = []
with open(self.__pathTestFileStop, "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
with open(self.__pathOutputFile3, "w") as ofh:
pWr = PdbxWriter(ofh)
pWr.write(myDataList)
self.assertEqual(len(myDataList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
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 _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 testPdbxFileCase(self):
"""Test case sensitive PdxWriter"""
if os.path.exists(self.__pathOutputFile):
os.unlink(self.__pathOutputFile)
curContainer = self.__generateData()
myDataList = [curContainer]
try:
with open(self.__pathOutputFile, "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
self.__testReaders(self.__pathOutputFile)
def testRowDictInitialization(self):
"""Test case - Row dictionary initialization of a data category and data block
"""
try:
#
rLen = 10
fn = self.__pathOutputFile5
attributeNameList = ["a", "b", "c", "d"]
rowList = [{"a": 1, "b": 2, "c": 3, "d": 4} for i in range(rLen)]
nameCat = "myCategory"
#
#
curContainer = DataContainer("myblock")
aCat = DataCategory(nameCat, attributeNameList, rowList)
aCat.append({"a": 1, "b": 2, "c": 3, "d": 4})
aCat.append({"a": 1, "b": 2, "c": 3, "d": 4})
aCat.extend(rowList)
curContainer.append(aCat)
aCat.renameAttributes({"a": "aa", "b": "bb", "c": "cc", "d": "dd"})
aCat.setName("renamedCategory")
#
#
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()
logger.debug("Recovered data category %s", name)
logger.debug("Attribute list %r", repr(aList))
logger.debug("Row list %r", repr(rList))
self.assertEqual(len(myContainerList), 1)
self.assertEqual(len(rList), 2 * rLen + 2)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_single_row_file(self, rw_data):
myDataList = []
with open(str(rw_data['pathTestFile']), "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
myBlock = myDataList[0]
myCat = myBlock.getObj('symmetry')
print("----attribute list %r\n" % myCat.getAttributeList())
row = myCat.getRow(0)
print("----ROW %r\n" % row)
#
# myCat.dumpIt()
with open(str(rw_data['pathOutputFile2']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
def test_update_data_file(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.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(str(rw_data['pathOutputFile1']), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
myDataList = []
ifh = open(str(rw_data['pathOutputFile1']), "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
myBlock = myDataList[0]
myCat = myBlock.getObj('pdbx_seqtool_mapping_ref')
for iRow in range(0, myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id', iRow)
myCat.setValue(100, 'ref_mon_num', iRow)
with open(str(rw_data['pathOutputFile2']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
def test_update_data_file(self, writer_paths):
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((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)
with open(str(writer_paths['pathOutputFile1']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
#
# Read and update the data -
#
myDataList = []
with open(str(writer_paths['pathOutputFile1']), "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(myDataList)
#
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(str(writer_paths['pathOutputFile2']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
def test_row_list_initialization(self, rw_data):
fn = rw_data['pathOutputFile4']
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)
curContainer.append(aCat)
myContainerList = []
myContainerList.append(curContainer)
ofh = open(str(fn), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myContainerList)
ofh.close()
myContainerList = []
ifh = open(str(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()
print("Recovered data category %s\n" % name)
print("Attribute list %r\n" % repr(aList))
print("Row list %r\n" % repr(rList))
assert len(myContainerList) == 1
def testSingleRow(self):
"""Test case - read /write single row and null row in data file
"""
try:
#
myDataList = []
# ofh = open(self.__pathOutputFile1, "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.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"])
# aCat.dumpIt()
curContainer.append(aCat)
#
bCat = curContainer.getObj("pdbx_seqtool_mapping_ref")
logger.debug("----attribute list %r", bCat.getAttributeList())
row = bCat.getRow(0)
logger.debug("----ROW %r", row)
#
with open(self.__pathOutputFile2, "w") as ofh:
myDataList.append(curContainer)
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_row_dict_initialization(self, rw_data):
rLen = 10
fn = rw_data['pathOutputFile5']
attributeNameList = ['a', 'b', 'c', 'd']
rowList = [{'a': 1, 'b': 2, 'c': 3, 'd': 4} for i in range(rLen)]
nameCat = 'myCategory'
#
#
curContainer = DataContainer("myblock")
aCat = DataCategory(nameCat, attributeNameList, rowList)
aCat.append({'a': 1, 'b': 2, 'c': 3, 'd': 4})
aCat.append({'a': 1, 'b': 2, 'c': 3, 'd': 4})
aCat.extend(rowList)
curContainer.append(aCat)
aCat.renameAttributes({'a': 'aa', 'b': 'bb', 'c': 'cc', 'd': 'dd'})
aCat.setName('renamedCategory')
#
#
myContainerList = []
myContainerList.append(curContainer)
ofh = open(str(fn), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myContainerList)
ofh.close()
myContainerList = []
ifh = open(str(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()
print("Recovered data category %s\n" % name)
print("Attribute list %r\n" % repr(aList))
print("Row list %r\n" % repr(rList))
assert len(myContainerList) == 1
assert len(rList) == 2 * rLen + 2
def test_write_data_file(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.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])
aCat.append([7, 6, 5, 4, 3, 2, 1])
curContainer.append(aCat)
myDataList.append(curContainer)
with open(str(rw_data['pathOutputFile1']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
def test_write_data_file(self, writer_paths):
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(
(1, 2, 3, 4, '55555555555555555555555555555555555555555555', 6, 7))
aCat.append((1, 2, 3, 4, '5555', 6, 7))
aCat.append((1, 2, 3, 4, '5555555555', 6, 7))
aCat.append((1, 2, 3, 4, '5', 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
with open(str(writer_paths['pathOutputFile1']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.setAlignmentFlag(flag=True)
pdbxW.write(myDataList)
assert len(myDataList) == 1