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)
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 testSetValues(self):
"""Test case - value setters"""
try:
dcU = DataCategory("A", self.__attributeListMiss,
self.__rowListUnicodeMiss)
for i in range(0, dcU.getRowCount()):
dcU.setValue("newValue", attributeName="colM1", rowIndex=i)
self.assertTrue(
dcU.setValue("newValue",
attributeName="colM1",
rowIndex=dcU.getRowCount() + 5))
self.assertRaises(ValueError, dcU.setValue, "newValue", "colX", 0)
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 __extractExtra(self, xrt):
""" Separately extract and parse data from the input document related to EM graphs.
Args:
xrt: ElementTree root element
Returns:
(list): DataCategory objects
"""
rL = []
elV = xrt.find("EM_validation")
if not elV:
return rL
#
graphDataL = []
#
logger.debug("Starting extraExtract -- ")
gAtList = [
"graph_data_id", "graph_id", "title", "x_axis_title",
"x_axis_scale", "x_axis_units", "y_axis_title", "y_axis_scale",
"y_axis_units"
]
infObj = DataCategory("pdbx_vrpt_em_2d_graph_info", gAtList)
#
for el in elV:
logger.debug("-- EM element tag %r attrib count (%d): %r", el.tag,
len(list(el.attrib.keys())), list(el.attrib.keys()))
if el.tag == "RecommendedContourLevel" and "value" in el.attrib:
cObj = DataCategory(
"pdbx_vrpt_em_details",
attributeNameList=["ordinal", "recommended_contour_level"])
cObj.setValue(1, "ordinal", 0)
cObj.setValue(el.attrib["value"], "recommended_contour_level",
0)
rL.append(cObj)
elif el.tag == "map_value_distribution":
try:
dL = self.__getGraphDataElements(el, graphDataId="d_mvd")
cgD = self.__getCommonGraphAttributes(el)
if dL and cgD:
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
infObj.setValue("map_value_distribution", "graph_id",
iRow)
infObj.setValue("d_mvd", "graph_data_id", iRow)
cObj = DataCategory(
"pdbx_vrpt_em_graph_map_value_distribution",
attributeNameList=["graph_id"])
cObj.setValue("map_value_distribution", "graph_id", 0)
graphDataL.extend(dL)
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif el.tag == "volume_estimate":
try:
dL = self.__getGraphDataElements(el, graphDataId="d_ve")
cgD = self.__getCommonGraphAttributes(el)
if dL and cgD:
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
infObj.setValue("volume_estimate", "graph_id", iRow)
infObj.setValue("d_ve", "graph_data_id", iRow)
cObj = DataCategory(
"pdbx_vrpt_em_graph_volume_estimate",
attributeNameList=["graph_id"])
cObj.setValue("volume_estimate", "graph_id", 0)
graphDataL.extend(dL)
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif el.tag == "rotationally_averaged_power_spectrum":
try:
dL = self.__getGraphDataElements(el, graphDataId="d_raps")
cgD = self.__getCommonGraphAttributes(el)
if dL and cgD:
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
infObj.setValue("rotationally_averaged_power_spectrum",
"graph_id", iRow)
infObj.setValue("d_raps", "graph_data_id", iRow)
cObj = DataCategory(
"pdbx_vrpt_em_graph_rotationally_averaged_power_spectrum",
attributeNameList=["graph_id"])
cObj.setValue("rotationally_averaged_power_spectrum",
"graph_id", 0)
graphDataL.extend(dL)
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif el.tag == "atom_inclusion":
# backbone or all_atoms
try:
cObj = None
for cN in ["all_atoms", "backbone"]:
ch = el.find(cN)
abbrev = "aa" if cN == "all_atoms" else "bb"
if ch:
gId = "atom_inclusion_%s" % cN
gdId = "d_ai_%s" % abbrev
dL = self.__getGraphDataElements(ch,
graphDataId=gdId)
cgD = self.__getCommonGraphAttributes(ch)
if dL and cgD:
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
infObj.setValue(gId, "graph_id", iRow)
infObj.setValue(gdId, "graph_data_id", iRow)
#
if not cObj:
cObj = DataCategory(
"pdbx_vrpt_em_graph_atom_inclusion",
attributeNameList=["graph_id", "type"])
tRow = cObj.getRowCount()
cObj.setValue(gId, "graph_id", tRow)
cObj.setValue(cN, "type", tRow)
graphDataL.extend(dL)
if cObj.getRowCount():
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif el.tag == "fsc":
for ch in el:
logger.debug(
"-- Child fsc element tag %r attrib count (%d): %r",
ch.tag, len(list(ch.attrib.keys())),
list(ch.attrib.keys()))
if ch.tag == "resolution_intersections":
try:
atList = [
"ordinal", "resolution_units",
"spatial_frequency_units", "correlation",
"resolution", "spatial_frequency", "curve",
"type"
]
rObj = DataCategory(
"pdbx_vrpt_em_resolution_intersections",
atList)
ru = ch.attrib[
"resolution_unit"] if "resolution_unit" in ch.attrib else "?"
sfu = ch.attrib[
"spatial_frequency_unit"] if "spatial_frequency_unit" in ch.attrib else "?"
ii = 0
for gch in ch:
if gch.tag == "intersection":
for at in [
"correlation", "resolution",
"spatial_frequency", "curve",
"type"
]:
atV = gch.attrib[
at] if at in gch.attrib else "?"
rObj.setValue(atV, at, ii)
rObj.setValue(ru, "resolution_units", ii)
rObj.setValue(sfu,
"spatial_frequency_units",
ii)
rObj.setValue(ii + 1, "ordinal", ii)
ii += 1
if rObj.getRowCount():
rL.append(rObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif ch.tag == "fsc_curves":
try:
iCount = 0
cObj = None
for gch in ch:
if gch.tag == "fsc_curve":
iCount += 1
gdId = "fsc_%d" % iCount
dL = self.__getGraphDataElements(
gch, graphDataId=gdId)
cgD = self.__getCommonGraphAttributes(gch)
curveName = gch.attrib[
"curve_name"] if "curve_name" in gch.attrib else "?"
gId = curveName
fscType = gch.attrib[
"type"] if "type" in gch.attrib else "?"
if dL and cgD and curveName != "?":
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
#
infObj.setValue(gId, "graph_id", iRow)
infObj.setValue(
gdId, "graph_data_id", iRow)
#
iRow = iCount - 1
if not cObj:
cObj = DataCategory(
"pdbx_vrpt_em_graph_fsc_curve",
attributeNameList=[
"graph_id", "type",
"curve_name"
])
cObj.setValue(gId, "graph_id", iRow)
cObj.setValue(fscType, "type", iRow)
cObj.setValue(curveName, "curve_name",
iRow)
graphDataL.extend(dL)
if cObj:
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
elif ch.tag == "fsc_indicator_curves":
try:
iCount = 0
cObj = None
for gch in ch:
if gch.tag == "fsc_indicator_curve":
iCount += 1
gdId = "fsc_i_%d" % iCount
dL = self.__getGraphDataElements(
gch, graphDataId=gdId)
cgD = self.__getCommonGraphAttributes(gch)
curveName = gch.attrib[
"curve_name"] if "curve_name" in gch.attrib else "?"
gId = curveName
fscType = gch.attrib[
"type"] if "type" in gch.attrib else "?"
dataCurveName = gch.attrib[
"data_curve"] if "data_curve" in gch.attrib else "?"
if dL and cgD and curveName != "?" and dataCurveName != "?":
iRow = infObj.getRowCount()
for k, v in cgD.items():
infObj.setValue(v, k, iRow)
#
infObj.setValue(gId, "graph_id", iRow)
infObj.setValue(
gdId, "graph_data_id", iRow)
#
iRow = iCount - 1
if not cObj:
cObj = DataCategory(
"pdbx_vrpt_em_graph_fsc_indicator_curve",
attributeNameList=[
"graph_id", "type",
"curve_name",
"data_curve_name"
])
cObj.setValue(gId, "graph_id", iRow)
cObj.setValue(fscType, "type", iRow)
cObj.setValue(curveName, "curve_name",
iRow)
cObj.setValue(dataCurveName,
"data_curve_name", iRow)
graphDataL.extend(dL)
if cObj:
rL.append(cObj)
except Exception as e:
logger.exception("Failing with %s", str(e))
#
# -- end of element processing
# -------
if infObj.getRowCount():
rL.append(infObj)
#
dObj = DataCategory(
"pdbx_vrpt_em_2d_graph_data",
["ordinal", "graph_data_id", "x_value", "y_value"])
for ii, dD in enumerate(graphDataL):
for k, v in dD.items():
dObj.setValue(v, k, ii)
dObj.setValue(ii + 1, "ordinal", ii)
rL.append(dObj)
return rL
