def testGetUcode(self):
"""Test case - Get all data items of type ucode
"""
print("\n")
try:
myIo = IoAdapter(raiseExceptions=True)
self.__containerList = myIo.readFile(
inputFilePath=self.__pathPdbxDictionary)
dApi = DictionaryApi(containerList=self.__containerList,
consolidate=True,
verbose=self.__verbose)
logger.debug(
"+++++++++++++++++++++++++++++++++++++++++++++++++++++++\n")
catNameList = dApi.getCategoryList()
for catName in catNameList:
itemNameList = dApi.getItemNameList(catName)
for itemName in itemNameList:
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
code = dApi.getTypeCode(categoryName, attributeName)
if (code == "ucode"):
print("Table: ", categoryName, "\tColumn: ",
attributeName, "\tType: ", code)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def test_dump_index(self, api_paths):
myIo = IoAdapter(raiseExceptions=True)
containerList = myIo.readFile(
inputFilePath=str(api_paths['pathPdbxDictionary']))
dApi = DictionaryApi(containerList=containerList, consolidate=True)
print("Index = %r\n" % dApi.getItemNameList('pdbx_nmr_spectral_dim'))
print("Index = %r\n" %
dApi.getAttributeNameList('pdbx_nmr_spectral_dim'))
catIndex = dApi.getCategoryIndex()
print("Index = %r\n" % catIndex['pdbx_nmr_spectral_dim'])
assert catIndex['pdbx_nmr_spectral_dim'] is not None
def testDumpIndex(self):
"""Test case - dump methods for dictionary metadata"""
try:
myIo = IoAdapter(raiseExceptions=True)
self.__containerList = myIo.readFile(inputFilePath=self.__pathPdbxDictionary)
dApi = DictionaryApi(containerList=self.__containerList, consolidate=True, verbose=self.__verbose)
if self.__verbose:
dApi.dumpCategoryIndex(fh=self.__lfh)
logger.debug("Index = %r\n", dApi.getItemNameList("pdbx_nmr_spectral_dim"))
logger.debug("Index = %r\n", dApi.getAttributeNameList("pdbx_nmr_spectral_dim"))
catIndex = dApi.getCategoryIndex()
logger.debug("Index = %r\n", catIndex["pdbx_nmr_spectral_dim"])
self.assertIsNotNone(catIndex["pdbx_nmr_spectral_dim"])
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
class DictionaryData(object):
def __init__(self):
basedir = os.path.join(os.path.dirname(__file__), "..", "dist")
self.dictPath = os.path.join(basedir, "mmcif_pdbx_v5_next.dic")
def readDictionary(self):
myIo = IoAdapterPy()
self.__containerList = myIo.readFile(inputFilePath=self.dictPath)
self._dApi = DictionaryApi(containerList=self.__containerList,
consolidate=True)
assert len(self.getGroups()) > 0, "Failed to load %s" % self.dictPath
def getGroups(self):
groupList = self._dApi.getCategoryGroups()
return groupList
def getTypeRegex(self, cat, attrib):
return self._dApi.getTypeRegex(cat, attrib)
def getTypeRegexAlt(self, cat, attrib):
return self._dApi.getTypeRegexAlt(cat, attrib)
def getDataTypeList(self):
""" Return list of tuples containing ('code','primitive_code','construct','detail' )
"""
return self._dApi.getDataTypeList()
def getEnumList(self, category, attribute, sortFlag=True):
return self._dApi.getEnumList(category, attribute, sortFlag)
def getEnumListAlt(self, category, attribute, sortFlag=True):
return self._dApi.getEnumListAlt(category, attribute, sortFlag)
def getEnumListAltWithDetail(self, category, attribute):
return self._dApi.getEnumListAltWithDetail(category, attribute)
def getAllCategory(self):
"""Returns list of all categories"""
return self._dApi.getCategoryList()
def getCategoryList(self):
return self._dApi.getCategoryList()
def getItemNameList(self, category):
return self._dApi.getItemNameList(category)
def wwPDBContext(self, catItem):
"""Returns true if category or item have local context"""
category, item = catItem.split('.')
if category[0] == "_":
category = category[1:]
#print "CHECKING ", category, item, self.__dictA.getCategoryContextList(category)
if self._dApi.getCategoryContextList(category) == ['WWPDB_LOCAL']:
return True
if self._dApi.getContextList(category, item) == ['WWPDB_LOCAL']:
return True
return False
def getCategoryItemEnum(self, itemName):
"""Returns any archive enum list"""
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
return self._dApi.getEnumList(categoryName, attributeName)
def getCategoryPdbxItemEnum(self, itemName):
"""Returns any DepUI enum list"""
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
return self._dApi.getEnumListAlt(categoryName, attributeName)
def getItemRelatedList(self, itemName):
categoryName = CifName.categoryPart(itemName)
attributeName = CifName.attributePart(itemName)
return self._dApi.getItemRelatedList(categoryName, attributeName)
def testClassifyByGroup(self):
"""Test case - organize dictionary items by classes: SAMPLE, MX, NMR, EM, STRUCTURE, and DB"""
try:
myIo = IoAdapter(raiseExceptions=True)
self.__containerList = myIo.readFile(
inputFilePath=self.__pathPdbxDictionary)
dApi = DictionaryApi(containerList=self.__containerList,
consolidate=True,
verbose=self.__verbose)
#
itemList = []
groupList = dApi.getCategoryGroups()
categoryList = dApi.getCategoryList()
for category in categoryList:
itemList.extend(dApi.getItemNameList(category))
itemList = sorted(set(itemList))
logger.info("Total category length %d", len(categoryList))
logger.info("Total definition length %d", len(itemList))
logger.info("group length %s", len(groupList))
logger.debug("groupList %r", groupList)
#
findUnlinked = False
if findUnlinked:
tSet = set(["pdbx_group", "inclusive_group"])
for category in categoryList:
gList = dApi.getCategoryGroupList(category)
gSet = set(gList)
if gSet == tSet:
logger.info("unqualified %s", category)
# logger.info("%s -> %r", category, gList)
if not gList:
logger.info("--- No category group assignment for %s",
category)
#
classD = {}
# Add category group members -
for groupName, className in self.__groupClassTupL:
categoryL = dApi.getCategoryGroupCategories(
groupName, followChildren=True)
for category in categoryL:
classD.setdefault(className, []).extend(
dApi.getItemNameList(category))
#
# Add unlinked categories
#
for category, className in self.__unlinkedCategoryClassTup:
classD.setdefault(className,
[]).extend(dApi.getItemNameList(category))
#
sumItem = 0
classItemD = {}
for className, itemL in classD.items():
numItem = len(set(itemL))
sumItem += numItem
logger.info("class %s items %d", className, len(set(itemL)))
for item in itemL:
classItemD[item] = True
#
logger.info("Sum classified items is %d", sumItem)
logger.info("classified items %d", len(classItemD))
#
logger.debug("classItemD.items() %r",
list(classItemD.items())[:10])
missingGroupL = []
jj = 0
for item in itemList:
if item not in classItemD:
jj += 1
category = CifName.categoryPart(item)
logger.info("%d item %r category %r", jj, item, category)
missingGroupL.extend(dApi.getCategoryGroupList(category))
#
logger.info("missing groups %r", sorted(set(missingGroupL)))
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()