def testDumpDictionary(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) # dApi.dumpCategoryIndex(fh=self.__lfh) # dApi.dumpEnumFeatures(fh=self.__lfh) # dApi.dumpFeatures(fh=self.__lfh) # dApi.dumpMethods(fh=self.__lfh) logger.debug( "+++++++++++++++++++++++++++++++++++++++++++++++++++++++\n") groupList = dApi.getCategoryGroups() logger.debug("groupList %s\n", groupList) for group in groupList: logger.debug("Group %s category list %s\n", group, dApi.getCategoryGroupCategories(groupName=group)) self.assertGreater(len(groupList), 10) except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
def test_dump_dictionary(self, api_paths): myIo = IoAdapter(raiseExceptions=True) containerList = myIo.readFile( inputFilePath=str(api_paths['pathPdbxDictionary'])) dApi = DictionaryApi(containerList=containerList, consolidate=True) print('+++++++++++++++++++++++++++++++++++++++++++++++++++++++\n') groupList = dApi.getCategoryGroups() print('groupList %s\n' % groupList) for group in groupList: print('Group %s category list %s\n' % (group, dApi.getCategoryGroupCategories(groupName=group))) assert len(groupList) > 10
def test_markup_category_group(self, in_tmpdir, test_files, out_file_name, groupSelectList): oFile = out_file_name rL = [] myIo = IoAdapter() containerList = myIo.readFile( str(test_files / "mmcif_pdbx_v5_next.dic")) dApi = DictionaryApi(containerList=containerList, consolidate=True) # groupList = dApi.getCategoryGroups() print('groupList %s\n' % groupList) for groupName in groupList: if groupSelectList and groupName not in groupSelectList: continue # # Goup header details # rL.append("# Category Group %s" % groupName) rL.append("") rL.append("") rL.append("%s" % dApi.getCategoryGroupDescription(groupName)) rL.append("") rL.append("---") rL.append("") catNameList = dApi.getCategoryGroupCategories(groupName=groupName) # cList = self.__sortIgnoreCase(catNameList) for catName in cList: print('Group %s category %s\n' % (groupName, catName)) catDescription = dApi.getCategoryDescription(category=catName) catExTupList = dApi.getCategoryExampleList(category=catName) keyItemNameList = dApi.getCategoryKeyList(category=catName) keyAttNameList = [ CifName.attributePart(k) for k in keyItemNameList ] # # Category header details # rL.append("## Category %s" % catName) rL.append("") rL.append("") rL.append(" %s" % catDescription) rL.append("") rL.append("---") rL.append("") if catExTupList: rL.extend( self.__formatTupListInset(catExTupList, tab=' ')) # # summary table # rL.append("") rL.append("---") rL.append("") rL.append( "| Attribute | Key | Required | Type | Units | Enumerated | Bounded |" ) rL.append( "| --------- | --- | -------- | ---- | ----- | ---------- | ------- |" ) aList = self.__sortIgnoreCase( dApi.getAttributeNameList(category=catName)) for attName in aList: isKey = attName in keyAttNameList attDescription = dApi.getDescription(category=catName, attribute=attName) attUnits = dApi.getUnits(category=catName, attribute=attName) attMandatory = dApi.getMandatoryCode(category=catName, attribute=attName) attTypeCode = dApi.getTypeCode(category=catName, attribute=attName) enumTupList = dApi.getEnumListWithDetail(category=catName, attribute=attName) if len(enumTupList) > 0: isEnum = True else: isEnum = False bL = dApi.getBoundaryList(category=catName, attribute=attName) if len(bL) > 0: isBounded = True else: isBounded = False rL.append( '| %s | %s | %s | %s | %s | %s | %s |' % (attName, self.__trB(isKey), attMandatory, attTypeCode, attUnits, self.__trB(isEnum), self.__trB(isBounded))) # rL.append("") rL.append("---") rL.append("") # for attName in aList: isKey = attName in keyAttNameList attMandatory = dApi.getMandatoryCode(category=catName, attribute=attName) # tN = '_' + catName + '.' + attName if isKey: tN = tN + ' (key)' elif attMandatory.upper() in ['YES', 'Y']: tN = tN + ' (required)' # rL.append("#### %s\n" % tN) rL.append("") attDescription = dApi.getDescription(category=catName, attribute=attName) rL.append(" %s\n" % attDescription) rL.append("") attUnits = dApi.getUnits(category=catName, attribute=attName) attTypeCode = dApi.getTypeCode(category=catName, attribute=attName) enumTupList = dApi.getEnumListWithDetail(category=catName, attribute=attName) if len(enumTupList) > 0: rL.append("") rL.append("---") rL.append("") rL.append("| Allowed Values | Detail |") rL.append("| -------------- | ------ |") for tup in enumTupList: if tup[1] and len(tup[1]) > 0: rL.append("| %s | %s |" % (tup[0], tup[1])) else: rL.append("| %s | %s |" % (tup[0], ' ')) rL.append("") # bL = dApi.getBoundaryList(category=catName, attribute=attName) btL = self.__processbounds(bL) if len(btL) > 0: tup = btL[0] rL.append("") rL.append("---") rL.append("") rL.append("| %s | %s |" % (tup[0], tup[1])) # rL.append("| ------------- | ------ |") for tup in btL[1:]: rL.append("| %s | %s |" % (tup[0], tup[1])) rL.append("") rL.append("") with open(str(oFile), 'w') as ofh: ofh.write('\n'.join(rL))
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()
def __testMarkupCategoryGroup(self, oFile, groupSelectList=None): """Test case - extract the content to be rendered -""" startTime = time.time() logger.debug("\nStarting at %s\n", time.strftime("%Y %m %d %H:%M:%S", time.localtime())) try: rL = [] myIo = IoAdapter() containerList = myIo.readFile(self.__pathPdbxV50Dictionary) dApi = DictionaryApi(containerList=containerList, consolidate=True, verbose=self.__verbose) # groupList = dApi.getCategoryGroups() logger.debug("groupList %s\n", groupList) for groupName in groupList: if groupSelectList and groupName not in groupSelectList: continue # # Goup header details # rL.append("# Category Group %s" % groupName) rL.append("") rL.append("") rL.append("%s" % dApi.getCategoryGroupDescription(groupName)) rL.append("") rL.append("---") rL.append("") catNameList = dApi.getCategoryGroupCategories( groupName=groupName) # cList = self.__sortIgnoreCase(catNameList) for catName in cList: logger.debug("Group %s category %s\n", groupName, catName) catDescription = dApi.getCategoryDescription( category=catName) catExTupList = dApi.getCategoryExampleList( category=catName) keyItemNameList = dApi.getCategoryKeyList(category=catName) keyAttNameList = [ CifName.attributePart(k) for k in keyItemNameList ] # # Category header details # rL.append("## Category %s" % catName) rL.append("") rL.append("") rL.append(" %s" % catDescription) rL.append("") rL.append("---") rL.append("") if catExTupList: rL.extend( self.__formatTupListInset(catExTupList, tab=" ")) # # summary table # rL.append("") rL.append("---") rL.append("") rL.append( "| Attribute | Key | Required | Type | Units | Enumerated | Bounded |" ) rL.append( "| --------- | --- | -------- | ---- | ----- | ---------- | ------- |" ) aList = self.__sortIgnoreCase( dApi.getAttributeNameList(category=catName)) for attName in aList: isKey = attName in keyAttNameList attDescription = dApi.getDescription(category=catName, attribute=attName) attUnits = dApi.getUnits(category=catName, attribute=attName) attMandatory = dApi.getMandatoryCode(category=catName, attribute=attName) attTypeCode = dApi.getTypeCode(category=catName, attribute=attName) enumTupList = dApi.getEnumListWithDetail( category=catName, attribute=attName) if enumTupList: isEnum = True else: isEnum = False bL = dApi.getBoundaryList(category=catName, attribute=attName) if bL: isBounded = True else: isBounded = False rL.append("| %s | %s | %s | %s | %s | %s | %s |" % (attName, self.__trB(isKey), attMandatory, attTypeCode, attUnits, self.__trB(isEnum), self.__trB(isBounded))) # rL.append("") rL.append("---") rL.append("") # for attName in aList: isKey = attName in keyAttNameList attMandatory = dApi.getMandatoryCode(category=catName, attribute=attName) # tN = "_" + catName + "." + attName if isKey: tN = tN + " (key)" elif attMandatory.upper() in ["YES", "Y"]: tN = tN + " (required)" # rL.append("#### %s\n" % tN) rL.append("") attDescription = dApi.getDescription(category=catName, attribute=attName) rL.append(" %s\n" % attDescription) rL.append("") attUnits = dApi.getUnits(category=catName, attribute=attName) attTypeCode = dApi.getTypeCode(category=catName, attribute=attName) enumTupList = dApi.getEnumListWithDetail( category=catName, attribute=attName) if enumTupList: rL.append("") rL.append("---") rL.append("") rL.append("| Allowed Values | Detail |") rL.append("| -------------- | ------ |") for tup in enumTupList: if tup[1]: rL.append("| %s | %s |" % (tup[0], tup[1])) else: rL.append("| %s | %s |" % (tup[0], " ")) rL.append("") # bL = dApi.getBoundaryList(category=catName, attribute=attName) btL = self.__processbounds(bL) if btL: tup = btL[0] rL.append("") rL.append("---") rL.append("") rL.append("| %s | %s |" % (tup[0], tup[1])) # rL.append("| ------------- | ------ |") for tup in btL[1:]: rL.append("| %s | %s |" % (tup[0], tup[1])) rL.append("") rL.append("") with open(oFile, "w") as ofh: ofh.write("\n".join(rL)) except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() endTime = time.time() logger.debug("\nCompleted at %s (%.2f seconds)", time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - startTime)