示例#1
0
    def testConsolidateDictionary(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, expandItemLinked=False, verbose=self.__verbose)
            for itemName in [
                "_entity.id",
                "_entity_poly_seq.num",
                "_atom_site.label_asym_id",
                "_struct_asym.id",
                "_chem_comp.id",
                "chem_comp_atom.comp_id",
                "chem_comp_bond.comp_id",
            ]:
                categoryName = CifName.categoryPart(itemName)
                attributeName = CifName.attributePart(itemName)
                logger.debug("Full parent list for  %s : %s\n", itemName, dApi.getFullParentList(categoryName, attributeName))
                logger.debug("Full child  list for  %s : %s\n", itemName, dApi.getFullChildList(categoryName, attributeName))
                logger.debug("Ultimate parent for  %s : %s\n", itemName, dApi.getUltimateParent(categoryName, attributeName))
                logger.debug("Type code for  %s : %s\n", itemName, dApi.getTypeCode(categoryName, attributeName))
                self.assertIsNotNone(dApi.getTypeCode(categoryName, attributeName))
        except Exception as e:
            logger.exception("Failing with %s", str(e))
            self.fail()
示例#2
0
    def test_consolidate_dictionary(self, api_paths):
        myIo = IoAdapter(raiseExceptions=True)
        containerList = myIo.readFile(
            inputFilePath=str(api_paths['pathPdbxDictionary']))
        dApi = DictionaryApi(containerList=containerList, consolidate=True)

        for itemName in [
                '_entity.id', '_entity_poly_seq.num',
                '_atom_site.label_asym_id', '_struct_asym.id', '_chem_comp.id',
                'chem_comp_atom.comp_id', 'chem_comp_bond.comp_id'
        ]:
            categoryName = CifName.categoryPart(itemName)
            attributeName = CifName.attributePart(itemName)
            print("Full parent list for  %s : %s\n" %
                  (itemName, dApi.getFullParentList(categoryName,
                                                    attributeName)))
            print(
                "Full child  list for  %s : %s\n" %
                (itemName, dApi.getFullChildList(categoryName, attributeName)))
            print("Ultimate parent for  %s : %s\n" %
                  (itemName, dApi.getUltimateParent(categoryName,
                                                    attributeName)))
            print("Type code for  %s : %s\n" %
                  (itemName, dApi.getTypeCode(categoryName, attributeName)))
            assert dApi.getTypeCode(categoryName, attributeName) is not None