Beispiel #1
0
    def test_gen_ddlm(self, in_tmpdir, test_files):
        myIo = IoAdapterPy()
        containerList = myIo.readFile(
            inputFilePath=str(test_files / 'mmcif_pdbx_v5_next.dic'))
        dApi = DictionaryApi(containerList=containerList, consolidate=True)
        parentD = dApi.getParentDictionary()
        #
        oCList = []
        dDef = DataContainer('mmcif_pdbx_ddlm_auto')
        dc = DataCategory("dictionary")
        dc.appendAttribute("title")
        dc.appendAttribute("class")
        dc.appendAttribute("version")
        dc.appendAttribute("date")
        dc.appendAttribute("ddl_conformance")
        dc.appendAttribute("text")
        dc.append([
            'mmcif_pdbx_ddlm_auto', 'Instance', 'latest', '2018-03-09',
            'ddlm best effort',
            'Software converted PDBx dictionary using DDLm semantics'
        ])
        dDef.append(dc)
        oCList.append(dDef)

        catIdx = dApi.getCategoryIndex()
        for catName in sorted(catIdx.keys()):
            attNameList = catIdx[catName]
            # created definition container -
            cDef = DefinitionContainer(catName)
            oCList.append(cDef)
            #
            dc = DataCategory("definition")
            dc.appendAttribute("id")
            dc.appendAttribute("scope")
            dc.appendAttribute("class")
            dc.appendAttribute("update")
            dc.append([catName, "Category", "Loop", "2018-03-09"])
            cDef.append(dc)
            val = dApi.getCategoryDescription(category=catName)
            dc = DataCategory("description")
            dc.appendAttribute("text")
            dc.append([val])
            cDef.append(dc)
            #
            dc = DataCategory("name")
            dc.appendAttribute("category_id")
            dc.appendAttribute("object_id")

            valList = dApi.getCategoryGroupList(category=catName)
            pcg = catName
            for val in valList:
                if val != 'inclusive_group':
                    pcg = val
                    break
            dc.append([catName, pcg])
            cDef.append(dc)

            valList = dApi.getCategoryKeyList(category=catName)
            if len(valList) < 1:
                print("Missing caegory key for category %s\n" % catName)
            else:
                dc = DataCategory("category")
                dc.appendAttribute("key_id")
                kItemName = CifName.itemName(catName, "synthetic_key")
                dc.append([kItemName])
                cDef.append(dc)

                iDef = DefinitionContainer(kItemName)
                self._makeKeyItem(catName, "synthetic_key", valList, iDef)
                oCList.append(iDef)

            for attName in attNameList:
                itemName = CifName.itemName(catName, attName)
                iDef = DefinitionContainer(itemName)

                oCList.append(iDef)

                #
                dc = DataCategory("definition")
                dc.appendAttribute("id")
                dc.appendAttribute("scope")
                dc.appendAttribute("class")
                dc.appendAttribute("update")
                dc.append([itemName, "Item", "Single", "2013-08-22"])
                iDef.append(dc)
                #
                val = dApi.getDescription(category=catName, attribute=attName)
                dc = DataCategory("description")
                dc.appendAttribute("text")
                dc.append([val])
                iDef.append(dc)
                #
                dc = DataCategory("name")
                dc.appendAttribute("category_id")
                dc.appendAttribute("object_id")
                #
                if itemName in parentD:
                    dc.appendAttribute("linked_item_id")
                    dc.append([catName, attName, parentD[itemName][0]])
                else:
                    dc.append([catName, attName])
                iDef.append(dc)
                #
                #
                aliasList = dApi.getItemAliasList(category=catName,
                                                  attribute=attName)
                if len(aliasList) > 0:
                    dc = DataCategory("alias")
                    dc.appendAttribute("definition_id")
                    for alias in aliasList:
                        dc.append([alias[0]])
                    iDef.append(dc)

                enList = dApi.getEnumListAltWithDetail(category=catName,
                                                       attribute=attName)

                tC = dApi.getTypeCode(category=catName, attribute=attName)
                tcontainer = 'Single'
                purpose = 'Describe'
                source = 'Recorded'
                contents = 'Text'
                #
                if tC is None:
                    self.__lfh.write("Missing data type attribute %s\n" %
                                     attName)
                elif tC in [
                        'code', 'atcode', 'name', 'idname', 'symop', 'fax',
                        'phone', 'email', 'code30', 'ec-type'
                ]:
                    purpose = 'Encode'
                    contents = 'Text'
                    source = 'Assigned'
                elif tC in ['ucode']:
                    purpose = 'Encode'
                    contents = 'Code'
                    source = 'Assigned'
                elif tC in ['line', 'uline', 'text']:
                    purpose = 'Describe'
                    source = 'Recorded'
                    contents = 'Text'
                elif tC in ['int']:
                    purpose = 'Number'
                    source = 'Recorded'
                    contents = 'Integer'
                elif tC in ['int-range']:
                    purpose = 'Number'
                    source = 'Recorded'
                    contents = 'Range'
                elif tC in ['float']:
                    purpose = 'Measurand'
                    source = 'Recorded'
                    contents = 'Real'
                elif tC in ['float-range']:
                    purpose = 'Measurand'
                    source = 'Recorded'
                    contents = 'Range'
                elif tC.startswith('yyyy'):
                    source = 'Assigned'
                    contents = 'Date'
                    purpose = 'Describe'

                if len(enList) > 0:
                    purpose = 'State'

                dc = DataCategory("type")
                dc.appendAttribute("purpose")
                dc.appendAttribute("source")
                dc.appendAttribute("contents")
                dc.appendAttribute("container")
                dc.append([purpose, source, contents, tcontainer])
                iDef.append(dc)
                #
                if (len(enList) > 0):
                    dc = DataCategory("enumeration_set")
                    dc.appendAttribute("state")
                    dc.appendAttribute("detail")
                    for en in enList:
                        dc.append([en[0], en[1]])
                    iDef.append(dc)

                dfv = dApi.getDefaultValue(category=catName, attribute=attName)
                bvList = dApi.getBoundaryList(category=catName,
                                              attribute=attName)
                if (((dfv is not None) and (dfv not in ['?', '.']))
                        or len(bvList) > 0):
                    row = []
                    dc = DataCategory("enumeration")
                    if dfv is not None:
                        dc.appendAttribute("default")
                        row.append(dfv)
                    if len(bvList) > 0:
                        dc.appendAttribute("range")
                        mminVp = -1000000
                        mmaxVp = 10000000
                        mminV = mmaxVp
                        mmaxV = mminVp
                        for bv in bvList:
                            minV = float(bv[0]) if bv[0] != '.' else mminVp
                            maxV = float(bv[1]) if bv[1] != '.' else mmaxVp
                            mminV = min(mminV, minV)
                            mmaxV = max(mmaxV, maxV)
                        if mminV == mminVp:
                            mminV = ''
                        if mmaxV == mmaxVp:
                            mmaxV = ''
                        row.append(str(mminV) + ":" + str(mmaxV))

                    dc.append(row)
                    iDef.append(dc)

        myIo.writeFile(outputFilePath="mmcif_pdbx_ddlm_auto.dic",
                       containerList=oCList)
    def testGenDDLm(self):
        """Generating alternative DDLm metadata format. (starting point)"""
        try:
            myIo = IoAdapterPy(self.__verbose, self.__lfh)
            self.__containerList = myIo.readFile(
                inputFilePath=self.__pathPdbxDictionary)
            dApi = DictionaryApi(containerList=self.__containerList,
                                 consolidate=True,
                                 verbose=self.__verbose)
            parentD = dApi.getParentDictionary()
            #
            oCList = []
            dDef = DataContainer("mmcif_pdbx_ddlm_auto")
            dc = DataCategory("dictionary")
            dc.appendAttribute("title")
            dc.appendAttribute("class")
            dc.appendAttribute("version")
            dc.appendAttribute("date")
            dc.appendAttribute("ddl_conformance")
            dc.appendAttribute("text")
            dc.append([
                "mmcif_pdbx_ddlm_auto", "Instance", "latest", "2018-03-09",
                "ddlm best effort",
                "Software converted PDBx dictionary using DDLm semantics"
            ])
            dDef.append(dc)
            oCList.append(dDef)

            catIdx = dApi.getCategoryIndex()
            for catName in sorted(catIdx.keys()):
                attNameList = catIdx[catName]
                # created definition container -
                cDef = DefinitionContainer(catName)
                oCList.append(cDef)
                #
                dc = DataCategory("definition")
                dc.appendAttribute("id")
                dc.appendAttribute("scope")
                dc.appendAttribute("class")
                dc.appendAttribute("update")
                dc.append([catName, "Category", "Loop", "2018-03-09"])
                cDef.append(dc)
                val = dApi.getCategoryDescription(category=catName)
                dc = DataCategory("description")
                dc.appendAttribute("text")
                dc.append([val])
                cDef.append(dc)
                #
                dc = DataCategory("name")
                dc.appendAttribute("category_id")
                dc.appendAttribute("object_id")

                valList = dApi.getCategoryGroupList(category=catName)
                pcg = catName
                for val in valList:
                    if val != "inclusive_group":
                        pcg = val
                        break
                dc.append([catName, pcg])
                cDef.append(dc)

                valList = dApi.getCategoryKeyList(category=catName)
                if not valList:
                    self.__lfh.write("Missing caegory key for category %s\n" %
                                     catName)
                else:
                    dc = DataCategory("category")
                    dc.appendAttribute("key_id")
                    kItemName = CifName.itemName(catName, "synthetic_key")
                    dc.append([kItemName])
                    cDef.append(dc)

                    iDef = DefinitionContainer(kItemName)
                    self.__makeKeyItem(catName, "synthetic_key", valList, iDef)
                    oCList.append(iDef)

                for attName in attNameList:
                    itemName = CifName.itemName(catName, attName)
                    iDef = DefinitionContainer(itemName)

                    oCList.append(iDef)

                    #
                    dc = DataCategory("definition")
                    dc.appendAttribute("id")
                    dc.appendAttribute("scope")
                    dc.appendAttribute("class")
                    dc.appendAttribute("update")
                    dc.append([itemName, "Item", "Single", "2013-08-22"])
                    iDef.append(dc)
                    #
                    val = dApi.getDescription(category=catName,
                                              attribute=attName)
                    dc = DataCategory("description")
                    dc.appendAttribute("text")
                    dc.append([val])
                    iDef.append(dc)
                    #
                    dc = DataCategory("name")
                    dc.appendAttribute("category_id")
                    dc.appendAttribute("object_id")
                    #
                    if itemName in parentD:
                        dc.appendAttribute("linked_item_id")
                        dc.append([catName, attName, parentD[itemName][0]])
                    else:
                        dc.append([catName, attName])
                    iDef.append(dc)
                    #
                    #
                    aliasList = dApi.getItemAliasList(category=catName,
                                                      attribute=attName)
                    if aliasList:
                        dc = DataCategory("alias")
                        dc.appendAttribute("definition_id")
                        for alias in aliasList:
                            dc.append([alias[0]])
                        iDef.append(dc)

                    enList = dApi.getEnumListAltWithDetail(category=catName,
                                                           attribute=attName)

                    tC = dApi.getTypeCode(category=catName, attribute=attName)
                    tcontainer = "Single"
                    purpose = "Describe"
                    source = "Recorded"
                    contents = "Text"
                    #
                    if tC is None:
                        self.__lfh.write("Missing data type attribute %s\n" %
                                         attName)
                    elif tC in [
                            "code", "atcode", "name", "idname", "symop", "fax",
                            "phone", "email", "code30", "ec-type"
                    ]:
                        purpose = "Encode"
                        contents = "Text"
                        source = "Assigned"
                    elif tC in ["ucode"]:
                        purpose = "Encode"
                        contents = "Code"
                        source = "Assigned"
                    elif tC in ["line", "uline", "text"]:
                        purpose = "Describe"
                        source = "Recorded"
                        contents = "Text"
                    elif tC in ["int"]:
                        purpose = "Number"
                        source = "Recorded"
                        contents = "Integer"
                    elif tC in ["int-range"]:
                        purpose = "Number"
                        source = "Recorded"
                        contents = "Range"
                    elif tC in ["float"]:
                        purpose = "Measurand"
                        source = "Recorded"
                        contents = "Real"
                    elif tC in ["float-range"]:
                        purpose = "Measurand"
                        source = "Recorded"
                        contents = "Range"
                    elif tC.startswith("yyyy"):
                        source = "Assigned"
                        contents = "Date"
                        purpose = "Describe"

                    if enList:
                        purpose = "State"

                    dc = DataCategory("type")
                    dc.appendAttribute("purpose")
                    dc.appendAttribute("source")
                    dc.appendAttribute("contents")
                    dc.appendAttribute("container")
                    dc.append([purpose, source, contents, tcontainer])
                    iDef.append(dc)
                    #
                    if enList:
                        dc = DataCategory("enumeration_set")
                        dc.appendAttribute("state")
                        dc.appendAttribute("detail")
                        for en in enList:
                            dc.append([en[0], en[1]])
                        iDef.append(dc)

                    dfv = dApi.getDefaultValue(category=catName,
                                               attribute=attName)
                    bvList = dApi.getBoundaryList(category=catName,
                                                  attribute=attName)
                    if ((dfv is not None) and
                        (dfv not in ["?", "."])) or bvList:
                        row = []
                        dc = DataCategory("enumeration")
                        if dfv is not None:
                            dc.appendAttribute("default")
                            row.append(dfv)
                        if bvList:
                            dc.appendAttribute("range")
                            mminVp = -1000000
                            mmaxVp = 10000000
                            mminV = mmaxVp
                            mmaxV = mminVp
                            for bv in bvList:
                                minV = float(bv[0]) if bv[0] != "." else mminVp
                                maxV = float(bv[1]) if bv[1] != "." else mmaxVp
                                mminV = min(mminV, minV)
                                mmaxV = max(mmaxV, maxV)
                            if mminV == mminVp:
                                mminV = ""
                            if mmaxV == mmaxVp:
                                mmaxV = ""
                            row.append(str(mminV) + ":" + str(mmaxV))

                        dc.append(row)
                        iDef.append(dc)

            myIo.writeFile(outputFilePath=os.path.join(
                HERE, "test-output", "mmcif_pdbx_ddlm_auto.dic"),
                           containerList=oCList)

        except Exception as e:
            logger.exception("Failing with %s", str(e))
            self.fail()