class RepoHoldingsDataPrepValidateTests(unittest.TestCase): def setUp(self): self.__verbose = True # self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") self.__pathConfig = os.path.join(TOPDIR, "rcsb", "db", "config", "exdb-config-example.yml") self.__cachePath = os.path.join(TOPDIR, "CACHE") self.__updateId = "2018_25" self.__export = False # configName = "site_info_configuration" self.__cfgOb = ConfigUtil(configPath=self.__pathConfig, defaultSectionName=configName, mockTopPath=self.__mockTopPath) self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=True) self.__sandboxPath = self.__cfgOb.getPath("RCSB_EXCHANGE_SANDBOX_PATH", sectionName=configName) # self.__mU = MarshalUtil(workPath=self.__cachePath) self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())) def tearDown(self): endTime = time.time() logger.debug("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime) def testValidateOptsStrict(self): updateId = self.__updateId schemaLevel = "full" eCount = self.__testValidateOpts(updateId, schemaLevel=schemaLevel) logger.info("Total validation errors schema level %s : %d", schemaLevel, eCount) self.assertTrue(eCount <= 1) @unittest.skip("Troubleshooting test") def testValidateOptsMin(self): updateId = self.__updateId schemaLevel = "min" eCount = self.__testValidateOpts(updateId, schemaLevel=schemaLevel) logger.info("Total validation errors schema level %s : %d", schemaLevel, eCount) self.assertTrue(eCount <= 1) def __testValidateOpts(self, updateId, schemaLevel="full"): schemaNames = ["repository_holdings"] collectionNames = { "repository_holdings": [ "repository_holdings_update_entry", "repository_holdings_current_entry", "repository_holdings_unreleased_entry", "repository_holdings_removed_entry", "repository_holdings_combined_entry", ], "entity_sequence_clusters": ["cluster_members", "cluster_provenance", "entity_members"], } # eCount = 0 for schemaName in schemaNames: for collectionName in collectionNames[schemaName]: _ = self.__schP.makeSchemaDef(schemaName, dataTyping="ANY", saveSchema=True) cD = self.__schP.makeSchema(schemaName, collectionName, encodingType="JSON", level=schemaLevel, saveSchema=True) dL = self.__getRepositoryHoldingsDocuments( schemaName, collectionName, updateId) if self.__export: savePath = os.path.join(HERE, "test-output", collectionName + ".json") self.__mU.doExport(savePath, dL, fmt="json", indent=3) # Raises exceptions for schema compliance. Draft4Validator.check_schema(cD) # valInfo = Draft4Validator(cD, format_checker=FormatChecker()) for ii, dD in enumerate(dL): logger.debug("Schema %s collection %s document %d", schemaName, collectionName, ii) try: cCount = 0 for error in sorted(valInfo.iter_errors(dD), key=str): logger.info( "schema %s collection %s path %s error: %s", schemaName, collectionName, error.path, error.message) logger.info(">>>") logger.info(">>> failing object is %r", dD) logger.info(">>>") eCount += 1 cCount += 1 # logger.debug("schema %s collection %s count %d", schemaName, collectionName, cCount) except Exception as e: logger.exception("Validation error %s", str(e)) return eCount def __getRepositoryHoldingsDocuments(self, schemaName, collectionName, updateId): """Test loading and processing operations for legacy holdings and status data.""" rL = [] try: rhdp = RepoHoldingsDataPrep(cfgOb=self.__cfgOb, sandboxPath=self.__sandboxPath, workPath=self.__cachePath) if collectionName == "repository_holdings_update_entry": rL = rhdp.getHoldingsUpdateEntry(updateId=updateId) self.assertGreaterEqual(len(rL), 10) logger.debug("update data length %r", len(rL)) # elif collectionName == "repository_holdings_current_entry": rL = rhdp.getHoldingsCurrentEntry(updateId=updateId) self.assertGreaterEqual(len(rL), 10) logger.debug("holdings data length %r", len(rL)) # elif collectionName == "repository_holdings_unreleased_entry": rL = rhdp.getHoldingsUnreleasedEntry(updateId=updateId) self.assertGreaterEqual(len(rL), 10) logger.debug("unreleased data length %r", len(rL)) # elif collectionName in ["repository_holdings_removed_entry"]: rL = rhdp.getHoldingsRemovedEntry(updateId=updateId) if collectionName == "repository_holdings_removed": self.assertGreaterEqual(len(rL), 10) logger.debug("removed data length %r", len(rL)) elif collectionName == "repository_holdings_combined_entry": rL = rhdp.getHoldingsCombinedEntry(updateId=updateId) self.assertGreaterEqual(len(rL), 10) logger.debug("holdings data length %r", len(rL)) # except Exception as e: logger.exception("%s %s failing with %s", schemaName, collectionName, str(e)) self.fail() return rL
class SchemaDataPrepValidateTests(unittest.TestCase): def setUp(self): self.__numProc = 2 # self.__fileLimit = 200 self.__fileLimit = None self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") self.__cachePath = os.path.join(TOPDIR, "CACHE") self.__configPath = os.path.join(TOPDIR, "rcsb", "db", "config", "exdb-config-example-ihm.yml") configName = "site_info_configuration" self.__configName = configName self.__cfgOb = ConfigUtil(configPath=self.__configPath, defaultSectionName=configName, mockTopPath=self.__mockTopPath) self.__mU = MarshalUtil(workPath=self.__cachePath) #self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=False, rebuildFlag=True) self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=True) self.__rpP = RepositoryProvider(cfgOb=self.__cfgOb, numProc=self.__numProc, fileLimit=self.__fileLimit, cachePath=self.__cachePath) # self.__birdRepoPath = self.__cfgOb.getPath("BIRD_REPO_PATH", sectionName=configName) # self.__fTypeRow = "drop-empty-attributes|drop-empty-tables|skip-max-width|convert-iterables|normalize-enums|translateXMLCharRefs" self.__fTypeCol = "drop-empty-tables|skip-max-width|convert-iterables|normalize-enums|translateXMLCharRefs" self.__verbose = True # self.__modulePathMap = self.__cfgOb.get("DICT_METHOD_HELPER_MODULE_PATH_MAP", sectionName=configName) self.__testDirPath = os.path.join(HERE, "test-output", "pdbx-files") self.__testIhmDirPath = os.path.join(HERE, "test-output", "ihm-files") self.__export = True # #self.__extraOpts = None # The following for extended parent/child info - self.__extraOpts = 'addParentRefs|addPrimaryKey' # self.__alldatabaseNameD = { "ihm_dev": ["ihm_dev"], "pdbx": ["pdbx", "pdbx_ext"], "pdbx_core": ["pdbx_core_entity", "pdbx_core_entry", "pdbx_core_assembly", "pdbx_core_entity_instance", "pdbx_core_entity_instance_validation"], "bird": ["bird"], "bird_family": ["family"], "chem_comp": ["chem_comp"], "bird_chem_comp": ["bird_chem_comp"], "bird_chem_comp_core": ["bird_chem_comp_core"], } self.__databaseNameD = { "pdbx_core": ["pdbx_core_entity", "pdbx_core_entry", "pdbx_core_assembly", "pdbx_core_entity_instance", "pdbx_core_entity_instance_validation"], "bird_chem_comp_core": ["bird_chem_comp_core"], } self.__mergeContentTypeD = {"pdbx_core": ["vrpt"]} # self.__databaseNameD = {"chem_comp_core": ["chem_comp_core"], "bird_chem_comp_core": ["bird_chem_comp_core"]} # self.__databaseNameD = {"ihm_dev_full": ["ihm_dev_full"]} # self.__databaseNameD = {"pdbx_core": ["pdbx_core_entity_instance_validation"]} # self.__databaseNameD = {"pdbx_core": ["pdbx_core_entity_monomer"]} self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())) def tearDown(self): endTime = time.time() logger.debug("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime) def testValidateOptsRepo(self): # schemaLevel = "min" schemaLevel = "full" inputPathList = None eCount = self.__testValidateOpts(databaseNameD=self.__databaseNameD, inputPathList=inputPathList, schemaLevel=schemaLevel, mergeContentTypeD=self.__mergeContentTypeD) logger.info("Total validation errors schema level %s : %d", schemaLevel, eCount) self.assertLessEqual(eCount, 1) @unittest.skip("Disable troubleshooting test") def testValidateOptsList(self): schemaLevel = "min" inputPathList = self.__mU.doImport(os.path.join(HERE, "test-output", "failed-path.list"), "list") # inputPathList = glob.glob(self.__testDirPath + "/*.cif") if not inputPathList: return True databaseNameD = {"pdbx_core": ["pdbx_core_entity", "pdbx_core_entry", "pdbx_core_entity_instance", "pdbx_core_entity_instance_validation"]} for ii, subList in enumerate(chunkList(inputPathList[::-1], 40)): if ii < 5: continue eCount = self.__testValidateOpts(databaseNameD=databaseNameD, inputPathList=subList, schemaLevel=schemaLevel, mergeContentTypeD=self.__mergeContentTypeD) logger.info("Chunk %d total validation errors schema level %s : %d", ii, schemaLevel, eCount) # self.assertGreaterEqual(eCount, 20) #@unittest.skip("Disable IHM troubleshooting test") def testValidateOptsIhmRepo(self): schemaLevel = "min" inputPathList = None self.__export = True databaseNameD = {"ihm_dev_full": ["ihm_dev_full"]} databaseNameD = {"ihm_dev": ["ihm_dev"]} eCount = self.__testValidateOpts(databaseNameD=databaseNameD, inputPathList=inputPathList, schemaLevel=schemaLevel, mergeContentTypeD=self.__mergeContentTypeD) logger.info("Total validation errors schema level %s : %d", schemaLevel, eCount) # self.assertGreaterEqual(eCount, 20) # #@unittest.skip("Disable IHM troubleshooting test") def testValidateOptsIhmList(self): #schemaLevel = "full" schemaLevel = "min" inputPathList = glob.glob(self.__testIhmDirPath + "/*.cif") if not inputPathList: return True #databaseNameD = {"ihm_dev_full": ["ihm_dev_full"]} databaseNameD = {"ihm_dev": ["ihm_dev"]} eCount = self.__testValidateOpts(databaseNameD=databaseNameD, inputPathList=inputPathList, schemaLevel=schemaLevel, mergeContentTypeD=self.__mergeContentTypeD) logger.info("Total validation errors schema level %s : %d", schemaLevel, eCount) # self.assertGreaterEqual(eCount, 20) # def __testValidateOpts(self, databaseNameD, inputPathList=None, schemaLevel="full", mergeContentTypeD=None): # eCount = 0 for databaseName in databaseNameD: mergeContentTypes = mergeContentTypeD[databaseName] if databaseName in mergeContentTypeD else None _ = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=True) pthList = inputPathList if inputPathList else self.__rpP.getLocatorObjList(databaseName, mergeContentTypes=mergeContentTypes) for collectionName in databaseNameD[databaseName]: cD = self.__schP.makeSchema(databaseName, collectionName, encodingType="JSON", level=schemaLevel, saveSchema=True, extraOpts=self.__extraOpts) # dL, cnL = self.__testPrepDocumentsFromContainers( pthList, databaseName, collectionName, styleType="rowwise_by_name_with_cardinality", mergeContentTypes=mergeContentTypes ) # Raises exceptions for schema compliance. try: Draft4Validator.check_schema(cD) except Exception as e: logger.error("%s %s schema validation fails with %s", databaseName, collectionName, str(e)) # valInfo = Draft4Validator(cD, format_checker=FormatChecker()) logger.info("Validating %d documents from %s %s", len(dL), databaseName, collectionName) for ii, dD in enumerate(dL): logger.debug("Schema %s collection %s document %d", databaseName, collectionName, ii) try: cCount = 0 #for error in sorted(valInfo.iter_errors(dD), key=str): # logger.info("schema %s collection %s (%s) path %s error: %s", databaseName, collectionName, cnL[ii], error.path, error.message) # logger.debug("Failing document %d : %r", ii, list(dD.items())) # eCount += 1 # cCount += 1 #if cCount > 0: # logger.info("schema %s collection %s container %s error count %d", databaseName, collectionName, cnL[ii], cCount) except Exception as e: logger.exception("Validation processing error %s", str(e)) return eCount def __testPrepDocumentsFromContainers(self, inputPathList, databaseName, collectionName, styleType="rowwise_by_name_with_cardinality", mergeContentTypes=None): """Test case - create loadable PDBx data from repository files """ try: sd, _, _, _ = self.__schP.getSchemaInfo(databaseName) # dP = DictionaryApiProviderWrapper(self.__cfgOb, self.__cachePath, useCache=False) dictApi = dP.getApiByName(databaseName) rP = DictMethodResourceProvider(self.__cfgOb, configName=self.__configName, cachePath=self.__cachePath, siftsAbbreviated="TEST") dmh = DictMethodRunner(dictApi, modulePathMap=self.__modulePathMap, resourceProvider=rP) # dtf = DataTransformFactory(schemaDefAccessObj=sd, filterType=self.__fTypeRow) sdp = SchemaDefDataPrep(schemaDefAccessObj=sd, dtObj=dtf, workPath=self.__cachePath, verbose=self.__verbose) containerList = self.__rpP.getContainerList(inputPathList) for container in containerList: cName = container.getName() logger.debug("Processing container %s", cName) dmh.apply(container) if self.__export: savePath = os.path.join(HERE, "test-output", cName + "-with-method.cif") #self.__mU.doExport(savePath, [container], fmt="mmcif") # tableIdExcludeList = sd.getCollectionExcluded(collectionName) tableIdIncludeList = sd.getCollectionSelected(collectionName) sliceFilter = sd.getCollectionSliceFilter(collectionName) sdp.setSchemaIdExcludeList(tableIdExcludeList) sdp.setSchemaIdIncludeList(tableIdIncludeList) # docList, containerNameList, _ = sdp.processDocuments( containerList, styleType=styleType, filterType=self.__fTypeRow, dataSelectors=["PUBLIC_RELEASE"], sliceFilter=sliceFilter, collectionName=collectionName ) docList = sdp.addDocumentPrivateAttributes(docList, collectionName) docList = sdp.addDocumentSubCategoryAggregates(docList, collectionName) # mergeS = "-".join(mergeContentTypes) if mergeContentTypes else "" if self.__export and docList: # for ii, doc in enumerate(docList[:1]): for ii, doc in enumerate(docList): cn = containerNameList[ii] fp = os.path.join(HERE, "test-output", "prep-%s-%s-%s-%s.json" % (cn, databaseName, collectionName, mergeS)) self.__mU.doExport(fp, [doc], fmt="json", indent=3) logger.debug("Exported %r", fp) # return docList, containerNameList except Exception as e: logger.exception("Failing with %s", str(e)) self.fail()
class SchemaDefBuildTests(unittest.TestCase): def setUp(self): self.__verbose = True mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") pathConfig = os.path.join(TOPDIR, "rcsb", "db", "config", "exdb-config-example.yml") configName = "site_info_configuration" self.__cachePath = os.path.join(TOPDIR, "CACHE") self.__cfgOb = ConfigUtil(configPath=pathConfig, defaultSectionName=configName, mockTopPath=mockTopPath) self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=False) # self.__validationLevels = self.__cfgOb.getList( "VALIDATION_LEVELS_TEST", sectionName="database_catalog_configuration") self.__encodingTypes = self.__cfgOb.getList( "ENCODING_TYPES_TEST", sectionName="database_catalog_configuration") # buildAll = True if buildAll: self.__databaseNameList = self.__cfgOb.getList( "DATABASE_NAMES_DEPLOYED", sectionName="database_catalog_configuration") self.__dataTypingList = self.__cfgOb.getList( "DATATYPING_DEPLOYED", sectionName="database_catalog_configuration") # else: self.__databaseNameList = self.__cfgOb.getList( "DATABASE_NAMES_TEST", sectionName="database_catalog_configuration") # self.__databaseNameList = ["repository_holdings"] self.__dataTypingList = self.__cfgOb.getList( "DATATYPING_TEST", sectionName="database_catalog_configuration") # self.__databaseNameList = ["sequence_clusters"] self.__saveSchema = True self.__compareDefSchema = False self.__compareSchema = False # self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())) def tearDown(self): endTime = time.time() logger.debug("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime) def testBuildSchemaDefs(self): try: for databaseName in self.__databaseNameList: for dataTyping in self.__dataTypingList: logger.debug("Building schema %s with types %s", databaseName, dataTyping) self.__schP.makeSchemaDef(databaseName, dataTyping=dataTyping, saveSchema=self.__saveSchema) if self.__compareDefSchema: self.__schP.schemaDefCompare(databaseName, dataTyping) except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() def testBuildCollectionSchema(self): schemaDifPathList = [] for databaseName in self.__databaseNameList: dD = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=False) sD = SchemaDefAccess(dD) for cd in sD.getCollectionInfo(): collectionName = cd["NAME"] for encodingType in self.__encodingTypes: if encodingType.lower() == "rcsb": continue for level in self.__validationLevels: self.__schP.makeSchema(databaseName, collectionName, encodingType=encodingType, level=level, saveSchema=self.__saveSchema) if self.__compareSchema and encodingType.lower( ) == "json": pth = self.__schP.jsonSchemaCompare( databaseName, collectionName, encodingType, level) if pth: schemaDifPathList.append(pth) if schemaDifPathList: logger.info("Path dif list %r", schemaDifPathList) def testCompareSchema(self): databaseName = "pdbx_core" collectionName = "pdbx_core_entry" encodingType = "json" level = "full" # oldPath = os.path.join( HERE, "test-saved-output", "json-full-db-pdbx_core-col-pdbx_core_entry.json") mU = MarshalUtil(workPath=os.path.join(HERE, "test-output")) sOld = mU.doImport(oldPath, fmt="json") sNew = self.__schP.makeSchema(databaseName, collectionName, encodingType=encodingType, level=level) numDif, difD = self.__schP.schemaCompare(sOld, sNew) logger.debug("numDiffs %d", numDif) self.assertGreaterEqual(numDif, 141) self.assertGreaterEqual(len(difD["changed"]), 160) logger.debug("difD %r", difD) @unittest.skip("Deprecated test") def testCompareSchemaCategories(self): """Compare common categories across schema definitions.""" try: sdCc = SchemaDefAccess( self.__schP.makeSchemaDef("chem_comp_core", dataTyping="ANY", saveSchema=False)) sdBcc = SchemaDefAccess( self.__schP.makeSchemaDef("bird_chem_comp_core", dataTyping="ANY", saveSchema=False)) # logger.info("") for schemaId in ["CHEM_COMP", "PDBX_CHEM_COMP_AUDIT"]: atCcL = sdCc.getAttributeIdList(schemaId) atBCcL = sdBcc.getAttributeIdList(schemaId) logger.debug("%s attributes (%d) %r", schemaId, len(atCcL), atCcL) logger.debug("%s attributes (%d) %r", schemaId, len(atBCcL), atBCcL) sDif = set(atCcL) - set(atBCcL) if sDif: logger.info("For %s attribute differences %r", schemaId, sDif) self.assertEqual(len(sDif), 0) except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() def testBuildColSchemaWithRefs(self): for databaseName in ["ihm_dev_full"]: dD = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=False) sD = SchemaDefAccess(dD) for cd in sD.getCollectionInfo(): collectionName = cd["NAME"] for schemaType in self.__encodingTypes: if schemaType.lower() == "rcsb": continue for level in self.__validationLevels: self.__schP.makeSchema( databaseName, collectionName, encodingType=schemaType, level=level, saveSchema=True, extraOpts="addParentRefs|addPrimaryKey")
class ClusterDataPrepValidateTests(unittest.TestCase): def setUp(self): self.__verbose = True # self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") self.__pathConfig = os.path.join(TOPDIR, "rcsb", "db", "config", "exdb-config-example.yml") self.__cachePath = os.path.join(TOPDIR, "CACHE") self.__updateId = "2018_25" # configName = "site_info_configuration" self.__cfgOb = ConfigUtil(configPath=self.__pathConfig, defaultSectionName=configName, mockTopPath=self.__mockTopPath) self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=True) # self.__sandboxPath = self.__cfgOb.getPath("RCSB_EXCHANGE_SANDBOX_PATH", sectionName=configName) # self.__dataSetId = "2018_23" self.__pathClusterData = self.__cfgOb.getPath("RCSB_SEQUENCE_CLUSTER_DATA_PATH", sectionName=configName) # self.__levels = ['100', '95', '90', '70', '50', '30'] self.__levels = ["100"] # self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())) def tearDown(self): endTime = time.time() logger.debug("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime) def testValidateOptsStrict(self): updateId = self.__updateId validationLevel = "full" eCount = self.__testValidateOpts(updateId, validationLevel=validationLevel) logger.info("Total validation errors validation level %s : %d", validationLevel, eCount) self.assertTrue(eCount <= 1) def __testValidateOpts(self, updateId, validationLevel="full"): _ = updateId databaseNames = ["sequence_clusters"] collectionNames = {"sequence_clusters": ["cluster_provenance", "cluster_members", "entity_members"]} # eCount = 0 for databaseName in databaseNames: for collectionName in collectionNames[databaseName]: _ = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=True) cD = self.__schP.makeSchema(databaseName, collectionName, encodingType="JSON", level=validationLevel, saveSchema=True) # dL = self.__getSequenceClusterData(collectionName, levels=self.__levels, dataSetId=self.__dataSetId, dataLocator=self.__pathClusterData) # Raises exceptions for schema compliance. Draft4Validator.check_schema(cD) # valInfo = Draft4Validator(cD, format_checker=FormatChecker()) for _, dD in enumerate(dL): # logger.debug("Schema %s collection %s document %d" % (schemaName, collectionName, ii)) try: cCount = 0 for error in sorted(valInfo.iter_errors(dD), key=str): logger.info("schema %s collection %s path %s error: %s", databaseName, collectionName, error.path, error.message) logger.info(">>> failing object is %r", dD) eCount += 1 cCount += 1 # logger.debug("schema %s collection %s count %d", databaseName, collectionName, cCount) except Exception as e: logger.exception("Validation error %s", str(e)) return eCount def __fetchProvenance(self): """Test case for fetching a provenance dictionary content.""" try: provKeyName = "rcsb_entity_sequence_cluster_prov" provU = ProvenanceProvider(self.__cfgOb, self.__cachePath, useCache=True) pD = provU.fetch() return pD[provKeyName] if provKeyName in pD else {} except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() def __getSequenceClusterData(self, collectionName, dataSetId=None, dataLocator=None, levels=None): """Test extraction on an example sequence cluster data set.""" try: # if collectionName == "cluster_provenance": return [self.__fetchProvenance()] # entitySchemaName = "rcsb_entity_sequence_cluster_list" clusterSchemaName = "rcsb_entity_sequence_cluster_identifer_list" cdp = ClusterDataPrep(workPath=self.__cachePath, entitySchemaName=entitySchemaName, clusterSchemaName=clusterSchemaName) cifD, docBySequenceD, docByClusterD = cdp.extract(dataSetId, clusterSetLocator=dataLocator, levels=levels, clusterType="entity") self.assertEqual(len(cifD), 1) self.assertEqual(len(docBySequenceD), 1) self.assertEqual(len(docByClusterD), 1) if collectionName == "entity_members": return docBySequenceD[entitySchemaName] elif collectionName == "cluster_members": return docByClusterD[clusterSchemaName] except Exception as e: logger.exception("Failing with %s", str(e)) self.fail() return None
def main(): parser = argparse.ArgumentParser() # defaultConfigName = "site_info_configuration" # parser.add_argument( "--update_chem_comp_ref", default=False, action="store_true", help="Update schema for Chemical Component reference definitions") parser.add_argument( "--update_chem_comp_core_ref", default=False, action="store_true", help="Update core schema for Chemical Component reference definitions") parser.add_argument( "--update_bird_chem_comp_ref", default=False, action="store_true", help="Update schema for Bird Chemical Component reference definitions") parser.add_argument( "--update_bird_chem_comp_core_ref", default=False, action="store_true", help= "Update core schema for Bird Chemical Component reference definitions") parser.add_argument("--update_bird_ref", default=False, action="store_true", help="Update schema for Bird reference definitions") parser.add_argument( "--update_bird_family_ref", default=False, action="store_true", help="Update schema for Bird Family reference definitions") parser.add_argument("--update_pdbx", default=False, action="store_true", help="Update schema for PDBx entry data") parser.add_argument("--update_pdbx_core", default=False, action="store_true", help="Update schema for PDBx core entry/entity data") parser.add_argument( "--update_pdbx_comp_model_core", default=False, action="store_true", help="Update schema for PDBx computational model core entry/entity data" ) # parser.add_argument("--update_repository_holdings", default=False, action="store_true", help="Update schema for repository holdings") parser.add_argument("--update_entity_sequence_clusters", default=False, action="store_true", help="Update schema for entity sequence clusters") parser.add_argument("--update_data_exchange", default=False, action="store_true", help="Update schema for data exchange status") parser.add_argument("--update_ihm_dev", default=False, action="store_true", help="Update schema for I/HM dev entry data") parser.add_argument("--update_drugbank_core", default=False, action="store_true", help="Update DrugBank schema") # parser.add_argument( "--update_config_all", default=False, action="store_true", help="Update using configuration settings (e.g. DATABASE_NAMES_ALL)") parser.add_argument( "--update_config_deployed", default=False, action="store_true", help= "Update using configuration settings (e.g. DATABASE_NAMES_DEPLOYED)") parser.add_argument( "--update_config_test", default=False, action="store_true", help="Update using configuration settings (e.g. DATABASE_NAMES_TEST)") # parser.add_argument("--config_path", default=None, help="Path to configuration options file") parser.add_argument("--config_name", default=defaultConfigName, help="Configuration section name") # parser.add_argument("--cache_path", default=None, help="Schema cache directory path") parser.add_argument( "--encoding_types", default=None, help="Schema encoding (rcsb|json|bson) (comma separated)") parser.add_argument( "--validation_levels", default=None, help="Schema validation level (full|min) (comma separated)") parser.add_argument("--compare_only", default=False, action="store_true", help="Perform comparison with cached schema") # parser.add_argument("--debug", default=False, action="store_true", help="Turn on verbose logging") parser.add_argument( "--mock", default=False, action="store_true", help="Use MOCK repository configuration for dependencies and testing") # parser.add_argument("--working_path", default=None, help="Working/alternative path for temporary and schema files") args = parser.parse_args() # debugFlag = args.debug if debugFlag: logger.setLevel(logging.DEBUG) # ----------------------- - ----------------------- - ----------------------- - ----------------------- - ----------------------- - # Configuration Details configPath = args.config_path configName = args.config_name cachePath = args.cache_path compareOnly = args.compare_only # encodingTypes = args.encoding_types.split( ",") if args.encoding_types else [] validationLevels = args.validation_levels.split( ",") if args.validation_levels else [] dataTypingList = ["ANY", "SQL"] if not configPath: configPath = os.getenv("DBLOAD_CONFIG_PATH", None) try: if os.access(configPath, os.R_OK): os.environ["DBLOAD_CONFIG_PATH"] = configPath logger.info("Using configuation path %s (%s)", configPath, configName) else: logger.error("Missing or access issue with config file %r", configPath) exit(1) mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") if args.mock else None cfgOb = ConfigUtil(configPath=configPath, defaultSectionName=defaultConfigName, mockTopPath=mockTopPath) if configName != defaultConfigName: cfgOb.replaceSectionName(defaultConfigName, configName) except Exception as e: logger.error("Missing or access issue with config file %r with %s", configPath, str(e)) exit(1) # databaseNameList = [] if args.update_chem_comp_ref: databaseNameList.append("chem_comp") if args.update_bird_chem_comp_ref: databaseNameList.append("bird_chem_comp") if args.update_chem_comp_core_ref: databaseNameList.append("chem_comp_core") if args.update_bird_chem_comp_core_ref: databaseNameList.append("bird_chem_comp_core") if args.update_bird_ref: databaseNameList.append("bird") if args.update_bird_family_ref: databaseNameList.append("bird_family") if args.update_pdbx: databaseNameList.append("pdbx") if args.update_pdbx_core: databaseNameList.append("pdbx_core") if args.update_pdbx_comp_model_core: databaseNameList.append("pdbx_comp_model_core") if args.update_repository_holdings: databaseNameList.append("repository_holdings") if args.update_entity_sequence_clusters: databaseNameList.append("sequence_clusters") if args.update_data_exchange: databaseNameList.append("data_exchange") if args.update_ihm_dev: databaseNameList.append("ihm_dev") if args.update_drugbank_core: databaseNameList.append("drugbank_core") if args.update_config_deployed: databaseNameList = cfgOb.getList( "DATABASE_NAMES_DEPLOYED", sectionName="database_catalog_configuration") dataTypingList = cfgOb.getList( "DATATYPING_DEPLOYED", sectionName="database_catalog_configuration") validationLevels = cfgOb.getList( "VALIDATION_LEVELS_DEPLOYED", sectionName="database_catalog_configuration") encodingTypes = cfgOb.getList( "ENCODING_TYPES_DEPLOYED", sectionName="database_catalog_configuration") if args.update_config_all: databaseNameList = cfgOb.getList( "DATABASE_NAMES_ALL", sectionName="database_catalog_configuration") dataTypingList = cfgOb.getList( "DATATYPING_ALL", sectionName="database_catalog_configuration") validationLevels = cfgOb.getList( "VALIDATION_LEVELS_ALL", sectionName="database_catalog_configuration") encodingTypes = cfgOb.getList( "ENCODING_TYPES_ALL", sectionName="database_catalog_configuration") if args.update_config_test: databaseNameList = cfgOb.getList( "DATABASE_NAMES_TEST", sectionName="database_catalog_configuration") dataTypingList = cfgOb.getList( "DATATYPING_TEST", sectionName="database_catalog_configuration") validationLevels = cfgOb.getList( "VALIDATION_LEVELS_TEST", sectionName="database_catalog_configuration") encodingTypes = cfgOb.getList( "ENCODING_TYPES_TEST", sectionName="database_catalog_configuration") # scnD = cfgOb.get("document_collection_names", sectionName="document_helper_configuration") # databaseNameList = list(set(databaseNameList)) logger.debug("Collections %s", list(scnD.items())) logger.debug("databaseNameList %s", databaseNameList) if compareOnly: schP = SchemaProvider(cfgOb, cachePath, useCache=True) difPathList = [] for databaseName in databaseNameList: for dataTyping in dataTypingList: logger.debug("Building schema %s with types %s", databaseName, dataTyping) pth = schP.schemaDefCompare(databaseName, dataTyping) if pth: difPathList.append(pth) if difPathList: logger.info("Schema definition difference path list %r", difPathList) difPathList = [] for databaseName in databaseNameList: dD = schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=False) sD = SchemaDefAccess(dD) for cd in sD.getCollectionInfo(): collectionName = cd["NAME"] for encodingType in encodingTypes: if encodingType.lower() != "json": continue for level in validationLevels: pth = schP.jsonSchemaCompare(databaseName, collectionName, encodingType, level) if pth: difPathList.append(pth) if difPathList: logger.info("JSON schema difference path list %r", difPathList) else: schP = SchemaProvider(cfgOb, cachePath, useCache=False) for databaseName in databaseNameList: for encodingType in encodingTypes: if encodingType == "rcsb": for dataTyping in dataTypingList: logger.info( "Creating schema definition for content type %s data typing %s", databaseName, dataTyping) schP.makeSchemaDef(databaseName, dataTyping=dataTyping, saveSchema=True) else: if databaseName in scnD: for dD in scnD[databaseName]: collectionName = dD["NAME"] for validationLevel in validationLevels: logger.info( "Creating %r schema for content type %s collection %s", encodingType, databaseName, collectionName) schP.makeSchema(databaseName, collectionName, encodingType=encodingType, level=validationLevel, saveSchema=True)
class ChemRefDataPrepValidateTests(unittest.TestCase): def setUp(self): self.__verbose = True # self.__mockTopPath = os.path.join(TOPDIR, "rcsb", "mock-data") self.__pathConfig = os.path.join(TOPDIR, "rcsb", "db", "config", "exdb-config-example.yml") self.__cachePath = os.path.join(TOPDIR, "CACHE") # self.__configName = "site_info_configuration" self.__cfgOb = ConfigUtil(configPath=self.__pathConfig, defaultSectionName=self.__configName, mockTopPath=self.__mockTopPath) self.__schP = SchemaProvider(self.__cfgOb, self.__cachePath, useCache=True) # self.__startTime = time.time() logger.debug("Starting %s at %s", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime())) def tearDown(self): endTime = time.time() logger.debug("Completed %s at %s (%.4f seconds)", self.id(), time.strftime("%Y %m %d %H:%M:%S", time.localtime()), endTime - self.__startTime) def testValidateFull(self): self.__validateChemRef("DrugBank", schemaLevel="full") def __validateChemRef(self, extResource, schemaLevel="full"): eCount = 0 if extResource == "DrugBank": schemaName = "drugbank_core" collectionNames = ["drugbank_core"] user = self.__cfgOb.get("_DRUGBANK_AUTH_USERNAME", sectionName=self.__configName) pw = self.__cfgOb.get("_DRUGBANK_AUTH_PASSWORD", sectionName=self.__configName) # cacheDir = self.__cfgOb.get("DRUGBANK_CACHE_DIR", sectionName=self.__configName) dbP = DrugBankProvider(cachePath=self.__cachePath, useCache=True, username=user, password=pw) # idD = dbP.getMapping() # crExt = ChemRefExtractor(self.__cfgOb) # idD = crExt.getChemCompAccesionMapping(extResource) dList = dbP.getDocuments() logger.info("Validating %d Drugbank documents", len(dList)) eCount = self.__validate(schemaName, collectionNames, dList, schemaLevel=schemaLevel) return eCount def __validate(self, databaseName, collectionNames, dList, schemaLevel="full"): eCount = 0 for collectionName in collectionNames: _ = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=True) cD = self.__schP.makeSchema(databaseName, collectionName, encodingType="JSON", level=schemaLevel, saveSchema=True) # Raises exceptions for schema compliance. Draft4Validator.check_schema(cD) # valInfo = Draft4Validator(cD, format_checker=FormatChecker()) for ii, dD in enumerate(dList): logger.debug("Database %s collection %s document %d", databaseName, collectionName, ii) try: cCount = 0 for error in sorted(valInfo.iter_errors(dD), key=str): logger.info( "database %s collection %s path %s error: %s", databaseName, collectionName, error.path, error.message) logger.info(">>> failing object is %r", dD) eCount += 1 cCount += 1 # logger.debug("database %s collection %s count %d", databaseName, collectionName, cCount) except Exception as e: logger.exception("Validation error %s", str(e)) return eCount
class ObjectValidator(object): """Utilities to extract and update object from the document object server with validation.""" def __init__(self, cfgOb, objectAdapter=None, cachePath=".", useCache=True, **kwargs): self.__cfgOb = cfgOb self.__oAdapt = objectAdapter self.__resourceName = "MONGO_DB" _ = kwargs self.__statusList = [] self.__schP = SchemaProvider(self.__cfgOb, cachePath, useCache=useCache) self.__valInst = None def __getValidator(self, databaseName, collectionName, schemaLevel="full"): _ = self.__schP.makeSchemaDef(databaseName, dataTyping="ANY", saveSchema=True) cD = self.__schP.makeSchema(databaseName, collectionName, encodingType="JSON", level=schemaLevel, saveSchema=True) # Raises exceptions for schema compliance. Draft4Validator.check_schema(cD) valInst = Draft4Validator(cD, format_checker=FormatChecker()) return valInst def __validateObj(self, databaseName, collectionName, rObj, label=""): try: eCount = 0 tId = rObj["rcsb_id"] if rObj and "rcsb_id" in rObj else "anonymous" for error in sorted(self.__valInst.iter_errors(rObj), key=str): logger.info( "Database %s collection %s (%s %r) path %s error: %s", databaseName, collectionName, label, tId, error.path, error.message) logger.debug(">>> Failing object is %r", rObj) eCount += 1 except Exception as e: logger.exception("Validation failing %s", str(e)) return eCount def doTransform(self, **kwargs): desp = DataExchangeStatus() statusStartTimestamp = desp.setStartTime() # databaseName = kwargs.get("databaseName", "pdbx_core") collectionName = kwargs.get("collectionName", "pdbx_core_entry") selectionQueryD = kwargs.get("selectionQuery", {}) fetchLimit = kwargs.get("fetchLimit", None) # # tU = TimeUtil() updateId = kwargs.get("updateId", tU.getCurrentWeekSignature()) # docSelectList = self.__selectObjectIds(databaseName, collectionName, selectionQueryD) docSelectList = docSelectList[:fetchLimit] if fetchLimit else docSelectList ok = self.__transform(databaseName, collectionName, docSelectList) # if updateId: okS = self.__updateStatus(updateId, databaseName, collectionName, ok, statusStartTimestamp) return ok and okS def __selectObjectIds(self, databaseName, collectionName, selectionQueryD): """Return a list of object identifiers for the input selection query.""" try: with Connection(cfgOb=self.__cfgOb, resourceName=self.__resourceName) as client: mg = MongoDbUtil(client) if mg.collectionExists(databaseName, collectionName): logger.info("%s %s document count is %d", databaseName, collectionName, mg.count(databaseName, collectionName)) qD = {} if selectionQueryD: qD.update(selectionQueryD) selectL = ["_id"] dL = mg.fetch(databaseName, collectionName, selectL, queryD=qD) logger.info("Selection %r fetch result count %d", selectL, len(dL)) except Exception as e: logger.exception("Failing with %s", str(e)) return dL # def __transform(self, databaseName, collectionName, docSelectList, logIncrement=100): """Return a list of object identifiers for the input selection query.""" # ok = True try: self.__valInst = self.__getValidator(databaseName, collectionName, schemaLevel="full") with Connection(cfgOb=self.__cfgOb, resourceName=self.__resourceName) as client: mg = MongoDbUtil(client) if mg.collectionExists(databaseName, collectionName): numDoc = len(docSelectList) for ii, dD in enumerate(docSelectList, 1): if "_id" not in dD: continue rObj = mg.fetchOne(databaseName, collectionName, "_id", dD["_id"]) del rObj["_id"] # fOk = True if self.__oAdapt: self.__validateObj(databaseName, collectionName, rObj, label="Original") fOk, rObj = self.__oAdapt.filter(rObj) self.__validateObj(databaseName, collectionName, rObj, label="Updated") if fOk: rOk = mg.replace(databaseName, collectionName, rObj, dD) if rOk is None: tId = rObj[ "rcsb_id"] if rObj and "rcsb_id" in rObj else "anonymous" logger.error("%r %r (%r) failing", databaseName, collectionName, tId) # logger.info("rObj.keys() %r", list(rObj.keys())) # logger.info("rObj.items() %s", rObj.items()) rOk = False ok = ok and rOk # if ii % logIncrement == 0 or ii == numDoc: logger.info("Replace status %r object (%d of %d)", ok, ii, numDoc) # except Exception as e: logger.exception("Failing with %s", str(e)) return ok def getLoadStatus(self): return self.__statusList def __updateStatus(self, updateId, databaseName, collectionName, status, startTimestamp): try: sFlag = "Y" if status else "N" desp = DataExchangeStatus() desp.setStartTime(tS=startTimestamp) desp.setObject(databaseName, collectionName) desp.setStatus(updateId=updateId, successFlag=sFlag) desp.setEndTime() self.__statusList.append(desp.getStatus()) return True except Exception as e: logger.exception("Failing with %s", str(e)) return False