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")
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 SchemaDefCompareTests(unittest.TestCase):
skipFlag = True
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=True)
#
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.__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)
@unittest.skipIf(skipFlag, "Troubleshooting test")
def testCompareSchemaDefs(self):
try:
difPathList = []
for databaseName in self.__databaseNameList:
for dataTyping in self.__dataTypingList:
logger.debug("Building schema %s with types %s",
databaseName, dataTyping)
pth = self.__schP.schemaDefCompare(databaseName,
dataTyping)
if pth:
difPathList.append(pth)
if difPathList:
logger.info("Schema definition difference path list %r",
[os.path.split(pth)[1] for pth in difPathList])
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
@unittest.skipIf(skipFlag, "Troubleshooting test")
def testCompareCollectionSchema(self):
try:
difPathList = []
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() != "json":
continue
for level in self.__validationLevels:
pth = self.__schP.jsonSchemaCompare(
databaseName, collectionName, encodingType,
level)
if pth:
difPathList.append(pth)
if difPathList:
logger.info("JSON schema difference path list %r",
[os.path.split(pth)[1] for pth in difPathList])
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
class SchemaProviderTests(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.__dataTypingList = self.__cfgOb.getList(
"DATATYPING_TEST",
sectionName="database_catalog_configuration")
#
self.__docHelper = DocumentDefinitionHelper(cfgOb=self.__cfgOb)
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 testSchemaAccessDefault(self):
for databaseName in self.__databaseNameList:
cDL = self.__docHelper.getCollectionInfo(databaseName)
for cD in cDL:
collectionName = cD["NAME"]
for encodingType in self.__encodingTypes:
if encodingType.lower() == "rcsb":
continue
for level in self.__validationLevels:
logger.debug("Loading ->%s %s %s %s", databaseName,
collectionName, encodingType, level)
sD = self.__schP.getJsonSchema(
databaseName,
collectionName,
encodingType=encodingType,
level=level)
self.assertTrue(sD is not None)
