116 lines
3.6 KiB
Python
116 lines
3.6 KiB
Python
#!/usr/bin/env python3
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"""
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Copyright 2018 EMBL - European Bioinformatics Institute
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing,
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software distributed under the License is distributed on an
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"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
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either express or implied. See the License for the specific
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language governing permissions and limitations under the
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License.
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"""
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import jsonschema
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import json
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import re
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class Validator(object):
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"""
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Validates FunPDBe JSON files
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"""
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def __init__(self, resource):
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self.resource = resource
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self.schema = None
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self.json_data = None
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self.error_log = None
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def load_json(self, path_to_file):
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"""
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Loads the user JSON
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:param path_to_file: String, path to JSON file
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:return: None
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"""
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self.json_data = self.parse_json(path_to_file)
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def load_schema(self, path_to_schema):
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"""
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Loads the FunPDBe schema
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:param path_to_schema: String, path to FunPDBe schema
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:return: None
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"""
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self.schema = self.parse_json(path_to_schema)
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def parse_json(self, path):
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"""
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Parses a FunPDBe JSON file and in case of file error
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or JSON error, the error message is saved to self.error_log
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:return: Bool, True is parsed, False if failed
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"""
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try:
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with open(path, "r") as json_file:
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try:
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return json.load(json_file)
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except json.decoder.JSONDecodeError as err:
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self.error_log = "JSON error: %s" % err
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return None
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except IOError as ioerr:
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self.error_log = "File error: %s" % ioerr
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return None
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def basic_checks(self):
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"""
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Performs basic data checks
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:return: Bool, True if valid, False if invalid
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"""
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if self.test_resource() and self.test_pdb_id():
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return True
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return False
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def test_resource(self):
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"""
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Check if data_resource field exists in the JSON,
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and if it is the same as the provided resource name
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:return: Bool, True if valid, False if invalid
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"""
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if "data_resource" not in self.json_data.keys():
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self.error_log = "No data resource name found"
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return False
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elif self.json_data["data_resource"] != self.resource:
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self.error_log = "Data resource name mismatch"
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return False
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return True
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def test_pdb_id(self):
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"""
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Check if PDB id exists in the JSON, and if it follows
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the PDB id pattern
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:return: Bool, True if valid, False if invalid
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"""
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if "pdb_id" not in self.json_data.keys():
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self.error_log = "No PDB id found"
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return False
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elif not re.match("^[1-9][a-zA-Z0-9]{3}$", self.json_data["pdb_id"]):
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self.error_log = "Invalid PDB id found"
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return False
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return True
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def validate_against_schema(self):
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"""
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Calls jsonschema.validate() to compare the JSON with
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the FunPDBe JSON schema
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:return: Bool, True is valid, False if invalid
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"""
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try:
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jsonschema.validate(self.json_data, self.schema)
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return True
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except jsonschema.exceptions.ValidationError as err:
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self.error_log = "JSON does not comply with schema: %s" % err
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return False
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