Initial commit of Validator() with tests

tests/validator_tests.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+
+"""
+Copyright 2018 EMBL - European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an
+"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+either express or implied. See the License for the specific
+language governing permissions and limitations under the
+License.
+"""
+
+import unittest
+from validator.validator import Validator
+
+
+class TestValidator(unittest.TestCase):
+
+    def test_no_file_at_path(self):
+        validator = Validator("resource_name")
+        validator.parse_json("invalid_path")
+        self.assertIn("File error", validator.error_log)
+
+    def test_json_parser(self):
+        validator = Validator("resource_name")
+        data = validator.parse_json("../data/test_data.json")
+        self.assertIsNotNone(data)
+        validator.parse_json("../data/test_data_malformed.json")
+        self.assertIn("JSON error", validator.error_log)
+
+    def test_basic_checks(self):
+        validator = Validator("test")
+        validator.json_data = {"data_resource": "test", "pdb_id": "1abc"}
+        print(validator.json_data)
+        self.assertTrue(validator.basic_checks())
+        validator.json_data = {"data_resource": "test"}
+        self.assertFalse(validator.basic_checks())
+        validator.json_data = {"pdb_id": "1abc"}
+        self.assertFalse(validator.basic_checks())
+
+    def test_no_resource_name(self):
+        validator = Validator("test")
+        validator.json_data = {"pdb_id": "1abc"}
+        self.assertFalse(validator.test_resource())
+
+    def test_resource_name_mismatch(self):
+        validator = Validator("test")
+        validator.json_data = {"data_resource": "test2", "pdb_id": "1abc"}
+        self.assertFalse(validator.test_resource())
+
+    def test_no_pdb_id(self):
+        validator = Validator("test")
+        validator.json_data = {"data_resource": "test"}
+        self.assertFalse(validator.test_pdb_id())
+
+    def test_invalid_pdb_id(self):
+        validator = Validator("test")
+        validator.json_data = {"data_resource": "test", "pdb_id": "invalid"}
+        self.assertFalse(validator.test_pdb_id())

validator/validator.py

@@ -0,0 +1,92 @@
+#!/usr/bin/env python3
+
+"""
+Copyright 2018 EMBL - European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an
+"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+either express or implied. See the License for the specific
+language governing permissions and limitations under the
+License.
+"""
+
+import jsonschema
+import json
+import re
+
+
+class Validator(object):
+    """
+    Validates FunPDBe JSON files
+    """
+
+    def __init__(self, resource):
+        self.resource = resource
+        self.schema = None
+        self.json_data = None
+        self.error_log = None
+
+    def load_json(self, path_to_file):
+        self.json_data = self.parse_json(path_to_file)
+
+    def load_schema(self, path_to_schema):
+        self.schema = self.parse_json(path_to_schema)
+
+    def parse_json(self, path):
+        """
+        Parses a FunPDBe JSON file and in case of file error
+        or JSON error, the error message is saved to self.error_log
+
+        :return: Bool, True is parsed, False if failed
+        """
+        try:
+            with open(path, "r") as json_file:
+                try:
+                    return json.load(json_file)
+                except json.decoder.JSONDecodeError as err:
+                    self.error_log = "JSON error: %s" % err
+                    return None
+        except IOError as ioerr:
+            self.error_log = "File error: %s" % ioerr
+            return None
+
+    def basic_checks(self):
+        if self.test_resource() and self.test_pdb_id():
+            return True
+        return False
+
+    def test_resource(self):
+        if "data_resource" not in self.json_data.keys():
+            self.error_log = "No data resource name found"
+            return False
+        elif self.json_data["data_resource"] != self.resource:
+            self.error_log = "Data resource name mismatch"
+            return False
+        return True
+
+    def test_pdb_id(self):
+        if "pdb_id" not in self.json_data.keys():
+            self.error_log = "No PDB id found"
+            return False
+        elif not re.match("^[1-9][a-zA-Z0-9]{3}$", self.json_data["pdb_id"]):
+            self.error_log = "Invalid PDB id found"
+            return False
+        return True
+
+    def validate_against_schema(self):
+        try:
+            jsonschema.validate(self.json_data, self.schema)
+            return True
+        except jsonschema.exceptions.ValidationError as err:
+            self.error_log = "JSON does not comply with schema: %s" % err
+            return False
+
+
+
+# TODO - Add the file path to the error log, if not empty
+# jsonschema.validate(json_data, self.json_schema)