Merge pull request #64 from harryhoch/master

basic validation test

.gitignore

@@ -1,3 +1,4 @@
 __pycache__
 .gitignore
-*~
+*~
+*#

.travis.yml

@@ -1,25 +1,6 @@
 language: python
 python:
  - "3.4"
-
-before_script:
- - mkdir -p bin
- - export PATH=$PATH:$PWD/bin
- - wget http:https://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools
- - wget http:https://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner
- - wget http:https://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar
- - wget http:https://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar
- - chmod +x bin/*
-
-# command to run tests
-script: make test
-
-# whitelist
-branches:
- only:
- - master
-
-notifications:
- email:
- - [email protected]
+install: "pip install -r requirements.txt"
+script: sh test/scriptrunner.sh
 

requirements.txt

@@ -0,0 +1,2 @@
+jsonschema
+python_jsonschema_objects

test/json_validation_test.py

@@ -0,0 +1,36 @@
+import unittest
+import os
+import json
+from jsonschema import validate, ValidationError, SchemaError,Draft4Validator
+import python_jsonschema_objects as jsonobjects
+from python_jsonschema_objects import ValidationError as ValidationException
+
+
+
+class ValidatorTestCase(unittest.TestCase):
+ """
+ Test various json validators, jsonschema seems to be a popular
+ lib, warlock and python-jsonschema-objects are build off
+ of jsonschema and also include json to python object mappers
+
+ The goal of this is to experiment with library options but these
+ could eventually be integrated into the phenopacket python api
+
+ As a first pass, testing that the journal example is incorrect
+ and the rest are correct. These could be expanded in the future
+ as appropriate
+ """
+
+ def test_valid_schema(self):
+
+ schema_path = "../schema/phenopacket-schema.json"
+
+ schema_fh = open(os.path.join(os.path.dirname(__file__), schema_path), 'r')
+ schema = json.load(schema_fh)
+ schema_fh.close()
+
+ ## call validator
+ Draft4Validator.check_schema(schema)
+
+if __name__ == '__main__':
+ unittest.main()

test/phenopacket_validator.py

@@ -0,0 +1,67 @@
+import unittest
+import os
+import json
+from jsonschema import validate, ValidationError, SchemaError
+import python_jsonschema_objects as jsonobjects
+import getopt,sys
+
+
+
+def main():
+
+ schema_path = "../schema/phenopacket-schema.json"
+
+ try:
+ opts,args = getopt.getopt(sys.argv[1:],"s:",["schema="])
+ except getopt.GetoptError as err:
+ usage()
+ sys.exit(2)
+
+ for o,a in opts:
+ if o in ("-s","--schema"):
+ schema_path=a
+ else:
+ assert False, "unhandled option"
+ exfile = args[0]
+
+ # try: 
+ schema_fh = open(os.path.join(os.path.dirname(__file__), schema_path), 'r')
+ schema = json.load(schema_fh)
+ schema_fh.close()
+# except json.decoder.JSONDecodeError:
+# print("Schema file ", schema_path, " does not contain a valid JSON file")
+# sys.exit(1)
+
+
+ try:
+ file_fh = open(exfile,'r')
+ data = json.load(file_fh)
+ file_fh.close()
+ except IOError:
+ print ("Could not read phenopacket file ",exfile)
+ sys.exit(2)
+ except json.decoder.JSONDecodeError:
+ print("Phenopacket file ", exfile, " does not contain a valid JSON file")
+ sys.exit(3)
+
+
+ # http:https://python-jsonschema.readthedocs.org/en/latest/errors/
+ try:
+ print("running validator");
+ validate(data,schema)
+ print("Valid phenopacket")
+ except SchemaError as s:
+ print ("Schema error in schema ", schema_path)
+ print (s.message)
+ except ValidationError as e:
+ print("Invalid phenopacket found in ",exfile)
+ print(e.message) 
+
+
+
+def usage():
+ print('Usage: '+sys.argv[0]+' -s <schemafile> [option]')
+ print(' '+sys.argv[0]+' --schema=<schemafile> [option]')
+
+if __name__ == '__main__':
+ main()

test/scriptrunner.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+python ./test/json_validation_test.py