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# -*- coding: utf-8 -*-
"""This module tests the to_json functions for all of the database models."""
import datetime
import json
import unittest
from pybel.constants import (
CITATION_TYPE_PUBMED,
IDENTIFIER,
METADATA_AUTHORS,
METADATA_CONTACT,
METADATA_COPYRIGHT,
METADATA_DESCRIPTION,
METADATA_DISCLAIMER,
METADATA_LICENSES,
METADATA_NAME,
METADATA_VERSION,
NAME,
NAMESPACE,
NAMESPACE_DOMAIN_OTHER,
)
from pybel.language import citation_dict
from pybel.manager.models import Citation, Namespace, NamespaceEntry, Network
from pybel.testing.utils import n
class TestNetwork(unittest.TestCase):
def setUp(self):
self.name = n()
self.version = n()
self.created = datetime.datetime.utcnow()
self.model = Network(
name=self.name,
version=self.version,
created=self.created,
)
self.expected = {
METADATA_NAME: self.name,
METADATA_VERSION: self.version,
"created": str(self.created),
}
def test_to_json(self):
model_json = self.model.to_json()
self.assertIn(METADATA_NAME, model_json)
self.assertEqual(self.name, model_json[METADATA_NAME])
self.assertIn(METADATA_VERSION, model_json)
self.assertEqual(self.version, model_json[METADATA_VERSION])
self.assertIn("created", model_json)
self.assertEqual(str(self.created), model_json["created"])
self.assertEqual(self.expected, model_json)
def test_dump(self):
json.dumps(self.model)
def test_network(self):
self.expected[METADATA_AUTHORS] = self.model.authors = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected[METADATA_CONTACT] = self.model.contact = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected[METADATA_DESCRIPTION] = self.model.description = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected[METADATA_COPYRIGHT] = self.model.copyright = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected[METADATA_DISCLAIMER] = self.model.disclaimer = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected[METADATA_LICENSES] = self.model.licenses = n()
self.assertEqual(self.expected, self.model.to_json())
self.expected["id"] = None
self.assertEqual(self.expected, self.model.to_json(include_id=True))
class TestModels(unittest.TestCase):
def test_namespace_url(self):
uploaded = datetime.datetime.now()
model = Namespace(
keyword="TEST",
url="http://test.com",
name="Test Namespace",
domain=NAMESPACE_DOMAIN_OTHER,
species="9606",
version="1.0.0",
author="Charles Tapley Hoyt",
contact="cthoyt@gmail.com",
uploaded=uploaded,
)
expected = dict(
keyword="TEST",
url="http://test.com",
name="Test Namespace",
version="1.0.0",
)
self.assertEqual(model.to_json(), expected)
expected["id"] = model.id = 1
self.assertEqual(model.to_json(include_id=True), expected)
def test_namespace_pattern(self):
uploaded = datetime.datetime.now()
model = Namespace(
keyword="TEST",
pattern=r"\w+",
name="Test Namespace",
domain=NAMESPACE_DOMAIN_OTHER,
species="9606",
version="1.0.0",
author="Charles Tapley Hoyt",
contact="cthoyt@gmail.com",
uploaded=uploaded,
)
expected = dict(
keyword="TEST",
pattern=r"\w+",
name="Test Namespace",
version="1.0.0",
)
self.assertEqual(model.to_json(), expected)
def test_namespace_entry(self):
model = NamespaceEntry(name="entry", namespace=Namespace(keyword="test"))
expected = {
NAMESPACE: "test",
NAME: "entry",
}
self.assertEqual(model.to_json(), expected)
expected["id"] = model.id = 1
self.assertEqual(model.to_json(include_id=True), expected)
expected[IDENTIFIER] = model.identifier = "test:00001"
self.assertEqual(model.to_json(include_id=True), expected)
def test_citation(self):
db_id = n()
model = Citation(
db=CITATION_TYPE_PUBMED,
db_id=db_id,
)
expected = citation_dict(namespace=CITATION_TYPE_PUBMED, identifier=db_id)
self.assertEqual(expected, model.to_json())
expected[NAME] = model.title = n()
self.assertEqual(expected, model.to_json())
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