29 tests/test_import.py
View file
@@ -1,13 +1,42 @@
import logging
import os
import unittest

import pybel
from pybel.manager import NamespaceCache
from pybel.parser import BelParser
from tests.constants import TestTokenParserBase, PYBEL_TEST_ALL

logging.getLogger('requests').setLevel(logging.WARNING)

dir_path = os.path.dirname(os.path.realpath(__file__))


@unittest.skipUnless(PYBEL_TEST_ALL, 'not enough memory on Travis-CI for this test')
class TestCacheIntegration(unittest.TestCase):
def test_cached_winning(self):
path = os.path.join(dir_path, 'bel', 'test_bel_3.bel')

c_path = 'sqlite://'

c = NamespaceCache(conn=c_path, setup_default_cache=False)

with open(path) as f:
g = pybel.BELGraph(f, ns_cache_path=c)

expected_document_metadata = {
'Name': "PyBEL Test Document",
"Description": "Made for testing PyBEL parsing",
'Version': "1.6",
'Copyright': "Copyright (c) Charles Tapley Hoyt. All Rights Reserved.",
'Authors': "Charles Tapley Hoyt",
'Licenses': "Other / Proprietary",
'ContactInfo': "charles.hoyt@scai.fraunhofer.de"
}

self.assertEqual(expected_document_metadata, g.metadata_parser.document_metadata)


@unittest.skipUnless(PYBEL_TEST_ALL, 'not enough memory on Travis-CI for this test')
class TestImport(unittest.TestCase):
def test_full(self):
52 tests/test_manager_namespaceCache.py
View file
@@ -2,53 +2,23 @@
import unittest
from datetime import datetime

from pybel.manager.defaults import default_namespaces as expected_keys
from pybel.manager.namespace_cache import NamespaceCache

dir_path = os.path.dirname(os.path.realpath(__file__))

test_ns1 = 'file:///' + os.path.join(dir_path, 'bel', 'test_ns_1.belns')
test_ns2 = 'file:///' + os.path.join(dir_path, 'bel', "test_ns_1_updated.belns")

expected_keys = [
'http://resource.belframework.org/belframework/20150611/namespace/mesh-cellular-structures-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/chebi.belns',
'http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns',
'http://resource.belframework.org/belframework/20150611/namespace/disease-ontology-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/selventa-protein-families.belns',
'http://resource.belframework.org/belframework/20150611/namespace/affy-probeset-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/go-biological-process.belns',
'http://resource.belframework.org/belframework/20150611/namespace/go-cellular-component-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/disease-ontology.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-chemicals.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-cellular-structures.belns',
'http://resource.belframework.org/belframework/20150611/namespace/go-cellular-component.belns',
'http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-chemicals.belns',
'http://resource.belframework.org/belframework/20150611/namespace/swissprot.belns',
'http://resource.belframework.org/belframework/20150611/namespace/rgd-rat-genes.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-processes.belns',
'http://resource.belframework.org/belframework/20150611/namespace/selventa-named-complexes.belns',
'http://resource.belframework.org/belframework/20150611/namespace/chebi-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-chemicals-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/swissprot-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-diseases.belns',
'http://resource.belframework.org/belframework/20150611/namespace/go-biological-process-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mesh-processes-ids.belns',
'http://resource.belframework.org/belframework/20150611/namespace/mgi-mouse-genes.belns'
]


class TestNsCache(unittest.TestCase):
def setUp(self):
self.test_db = 'sqlite://'
self.data = os.path.join(dir_path, 'bel')

self.test_namespace = {
'url': 'file:///' + self.data,
'namespaces': ['test_ns_1.belns']
}
self.test_namespace = [
test_ns1
]

self.expected_test_cache = {
test_ns1: {
@@ -92,11 +62,11 @@ def test_setup(self):

def test_allreadyIn(self):

test_db = NamespaceCache(self.test_db)
test_db = NamespaceCache(self.test_db, setup_default_cache=False)
test_db.setup_database()

for namespace in self.test_namespace['namespaces']:
namespace_exists = test_db.check_namespace(os.path.join(self.test_namespace['url'], namespace))
for namespace in self.test_namespace:
namespace_exists = test_db.check_namespace(namespace)
self.assertIsNone(namespace_exists)

def test_importing(self):
@@ -112,7 +82,7 @@ def test_importing(self):
'contact': 'charles.hoyt@scai.fraunhofer.de'
}

test_db = NamespaceCache(self.test_db)
test_db = NamespaceCache(self.test_db, setup_default_cache=False)
test_db.setup_database(drop_existing=True)
test_db.ensure_cache(self.test_namespace)
print(test_db.cache)
@@ -155,7 +125,7 @@ def test_update_namespace(self):
}
}

test_db = NamespaceCache(self.test_db)
test_db = NamespaceCache(self.test_db, setup_default_cache=False)
test_db.setup_database(drop_existing=True)
test_db.ensure_cache(self.test_namespace)

@@ -170,7 +140,7 @@ def test_update_namespace(self):
self.assertEqual(expected_cache_dict2, test_db.cache)
self.assertNotEqual(expected_cache_dict3, test_db.cache)

test_db2 = NamespaceCache(self.test_db)
test_db2 = NamespaceCache(self.test_db, setup_default_cache=False)
test_db2.setup_database(drop_existing=True)
test_db2.ensure_cache(self.test_namespace)

@@ -183,7 +153,7 @@ def test_update_namespace(self):
self.assertEqual(expected_cache_dict3, test_db2.cache)

def test_update_namespaceCache(self):
test_db = NamespaceCache(self.test_db)
test_db = NamespaceCache(self.test_db, setup_default_cache=False)
test_db.update_namespace_cache()
test_db_keys = test_db.cache.keys()
for db_key in expected_keys: