def test_type_restricted(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res, pid = epidb.add_project("ENCODE", "desc", self.admin_key)
self.assertSuccess(res, pid)
res, emid = epidb.add_epigenetic_mark("Methylation", "desc", {"category": "DNA Methylation"}, self.admin_key)
self.assertSuccess(res, emid)
res, bsid = epidb.add_biosource("K562", "desc", {}, self.admin_key)
self.assertSuccess(res, bsid)
res, ids = epidb.search("desc", None, self.admin_key)
self.assertSuccess(res, ids)
self.assertTrue([pid, 'ENCODE', 'projects'] in ids)
self.assertTrue([emid, 'Methylation', 'epigenetic_marks'] in ids)
self.assertTrue([bsid, 'K562', 'biosources'] in ids)
self.assertEqual(len(ids), 3)
res, ids = epidb.search("desc", "projects", self.admin_key)
self.assertSuccess(res, ids)
self.assertTrue([pid, 'ENCODE', 'projects'] in ids)
self.assertEqual(len(ids), 1)
res, ids = epidb.search("desc", ["epigenetic_marks", "biosources"], self.admin_key)
self.assertSuccess(res, ids)
self.assertTrue([emid, 'Methylation', 'epigenetic_marks'] in ids)
self.assertTrue([bsid, 'K562', 'biosources'] in ids)
self.assertEqual(len(ids), 2)
def test_remove_epigenetic_mark(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
regions_data = helpers.load_bed("hg19_chr1_1")
format = data_info.EXPERIMENTS["hg19_chr1_1"]["format"]
(res, epigenetic_mark_id) = epidb.add_epigenetic_mark(
"H3K666ac3", "acetil metal \,,,/",
{"category": "heavy histone metal"}, self.admin_key)
self.assertSuccess(res, epigenetic_mark_id)
# adding two experiments with the same data should work
res, eid = epidb.add_experiment("test_exp1", "hg19", "H3K666ac3",
sample_id, "tech1", "ENCODE", "desc1",
regions_data, format, None,
self.admin_key)
self.assertSuccess(res)
res = epidb.remove(epigenetic_mark_id, self.admin_key)
self.assertFailure(res)
res = epidb.remove(eid, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(epigenetic_mark_id, self.admin_key)
self.assertSuccess(res)
def test_result_ids_reuse(self):
"""
Test the request-ID's returned by list_requests
"""
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
s, id = epidb.add_epigenetic_mark("DNA Methylation", "", {}, self.admin_key)
self.assertSuccess(s, id)
s, query_id = epidb.select_regions(None, "hg19", "DNA Methylation", None, None, None, "chr1", None, None, self.admin_key)
self.assertSuccess(s, query_id)
requests = []
for i in xrange(0, 10):
s, request_id = epidb.get_regions(query_id, "CHROMOSOME,START,END", self.admin_key)
self.assertSuccess(s, request_id)
requests.append(request_id)
s, requests_list = epidb.list_requests(None, self.admin_key)
self.assertSuccess(s, requests_list)
for _id, status in requests_list:
self.assertTrue(_id in requests)
requests_ids = [r[0] for r in requests_list]
self.assertEquals(len(requests_ids), 1)
def test_epigenetic_mark_info(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res, emid = epidb.add_epigenetic_mark("Methylation", "DNA Methylation", {"category":"DNA Methylation"}, self.admin_key)
self.assertSuccess(res, emid)
res, data = epidb.info(emid, self.admin_key)
self.assertEqual(data[0]['name'], "Methylation")
self.assertEqual(data[0]['description'], "DNA Methylation")
self.assertEqual(data[0]['extra_metadata']['category'], "DNA Methylation")
self.assertEqual(data[0]['user'], "test_admin")
self.assertEqual(data[0]['_id'], emid)
def test_epigenetic_mark(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res, emid1 = epidb.add_epigenetic_mark("Methylation", "DNA Methylation", {"category": "DNA Methylation"}, self.admin_key)
self.assertSuccess(res, emid1)
res, emid2 = epidb.add_epigenetic_mark("Methyl450", "DNA Methylation Infinium HumanMethylation450 BeadChip", {"category": "DNA Methylation"}, self.admin_key)
self.assertSuccess(res, emid2)
res, emid3 = epidb.add_epigenetic_mark("OpenChromDnase", "Open Chromatin DNaseI", {"category": "open chromatin"}, self.admin_key)
self.assertSuccess(res, emid3)
res, emid4 = epidb.add_epigenetic_mark("DNaseI", "DNaseI hypersensitive sites ", {"category": "open chromatin"}, self.admin_key)
self.assertSuccess(res, emid4)
self.assertEqual(res, "okay")
res, ids = epidb.search("Methylation", None, self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], emid1)
self.assertEqual(ids[1][0], emid2)
res, ids = epidb.search("DNA", None, self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], emid1)
self.assertEqual(ids[1][0], emid2)
res, ids = epidb.search("Dnasei", None, self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], emid4)
self.assertEqual(ids[1][0], emid3)
res, ids = epidb.search(emid4, None, self.admin_key)
self.assertSuccess(res, ids)
self.assertEqual(ids[0][0], emid4)
def test_request_info_permission(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_full(epidb)
s, user = epidb.add_user("user1", "*****@*****.**", "test", self.admin_key)
id, user_key = user
s, _id = epidb.modify_user_admin(id, "permission_level", "INCLUDE_COLLECTION_TERMS", self.admin_key)
self.assertSuccess(s, _id)
s, id = epidb.add_epigenetic_mark("DNA Methylation", "", {}, user_key)
self.assertSuccess(s, id)
s, query_id = epidb.select_regions(None, "hg19", "DNA Methylation", None, None, None, "chr1", None, None, user_key)
self.assertSuccess(s, query_id)
s, request_id = epidb.get_regions(query_id, "CHROMOSOME,START,END", user_key)
s, info = epidb.info(request_id, user_key)
self.assertSuccess(s, info)
s, info = epidb.info(request_id, self.admin_key)
self.assertSuccess(s, info)
