1- from comptox_ai .db import GraphDB
1+ import os
2+ import warnings
23
34import pytest
4- import warnings
5- import os
5+
6+ from comptox_ai . db import GraphDB
67
78TEST_DIR = os .path .dirname (os .path .realpath (__file__ ))
89
910
1011# Module-level scope so we don't keep reconnecting with every test
1112@pytest .fixture (scope = "module" )
1213def G ():
13- G = GraphDB (verbose = True , hostname = "neo4j.comptox.ai" )
14- return G
14+ G = GraphDB (verbose = True , hostname = "neo4j.comptox.ai" )
15+ return G
16+
1517
1618class TestGraphDB (object ):
17-
18- < << << << HEAD
19- == == == =
20-
21- >> >> >> > master
22- def test_neo4j_connection_does_exist (self , G ):
23- with warnings .catch_warnings ():
24- # Supress the ExperimentalWarning for now
25- warnings .simplefilter ("ignore" )
26- assert G ._driver .verify_connectivity () is not None
27-
28- def test_cypher_query_does_run (self , G ):
29- x = G .run_cypher ("RETURN 'hello';" )
30- assert len (x [0 ]) > 0
31-
32- def test_dsstox_to_casrn_converts (self , G ):
33- converted_ids = G .convert_ids (
34- node_type = 'Chemical' ,
35- from_id = 'xrefDTXSID' ,
36- to_id = 'xrefCasRN' ,
37- ids = ['DTXSID40857898' , 'DTXSID40858749' ]
38- )
39-
40- # Hopefully DSSTOX -> CASRN mappings are stable between versions...
41- assert converted_ids == ['69313-80-0' , '4559-79-9' ]
42-
43- ## THE FOLLOWING ARE OBSOLETE UNTIL GDS GRAPH CATALOG IS COMPATIBLE WITH
44- # def test_raise_when_config_file_not_found(self):
45- # with pytest.raises(RuntimeError) as e_info:
46- # G_pre = GraphDB(config_file="/dev/null")
47-
48- # def test_raise_when_bad_config_given(self):
49- # bad_config_file = os.path.join(TEST_DIR, 'badconfig.txt')
50- # with pytest.raises(RuntimeError) as e_info:
51- # G_pre = GraphDB(config_file=bad_config_file)
52-
53- # def test_raise_when_database_unavailable(self):
54- # unavail_config_file = os.path.join(TEST_DIR, 'unavailconfig.txt')
55- # with pytest.raises(RuntimeError) as e_info:
56- # G_pre = GraphDB(config_file=unavail_config_file)
57- ## STRING PROPERTIES:
58-
59- # def test_gds_list_existing_graphs(self, G):
60- # x = G.list_existing_graphs()
61- # assert isinstance(x, list)
62-
63- # def test_gds_delete_existing_graphs(self, G):
64- # x = G.drop_all_existing_graphs()
65-
66- # y = G.list_existing_graphs()
67-
68- # assert len(y) is 0
69-
70- # def test_gds_create_graph_native_projection(self, G):
71- # newgraph1 = G.build_graph_native_projection(
72- # "testgraph1",
73- # ["Chemical", "Disease"],
74- # "*",
75- # )
76-
77- # def test_gds_new_num_graphs_is_1(self, G):
78- # y = G.list_existing_graphs()
79- # assert len(y) == 1
80-
81- # def test_gds_delete_graph_native_projection(self, G):
82- # x = G.drop_existing_graph("testgraph1")
83- # assert x['graphName'] == "testgraph1"
84-
85- # def test_gds_create_graph_cypher_projection(self, G):
86- # newgraph2 = G.build_graph_cypher_projection(
87- # "testgraph2",
88- # "MATCH (n) WHERE n:Chemical OR n:Disease RETURN id(n) AS id, labels(n) AS labels",
89- # "MATCH (c:Chemical)-->(d:Disease) RETURN id(c) as source, id(d) as target"
90- # )
91-
92- # def test_gds_delete_graph_cypher_projection(self, G):
93- # # Note: this test will fail if the previous test fails
94- # x = G.drop_existing_graph("testgraph2")
95- # assert x['graphName'] == "testgraph2"
19+
20+ def test_neo4j_connection_does_exist (self , G ):
21+ with warnings .catch_warnings ():
22+ # Supress the ExperimentalWarning for now
23+ warnings .simplefilter ("ignore" )
24+ assert G ._driver .verify_connectivity () is not None
25+
26+ def test_cypher_query_does_run (self , G ):
27+ x = G .run_cypher ("RETURN 'hello';" )
28+ assert len (x [0 ]) > 0
29+
30+ def test_dsstox_to_casrn_converts (self , G ):
31+ converted_ids = G .convert_ids (
32+ node_type = 'Chemical' ,
33+ from_id = 'xrefDTXSID' ,
34+ to_id = 'xrefCasRN' ,
35+ ids = ['DTXSID40857898' , 'DTXSID40858749' ]
36+ )
37+
38+ # Hopefully DSSTOX -> CASRN mappings are stable between versions...
39+ assert converted_ids == ['69313-80-0' , '4559-79-9' ]
40+
41+ # THE FOLLOWING ARE OBSOLETE UNTIL GDS GRAPH CATALOG IS COMPATIBLE WITH
42+ # def test_raise_when_config_file_not_found(self):
43+ # with pytest.raises(RuntimeError) as e_info:
44+ # G_pre = GraphDB(config_file="/dev/null")
45+
46+ # def test_raise_when_bad_config_given(self):
47+ # bad_config_file = os.path.join(TEST_DIR, 'badconfig.txt')
48+ # with pytest.raises(RuntimeError) as e_info:
49+ # G_pre = GraphDB(config_file=bad_config_file)
50+
51+ # def test_raise_when_database_unavailable(self):
52+ # unavail_config_file = os.path.join(TEST_DIR, 'unavailconfig.txt')
53+ # with pytest.raises(RuntimeError) as e_info:
54+ # G_pre = GraphDB(config_file=unavail_config_file)
55+ # STRING PROPERTIES:
56+
57+ # def test_gds_list_existing_graphs(self, G):
58+ # x = G.list_existing_graphs()
59+ # assert isinstance(x, list)
60+
61+ # def test_gds_delete_existing_graphs(self, G):
62+ # x = G.drop_all_existing_graphs()
63+
64+ # y = G.list_existing_graphs()
65+
66+ # assert len(y) is 0
67+
68+ # def test_gds_create_graph_native_projection(self, G):
69+ # newgraph1 = G.build_graph_native_projection(
70+ # "testgraph1",
71+ # ["Chemical", "Disease"],
72+ # "*",
73+ # )
74+
75+ # def test_gds_new_num_graphs_is_1(self, G):
76+ # y = G.list_existing_graphs()
77+ # assert len(y) == 1
78+
79+ # def test_gds_delete_graph_native_projection(self, G):
80+ # x = G.drop_existing_graph("testgraph1")
81+ # assert x['graphName'] == "testgraph1"
82+
83+ # def test_gds_create_graph_cypher_projection(self, G):
84+ # newgraph2 = G.build_graph_cypher_projection(
85+ # "testgraph2",
86+ # "MATCH (n) WHERE n:Chemical OR n:Disease RETURN id(n) AS id, labels(n) AS labels",
87+ # "MATCH (c:Chemical)-->(d:Disease) RETURN id(c) as source, id(d) as target"
88+ # )
89+
90+ # def test_gds_delete_graph_cypher_projection(self, G):
91+ # # Note: this test will fail if the previous test fails
92+ # x = G.drop_existing_graph("testgraph2")
93+ # assert x['graphName'] == "testgraph2"
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