Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EBIFetchClientTest	31	36	3	0.00%	Show methods

Class EBIFetchClientTest

Class EBIFetchClientTest	Line # 31	Total Statements 36	Complexity 3	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3434	2.02	1.01	0.0 0.00%
testBuildUrl() : void   testBuildUrl() : void	4444	4.04	1.01	0.0 0.00%
testParseIds() : void   testParseIds() : void	7878	30.030	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ws.ebi;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import jalview.gui.JvOptionPane;
27
28		import org.testng.annotations.BeforeClass;
29		import org.testng.annotations.Test;
30
		0% Uncovered Elements: 39 (39) Complexity: 3 Complexity Density: 0.08
31		public class EBIFetchClientTest
32		{
33
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
34	0	@BeforeClass(alwaysRun = true)...
35		public void setUpJvOptionPane()
36		{
37	0	JvOptionPane.setInteractiveMode(false);
38	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
39		}
40
41		/**
42		* Test method that constructs URL to fetch from
43		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
44	0	@Test(groups = "Functional")...
45		public void testBuildUrl()
46		{
47		/*
48		* EMBL
49		*/
50	0	assertEquals(
51		"https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
52		EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
53
54		/*
55		* EMBLCDS
56		*/
57	0	assertEquals(
58		"https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
59		EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
60
61		/*
62		* PDB / pdb
63		*/
64	0	assertEquals("https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
65		EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
66
67		/*
68		* PDB / mmCIF
69		*/
70	0	assertEquals(
71		"https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
72		EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
73		}
74
75		/**
76		* Test method that parses db:id;id;id
77		*/
		0% Uncovered Elements: 30 (30) Complexity: 1 Complexity Density: 0.03 4-
78	0	@Test(groups = "Functional")...
79		public void testParseIds()
80		{
81		/*
82		* pdb, two accessions
83		*/
84	0	StringBuilder queries = new StringBuilder();
85	0	String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
86	0	assertEquals("pdb", db);
87	0	assertEquals("3a6s,1A70", queries.toString());
88
89		/*
90		* pdb specified on second accession
91		*/
92	0	queries.setLength(0);
93	0	queries = new StringBuilder();
94	0	db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
95	0	assertEquals("pdb", db);
96	0	assertEquals("3a6s,1A70", queries.toString());
97
98		/*
99		* uniprot, one accession
100		*/
101	0	queries.setLength(0);
102	0	db = EBIFetchClient.parseIds("uniprot:P00340", queries);
103	0	assertEquals("uniprot", db);
104	0	assertEquals("P00340", queries.toString());
105
106		/*
107		* uniprot, one accession, appending to existing queries
108		*/
109	0	queries.setLength(0);
110	0	queries.append("P30419");
111	0	db = EBIFetchClient.parseIds("uniprot:P00340", queries);
112	0	assertEquals("uniprot", db);
113	0	assertEquals("P30419,P00340", queries.toString());
114
115		/*
116		* pdb and uniprot mixed - rejected
117		*/
118	0	queries.setLength(0);
119	0	db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
120	0	assertNull(db);
121	0	assertEquals("3a6s,1a70", queries.toString());
122
123		/*
124		* pdb and PDB mixed - ok
125		*/
126	0	queries.setLength(0);
127	0	db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
128	0	assertEquals("PDB", db);
129	0	assertEquals("3a6s,1a70,1QIP", queries.toString());
130
131		/*
132		* no database (improper format)
133		*/
134	0	queries.setLength(0);
135	0	db = EBIFetchClient.parseIds("P00340", queries);
136	0	assertNull(db);
137	0	assertEquals("P00340", queries.toString());
138		}
139		}