JAL-2388 New iterators and tests
[jalview.git] / test / jalview / ws / ebi / EBIFetchClientTest.java
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
31 public class EBIFetchClientTest
32 {
33
34   @BeforeClass(alwaysRun = true)
35   public void setUpJvOptionPane()
36   {
37     JvOptionPane.setInteractiveMode(false);
38     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
39   }
40
41   /**
42    * Test method that constructs URL to fetch from
43    */
44   @Test(groups = "Functional")
45   public void testBuildUrl()
46   {
47     /*
48      * EMBL
49      */
50     assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
51             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
52
53     /*
54      * EMBLCDS
55      */
56     assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
57             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
58
59     /*
60      * Uniprot
61      */
62     assertEquals(
63             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
64             EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
65
66     /*
67      * PDB / pdb
68      */
69     assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
70             EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
71
72     /*
73      * PDB / mmCIF
74      */
75     assertEquals(
76             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
77             EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
78   }
79
80   /**
81    * Test method that parses db:id;id;id
82    */
83   @Test(groups = "Functional")
84   public void testParseIds()
85   {
86     /*
87      * pdb, two accessions
88      */
89     StringBuilder queries = new StringBuilder();
90     String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
91     assertEquals("pdb", db);
92     assertEquals("3a6s,1A70", queries.toString());
93
94     /*
95      * pdb specified on second accession
96      */
97     queries.setLength(0);
98     queries = new StringBuilder();
99     db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
100     assertEquals("pdb", db);
101     assertEquals("3a6s,1A70", queries.toString());
102
103     /*
104      * uniprot, one accession
105      */
106     queries.setLength(0);
107     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
108     assertEquals("uniprot", db);
109     assertEquals("P00340", queries.toString());
110
111     /*
112      * uniprot, one accession, appending to existing queries
113      */
114     queries.setLength(0);
115     queries.append("P30419");
116     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
117     assertEquals("uniprot", db);
118     assertEquals("P30419,P00340", queries.toString());
119
120     /*
121      * pdb and uniprot mixed - rejected
122      */
123     queries.setLength(0);
124     db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
125     assertNull(db);
126     assertEquals("3a6s,1a70", queries.toString());
127
128     /*
129      * pdb and PDB mixed - ok
130      */
131     queries.setLength(0);
132     db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
133     assertEquals("PDB", db);
134     assertEquals("3a6s,1a70,1QIP", queries.toString());
135
136     /*
137      * no database (improper format)
138      */
139     queries.setLength(0);
140     db = EBIFetchClient.parseIds("P00340", queries);
141     assertNull(db);
142     assertEquals("P00340", queries.toString());
143   }
144 }