Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
UrlProviderTest | 37 | 32 | 5 |
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.urls; | |
22 | ||
23 | import jalview.urls.api.UrlProviderI; | |
24 | import jalview.urls.desktop.DesktopUrlProviderFactory; | |
25 | import jalview.util.UrlConstants; | |
26 | ||
27 | import java.io.BufferedWriter; | |
28 | import java.io.File; | |
29 | import java.io.FileWriter; | |
30 | import java.io.IOException; | |
31 | import java.util.List; | |
32 | ||
33 | import org.testng.Assert; | |
34 | import org.testng.annotations.BeforeMethod; | |
35 | import org.testng.annotations.Test; | |
36 | ||
37 | public class UrlProviderTest | |
38 | { | |
39 | ||
40 | // Test identifiers.org download file | |
41 | private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\"," | |
42 | + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\"," | |
43 | + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\"," | |
44 | + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\"," | |
45 | + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"}," | |
46 | + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\"," | |
47 | + "\"url\":\"http://identifiers.org/interpro\"}," | |
48 | + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\"" | |
49 | + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}"; | |
50 | ||
51 | private UrlProviderI prov; | |
52 | ||
53 | 3 | @BeforeMethod(alwaysRun = true) |
54 | public void setup() | |
55 | { | |
56 | // make a dummy identifiers.org download file | |
57 | 3 | File temp = null; |
58 | ||
59 | 3 | try |
60 | { | |
61 | 3 | temp = File.createTempFile("tempfile", ".tmp"); |
62 | 3 | temp.deleteOnExit(); |
63 | 3 | BufferedWriter bw = new BufferedWriter(new FileWriter(temp)); |
64 | 3 | bw.write(testIdOrgString); |
65 | 3 | bw.close(); |
66 | } catch (IOException e) | |
67 | { | |
68 | 0 | System.out.println( |
69 | "Error initialising UrlProviderTest test: " + e.getMessage()); | |
70 | } | |
71 | ||
72 | 3 | IdOrgSettings.setDownloadLocation(temp.getPath()); |
73 | ||
74 | 3 | String defaultUrlString = "No default"; |
75 | 3 | String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|" |
76 | + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$"; | |
77 | 3 | String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$"; |
78 | ||
79 | 3 | DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory( |
80 | defaultUrlString, cachedUrlList, userUrlList); | |
81 | 3 | prov = factory.createUrlProvider(); |
82 | } | |
83 | ||
84 | 1 | @Test(groups = { "Functional" }) |
85 | public void testInitUrlProvider() | |
86 | { | |
87 | 1 | String emblUrl = UrlConstants.DEFAULT_STRING.substring( |
88 | UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1, | |
89 | UrlConstants.DEFAULT_STRING.length()); | |
90 | ||
91 | // chooses EMBL url when default Url id does not exist in provided url lists | |
92 | 1 | Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL); |
93 | 1 | Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"), |
94 | emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN")); | |
95 | ||
96 | 1 | List<String> menulinks = prov.getLinksForMenu(); |
97 | 1 | List<UrlLinkDisplay> allLinks = prov.getLinksForTable(); |
98 | ||
99 | // 9 links in provider - 4 from id file, 4 custom links, 1 additional | |
100 | // default | |
101 | 1 | Assert.assertEquals(allLinks.size(), 9); |
102 | ||
103 | // 6 links in menu (cachedUrlList) + new default | |
104 | 1 | Assert.assertEquals(menulinks.size(), 6); |
105 | ||
106 | 1 | Assert.assertTrue( |
107 | menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$")); | |
108 | 1 | Assert.assertTrue( |
109 | menulinks.contains("Test2|http://test2/$DB_ACCESSION$")); | |
110 | 1 | Assert.assertTrue( |
111 | menulinks.contains("Test3|http://test3/$SEQUENCE_ID$")); | |
112 | 1 | Assert.assertTrue(menulinks.contains( |
113 | "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot")); | |
114 | 1 | Assert.assertTrue(menulinks.contains( |
115 | "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro")); | |
116 | 1 | Assert.assertTrue(menulinks.contains( |
117 | UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl)); | |
118 | } | |
119 | ||
120 | 1 | @Test(groups = { "Functional" }) |
121 | public void testSetDefaultUrl() | |
122 | { | |
123 | // set custom url as default | |
124 | 1 | Assert.assertTrue(prov.setPrimaryUrl("Test1")); |
125 | 1 | Assert.assertEquals(prov.getPrimaryUrlId(), "Test1"); |
126 | ||
127 | // set identifiers url as default | |
128 | 1 | Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011")); |
129 | 1 | Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011"); |
130 | } | |
131 | ||
132 | 1 | @Test( |
133 | groups = | |
134 | { "Functional" }, | |
135 | expectedExceptions = | |
136 | { IllegalArgumentException.class }) | |
137 | public void testSetDefaultUrlWrongly() | |
138 | { | |
139 | // don't allow default to be a non-key | |
140 | 1 | prov.setPrimaryUrl("not-a-key"); |
141 | } | |
142 | } |