JAL-2505 removed SequenceFeature constructor JAL-1641 include
[jalview.git] / test / jalview / urls / IdentifiersUrlProviderTest.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
22 package jalview.urls;
23
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
26 import static org.testng.AssertJUnit.assertTrue;
27
28 import jalview.urls.api.UrlProviderI;
29
30 import java.io.File;
31 import java.io.FileWriter;
32 import java.util.Arrays;
33 import java.util.HashMap;
34 import java.util.Vector;
35
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.Test;
38
39 public class IdentifiersUrlProviderTest
40 {
41   private static final String testIdOrgFile = "{\"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 static final String[] dlinks = {
52       "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot",
53       "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
54       "ENA|http://identifiers.org/ena.embl/$DB_ACCESSION$|ena.embl" };
55
56   private static final String[] dlinks1 = {
57       "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
58       "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
59
60   private static final String[] dlinks2 = {
61       "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
62       "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
63
64   private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
65           + "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
66           + "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
67
68   private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
69
70   private static final Vector<String> displayLinks = new Vector<String>(
71         Arrays.asList(dlinks));
72   
73   private static final Vector<String> unselDisplayLinks = new Vector<String>(
74           Arrays.asList(unselDlinks));
75
76   private static final Vector<String> displayLinks1 = new Vector<String>(
77           Arrays.asList(dlinks1));
78
79   private static final Vector<String> displayLinks2 = new Vector<String>(
80           Arrays.asList(dlinks2));
81
82   private static final HashMap<String, String> urlMap = new HashMap<String, String>()
83   {
84     {
85       put("MIR:00000005", "http://identifiers.org/uniprot/$DB_ACCESSION$");
86       put("MIR:00000011", "http://identifiers.org/interpro/$DB_ACCESSION$");
87       put("MIR:00000372", "http://identifiers.org/ena.embl/$DB_ACCESSION$");
88     }
89   };
90
91   private String testfile = "";
92
93
94   @BeforeClass(alwaysRun = true)
95   public void setup()
96   {
97     // setup test ids in a file
98     File outFile = null;
99     try
100     {
101       outFile = File.createTempFile("testidsfile", "txt");
102       outFile.deleteOnExit();
103
104       FileWriter fw = new FileWriter(outFile);
105       fw.write(testIdOrgFile);
106       fw.close();
107
108       testfile = outFile.getAbsolutePath();
109
110     } catch (Exception ex)
111     {
112       System.err.println(ex);
113     }
114
115     IdOrgSettings.setDownloadLocation(testfile);
116   }
117
118   /*
119    * Test urls are set and returned correctly
120    */
121   @Test(groups = { "Functional" })
122   public void testUrlLinks()
123   {
124     // creation from cached id list
125     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
126     UrlProviderI idProv = new IdentifiersUrlProvider(idList);
127     
128     assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
129
130     // because UrlProvider does not guarantee order of links, we can't just
131     // compare the output of writeUrlsAsString to a string, hence the hoops here
132     String result = idProv.writeUrlsAsString(true);
133     UrlProviderI up = new IdentifiersUrlProvider(result);
134     assertTrue(displayLinks.containsAll(up.getLinksForMenu()));
135
136     result = idProv.writeUrlsAsString(false);
137     up = new IdentifiersUrlProvider(result);
138     assertTrue(unselDisplayLinks.containsAll(up.getLinksForMenu()));
139
140   }
141
142   /*
143    * Test default is set and returned correctly
144    */
145   @Test(groups = { "Functional" })
146   public void testDefaultUrl()
147   {
148     // creation from cached id list
149     String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
150     UrlProviderI idProv = new IdentifiersUrlProvider(idList);
151     
152     // initially no default
153     assertEquals(null, idProv.getPrimaryUrl("seqid"));
154     
155     // set and then retrieve default
156     assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
157     assertEquals("http://identifiers.org/uniprot/seqid",
158             idProv.getPrimaryUrl("seqid"));
159
160     // ids less than length 4 return null
161     assertEquals(null,
162             idProv.getPrimaryUrl("123"));
163
164     // attempt to set bad default
165     assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
166     // default set to null (as default should have been set elsewhere)
167     assertEquals(null, idProv.getPrimaryUrl("seqid"));
168
169     // chooseDefaultUrl not implemented for IdentifiersUrlProvider
170     assertEquals(null, idProv.choosePrimaryUrl());
171   }
172 }