2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
24 import static jalview.util.UrlConstants.DELIM;
25 import static jalview.util.UrlConstants.SEP;
26 import static jalview.util.UrlConstants.SEQUENCE_ID;
28 import jalview.urls.api.UrlProviderI;
29 import jalview.util.MessageManager;
31 import java.io.BufferedWriter;
33 import java.io.FileWriter;
34 import java.io.IOException;
35 import java.util.ArrayList;
36 import java.util.List;
38 import javax.swing.event.TableModelListener;
40 import org.testng.Assert;
41 import org.testng.annotations.BeforeMethod;
42 import org.testng.annotations.Test;
44 public class UrlLinkTableModelTest {
46 private static final String inmenu = "TEST|http://someurl.blah/$DB_ACCESSION$|"
47 + "ANOTHER|http://test/t$SEQUENCE_ID$|"
48 + "TEST2|http://address/$SEQUENCE_ID$|SRS|"
49 + "http://theSRSlink/$SEQUENCE_ID$|"
50 + "MIR:00000005|MIR:00000011|MIR:00000372";
52 private static final String notinmenu = "Not1|http://not.in.menu/$DB_ACCESSION$|"
53 + "Not2|http://not.in.menu.either/$DB_ACCESSION$";
55 // Test identifiers.org download file
56 private static final String testIdOrgString = "[{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
57 + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
58 + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
59 + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
60 + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
61 + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
62 + "\"url\":\"http://identifiers.org/interpro\"},"
63 + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
64 + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]";
66 private UrlProviderI prov;
68 @BeforeMethod(alwaysRun = true)
71 // set up UrlProvider data as the source for the TableModel
72 // the data gets updated by the TableModel, so needs to be reinitialised for
75 // make a dummy identifiers.org download file
79 temp = File.createTempFile("tempfile", ".tmp");
81 BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
82 bw.write(testIdOrgString);
84 } catch (IOException e)
86 System.out.println("Error initialising UrlLinkTableModel test: "
90 // set up custom and identifiers.org url providers
91 IdOrgSettings.setDownloadLocation(temp.getPath());
92 IdentifiersUrlProvider idprov = new IdentifiersUrlProvider(inmenu);
93 CustomUrlProvider cprov = new CustomUrlProvider(inmenu, notinmenu);
94 List<UrlProviderI> provlist = new ArrayList<UrlProviderI>();
98 prov = new UrlProvider("TEST2", provlist);
102 * Test that the table model is correctly initialised
103 * Display columns and default row are set; data provider listening event set up
105 @Test(groups = { "Functional" })
106 public void testInitialisation()
111 UrlLinkTableModel m = new UrlLinkTableModel(prov);
113 // exactly one table model listener
114 TableModelListener[] listeners = m
115 .getListeners(TableModelListener.class);
116 Assert.assertEquals(listeners.length, 1);
118 // default row exists, there is exactly 1, and it matches the supplied
121 for (int row = 0; row < m.getRowCount(); row++)
123 boolean isDefault = (boolean) m.getValueAt(row, defaultCol);
127 String defaultName = (String) m.getValueAt(row, nameCol);
128 Assert.assertEquals(defaultName, "TEST2");
131 Assert.assertEquals(count, 1);
135 * Test row and column counts
137 @Test(groups = { "Functional" })
138 public void testCounts()
140 UrlLinkTableModel m = new UrlLinkTableModel(prov);
142 // correct numbers of column and rows
143 Assert.assertEquals(m.getColumnCount(), 4);
144 Assert.assertEquals(m.getRowCount(), 10);
150 @Test(groups = { "Functional" })
151 public void testColumns()
153 UrlLinkTableModel m = new UrlLinkTableModel(prov);
155 // check column names
156 Assert.assertEquals(m.getColumnName(0),
157 MessageManager.formatMessage("label.name"));
158 Assert.assertEquals(m.getColumnName(1),
159 MessageManager.formatMessage("label.url"));
160 Assert.assertEquals(m.getColumnName(2),
161 MessageManager.formatMessage("label.inmenu"));
162 Assert.assertEquals(m.getColumnName(3),
163 MessageManager.formatMessage("label.default"));
165 // check column classes
166 Assert.assertEquals(m.getColumnClass(0), String.class);
167 Assert.assertEquals(m.getColumnClass(1), String.class);
168 Assert.assertEquals(m.getColumnClass(2), Boolean.class);
169 Assert.assertEquals(m.getColumnClass(3), Boolean.class);
175 @Test(groups = { "Functional" })
176 public void testRowInsert()
178 UrlLinkTableModel m = new UrlLinkTableModel(prov);
180 m.insertRow("newname", "newurl");
182 // check table has new row inserted
183 Assert.assertEquals(m.getValueAt(10, 0), "newname");
184 Assert.assertEquals(m.getValueAt(10, 1), "newurl");
185 Assert.assertEquals(m.getValueAt(10, 2), true);
186 Assert.assertEquals(m.getValueAt(10, 3), false);
188 // check data source has new row insrte
189 Assert.assertTrue(prov.getLinksForMenu().contains(
190 "newname" + SEP + "newurl"));
196 @Test(groups = { "Functional" })
197 public void testRowDelete()
199 UrlLinkTableModel m = new UrlLinkTableModel(prov);
201 // get name and url at row 0
202 String name = (String) m.getValueAt(0, 0);
203 String url = (String) m.getValueAt(0, 1);
207 // check table no longer has row 0 elements in it
208 for (int row = 0; row < m.getRowCount(); row++)
210 Assert.assertNotEquals(m.getValueAt(row, 0), name);
213 // check data source likewise
214 Assert.assertFalse(prov.getLinksForMenu().contains(name + SEP + url));
218 * Test value setting and getting
220 @Test(groups = { "Functional" })
221 public void testValues()
223 UrlLinkTableModel m = new UrlLinkTableModel(prov);
225 // get original default
227 boolean isDefault = false;
228 for (olddefault = 0; olddefault < m.getRowCount() && !isDefault; olddefault++)
230 isDefault = (boolean) m.getValueAt(olddefault, 3);
233 // set new values, one in each row
234 m.setValueAt("namechanged", 6, 0);
235 m.setValueAt("urlchanged", 7, 1);
236 m.setValueAt(false, 8, 2);
237 m.setValueAt(true, 6, 3);
239 // check values updated in table
240 Assert.assertEquals(m.getValueAt(6, 0), "namechanged");
241 Assert.assertEquals(m.getValueAt(7, 1), "urlchanged");
242 Assert.assertFalse((boolean) m.getValueAt(8, 2));
243 Assert.assertTrue((boolean) m.getValueAt(6, 3));
244 Assert.assertFalse((boolean) m.getValueAt(olddefault, 3));
246 // check default row is exactly one row still
247 for (int row = 0; row < m.getRowCount(); row++)
249 isDefault = (boolean) m.getValueAt(row, 3);
251 // if isDefault is true, row is 9
252 // if isDefault is false, row is not 9
253 Assert.assertFalse(isDefault && !(row == 6));
256 // check table updated
257 Assert.assertTrue(prov.writeUrlsAsString(true).contains("namechanged" +SEP + m.getValueAt(6, 1)));
258 Assert.assertTrue(prov.writeUrlsAsString(true).contains(m.getValueAt(7,0) + SEP + "urlchanged"));
259 Assert.assertTrue(prov.writeUrlsAsString(false).contains(
260 (String) m.getValueAt(8, 0)));
261 Assert.assertEquals(prov.getDefaultUrl("seqid"), m.getValueAt(6, 1)
262 .toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
267 * Test cell editability
269 @Test(groups = { "Functional" })
270 public void testEditable()
272 UrlLinkTableModel m = new UrlLinkTableModel(prov);
274 for (int row = 0; row < m.getRowCount(); row++)
276 Assert.assertFalse(m.isCellEditable(row, 0));
277 Assert.assertFalse(m.isCellEditable(row, 1));
278 Assert.assertTrue(m.isCellEditable(row, 2));
280 if ((row == 4) || (row == 6) || (row == 7))
282 Assert.assertTrue(m.isCellEditable(row, 3));
286 Assert.assertFalse(m.isCellEditable(row, 3));