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
47 private static final String inmenu = "TEST|http://someurl.blah/$DB_ACCESSION$|"
48 + "ANOTHER|http://test/t$SEQUENCE_ID$|"
49 + "TEST2|http://address/$SEQUENCE_ID$|SRS|"
50 + "http://theSRSlink/$SEQUENCE_ID$|"
51 + "MIR:00000005|MIR:00000011|MIR:00000372";
53 private static final String notinmenu = "Not1|http://not.in.menu/$DB_ACCESSION$|"
54 + "Not2|http://not.in.menu.either/$DB_ACCESSION$";
56 private static final String testIdOrgString = "{\"Local\": [{\"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()
112 UrlLinkTableModel m = new UrlLinkTableModel(prov);
114 // exactly one table model listener
115 TableModelListener[] listeners = m
116 .getListeners(TableModelListener.class);
117 Assert.assertEquals(listeners.length, 1);
119 // default row exists, there is exactly 1, and it matches the supplied
122 for (int row = 0; row < m.getRowCount(); row++)
124 boolean isDefault = (boolean) m.getValueAt(row, defaultCol);
128 String defaultDBName = (String) m.getValueAt(row, dbCol);
129 Assert.assertEquals(defaultDBName, "TEST2");
131 String defaultDesc = (String) m.getValueAt(row, descCol);
132 Assert.assertEquals(defaultDesc, "TEST2");
135 Assert.assertEquals(count, 1);
139 * Test row and column counts
141 @Test(groups = { "Functional" })
142 public void testCounts()
144 UrlLinkTableModel m = new UrlLinkTableModel(prov);
146 // correct numbers of column and rows
147 Assert.assertEquals(m.getColumnCount(), 5);
148 Assert.assertEquals(m.getRowCount(), 10);
154 @Test(groups = { "Functional" })
155 public void testColumns()
157 UrlLinkTableModel m = new UrlLinkTableModel(prov);
159 // check column names
160 Assert.assertEquals(m.getColumnName(0),
161 MessageManager.formatMessage("label.database"));
162 Assert.assertEquals(m.getColumnName(1),
163 MessageManager.formatMessage("label.name"));
164 Assert.assertEquals(m.getColumnName(2),
165 MessageManager.formatMessage("label.url"));
166 Assert.assertEquals(m.getColumnName(3),
167 MessageManager.formatMessage("label.inmenu"));
168 Assert.assertEquals(m.getColumnName(4),
169 MessageManager.formatMessage("label.primary"));
171 // check column classes
172 Assert.assertEquals(m.getColumnClass(0), String.class);
173 Assert.assertEquals(m.getColumnClass(1), String.class);
174 Assert.assertEquals(m.getColumnClass(2), String.class);
175 Assert.assertEquals(m.getColumnClass(3), Boolean.class);
176 Assert.assertEquals(m.getColumnClass(4), Boolean.class);
182 @Test(groups = { "Functional" })
183 public void testRowInsert()
185 UrlLinkTableModel m = new UrlLinkTableModel(prov);
187 m.insertRow("newname", "newurl");
189 // check table has new row inserted
190 Assert.assertEquals(m.getValueAt(10, 0), "newname");
191 Assert.assertEquals(m.getValueAt(10, 1), "newname");
192 Assert.assertEquals(m.getValueAt(10, 2), "newurl");
193 Assert.assertEquals(m.getValueAt(10, 3), true);
194 Assert.assertEquals(m.getValueAt(10, 4), false);
196 // check data source has new row insrte
198 prov.getLinksForMenu().contains("newname" + SEP + "newurl"));
204 @Test(groups = { "Functional" })
205 public void testRowDelete()
207 UrlLinkTableModel m = new UrlLinkTableModel(prov);
209 // get name and url at row 0
210 String name = (String) m.getValueAt(0, 0);
211 String url = (String) m.getValueAt(0, 1);
215 // check table no longer has row 0 elements in it
216 for (int row = 0; row < m.getRowCount(); row++)
218 Assert.assertNotEquals(m.getValueAt(row, 0), name);
221 // check data source likewise
222 Assert.assertFalse(prov.getLinksForMenu().contains(name + SEP + url));
226 * Test value setting and getting
228 @Test(groups = { "Functional" })
229 public void testValues()
231 UrlLinkTableModel m = new UrlLinkTableModel(prov);
233 // get original default
235 boolean isDefault = false;
236 for (olddefault = 0; olddefault < m.getRowCount()
237 && !isDefault; olddefault++)
239 isDefault = (boolean) m.getValueAt(olddefault, 3);
242 // set new values, one in each row
243 m.setValueAt("dbnamechanged", 6, 0);
244 m.setValueAt("descchanged", 6, 1);
245 m.setValueAt("urlchanged", 7, 2);
246 m.setValueAt(false, 8, 3);
247 m.setValueAt(true, 6, 4);
249 m.setValueAt("dbnamechanged", 5, 0);
251 // check values updated in table
252 Assert.assertEquals(m.getValueAt(6, 0), "descchanged"); // custom url can't
254 Assert.assertEquals(m.getValueAt(6, 1), "descchanged");
255 Assert.assertEquals(m.getValueAt(7, 2), "urlchanged");
256 Assert.assertFalse((boolean) m.getValueAt(8, 3));
257 Assert.assertTrue((boolean) m.getValueAt(6, 4));
258 Assert.assertFalse((boolean) m.getValueAt(olddefault, 4));
260 Assert.assertEquals(m.getValueAt(5, 0), "dbnamechanged");
262 // check default row is exactly one row still
263 for (int row = 0; row < m.getRowCount(); row++)
265 isDefault = (boolean) m.getValueAt(row, 4);
267 // if isDefault is true, row is 9
268 // if isDefault is false, row is not 9
269 Assert.assertFalse(isDefault && !(row == 6));
272 // check table updated
273 Assert.assertTrue(prov.writeUrlsAsString(true)
274 .contains("descchanged" + SEP + m.getValueAt(6, 2)));
275 Assert.assertTrue(prov.writeUrlsAsString(true)
276 .contains(m.getValueAt(7, 1) + SEP + "urlchanged"));
277 Assert.assertTrue(prov.writeUrlsAsString(false)
278 .contains((String) m.getValueAt(8, 1)));
279 Assert.assertEquals(prov.getPrimaryUrl("seqid"), m.getValueAt(6, 2)
280 .toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
284 * Test cell editability
286 @Test(groups = { "Functional" })
287 public void testEditable()
289 UrlLinkTableModel m = new UrlLinkTableModel(prov);
291 for (int row = 0; row < m.getRowCount(); row++)
293 Assert.assertFalse(m.isCellEditable(row, 0));
294 Assert.assertFalse(m.isCellEditable(row, 1));
295 Assert.assertFalse(m.isCellEditable(row, 2));
296 Assert.assertTrue(m.isCellEditable(row, 3));
298 if ((row == 4) || (row == 6) || (row == 7))
300 Assert.assertTrue(m.isCellEditable(row, 4));
304 Assert.assertFalse(m.isCellEditable(row, 4));
310 * Test row 'deletability'
312 @Test(groups = { "Functional" })
313 public void testDeletable()
315 UrlLinkTableModel m = new UrlLinkTableModel(prov);
317 for (int row = 0; row < m.getRowCount(); row++)
321 Assert.assertTrue(m.isRowDeletable(row));
325 Assert.assertFalse(m.isRowDeletable(row));
331 * Test indirect row editability
333 @Test(groups = { "Functional" })
334 public void testRowEditable()
336 UrlLinkTableModel m = new UrlLinkTableModel(prov);
338 for (int row = 0; row < m.getRowCount(); row++)
342 Assert.assertTrue(m.isRowEditable(row));
346 Assert.assertFalse(m.isRowEditable(row));