Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UrlLinkTableModelTest	44	104	25	0.9926470599.3%	Show methods

Class UrlLinkTableModelTest

Class UrlLinkTableModelTest	Line # 44	Total Statements 104	Complexity 25	TOTAL Coverage 0.9926470599.3%
setup() : void   setup() : void	6868	15.015	2.02	0.93333334 0.9333333493.3%
testInitialisation() : void   testInitialisation() : void	105105	16.016	3.03	1.0 1.0100%
testCounts() : void   testCounts() : void	141141	3.03	1.01	1.0 1.0100%
testColumns() : void   testColumns() : void	154154	11.011	1.01	1.0 1.0100%
testRowInsert() : void   testRowInsert() : void	182182	8.08	1.01	1.0 1.0100%
testRowDelete() : void   testRowDelete() : void	204204	7.07	2.02	1.0 1.0100%
testValues() : void   testValues() : void	228228	25.025	4.04	1.0 1.0100%
testEditable() : void   testEditable() : void	286286	9.09	5.05	1.0 1.0100%
testDeletable() : void   testDeletable() : void	312312	5.05	3.03	1.0 1.0100%
testRowEditable() : void   testRowEditable() : void	333333	5.05	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22058824	jalview.urls.UrlLinkTableModelTest.testValuesjalview.urls.UrlLinkTableModelTest.testValues	1PASS
	0.15441176	jalview.urls.UrlLinkTableModelTest.testInitialisationjalview.urls.UrlLinkTableModelTest.testInitialisation	1PASS
	0.10294118	jalview.urls.UrlLinkTableModelTest.testEditablejalview.urls.UrlLinkTableModelTest.testEditable	1PASS
	0.0882353	jalview.urls.UrlLinkTableModelTest.testColumnsjalview.urls.UrlLinkTableModelTest.testColumns	1PASS
	0.073529415	jalview.urls.UrlLinkTableModelTest.testRowEditablejalview.urls.UrlLinkTableModelTest.testRowEditable	1PASS
	0.073529415	jalview.urls.UrlLinkTableModelTest.testRowDeletejalview.urls.UrlLinkTableModelTest.testRowDelete	1PASS
	0.073529415	jalview.urls.UrlLinkTableModelTest.testDeletablejalview.urls.UrlLinkTableModelTest.testDeletable	1PASS
	0.066176474	jalview.urls.UrlLinkTableModelTest.testRowInsertjalview.urls.UrlLinkTableModelTest.testRowInsert	1PASS
	0.029411765	jalview.urls.UrlLinkTableModelTest.testCountsjalview.urls.UrlLinkTableModelTest.testCounts	1PASS

 

Source view

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 jalview.util.UrlConstants.DELIM;
25		import static jalview.util.UrlConstants.SEP;
26		import static jalview.util.UrlConstants.SEQUENCE_ID;
27
28		import jalview.urls.api.UrlProviderI;
29		import jalview.util.MessageManager;
30
31		import java.io.BufferedWriter;
32		import java.io.File;
33		import java.io.FileWriter;
34		import java.io.IOException;
35		import java.util.ArrayList;
36		import java.util.List;
37
38		import javax.swing.event.TableModelListener;
39
40		import org.testng.Assert;
41		import org.testng.annotations.BeforeMethod;
42		import org.testng.annotations.Test;
43
		99.3% Uncovered Elements: 1 (136) Complexity: 25 Complexity Density: 0.24
44		public class UrlLinkTableModelTest
45		{
46
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";
52
53		private static final String notinmenu = "Not1|http://not.in.menu/$DB_ACCESSION$|"
54		+ "Not2|http://not.in.menu.either/$DB_ACCESSION$";
55
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\"}]}";
65
66		private UrlProviderI prov;
67
		93.3% Uncovered Elements: 1 (15) Complexity: 2 Complexity Density: 0.13
68	9	@BeforeMethod(alwaysRun = true)...
69		public void setup()
70		{
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
73		// each test
74
75		// make a dummy identifiers.org download file
76	9	File temp = null;
77	9	try
78		{
79	9	temp = File.createTempFile("tempfile", ".tmp");
80	9	temp.deleteOnExit();
81	9	BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
82	9	bw.write(testIdOrgString);
83	9	bw.close();
84		} catch (IOException e)
85		{
86	0	System.out.println("Error initialising UrlLinkTableModel test: "
87		+ e.getMessage());
88		}
89
90		// set up custom and identifiers.org url providers
91	9	IdOrgSettings.setDownloadLocation(temp.getPath());
92	9	IdentifiersUrlProvider idprov = new IdentifiersUrlProvider(inmenu);
93	9	CustomUrlProvider cprov = new CustomUrlProvider(inmenu, notinmenu);
94	9	List<UrlProviderI> provlist = new ArrayList<UrlProviderI>();
95	9	provlist.add(idprov);
96	9	provlist.add(cprov);
97
98	9	prov = new UrlProvider("TEST2", provlist);
99		}
100
101		/*
102		* Test that the table model is correctly initialised
103		* Display columns and default row are set; data provider listening event set up
104		*/
		100% Uncovered Elements: 0 (20) Complexity: 3 Complexity Density: 0.19 1PASS
105	1	@Test(groups = { "Functional" })...
106		public void testInitialisation()
107		{
108	1	int defaultCol = 4;
109	1	int dbCol = 0;
110	1	int descCol = 1;
111
112	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
113
114		// exactly one table model listener
115	1	TableModelListener[] listeners = m
116		.getListeners(TableModelListener.class);
117	1	Assert.assertEquals(listeners.length, 1);
118
119		// default row exists, there is exactly 1, and it matches the supplied
120		// default
121	1	int count = 0;
122	11	for (int row = 0; row < m.getRowCount(); row++)
123		{
124	10	boolean isDefault = (boolean) m.getValueAt(row, defaultCol);
125	10	if (isDefault)
126		{
127	1	count++;
128	1	String defaultDBName = (String) m.getValueAt(row, dbCol);
129	1	Assert.assertEquals(defaultDBName, "TEST2");
130
131	1	String defaultDesc = (String) m.getValueAt(row, descCol);
132	1	Assert.assertEquals(defaultDesc, "TEST2");
133		}
134		}
135	1	Assert.assertEquals(count, 1);
136		}
137
138		/*
139		* Test row and column counts
140		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33 1PASS
141	1	@Test(groups = { "Functional" })...
142		public void testCounts()
143		{
144	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
145
146		// correct numbers of column and rows
147	1	Assert.assertEquals(m.getColumnCount(), 5);
148	1	Assert.assertEquals(m.getRowCount(), 10);
149		}
150
151		/*
152		* Test column access
153		*/
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
154	1	@Test(groups = { "Functional" })...
155		public void testColumns()
156		{
157	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
158
159		// check column names
160	1	Assert.assertEquals(m.getColumnName(0),
161		MessageManager.formatMessage("label.database"));
162	1	Assert.assertEquals(m.getColumnName(1),
163		MessageManager.formatMessage("label.name"));
164	1	Assert.assertEquals(m.getColumnName(2),
165		MessageManager.formatMessage("label.url"));
166	1	Assert.assertEquals(m.getColumnName(3),
167		MessageManager.formatMessage("label.inmenu"));
168	1	Assert.assertEquals(m.getColumnName(4),
169		MessageManager.formatMessage("label.primary"));
170
171		// check column classes
172	1	Assert.assertEquals(m.getColumnClass(0), String.class);
173	1	Assert.assertEquals(m.getColumnClass(1), String.class);
174	1	Assert.assertEquals(m.getColumnClass(2), String.class);
175	1	Assert.assertEquals(m.getColumnClass(3), Boolean.class);
176	1	Assert.assertEquals(m.getColumnClass(4), Boolean.class);
177		}
178
179		/*
180		* Test row insertion
181		*/
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
182	1	@Test(groups = { "Functional" })...
183		public void testRowInsert()
184		{
185	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
186
187	1	m.insertRow("newname", "newurl");
188
189		// check table has new row inserted
190	1	Assert.assertEquals(m.getValueAt(10, 0), "newname");
191	1	Assert.assertEquals(m.getValueAt(10, 1), "newname");
192	1	Assert.assertEquals(m.getValueAt(10, 2), "newurl");
193	1	Assert.assertEquals(m.getValueAt(10, 3), true);
194	1	Assert.assertEquals(m.getValueAt(10, 4), false);
195
196		// check data source has new row insrte
197	1	Assert.assertTrue(
198		prov.getLinksForMenu().contains("newname" + SEP + "newurl"));
199		}
200
201		/*
202		* Test row deletion
203		*/
		100% Uncovered Elements: 0 (9) Complexity: 2 Complexity Density: 0.29 1PASS
204	1	@Test(groups = { "Functional" })...
205		public void testRowDelete()
206		{
207	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
208
209		// get name and url at row 0
210	1	String name = (String) m.getValueAt(0, 0);
211	1	String url = (String) m.getValueAt(0, 1);
212
213	1	m.removeRow(0);
214
215		// check table no longer has row 0 elements in it
216	10	for (int row = 0; row < m.getRowCount(); row++)
217		{
218	9	Assert.assertNotEquals(m.getValueAt(row, 0), name);
219		}
220
221		// check data source likewise
222	1	Assert.assertFalse(prov.getLinksForMenu().contains(name + SEP + url));
223		}
224
225		/*
226		* Test value setting and getting
227		*/
		100% Uncovered Elements: 0 (29) Complexity: 4 Complexity Density: 0.16 1PASS
228	1	@Test(groups = { "Functional" })...
229		public void testValues()
230		{
231	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
232
233		// get original default
234	1	int olddefault;
235	1	boolean isDefault = false;
236	2	for (olddefault = 0; olddefault < m.getRowCount()
237		&& !isDefault; olddefault++)
238		{
239	1	isDefault = (boolean) m.getValueAt(olddefault, 3);
240		}
241
242		// set new values, one in each row
243	1	m.setValueAt("dbnamechanged", 6, 0);
244	1	m.setValueAt("descchanged", 6, 1);
245	1	m.setValueAt("urlchanged", 7, 2);
246	1	m.setValueAt(false, 8, 3);
247	1	m.setValueAt(true, 6, 4);
248
249	1	m.setValueAt("dbnamechanged", 5, 0);
250
251		// check values updated in table
252	1	Assert.assertEquals(m.getValueAt(6, 0), "descchanged"); // custom url can't
253		// change db name
254	1	Assert.assertEquals(m.getValueAt(6, 1), "descchanged");
255	1	Assert.assertEquals(m.getValueAt(7, 2), "urlchanged");
256	1	Assert.assertFalse((boolean) m.getValueAt(8, 3));
257	1	Assert.assertTrue((boolean) m.getValueAt(6, 4));
258	1	Assert.assertFalse((boolean) m.getValueAt(olddefault, 4));
259
260	1	Assert.assertEquals(m.getValueAt(5, 0), "dbnamechanged");
261
262		// check default row is exactly one row still
263	11	for (int row = 0; row < m.getRowCount(); row++)
264		{
265	10	isDefault = (boolean) m.getValueAt(row, 4);
266
267		// if isDefault is true, row is 9
268		// if isDefault is false, row is not 9
269	10	Assert.assertFalse(isDefault && !(row == 6));
270		}
271
272		// check table updated
273	1	Assert.assertTrue(prov.writeUrlsAsString(true)
274		.contains("descchanged" + SEP + m.getValueAt(6, 2)));
275	1	Assert.assertTrue(prov.writeUrlsAsString(true)
276		.contains(m.getValueAt(7, 1) + SEP + "urlchanged"));
277	1	Assert.assertTrue(prov.writeUrlsAsString(false)
278		.contains((String) m.getValueAt(8, 1)));
279	1	Assert.assertEquals(prov.getPrimaryUrl("seqid"), m.getValueAt(6, 2)
280		.toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
281		}
282
283		/*
284		* Test cell editability
285		*/
		100% Uncovered Elements: 0 (13) Complexity: 5 Complexity Density: 0.56 1PASS
286	1	@Test(groups = { "Functional" })...
287		public void testEditable()
288		{
289	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
290
291	11	for (int row = 0; row < m.getRowCount(); row++)
292		{
293	10	Assert.assertFalse(m.isCellEditable(row, 0));
294	10	Assert.assertFalse(m.isCellEditable(row, 1));
295	10	Assert.assertFalse(m.isCellEditable(row, 2));
296	10	Assert.assertTrue(m.isCellEditable(row, 3));
297
298	10	if ((row == 4) || (row == 6) || (row == 7))
299		{
300	3	Assert.assertTrue(m.isCellEditable(row, 4));
301		}
302		else
303		{
304	7	Assert.assertFalse(m.isCellEditable(row, 4));
305		}
306		}
307		}
308
309		/*
310		* Test row 'deletability'
311		*/
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.6 1PASS
312	1	@Test(groups = { "Functional" })...
313		public void testDeletable()
314		{
315	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
316
317	11	for (int row = 0; row < m.getRowCount(); row++)
318		{
319	10	if (row > 4)
320		{
321	5	Assert.assertTrue(m.isRowDeletable(row));
322		}
323		else
324		{
325	5	Assert.assertFalse(m.isRowDeletable(row));
326		}
327		}
328		}
329
330		/*
331		* Test indirect row editability
332		*/
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.6 1PASS
333	1	@Test(groups = { "Functional" })...
334		public void testRowEditable()
335		{
336	1	UrlLinkTableModel m = new UrlLinkTableModel(prov);
337
338	11	for (int row = 0; row < m.getRowCount(); row++)
339		{
340	10	if (row > 3)
341		{
342	6	Assert.assertTrue(m.isRowEditable(row));
343		}
344		else
345		{
346	4	Assert.assertFalse(m.isRowEditable(row));
347		}
348		}
349		}
350		}