Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFetcherTest	42	90	35	0.095890419.6%	Show methods

Class SequenceFetcherTest

Class SequenceFetcherTest	Line # 42	Total Statements 90	Complexity 35	TOTAL Coverage 0.095890419.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	1.0 1.0100%
testNoDuplicatesInFetchDbRefs() : void   testNoDuplicatesInFetchDbRefs() : void	5252	10.010	4.04	0.625 0.62562.5%
main(String[]) : void   main(String[]) : void	8383	26.026	11.011	0.0 0.00%
testRetrieval(String,DbSourceProxy,String) : void   testRetrieval(String,DbSourceProxy,String) : void	151151	52.052	19.019	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.07534247	jalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefsjalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefs	1PASS

 

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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.ws;
22
23		import jalview.analysis.CrossRef;
24		import jalview.datamodel.Alignment;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.DBRefSource;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29		import jalview.ws.seqfetcher.ASequenceFetcher;
30		import jalview.ws.seqfetcher.DbSourceProxy;
31
32		import java.util.Enumeration;
33		import java.util.HashMap;
34		import java.util.List;
35		import java.util.Map;
36		import java.util.Vector;
37
38		import org.testng.Assert;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		9.6% Uncovered Elements: 132 (146) Complexity: 35 Complexity Density: 0.39
42		public class SequenceFetcherTest
43		{
44
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	1	JvOptionPane.setInteractiveMode(false);
49	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
		62.5% Uncovered Elements: 6 (16) Complexity: 4 Complexity Density: 0.4 1PASS
52	1	@Test(groups = "Functional")...
53		public void testNoDuplicatesInFetchDbRefs()
54		{
55	1	Map<String, List<DbSourceProxy>> seen = new HashMap<>();
56	1	jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher();
57	1	String dupes = "";
58		// for (String src : sfetcher.getOrderedSupportedSources())
59	1	for (String src : sfetcher.getNonAlignmentSources())
60		{
61	5	List<DbSourceProxy> seenitem = seen.get(src);
62	5	if (seenitem != null)
63		{
64	0	dupes += (dupes.length() > 0 ? "," : "") + src;
65		}
66		else
67		{
68	5	seen.put(src, sfetcher.getSourceProxy(src));
69		}
70		}
71	1	if (dupes.length() > 0)
72		{
73	0	Assert.fail("Duplicate sources : " + dupes);
74		}
75		}
76
77		/**
78		* simple run method to test dbsources.
79		*
80		* @param argv
81		* @j2sIgnore
82		*/
		0% Uncovered Elements: 40 (40) Complexity: 11 Complexity Density: 0.42
83	0	public static void main(String[] argv)...
84		{
85		// TODO: extracted from SequenceFetcher - convert to network dependent
86		// functional integration test with
87		// assertions
88
89	0	String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
90		+ "With no arguments, all DbSources will be queried with their test Accession number.\n"
91		+ "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
92		+ "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
93
94	0	if (argv != null && argv.length > 0)
95		{
96	0	String targs[] = new String[argv.length - 1];
97	0	System.arraycopy(argv, 1, targs, 0, targs.length);
98	0	argv = targs;
99		}
100	0	if (argv != null && argv.length > 0)
101		{
102	0	List<DbSourceProxy> sps = new SequenceFetcher()
103		.getSourceProxy(argv[0]);
104
105	0	if (sps != null)
106		{
107	0	for (DbSourceProxy sp : sps)
108		{
109	0	AlignmentI al = null;
110	0	try
111		{
112	0	testRetrieval(argv[0], sp,
113	0	argv.length > 1 ? argv[1] : sp.getTestQuery());
114		} catch (Exception e)
115		{
116	0	e.printStackTrace();
117	0	System.err.println("Error when retrieving "
118	0	+ (argv.length > 1 ? argv[1] : sp.getTestQuery())
119		+ " from " + argv[0] + "\nUsage: " + usage);
120		}
121		}
122	0	return;
123		}
124		else
125		{
126	0	System.err.println("Can't resolve " + argv[0]
127		+ " as a database name. Allowed values are :\n"
128		+ new SequenceFetcher().getSupportedDb());
129		}
130	0	System.out.println(usage);
131	0	return;
132		}
133	0	ASequenceFetcher sfetcher = new SequenceFetcher();
134	0	String[] dbSources = sfetcher.getSupportedDb();
135	0	for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
136		{
137	0	String db = dbSources[dbsource];
138		// skip me
139	0	if (db.equals(DBRefSource.PDB))
140		{
141	0	continue;
142		}
143	0	for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
144		{
145	0	testRetrieval(db, sp, sp.getTestQuery());
146		}
147		}
148
149		}
150
		0% Uncovered Elements: 84 (84) Complexity: 19 Complexity Density: 0.37
151	0	private static void testRetrieval(String db, DbSourceProxy sp,...
152		String testQuery)
153		{
154	0	AlignmentI ds = null;
155	0	Vector<Object[]> noProds = new Vector<>();
156	0	System.out.println("Source: " + sp.getDbName() + " (" + db
157		+ "): retrieving test:" + sp.getTestQuery());
158		{
159	0	AlignmentI al = null;
160	0	try
161		{
162	0	al = sp.getSequenceRecords(testQuery);
163	0	if (al != null && al.getHeight() > 0)
164		{
165	0	boolean dna = sp.isDnaCoding();
166	0	al.setDataset(null);
167	0	AlignmentI alds = al.getDataset();
168		// try and find products
169	0	CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds);
170	0	List<String> types = crossRef.findXrefSourcesForSequences(dna);
171	0	if (types != null)
172		{
173	0	System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
174	0	for (String source : types)
175		{
176	0	System.out.println("Type: " + source);
177	0	SequenceI[] prod = crossRef.findXrefSequences(source, dna)
178		.getSequencesArray();
179	0	System.out.println(
180	0	"Found " + ((prod == null) ? "no" : "" + prod.length)
181		+ " products");
182	0	if (prod != null)
183		{
184	0	for (int p = 0; p < prod.length; p++)
185		{
186	0	System.out.println(
187		"Prod " + p + ": " + prod[p].getDisplayId(true));
188		}
189		}
190		}
191		}
192		else
193		{
194	0	noProds.addElement(
195	0	(dna ? new Object[]
196		{ al, al } : new Object[] { al }));
197		}
198
199		}
200		} catch (Exception ex)
201		{
202	0	System.out.println("ERROR:Failed to retrieve test query.");
203	0	ex.printStackTrace(System.out);
204		}
205
206	0	if (al == null)
207		{
208	0	System.out.println("ERROR:No alignment retrieved.");
209	0	StringBuffer raw = sp.getRawRecords();
210	0	if (raw != null)
211		{
212	0	System.out.println(raw.toString());
213		}
214		else
215		{
216	0	System.out.println("ERROR:No Raw results.");
217		}
218		}
219		else
220		{
221	0	System.out.println("Retrieved " + al.getHeight() + " sequences.");
222	0	if (ds == null)
223		{
224	0	ds = al.getDataset();
225		}
226		else
227		{
228	0	ds.append(al.getDataset());
229	0	al.setDataset(ds);
230		}
231		}
232	0	System.out.flush();
233	0	System.err.flush();
234		}
235	0	if (noProds.size() > 0)
236		{
237	0	Enumeration<Object[]> ts = noProds.elements();
238	0	while (ts.hasMoreElements())
239
240		{
241	0	Object[] typeSq = ts.nextElement();
242	0	boolean dna = (typeSq.length > 1);
243	0	AlignmentI al = (AlignmentI) typeSq[0];
244	0	System.out.println("Trying getProducts for "
245		+ al.getSequenceAt(0).getDisplayId(true));
246	0	System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));
247		// have a bash at finding the products amongst all the retrieved
248		// sequences.
249	0	SequenceI[] seqs = al.getSequencesArray();
250	0	Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
251		dna);
252	0	System.out.println("Found "
253	0	+ ((prodal == null) ? "no" : "" + prodal.getHeight())
254		+ " products");
255	0	if (prodal != null)
256		{
257	0	SequenceI[] prod = prodal.getSequencesArray(); // note
258		// should
259		// test
260		// rather
261		// than
262		// throw
263		// away
264		// codon
265		// mapping
266		// (if
267		// present)
268	0	for (int p = 0; p < prod.length; p++)
269		{
270	0	System.out.println(
271		"Prod " + p + ": " + prod[p].getDisplayId(true));
272		}
273		}
274		}
275		}
276		}
277		}