Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DbRefFetcherTest	58	71	14	0.00%	Show methods

Class DbRefFetcherTest

Class DbRefFetcherTest	Line # 58	Total Statements 71	Complexity 14	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	6161	2.02	1.01	0.0 0.00%
setUpBeforeClass() : void   setUpBeforeClass() : void	7171	1.01	1.01	0.0 0.00%
tearDownAfterClass() : void   tearDownAfterClass() : void	8080	0.00	1.01	-1.0 -1.0 -
checkUniprotCanonicalFlagSet() : void   checkUniprotCanonicalFlagSet() : void	8585	11.011	1.01	0.0 0.00%
testStandardProtDbs() : void   testStandardProtDbs() : void	112112	20.020	5.05	0.0 0.00%
testEmblUniprotProductRecovery() : void   testEmblUniprotProductRecovery() : void	161161	4.04	1.01	0.0 0.00%
testEmblCDSUniprotProductRecovery() : void   testEmblCDSUniprotProductRecovery() : void	177177	4.04	1.01	0.0 0.00%
verifyProteinNucleotideXref(String,DbSourceProxy) : void   verifyProteinNucleotideXref(String,DbSourceProxy) : void	194194	20.020	1.01	0.0 0.00%
testAlphaFoldClien() : void   testAlphaFoldClien() : void	238238	9.09	2.02	0.0 0.00%

 

Contributing tests

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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.seqfetcher;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertNotNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import java.util.ArrayList;
29		import java.util.Arrays;
30		import java.util.List;
31
32		import org.junit.Assert;
33		import org.testng.annotations.AfterClass;
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
37		import jalview.analysis.CrossRef;
38		import jalview.datamodel.AlignmentAnnotation;
39		import jalview.datamodel.AlignmentI;
40		import jalview.datamodel.DBRefEntry;
41		import jalview.datamodel.DBRefSource;
42		import jalview.datamodel.FeatureProperties;
43		import jalview.datamodel.Sequence;
44		import jalview.datamodel.SequenceFeature;
45		import jalview.datamodel.SequenceI;
46		import jalview.gui.JvOptionPane;
47		import jalview.util.DBRefUtils;
48		import jalview.ws.DBRefFetcher;
49		import jalview.ws.SequenceFetcher;
50		import jalview.ws.dbsources.EBIAlfaFold;
51		import jalview.ws.dbsources.Pdb;
52		import jalview.ws.dbsources.Uniprot;
53
54		/**
55		* @author jimp
56		*
57		*/
		0% Uncovered Elements: 88 (88) Complexity: 14 Complexity Density: 0.2
58		public class DbRefFetcherTest
59		{
60
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
61	0	@BeforeClass(alwaysRun = true)...
62		public void setUpJvOptionPane()
63		{
64	0	JvOptionPane.setInteractiveMode(false);
65	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
66		}
67
68		/**
69		* @throws java.lang.Exception
70		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@BeforeClass(alwaysRun = true)...
72		public static void setUpBeforeClass() throws Exception
73		{
74	0	jalview.bin.Console.initLogger();
75		}
76
77		/**
78		* @throws java.lang.Exception
79		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
80	0	@AfterClass(alwaysRun = true)...
81		public static void tearDownAfterClass() throws Exception
82		{
83		}
84
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09 4-
85	0	@Test(groups = { "Network" })...
86		public void checkUniprotCanonicalFlagSet()
87		{
88		// TODO - mock this - for moment it is a live request.
89	0	SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
90		"MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
91		+ "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
92		+ "LTA");
93	0	DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
94	0	dbr.fetchDBRefs(true);
95	0	List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
96	0	assertNotNull(primRefs);
97	0	assertTrue(primRefs.size() > 0);
98	0	boolean canonicalUp = false;
99	0	for (DBRefEntry ref : primRefs)
100		{
101	0	assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
102	0	canonicalUp |= ref.isCanonical();
103		}
104	0	assertTrue("No Canonical Uniprot reference detected", canonicalUp);
105		}
106
107		/**
108		* Tests that standard protein database sources include Uniprot (as the first)
109		* and also PDB. (Additional sources are dependent on availability of DAS
110		* services.)
111		*/
		0% Uncovered Elements: 26 (26) Complexity: 5 Complexity Density: 0.25 4-
112	0	@Test(groups = { "Functional" })...
113		public void testStandardProtDbs()
114		{
115	0	List<String> defdb = new ArrayList<String>();
116	0	defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
117	0	defdb.add(DBRefSource.PDB);
118	0	List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
119	0	SequenceFetcher sfetcher = new SequenceFetcher();
120	0	boolean pdbFound = false;
121
122	0	for (String ddb : defdb)
123		{
124	0	List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
125
126	0	if (srcesfordb != null)
127		{
128		// TODO is this right? get duplicate entries
129	0	srces.addAll(srcesfordb);
130		}
131		}
132
133	0	int i = 0;
134	0	int uniprotPos = -1;
135	0	for (DbSourceProxy s : srces)
136		{
137	0	if (s instanceof Uniprot && uniprotPos == -1)
138		{
139	0	uniprotPos = i;
140		}
141	0	if (s instanceof Pdb)
142		{
143	0	pdbFound = true;
144		}
145	0	i++;
146		}
147
148	0	assertTrue("Failed to find Uniprot source as first source amongst "
149		+ srces.size() + " sources (source was at position "
150		+ uniprotPos + ")", uniprotPos == 0);
151	0	assertTrue("Failed to find PDB source amongst " + srces.size()
152		+ " sources", pdbFound);
153		}
154
155		/**
156		* Tests retrieval of one entry from EMBL. Test is dependent on availability
157		* of network and the EMBL service.
158		*
159		* @throws Exception
160		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
161	0	@Test(groups = { "External" })...
162		public void testEmblUniprotProductRecovery() throws Exception
163		{
164	0	String retrievalId = "V00488";
165	0	DbSourceProxy embl = new SequenceFetcher()
166		.getSourceProxy(DBRefSource.EMBL).get(0);
167	0	assertNotNull("Couldn't find the EMBL retrieval client", embl);
168	0	verifyProteinNucleotideXref(retrievalId, embl);
169		}
170
171		/**
172		* Tests retrieval of one entry from EMBLCDS. Test is dependent on
173		* availability of network and the EMBLCDS service.
174		*
175		* @throws Exception
176		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
177	0	@Test(groups = { "External" })...
178		public void testEmblCDSUniprotProductRecovery() throws Exception
179		{
180	0	String retrievalId = "AAH29712";
181	0	DbSourceProxy embl = new SequenceFetcher()
182		.getSourceProxy(DBRefSource.EMBLCDS).get(0);
183	0	assertNotNull("Couldn't find the EMBL retrieval client", embl);
184	0	verifyProteinNucleotideXref(retrievalId, embl);
185		}
186
187		/**
188		* Helper method to perform database retrieval and verification of results.
189		*
190		* @param retrievalId
191		* @param embl
192		* @throws Exception
193		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05
194	0	private void verifyProteinNucleotideXref(String retrievalId,...
195		DbSourceProxy embl) throws Exception
196		{
197	0	AlignmentI alsq = embl.getSequenceRecords(retrievalId);
198	0	assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
199	0	assertEquals("Didn't retrieve right number of records", 1,
200		alsq.getHeight());
201	0	SequenceI seq = alsq.getSequenceAt(0);
202	0	assertEquals("Wrong sequence name",
203		embl.getDbSource() + "|" + retrievalId, seq.getName());
204	0	List<SequenceFeature> sfs = seq.getSequenceFeatures();
205	0	assertFalse("Sequence features missing", sfs.isEmpty());
206	0	assertTrue("Feature not CDS", FeatureProperties
207		.isCodingFeature(embl.getDbSource(), sfs.get(0).getType()));
208	0	assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
209	0	List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
210		new String[]
211		{ DBRefSource.UNIPROT });
212	0	assertNotNull(dr);
213	0	assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
214	0	assertEquals("Expected cross reference map to be one amino acid",
215		dr.get(0).getMap().getMappedWidth(), 1);
216	0	assertEquals("Expected local reference map to be 3 nucleotides",
217		dr.get(0).getMap().getWidth(), 3);
218	0	AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
219		.findXrefSequences(dr.get(0).getSource(), true);
220	0	assertNotNull(
221		"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
222		sprods);
223	0	assertEquals("Didn't xref right number of records", 1,
224		sprods.getHeight());
225	0	SequenceI proteinSeq = sprods.getSequenceAt(0);
226	0	assertEquals(proteinSeq.getSequenceAsString(),
227		dr.get(0).getMap().getTo().getSequenceAsString());
228	0	assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
229		proteinSeq.getName());
230		}
231
232		/**
233		* Tests retrieval of one entry from EMBLCDS. Test is dependent on
234		* availability of network and the EMBLCDS service.
235		*
236		* @throws Exception
237		*/
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22 4-
238	0	@Test(groups = { "External" })...
239		public void testAlphaFoldClien() throws Exception
240		{
241	0	DbSourceProxy alphafold = new EBIAlfaFold();
242	0	AlignmentI resp = alphafold
243		.getSequenceRecords(alphafold.getTestQuery());
244	0	assertNotNull(resp);
245	0	assertEquals("One sequence only", resp.getHeight(), 1);
246	0	for (AlignmentAnnotation aa : resp.getAlignmentAnnotation())
247		{
248	0	if (aa.graph == AlignmentAnnotation.CONTACT_MAP)
249		{
250	0	assertTrue("Contact map didn't provide valid contact",
251		resp.getContactListFor(aa, 1).getContactAt(1) != -1d);
252		// test passes
253	0	return;
254		}
255		}
256	0	Assert.fail("No pAE matrix found for alphafold structure.");
257		}
258
259		}