Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RemoteFormatTest	60	35	4	0.1282051412.8%	Show methods

Class RemoteFormatTest

Class RemoteFormatTest	Line # 60	Total Statements 35	Complexity 4	TOTAL Coverage 0.1282051412.8%
setUp() : void   setUp() : void	6464	4.04	1.01	1.0 1.0100%
getAccessions() : Object[][]   getAccessions() : Object[][]	7777	1.01	1.01	0.0 0.00%
testFetchAccession(String,String) : void   testFetchAccession(String,String) : void	9191	10.010	1.01	0.0 0.00%
testUniprotFreeTextSearch() : void   testUniprotFreeTextSearch() : void	113113	20.020	1.01	0.0 0.00%

 

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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.dbsources;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotNull;
26		import static org.testng.Assert.assertTrue;
27
28		import jalview.analysis.AlignSeq;
29		import jalview.bin.Cache;
30		import jalview.datamodel.AlignmentI;
31		import jalview.datamodel.DBRefSource;
32		import jalview.datamodel.SequenceI;
33		import jalview.ext.ensembl.EnsemblGenomes;
34		import jalview.fts.api.FTSData;
35		import jalview.fts.api.FTSDataColumnI;
36		import jalview.fts.api.FTSRestClientI;
37		import jalview.fts.core.FTSRestRequest;
38		import jalview.fts.core.FTSRestResponse;
39		import jalview.fts.service.uniprot.UniProtFTSRestClient;
40		import jalview.ws.SequenceFetcher;
41		import jalview.ws.seqfetcher.DbSourceProxy;
42
43		import java.util.ArrayList;
44		import java.util.List;
45
46		import org.testng.annotations.BeforeTest;
47		import org.testng.annotations.DataProvider;
48		import org.testng.annotations.Test;
49
50		/**
51		* A class to verify that remotely fetched data has an expected format and can
52		* be successfully processed by Jalview. This is intended as a first line of
53		* defence and early warning of service affecting changes to data fetched
54		* externally.
55		* <p>
56		* This is class is not intended to cover remote services e.g. alignment. Nor
57		* should it duplicate tests already provided by other classes (such as
58		* PDBFTSRestClientTest). Or maybe we will relocate those tests here...
59		*/
		12.8% Uncovered Elements: 34 (39) Complexity: 4 Complexity Density: 0.11
60		public class RemoteFormatTest
61		{
62		SequenceFetcher sf;
63
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
64	4	@BeforeTest(alwaysRun = true)...
65		public void setUp() throws Exception
66		{
67	4	Cache.loadProperties("test/jalview/io/testProps.jvprops");
68		// ensure 'add annotation from structure' is selected
69	4	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
70		Boolean.TRUE.toString());
71	4	Cache.applicationProperties.setProperty("ADD_SS_ANN",
72		Boolean.TRUE.toString());
73
74	4	sf = new SequenceFetcher();
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@DataProvider(name = "AccessionData")...
78		protected Object[][] getAccessions()
79		{
80	0	return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
81		{ DBRefSource.PDB, "1QIP" },
82		{ DBRefSource.EMBL, "X53828" },
83		{ DBRefSource.EMBLCDS, "CAA37824" },
84		{ DBRefSource.ENSEMBL, "ENSG00000157764" },
85		{ new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
86		{ new PfamFull().getDbSource(), "PF03760" },
87		{ new PfamSeed().getDbSource(), "PF03760" },
88		{ new RfamSeed().getDbSource(), "RF00014" } };
89		}
90
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
91	0	@Test(groups = "Network", dataProvider = "AccessionData")...
92		public void testFetchAccession(String dbSource, String accessionId)
93		throws Exception
94		{
95	0	System.out.println("Fetching " + accessionId + " from " + dbSource);
96	0	List<DbSourceProxy> sps = sf.getSourceProxy(dbSource);
97	0	assertFalse(sps.isEmpty());
98	0	AlignmentI al = sps.get(0).getSequenceRecords(accessionId);
99	0	assertNotNull(al);
100	0	assertTrue(al.getHeight() > 0);
101	0	SequenceI sq = al.getSequenceAt(0);
102		// suppress this check as only Uniprot and PDB acquire PDB refs
103		// assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
104	0	assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
105		// suppress this test as only certain databases provide 'primary' dbrefs
106		// assertFalse(sq.getPrimaryDBRefs().isEmpty());
107	0	int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
108		.length();
109	0	assertEquals(sq.getEnd() - sq.getStart() + 1, length,
110		"Sequence start/end doesn't match number of residues in sequence");
111		}
112
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
113	0	@Test(groups = { "Network" })...
114		public void testUniprotFreeTextSearch() throws Exception
115		{
116	0	List<FTSDataColumnI> wantedFields = new ArrayList<>();
117	0	FTSRestClientI client = UniProtFTSRestClient.getInstance();
118	0	wantedFields.add(client.getDataColumnByNameOrCode("id"));
119	0	wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
120	0	wantedFields.add(client.getDataColumnByNameOrCode("organism"));
121	0	wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
122	0	wantedFields.add(client.getDataColumnByNameOrCode("length"));
123
124	0	FTSRestRequest request = new FTSRestRequest();
125	0	request.setAllowEmptySeq(false);
126	0	request.setResponseSize(100);
127	0	request.setFieldToSearchBy("Search All");
128	0	request.setSearchTerm("metanephrops"); // lobster!
129	0	request.setWantedFields(wantedFields);
130
131	0	FTSRestResponse response;
132	0	response = client.executeRequest(request);
133	0	assertTrue(response.getNumberOfItemsFound() > 20);
134	0	assertTrue(response.getSearchSummary() != null);
135	0	assertTrue(response.getSearchSummary().size() > 20);
136		// verify we successfully filtered out the header row (JAL-2485)
137	0	FTSData header = response.getSearchSummary().iterator().next();
138	0	assertFalse(
139		header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"),
140		"Failed to filter out summary header row");
141		}
142		}