Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RemoteFormatTest	40	35	4	0.1282051412.8%	Show methods

Class RemoteFormatTest

Class RemoteFormatTest	Line # 40	Total Statements 35	Complexity 4	TOTAL Coverage 0.1282051412.8%
setUp() : void   setUp() : void	4444	4.04	1.01	1.0 1.0100%
getAccessions() : Object[][]   getAccessions() : Object[][]	5757	1.01	1.01	0.0 0.00%
testFetchAccession(String,String) : void   testFetchAccession(String,String) : void	7070	10.010	1.01	0.0 0.00%
testUniprotFreeTextSearch() : void   testUniprotFreeTextSearch() : void	9292	20.020	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.ws.dbsources;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertNotNull;
6		import static org.testng.Assert.assertTrue;
7
8		import jalview.analysis.AlignSeq;
9		import jalview.bin.Cache;
10		import jalview.datamodel.AlignmentI;
11		import jalview.datamodel.DBRefSource;
12		import jalview.datamodel.SequenceI;
13		import jalview.ext.ensembl.EnsemblGenomes;
14		import jalview.fts.api.FTSData;
15		import jalview.fts.api.FTSDataColumnI;
16		import jalview.fts.api.FTSRestClientI;
17		import jalview.fts.core.FTSRestRequest;
18		import jalview.fts.core.FTSRestResponse;
19		import jalview.fts.service.uniprot.UniProtFTSRestClient;
20		import jalview.ws.SequenceFetcher;
21		import jalview.ws.seqfetcher.DbSourceProxy;
22
23		import java.util.ArrayList;
24		import java.util.List;
25
26		import org.testng.annotations.BeforeTest;
27		import org.testng.annotations.DataProvider;
28		import org.testng.annotations.Test;
29
30		/**
31		* A class to verify that remotely fetched data has an expected format and can
32		* be successfully processed by Jalview. This is intended as a first line of
33		* defence and early warning of service affecting changes to data fetched
34		* externally.
35		* <p>
36		* This is class is not intended to cover remote services e.g. alignment. Nor
37		* should it duplicate tests already provided by other classes (such as
38		* PDBFTSRestClientTest). Or maybe we will relocate those tests here...
39		*/
		12.8% Uncovered Elements: 34 (39) Complexity: 4 Complexity Density: 0.11
40		public class RemoteFormatTest
41		{
42		SequenceFetcher sf;
43
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
44	1	@BeforeTest(alwaysRun = true)...
45		public void setUp() throws Exception
46		{
47	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
48		// ensure 'add annotation from structure' is selected
49	1	Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
50		Boolean.TRUE.toString());
51	1	Cache.applicationProperties.setProperty("ADD_SS_ANN",
52		Boolean.TRUE.toString());
53
54	1	sf = new SequenceFetcher();
55		}
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	@DataProvider(name = "AccessionData")...
58		protected Object[][] getAccessions()
59		{
60	0	return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
61		{ DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
62		{ DBRefSource.EMBLCDS, "CAA37824" },
63		{ DBRefSource.ENSEMBL, "ENSG00000157764" },
64		{ new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
65		{ new PfamFull().getDbSource(), "PF03760" },
66		{ new PfamSeed().getDbSource(), "PF03760" },
67		{ new RfamSeed().getDbSource(), "RF00014" } };
68		}
69
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1 4-
70	0	@Test(groups = "Network", dataProvider = "AccessionData")...
71		public void testFetchAccession(String dbSource, String accessionId)
72		throws Exception
73		{
74	0	System.out.println("Fetching " + accessionId + " from " + dbSource);
75	0	List<DbSourceProxy> sps = sf.getSourceProxy(dbSource);
76	0	assertFalse(sps.isEmpty());
77	0	AlignmentI al = sps.get(0).getSequenceRecords(accessionId);
78	0	assertNotNull(al);
79	0	assertTrue(al.getHeight() > 0);
80	0	SequenceI sq = al.getSequenceAt(0);
81		// suppress this check as only Uniprot and PDB acquire PDB refs
82		// assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
83	0	assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
84		// suppress this test as only certain databases provide 'primary' dbrefs
85		// assertFalse(sq.getPrimaryDBRefs().isEmpty());
86	0	int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
87		.length();
88	0	assertEquals(sq.getEnd() - sq.getStart() + 1, length,
89		"Sequence start/end doesn't match number of residues in sequence");
90		}
91
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
92	0	@Test(groups = { "Network" })...
93		public void testUniprotFreeTextSearch() throws Exception
94		{
95	0	List<FTSDataColumnI> wantedFields = new ArrayList<>();
96	0	FTSRestClientI client = UniProtFTSRestClient.getInstance();
97	0	wantedFields.add(client.getDataColumnByNameOrCode("id"));
98	0	wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
99	0	wantedFields.add(client.getDataColumnByNameOrCode("organism"));
100	0	wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
101	0	wantedFields.add(client.getDataColumnByNameOrCode("length"));
102
103	0	FTSRestRequest request = new FTSRestRequest();
104	0	request.setAllowEmptySeq(false);
105	0	request.setResponseSize(100);
106	0	request.setFieldToSearchBy("Search All");
107	0	request.setSearchTerm("metanephrops"); // lobster!
108	0	request.setWantedFields(wantedFields);
109
110	0	FTSRestResponse response;
111	0	response = client.executeRequest(request);
112	0	assertTrue(response.getNumberOfItemsFound() > 20);
113	0	assertTrue(response.getSearchSummary() != null);
114	0	assertTrue(response.getSearchSummary().size() > 20);
115		// verify we successfully filtered out the header row (JAL-2485)
116	0	FTSData header = response.getSearchSummary().iterator().next();
117	0	assertFalse(
118		header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"),
119		"Failed to filter out summary header row");
120		}
121		}