/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import jalview.analysis.AlignSeq;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.ext.ensembl.EnsemblGenomes;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.uniprot.UniProtFTSRestClient;
import jalview.ws.SequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
import java.util.List;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
/**
* A class to verify that remotely fetched data has an expected format and can
* be successfully processed by Jalview. This is intended as a first line of
* defence and early warning of service affecting changes to data fetched
* externally.
*
* This is class is not intended to cover remote services e.g. alignment. Nor
* should it duplicate tests already provided by other classes (such as
* PDBFTSRestClientTest). Or maybe we will relocate those tests here...
*/
public class RemoteFormatTest
{
SequenceFetcher sf;
@BeforeTest(alwaysRun = true)
public void setUp() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
sf = new SequenceFetcher();
}
@DataProvider(name = "AccessionData")
protected Object[][] getAccessions()
{
return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
{ DBRefSource.PDB, "1QIP" },
{ DBRefSource.EMBL, "X53828" },
{ DBRefSource.EMBLCDS, "CAA37824" },
{ DBRefSource.ENSEMBL, "ENSG00000157764" },
{ new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
{ new PfamFull().getDbSource(), "PF03760" },
{ new PfamSeed().getDbSource(), "PF03760" },
{ new RfamSeed().getDbSource(), "RF00014" } };
}
@Test(groups = "Network", dataProvider = "AccessionData")
public void testFetchAccession(String dbSource, String accessionId)
throws Exception
{
System.out.println("Fetching " + accessionId + " from " + dbSource);
List sps = sf.getSourceProxy(dbSource);
assertFalse(sps.isEmpty());
AlignmentI al = sps.get(0).getSequenceRecords(accessionId);
assertNotNull(al);
assertTrue(al.getHeight() > 0);
SequenceI sq = al.getSequenceAt(0);
// suppress this check as only Uniprot and PDB acquire PDB refs
// assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
// suppress this test as only certain databases provide 'primary' dbrefs
// assertFalse(sq.getPrimaryDBRefs().isEmpty());
int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
.length();
assertEquals(sq.getEnd() - sq.getStart() + 1, length,
"Sequence start/end doesn't match number of residues in sequence");
}
@Test(groups = { "Network" })
public void testUniprotFreeTextSearch() throws Exception
{
List wantedFields = new ArrayList<>();
FTSRestClientI client = UniProtFTSRestClient.getInstance();
wantedFields.add(client.getDataColumnByNameOrCode("id"));
wantedFields.add(client.getDataColumnByNameOrCode("entry name"));
wantedFields.add(client.getDataColumnByNameOrCode("organism"));
wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
wantedFields.add(client.getDataColumnByNameOrCode("length"));
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
request.setFieldToSearchBy("Search All");
request.setSearchTerm("metanephrops"); // lobster!
request.setWantedFields(wantedFields);
FTSRestResponse response;
response = client.executeRequest(request);
assertTrue(response.getNumberOfItemsFound() > 20);
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getSearchSummary().size() > 20);
// verify we successfully filtered out the header row (JAL-2485)
FTSData header = response.getSearchSummary().iterator().next();
assertFalse(
header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"),
"Failed to filter out summary header row");
}
}