package jalview.ws.dbsources;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
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.BeforeMethod;
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.
 * <p>
 * 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;

  @Test(groups = "Network")
  public void testFetchUniprot() throws Exception
  {
    List<DbSourceProxy> sps = sf.getSourceProxy(DBRefSource.UNIPROT);
    assertFalse(sps.isEmpty());
    AlignmentI response = sps.get(0).getSequenceRecords("P30419");
    assertNotNull(response);
    assertEquals(response.getHeight(), 1);
    SequenceI sq = response.getSequenceAt(0);
    assertTrue("No PDBEntry on sequence.", sq.getAllPDBEntries().size() > 0);
    assertTrue("No DBRef on sequence.", sq.getDBRefs().length > 0);
    List<DBRefEntry> dbr = sq.getPrimaryDBRefs();
    assertFalse(dbr.isEmpty());
    assertEquals(
            "Sequence start/end doesn't match number of residues in sequence",
            sq.getEnd() - sq.getStart() + 1, sq.getLength());
  }

  @Test(groups = "Network")
  public void testFetchPdb()
  {
    // 1QIP
  }

  @Test(groups = "Network")
  public void testFetchEmbl()
  {
    // X53828
  }

  @Test(groups = "Network")
  public void testFetchEmblCDS()
  {
    // CAA37824
  }

  @Test(groups = "Network")
  public void testFetchEnsembl()
  {
    // ENSG00000157764
  }

  @Test(groups = "Network")
  public void testFetchEnsemblGenomes()
  {
    // DDB_G0283883
  }

  @Test(groups = "Network")
  public void testFetchPfamSeed()
  {
    // PF03760
  }

  @Test(groups = "Network")
  public void testFetchPfamFull()
  {
    // PF03760
  }

  @Test(groups = "Network")
  public void testFetchRfamSeed()
  {
    // RF00014
  }

  @Test(groups = { "Network" })
  public void testUniprotFreeTextSearch() throws Exception
  {
    List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
    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("Failed to filter out summary header row",
            header.getSummaryData()[0].toString().equalsIgnoreCase("Entry"));
  }

  @BeforeMethod(alwaysRun = true)
  public void setUp() throws Exception
  {
    Cache.loadProperties("test/jalview/io/testProps.jvprops");
    // ensure 'add annotation from structure' is selected
    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
            Boolean.TRUE.toString());
    Cache.applicationProperties.setProperty("ADD_SS_ANN",
            Boolean.TRUE.toString());
  
    sf = new SequenceFetcher(false);
  }
}