package jalview.ext.ensembl;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.FileParse;

import java.lang.reflect.Method;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
import java.util.List;

import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;


public class EnsemblSeqProxyTest
{
  private static final Object[][] allSeqs = new Object[][] {
      {
          new EnsemblProtein(),
          "CCDS5863.1",
          ">CCDS5863.1\n"
                  + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
                  + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
                  + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
                  + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
                  + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
                  + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
                  + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
                  + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
                  + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
                  + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
                  + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                  + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
      {
          new EnsemblCdna(),
          "CCDS5863.1",
          ">CCDS5863.1\n"
                  + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
                  + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
                  + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
                  + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
                  + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
                  + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
                  + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
                  + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
                  + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
                  + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
                  + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
                  + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
                  + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
                  + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
                  + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
                  + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
                  + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
                  + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
                  + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
                  + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
                  + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
                  + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
                  + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
                  + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
                  + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
                  + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
                  + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
                  + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
                  + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
                  + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
                  + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
                  + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
                  + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
                  + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
                  + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
                  + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
                  + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
                  + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
                  + "GGTGCGTTTCCTGTCCACTGA\n" },
      {
          new EnsemblProtein(),
          "ENSP00000288602",
          ">ENSP00000288602\n"
                  + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
                  + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
                  + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
                  + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
                  + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
                  + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
                  + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
                  + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
                  + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
                  + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
                  + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                  + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };

  @DataProvider(name = "queries")
  public Object[][] createQueryData(Method m)
  {
    return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
  }

  @Test(dataProvider = "queries")
  public void testIsValidReference(String query) throws Exception
  {
    EnsemblSequenceFetcher esq = new EnsemblProtein();
    Assert.assertTrue(esq.isValidReference(query),
            "Expected reference string " + query
                    + " to be valid for regex "
                    + esq.getAccessionValidator().toString());
  }

  @DataProvider(name = "ens_seqs")
  public Object[][] createData(Method m)
  {
    System.out.println(m.getName());
    return allSeqs;
  }

  @Test(dataProvider = "ens_seqs", suiteName = "live")
  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
          throws Exception
  {
    FileParse fp = proxy.getSequenceReader(Arrays
            .asList(new String[]
    { sq }));
    SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
    FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
    SequenceI[] trueSqs = trueRes.getSeqsAsArray();
    Assert.assertEquals(sqs.length, trueSqs.length,
            "Different number of sequences retrieved for query " + sq);
    Alignment ral = new Alignment(sqs);
    for (SequenceI tr : trueSqs)
    {
      SequenceI[] rseq;
      Assert.assertNotNull(
              rseq = ral.findSequenceMatch(tr.getName()),
              "Couldn't find sequences matching expected sequence "
                      + tr.getName());
      Assert.assertEquals(rseq.length, 1,
              "Expected only one sequence for sequence ID " + tr.getName());
      Assert.assertEquals(
              rseq[0].getSequenceAsString(),
              tr.getSequenceAsString(),
              "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                      + tr.getSequenceAsString() + "\n" + "Got:"
                      + rseq[0].getSequenceAsString());
  
    }
  }

  @Test(suiteName = "live")
  public void testLiveCheckEnsembl()
  {
    EnsemblRestClient sf = new EnsemblRestClient()
    {

      @Override
      public String getDbName()
      {
        // TODO Auto-generated method stub
        return null;
      }

      @Override
      public AlignmentI getSequenceRecords(String queries) throws Exception
      {
        // TODO Auto-generated method stub
        return null;
      }

      @Override
      protected URL getUrl(List<String> ids) throws MalformedURLException
      {
        // TODO Auto-generated method stub
        return null;
      }

      @Override
      public boolean useGetRequest()
      {
        // TODO Auto-generated method stub
        return false;
      }

      @Override
      public String getRequestMimeType()
      {
        // TODO Auto-generated method stub
        return null;
      }

      @Override
      public String getResponseMimeType()
      {
        // TODO Auto-generated method stub
        return null;
      }

    };
    boolean isAvailable = sf.isEnsemblAvailable();
    System.out.println("Ensembl is "
            + (isAvailable ? "UP!"
                    : "DOWN or unreachable ******************* BAD!"));
  }
}