test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

   1 package jalview.ext.ensembl;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.io.AppletFormatAdapter;
   7 import jalview.io.FastaFile;
   8 import jalview.io.FileParse;
   9
  10 import java.lang.reflect.Method;
  11 import java.net.MalformedURLException;
  12 import java.net.URL;
  13 import java.util.Arrays;
  14 import java.util.List;
  15
  16 import org.testng.Assert;
  17 import org.testng.annotations.DataProvider;
  18 import org.testng.annotations.Test;
  19
  20
  21 public class EnsemblSeqProxyTest
  22 {
  23   private static final Object[][] allSeqs = new Object[][] {
  24       {
  25           new EnsemblProtein(),
  26           "CCDS5863.1",
  27           ">CCDS5863.1\n"
  28                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  29                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  30                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  31                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  32                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  33                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  34                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  35                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  36                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  37                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  38                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  39                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  40                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  41       {
  42           new EnsemblCdna(),
  43           "CCDS5863.1",
  44           ">CCDS5863.1\n"
  45                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  46                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  47                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  48                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  49                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  50                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  51                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  52                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  53                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  54                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  55                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  56                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  57                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  58                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  59                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  60                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  61                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  62                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  63                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  64                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  65                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  66                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  67                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  68                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  69                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  70                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  71                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  72                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  73                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  74                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  75                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  76                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  77                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  78                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  79                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  80                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  81                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  82                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  83                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  84       {
  85           new EnsemblProtein(),
  86           "ENSP00000288602",
  87           ">ENSP00000288602\n"
  88                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  89                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  90                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  91                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  92                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  93                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  94                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  95                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  96                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  97                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  98                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  99                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 100                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 101
 102   @DataProvider(name = "queries")
 103   public Object[][] createQueryData(Method m)
 104   {
 105     return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
 106   }
 107
 108   @Test(dataProvider = "queries")
 109   public void testIsValidReference(String query) throws Exception
 110   {
 111     EnsemblSequenceFetcher esq = new EnsemblProtein();
 112     Assert.assertTrue(esq.isValidReference(query),
 113             "Expected reference string " + query
 114                     + " to be valid for regex "
 115                     + esq.getAccessionValidator().toString());
 116   }
 117
 118   @DataProvider(name = "ens_seqs")
 119   public Object[][] createData(Method m)
 120   {
 121     System.out.println(m.getName());
 122     return allSeqs;
 123   }
 124
 125   @Test(dataProvider = "ens_seqs", suiteName = "live")
 126   public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
 127           throws Exception
 128   {
 129     FileParse fp = proxy.getSequenceReader(Arrays
 130             .asList(new String[]
 131     { sq }));
 132     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 133     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 134     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 135     Assert.assertEquals(sqs.length, trueSqs.length,
 136             "Different number of sequences retrieved for query " + sq);
 137     Alignment ral = new Alignment(sqs);
 138     for (SequenceI tr : trueSqs)
 139     {
 140       SequenceI[] rseq;
 141       Assert.assertNotNull(
 142               rseq = ral.findSequenceMatch(tr.getName()),
 143               "Couldn't find sequences matching expected sequence "
 144                       + tr.getName());
 145       Assert.assertEquals(rseq.length, 1,
 146               "Expected only one sequence for sequence ID " + tr.getName());
 147       Assert.assertEquals(
 148               rseq[0].getSequenceAsString(),
 149               tr.getSequenceAsString(),
 150               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 151                       + tr.getSequenceAsString() + "\n" + "Got:"
 152                       + rseq[0].getSequenceAsString());
 153
 154     }
 155   }
 156
 157   @Test(suiteName = "live")
 158   public void testLiveCheckEnsembl()
 159   {
 160     EnsemblRestClient sf = new EnsemblRestClient()
 161     {
 162
 163       @Override
 164       public String getDbName()
 165       {
 166         // TODO Auto-generated method stub
 167         return null;
 168       }
 169
 170       @Override
 171       public AlignmentI getSequenceRecords(String queries) throws Exception
 172       {
 173         // TODO Auto-generated method stub
 174         return null;
 175       }
 176
 177       @Override
 178       protected URL getUrl(List<String> ids) throws MalformedURLException
 179       {
 180         // TODO Auto-generated method stub
 181         return null;
 182       }
 183
 184       @Override
 185       public boolean useGetRequest()
 186       {
 187         // TODO Auto-generated method stub
 188         return false;
 189       }
 190
 191       @Override
 192       public String getRequestMimeType()
 193       {
 194         // TODO Auto-generated method stub
 195         return null;
 196       }
 197
 198       @Override
 199       public String getResponseMimeType()
 200       {
 201         // TODO Auto-generated method stub
 202         return null;
 203       }
 204
 205     };
 206     boolean isAvailable = sf.isEnsemblAvailable();
 207     System.out.println("Ensembl is "
 208             + (isAvailable ? "UP!"
 209                     : "DOWN or unreachable ******************* BAD!"));
 210   }
 211 }