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;
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[][] createData(Method m)
+ public Object[][] createQueryData(Method m)
{
return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
}
@Test(dataProvider = "queries")
public void testIsValidReference(String query) throws Exception
{
- EnsemblSeqProxy esq = new EnsemblProtein();
+ 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!"));
+ }
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff