test/jalview/ws/ebi/EBIFetchClientTest.java

   1 package jalview.ws.ebi;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertNull;
   5
   6 import org.testng.annotations.Test;
   7
   8 public class EBIFetchClientTest
   9 {
  10   /**
  11    * Test method that constructs URL to fetch from
  12    */
  13   @Test(groups = "Functional")
  14   public void testBuildUrl()
  15   {
  16     /*
  17      * EMBL
  18      */
  19     assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
  20             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
  21
  22     /*
  23      * EMBLCDS
  24      */
  25     assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
  26             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
  27
  28     /*
  29      * Uniprot
  30      */
  31     assertEquals(
  32             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
  33             EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
  34
  35     /*
  36      * PDB / pdb
  37      */
  38     assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
  39             EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
  40
  41     /*
  42      * PDB / mmCIF
  43      */
  44     assertEquals(
  45             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
  46             EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
  47   }
  48
  49   /**
  50    * Test method that parses db:id;id;id
  51    */
  52   @Test(groups = "Functional")
  53   public void testParseIds()
  54   {
  55     /*
  56      * pdb, two accessions
  57      */
  58     StringBuilder queries = new StringBuilder();
  59     String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
  60     assertEquals("pdb", db);
  61     assertEquals("3a6s,1A70", queries.toString());
  62
  63     /*
  64      * pdb specified on second accession
  65      */
  66     queries.setLength(0);
  67     queries = new StringBuilder();
  68     db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
  69     assertEquals("pdb", db);
  70     assertEquals("3a6s,1A70", queries.toString());
  71
  72     /*
  73      * uniprot, one accession
  74      */
  75     queries.setLength(0);
  76     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
  77     assertEquals("uniprot", db);
  78     assertEquals("P00340", queries.toString());
  79
  80     /*
  81      * uniprot, one accession, appending to existing queries
  82      */
  83     queries.setLength(0);
  84     queries.append("P30419");
  85     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
  86     assertEquals("uniprot", db);
  87     assertEquals("P30419,P00340", queries.toString());
  88
  89     /*
  90      * pdb and uniprot mixed - rejected
  91      */
  92     queries.setLength(0);
  93     db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
  94     assertNull(db);
  95     assertEquals("3a6s,1a70", queries.toString());
  96
  97     /*
  98      * pdb and PDB mixed - ok
  99      */
 100     queries.setLength(0);
 101     db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
 102     assertEquals("PDB", db);
 103     assertEquals("3a6s,1a70,1QIP", queries.toString());
 104
 105     /*
 106      * no database (improper format)
 107      */
 108     queries.setLength(0);
 109     db = EBIFetchClient.parseIds("P00340", queries);
 110     assertNull(db);
 111     assertEquals("P00340", queries.toString());
 112   }
 113 }