test/jalview/ws/ebi/EBIFetchClientTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ws.ebi;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNull;
  25
  26 import org.testng.annotations.Test;
  27
  28 public class EBIFetchClientTest
  29 {
  30   /**
  31    * Test method that constructs URL to fetch from
  32    */
  33   @Test(groups = "Functional")
  34   public void testBuildUrl()
  35   {
  36     /*
  37      * EMBL
  38      */
  39     assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
  40             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
  41
  42     /*
  43      * EMBLCDS
  44      */
  45     assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
  46             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
  47
  48     /*
  49      * Uniprot
  50      */
  51     assertEquals(
  52             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
  53             EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
  54
  55     /*
  56      * PDB / pdb
  57      */
  58     assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
  59             EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
  60
  61     /*
  62      * PDB / mmCIF
  63      */
  64     assertEquals(
  65             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
  66             EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
  67   }
  68
  69   /**
  70    * Test method that parses db:id;id;id
  71    */
  72   @Test(groups = "Functional")
  73   public void testParseIds()
  74   {
  75     /*
  76      * pdb, two accessions
  77      */
  78     StringBuilder queries = new StringBuilder();
  79     String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
  80     assertEquals("pdb", db);
  81     assertEquals("3a6s,1A70", queries.toString());
  82
  83     /*
  84      * pdb specified on second accession
  85      */
  86     queries.setLength(0);
  87     queries = new StringBuilder();
  88     db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
  89     assertEquals("pdb", db);
  90     assertEquals("3a6s,1A70", queries.toString());
  91
  92     /*
  93      * uniprot, one accession
  94      */
  95     queries.setLength(0);
  96     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
  97     assertEquals("uniprot", db);
  98     assertEquals("P00340", queries.toString());
  99
 100     /*
 101      * uniprot, one accession, appending to existing queries
 102      */
 103     queries.setLength(0);
 104     queries.append("P30419");
 105     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
 106     assertEquals("uniprot", db);
 107     assertEquals("P30419,P00340", queries.toString());
 108
 109     /*
 110      * pdb and uniprot mixed - rejected
 111      */
 112     queries.setLength(0);
 113     db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
 114     assertNull(db);
 115     assertEquals("3a6s,1a70", queries.toString());
 116
 117     /*
 118      * pdb and PDB mixed - ok
 119      */
 120     queries.setLength(0);
 121     db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
 122     assertEquals("PDB", db);
 123     assertEquals("3a6s,1a70,1QIP", queries.toString());
 124
 125     /*
 126      * no database (improper format)
 127      */
 128     queries.setLength(0);
 129     db = EBIFetchClient.parseIds("P00340", queries);
 130     assertNull(db);
 131     assertEquals("P00340", queries.toString());
 132   }
 133 }