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 jalview.gui.JvOptionPane;
  27
  28 import org.testng.annotations.BeforeClass;
  29 import org.testng.annotations.Test;
  30
  31 public class EBIFetchClientTest
  32 {
  33
  34   @BeforeClass(alwaysRun = true)
  35   public void setUpJvOptionPane()
  36   {
  37     JvOptionPane.setInteractiveMode(false);
  38     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  39   }
  40
  41   /**
  42    * Test method that constructs URL to fetch from
  43    */
  44   @Test(groups = "Functional")
  45   public void testBuildUrl()
  46   {
  47     /*
  48      * EMBL
  49      */
  50     assertEquals("https://www.ebi.ac.uk/ena/data/view/x53838&display=xml",
  51             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
  52
  53     /*
  54      * EMBLCDS
  55      */
  56     assertEquals("https://www.ebi.ac.uk/ena/data/view/caa37824&display=xml",
  57             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
  58
  59     /*
  60      * Uniprot
  61      */
  62     assertEquals(
  63             "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml",
  64             EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml"));
  65
  66     /*
  67      * PDB / pdb
  68      */
  69     assertEquals("https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
  70             EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
  71
  72     /*
  73      * PDB / mmCIF
  74      */
  75     assertEquals(
  76             "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
  77             EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
  78   }
  79
  80   /**
  81    * Test method that parses db:id;id;id
  82    */
  83   @Test(groups = "Functional")
  84   public void testParseIds()
  85   {
  86     /*
  87      * pdb, two accessions
  88      */
  89     StringBuilder queries = new StringBuilder();
  90     String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
  91     assertEquals("pdb", db);
  92     assertEquals("3a6s,1A70", queries.toString());
  93
  94     /*
  95      * pdb specified on second accession
  96      */
  97     queries.setLength(0);
  98     queries = new StringBuilder();
  99     db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
 100     assertEquals("pdb", db);
 101     assertEquals("3a6s,1A70", queries.toString());
 102
 103     /*
 104      * uniprot, one accession
 105      */
 106     queries.setLength(0);
 107     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
 108     assertEquals("uniprot", db);
 109     assertEquals("P00340", queries.toString());
 110
 111     /*
 112      * uniprot, one accession, appending to existing queries
 113      */
 114     queries.setLength(0);
 115     queries.append("P30419");
 116     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
 117     assertEquals("uniprot", db);
 118     assertEquals("P30419,P00340", queries.toString());
 119
 120     /*
 121      * pdb and uniprot mixed - rejected
 122      */
 123     queries.setLength(0);
 124     db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
 125     assertNull(db);
 126     assertEquals("3a6s,1a70", queries.toString());
 127
 128     /*
 129      * pdb and PDB mixed - ok
 130      */
 131     queries.setLength(0);
 132     db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
 133     assertEquals("PDB", db);
 134     assertEquals("3a6s,1a70,1QIP", queries.toString());
 135
 136     /*
 137      * no database (improper format)
 138      */
 139     queries.setLength(0);
 140     db = EBIFetchClient.parseIds("P00340", queries);
 141     assertNull(db);
 142     assertEquals("P00340", queries.toString());
 143   }
 144 }