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(
  51             "https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
  52             EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
  53
  54     /*
  55      * EMBLCDS
  56      */
  57     assertEquals(
  58             "https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
  59             EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
  60
  61     /*
  62      * PDB / pdb
  63      */
  64     assertEquals("https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb",
  65             EBIFetchClient.buildUrl("3A6S", "PDB", "pdb"));
  66
  67     /*
  68      * PDB / mmCIF
  69      */
  70     assertEquals(
  71             "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF",
  72             EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF"));
  73   }
  74
  75   /**
  76    * Test method that parses db:id;id;id
  77    */
  78   @Test(groups = "Functional")
  79   public void testParseIds()
  80   {
  81     /*
  82      * pdb, two accessions
  83      */
  84     StringBuilder queries = new StringBuilder();
  85     String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries);
  86     assertEquals("pdb", db);
  87     assertEquals("3a6s,1A70", queries.toString());
  88
  89     /*
  90      * pdb specified on second accession
  91      */
  92     queries.setLength(0);
  93     queries = new StringBuilder();
  94     db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries);
  95     assertEquals("pdb", db);
  96     assertEquals("3a6s,1A70", queries.toString());
  97
  98     /*
  99      * uniprot, one accession
 100      */
 101     queries.setLength(0);
 102     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
 103     assertEquals("uniprot", db);
 104     assertEquals("P00340", queries.toString());
 105
 106     /*
 107      * uniprot, one accession, appending to existing queries
 108      */
 109     queries.setLength(0);
 110     queries.append("P30419");
 111     db = EBIFetchClient.parseIds("uniprot:P00340", queries);
 112     assertEquals("uniprot", db);
 113     assertEquals("P30419,P00340", queries.toString());
 114
 115     /*
 116      * pdb and uniprot mixed - rejected
 117      */
 118     queries.setLength(0);
 119     db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries);
 120     assertNull(db);
 121     assertEquals("3a6s,1a70", queries.toString());
 122
 123     /*
 124      * pdb and PDB mixed - ok
 125      */
 126     queries.setLength(0);
 127     db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries);
 128     assertEquals("PDB", db);
 129     assertEquals("3a6s,1a70,1QIP", queries.toString());
 130
 131     /*
 132      * no database (improper format)
 133      */
 134     queries.setLength(0);
 135     db = EBIFetchClient.parseIds("P00340", queries);
 136     assertNull(db);
 137     assertEquals("P00340", queries.toString());
 138   }
 139 }