test/jalview/io/IdentifyFileTest.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.io;
  22
  23 import static org.testng.AssertJUnit.assertFalse;
  24 import static org.testng.AssertJUnit.assertSame;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import java.io.FileNotFoundException;
  28
  29 import org.testng.Assert;
  30 import org.testng.annotations.BeforeClass;
  31 import org.testng.annotations.DataProvider;
  32 import org.testng.annotations.Test;
  33
  34 import jalview.gui.JvOptionPane;
  35
  36 public class IdentifyFileTest
  37 {
  38
  39   @BeforeClass(alwaysRun = true)
  40   public void setUpJvOptionPane()
  41   {
  42     JvOptionPane.setInteractiveMode(false);
  43     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  44   }
  45
  46   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
  47   public void testIdentify(String data, FileFormatI expectedFileType)
  48           throws FileFormatException, FileNotFoundException
  49   {
  50     DataSourceType protocol = DataSourceType.FILE;
  51     IdentifyFile ider = new IdentifyFile();
  52     FileFormatI actualFiletype = ider.identify(data, protocol);
  53     Assert.assertSame(actualFiletype, expectedFileType,
  54             "File identification Failed!");
  55   }
  56
  57   /**
  58    * Additional tests for Jalview features file
  59    *
  60    * @throws FileFormatException
  61    */
  62   @Test(groups = "Functional")
  63   public void testIdentify_featureFile()
  64           throws FileFormatException, FileNotFoundException
  65   {
  66     IdentifyFile ider = new IdentifyFile();
  67
  68     /*
  69      * Jalview format with features only, no feature colours
  70      */
  71     String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
  72             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
  73     assertSame(FileFormat.Features,
  74             ider.identify(data, DataSourceType.PASTE));
  75
  76     /*
  77      * Jalview feature colour followed by GFF format feature data
  78      */
  79     data = "METAL\tcc9900\n" + "GFF\n"
  80             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
  81     assertSame(FileFormat.Features,
  82             ider.identify(data, DataSourceType.PASTE));
  83
  84     /*
  85      * Feature with '<' in the name (JAL-2098)
  86      */
  87     data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
  88     assertSame(FileFormat.Features,
  89             ider.identify(data, DataSourceType.PASTE));
  90   }
  91
  92   @DataProvider(name = "identifyFiles")
  93   public Object[][] IdentifyFileDP()
  94   {
  95     return new Object[][] { { "examples/example.json", FileFormat.Json },
  96         { "examples/plantfdx.fa", FileFormat.Fasta },
  97         { "examples/dna_interleaved.phy", FileFormat.Phylip },
  98         { "examples/2GIS.pdb", FileFormat.PDB },
  99         { "examples/RF00031_folded.stk", FileFormat.Stockholm },
 100         { "examples/testdata/test.rnaml", FileFormat.Rnaml },
 101         { "examples/testdata/test.aln", FileFormat.Clustal },
 102         { "examples/testdata/test.pfam", FileFormat.Pfam },
 103         { "examples/testdata/test.msf", FileFormat.MSF },
 104         { "examples/testdata/test.pir", FileFormat.PIR },
 105         { "examples/testdata/test.html", FileFormat.Html },
 106         { "examples/testdata/test.pileup", FileFormat.Pileup },
 107         { "examples/testdata/test.blc", FileFormat.BLC },
 108         { "test/jalview/io/J03321.embl.txt", FileFormat.Embl },
 109         { "test/jalview/io/J03321.gb", FileFormat.GenBank },
 110         { "examples/exampleFeatures.txt", FileFormat.Features },
 111         { "examples/testdata/simpleGff3.gff", FileFormat.Features },
 112         { "examples/testdata/test.jvp", FileFormat.Jalview },
 113         { "examples/testdata/test.cif", FileFormat.MMCif },
 114         { "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
 115             FileFormat.Fasta },
 116         { "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix },
 117         { "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix }
 118         // { "examples/testdata/test.amsa", "AMSA" },
 119         // { "examples/test.jnet", "JnetFile" },
 120     };
 121   }
 122
 123   @Test(groups = "Functional")
 124   public void testLooksLikeFeatureData()
 125   {
 126     IdentifyFile id = new IdentifyFile();
 127     assertFalse(id.looksLikeFeatureData(null));
 128     assertFalse(id.looksLikeFeatureData(""));
 129     // too few columns:
 130     assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
 131     // GFF format:
 132     assertTrue(
 133             id.looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
 134     // Jalview format:
 135     assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
 136     // non-numeric start column:
 137     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
 138     // non-numeric start column:
 139     assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
 140   }
 141
 142   @Test(groups = "Network", dataProvider = "urlTargetsAndExceptions")
 143   public void testExceptions(String url,
 144           Class<? extends Exception> expectedExceptionClass,
 145           FileFormatI expectedFormat)
 146   {
 147     Class<? extends Exception> actualExceptionClass = null;
 148     FileFormatI actualFormat = null;
 149     try
 150     {
 151       actualFormat = new IdentifyFile().identify(url, DataSourceType.URL);
 152     } catch (FileFormatException | FileNotFoundException e)
 153     {
 154       Assert.assertNull(expectedFormat,
 155               "Exception occurred when expecting an identifiable format.");
 156       Assert.assertNotNull(expectedExceptionClass,
 157               "An unexpected exception occurred: '" + e.getMessage() + "'");
 158       Assert.assertEquals(e.getClass(), expectedExceptionClass,
 159               "Got the wrong kind of exception.");
 160       actualExceptionClass = e.getClass();
 161     }
 162
 163     if (expectedExceptionClass != null)
 164     {
 165       Assert.assertEquals(actualExceptionClass, expectedExceptionClass,
 166               "Expected an exception but got the wrong one.");
 167     }
 168
 169   }
 170
 171   @DataProvider(name = "urlTargetsAndExceptions")
 172   public Object[][] urlTargetsAndExceptions()
 173   {
 174     /*
 175     String targetUrl,
 176     String finalUrl,
 177     String foundInFirstLine,
 178     */
 179     return new Object[][] {
 180         //
 181         /*
 182         { "http://jalview.org/examples/uniref50.fa", null,
 183             FileFormat.Fasta },
 184         { "https://www.jalview.org/examples/NOFILE.fa",
 185             FileNotFoundException.class, null },
 186         { "https://NOSERVER.jalview.org/", FileNotFoundException.class,
 187             null },
 188          */
 189         { "https://www.jalview.org/schools/Jalview_Schools_Workbook_200.jpg",
 190             FileFormatException.class, null },
 191         /*
 192          */
 193         //
 194     };
 195   }
 196
 197 }