X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Furls%2FUrlLinkTableModelTest.java;fp=test%2Fjalview%2Furls%2FUrlLinkTableModelTest.java;h=ab190ef46d7ccc4c5624cad576ed4abb39b816e1;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=0000000000000000000000000000000000000000;hpb=9debcac658224e1a84ddff4c4fd9f696e812913f;p=jalview.git

diff --git a/test/jalview/urls/UrlLinkTableModelTest.java b/test/jalview/urls/UrlLinkTableModelTest.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import static jalview.util.UrlConstants.DELIM;
+import static jalview.util.UrlConstants.SEP;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+
+import jalview.urls.api.UrlProviderI;
+import jalview.util.MessageManager;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.event.TableModelListener;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class UrlLinkTableModelTest {
+
+  private static final String inmenu = "TEST|http://someurl.blah/$DB_ACCESSION$|"
+          + "ANOTHER|http://test/t$SEQUENCE_ID$|"
+          + "TEST2|http://address/$SEQUENCE_ID$|SRS|"
+          + "http://theSRSlink/$SEQUENCE_ID$|"
+          + "MIR:00000005|MIR:00000011|MIR:00000372";
+
+  private static final String notinmenu = "Not1|http://not.in.menu/$DB_ACCESSION$|"
+          + "Not2|http://not.in.menu.either/$DB_ACCESSION$";
+
+  private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
+          + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
+          + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
+          + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
+          + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
+          + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
+          + "\"url\":\"http://identifiers.org/interpro\"},"
+          + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+          + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
+
+  private UrlProviderI prov;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setup()
+  {
+    // set up UrlProvider data as the source for the TableModel
+    // the data gets updated by the TableModel, so needs to be reinitialised for
+    // each test
+
+    // make a dummy identifiers.org download file
+    File temp = null;
+    try
+    {
+      temp = File.createTempFile("tempfile", ".tmp");
+      temp.deleteOnExit();
+      BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
+      bw.write(testIdOrgString);
+      bw.close();
+    } catch (IOException e)
+    {
+      System.out.println("Error initialising UrlLinkTableModel test: "
+              + e.getMessage());
+    }
+
+    // set up custom and identifiers.org url providers
+    IdOrgSettings.setDownloadLocation(temp.getPath());
+    IdentifiersUrlProvider idprov = new IdentifiersUrlProvider(inmenu);
+    CustomUrlProvider cprov = new CustomUrlProvider(inmenu, notinmenu);
+    List<UrlProviderI> provlist = new ArrayList<UrlProviderI>();
+    provlist.add(idprov);
+    provlist.add(cprov);
+
+    prov = new UrlProvider("TEST2", provlist);
+  }
+
+  /*
+   * Test that the table model is correctly initialised
+   * Display columns and default row are set; data provider listening event set up
+   */
+  @Test(groups = { "Functional" })
+  public void testInitialisation()
+  {
+    int defaultCol = 4;
+    int dbCol = 0;
+    int descCol = 1;
+
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    // exactly one table model listener
+    TableModelListener[] listeners = m
+            .getListeners(TableModelListener.class);
+    Assert.assertEquals(listeners.length, 1);
+
+    // default row exists, there is exactly 1, and it matches the supplied
+    // default
+    int count = 0;
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      boolean isDefault = (boolean) m.getValueAt(row, defaultCol);
+      if (isDefault)
+      {
+        count++;
+        String defaultDBName = (String) m.getValueAt(row, dbCol);
+        Assert.assertEquals(defaultDBName, "TEST2");
+
+        String defaultDesc = (String) m.getValueAt(row, descCol);
+        Assert.assertEquals(defaultDesc, "TEST2");
+      }
+    }
+    Assert.assertEquals(count, 1);
+  }
+
+  /*
+   * Test row and column counts
+   */
+  @Test(groups = { "Functional" })
+  public void testCounts()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    // correct numbers of column and rows
+    Assert.assertEquals(m.getColumnCount(), 5);
+    Assert.assertEquals(m.getRowCount(), 10);
+  }
+
+  /*
+   * Test column access
+   */
+  @Test(groups = { "Functional" })
+  public void testColumns()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    // check column names
+    Assert.assertEquals(m.getColumnName(0),
+            MessageManager.formatMessage("label.database"));
+    Assert.assertEquals(m.getColumnName(1),
+            MessageManager.formatMessage("label.name"));
+    Assert.assertEquals(m.getColumnName(2),
+            MessageManager.formatMessage("label.url"));
+    Assert.assertEquals(m.getColumnName(3),
+            MessageManager.formatMessage("label.inmenu"));
+    Assert.assertEquals(m.getColumnName(4),
+            MessageManager.formatMessage("label.primary"));
+
+    // check column classes
+    Assert.assertEquals(m.getColumnClass(0), String.class);
+    Assert.assertEquals(m.getColumnClass(1), String.class);
+    Assert.assertEquals(m.getColumnClass(2), String.class);
+    Assert.assertEquals(m.getColumnClass(3), Boolean.class);
+    Assert.assertEquals(m.getColumnClass(4), Boolean.class);
+  }
+
+  /*
+   * Test row insertion
+   */
+  @Test(groups = { "Functional" })
+  public void testRowInsert()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    m.insertRow("newname", "newurl");
+
+    // check table has new row inserted
+    Assert.assertEquals(m.getValueAt(10, 0), "newname");
+    Assert.assertEquals(m.getValueAt(10, 1), "newname");
+    Assert.assertEquals(m.getValueAt(10, 2), "newurl");
+    Assert.assertEquals(m.getValueAt(10, 3), true);
+    Assert.assertEquals(m.getValueAt(10, 4), false);
+
+    // check data source has new row insrte
+    Assert.assertTrue(prov.getLinksForMenu().contains(
+            "newname" + SEP + "newurl"));
+  }
+
+  /*
+   * Test row deletion
+   */
+  @Test(groups = { "Functional" })
+  public void testRowDelete()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    // get name and url at row 0
+    String name = (String) m.getValueAt(0, 0);
+    String url = (String) m.getValueAt(0, 1);
+
+    m.removeRow(0);
+
+    // check table no longer has row 0 elements in it
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      Assert.assertNotEquals(m.getValueAt(row, 0), name);
+    }
+
+    // check data source likewise
+    Assert.assertFalse(prov.getLinksForMenu().contains(name + SEP + url));
+  }
+
+  /*
+   * Test value setting and getting
+   */
+  @Test(groups = { "Functional" })
+  public void testValues()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    // get original default
+    int olddefault;
+    boolean isDefault = false;
+    for (olddefault = 0; olddefault < m.getRowCount() && !isDefault; olddefault++)
+    {
+      isDefault = (boolean) m.getValueAt(olddefault, 3);
+    }
+
+    // set new values, one in each row
+    m.setValueAt("dbnamechanged", 6, 0);
+    m.setValueAt("descchanged", 6, 1);
+    m.setValueAt("urlchanged", 7, 2);
+    m.setValueAt(false, 8, 3);
+    m.setValueAt(true, 6, 4);
+
+    m.setValueAt("dbnamechanged", 5, 0);
+
+    // check values updated in table
+    Assert.assertEquals(m.getValueAt(6, 0), "descchanged"); // custom url can't
+                                                            // change db name
+    Assert.assertEquals(m.getValueAt(6, 1), "descchanged");
+    Assert.assertEquals(m.getValueAt(7, 2), "urlchanged");
+    Assert.assertFalse((boolean) m.getValueAt(8, 3));
+    Assert.assertTrue((boolean) m.getValueAt(6, 4));
+    Assert.assertFalse((boolean) m.getValueAt(olddefault, 4));
+
+    Assert.assertEquals(m.getValueAt(5, 0), "dbnamechanged");
+
+    // check default row is exactly one row still
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      isDefault = (boolean) m.getValueAt(row, 4);
+
+      // if isDefault is true, row is 9
+      // if isDefault is false, row is not 9
+      Assert.assertFalse(isDefault && !(row == 6));
+    }
+
+    // check table updated
+    Assert.assertTrue(prov.writeUrlsAsString(true).contains(
+            "descchanged" + SEP + m.getValueAt(6, 2)));
+    Assert.assertTrue(prov.writeUrlsAsString(true).contains(
+            m.getValueAt(7, 1) + SEP + "urlchanged"));
+    Assert.assertTrue(prov.writeUrlsAsString(false).contains(
+            (String) m.getValueAt(8, 1)));
+    Assert.assertEquals(prov.getPrimaryUrl("seqid"), m.getValueAt(6, 2)
+            .toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
+  }
+
+  /*
+   * Test cell editability
+   */
+  @Test(groups = { "Functional" })
+  public void testEditable()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      Assert.assertFalse(m.isCellEditable(row, 0));
+      Assert.assertFalse(m.isCellEditable(row, 1));
+      Assert.assertFalse(m.isCellEditable(row, 2));
+      Assert.assertTrue(m.isCellEditable(row, 3));
+
+      if ((row == 4) || (row == 6) || (row == 7))
+      {
+        Assert.assertTrue(m.isCellEditable(row, 4));
+      }
+      else
+      {
+        Assert.assertFalse(m.isCellEditable(row, 4));
+      }
+    }
+  }
+
+  /*
+   * Test row 'deletability'
+   */
+  @Test(groups = { "Functional" })
+  public void testDeletable()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      if (row > 4)
+      {
+        Assert.assertTrue(m.isRowDeletable(row));
+      }
+      else
+      {
+        Assert.assertFalse(m.isRowDeletable(row));
+      }
+    }
+  }
+
+  /*
+   * Test indirect row editability
+   */
+  @Test(groups = { "Functional" })
+  public void testRowEditable()
+  {
+    UrlLinkTableModel m = new UrlLinkTableModel(prov);
+
+    for (int row = 0; row < m.getRowCount(); row++)
+    {
+      if (row > 3)
+      {
+        Assert.assertTrue(m.isRowEditable(row));
+      }
+      else
+      {
+        Assert.assertFalse(m.isRowEditable(row));
+      }
+    }
+  }
+}