X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Furls%2FUrlLinkTableModelTest.java;fp=test%2Fjalview%2Furls%2FUrlLinkTableModelTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=ab190ef46d7ccc4c5624cad576ed4abb39b816e1;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/urls/UrlLinkTableModelTest.java b/test/jalview/urls/UrlLinkTableModelTest.java
deleted file mode 100644
index ab190ef..0000000
--- a/test/jalview/urls/UrlLinkTableModelTest.java
+++ /dev/null
@@ -1,348 +0,0 @@
-/*
- * 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));
-      }
-    }
-  }
-}