+++ /dev/null
-/*
- * 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));
- }
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff