{
return null;
}
+
+ @Override
+ public boolean contains(String id)
+ {
+ return (urls.containsKey(id));
+ }
}
customProvider = findCustomProvider();
// check that the defaultUrl still exists
- if (!setDefaultUrl(defaultUrlString))
+ if (!contains(defaultUrlString))
{
// if the defaultUrl can't be found in any of the providers
// set up a custom default url
chooseDefaultUrl();
}
+ else
+ {
+ setDefaultUrl(defaultUrlString);
+ }
}
/*
outcome = true;
}
}
+ if (!outcome)
+ {
+ throw new IllegalArgumentException();
+ }
+ return outcome;
+ }
+
+ @Override
+ public boolean contains(String id)
+ {
+ boolean outcome = false;
+ for (UrlProviderI p : providers)
+ {
+ if (p.contains(id))
+ {
+ outcome = true;
+ }
+ }
return outcome;
}
{
for (UrlProviderI p : providers)
{
- p.setDefaultUrl(null);
p.setUrlData(links);
}
}
{
/**
- * Get names and urls in as strings for display
+ * Get names and urls in the UrlProvider as strings for display
*
*/
Vector<String> getLinksForMenu();
String getDefaultUrlId();
/**
- * Get the target of thelink for the default URL
+ * Get the target of the link for the default URL
*
* @seqid sequence id for which to build link
* @return target of link for the default URL
*
* @param id
* the id of the URL to set as default
- * @return true if setting was successful, false otherwise
+ * @return true if setting is successful
+ * @throws IllegalArgumentException
+ * if id does not exist as a url in the UrlProvider
*/
- boolean setDefaultUrl(String id);
+ boolean setDefaultUrl(String id) throws IllegalArgumentException;
+
+ /**
+ * Test if UrlProvider contains a url
+ *
+ * @param id
+ * to test for
+ * @return true of UrlProvider contains this id, false otherwise
+ */
+ boolean contains(String id);
/**
* Write out all URLs as a string suitable for serialising
--- /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 jalview.util.UrlConstants;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class AppletUrlProviderFactoryTest {
+
+ @Test(groups = { "Functional" })
+ public void testCreateUrlProvider()
+ {
+ final String defaultUrl = UrlConstants.DEFAULT_STRING.substring(
+ UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
+ UrlConstants.DEFAULT_STRING.length());
+ Map<String, String> urlList = new HashMap<String, String>()
+ {
+ {
+ put("Test1", "http://identifiers.org/uniprot/$DB_ACCESSION$");
+ put("Test2", defaultUrl);
+ }
+ };
+
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory("Test2",
+ urlList);
+ UrlProviderI prov = factory.createUrlProvider();
+
+ // default url correctly set
+ Assert.assertEquals(prov.getDefaultUrlId(), "Test2");
+ Assert.assertEquals(prov.getDefaultUrl("FER_CAPAN"),
+ defaultUrl.replace("$SEQUENCE_ID$",
+ "FER_CAPAN"));
+
+ List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
+
+ // 2 links in provider
+ Assert.assertEquals(allLinks.size(), 2);
+
+ // first link set correctly
+ Assert.assertEquals(allLinks.get(0).getId(), "Test1");
+ Assert.assertEquals(allLinks.get(0).getName(), "Test1");
+ Assert.assertEquals(allLinks.get(0).getUrl(),
+ "http://identifiers.org/uniprot/$DB_ACCESSION$");
+ Assert.assertFalse(allLinks.get(0).getIsDefault());
+ Assert.assertTrue(allLinks.get(0).getIsSelected());
+
+ // second link set correctly
+ Assert.assertEquals(allLinks.get(1).getId(), "Test2");
+ Assert.assertEquals(allLinks.get(1).getName(), "Test2");
+ Assert.assertEquals(allLinks.get(1).getUrl(), defaultUrl);
+ Assert.assertTrue(allLinks.get(1).getIsDefault());
+ Assert.assertTrue(allLinks.get(1).getIsSelected());
+ }
+}
--- /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 java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Vector;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class DesktopUrlProviderFactoryTest
+{
+ // Test identifiers.org download file
+ private static final String testIdOrgString = "[{\"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\"}]";
+
+ @BeforeMethod(alwaysRun = true)
+ public void setup()
+ {
+ // 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 DesktopUrlProviderFactoryTest test: "
+ + e.getMessage());
+ }
+
+ IdOrgSettings.setDownloadLocation(temp.getPath());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCreateUrlProvider()
+ {
+ String defaultUrlString = "Test1";
+ String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
+ String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
+ + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
+ String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
+
+ DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
+ defaultUrlString, cachedUrlList, userUrlList);
+ UrlProviderI prov = factory.createUrlProvider();
+
+ // default url correctly set
+ Assert.assertEquals(prov.getDefaultUrlId(), "Test1");
+ Assert.assertEquals(prov.getDefaultUrl("FER_CAPAN"),
+ defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
+
+ Vector<String> menulinks = prov.getLinksForMenu();
+ List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
+
+ // 8 links in provider - 4 from id file, 4 custom links
+ Assert.assertEquals(allLinks.size(), 8);
+
+ // 5 links in menu (cachedUrlList)
+ Assert.assertEquals(menulinks.size(), 5);
+
+ Assert.assertTrue(menulinks
+ .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks
+ .contains("Test2|http://test2/$DB_ACCESSION$"));
+ Assert.assertTrue(menulinks
+ .contains("Test3|http://test3/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks
+ .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$"));
+ Assert.assertTrue(menulinks
+ .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$"));
+ }
+}
package jalview.urls;
-import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.DELIM;
import static jalview.util.UrlConstants.SEP;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.util.MessageManager;
provlist.add(idprov);
provlist.add(cprov);
- prov = new UrlProvider("MIR:00000005", provlist);
+ prov = new UrlProvider("TEST2", provlist);
}
/*
{
count++;
String defaultName = (String) m.getValueAt(row, nameCol);
- Assert.assertEquals(defaultName, "UniProt Knowledgebase");
+ Assert.assertEquals(defaultName, "TEST2");
}
}
Assert.assertEquals(count, 1);
isDefault = (boolean) m.getValueAt(olddefault, 3);
}
- // set new values, one in each row - uneditable
+ // set new values, one in each row
m.setValueAt("namechanged", 6, 0);
m.setValueAt("urlchanged", 7, 1);
m.setValueAt(false, 8, 2);
- m.setValueAt(true, 9, 3);
+ m.setValueAt(true, 6, 3);
// check values updated in table
Assert.assertEquals(m.getValueAt(6, 0), "namechanged");
Assert.assertEquals(m.getValueAt(7, 1), "urlchanged");
Assert.assertFalse((boolean) m.getValueAt(8, 2));
- Assert.assertTrue((boolean) m.getValueAt(9, 3));
+ Assert.assertTrue((boolean) m.getValueAt(6, 3));
Assert.assertFalse((boolean) m.getValueAt(olddefault, 3));
// check default row is exactly one row still
// if isDefault is true, row is 9
// if isDefault is false, row is not 9
- Assert.assertFalse(isDefault && !(row == 9));
+ Assert.assertFalse(isDefault && !(row == 6));
}
// check table updated
Assert.assertTrue(prov.writeUrlsAsString(true).contains(m.getValueAt(7,0) + SEP + "urlchanged"));
Assert.assertTrue(prov.writeUrlsAsString(false).contains(
(String) m.getValueAt(8, 0)));
- Assert.assertEquals(prov.getDefaultUrl("seqid"), m.getValueAt(9, 1)
- .toString().replace(DELIM + DB_ACCESSION + DELIM, "seqid"));
+ Assert.assertEquals(prov.getDefaultUrl("seqid"), m.getValueAt(6, 1)
+ .toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
}
Assert.assertFalse(m.isCellEditable(row, 0));
Assert.assertFalse(m.isCellEditable(row, 1));
Assert.assertTrue(m.isCellEditable(row, 2));
- Assert.assertTrue(m.isCellEditable(row, 3));
+
+ if ((row == 4) || (row == 6) || (row == 7))
+ {
+ Assert.assertTrue(m.isCellEditable(row, 3));
+ }
+ else
+ {
+ Assert.assertFalse(m.isCellEditable(row, 3));
+ }
}
}
}
--- /dev/null
+package jalview.urls;
+
+import jalview.util.UrlConstants;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Vector;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+
+public class UrlProviderTest {
+
+ // Test identifiers.org download file
+ private static final String testIdOrgString = "[{\"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()
+ {
+ // 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 UrlProviderTest test: "
+ + e.getMessage());
+ }
+
+ IdOrgSettings.setDownloadLocation(temp.getPath());
+
+ String defaultUrlString = "No default";
+ String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
+ + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
+ String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
+
+ DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
+ defaultUrlString, cachedUrlList, userUrlList);
+ prov = factory.createUrlProvider();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testInitUrlProvider()
+ {
+ String emblUrl = UrlConstants.DEFAULT_STRING.substring(
+ UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
+ UrlConstants.DEFAULT_STRING.length());
+
+ // chooses EMBL url when default Url id does not exist in provided url lists
+ Assert.assertEquals(prov.getDefaultUrlId(), UrlConstants.DEFAULT_LABEL);
+ Assert.assertEquals(prov.getDefaultUrl("FER_CAPAN"),
+ emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
+
+ Vector<String> menulinks = prov.getLinksForMenu();
+ List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
+
+ // 9 links in provider - 4 from id file, 4 custom links, 1 additional
+ // default
+ Assert.assertEquals(allLinks.size(), 9);
+
+ // 6 links in menu (cachedUrlList) + new default
+ Assert.assertEquals(menulinks.size(), 6);
+
+ Assert.assertTrue(menulinks
+ .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks
+ .contains("Test2|http://test2/$DB_ACCESSION$"));
+ Assert.assertTrue(menulinks
+ .contains("Test3|http://test3/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks
+ .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$"));
+ Assert.assertTrue(menulinks
+ .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$"));
+ Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
+ + UrlConstants.SEP + emblUrl));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetDefaultUrl()
+ {
+ // set custom url as default
+ Assert.assertTrue(prov.setDefaultUrl("Test1"));
+ Assert.assertEquals(prov.getDefaultUrlId(), "Test1");
+
+ // set identifiers url as default
+ Assert.assertTrue(prov.setDefaultUrl("MIR:00000011"));
+ Assert.assertEquals(prov.getDefaultUrlId(), "MIR:00000011");
+ }
+
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testSetDefaultUrlWrongly()
+ {
+ // don't allow default to be a non-key
+ prov.setDefaultUrl("not-a-key");
+ }
+}
git://source.jalview.org / jalview.git / commitdiff