/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.urls;
import jalview.urls.api.UrlProviderI;
import jalview.urls.desktop.DesktopUrlProviderFactory;
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 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 = "{\"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()
{
// 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.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
List menulinks = prov.getLinksForMenu();
List 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/$DB_ACCESSION$|uniprot"));
Assert.assertTrue(menulinks.contains(
"InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
Assert.assertTrue(menulinks.contains(
UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
}
@Test(groups = { "Functional" })
public void testSetDefaultUrl()
{
// set custom url as default
Assert.assertTrue(prov.setPrimaryUrl("Test1"));
Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
// set identifiers url as default
Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
}
@Test(
groups =
{ "Functional" },
expectedExceptions =
{ IllegalArgumentException.class })
public void testSetDefaultUrlWrongly()
{
// don't allow default to be a non-key
prov.setPrimaryUrl("not-a-key");
}
}