+++ /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.util;
-
-import static jalview.util.UrlConstants.DB_ACCESSION;
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.Sequence;
-import jalview.gui.JvOptionPane;
-
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class UrlLinkTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- final static String DB = "Test";
-
- final static String URL_PREFIX = "http://www.jalview.org/";
-
- final static String URL_SUFFIX = "/blah";
-
- final static String SEP = "|";
-
- final static String DELIM = "$";
-
- final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=";
-
- final static String REGEX_RUBBISH = "=/[0-9]++/=";
-
- /**
- * Test URL link creation when the input string has no regex
- */
- @Test(groups = { "Functional" })
- public void testUrlLinkCreationNoRegex()
- {
- // SEQUENCE_ID
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
- + DELIM + URL_SUFFIX);
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrlPrefix());
- assertEquals(URL_SUFFIX, ul.getUrlSuffix());
- assertTrue(ul.isDynamic());
- assertFalse(ul.usesDBAccession());
- assertNull(ul.getRegexReplace());
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // DB_ACCESSION
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
- + URL_SUFFIX);
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrlPrefix());
- assertEquals(URL_SUFFIX, ul.getUrlSuffix());
- assertTrue(ul.isDynamic());
- assertTrue(ul.usesDBAccession());
- assertNull(ul.getRegexReplace());
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // Not dynamic
- ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix());
- assertFalse(ul.isDynamic());
- assertFalse(ul.usesDBAccession());
- assertNull(ul.getRegexReplace());
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
- }
-
- /**
- * Test URL link creation when the input string has regex
- */
- @Test(groups = { "Functional" })
- public void testUrlLinkCreationWithRegex()
- {
- // SEQUENCE_ID
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
- + REGEX_NESTED + DELIM + URL_SUFFIX);
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrlPrefix());
- assertEquals(URL_SUFFIX, ul.getUrlSuffix());
- assertTrue(ul.isDynamic());
- assertFalse(ul.usesDBAccession());
- assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
- ul.getRegexReplace());
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // DB_ACCESSION
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
- + REGEX_NESTED + DELIM + URL_SUFFIX);
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrlPrefix());
- assertEquals(URL_SUFFIX, ul.getUrlSuffix());
- assertTrue(ul.isDynamic());
- assertTrue(ul.usesDBAccession());
- assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
- ul.getRegexReplace());
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // invalid regex
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
- + REGEX_RUBBISH + DELIM + URL_SUFFIX);
- assertEquals(DB, ul.getTarget());
- assertEquals(DB, ul.getLabel());
- assertEquals(URL_PREFIX, ul.getUrlPrefix());
- assertEquals(URL_SUFFIX, ul.getUrlSuffix());
- assertTrue(ul.isDynamic());
- assertTrue(ul.usesDBAccession());
- assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
- ul.getRegexReplace());
- assertFalse(ul.isValid());
- assertEquals(
- "Invalid Regular Expression : '"
- + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
- + "'\n",
- ul.getInvalidMessage());
- }
-
- /**
- * Test construction of link by substituting sequence id or name
- */
- @Test(groups = { "Functional" })
- public void testMakeUrlNoRegex()
- {
- // Single non-regex
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
- + DELIM + URL_SUFFIX);
- String idstring = "FER_CAPAA";
- String[] urls = ul.makeUrls(idstring, true);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
-
- urls = ul.makeUrls(idstring, false);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
- }
-
- /**
- * Test construction of link by substituting sequence id or name using regular
- * expression
- */
- @Test(groups = { "Functional" })
- public void testMakeUrlWithRegex()
- {
- // Unused regex
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
- + REGEX_NESTED + DELIM + URL_SUFFIX);
- String idstring = "FER_CAPAA";
- String[] urls = ul.makeUrls(idstring, true);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- urls = ul.makeUrls(idstring, false);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // nested regex
- idstring = "Label:gi|9234|pdb|102L|A";
- urls = ul.makeUrls(idstring, true);
-
- assertEquals(2, urls.length);
- assertEquals("9234", urls[0]);
- assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- urls = ul.makeUrls(idstring, false);
-
- assertEquals(2, urls.length);
- assertEquals("9234", urls[0]);
- assertEquals(URL_PREFIX + "9234" + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // unmatched regex
- idstring = "this does not match";
- urls = ul.makeUrls(idstring, true);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- urls = ul.makeUrls(idstring, false);
-
- assertEquals(2, urls.length);
- assertEquals(idstring, urls[0]);
- assertEquals(URL_PREFIX + idstring + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
-
- // empty idstring
- idstring = "";
- urls = ul.makeUrls(idstring, true);
-
- assertNull(urls);
-
- urls = ul.makeUrls(idstring, false);
-
- assertEquals(2, urls.length);
- assertEquals("", urls[0]);
- assertEquals(URL_PREFIX + URL_SUFFIX, urls[1]);
- assertTrue(ul.isValid());
- assertNull(ul.getInvalidMessage());
- }
-
- /**
- * Test creating links with null sequence
- */
- @Test(groups = { "Functional" })
- public void testCreateLinksFromNullSequence()
- {
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
- + DELIM + URL_SUFFIX);
-
- Map<String, List<String>> linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(null, linkset);
-
- String key = DB + SEP + URL_PREFIX;
- assertEquals(1, linkset.size());
- assertTrue(linkset.containsKey(key));
- assertEquals(DB, linkset.get(key).get(0));
- assertEquals(DB, linkset.get(key).get(1));
- assertEquals(null, linkset.get(key).get(2));
- assertEquals(URL_PREFIX, linkset.get(key).get(3));
- }
-
- /**
- * Test creating links with non-dynamic urlLink
- */
- @Test(groups = { "Functional" })
- public void testCreateLinksForNonDynamic()
- {
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
-
- Map<String, List<String>> linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(null, linkset);
-
- String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
- assertEquals(1, linkset.size());
- assertTrue(linkset.containsKey(key));
- assertEquals(DB, linkset.get(key).get(0));
- assertEquals(DB, linkset.get(key).get(1));
- assertEquals(null, linkset.get(key).get(2));
- assertEquals(URL_PREFIX + URL_SUFFIX, linkset.get(key).get(3));
- }
-
- /**
- * Test creating links
- */
- @Test(groups = { "Functional" })
- public void testCreateLinksFromSequence()
- {
-
- // create list of links and list of DBRefs
- List<String> links = new ArrayList<>();
- List<DBRefEntry> refs = new ArrayList<>();
-
- // links as might be added into Preferences | Connections dialog
- links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
- + SEQUENCE_ID + "$");
- links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
- + "$");
- links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
- + DB_ACCESSION + "$");
-
- // make seq0 dbrefs
- refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
- refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
- refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
- refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
-
- Sequence seq0 = new Sequence("FER1", "AKPNGVL");
-
- // add all the dbrefs to the sequence
- seq0.addDBRef(refs.get(0));
- seq0.addDBRef(refs.get(1));
- seq0.addDBRef(refs.get(2));
- seq0.addDBRef(refs.get(3));
- seq0.createDatasetSequence();
-
- // Test where link takes a sequence id as replacement
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
- + DELIM + URL_SUFFIX);
-
- Map<String, List<String>> linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(seq0, linkset);
-
- String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName()
- + URL_SUFFIX;
- assertEquals(1, linkset.size());
- assertTrue(linkset.containsKey(key));
- assertEquals(DB, linkset.get(key).get(0));
- assertEquals(DB, linkset.get(key).get(1));
- assertEquals(seq0.getName(), linkset.get(key).get(2));
- assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, linkset.get(key)
- .get(3));
-
- // Test where link takes a db annotation id and only has one dbref
- ul = new UrlLink(links.get(1));
- linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(seq0, linkset);
-
- key = "P83527|http://www.uniprot.org/uniprot/P83527";
- assertEquals(linkset.size(), 1);
- assertTrue(linkset.containsKey(key));
- assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0));
- assertEquals(DBRefSource.UNIPROT + SEP + "P83527", linkset.get(key)
- .get(1));
- assertEquals("P83527", linkset.get(key).get(2));
- assertEquals("http://www.uniprot.org/uniprot/P83527", linkset.get(key)
- .get(3));
-
- // Test where link takes a db annotation id and has multiple dbrefs
- ul = new UrlLink(links.get(2));
- linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(seq0, linkset);
- assertEquals(3, linkset.size());
-
- // check each link made it in correctly
- key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041";
- assertTrue(linkset.containsKey(key));
- assertEquals("INTERPRO", linkset.get(key).get(0));
- assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1));
- assertEquals("IPR001041", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", linkset
- .get(key).get(3));
-
- key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
- assertTrue(linkset.containsKey(key));
- assertEquals("INTERPRO", linkset.get(key).get(0));
- assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1));
- assertEquals("IPR006058", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", linkset
- .get(key).get(3));
-
- key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
- assertTrue(linkset.containsKey(key));
- assertEquals("INTERPRO", linkset.get(key).get(0));
- assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1));
- assertEquals("IPR012675", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", linkset
- .get(key).get(3));
-
- // Test where there are no matching dbrefs for the link
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
- + URL_SUFFIX);
- linkset = new LinkedHashMap<>();
- ul.createLinksFromSeq(seq0, linkset);
- assertTrue(linkset.isEmpty());
- }
-
- /**
- * Test links where label and target are both included
- */
- @Test(groups = { "Functional" })
- public void testLinksWithTargets()
- {
- UrlLink ul = new UrlLink(
- "Protein Data Bank | http://www.identifiers.org/pdb/$"
- + DB_ACCESSION + "$" + " | pdb");
-
- assertEquals("Protein Data Bank", ul.getLabel());
- assertEquals("pdb", ul.getTarget());
- assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
- ul.getUrlWithToken());
-
- assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
- + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
-
- ul = new UrlLink("Protein Data Bank",
- "http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$", "pdb");
-
- assertEquals("Protein Data Bank", ul.getLabel());
- assertEquals("pdb", ul.getTarget());
- assertEquals("http://www.identifiers.org/pdb/$" + DB_ACCESSION + "$",
- ul.getUrlWithToken());
-
- assertEquals("Protein Data Bank|http://www.identifiers.org/pdb/$"
- + DB_ACCESSION + "$" + "|pdb", ul.toStringWithTarget());
-
- }
-
- @Test(groups = { "Functional" })
- public void testLinkComparator()
- {
- Comparator<String> c = UrlLink.LINK_COMPARATOR;
- assertEquals(0, c.compare(null, null));
- assertEquals(0, c.compare(null, "x"));
- assertEquals(0, c.compare("y", null));
-
- /*
- * SEQUENCE_ID templates should come before DB_ACCESSION templates
- */
- String dbRefUrl = "Cath|http://www.cathdb.info/version/v4_2_0/superfamily/$DB_ACCESSION$";
- String seqIdUrl = "EBI|https://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
- assertTrue(c.compare(seqIdUrl, dbRefUrl) < 0);
- assertTrue(c.compare(dbRefUrl, seqIdUrl) > 0);
-
- String interpro = "Interpro|https://www.ebi.ac.uk/interpro/entry/$DB_ACCESSION$";
- String prosite = "ProSite|https://prosite.expasy.org/PS00197";
- assertTrue(c.compare(interpro, prosite) < 0);
- assertTrue(c.compare(prosite, interpro) > 0);
- }
-}
git://source.jalview.org / jalview.git / blobdiff