X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FUrlLinkTest.java;fp=test%2Fjalview%2Futil%2FUrlLinkTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=c7d37b097a20e805f9961857208633fc65ef691d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
deleted file mode 100644
index c7d37b0..0000000
--- a/test/jalview/util/UrlLinkTest.java
+++ /dev/null
@@ -1,464 +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.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);
-  }
-}