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Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet
[jalview.git] / test / jalview / util / UrlLinkTest.java
diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
index 875dd7f..c7d37b0 100644 (file)
--- a/test/jalview/util/UrlLinkTest.java
+++ b/test/jalview/util/UrlLinkTest.java
@@ -20,8 +20,8 @@
  */
 package jalview.util;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
@@ -30,17 +30,27 @@ 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/";
@@ -61,39 +71,39 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testUrlLinkCreationNoRegex()
   {
-    // SEQUENCE_NAME
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    // SEQUENCE_ID
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
-    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX, ul.getUrl_prefix());
-    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertEquals(URL_PREFIX, ul.getUrlPrefix());
+    assertEquals(URL_SUFFIX, ul.getUrlSuffix());
     assertTrue(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertNull(ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
 
-    // SEQUENCE_ID
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+    // DB_ACCESSION
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
             + URL_SUFFIX);
-    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX, ul.getUrl_prefix());
-    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertEquals(URL_PREFIX, ul.getUrlPrefix());
+    assertEquals(URL_SUFFIX, ul.getUrlSuffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    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.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
+    assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrlPrefix());
     assertFalse(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertNull(ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
@@ -105,43 +115,43 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testUrlLinkCreationWithRegex()
   {
-    // SEQUENCE_NAME
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    // SEQUENCE_ID
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + REGEX_NESTED + DELIM + URL_SUFFIX);
-    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX, ul.getUrl_prefix());
-    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertEquals(URL_PREFIX, ul.getUrlPrefix());
+    assertEquals(URL_SUFFIX, ul.getUrlSuffix());
     assertTrue(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
             ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
 
-    // SEQUENCE_ID
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+    // DB_ACCESSION
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
             + REGEX_NESTED + DELIM + URL_SUFFIX);
-    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX, ul.getUrl_prefix());
-    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertEquals(URL_PREFIX, ul.getUrlPrefix());
+    assertEquals(URL_SUFFIX, ul.getUrlSuffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    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 + SEQUENCE_ID
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
             + REGEX_RUBBISH + DELIM + URL_SUFFIX);
-    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getTarget());
     assertEquals(DB, ul.getLabel());
-    assertEquals(URL_PREFIX, ul.getUrl_prefix());
-    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertEquals(URL_PREFIX, ul.getUrlPrefix());
+    assertEquals(URL_SUFFIX, ul.getUrlSuffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    assertTrue(ul.usesDBAccession());
     assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
             ul.getRegexReplace());
     assertFalse(ul.isValid());
@@ -159,7 +169,7 @@ public class UrlLinkTest
   public void testMakeUrlNoRegex()
   {
     // Single non-regex
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
     String idstring = "FER_CAPAA";
     String[] urls = ul.makeUrls(idstring, true);
@@ -183,7 +193,7 @@ public class UrlLinkTest
   public void testMakeUrlWithRegex()
   {
     // Unused regex
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+    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);
@@ -259,19 +269,19 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testCreateLinksFromNullSequence()
   {
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
 
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    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(linkset.get(key).get(0), DB.toUpperCase());
-    assertEquals(linkset.get(key).get(1), DB);
-    assertEquals(linkset.get(key).get(2), null);
-    assertEquals(linkset.get(key).get(3), URL_PREFIX);
+    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));
   }
 
   /**
@@ -282,16 +292,16 @@ public class UrlLinkTest
   {
     UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
 
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    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(linkset.get(key).get(0), DB.toUpperCase());
-    assertEquals(linkset.get(key).get(1), DB);
-    assertEquals(linkset.get(key).get(2), null);
-    assertEquals(linkset.get(key).get(3), URL_PREFIX + URL_SUFFIX);
+    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));
   }
 
   /**
@@ -302,16 +312,16 @@ public class UrlLinkTest
   {
 
     // create list of links and list of DBRefs
-    List<String> links = new ArrayList<String>();
-    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+    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=$"
-            + SEQUENCE_NAME + "$");
-    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + SEQUENCE_ID
+            + SEQUENCE_ID + "$");
+    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
             + "$");
     links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
-            + SEQUENCE_ID + "$");
+            + DB_ACCESSION + "$");
 
     // make seq0 dbrefs
     refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
@@ -329,74 +339,126 @@ public class UrlLinkTest
     seq0.createDatasetSequence();
 
     // Test where link takes a sequence id as replacement
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
 
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    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(linkset.get(key).get(0), DB.toUpperCase());
-    assertEquals(linkset.get(key).get(1), DB);
-    assertEquals(linkset.get(key).get(2), seq0.getName());
-    assertEquals(linkset.get(key).get(3), URL_PREFIX + seq0.getName()
-            + URL_SUFFIX);
+    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<String, List<String>>();
+    linkset = new LinkedHashMap<>();
     ul.createLinksFromSeq(seq0, linkset);
 
     key = "P83527|http://www.uniprot.org/uniprot/P83527";
-    assertEquals(1, linkset.size());
+    assertEquals(linkset.size(), 1);
     assertTrue(linkset.containsKey(key));
-    assertEquals(linkset.get(key).get(0), DBRefSource.UNIPROT);
-    assertEquals(linkset.get(key).get(1), DBRefSource.UNIPROT + SEP
-            + "P83527");
-    assertEquals(linkset.get(key).get(2), "P83527");
-    assertEquals(linkset.get(key).get(3),
-            "http://www.uniprot.org/uniprot/P83527");
+    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<String, List<String>>();
+    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(linkset.get(key).get(0), "INTERPRO");
-    assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR001041");
-    assertEquals(linkset.get(key).get(2), "IPR001041");
-    assertEquals(linkset.get(key).get(3),
-            "http://www.ebi.ac.uk/interpro/entry/IPR001041");
+    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(linkset.get(key).get(0), "INTERPRO");
-    assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR006058");
-    assertEquals(linkset.get(key).get(2), "IPR006058");
-    assertEquals(linkset.get(key).get(3),
-            "http://www.ebi.ac.uk/interpro/entry/IPR006058");
+    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(linkset.get(key).get(0), "INTERPRO");
-    assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR012675");
-    assertEquals(linkset.get(key).get(2), "IPR012675");
-    assertEquals(linkset.get(key).get(3),
-            "http://www.ebi.ac.uk/interpro/entry/IPR012675");
+    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 + SEQUENCE_ID + DELIM
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
             + URL_SUFFIX);
-    linkset = new LinkedHashMap<String, List<String>>();
+    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);
+  }
 }