JAL-2282 URLLink unit tests updated

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index e14ff63..218da6c 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -83,7 +83,7 @@ public class UrlLink
       target = link.substring(0, sep);
       sep = link.lastIndexOf("|");
       label = link.substring(0, sep);
-      url_prefix = link.substring(sep + 1);
+      url_prefix = link.substring(sep + 1).trim();
       regexReplace = null; // implies we trim any prefix if necessary //
       // regexReplace=".*\\|?(.*)";
       url_suffix = null;
@@ -331,7 +331,7 @@ public class UrlLink
    */
   protected void parseUrl(String link, String varName, int sqidPos, int sep)
   {
-    url_prefix = link.substring(sep + 1, sqidPos);
+    url_prefix = link.substring(sep + 1, sqidPos).trim();
 
     // delimiter at start of regex: e.g. $SEQUENCE_ID=/
     String startDelimiter = "$" + varName + "=/";
@@ -384,10 +384,12 @@ public class UrlLink
   }
 
   /**
+   * Create a set of URL links for a sequence
    * 
-   * @param urlLink
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
   public void createLinksFromSeq(final SequenceI seq,
           Map<String, List<String>> linkset)
@@ -406,8 +408,9 @@ public class UrlLink
    * Create a static URL link
    * 
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
-  public void createStaticLink(Map<String, List<String>> linkset)
+  protected void createStaticLink(Map<String, List<String>> linkset)
   {
     if (!linkset.containsKey(label + "|" + getUrl_prefix()))
     {
@@ -418,12 +421,14 @@ public class UrlLink
   }
 
   /**
-   * Create a dynamic URL link
+   * Create dynamic URL links
    * 
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
-  public void createDynamicLinks(final SequenceI seq,
+  protected void createDynamicLinks(final SequenceI seq,
           Map<String, List<String>> linkset)
   {
     // collect id string too
@@ -446,14 +451,14 @@ public class UrlLink
         for (int r = 0; r < dbr.length; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), linkset, true);
+          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
         }
       }
     }
     else if (!usesSeqId() && id != null) // link is name
     {
       // create Bare ID link for this URL
-      createBareURLLink(id, linkset, false);
+      createBareURLLink(id, false, linkset);
     }
 
     // Create urls from description but only for URL links which are regex
@@ -461,15 +466,16 @@ public class UrlLink
     if (descr != null && getRegexReplace() != null)
     {
       // create link for this URL from description where regex matches
-      createBareURLLink(descr, linkset, false);
+      createBareURLLink(descr, false, linkset);
     }
   }
 
   /*
    * Create a bare URL Link
+   * Returns map where key = id | link, and value = [target, label, id, link]
    */
-  protected void createBareURLLink(String id,
-          Map<String, List<String>> linkset, Boolean combineLabel)
+  protected void createBareURLLink(String id, Boolean combineLabel,
+          Map<String, List<String>> linkset)
   {
     String[] urls = makeUrls(id, true);
     if (urls != null)
@@ -481,6 +487,7 @@ public class UrlLink
           String thisLabel = label;
           if (combineLabel)
           {
+            // incorporate label with idstring
             thisLabel = label + "|" + urls[u];
           }
 

diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
index 45ef6af..875dd7f 100644 (file)
--- a/test/jalview/util/UrlLinkTest.java
+++ b/test/jalview/util/UrlLinkTest.java
@@ -27,6 +27,15 @@ 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 java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
 import org.testng.annotations.Test;
 
 public class UrlLinkTest
@@ -167,7 +176,8 @@ public class UrlLinkTest
   }
 
   /**
-   * Test construction of link by substituting sequence id or name
+   * Test construction of link by substituting sequence id or name using regular
+   * expression
    */
   @Test(groups = { "Functional" })
   public void testMakeUrlWithRegex()
@@ -243,4 +253,150 @@ public class UrlLinkTest
     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_NAME
+            + DELIM + URL_SUFFIX);
+
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    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);
+  }
+
+  /**
+   * 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<String, List<String>>();
+    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);
+  }
+
+  /**
+   * Test creating links
+   */
+  @Test(groups = { "Functional" })
+  public void testCreateLinksFromSequence()
+  {
+
+    // create list of links and list of DBRefs
+    List<String> links = new ArrayList<String>();
+    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+    // 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/$" + SEQUENCE_ID
+            + "$");
+    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+            + SEQUENCE_ID + "$");
+
+    // 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_NAME
+            + DELIM + URL_SUFFIX);
+
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    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);
+
+    // 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>>();
+    ul.createLinksFromSeq(seq0, linkset);
+
+    key = "P83527|http://www.uniprot.org/uniprot/P83527";
+    assertEquals(1, linkset.size());
+    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");
+
+    // Test where link takes a db annotation id and has multiple dbrefs
+    ul = new UrlLink(links.get(2));
+    linkset = new LinkedHashMap<String, List<String>>();
+    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");
+
+    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");
+
+    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");
+
+    // Test where there are no matching dbrefs for the link
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+            + URL_SUFFIX);
+    linkset = new LinkedHashMap<String, List<String>>();
+    ul.createLinksFromSeq(seq0, linkset);
+    assertTrue(linkset.isEmpty());
+  }
+
 }