Unit tests for UrlLink

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index f9dda09..872f432 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -86,6 +86,7 @@ public class UrlLink
     label = label.trim();
     target = target.trim();
     target = target.toUpperCase(); // DBRefEntry uppercases DB names
+    // NB getCanonicalName might be better but does not currently change case
   }
 
   /**
@@ -261,13 +262,14 @@ public class UrlLink
   @Override
   public String toString()
   {
+    String var = (uses_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+
     return label
             + "|"
             + url_prefix
-            + (dynamic ? ("$" + SEQUENCE_ID + ((regexReplace != null) ? "="
+            + (dynamic ? ("$" + var + ((regexReplace != null) ? "="
                     + regexReplace + "=$" : "$")) : "")
             + ((url_suffix == null) ? "" : url_suffix);
-
   }
 
   /**

diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
new file mode 100644 (file)
index 0000000..45ef6af
--- /dev/null
+++ b/test/jalview/util/UrlLinkTest.java
@@ -0,0 +1,246 @@
+/*
+ * 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.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;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.Test;
+
+public class UrlLinkTest
+{
+
+  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_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+            + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    assertNull(ul.getRegexReplace());
+    assertTrue(ul.isValid());
+    assertNull(ul.getInvalidMessage());
+
+    // SEQUENCE_ID
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+            + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    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.getLabel());
+    assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
+    assertFalse(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    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_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+            + REGEX_NESTED + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertFalse(ul.usesSeqId());
+    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
+            + REGEX_NESTED + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    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
+            + REGEX_RUBBISH + DELIM + URL_SUFFIX);
+    assertEquals(DB.toUpperCase(), ul.getTarget());
+    assertEquals(DB, ul.getLabel());
+    assertEquals(URL_PREFIX, ul.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    assertTrue(ul.isDynamic());
+    assertTrue(ul.usesSeqId());
+    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_NAME
+            + 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
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeUrlWithRegex()
+  {
+    // Unused regex
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+            + 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());
+  }
+
+}