X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FUrlLinkTest.java;fp=test%2Fjalview%2Futil%2FUrlLinkTest.java;h=f219fb86bc5f96b691b058e0c4992b0d2ad189ff;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=0000000000000000000000000000000000000000;hpb=02e38bb826828ab2991584cf4b737c0138cb6c44;p=jalview.git

diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
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+/*
+ * 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 java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+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_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.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    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.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    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.getUrl_prefix());
+    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.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    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.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    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.getUrl_prefix());
+    assertEquals(URL_SUFFIX, ul.getUrl_suffix());
+    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<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);
+    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);
+    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_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<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);
+    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 + DB_ACCESSION + DELIM
+            + URL_SUFFIX);
+    linkset = new LinkedHashMap<String, List<String>>();
+    ul.createLinksFromSeq(seq0, linkset);
+    assertTrue(linkset.isEmpty());
+  }
+
+}