Merge branch 'develop' into bug/JAL-1608createGroups

[jalview.git] / test / jalview / urls / DesktopUrlProviderFactoryTest.java

diff --git a/test/jalview/urls/DesktopUrlProviderFactoryTest.java b/test/jalview/urls/DesktopUrlProviderFactoryTest.java
new file mode 100644 (file)
index 0000000..cc55034
--- /dev/null
+++ b/test/jalview/urls/DesktopUrlProviderFactoryTest.java
@@ -0,0 +1,109 @@
+/*
+ * 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.urls;
+
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class DesktopUrlProviderFactoryTest
+{
+  private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
+          + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
+          + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
+          + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
+          + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
+          + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
+          + "\"url\":\"http://identifiers.org/interpro\"},"
+          + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+          + "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
+
+  @BeforeMethod(alwaysRun = true)
+  public void setup()
+  {
+    // make a dummy identifiers.org download file
+    File temp = null;
+
+    try
+    {
+      temp = File.createTempFile("tempfile", ".tmp");
+      temp.deleteOnExit();
+      BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
+      bw.write(testIdOrgString);
+      bw.close();
+    } catch (IOException e)
+    {
+      System.out
+              .println("Error initialising DesktopUrlProviderFactoryTest test: "
+                      + e.getMessage());
+    }
+
+    IdOrgSettings.setDownloadLocation(temp.getPath());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCreateUrlProvider()
+  {
+    String defaultUrlString = "Test1";
+    String defaultUrl = "http://blah.blah/$SEQUENCE_ID$";
+    String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
+            + "Test2|http://test2/$DB_ACCESSION$|Test3|http://test3/$SEQUENCE_ID$";
+    String userUrlList = "MIR:00000372|Test4|httpL//another.url/$SEQUENCE_ID$";
+
+    DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
+            defaultUrlString, cachedUrlList, userUrlList);
+    UrlProviderI prov = factory.createUrlProvider();
+
+    // default url correctly set
+    Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
+    Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
+            defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
+
+    List<String> menulinks = prov.getLinksForMenu();
+    List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
+
+    // 8 links in provider - 4 from id file, 4 custom links
+    Assert.assertEquals(allLinks.size(), 8);
+
+    // 5 links in menu (cachedUrlList)
+    Assert.assertEquals(menulinks.size(), 5);
+
+    Assert.assertTrue(menulinks
+            .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
+    Assert.assertTrue(menulinks
+            .contains("Test2|http://test2/$DB_ACCESSION$"));
+    Assert.assertTrue(menulinks
+            .contains("Test3|http://test3/$SEQUENCE_ID$"));
+    Assert.assertTrue(menulinks
+            .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
+    Assert.assertTrue(menulinks
+            .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
+  }
+}