Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/test/jalview/urls/UrlProviderTest.java b/test/jalview/urls/UrlProviderTest.java
new file mode 100644 (file)
index 0000000..460ebe9
--- /dev/null
+++ b/test/jalview/urls/UrlProviderTest.java
@@ -0,0 +1,120 @@
+package jalview.urls;
+
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.UrlConstants;
+
+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 UrlProviderTest {
+  
+  // Test identifiers.org download file
+  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\"}]}";
+
+  private UrlProviderI prov;
+
+  @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 UrlProviderTest test: "
+              + e.getMessage());
+   }
+
+   IdOrgSettings.setDownloadLocation(temp.getPath());
+
+    String defaultUrlString = "No default";
+    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);
+    prov = factory.createUrlProvider();
+ }
+
+  @Test(groups = { "Functional" })
+  public void testInitUrlProvider()
+  {
+    String emblUrl = UrlConstants.DEFAULT_STRING.substring(
+            UrlConstants.DEFAULT_STRING.indexOf(UrlConstants.SEP) + 1,
+            UrlConstants.DEFAULT_STRING.length());
+
+    // chooses EMBL url when default Url id does not exist in provided url lists
+    Assert.assertEquals(prov.getPrimaryUrlId(), UrlConstants.DEFAULT_LABEL);
+    Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
+            emblUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
+
+    List<String> menulinks = prov.getLinksForMenu();
+    List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
+
+    // 9 links in provider - 4 from id file, 4 custom links, 1 additional
+    // default
+    Assert.assertEquals(allLinks.size(), 9);
+
+    // 6 links in menu (cachedUrlList) + new default
+    Assert.assertEquals(menulinks.size(), 6);
+
+    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"));
+    Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
+            + UrlConstants.SEP + emblUrl));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetDefaultUrl()
+  {
+    // set custom url as default
+    Assert.assertTrue(prov.setPrimaryUrl("Test1"));
+    Assert.assertEquals(prov.getPrimaryUrlId(), "Test1");
+
+    // set identifiers url as default
+    Assert.assertTrue(prov.setPrimaryUrl("MIR:00000011"));
+    Assert.assertEquals(prov.getPrimaryUrlId(), "MIR:00000011");
+  }
+
+  @Test(
+    groups = { "Functional" },
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDefaultUrlWrongly()
+  {
+    // don't allow default to be a non-key
+    prov.setPrimaryUrl("not-a-key");
+  }
+}