package jalview.io;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
+import jalview.json.binding.v1.BioJSReleasePojo;
+import jalview.json.binding.v1.BioJSRepositoryPojo;
+import java.io.File;
import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.TreeMap;
+import org.junit.Assert;
import org.junit.Test;
-import com.json.JSONException;
public class BioJsHTMLOutputTest
{
-
@Test
public void getJalviewAlignmentAsJsonString()
{
- BioJsHTMLOutput bioJsHtmlOuput = new BioJsHTMLOutput(null, null);
- bioJsHtmlOuput.setGlobalColorScheme("Zappo");
-
- Sequence[] seqs = new Sequence[1];
- Sequence seq = new Sequence("name", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
- // SequenceFeature seqFeature = new SequenceFeature("type", "desc",
- // "status", 1, 5, "jalview");
- // seq.addSequenceFeature(seqFeature);
- seq.setDatasetSequence(seq);
- seqs[0] = seq;
-
- Alignment al = new Alignment(seqs);
+ String bjsTemplate = null;
try
{
- String generatedJson = bioJsHtmlOuput
- .getJalviewAlignmentAsJsonString(al);
- org.junit.Assert
- .assertEquals(
- generatedJson.toLowerCase(),
- "{\"globalColorScheme\":\"zappo\",\"seqs\":[{\"id\":\"1\",\"start\":1,\"name\":\"name/1-26\",\"features\":[],\"seq\":\"ABCDEFGHIJKLMNOPQRSTUVWXYZ\",\"end\":26}]}"
- .toLowerCase());
- System.out.println("Output : " + generatedJson);
+ BioJsHTMLOutput.updateBioJS();
+ try
+ {
+ // allow the update some three seconds to complete before getting latest
+ // version of BioJS template
+ Thread.sleep(1000 * 3);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ bjsTemplate = BioJsHTMLOutput.getBioJsTemplateAsString();
+ // System.out.println(bjsTemplate);
} catch (IOException e)
{
e.printStackTrace();
- } catch (JSONException e)
+ }
+ Assert.assertNotNull(bjsTemplate);
+ }
+
+ @Test(expected = NullPointerException.class)
+ public void expectedNullPointerException()
+ {
+ try
+ {
+ BioJsHTMLOutput.refreshBioJSVersionsInfo(null);
+ } catch (URISyntaxException e)
{
+ Assert.fail("Expception occured while testing!");
e.printStackTrace();
}
}
+ @Test
+ public void getBioJsMSAVersions()
+ {
+ TreeMap<String, File> versions = null;
+ try
+ {
+ BioJsHTMLOutput
+ .refreshBioJSVersionsInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ versions = BioJsHTMLOutput.getBioJsMSAVersions();
+ } catch (URISyntaxException e)
+ {
+ Assert.fail("Expception occured while testing!");
+ e.printStackTrace();
+ }
+ Assert.assertNotNull("No versions found", versions);
+ Assert.assertTrue("One or more Templates required", versions.size() > 0);
+ System.out
+ .println("Number of discovered versions : "
+ + versions.size());
+ for (String v : versions.keySet())
+ {
+ System.out.println("version : " + v);
+ System.out.println("File : " + versions.get(v));
+ }
+
+ System.out.println("\nCurrent latest version : "
+ + BioJsHTMLOutput.getCurrentBJSTemplateFile());
+ Assert.assertNotNull("Latest BioJsMSA version NOT found!",
+ BioJsHTMLOutput.getCurrentBJSTemplateFile());
+
+ }
+
+ @Test
+ public void testBioJsUpdate()
+ {
+ String url = BioJsHTMLOutput.BJS_TEMPLATE_GIT_REPO;
+ Assert.assertTrue("URL not reacable : " + url, urlIsReachable(url));
+ String response = BioJsHTMLOutput.getURLContentAsString(url);
+ Assert.assertNotNull("Null response read from url!", response);
+ BioJSRepositoryPojo repository = new BioJSRepositoryPojo(response);
+ System.out.println(">>> description : " + repository.getDescription());
+ System.out
+.println(">>> latest version : "
+ + repository.getLatestReleaseVersion());
+ System.out.println(">>> repo count : "
+ + repository.getReleases().size());
+ for (BioJSReleasePojo release : repository.getReleases())
+ {
+ System.out.println("repo type : " + release.getType());
+ System.out.println("url : " + release.getUrl());
+ System.out.println("release version : " + release.getVersion());
+ }
+ }
+
+ private static boolean urlIsReachable(String urlString)
+ {
+ try
+ {
+ final URL url = new URL(urlString);
+ final URLConnection conn = url.openConnection();
+ conn.connect();
+ return true;
+ } catch (MalformedURLException e)
+ {
+ throw new RuntimeException(e);
+ } catch (IOException e)
+ {
+ return false;
+ }
+ }
}