+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.io;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
+import java.io.File;
import java.io.IOException;
-import java.util.Iterator;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.TreeMap;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-import org.json.simple.parser.ParseException;
-import org.junit.Assert;
-import org.junit.Test;
-
-import com.json.JSONException;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
public class BioJsHTMLOutputTest
{
-
- @Test
+ @Test(groups = { "Functional" })
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
{
+ 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();
+ }
+ Assert.assertNotNull(bjsTemplate);
+ }
- JSONParser jsonParser = new JSONParser();
- String actualJsonString = bioJsHtmlOuput
- .getJalviewAlignmentAsJsonString(al);
-
- JSONObject actualJsonObj = (JSONObject) jsonParser.parse(actualJsonString);
-
- System.out.println("Output : " + actualJsonString);
- Assert.assertTrue(actualJsonObj.get("globalColorScheme") != null);
- Assert.assertTrue((actualJsonObj.get("globalColorScheme").toString()).equals("zappo"));
-
- Assert.assertTrue(actualJsonObj.get("webStartUrl") != null);
- Assert.assertTrue((actualJsonObj.get("webStartUrl").toString())
- .equals("http://www.jalview.org/services/launchApp"));
-
- JSONArray actualSeqJsonObj = (JSONArray) actualJsonObj.get("seqs");
- Assert.assertTrue(actualSeqJsonObj != null);
- Assert.assertTrue(actualSeqJsonObj.size() == 1);
-
- @SuppressWarnings("unchecked")
- Iterator<JSONObject> jsonIter = actualSeqJsonObj.iterator();
- JSONObject jsonSeq = jsonIter.next();
- Assert.assertTrue(jsonSeq != null);
-
- Assert.assertTrue(jsonSeq.get("name") != null);
- Assert.assertTrue((jsonSeq.get("name").toString())
- .equals("name/1-26"));
-
- Assert.assertTrue(jsonSeq.get("seq") != null);
- Assert.assertTrue((jsonSeq.get("seq").toString())
- .equals("ABCDEFGHIJKLMNOPQRSTUVWXYZ"));
-
- Assert.assertTrue(jsonSeq.get("id") != null);
- Assert.assertTrue((jsonSeq.get("id").toString()).equals("1"));
+ @Test(
+ groups = { "Functional" },
+ expectedExceptions = NullPointerException.class)
+ public void expectedNullPointerException()
+ {
+ try
+ {
+ BioJsHTMLOutput.refreshBioJSVersionsInfo(null);
+ } catch (URISyntaxException e)
+ {
+ AssertJUnit.fail("Expception occured while testing!");
+ e.printStackTrace();
+ }
+ }
- Assert.assertTrue(jsonSeq.get("start") != null);
- Assert.assertTrue((jsonSeq.get("start").toString()).equals("1"));
+ @Test(groups = { "Functional" })
+ public void getBioJsMSAVersions()
+ {
+ TreeMap<String, File> versions = null;
+ try
+ {
+ BioJsHTMLOutput
+ .refreshBioJSVersionsInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ versions = BioJsHTMLOutput.getBioJsMSAVersions();
+ } catch (URISyntaxException e)
+ {
+ AssertJUnit.fail("Expception occured while testing!");
+ e.printStackTrace();
+ }
+ AssertJUnit.assertNotNull("No versions found", versions);
+ AssertJUnit.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));
+ }
- Assert.assertTrue(jsonSeq.get("end") != null);
- Assert.assertTrue((jsonSeq.get("end").toString()).equals("26"));
+ System.out.println("\nCurrent latest version : "
+ + BioJsHTMLOutput.getCurrentBJSTemplateFile());
+ AssertJUnit.assertNotNull("Latest BioJsMSA version NOT found!",
+ BioJsHTMLOutput.getCurrentBJSTemplateFile());
- Assert.assertTrue(jsonSeq.get("features") != null);
- Assert.assertTrue(jsonSeq.get("features").toString().equals("[]"));
+ }
+ @Test(groups = { "Network" })
+ public void testBioJsUpdate()
+ {
+ String url = BioJsHTMLOutput.BJS_TEMPLATE_GIT_REPO;
+ AssertJUnit
+ .assertTrue("URL not reacable : " + url, urlIsReachable(url));
+ String response = BioJsHTMLOutput.getURLContentAsString(url);
+ AssertJUnit.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());
+ }
+ }
- } catch (IOException e)
+ private static boolean urlIsReachable(String urlString)
+ {
+ try
{
- e.printStackTrace();
- } catch (JSONException e)
+ final URL url = new URL(urlString);
+ final URLConnection conn = url.openConnection();
+ conn.connect();
+ return true;
+ } catch (MalformedURLException e)
{
- e.printStackTrace();
- } catch (ParseException e)
+ throw new RuntimeException(e);
+ } catch (IOException e)
{
- e.printStackTrace();
+ return false;
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff