--- /dev/null
+/*
+ * 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.ws.jabaws;
+
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
+public class AAConAnnotAndSettingsIO
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ public static String testseqs = "examples/uniref50.fa";
+
+ public static Jws2Discoverer disc;
+
+ public static List<ServiceWithParameters[]> aacon;
+
+ jalview.ws.jws2.SeqAnnotationServiceCalcWorker aaconClient;
+
+ public static jalview.gui.AlignFrame af = null;
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.initLogger();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
+
+
+ aacon = new ArrayList<>();
+ for (ServiceWithParameters svc : disc.getServices())
+ {
+ if (svc.getNameURI().toLowerCase().contains("aacon"))
+ {
+ aacon.add(new ServiceWithParameters[] { svc });
+ }
+ }
+
+ for (ServiceWithParameters svc : SlivkaWSDiscoverer.getServices())
+ {
+ if (svc.getNameURI().toLowerCase().contains("aacon"))
+ {
+ aacon.add(new ServiceWithParameters[] { svc });
+ }
+ }
+ assertTrue("Couldn't discover any AACon services to use to test.",
+ aacon.size() > 0);
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ if (af != null)
+ {
+ af.setVisible(false);
+ af.dispose();
+ af = null;
+ }
+ }
+
+ @DataProvider(name = "aacons")
+ public Object[][] getAaconArray()
+ {
+
+ Object[][] rtn = new Object[aacon.size()][1];
+ int i = 0;
+ for (ServiceWithParameters[] aa : aacon)
+ {
+ rtn[i++] = aa;
+ }
+ return rtn;
+ }
+ /**
+ * Run AACon on an alignment with defaults and verify Just Shenkin annotation
+ * appears
+ */
+ @Test(groups = { "External", "Network" }, dataProvider = "aacons")
+ public void testAAConAnnotAndRecovery(ServiceWithParameters service)
+ {
+ jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+ AlignFrame _af = fl.LoadFileWaitTillLoaded(testseqs,
+ jalview.io.DataSourceType.FILE);
+ assertNotNull("Couldn't load test data ('" + testseqs + "')", _af);
+ af = _af;
+ try
+ {
+ testAAConClient(_af, service);
+ } finally
+ {
+ af = null;
+ _af.setVisible(false);
+ _af.dispose();
+ _af = null;
+
+ }
+ }
+
+ /**
+ * triggers the given aacon worker on the alignment, waits for 5s and gives up
+ * or verifies SHENKIN annotation is produced.
+ *
+ * @param af
+ * - test data in an alignment frame
+ * @param aacon
+ * - the service to test
+ */
+ static void testAAConClient(AlignFrame af, ServiceWithParameters aacon)
+ {
+ SeqAnnotationServiceCalcWorker aaconClient = new SeqAnnotationServiceCalcWorker(
+ aacon, af, null,
+ null);
+ long current = System.currentTimeMillis(), limit = 15;
+ af.getViewport().getCalcManager().startWorker(aaconClient);
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
+ assertTrue(
+ "Waited " + limit + "s for " + aacon.getHostURL()
+ + " - giving up.",
+ (System.currentTimeMillis() - current) < limit * 1000);
+ } while (af.getViewport().getCalcManager().isWorking());
+ AlignmentI orig_alig = af.getViewport().getAlignment();
+ boolean foundShenkin = false;
+ Iterable<AlignmentAnnotation> _aa=orig_alig
+ .findAnnotation(aacon.getAlignAnalysisUI().getCalcId());
+ assertTrue("No annotation from service",
+ _aa != null && _aa.iterator().hasNext());
+
+ for (AlignmentAnnotation aa : _aa)
+ {
+ assertTrue("AACon annotation not marked as autocalculated!",
+ aa.autoCalculated);
+ if ("shenkin".equals(aa.label.toLowerCase()))
+ {
+ foundShenkin = true;
+ break;
+ }
+ }
+ assertTrue("Failed to locate 'SHENKIN' annotation row.", foundShenkin);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff