+/*
+ * 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.jws2;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.WrongParameterException;
+
+import jalview.bin.Cache;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+public class ParameterUtilsTest
+{
+ /*
+ * To limit tests to specify services, add them to this list; leave list empty
+ * to test all
+ */
+ private static List<String> serviceTests = new ArrayList<String>();
+
+ private static Jws2Discoverer disc = null;
+
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ serviceTests.add("AAConWS".toLowerCase());
+ Cache.initLogger();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+ }
+
+ @Test
+ public void testWriteParameterSet() throws WrongParameterException
+ {
+ for (Jws2Instance service : disc.getServices())
+ {
+ if (isForTesting(service))
+ {
+
+ List<Preset> prl = null;
+ PresetManager prman = service.getPresets();
+ if (prman == null)
+ {
+ continue;
+ }
+ prl = prman.getPresets();
+ if (prl == null)
+ {
+ continue;
+ }
+ for (Preset pr : prl)
+ {
+ List<String> writeparam = null;
+ List<String> readparam = null;
+ writeparam = ParameterUtils.writeParameterSet(
+ pr.getArguments(service.getRunnerConfig()), " ");
+ List<Option> pset = ParameterUtils.processParameters(writeparam,
+ service.getRunnerConfig(), " ");
+ readparam = ParameterUtils.writeParameterSet(pset, " ");
+ Iterator<String> o = pr.getOptions().iterator();
+ Iterator<String> s = writeparam.iterator();
+ Iterator<String> t = readparam.iterator();
+ boolean failed = false;
+ while (s.hasNext() && t.hasNext())
+ {
+ String on = o.next();
+ String sn = s.next();
+ String st = t.next();
+ final String errorMsg = "Original was " + on + " Phase 1 wrote " + sn
+ + "\tPhase 2 wrote " + st;
+ assertEquals(errorMsg, sn, st);
+ assertEquals(errorMsg, sn, on);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns true if the service is in the list of the ones we chose to test,
+ * _or_ the list is empty (test all)
+ *
+ * @param service
+ * @return
+ */
+ public boolean isForTesting(Jws2Instance service)
+ {
+ return serviceTests.size() == 0
+ || serviceTests.contains(service.serviceType.toLowerCase());
+ }
+
+ @Test
+ public void testCopyOption()
+ {
+ for (Jws2Instance service : disc.getServices())
+ {
+ if (isForTesting(service))
+ {
+ List<Option<?>> options = service.getRunnerConfig().getOptions();
+ for (Option<?> o : options)
+ {
+ System.out.println("Testing copyOption for option " + o.getName()
+ + " of " + service.getActionText());
+ Option<?> cpy = ParameterUtils.copyOption(o);
+ assertTrue(cpy.equals(o));
+ assertEquals(cpy.getName(), o.getName());
+ assertFalse(cpy == o);
+ // todo more assertions?
+ }
+ }
+ }
+ }
+
+ /**
+ */
+ @Test
+ public void testCopyParameter()
+ {
+ for (Jws2Instance service : disc.getServices())
+ {
+ if (isForTesting(service))
+ {
+ List<Parameter> parameters = service.getRunnerConfig()
+ .getParameters();
+ for (Parameter o : parameters)
+ {
+ System.out.println("Testing copyParameter for parameter "
+ + o.getName() + " of " + service.getActionText());
+ Parameter cpy = ParameterUtils.copyParameter(o);
+ assertTrue(cpy.equals(o));
+ assertFalse(cpy == o);
+ assertEquals(cpy.getName(), o.getName());
+ // todo more assertions?
+ }
+ }
+ }
+ }
+}