2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.jabaws;
23 import java.util.Locale;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.bin.Cache;
28 import jalview.bin.Console;
29 import jalview.datamodel.AlignmentAnnotation;
30 import jalview.datamodel.AlignmentI;
31 import jalview.gui.JvOptionPane;
32 import jalview.io.AnnotationFile;
33 import jalview.io.DataSourceType;
34 import jalview.io.FileFormat;
35 import jalview.io.FormatAdapter;
36 import jalview.io.StockholmFileTest;
37 import jalview.project.Jalview2XML;
38 import jalview.ws.api.ServiceWithParameters;
39 import jalview.ws.jws2.JabaParamStore;
40 import jalview.ws.jws2.Jws2Discoverer;
41 import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
42 import jalview.ws.jws2.SequenceAnnotationWSClient;
43 import jalview.ws.jws2.jabaws2.Jws2Instance;
44 import jalview.ws.params.AutoCalcSetting;
46 import java.awt.Component;
48 import java.util.ArrayList;
49 import java.util.List;
51 import javax.swing.JMenu;
52 import javax.swing.JMenuItem;
54 import org.testng.Assert;
55 import org.testng.annotations.AfterClass;
56 import org.testng.annotations.BeforeClass;
57 import org.testng.annotations.Test;
59 import compbio.metadata.Argument;
60 import compbio.metadata.WrongParameterException;
63 * All methods in this class are set to the Network group because setUpBeforeClass will fail
64 * if there is no network.
66 @Test(singleThreaded = true)
67 public class RNAStructExportImport
70 @BeforeClass(alwaysRun = true)
71 public void setUpJvOptionPane()
73 JvOptionPane.setInteractiveMode(false);
74 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
77 private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
79 public static String testseqs = "examples/RF00031_folded.stk";
81 public static Jws2Discoverer disc;
83 public static Jws2Instance rnaalifoldws;
85 SeqAnnotationServiceCalcWorker alifoldClient;
87 public static jalview.gui.AlignFrame af = null;
89 @BeforeClass(alwaysRun = true)
90 public static void setUpBeforeClass() throws Exception
92 Cache.loadProperties("test/jalview/io/testProps.jvprops");
94 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
96 while (disc.isRunning())
98 // don't get services until discoverer has finished
102 for (ServiceWithParameters svc : disc.getServices())
105 if (svc.getServiceType().toLowerCase(Locale.ROOT)
106 .contains("rnaalifoldws"))
108 rnaalifoldws = (Jws2Instance) svc;
112 System.out.println("State of rnaalifoldws: " + rnaalifoldws);
114 if (rnaalifoldws == null)
116 Assert.fail("no web service");
119 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
121 af = fl.LoadFileWaitTillLoaded(testseqs,
122 jalview.io.DataSourceType.FILE);
124 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
126 // remove any existing annotation
127 List<AlignmentAnnotation> aal = new ArrayList<>();
128 for (AlignmentAnnotation rna : af.getViewport().getAlignment()
129 .getAlignmentAnnotation())
136 for (AlignmentAnnotation rna : aal)
138 af.getViewport().getAlignment().deleteAnnotation(rna);
140 af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
144 @AfterClass(alwaysRun = true)
145 public static void tearDownAfterClass() throws Exception
149 af.setVisible(false);
151 File f = new File(JAR_FILE_NAME);
159 @Test(groups = { "Network" })
160 public void testRNAAliFoldValidStructure()
163 alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
166 af.getViewport().getCalcManager().startWorker(alifoldClient);
173 } catch (InterruptedException x)
176 } while (af.getViewport().getCalcManager().isWorking());
178 AlignmentI orig_alig = af.getViewport().getAlignment();
179 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
181 if (alifoldClient.involves(aa))
186 "Did not create valid structure from RNAALiFold prediction",
193 @Test(groups = { "Network" })
194 public void testRNAStructExport()
197 alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
200 af.getViewport().getCalcManager().startWorker(alifoldClient);
207 } catch (InterruptedException x)
210 } while (af.getViewport().getCalcManager().isWorking());
212 AlignmentI orig_alig = af.getViewport().getAlignment();
213 // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
214 // annotation is mistakenly recognised as an RNA annotation row when read in
215 // as an annotation file. bug is JAL-3122
216 verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
220 static void verifyAnnotationFileIO(String testname, AlignmentI al)
224 // what format would be appropriate for RNAalifold annotations?
225 String aligfileout = FileFormat.Pfam.getWriter(null)
226 .print(al.getSequencesArray(), true);
228 String anfileout = new AnnotationFile()
229 .printAnnotationsForAlignment(al);
230 assertNotNull("Test " + testname
231 + "\nAlignment annotation file was not regenerated. Null string",
233 assertTrue("Test " + testname
234 + "\nAlignment annotation file was not regenerated. Empty string",
235 anfileout.length() > "JALVIEW_ANNOTATION".length());
238 "Output annotation file:\n" + anfileout + "\n<<EOF\n");
240 // again what format would be appropriate?
241 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
242 DataSourceType.PASTE, FileFormat.Pfam);
243 assertTrue("Test " + testname
244 + "\nregenerated annotation file did not annotate alignment.",
245 new AnnotationFile().readAnnotationFile(al_new, anfileout,
246 DataSourceType.PASTE));
248 // test for consistency in io
249 StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
252 } catch (Exception e)
256 Assert.fail("Test " + testname
257 + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
260 @Test(groups = { "Network" })
261 public void testRnaalifoldSettingsRecovery()
263 List<Argument> opts = new ArrayList<>();
264 for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
267 if (rg.getDescription().contains("emperature"))
272 } catch (WrongParameterException q)
274 Assert.fail("Couldn't set the temperature parameter "
275 + q.getStackTrace());
279 if (rg.getDescription().contains("max"))
284 alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
285 JabaParamStore.getJwsArgsfromJaba(opts));
287 af.getViewport().getCalcManager().startWorker(alifoldClient);
294 } catch (InterruptedException x)
298 } while (af.getViewport().getCalcManager().isWorking());
299 AutoCalcSetting oldacs = af.getViewport()
300 .getCalcIdSettingsFor(alifoldClient.getCalcId());
301 String oldsettings = oldacs.getWsParamFile();
302 // write out parameters
303 jalview.gui.AlignFrame nalf = null;
304 assertTrue("Couldn't write out the Jar file", new Jalview2XML(false)
305 .saveAlignment(af, JAR_FILE_NAME, "trial parameter writeout"));
306 assertTrue("Couldn't read back the Jar file",
307 (nalf = new Jalview2XML(false)
308 .loadJalviewAlign(JAR_FILE_NAME)) != null);
311 AutoCalcSetting acs = af.getViewport()
312 .getCalcIdSettingsFor(alifoldClient.getCalcId());
313 assertTrue("Calc ID settings not recovered from viewport stash",
316 "Serialised Calc ID settings not identical to those recovered from viewport stash",
317 acs.getWsParamFile().equals(oldsettings));
318 JMenu nmenu = new JMenu();
319 new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
321 assertTrue("Couldn't get menu entry for service",
322 nmenu.getItemCount() > 0);
323 for (Component itm : nmenu.getMenuComponents())
325 if (itm instanceof JMenuItem)
327 JMenuItem i = (JMenuItem) itm;
328 if (i.getText().equals(
329 rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
336 while (af.getViewport().isCalcInProgress())
341 } catch (Exception x)
346 AutoCalcSetting acs2 = af.getViewport()
347 .getCalcIdSettingsFor(alifoldClient.getCalcId());
349 "Calc ID settings after recalculation has not been recovered.",
350 acs2.getWsParamFile().equals(oldsettings));