BeautiBase.java

package test.beast.app.beauti;



import static org.fest.assertions.Assertions.assertThat;
import static org.fest.swing.edt.GuiActionRunner.execute;
import static org.fest.swing.finder.JFileChooserFinder.findFileChooser;

import java.awt.Dimension;
import java.awt.FileDialog;
import java.awt.event.KeyEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;

import javax.swing.JFrame;

import org.fest.swing.annotation.RunsInEDT;
import org.fest.swing.edt.GuiQuery;
import org.fest.swing.edt.GuiTask;
import org.fest.swing.fixture.FrameFixture;
import org.fest.swing.fixture.JFileChooserFixture;
import org.fest.swing.fixture.JTabbedPaneFixture;
import org.fest.swing.fixture.JTableFixture;
import org.fest.swing.junit.testcase.FestSwingJUnitTestCase;

import beast.app.beauti.Beauti;
import beast.app.beauti.BeautiDoc;
import beast.app.util.Utils;
import beast.core.BEASTInterface;
import beast.core.BEASTObject;
import beast.core.Distribution;
import beast.core.Function;
import beast.core.Logger;
import beast.core.MCMC;
import beast.core.Operator;
import beast.core.State;
import beast.core.StateNode;
import beast.core.parameter.Parameter;
import beast.core.util.CompoundDistribution;
import beast.math.distributions.Prior;
import beast.util.XMLParser;



/**
 * Basic test methods for Beauti  
 * 
 */
public class BeautiBase extends FestSwingJUnitTestCase {

	protected FrameFixture beautiFrame;
	protected Beauti beauti;
	protected BeautiDoc doc;

	@Override
	protected void onSetUp() {
		beautiFrame = new FrameFixture(robot(), createNewEditor());
		beautiFrame.show();
		beautiFrame.resizeTo(new Dimension(1224, 786));
		JTabbedPaneFixture f = beautiFrame.tabbedPane();
		beauti = (Beauti) f.target;
		doc = beauti.doc;
	}

	@RunsInEDT
	private static JFrame createNewEditor() {
		return execute(new GuiQuery<JFrame>() {
			@Override
			protected JFrame executeInEDT() throws Throwable {
				Beauti beauti = Beauti.main2(new String[] {});
				return beauti.frame;
			}
		});
	}

	String priorsAsString() {
		CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
		List<Distribution> priors = prior.pDistributions.get();
		return "assertPriorsEqual" + pluginListAsString(priors);
	}
	
	String stateAsString() {
		State state = (State) doc.pluginmap.get("state");
		List<StateNode> stateNodes = state.stateNodeInput.get();
		return "assertStateEquals" + pluginListAsString(stateNodes);
	}

	String operatorsAsString() {
		MCMC mcmc = (MCMC) doc.mcmc.get();
		List<Operator> operators = mcmc.operatorsInput.get();
		return "assertOperatorsEqual" + pluginListAsString(operators);
	}
	
	String traceLogAsString() {
		Logger logger = (Logger) doc.pluginmap.get("tracelog");
		List<BEASTObject> logs = logger.loggersInput.get();
		return "assertTraceLogEqual" + pluginListAsString(logs);
	}

	
	private String pluginListAsString(List<?> list) {
		if (list.size() == 0) {
			return "";
		}
		StringBuffer bf = new StringBuffer();
		for (Object o : list) {
			BEASTObject beastObject = (BEASTObject) o;
			bf.append('"');
			bf.append(beastObject.getID());
			bf.append("\", ");
		}
		String str = bf.toString();
		return "(" + str.substring(0, str.length()-2) + ");";
	}

	void assertPriorsEqual(String... ids) {
		System.err.println("assertPriorsEqual");
		CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
		List<Distribution> priors = prior.pDistributions.get();
		for (String id : ids) {
			boolean found = false;
			for (BEASTObject node : priors) {
				if (node.getID().equals(id)) {
					found = true;
				}
			}
			assertThat(found).as("Could not find beastObject with ID " + id).isEqualTo(true);
		}
		List<String> extras = new ArrayList<>();
		for (BEASTObject node : priors) {
			boolean found = false;
			for (String id : ids) {
				if (node.getID().equals(id)) {
					found = true;
				}
			}
			if (!found) {
				extras.add(node.getID());
			}
		}
		if (extras.size() != 0) {
			System.err.println("Extra ids found: " + Arrays.toString(extras.toArray(new String[]{})));
		}
		assertThat(ids.length).as("list of beastObjects do not match").isEqualTo(priors.size());;
	}

	private void asserListsEqual(List<?> list, String[] ids) {
		// check all ids are in list
		for (String id : ids) {
			boolean found = false;
			for (Object o: list) {
				BEASTObject node = (BEASTObject) o;
				if (node.getID().equals(id)) {
					found = true;
					break;
				}
			}
			assertThat(found).as("Could not find beastObject with ID " + id).isEqualTo(true);
		}
		// check all items in list have a unique ie
		Set<String> idsInList = new HashSet<String>();
		Set<String> duplicates = new HashSet<String>();
		for (Object o : list) {
			String id = ((BEASTObject) o).getID();
			if (idsInList.contains(id)) {
				duplicates.add(id);
			} else {
				idsInList.add(id);
			}
		}
		assertThat(duplicates.size()).as("Duplicate ids found: " + Arrays.toString(duplicates.toArray())).isEqualTo(0);
		
		if (list.size() != ids.length) {
			// list.size > ids.length, otherwise it would have been picked up above
			List<String> extraIDs = new ArrayList<String>(); 
			for (Object o : list) {
				String id = ((BEASTObject) o).getID();
				boolean found = false;
				for (String id2 : ids) {
					if (id2.equals(id)) {
						found = true;
						break;
					}
				}
				if (!found) {
					extraIDs.add(id);
				}
			}
			assertThat(ids.length).as("list of beastObjects do not match: found extra items " + Arrays.toString(extraIDs.toArray())).isEqualTo(list.size());
		}
	}

	void assertStateEquals(String... ids) {
		System.err.println("assertStateEquals");
		State state = (State) doc.pluginmap.get("state");
		List<StateNode> stateNodes = state.stateNodeInput.get();
		asserListsEqual(stateNodes, ids);
	}

	void assertOperatorsEqual(String... ids) {
		System.err.println("assertOperatorsEqual");
		MCMC mcmc = (MCMC) doc.mcmc.get();
		List<Operator> operators = mcmc.operatorsInput.get();
		asserListsEqual(operators, ids);
	}

	void assertTraceLogEqual(String... ids) {
		System.err.println("assertTraceLogEqual");
		Logger logger = (Logger) doc.pluginmap.get("tracelog");
		List<BEASTObject> logs = logger.loggersInput.get();
		asserListsEqual(logs, ids);
	}

	void assertArrayEquals(Object [] o, String array) {
		String str = array.substring(1, array.length() - 1);
		String [] strs = str.split(", ");
		for (int i = 0; i < o.length && i < strs.length; i++) {
			assertThat(strs[i]).as("expected array value " + strs[i] + " instead of " + o[i].toString()).isEqualTo(o[i].toString());
		}
		assertThat(o.length).as("arrays do not match: different lengths").isEqualTo(strs.length);
	}
	
	void assertParameterCountInPriorIs(int i) {
		// count nr of parameters in Prior objects in prior
		// including those for prior distributions (Normal, etc)
		// useful to make sure they do (or do not) get linked
		Set<Function> parameters = new LinkedHashSet<>();
		CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
		for (Distribution p : prior.pDistributions.get()) {
			if (p instanceof Prior) {
				Prior p2 = (Prior) p;
				parameters.add(p2.m_x.get());
				for (BEASTInterface o : p2.distInput.get().listActiveBEASTObjects()) {
					if (o instanceof Parameter) {
						parameters.add((Parameter<?>) o);
					}
				}
			}
		}
		System.err.println("Number of parameters in prior = " + parameters.size());
		if (i >= 0) {
			assertThat(parameters.size()).as("Expected " + i + " parameters in prior").isEqualTo(i);
		}
	}
	
	void printBeautiState(JTabbedPaneFixture f) throws InterruptedException {
        doc.scrubAll(true, false);
		//f.selectTab("MCMC");
		System.err.println(stateAsString());
		System.err.println(operatorsAsString());
		System.err.println(priorsAsString());
		System.err.println(traceLogAsString());
	}


	void printTableContents(JTableFixture t) {
		String [][] contents = t.contents();
		for (int i = 0; i < contents.length; i++) {
			System.err.print("\"" + Arrays.toString(contents[i]));
			if (i < contents.length - 1) {
				System.err.print("*\" +");
			} else {
				System.err.print("\"");
			}
			System.err.println();
		}
	}
	
	void checkTableContents(JTableFixture t, String str) {
		String [][] contents = t.contents();
		String [] strs = str.split("\\*");
		assertThat(contents.length).as("tables do not match: different #rows").isEqualTo(strs.length);
		for (int i = 0; i < contents.length; i++) {
			assertArrayEquals(contents[i], strs[i]);
		}
	}

	void warning(String str) {
		System.err.println("\n\n=====================================================\n");
		System.err.println(str);
		System.err.println("\n=====================================================\n\n");
	}
	
	void makeSureXMLParses() {
		warning("Make sure that XML that BEAUti produces parses");
		File XMLFile = new File(org.fest.util.Files.temporaryFolder() + "/x.xml");
		if (XMLFile.exists()) {
			XMLFile.delete();
		}
		
		saveFile(""+org.fest.util.Files.temporaryFolder(), "x.xml");

//		JFileChooserFixture fileChooser = findFileChooser().using(robot());
//		fileChooser.setCurrentDirectory(org.fest.util.Files.temporaryFolder());
//		fileChooser.selectFile(new File("x.xml")).approve();
		
		XMLParser parser = new XMLParser();
		XMLFile = new File(org.fest.util.Files.temporaryFolder() + "/x.xml");
		try {
			parser.parseFile(XMLFile);
		} catch (Exception e) {
			e.printStackTrace();
			assertThat(0).as("Parser exception: " + e.getMessage()).isEqualTo(1);
		}
	}

	protected void saveFile(String dir, String file) {
		if (!Utils.isMac()) {
			beautiFrame.menuItemWithPath("File", "Save As").click();
			JFileChooserFixture fileChooser = findFileChooser().using(robot());
			fileChooser.setCurrentDirectory(new File(dir));
			fileChooser.selectFile(new File(file)).approve();
		} else {
			_file = new File(dir + "/" + file);
			execute(new GuiTask() {
		        @Override
				protected void executeInEDT() {
		        	try {
		        		beauti.doc.save(_file);
		        	} catch (Exception e) {
						e.printStackTrace();
					}
		        }
		    });
			
		}	
	}

	// for handling file open events on Mac
	FileDialog fileDlg = null;
	String _dir;
	File _file;

	void importAlignment(String dir, File ... files) {
		if (!Utils.isMac()) {
			beautiFrame.menuItemWithPath("File", "Import Alignment").click();
			JFileChooserFixture fileChooser = findFileChooser().using(robot());
			fileChooser.setCurrentDirectory(new File(dir));
			fileChooser.selectFiles(files).approve();
			// close down any popup message
			robot().pressKey(KeyEvent.VK_ESCAPE);
		} else {
			this._dir = dir;
			for (File file : files) {
				_file = new File(dir + "/" + file.getName());
				execute(new GuiTask() {
			        @Override
					protected void executeInEDT() {
			        	try {
			        		beauti.doc.importNexus(_file);
			    			beauti.refreshPanel();
			        	} catch (Exception e) {
							e.printStackTrace();
						}
			        }
			    });
			}
		}			
	}

	
//	void openFile(String dir, String file) {
//		if (!Utils.isMac() && false) {
//			JFileChooserFixture fileChooser = findFileChooser().using(robot());
//			fileChooser.setCurrentDirectory(new File(dir));
//			fileChooser.selectFile(new File(file)).approve();
//		} else {
//			fileDlg = null;
//			this._dir = dir;
//			this._file = file;
//			DialogFixture dialog = WindowFinder.findDialog(FileDialog.class).using(robot());
//			fileDlg = (FileDialog) dialog.target;
//					
//			execute(new GuiTask() {
//		        protected void executeInEDT() {
//		          fileDlg.setDirectory(_dir);
//		          fileDlg.setFile(_file);
//		        }
//		    });
//			robot().click(
//		    	robot().finder().find(new ComponentMatcher() {
//		    		@Override
//		    		public boolean matches(Component c) {
//		    			if (c.getName() == null) {
//		    				return false;
//		    			}
//		    			System.err.println(c.getName());
//		    			if (c instanceof Button) {
//		    				System.err.println(">>>" + ((Button)c).getLabel());
//		    			}
//		    			return (c.getName().equals("button0") || c.getName().equals("button3"));
//		    		}
//		    	})
//		    );
//		}
//	}
	

	
}