Java tutorial
/* This file is part of RUbioSeq-GUI. RUbioSeq-GUI 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. RUbioSeq-GUI 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 RUbioSeq-GUI. If not, see <http://www.gnu.org/licenses/>. */ package es.uvigo.ei.sing.rubioseq.gui.view.models.experiments; import java.io.File; import java.io.IOException; import java.lang.reflect.InvocationTargetException; import java.util.LinkedList; import java.util.List; import javax.persistence.EntityManager; import javax.persistence.PersistenceContext; import javax.persistence.PersistenceContextType; import org.apache.commons.beanutils.BeanUtils; import org.zkoss.bind.annotation.BindingParam; import org.zkoss.bind.annotation.Command; import org.zkoss.bind.annotation.DependsOn; import org.zkoss.bind.annotation.Init; import org.zkoss.bind.annotation.NotifyChange; import org.zkoss.zk.ui.Executions; import org.zkoss.zk.ui.Session; import org.zkoss.zk.ui.Sessions; import org.zkoss.zul.Messagebox; import es.uvigo.ei.sing.rubioseq.Experiment; import es.uvigo.ei.sing.rubioseq.ExperimentType; import es.uvigo.ei.sing.rubioseq.User; import es.uvigo.ei.sing.rubioseq.gui.macros.RUbioSeqFile; import es.uvigo.ei.sing.rubioseq.gui.view.models.EditExperimentModel; import es.uvigo.ei.sing.rubioseq.gui.view.models.ExecuteExperimentModel; /** * * @author hlfernandez * */ public class CopyNumberVariationExperimentModel { @PersistenceContext(type = PersistenceContextType.EXTENDED) private EntityManager em; private CopyNumberVariationExperiment experiment = new CopyNumberVariationExperiment(); private RUbioSeqFile outputFilePathRSFile; private boolean selectOutputFile; private String outputFilePath = "/home/hlfernandez/Tmp"; private String outputFileName = "experiment.xml"; private RUbioSeqFile currentExperimentFile; @Init public void init() { RUbioSeqFile editFile = (RUbioSeqFile) Sessions.getCurrent() .getAttribute(EditExperimentModel.EDIT_EXPERIMENT_FILE); if (editFile != null) { this.outputFilePathRSFile = new RUbioSeqFile(new File(editFile.getFile().getParent()), editFile.getDatastore()); this.outputFilePath = editFile.getFile().getParent(); this.outputFileName = editFile.getFile().getName(); Object data = Sessions.getCurrent().getAttribute(EditExperimentModel.EDIT_EXPERIMENT_DATA); if (data != null) { this.experiment = (CopyNumberVariationExperiment) data; } // try{ // this.experiment.loadDataFromFile(editFile.getFile()); // } catch(InvalidRubioSeqParameterException e){ // Sessions.getCurrent().setAttribute(EditExperimentModel.EDIT_EXPERIMENT_FILE, editFile); // Sessions.getCurrent().setAttribute(EditExperimentModel.EDIT_EXPERIMENT_ERROR_MSG, e.getMessage()); // Executions.getCurrent().sendRedirect("edit-experiment.zul"); // return; // } } Sessions.getCurrent().removeAttribute(EditExperimentModel.EDIT_EXPERIMENT_DATA); Sessions.getCurrent().removeAttribute(EditExperimentModel.EDIT_EXPERIMENT_FILE); } @SuppressWarnings("unchecked") public List<Experiment> getUserexperiments() { final Session webSession = Sessions.getCurrent(); String username = ((User) webSession.getAttribute("user")).getUsername(); return (List<Experiment>) this.em.createQuery("SELECT e FROM Experiment e where e.user='" + username + "'") .getResultList(); } @NotifyChange({ "selectOutputFile" }) @Command public void selectOutputFile() { this.selectOutputFile = true; } @NotifyChange({ "selectOutputFile" }) @Command public void cancelSelectOutputFile() { this.selectOutputFile = false; } public boolean isSelectOutputFile() { return selectOutputFile; } @NotifyChange({ "selectOutputFile", "currentExperimentFile" }) @Command public void generateXMLConfigurationFile() { File output = new File(this.outputFilePath, this.outputFileName); File outputDirectory = new File(this.outputFilePath); if (outputDirectory.isDirectory()) { if (outputDirectory.canWrite()) { try { experiment.generateXMLConfigurationFile(output); this.currentExperimentFile = new RUbioSeqFile(output, outputFilePathRSFile.getDatastore()); Messagebox.show("Configuration saved", "OK", Messagebox.OK, Messagebox.INFORMATION); } catch (IOException e) { Messagebox.show("Error saving configuration", "Error", Messagebox.OK, Messagebox.ERROR); this.currentExperimentFile = null; e.printStackTrace(); } this.selectOutputFile = false; } else { this.currentExperimentFile = null; Messagebox.show("Cannot write to file " + output.getName(), "Invalid file", Messagebox.OK, Messagebox.ERROR); } } else { this.currentExperimentFile = null; Messagebox.show(this.outputFilePath + " is not a directory.", "Invalid file", Messagebox.OK, Messagebox.ERROR); } if (this.executeExperiment) { this.executeExperiment(); this.executeExperiment = false; } } public CopyNumberVariationExperiment getExperiment() { return experiment; } public void setExperiment(CopyNumberVariationExperiment experiment) { this.experiment = experiment; } public EntityManager getEm() { return em; } public void setEm(EntityManager em) { this.em = em; } /* * Samples Management */ private Sample currentSample; private Sample currentTmpSample; private boolean edit = false; public Sample getCurrentSample() { return currentSample; } public void setCurrentSample(Sample currentSample) { this.currentSample = currentSample; } public Sample getCurrentTmpSample() { return currentTmpSample; } public void setCurrentTmpSample(Sample currentTmpSample) { this.currentTmpSample = currentTmpSample; } @NotifyChange({ "currentSample", "currentTmpSample" }) @Command public void addSample() { this.edit = false; this.currentSample = new Sample(); this.currentTmpSample = new Sample(); } @NotifyChange({ "currentSample", "samples", "mandatoryHeight" }) @Command public void saveSample() { if (!this.edit) { experiment.getSamples().add(this.currentSample); } else { } this.edit = false; this.currentSample = null; this.currentTmpSample = null; } @NotifyChange({ "currentSample" }) @Command public void cancelEdit() { this.currentSample = null; this.currentTmpSample = null; } public String getOutputFileName() { return outputFileName; } public void setOutputFileName(String outputFileName) { this.outputFileName = outputFileName; } public RUbioSeqFile getOutputFilePath() { return outputFilePathRSFile; } public void setOutputFilePath(RUbioSeqFile outputFilePathRSFile) { this.outputFilePathRSFile = outputFilePathRSFile; this.outputFilePath = this.outputFilePathRSFile.getFile().getAbsolutePath(); } public List<Sample> getSamples() { return experiment.getSamples(); } public void setSamples(List<Sample> samples) { experiment.setSamples(samples); } @DependsOn({ "currentTmpSample.sampleType", "currentTmpSample.sampleName", "currentTmpSample.sampleFiles", "currentTmpSample.sampleSuffix" }) public boolean isEnabledSaveSampleButton() { if (this.currentTmpSample == null) { return false; } if (this.currentTmpSample.getSampleFiles() != null && this.currentTmpSample.getSampleName() != null && this.currentTmpSample.getSampleSuffix() != null && this.currentTmpSample.getSampleType() != null && !this.currentTmpSample.getSampleFiles().equals("") && !this.currentTmpSample.getSampleName().equals("") && !this.currentTmpSample.getSampleSuffix().equals("")) { return true; } else return false; } @NotifyChange({ "currentSample", "samples" }) @Command public void editSample(@BindingParam("sample") Sample sample) { this.edit = true; this.currentSample = sample; this.currentTmpSample = new Sample(); try { BeanUtils.copyProperties(this.currentTmpSample, this.currentSample); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (InvocationTargetException e) { e.printStackTrace(); } } @NotifyChange({ "samples", "mandatoryHeight" }) @Command public void deleteSample(@BindingParam("sample") Sample sample) { this.experiment.getSamples().remove(sample); } /* * KnownIndels Management */ private KnownIndels currentKnownIndels; private KnownIndels currentTmpKnownIndels; private boolean editKnownIndels = false; private boolean executeExperiment = false; public KnownIndels getCurrentKnownIndels() { return currentKnownIndels; } public void setCurrentKnownIndels(KnownIndels currentKnownIndels) { this.currentKnownIndels = currentKnownIndels; } public KnownIndels getCurrentTmpKnownIndels() { return currentTmpKnownIndels; } public void setCurrentTmpKnownIndels(KnownIndels currentKnownIndels) { this.currentKnownIndels = currentKnownIndels; } @NotifyChange({ "currentKnownIndels", "currentTmpKnownIndels" }) @Command public void addKnownIndels() { this.editKnownIndels = false; this.currentKnownIndels = new KnownIndels(); this.currentTmpKnownIndels = new KnownIndels(); } @NotifyChange({ "currentKnownIndels", "knownIndels", "optionalHeight" }) @Command public void saveKnownIndels() { if (!this.editKnownIndels) { experiment.getKnownIndels().add(this.currentKnownIndels); } else { // It is saved automatically by the @save annotation before saveHardFilter in the .zul } this.editKnownIndels = false; this.currentKnownIndels = null; this.currentTmpKnownIndels = null; } @NotifyChange({ "currentKnownIndels" }) @Command public void cancelEditKnownIndels() { this.currentKnownIndels = null; this.currentTmpKnownIndels = null; } @NotifyChange({ "currentKnownIndels" }) @Command public void editKnownIndels(@BindingParam("knownIndels") KnownIndels knownIndels) { this.editKnownIndels = true; this.currentKnownIndels = knownIndels; this.currentTmpKnownIndels = new KnownIndels(); try { BeanUtils.copyProperties(this.currentTmpKnownIndels, this.currentKnownIndels); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (InvocationTargetException e) { e.printStackTrace(); } } @NotifyChange({ "knownIndels", "optionalHeight" }) @Command public void deleteKnownIndels(@BindingParam("knownIndels") KnownIndels knownIndels) { this.experiment.getKnownIndels().remove(knownIndels); } public List<KnownIndels> getKnownIndels() { return experiment.getKnownIndels(); } public void setKnownIndels(List<KnownIndels> knownIndels) { experiment.setKnownIndels(knownIndels); } @DependsOn({ "currentTmpKnownIndels.file" }) public boolean isEnabledSaveKnownIndelsButton() { if (this.currentTmpKnownIndels == null) { return false; } if (this.currentTmpKnownIndels.getFile() != null && !this.currentTmpKnownIndels.getFile().equals("")) { return true; } else return false; } @DependsOn({ "knownIndels" }) public boolean isKnownIndelsGridVisible() { return this.experiment.getKnownIndels().size() > 0; } @DependsOn({ "experiment.genRefPath", "experiment.dbSnpAnnotPath", "experiment.intervalsPath", "experiment.indelAnnotPath", "experiment.plattform", "experiment.dirOutBase", "experiment.baseline", "experiment.projectId", "experiment.dataInDirpreProcess", "samples" }) public boolean isEnabledExportButton() { if (experiment.getGenRefPath() == null || experiment.getDbSnpAnnotPath() == null || experiment.getIntervalsPath() == null || experiment.getIndelAnnotPath() == null || experiment.getPlattform() == null || experiment.getDirOutBase() == null || experiment.getProjectId() == null || experiment.getDataInDirpreProcess() == null || this.getSamples().size() == 0 || !experiment.checkPaths()) { return false; } return true; } public boolean isStringOk(String str) { if (str == null || str.equals("")) { return false; } return true; } @NotifyChange({ "experiment", "knownIndels" }) @Command("restoreKnownIndels") public void restoreKnownIndels() { experiment.setKnownIndels(new LinkedList<KnownIndels>()); } @NotifyChange("experiment") @Command("restoreCheckCasava") public void restoreCheckCasava() { experiment.setCheckCasava(experiment.getCheckCasava_DV()); } @NotifyChange("experiment") @Command("restoreUserName") public void restoreUserName() { experiment.setUserName(experiment.getUserName_DV()); } @NotifyChange("experiment") @Command("restoreFastqc") public void restoreFastqc() { experiment.setFastqc(experiment.getFastqc_DV()); } @NotifyChange("experiment") @Command("restoreMDFlag") public void restoreMDFlag() { experiment.setmDFlag(experiment.getmDFlag_DV()); } @NotifyChange("experiment") @Command("restoreExtraContra") public void restoreExtraContra() { experiment.setExtraContra(experiment.getExtraContra_DV()); } @NotifyChange("experiment") @Command("restoreBaseline") public void restoreBaseline() { experiment.setBaseline(experiment.getBaseline_DV()); } @NotifyChange("experiment") @Command("restorequeueSGEProject") public void restorequeueSGEProject() { experiment.setQueueSGEProject(experiment.getQueueSGEProject_DV()); } @DependsOn("currentExperimentFile") public boolean isEnabledExecuteExperimentButton() { return this.currentExperimentFile != null; } @NotifyChange({ "selectOutputFile" }) @Command public void saveBeforeExecuteExperiment() { this.selectOutputFile = true; this.executeExperiment = true; } @Command public void executeExperiment() { Sessions.getCurrent().setAttribute(ExecuteExperimentModel.EXPERIMENT_FILE, new ExecuteExperimentModel.ExperimentFile(this.currentExperimentFile, ExperimentType.CNV)); Executions.getCurrent().sendRedirect("/experiments/execute-experiment.zul"); } private static final int minMandatoryHeight = 680; private static final int minOptionalHeight = 650; private int getMinOptionalHeight() { int toret = minOptionalHeight + this.experiment.getKnownIndels().size() * 40; return toret; } private int getMinMandatoryHeight() { int toret = minMandatoryHeight + this.experiment.getSamples().size() * 40; return toret; } public String getMandatoryHeight() { return String.valueOf(getMinMandatoryHeight()) + "px"; } public String getOptionalHeight() { return String.valueOf(getMinOptionalHeight()) + "px"; } @DependsOn("enabledExportButton") public String getExportButtonClass() { if (isEnabledExportButton()) { return "actionButton"; } else { return ""; } } }