org.eclipse.stem/models/epidemiology/org.eclipse.stem.ui.diseasemodels/src/org/eclipse/stem/ui/wizards/NewInfectorWizard.java - stem/org.eclipse.stem - Git at Google

 // NewInfectorWizard.java
 package org.eclipse.stem.ui.wizards;

 /*******************************************************************************
  * Copyright (c) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018
  * IBM Corporation, BfR, and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v2.0
  * which accompanies this distribution, and is available at
  * https://www.eclipse.org/legal/epl-2.0/
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation and new features
  *     Bundesinstitut für Risikobewertung - Pajek Graph interface, new Veterinary Models
  *******************************************************************************/

 import java.util.List;

 import org.eclipse.core.commands.AbstractHandler;
 import org.eclipse.core.commands.ExecutionEvent;
 import org.eclipse.core.commands.ExecutionException;
 import org.eclipse.core.commands.IHandler;
 import org.eclipse.jface.viewers.StructuredSelection;
 import org.eclipse.jface.wizard.WizardDialog;
 import org.eclipse.stem.analysis.impl.ReferenceScenarioDataMapImpl;
 import org.eclipse.stem.analysis.impl.ReferenceScenarioDataMapImpl.ReferenceScenarioDataInstance;
 import org.eclipse.stem.analysis.util.CSVscenarioLoader;
 import org.eclipse.stem.core.STEMURI;
 import org.eclipse.stem.core.common.Identifiable;
 import org.eclipse.stem.core.common.util.LogInitializationException;
 import org.eclipse.stem.core.model.NodeDecorator;
 import org.eclipse.stem.diseasemodels.standard.InfectorInoculatorCollection;
 import org.eclipse.stem.diseasemodels.standard.SIInfector;
 import org.eclipse.stem.diseasemodels.standard.SIRInoculator;
 import org.eclipse.stem.diseasemodels.standard.StandardFactory;
 import org.eclipse.stem.diseasemodels.standard.StandardPackage;
 import org.eclipse.stem.diseasemodels.standard.impl.SIRInoculatorImpl;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.events.SelectionEvent;
 import org.eclipse.swt.events.SelectionListener;
 import org.eclipse.swt.widgets.Composite;
 import org.eclipse.ui.IWorkbenchWindow;
 import org.eclipse.ui.handlers.HandlerUtil;

 /**
  * This class represents
  */
 public class NewInfectorWizard extends NewIdentifiableWizard {

 	private NewInfectorPage nip = null;

 	/**
 	 * Constructor
 	 */
 	public NewInfectorWizard() {
 		// Nothing
 	}

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getWizardTitle()
 	 */
 	@Override
 	protected String getWizardTitle() {
 		return DiseaseWizardMessages.getString("NInfectorWiz.wizard_title"); //$NON-NLS-1$
 	}

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createNewIdentifiablePage()
 	 */
 	@Override
 	protected NewIdentifiablePage createNewIdentifiablePage() {
 		nip = new NewInfectorPage(DiseaseWizardMessages.getString("NInfectorWiz.page_title")); //$NON-NLS-1$
 		nip.setTitle(DiseaseWizardMessages.getString("NInfectorWiz.page_title")); //$NON-NLS-1$
 		nip.setDescription(DiseaseWizardMessages.getString("NInfectorWiz.page_description")); //$NON-NLS-1$

 		this.setHelpContextId("org.eclipse.stem.doc.newinfectorinoculator_contextid");

 		return nip;
 	} // createNewIdentifiablePage

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createDublinCorePage()
 	 */
 	@Override
 	protected DublinCorePage createDublinCorePage() {
 		return new DublinCorePage() {
 			/**
 			 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard.DublinCorePage#initializeDCFields()
 			 */
 			@Override
 			protected void initializeDCAttributes() {
 				super.initializeDCAttributes();
 				format.setText(StandardPackage.eNS_URI);
 				format.setEnabled(false);
 				// type.setText("undefined");
 				// type.setText(STEMURI.SCENARIO_TYPE_URI.toString());
 				type.setEnabled(false);
 			}
 		}; // DublinCorePage
 	}

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createIdentifiable()
 	 */
 	@Override
 	protected Identifiable createIdentifiable() {
 		final NodeDecorator retValue = nip.getInfector();
 		retValue.setDublinCore(newDublinCorePage.createDublinCore());
 		return retValue;
 	} // createSpecificIdentifiable

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getSerializationFolderName()
 	 */
 	@Override
 	protected String getSerializationFolderName() {
 		return NewSTEMProjectWizard.DECORATORS_FOLDER_NAME;
 	}

 	/**
 	 * @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getSerializationFileNameExtension()
 	 */
 	@Override
 	protected String getSerializationFileNameExtension() {
 		return StandardPackage.eNAME;
 	}

 	protected static class NewInfectorPage extends NewIdentifiablePage {

 		private InfectorDefinitionComposite idc;

 		/**
 		 * @param pageName
 		 */
 		protected NewInfectorPage(String pageName) {
 			super(pageName);
 		}

 		/**
 		 * @return
 		 */
 		public NodeDecorator getInfector() {
 			if(!idc.isFromFile()) {
 				SIInfector retValue = null;
 				if(idc.isInfectorMode()) {
 					retValue = StandardFactory.eINSTANCE.createSIInfector();
 					retValue.setTargetFeature("i"); // default for infector
 				} else {
 					retValue = StandardFactory.eINSTANCE.createSIRInoculator();
 					retValue.setTargetFeature("r"); // default for inoculator
 				}
 				retValue.setDiseaseName(idc.getDiseaseName());
 				retValue.setPopulationIdentifier(idc.getPopulation());
 				retValue.setTargetISOKey(idc.getIsoKey());
 				retValue.setTargetURI(idc.getTargetURI());
 				if(idc.isInfectorMode() && idc.isPercentage()) {
 					retValue.setInfectPercentage(true);
 					retValue.setInfectiousCount(idc.getNumber());
 				} else if(idc.isInfectorMode() && !idc.isPercentage()) {
 					retValue.setInfectPercentage(false);
 					retValue.setInfectiousCount(idc.getNumber());
 				} else if( idc.isPercentage()){
 					((SIRInoculatorImpl) retValue).setInoculatedPercentage(idc.getNumber());

 					((SIRInoculatorImpl) retValue).setInoculatePercentage(true);
 					// just to be sure - since this is NOT and Infector
 					retValue.setInfectiousCount(0.0);
 				} else {
 					((SIRInoculatorImpl) retValue).setInoculatedPercentage(idc.getNumber());
 					((SIRInoculatorImpl) retValue).setInoculatePercentage(false);
 					// just to be sure - since this is NOT and Infector
 					retValue.setInfectiousCount(0.0);
 				}
 				return retValue;
 			} else {
 				// We need to create a InfectorInoculatorList object
 				// and read the data from file

 				String folder = idc.getImportFolder();
 				ReferenceScenarioDataMapImpl  map = null;
 				List<Integer>resolutions = null;
 				try {
 					CSVscenarioLoader loader = new CSVscenarioLoader(folder);
 					//resolutions = loader.getResolutions();
 					map = loader.parseAllFiles();
 				} catch(LogInitializationException sie) {
 					org.eclipse.stem.diseasemodels.Activator.logError(sie.getMessage(), sie);
 					return null;
 				}
 				InfectorInoculatorCollection iic = StandardFactory.eINSTANCE.createInfectorInoculatorCollection();
 				iic.setImportFolder(folder);
 				for(String location : map.getLocations()) {
 					ReferenceScenarioDataInstance instance = map.getLocation(location);
 					List<String>counts = null;
 					List<String>denom = null;
 					if(idc.isInfectorMode())
 						counts = instance.getData(CSVscenarioLoader.I_TYPE);
 					else
 						counts = instance.getData(CSVscenarioLoader.R_TYPE);
 					if(idc.isPercentage())
 						denom = instance.getData(CSVscenarioLoader.POP_COUNT_KEY);

 					// Use first row only
 					double dcount = 0.0;

 					if(idc.isFirstRow())
 						dcount = Double.parseDouble(counts.get(0));
 					else if(idc.isLastRow())
 						dcount = Double.parseDouble(counts.get(counts.size()-1));
 					else
 						dcount = Double.parseDouble(counts.get(idc.getSelectecRow()));

 					double ddenom = 1.0;
 					if(idc.isPercentage())
 						if(idc.isFirstRow())
 							ddenom = (Double.parseDouble(denom.get(0)) / 100.0);
 						else if(idc.isLastRow())
 							ddenom = (Double.parseDouble(denom.get(counts.size()-1)) / 100.0);
 						else
 							ddenom = (Double.parseDouble(denom.get(idc.getSelectecRow())) / 100.0);

 					SIInfector infector = null;
 					if(idc.isInfectorMode()) {
 						infector = StandardFactory.eINSTANCE.createSIInfector();
 						infector.setInfectPercentage(idc.isPercentage());
 						infector.setInfectiousCount(dcount/ddenom);
 						infector.setURI(STEMURI.createURI(STEMURI.generateUniquePart()+"/infect_"+location));
 					}
 					else {
 						infector = StandardFactory.eINSTANCE.createSIRInoculator();
 						((SIRInoculator)infector).setInoculatePercentage(idc.isPercentage());
 						((SIRInoculator)infector).setInoculatedPercentage(dcount/ddenom);
 						infector.setURI(STEMURI.createURI(STEMURI.generateUniquePart()+"/inoculate_"+location));
 					}
 					infector.setDiseaseName(idc.getDiseaseName());
 					infector.setPopulationIdentifier(idc.getPopulation());
 					infector.setTargetISOKey(location);
 					iic.getList().add(infector);
 				}
 				return iic;
 			}
 		} // getInfector

 		@Override
 		protected Composite createSpecificComposite(final Composite parent) {
 			idc = new InfectorDefinitionComposite(parent, SWT.NONE,
 					projectValidator, super.getSelectedProject());

 			final NewInfectorWizard.NewInfectorPage self = this;

 			this.projectNamesCombo.addSelectionListener(new SelectionListener() {

 				public void widgetSelected(SelectionEvent arg0) {
 					idc.setProject(self.getSelectedProject());
 				}

 				public void widgetDefaultSelected(SelectionEvent arg0) {

 				}
 			});

 			return idc;
 		} // createSpecificComposite

 		@Override
 		protected boolean validatePage() {
 			boolean retValue = super.validatePage();
 			if (retValue) {
 				setErrorMessage(null);
 				retValue = idc.validate();
 				// Error?
 				if (!retValue) {
 					// Yes
 					setErrorMessage(idc.getErrorMessage());
 				} // if
 			}
 			return retValue;
 		} // validatePage
 	} // NewInfectorPage

 	/**
 	 * This class is a {@link IHandler} for the command that creates a
 	 * {@link NewInfectorWizard}
 	 */
 	public static class NewInfectorWizardCommandHandler extends AbstractHandler
 			implements IHandler {

 		/**
 		 * @see org.eclipse.core.commands.AbstractHandler#execute(org.eclipse.core.commands.ExecutionEvent)
 		 */
 		public Object execute(final ExecutionEvent executionEvent)
 				throws ExecutionException {
 			final IWorkbenchWindow window = HandlerUtil
 					.getActiveWorkbenchWindowChecked(executionEvent);
 			final NewInfectorWizard wizard = new NewInfectorWizard();
 			wizard.init(window.getWorkbench(), StructuredSelection.EMPTY);
 			final WizardDialog wizardDialog = new STEMWizardDialog(window
 					.getShell(), wizard);
 			wizardDialog.open();
 			return null;
 		} // execute
 	} // NewInfectorWizardCommandHandler
 } // NewInfectorWizard
	// NewInfectorWizard.java
	package org.eclipse.stem.ui.wizards;

	/*******************************************************************************
	* Copyright (c) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018
	* IBM Corporation, BfR, and others.
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v2.0
	* which accompanies this distribution, and is available at
	* https://www.eclipse.org/legal/epl-2.0/
	*
	* Contributors:
	* IBM Corporation - initial API and implementation and new features
	* Bundesinstitut für Risikobewertung - Pajek Graph interface, new Veterinary Models
	*******************************************************************************/

	import java.util.List;

	import org.eclipse.core.commands.AbstractHandler;
	import org.eclipse.core.commands.ExecutionEvent;
	import org.eclipse.core.commands.ExecutionException;
	import org.eclipse.core.commands.IHandler;
	import org.eclipse.jface.viewers.StructuredSelection;
	import org.eclipse.jface.wizard.WizardDialog;
	import org.eclipse.stem.analysis.impl.ReferenceScenarioDataMapImpl;
	import org.eclipse.stem.analysis.impl.ReferenceScenarioDataMapImpl.ReferenceScenarioDataInstance;
	import org.eclipse.stem.analysis.util.CSVscenarioLoader;
	import org.eclipse.stem.core.STEMURI;
	import org.eclipse.stem.core.common.Identifiable;
	import org.eclipse.stem.core.common.util.LogInitializationException;
	import org.eclipse.stem.core.model.NodeDecorator;
	import org.eclipse.stem.diseasemodels.standard.InfectorInoculatorCollection;
	import org.eclipse.stem.diseasemodels.standard.SIInfector;
	import org.eclipse.stem.diseasemodels.standard.SIRInoculator;
	import org.eclipse.stem.diseasemodels.standard.StandardFactory;
	import org.eclipse.stem.diseasemodels.standard.StandardPackage;
	import org.eclipse.stem.diseasemodels.standard.impl.SIRInoculatorImpl;
	import org.eclipse.swt.SWT;
	import org.eclipse.swt.events.SelectionEvent;
	import org.eclipse.swt.events.SelectionListener;
	import org.eclipse.swt.widgets.Composite;
	import org.eclipse.ui.IWorkbenchWindow;
	import org.eclipse.ui.handlers.HandlerUtil;

	/**
	* This class represents
	*/
	public class NewInfectorWizard extends NewIdentifiableWizard {

	private NewInfectorPage nip = null;

	/**
	* Constructor
	*/
	public NewInfectorWizard() {
	// Nothing
	}

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getWizardTitle()
	*/
	@Override
	protected String getWizardTitle() {
	return DiseaseWizardMessages.getString("NInfectorWiz.wizard_title"); //$NON-NLS-1$
	}

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createNewIdentifiablePage()
	*/
	@Override
	protected NewIdentifiablePage createNewIdentifiablePage() {
	nip = new NewInfectorPage(DiseaseWizardMessages.getString("NInfectorWiz.page_title")); //$NON-NLS-1$
	nip.setTitle(DiseaseWizardMessages.getString("NInfectorWiz.page_title")); //$NON-NLS-1$
	nip.setDescription(DiseaseWizardMessages.getString("NInfectorWiz.page_description")); //$NON-NLS-1$

	this.setHelpContextId("org.eclipse.stem.doc.newinfectorinoculator_contextid");

	return nip;
	} // createNewIdentifiablePage

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createDublinCorePage()
	*/
	@Override
	protected DublinCorePage createDublinCorePage() {
	return new DublinCorePage() {
	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard.DublinCorePage#initializeDCFields()
	*/
	@Override
	protected void initializeDCAttributes() {
	super.initializeDCAttributes();
	format.setText(StandardPackage.eNS_URI);
	format.setEnabled(false);
	// type.setText("undefined");
	// type.setText(STEMURI.SCENARIO_TYPE_URI.toString());
	type.setEnabled(false);
	}
	}; // DublinCorePage
	}

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#createIdentifiable()
	*/
	@Override
	protected Identifiable createIdentifiable() {
	final NodeDecorator retValue = nip.getInfector();
	retValue.setDublinCore(newDublinCorePage.createDublinCore());
	return retValue;
	} // createSpecificIdentifiable

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getSerializationFolderName()
	*/
	@Override
	protected String getSerializationFolderName() {
	return NewSTEMProjectWizard.DECORATORS_FOLDER_NAME;
	}

	/**
	* @see org.eclipse.stem.ui.wizards.NewIdentifiableWizard#getSerializationFileNameExtension()
	*/
	@Override
	protected String getSerializationFileNameExtension() {
	return StandardPackage.eNAME;
	}

	protected static class NewInfectorPage extends NewIdentifiablePage {

	private InfectorDefinitionComposite idc;

	/**
	* @param pageName
	*/
	protected NewInfectorPage(String pageName) {
	super(pageName);
	}

	/**
	* @return
	*/
	public NodeDecorator getInfector() {
	if(!idc.isFromFile()) {
	SIInfector retValue = null;
	if(idc.isInfectorMode()) {
	retValue = StandardFactory.eINSTANCE.createSIInfector();
	retValue.setTargetFeature("i"); // default for infector
	} else {
	retValue = StandardFactory.eINSTANCE.createSIRInoculator();
	retValue.setTargetFeature("r"); // default for inoculator
	}
	retValue.setDiseaseName(idc.getDiseaseName());
	retValue.setPopulationIdentifier(idc.getPopulation());
	retValue.setTargetISOKey(idc.getIsoKey());
	retValue.setTargetURI(idc.getTargetURI());
	if(idc.isInfectorMode() && idc.isPercentage()) {
	retValue.setInfectPercentage(true);
	retValue.setInfectiousCount(idc.getNumber());
	} else if(idc.isInfectorMode() && !idc.isPercentage()) {
	retValue.setInfectPercentage(false);
	retValue.setInfectiousCount(idc.getNumber());
	} else if( idc.isPercentage()){
	((SIRInoculatorImpl) retValue).setInoculatedPercentage(idc.getNumber());

	((SIRInoculatorImpl) retValue).setInoculatePercentage(true);
	// just to be sure - since this is NOT and Infector
	retValue.setInfectiousCount(0.0);
	} else {
	((SIRInoculatorImpl) retValue).setInoculatedPercentage(idc.getNumber());
	((SIRInoculatorImpl) retValue).setInoculatePercentage(false);
	// just to be sure - since this is NOT and Infector
	retValue.setInfectiousCount(0.0);
	}
	return retValue;
	} else {
	// We need to create a InfectorInoculatorList object
	// and read the data from file

	String folder = idc.getImportFolder();
	ReferenceScenarioDataMapImpl map = null;
	List<Integer>resolutions = null;
	try {
	CSVscenarioLoader loader = new CSVscenarioLoader(folder);
	//resolutions = loader.getResolutions();
	map = loader.parseAllFiles();
	} catch(LogInitializationException sie) {
	org.eclipse.stem.diseasemodels.Activator.logError(sie.getMessage(), sie);
	return null;
	}
	InfectorInoculatorCollection iic = StandardFactory.eINSTANCE.createInfectorInoculatorCollection();
	iic.setImportFolder(folder);
	for(String location : map.getLocations()) {
	ReferenceScenarioDataInstance instance = map.getLocation(location);
	List<String>counts = null;
	List<String>denom = null;
	if(idc.isInfectorMode())
	counts = instance.getData(CSVscenarioLoader.I_TYPE);
	else
	counts = instance.getData(CSVscenarioLoader.R_TYPE);
	if(idc.isPercentage())
	denom = instance.getData(CSVscenarioLoader.POP_COUNT_KEY);

	// Use first row only
	double dcount = 0.0;

	if(idc.isFirstRow())
	dcount = Double.parseDouble(counts.get(0));
	else if(idc.isLastRow())
	dcount = Double.parseDouble(counts.get(counts.size()-1));
	else
	dcount = Double.parseDouble(counts.get(idc.getSelectecRow()));

	double ddenom = 1.0;
	if(idc.isPercentage())
	if(idc.isFirstRow())
	ddenom = (Double.parseDouble(denom.get(0)) / 100.0);
	else if(idc.isLastRow())
	ddenom = (Double.parseDouble(denom.get(counts.size()-1)) / 100.0);
	else
	ddenom = (Double.parseDouble(denom.get(idc.getSelectecRow())) / 100.0);

	SIInfector infector = null;
	if(idc.isInfectorMode()) {
	infector = StandardFactory.eINSTANCE.createSIInfector();
	infector.setInfectPercentage(idc.isPercentage());
	infector.setInfectiousCount(dcount/ddenom);
	infector.setURI(STEMURI.createURI(STEMURI.generateUniquePart()+"/infect_"+location));
	}
	else {
	infector = StandardFactory.eINSTANCE.createSIRInoculator();
	((SIRInoculator)infector).setInoculatePercentage(idc.isPercentage());
	((SIRInoculator)infector).setInoculatedPercentage(dcount/ddenom);
	infector.setURI(STEMURI.createURI(STEMURI.generateUniquePart()+"/inoculate_"+location));
	}
	infector.setDiseaseName(idc.getDiseaseName());
	infector.setPopulationIdentifier(idc.getPopulation());
	infector.setTargetISOKey(location);
	iic.getList().add(infector);
	}
	return iic;
	}
	} // getInfector

	@Override
	protected Composite createSpecificComposite(final Composite parent) {
	idc = new InfectorDefinitionComposite(parent, SWT.NONE,
	projectValidator, super.getSelectedProject());

	final NewInfectorWizard.NewInfectorPage self = this;

	this.projectNamesCombo.addSelectionListener(new SelectionListener() {

	public void widgetSelected(SelectionEvent arg0) {
	idc.setProject(self.getSelectedProject());
	}

	public void widgetDefaultSelected(SelectionEvent arg0) {

	}
	});

	return idc;
	} // createSpecificComposite

	@Override
	protected boolean validatePage() {
	boolean retValue = super.validatePage();
	if (retValue) {
	setErrorMessage(null);
	retValue = idc.validate();
	// Error?
	if (!retValue) {
	// Yes
	setErrorMessage(idc.getErrorMessage());
	} // if
	}
	return retValue;
	} // validatePage
	} // NewInfectorPage

	/**
	* This class is a {@link IHandler} for the command that creates a
	* {@link NewInfectorWizard}
	*/
	public static class NewInfectorWizardCommandHandler extends AbstractHandler
	implements IHandler {

	/**
	* @see org.eclipse.core.commands.AbstractHandler#execute(org.eclipse.core.commands.ExecutionEvent)
	*/
	public Object execute(final ExecutionEvent executionEvent)
	throws ExecutionException {
	final IWorkbenchWindow window = HandlerUtil
	.getActiveWorkbenchWindowChecked(executionEvent);
	final NewInfectorWizard wizard = new NewInfectorWizard();
	wizard.init(window.getWorkbench(), StructuredSelection.EMPTY);
	final WizardDialog wizardDialog = new STEMWizardDialog(window
	.getShell(), wizard);
	wizardDialog.open();
	return null;
	} // execute
	} // NewInfectorWizardCommandHandler
	} // NewInfectorWizard