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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.preference;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.lang.reflect.Field;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Properties;
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import java.util.Set;
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import java.util.StringTokenizer;
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import java.util.UUID;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.log4j.Logger;
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import org.eclipse.core.runtime.preferences.ConfigurationScope;
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import org.eclipse.core.runtime.preferences.IEclipsePreferences;
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import org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement;
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import org.eclipse.jface.preference.IPreferenceStore;
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import org.eclipse.jface.window.Window;
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import org.eclipse.swt.widgets.Composite;
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import org.eclipse.swt.widgets.Control;
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import org.eclipse.swt.widgets.Shell;
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import org.eclipse.ui.PlatformUI;
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import org.osgi.service.prefs.BackingStoreException;
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import org.osgi.service.prefs.Preferences;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.ITermTreeService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.api.service.config.FindTaxaAndNamesConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
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import eu.etaxonomy.cdm.model.common.ICdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference.PrefKey;
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import eu.etaxonomy.cdm.model.metadata.IPreferencePredicate;
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import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
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import eu.etaxonomy.cdm.model.metadata.PreferenceSubject;
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import eu.etaxonomy.cdm.model.metadata.TermDisplayEnum;
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import eu.etaxonomy.cdm.model.metadata.TermOrder;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.term.IDefinedTerm;
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import eu.etaxonomy.cdm.model.term.ISimpleTerm;
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import eu.etaxonomy.cdm.model.term.TermBase;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.model.term.VocabularyEnum;
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import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;
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import eu.etaxonomy.cdm.strategy.match.FieldMatcher;
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import eu.etaxonomy.cdm.strategy.match.IMatchStrategy;
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import eu.etaxonomy.cdm.strategy.match.MatchException;
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import eu.etaxonomy.cdm.strategy.match.MatchMode;
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import eu.etaxonomy.taxeditor.editor.definedterm.input.TermEditorInput;
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import eu.etaxonomy.taxeditor.model.AbstractUtility;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.model.NomenclaturalCodeHelper;
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import eu.etaxonomy.taxeditor.remoting.source.ICdmRemoteSource;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.store.TermStore;
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import eu.etaxonomy.taxeditor.store.internal.TaxeditorStorePlugin;
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import eu.etaxonomy.taxeditor.ui.dialog.DefaultLanguageDialog;
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/**
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* <p>
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* PreferencesUtil class.
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* </p>
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*
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* @author p.ciardelli
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* @author n.hoffmann
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* @created 05.12.2008
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*/
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public class PreferencesUtil implements IPreferenceKeys {
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private final static String EDITOR_PREFERENCES_NODE = "eu.etaxonomy.taxeditor";
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public static final String PREFERRED_TERMS_CHANGE = "preferred_terms";
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public static final String P2_REPOSITORIES_DELIM = ",";
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public static final String P2_REPOSITORY_FIELDS_DELIM = ";";
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public static final String SUBJECT_DELIM = "/";
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private static TermTree<Feature> preferredNameFeatureTree;
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private static TermTree<Feature> preferredTaxonFeatureTree;
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private final static Logger logger = Logger.getLogger(PreferencesUtil.class);
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public static IPreferenceStore getPreferenceStore() {
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return TaxeditorStorePlugin.getDefault().getPreferenceStore();
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}
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public static String[] extractSubjectParts(String subject){
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String[] result = subject.split("/");
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return result;
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}
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public static IEclipsePreferences getEditorPreferences(){
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return ConfigurationScope.INSTANCE.getNode(EDITOR_PREFERENCES_NODE);
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}
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public static String getPreferenceValue(PrefKey prefKey){
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try {
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if(getEditorPreferences().nodeExists(prefKey.getPredicate())){
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Preferences predicateNode = getEditorPreferences().node(prefKey.getPredicate());
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String[] splittedSubject = extractSubjectParts(prefKey.getSubject());
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String value = predicateNode.get(splittedSubject[splittedSubject.length-1], PreferencePredicate.getByKey(prefKey.getPredicate()).getDefaultValue() != null? PreferencePredicate.getByKey(prefKey.getPredicate()).getDefaultValue().toString(): "");
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int index = splittedSubject.length -2;
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while (value != null && index >= 0){
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value = predicateNode.get(splittedSubject[index], prefKey.getPredicate());
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index--;
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}
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return value;
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}
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} catch (BackingStoreException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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return null;
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}
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public static List<CdmPreference> getPreference(PreferencePredicate prefPredicate){
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try {
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List<CdmPreference> prefs = new ArrayList<>();
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CdmPreference pref;
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PreferenceSubject subject;
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if(getEditorPreferences().nodeExists(prefPredicate.getKey())){
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Preferences predicateNode = getEditorPreferences().node(prefPredicate.getKey());
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for (String childName: predicateNode.childrenNames()){
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Preferences child = predicateNode.node(childName);
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String subjectString = "";
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subjectString = createSubjectStringForChildNodes(childName, child);
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String value = child.get(subjectString, "");
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subject = PreferenceSubject.NewInstance(subjectString);
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pref = CdmPreference.NewInstance(subject, prefPredicate, value);
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prefs.add(pref);
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}
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}
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} catch (BackingStoreException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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return null;
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}
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private static String createSubjectStringForChildNodes(String subject, Preferences parent) {
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try {
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for (String childName: parent.childrenNames()){
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subject = childName+SUBJECT_DELIM+subject;
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Preferences child = parent.node(childName);
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createSubjectStringForChildNodes(subject, child);
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}
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} catch (BackingStoreException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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return subject;
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}
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private static String prefKey(String name) {
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return name + "_"+ ((ICdmRemoteSource)CdmStore.getActiveCdmSource()).toString();
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}
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public static String prefOverrideKey(String name) {
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return name + "_OVERRIDE_";
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}
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public static void setStringValue(String name, String value) {
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if (value != null){
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getPreferenceStore().setValue(prefKey(name), value);
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}else{
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getPreferenceStore().setToDefault(prefKey(name));
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}
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}
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public static void setIntValue(String name, int value) {
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getPreferenceStore().setValue(prefKey(name), value);
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}
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public static void setBooleanValue(String name, boolean value) {
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getPreferenceStore().setValue(prefKey(name), value);
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}
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public static void setDoubleValue(String name, double value) {
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getPreferenceStore().setValue(prefKey(name), value);
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}
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public static void setFloatValue(String name, float value) {
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getPreferenceStore().setValue(prefKey(name), value);
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}
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public static void setLongValue(String name, long value) {
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getPreferenceStore().setValue(prefKey(name), value);
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}
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public static String getStringValue(String name, boolean local) {
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CdmPreference pref = getDBPreferenceValue(name);
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boolean override = getOverrideForPreference(name);
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if (local || (pref == null && override)|| (pref != null && pref.isAllowOverride() && override)){
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//local preference
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String dbSpecific = prefKey(name);
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if (getPreferenceStore().contains(dbSpecific)){
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return getPreferenceStore().getString(dbSpecific);
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}
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}else if (pref != null){
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//db preference
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if (pref.getValue() == null){
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Object result = PreferencePredicate.getByKey(pref.getPredicate()).getDefaultValue();
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if (result instanceof String){
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return (String)result;
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}else{
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return result.toString();
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}
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}
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return pref.getValue();
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}
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//no override but default value
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IPreferencePredicate<?> pred = PreferencePredicate.getByKey(name);
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if (pred != null){
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if (pred.getDefaultValue() instanceof String){
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return (String)pred.getDefaultValue();
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}else if (pred.getDefaultValue() != null){
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return pred.getDefaultValue().toString();
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}
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}
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return null;
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}
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public static String getStringValue(String name){
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return getStringValue(name, false);
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}
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private static CdmPreference getDBPreferenceValue(String name) {
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CdmPreferenceCache cache = CdmPreferenceCache.instance();
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CdmPreference pref = null;
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pref = cache.get(name);
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return pref;
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}
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public static int getIntValue(String name, boolean local) {
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CdmPreference pref= getDBPreferenceValue(name);
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String prefValue = null;
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if (pref != null){
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prefValue = pref.getValue();
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}
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Integer result = null;
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try{
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result = Integer.parseInt(prefValue);
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}catch(NumberFormatException e){
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logger.debug("Preference value of " + name + " is not an integer");
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}
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boolean override = getOverrideForPreference(name);
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if (local || (pref == null && override) || (pref != null && pref.isAllowOverride() && override)){
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String dbSpecific = prefKey(name);
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if (getPreferenceStore().contains(dbSpecific)){
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result = getPreferenceStore().getInt(dbSpecific);
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}
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}
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if (result == null){
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IPreferencePredicate<?> pred = PreferencePredicate.getByKey(name);
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if (pred != null){
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if (pred.getDefaultValue() instanceof Integer){
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result = (Integer)pred.getDefaultValue();
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}else if (pred.getDefaultValue() != null){
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try{
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result = Integer.valueOf(pred.getDefaultValue().toString());
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}catch(NumberFormatException e){
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logger.debug("Preference value of " + name + " is not a number");
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result = 0;
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}
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}
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}
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//if no default value available
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if (result == null){
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result = 0;
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}
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}
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return result;
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}
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310
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311
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public static boolean getBooleanValue(String name) {
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Boolean result = getBooleanValue(name, false);
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if (result == null){
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return false;
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}else{
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return result;
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}
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}
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320
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public static Boolean getBooleanValue(String name, boolean local) {
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321
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if (CdmStore.isActive()){
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CdmPreference pref = getDBPreferenceValue(name);
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String overrideKey = createPreferenceString(createOverridePreferenceString(name));
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boolean override = getPreferenceStore().getBoolean(overrideKey);
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if (local || (pref == null && override)|| (pref != null && pref.isAllowOverride() && override)){
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//local preference
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String dbSpecific = prefKey(name);
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return getPreferenceStore().getBoolean(dbSpecific);
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}else if (pref != null){
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//db preference is available and override == false
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if (pref.getValue() == null){
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Object result = PreferencePredicate.getByKey(pref.getPredicate()).getDefaultValue();
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if (result instanceof Boolean){
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return (Boolean)result;
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}else{
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return Boolean.valueOf(result.toString());
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}
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}
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return Boolean.valueOf(pref.getValue());
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}
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//no override but default value
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IPreferencePredicate<?> pred = PreferencePredicate.getByKey(name);
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344
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if (pred != null){
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345
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if (pred.getDefaultValue() instanceof Boolean){
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return (Boolean)pred.getDefaultValue();
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}else if (pred.getDefaultValue() != null){
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return Boolean.valueOf(pred.getDefaultValue().toString());
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}
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}
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return false;
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}else{
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// no connection to db, use local preference
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return getPreferenceStore().getBoolean(name);
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}
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}
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358
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public static float getFloatValue(String name, boolean local) {
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359
|
CdmPreference pref = getDBPreferenceValue(name);
|
|
360
|
String prefValue = null;
|
|
361
|
if (pref != null){
|
|
362
|
prefValue = pref.getValue();
|
|
363
|
}
|
|
364
|
Float result = null;
|
|
365
|
try{
|
|
366
|
if (prefValue != null){
|
|
367
|
result = Float.parseFloat(prefValue);
|
|
368
|
}
|
|
369
|
}catch(NumberFormatException e){
|
|
370
|
logger.debug("Preference value of " + name + " is not a float");
|
|
371
|
}
|
|
372
|
|
|
373
|
boolean override = getOverrideForPreference(name);
|
|
374
|
|
|
375
|
if (local || pref == null || (pref.isAllowOverride() && override)){
|
|
376
|
String dbSpecific = prefKey(name);
|
|
377
|
if (getPreferenceStore().contains(dbSpecific)){
|
|
378
|
result = getPreferenceStore().getFloat(dbSpecific);
|
|
379
|
}else{
|
|
380
|
IPreferencePredicate<?> pred = PreferencePredicate.getByKey(name);
|
|
381
|
if (pred != null){
|
|
382
|
if (pred.getDefaultValue() instanceof Float){
|
|
383
|
return (float)pred.getDefaultValue();
|
|
384
|
}else if (pred.getDefaultValue() != null){
|
|
385
|
return Float.valueOf(pred.getDefaultValue().toString());
|
|
386
|
}
|
|
387
|
}
|
|
388
|
return 0;
|
|
389
|
}
|
|
390
|
}
|
|
391
|
return result;
|
|
392
|
}
|
|
393
|
|
|
394
|
public static CdmPreference setPreferredNomenclaturalCode(
|
|
395
|
String preferenceValue, boolean local) {
|
|
396
|
if (local){
|
|
397
|
setStringValue(PreferencePredicate.NomenclaturalCode.getKey(),
|
|
398
|
preferenceValue);
|
|
399
|
}
|
|
400
|
else{
|
|
401
|
ICdmRepository controller;
|
|
402
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
403
|
if (controller == null){
|
|
404
|
return null;
|
|
405
|
}
|
|
406
|
PrefKey key = null;
|
|
407
|
try{
|
|
408
|
key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
|
|
409
|
}catch (Exception e){
|
|
410
|
System.out.println(e.getStackTrace());
|
|
411
|
}
|
|
412
|
CdmPreference preference = null;
|
|
413
|
|
|
414
|
if (preferenceValue == null){
|
|
415
|
preference = controller.getPreferenceService().find(key);
|
|
416
|
if (preference == null){
|
|
417
|
return null;
|
|
418
|
} else{
|
|
419
|
setStringValue(PreferencePredicate.NomenclaturalCode.getKey(),
|
|
420
|
preference.getValue());
|
|
421
|
|
|
422
|
return preference;
|
|
423
|
}
|
|
424
|
} else{
|
|
425
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode, preferenceValue);
|
|
426
|
controller.getPreferenceService().set(preference);
|
|
427
|
|
|
428
|
}
|
|
429
|
}
|
|
430
|
return null;
|
|
431
|
}
|
|
432
|
|
|
433
|
public static void setPreferredNomenclaturalCode(
|
|
434
|
CdmPreference preference) {
|
|
435
|
|
|
436
|
ICdmRepository controller;
|
|
437
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
438
|
if (controller == null){
|
|
439
|
return;
|
|
440
|
}
|
|
441
|
|
|
442
|
if (preference == null){
|
|
443
|
PrefKey key = null;
|
|
444
|
try{
|
|
445
|
key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
|
|
446
|
}catch (Exception e){
|
|
447
|
System.out.println(e.getStackTrace());
|
|
448
|
}
|
|
449
|
controller.getPreferenceService().remove(key);
|
|
450
|
}else{
|
|
451
|
controller.getPreferenceService().set(preference);
|
|
452
|
}
|
|
453
|
}
|
|
454
|
|
|
455
|
public static NomenclaturalCode getPreferredNomenclaturalCode() {
|
|
456
|
|
|
457
|
String nomString = getStringValue(PreferencePredicate.NomenclaturalCode.getKey());
|
|
458
|
return getPreferredNomenclaturalCode(nomString);
|
|
459
|
}
|
|
460
|
|
|
461
|
public static NomenclaturalCode getPreferredNomenclaturalCode(String preferenceKeyNomenclaturalCode) {
|
|
462
|
|
|
463
|
for (NomenclaturalCode code : NomenclaturalCodeHelper.getAllCodes()) {
|
|
464
|
if (getPreferenceKey(code).equals(preferenceKeyNomenclaturalCode) || code.getKey().equals(preferenceKeyNomenclaturalCode)) {
|
|
465
|
return code;
|
|
466
|
}
|
|
467
|
}
|
|
468
|
return null;
|
|
469
|
}
|
|
470
|
|
|
471
|
public static boolean isShowTaxonAssociations(){
|
|
472
|
boolean result = getBooleanValue(PreferencePredicate.ShowTaxonAssociations.getKey());
|
|
473
|
return result;
|
|
474
|
}
|
|
475
|
|
|
476
|
public static boolean isShowLifeForm(){
|
|
477
|
boolean result = getBooleanValue(PreferencePredicate.ShowLifeForm.getKey());
|
|
478
|
return result;
|
|
479
|
}
|
|
480
|
|
|
481
|
public static boolean isDeterminationOnlyForFieldUnits(){
|
|
482
|
boolean result = getBooleanValue(PreferencePredicate.DeterminationOnlyForFieldUnits.getKey());
|
|
483
|
return result;
|
|
484
|
}
|
|
485
|
|
|
486
|
public static boolean isCollectingAreaInGeneralSection(){
|
|
487
|
boolean result = getBooleanValue(PreferencePredicate.ShowCollectingAreasInGeneralSection.getKey());
|
|
488
|
return result;
|
|
489
|
}
|
|
490
|
|
|
491
|
public static CdmPreference getPreferenceFromDB(IPreferencePredicate<?> predicate){
|
|
492
|
ICdmRepository controller;
|
|
493
|
CdmPreference pref = null;
|
|
494
|
|
|
495
|
try{
|
|
496
|
if(CdmStore.isActive()){
|
|
497
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
498
|
PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), predicate);
|
|
499
|
pref = controller.getPreferenceService().find(key);
|
|
500
|
}
|
|
501
|
}catch(Exception e){
|
|
502
|
e.printStackTrace();
|
|
503
|
}
|
|
504
|
|
|
505
|
return pref;
|
|
506
|
}
|
|
507
|
|
|
508
|
public static List<CdmPreference> getPreferencesFromDB(IPreferencePredicate<?> predicate){
|
|
509
|
ICdmRepository controller;
|
|
510
|
List<CdmPreference> prefs = null;
|
|
511
|
|
|
512
|
try{
|
|
513
|
if(CdmStore.isActive()){
|
|
514
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
515
|
PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), predicate);
|
|
516
|
prefs = controller.getPreferenceService().list(predicate);
|
|
517
|
}
|
|
518
|
}catch(Exception e){
|
|
519
|
e.printStackTrace();
|
|
520
|
}
|
|
521
|
|
|
522
|
return prefs;
|
|
523
|
|
|
524
|
}
|
|
525
|
|
|
526
|
public static void setPreferencesToDB(CdmPreference preference, boolean setDefault){
|
|
527
|
ICdmRepository controller;
|
|
528
|
try{
|
|
529
|
if(CdmStore.isActive()){
|
|
530
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
531
|
|
|
532
|
if (setDefault){
|
|
533
|
controller.getPreferenceService().remove(preference.getKey());
|
|
534
|
}else{
|
|
535
|
controller.getPreferenceService().set(preference);
|
|
536
|
}
|
|
537
|
}
|
|
538
|
}catch(Exception e){
|
|
539
|
e.printStackTrace();
|
|
540
|
}
|
|
541
|
}
|
|
542
|
|
|
543
|
public static CdmPreference getPreferenceFromDB(PrefKey key){
|
|
544
|
ICdmRepository controller;
|
|
545
|
CdmPreference pref = null;
|
|
546
|
|
|
547
|
try{
|
|
548
|
if(CdmStore.isActive()){
|
|
549
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
550
|
pref = controller.getPreferenceService().find(key);
|
|
551
|
}
|
|
552
|
}catch(Exception e){
|
|
553
|
e.printStackTrace();
|
|
554
|
}
|
|
555
|
|
|
556
|
return pref;
|
|
557
|
|
|
558
|
}
|
|
559
|
|
|
560
|
public static void setPreferenceToDB(CdmPreference preference){
|
|
561
|
ICdmRepository controller;
|
|
562
|
try{
|
|
563
|
if(CdmStore.isActive()){
|
|
564
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
565
|
if (preference.getValue() == null && preference.isAllowOverride()){
|
|
566
|
controller.getPreferenceService().remove(preference.getKey());
|
|
567
|
}else{
|
|
568
|
controller.getPreferenceService().set(preference);
|
|
569
|
}
|
|
570
|
CdmPreferenceCache.instance().put(preference);
|
|
571
|
}
|
|
572
|
}catch(Exception e){
|
|
573
|
e.printStackTrace();
|
|
574
|
}
|
|
575
|
}
|
|
576
|
|
|
577
|
public static String getPreferredDefaultLangugae(){
|
|
578
|
String preferredLanguage = getStringValue(DEFAULT_LANGUAGE_EDITOR, true);
|
|
579
|
if(StringUtils.isNotEmpty(preferredLanguage) && StringUtils.isNotBlank(preferredLanguage)){
|
|
580
|
return preferredLanguage;
|
|
581
|
}
|
|
582
|
return null;
|
|
583
|
}
|
|
584
|
|
|
585
|
public static boolean isShowMediaPreview(){
|
|
586
|
boolean isShowMediaPreview = getBooleanValue(SHOW_MEDIA_PREVIEW, true);
|
|
587
|
return isShowMediaPreview;
|
|
588
|
}
|
|
589
|
|
|
590
|
/**
|
|
591
|
* Get the match strategy for the given class that was stored in preferences
|
|
592
|
* or the default strategy if it was not stored in preferences
|
|
593
|
*
|
|
594
|
* @param clazz
|
|
595
|
* a {@link java.lang.Class} object.
|
|
596
|
* @return a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy} object.
|
|
597
|
*/
|
|
598
|
public static IMatchStrategy getMatchStrategy(Class<?> clazz) {
|
|
599
|
String className = clazz.getName();
|
|
600
|
if (getBooleanValue(MATCH_STRATEGY_PREFIX + className, true)) {
|
|
601
|
IMatchStrategy matchStrategy = getDefaultMatchStrategy(clazz);
|
|
602
|
|
|
603
|
//TODO CacheMatchers (or multiple field matchers in future) are missing here
|
|
604
|
for (FieldMatcher fieldMatcher : matchStrategy.getMatching().getFieldMatchers(false)) {
|
|
605
|
String fieldName = fieldMatcher.getPropertyName();
|
|
606
|
String matchModeName = getStringValue(
|
|
607
|
getMatchStrategyFieldName(className, fieldName), true);
|
|
608
|
MatchMode matchMode = MatchMode.valueOf(matchModeName);
|
|
609
|
try {
|
|
610
|
matchStrategy.setMatchMode(fieldName, matchMode);
|
|
611
|
} catch (MatchException e) {
|
|
612
|
MessagingUtils.error(PreferencesUtil.class, e);
|
|
613
|
throw new RuntimeException(e);
|
|
614
|
}
|
|
615
|
}
|
|
616
|
|
|
617
|
return matchStrategy;
|
|
618
|
}
|
|
619
|
return getDefaultMatchStrategy(clazz);
|
|
620
|
}
|
|
621
|
|
|
622
|
/**
|
|
623
|
* Stores a matchStrategy into the preference store.
|
|
624
|
*
|
|
625
|
* @param matchStrategy
|
|
626
|
* a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy}
|
|
627
|
* object.
|
|
628
|
*/
|
|
629
|
public static void setMatchStrategy(IMatchStrategy matchStrategy) {
|
|
630
|
String className = "ANY class"; //FIXME was: matchStrategy.getMatchClass().getName(); seems currently not in use
|
|
631
|
setBooleanValue(MATCH_STRATEGY_PREFIX + className, true);
|
|
632
|
|
|
633
|
List<FieldMatcher> fieldMatchers = matchStrategy.getMatching().getFieldMatchers(false);
|
|
634
|
|
|
635
|
for (FieldMatcher fieldMatcher : fieldMatchers) {
|
|
636
|
String fieldName = fieldMatcher.getPropertyName();
|
|
637
|
setStringValue(
|
|
638
|
getMatchStrategyFieldName(className, fieldName),
|
|
639
|
fieldMatcher.getMatchMode().name());
|
|
640
|
}
|
|
641
|
}
|
|
642
|
|
|
643
|
/**
|
|
644
|
* Helper method to create the preference property for a match field.
|
|
645
|
*
|
|
646
|
* @param className
|
|
647
|
* @param fieldName
|
|
648
|
* @return
|
|
649
|
*/
|
|
650
|
private static String getMatchStrategyFieldName(String className,
|
|
651
|
String fieldName) {
|
|
652
|
return MATCH_STRATEGY_PREFIX + className + "." + fieldName;
|
|
653
|
}
|
|
654
|
|
|
655
|
/**
|
|
656
|
* Returns the default match strategy for a given class.
|
|
657
|
*
|
|
658
|
* @param clazz
|
|
659
|
* a {@link java.lang.Class} object.
|
|
660
|
* @return a {@link eu.etaxonomy.cdm.strategy.match.IMatchStrategy} object.
|
|
661
|
*/
|
|
662
|
public static IMatchStrategy getDefaultMatchStrategy(Class clazz) {
|
|
663
|
return DefaultMatchStrategy.NewInstance(clazz);
|
|
664
|
}
|
|
665
|
|
|
666
|
public static String getDateFormatPattern() {
|
|
667
|
// TODO make this configurable in properties
|
|
668
|
String pattern = "Y-M-d H:m";
|
|
669
|
return pattern;
|
|
670
|
}
|
|
671
|
|
|
672
|
public static <T extends TermBase> void addTermToPreferredTerms(T term) {
|
|
673
|
|
|
674
|
// VocabularyEnum vocabulary =
|
|
675
|
// VocabularyEnum.getVocabularyEnum(term.getClass());
|
|
676
|
//
|
|
677
|
// getPreferenceStore().setValue(getPreferenceKey(term),
|
|
678
|
// VocabularyStore.getTermVocabulary(vocabulary).getTerms().contains(term));
|
|
679
|
//
|
|
680
|
// firePreferencesChanged(term.getClass());
|
|
681
|
}
|
|
682
|
|
|
683
|
/**
|
|
684
|
* Construct a unique key using the CdmBase object's uuid
|
|
685
|
*
|
|
686
|
* @param cdmBase
|
|
687
|
* @return
|
|
688
|
*/
|
|
689
|
private static String getPreferenceKey(ICdmBase cdmBase) {
|
|
690
|
cdmBase = HibernateProxyHelper.deproxy(cdmBase);
|
|
691
|
|
|
692
|
String key = cdmBase.getClass().getName().concat(".")
|
|
693
|
.concat(cdmBase.getUuid().toString());
|
|
694
|
if (key.contains("javassist")) {
|
|
695
|
MessagingUtils.info("proxy");
|
|
696
|
}
|
|
697
|
return key;
|
|
698
|
}
|
|
699
|
|
|
700
|
/**
|
|
701
|
* Construct a unique key using the CdmBase object's uuid
|
|
702
|
*
|
|
703
|
* @param cdmBase
|
|
704
|
* @return
|
|
705
|
*/
|
|
706
|
public static String getPreferenceKey(ISimpleTerm<?> simpleTerm) {
|
|
707
|
simpleTerm = HibernateProxyHelper.deproxy(simpleTerm);
|
|
708
|
String key = simpleTerm.getClass().getName().concat(".")
|
|
709
|
.concat(simpleTerm.getUuid().toString());
|
|
710
|
if (key.contains("javassist")) {
|
|
711
|
MessagingUtils.warn(PreferencesUtil.class,
|
|
712
|
"Trying to persist a preference based on a proxy class.");
|
|
713
|
}
|
|
714
|
return key;
|
|
715
|
}
|
|
716
|
|
|
717
|
/**
|
|
718
|
* Construct a unique key using the CdmBase object's uuid
|
|
719
|
*/
|
|
720
|
public static String getPreferenceKey(IDefinedTerm definedTerm) {
|
|
721
|
definedTerm = HibernateProxyHelper.deproxy(definedTerm);
|
|
722
|
String key = definedTerm.getClass().getName().concat(".")
|
|
723
|
.concat(definedTerm.getUuid().toString());
|
|
724
|
if (key.contains("javassist")) {
|
|
725
|
MessagingUtils.warn(PreferencesUtil.class,
|
|
726
|
"Trying to persist a preference based on a proxy class.");
|
|
727
|
}
|
|
728
|
return key;
|
|
729
|
}
|
|
730
|
|
|
731
|
/**
|
|
732
|
* Retrieves search preferences from the preference store
|
|
733
|
*
|
|
734
|
* @return an {@link ITaxonServiceConfigurator} to pass to search methods
|
|
735
|
*/
|
|
736
|
public static IFindTaxaAndNamesConfigurator getSearchConfigurator() {
|
|
737
|
IFindTaxaAndNamesConfigurator configurator = initializeSearchConfigurator();
|
|
738
|
|
|
739
|
configurator.setDoTaxa(PreferencesUtil.getPreferenceStore().contains(IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_TAXA)? PreferencesUtil.getPreferenceStore().getBoolean(
|
|
740
|
IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_TAXA): true);
|
|
741
|
configurator.setDoSynonyms(PreferencesUtil.getPreferenceStore().contains(IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_SYNONYMS)? PreferencesUtil.getPreferenceStore().getBoolean(
|
|
742
|
IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_SYNONYMS): true);
|
|
743
|
configurator.setDoNamesWithoutTaxa(PreferencesUtil.getPreferenceStore().contains(IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_NAMES)? PreferencesUtil.getPreferenceStore().getBoolean(
|
|
744
|
IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_NAMES): true);
|
|
745
|
configurator.setDoTaxaByCommonNames(PreferencesUtil.getPreferenceStore().contains(IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES)? PreferencesUtil.getPreferenceStore().getBoolean(
|
|
746
|
IPreferenceKeys.TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES): true);
|
|
747
|
//configurator.setMatchMode(eu.etaxonomy.cdm.persistence.query.MatchMode.valueOf(getStringValue(TAXON_SERVICE_CONFIGURATOR_MATCH_MODE)));
|
|
748
|
|
|
749
|
return configurator;
|
|
750
|
}
|
|
751
|
|
|
752
|
/**
|
|
753
|
* create new preferences, setting all search options to true
|
|
754
|
*
|
|
755
|
* @return a
|
|
756
|
* {@link eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator}
|
|
757
|
* object.
|
|
758
|
*/
|
|
759
|
public static IFindTaxaAndNamesConfigurator initializeSearchConfigurator() {
|
|
760
|
IFindTaxaAndNamesConfigurator configurator = FindTaxaAndNamesConfiguratorImpl.NewInstance();
|
|
761
|
|
|
762
|
configurator.setDoTaxa(true);
|
|
763
|
configurator.setDoSynonyms(true);
|
|
764
|
configurator.setDoNamesWithoutTaxa(true);
|
|
765
|
configurator.setDoTaxaByCommonNames(true);
|
|
766
|
|
|
767
|
configurator.setTaxonPropertyPath(Arrays.asList("$", "titleCache",
|
|
768
|
"name", "name.$", "relationsFromThisTaxon.$"));
|
|
769
|
|
|
770
|
configurator.setSynonymPropertyPath(Arrays.asList("$", "titleCache",
|
|
771
|
"name", "name.$", "synonyms.relatedTo.*"));
|
|
772
|
|
|
773
|
// DEFAULT VALUES
|
|
774
|
// match mode is a simple like, actually all other match modes are kind
|
|
775
|
// of bogus
|
|
776
|
configurator
|
|
777
|
.setMatchMode(eu.etaxonomy.cdm.persistence.query.MatchMode.ANYWHERE);
|
|
778
|
// we set page number and size here as this should always be unlimited
|
|
779
|
configurator.setPageNumber(0);
|
|
780
|
// TODO currently limit results to 10000
|
|
781
|
configurator.setPageSize(10000);
|
|
782
|
//setSearchConfigurator(configurator) ;
|
|
783
|
return configurator;
|
|
784
|
}
|
|
785
|
|
|
786
|
/**
|
|
787
|
* Store search preferences
|
|
788
|
*
|
|
789
|
* @param configurator
|
|
790
|
* a
|
|
791
|
* {@link eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator}
|
|
792
|
* object.
|
|
793
|
*/
|
|
794
|
public static void setSearchConfigurator(
|
|
795
|
IFindTaxaAndNamesConfigurator configurator) {
|
|
796
|
getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_TAXA,
|
|
797
|
configurator.isDoTaxa());
|
|
798
|
getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_SYNONYMS,
|
|
799
|
configurator.isDoSynonyms());
|
|
800
|
getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_NAMES,
|
|
801
|
configurator.isDoNamesWithoutTaxa());
|
|
802
|
getPreferenceStore().setValue(TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES,
|
|
803
|
configurator.isDoTaxaByCommonNames());
|
|
804
|
}
|
|
805
|
|
|
806
|
public static void firePreferencesChanged(Class clazz) {
|
|
807
|
getPreferenceStore().firePropertyChangeEvent(PREFERRED_TERMS_CHANGE,
|
|
808
|
null, clazz);
|
|
809
|
}
|
|
810
|
|
|
811
|
|
|
812
|
public static String createPreferenceString(String property){
|
|
813
|
return prefKey(property);
|
|
814
|
}
|
|
815
|
public static String createOverridePreferenceString(String property){
|
|
816
|
return prefOverrideKey(property);
|
|
817
|
}
|
|
818
|
|
|
819
|
public static boolean getOverrideForPreference(String preferenceString){
|
|
820
|
return PreferencesUtil.getBooleanValue(PreferencesUtil.createOverridePreferenceString(preferenceString), true);
|
|
821
|
}
|
|
822
|
|
|
823
|
/**
|
|
824
|
* Set default values for preferences
|
|
825
|
*/
|
|
826
|
public static void setDefaults() {
|
|
827
|
|
|
828
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.EditMapServiceAccessPoint.getKey()),
|
|
829
|
"http://edit.africamuseum.be/edit_wp5/v1.2/rest_gen.php");
|
|
830
|
//FIXME : changed default for SHOULD_CONNECT_AT_STARTUP to false (ticket 3828) until resolution
|
|
831
|
getPreferenceStore().setDefault(createPreferenceString(SHOULD_CONNECT_AT_STARTUP), false);
|
|
832
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.MobotOpenUrlServiceAccessPoint.getKey()),
|
|
833
|
"http://www.biodiversitylibrary.org/openurl");
|
|
834
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.MobotOpenUrlServiceMaxWidth.getKey()), "1000");
|
|
835
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.MobotOpenUrlServiceMaxHeight.getKey()), "1000");
|
|
836
|
getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_TAXA, true);
|
|
837
|
getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_SYNONYMS, true);
|
|
838
|
getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_NAMES, true);
|
|
839
|
getPreferenceStore().setDefault(TAXON_SERVICE_CONFIGURATOR_COMMON_NAMES, true);
|
|
840
|
|
|
841
|
//Name Details
|
|
842
|
// getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.NameDetailsView.getKey()), new NameDetailsConfigurator(false).toString());
|
|
843
|
|
|
844
|
//Navigator preferences
|
|
845
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.TaxonNodeOrder.getKey()), NavigatorOrderEnum.RankAndNameOrder.getKey());
|
|
846
|
|
|
847
|
//getPreferenceStore().setDefault(createPreferenceString(Prefe), true);
|
|
848
|
|
|
849
|
getPreferenceStore().setDefault(createPreferenceString(SHOW_ADVANCED_MEDIA_SECTION), false);
|
|
850
|
|
|
851
|
getPreferenceStore().setDefault(createPreferenceString(SHOW_MEDIA_PREVIEW), false);
|
|
852
|
//override db preferences
|
|
853
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.AbcdImportConfig.getKey())), false);
|
|
854
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.NameDetailsView.getKey())), false);
|
|
855
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.CommonNameAreaVocabularies.getKey())), false);
|
|
856
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.CommonNameReferencesWithMarker.getKey()), false);
|
|
857
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.ShowTaxonNodeWizard.getKey()), Boolean.valueOf(PreferencePredicate.ShowTaxonNodeWizard.getDefaultValue().toString()));
|
|
858
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.ShowNamespaceInSource.getKey()), Boolean.valueOf(PreferencePredicate.ShowNamespaceInSource.getDefaultValue().toString()));
|
|
859
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.ShowIdInSource.getKey()), Boolean.valueOf(PreferencePredicate.ShowIdInSource.getDefaultValue().toString()));
|
|
860
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.DisableMultiClassification.getKey()), Boolean.valueOf(PreferencePredicate.DisableMultiClassification.getDefaultValue().toString()));
|
|
861
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.ShowImportExportMenu.getKey()), Boolean.valueOf(PreferencePredicate.ShowImportExportMenu.getDefaultValue().toString()));
|
|
862
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.ShowSpecimen.getKey()), Boolean.valueOf(PreferencePredicate.ShowSpecimen.getDefaultValue().toString()));
|
|
863
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.SearchForIdentifierAndTitleCache.getKey()), Boolean.valueOf(PreferencePredicate.SearchForIdentifierAndTitleCache.getDefaultValue().toString()));
|
|
864
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.SearchForIdentifierAndTitleCache.getKey())), false);
|
|
865
|
getPreferenceStore().setDefault(createPreferenceString(PreferencePredicate.SearchForIdentifierAsDefault.getKey()), Boolean.valueOf(PreferencePredicate.SearchForIdentifierAsDefault.getDefaultValue().toString()));
|
|
866
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.SearchForIdentifierAsDefault.getKey())), false);
|
|
867
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.ShowModifierFreeText.getKey())), false);
|
|
868
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.ShowModifier.getKey())), false);
|
|
869
|
getPreferenceStore().setDefault(createPreferenceString(prefOverrideKey(PreferencePredicate.DistributionEditorActivated.getKey())), false);
|
|
870
|
}
|
|
871
|
|
|
872
|
public static void checkNomenclaturalCode() {
|
|
873
|
// First time Editor is opened, no nomenclatural code has been set
|
|
874
|
if (PreferencesUtil.getPreferredNomenclaturalCode() == null) {
|
|
875
|
PreferencesUtil.setPreferredNomenclaturalCode(getPreferenceKey(NomenclaturalCode.ICNAFP), true);
|
|
876
|
}
|
|
877
|
}
|
|
878
|
|
|
879
|
public static void setNomenclaturalCodePreferences(){
|
|
880
|
ICdmRepository controller;
|
|
881
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
882
|
PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewDatabaseInstance(), PreferencePredicate.NomenclaturalCode);
|
|
883
|
CdmPreference preference = null;
|
|
884
|
if (controller == null){
|
|
885
|
return ;
|
|
886
|
}
|
|
887
|
preference = controller.getPreferenceService().find(key);
|
|
888
|
if (preference == null){
|
|
889
|
return;
|
|
890
|
}
|
|
891
|
// setBooleanValue(ALLOW_OVERRIDE_NOMENCLATURAL_CODE_KEY, preference.isAllowOverride());
|
|
892
|
|
|
893
|
int index = StringUtils.lastIndexOf(preference.getValue(), ".");
|
|
894
|
UUID uuid = UUID.fromString(preference.getValue().substring(index +1, preference.getValue().length()));
|
|
895
|
NomenclaturalCode preferredCode = NomenclaturalCode.getByUuid(uuid);
|
|
896
|
|
|
897
|
setStringValue(PreferencePredicate.NomenclaturalCode.getKey(),
|
|
898
|
getPreferenceKey(preferredCode));
|
|
899
|
}
|
|
900
|
|
|
901
|
public static void checkDefaultLanguage(){
|
|
902
|
if(PreferencesUtil.getPreferredDefaultLangugae() == null){
|
|
903
|
Shell shell = AbstractUtility.getShell();
|
|
904
|
int open = new DefaultLanguageDialog(shell).open();
|
|
905
|
if(open == Window.OK){
|
|
906
|
PlatformUI.getWorkbench().restart();
|
|
907
|
}
|
|
908
|
}else{
|
|
909
|
//TODO:In case of a reinstall, the config.ini will be overwritten
|
|
910
|
// here you create config.ini with the stored key from preferences
|
|
911
|
}
|
|
912
|
}
|
|
913
|
|
|
914
|
public static String getMapServiceAccessPoint() {
|
|
915
|
return getStringValue(PreferencePredicate.EditMapServiceAccessPoint.getKey());
|
|
916
|
}
|
|
917
|
|
|
918
|
public static boolean shouldConnectAtStartUp() {
|
|
919
|
//FIXME : force SHOULD_CONNECT_AT_STARTUP to false (ticket 3828) until resolution
|
|
920
|
//return getBooleanValue(SHOULD_CONNECT_AT_STARTUP);
|
|
921
|
return false;
|
|
922
|
}
|
|
923
|
|
|
924
|
public static TermTree<?> getDefaultFeatureTreeForTextualDescription() {
|
|
925
|
String uuidString = getStringValue(
|
|
926
|
FEATURE_TREE_DEFAULT_TEXT, true);
|
|
927
|
if (StringUtils.isBlank(uuidString)) {
|
|
928
|
return null;
|
|
929
|
}
|
|
930
|
TermTree<?> tree = CdmStore.getService(
|
|
931
|
ITermTreeService.class).load(UUID.fromString(uuidString));
|
|
932
|
|
|
933
|
if (tree == null || tree.getId() == 0) {
|
|
934
|
return null;
|
|
935
|
}
|
|
936
|
return tree;
|
|
937
|
}
|
|
938
|
|
|
939
|
public static TermTree<?> getDefaultFeatureTreeForStructuredDescription() {
|
|
940
|
String uuidString = getStringValue(
|
|
941
|
FEATURE_TREE_DEFAULT_STRUCTURE, true);
|
|
942
|
return StringUtils.isBlank(uuidString) ? null : CdmStore.getService(
|
|
943
|
ITermTreeService.class).load(UUID.fromString(uuidString));
|
|
944
|
}
|
|
945
|
|
|
946
|
public static void setSortRanksHierarchichally(boolean selection) {
|
|
947
|
setBooleanValue(PreferencePredicate.SortRanksHierarchichally.getKey(), selection);
|
|
948
|
}
|
|
949
|
|
|
950
|
public static boolean getSortRanksHierarchichally() {
|
|
951
|
return getBooleanValue(PreferencePredicate.SortRanksHierarchichally.getKey());
|
|
952
|
}
|
|
953
|
|
|
954
|
public static boolean isMultilanguageTextEditingCapability() {
|
|
955
|
return getBooleanValue(
|
|
956
|
PreferencePredicate.MultiLanguageTextEditing.getKey());
|
|
957
|
}
|
|
958
|
|
|
959
|
public static Language getGlobalLanguage() {
|
|
960
|
|
|
961
|
String languageUuidString = getStringValue(
|
|
962
|
GLOBAL_LANGUAGE_UUID, true);
|
|
963
|
|
|
964
|
if(!CdmStore.isActive()) {
|
|
965
|
MessagingUtils.noDataSourceWarningDialog(languageUuidString);
|
|
966
|
return null;
|
|
967
|
}
|
|
968
|
|
|
969
|
if (CdmUtils.isBlank(languageUuidString)) {
|
|
970
|
return Language.getDefaultLanguage();
|
|
971
|
}
|
|
972
|
|
|
973
|
UUID languageUuid = UUID.fromString(languageUuidString);
|
|
974
|
return (Language) CdmStore.getService(ITermService.class).load(
|
|
975
|
languageUuid);
|
|
976
|
}
|
|
977
|
|
|
978
|
public static void setGlobalLanguage(Language language) {
|
|
979
|
if(language != null) {
|
|
980
|
setStringValue(GLOBAL_LANGUAGE_UUID,language.getUuid().toString());
|
|
981
|
CdmStore.setDefaultLanguage(language);
|
|
982
|
}
|
|
983
|
}
|
|
984
|
|
|
985
|
public static Map<MarkerType, Boolean> getEditMarkerTypePreferences() {
|
|
986
|
List<MarkerType> markerTypes = CdmStore.getTermManager()
|
|
987
|
.getPreferredTerms(MarkerType.class);
|
|
988
|
|
|
989
|
Map<MarkerType, Boolean> result = new HashMap<>();
|
|
990
|
|
|
991
|
for (MarkerType markerType : markerTypes) {
|
|
992
|
String name = getMarkerTypeEditingPreferenceKey(markerType);
|
|
993
|
Boolean value = getBooleanValue(name);
|
|
994
|
result.put(markerType, value);
|
|
995
|
}
|
|
996
|
|
|
997
|
return result;
|
|
998
|
}
|
|
999
|
|
|
1000
|
public static void setEditMarkerTypePreferences(
|
|
1001
|
Map<MarkerType, Boolean> markerTypeEditingMap) {
|
|
1002
|
for (MarkerType markerType : markerTypeEditingMap.keySet()) {
|
|
1003
|
String name = getMarkerTypeEditingPreferenceKey(markerType);
|
|
1004
|
setBooleanValue(name,
|
|
1005
|
markerTypeEditingMap.get(markerType));
|
|
1006
|
}
|
|
1007
|
}
|
|
1008
|
|
|
1009
|
private static String getMarkerTypeEditingPreferenceKey(
|
|
1010
|
MarkerType markerType) {
|
|
1011
|
markerType = HibernateProxyHelper.deproxy(markerType);
|
|
1012
|
return markerType.getClass().getName() + EDIT_MARKER_TYPE_PREFIX;
|
|
1013
|
}
|
|
1014
|
|
|
1015
|
public static void setEditMarkerTypePreference(MarkerType markerType,
|
|
1016
|
boolean edit) {
|
|
1017
|
setBooleanValue(
|
|
1018
|
getMarkerTypeEditingPreferenceKey(markerType), edit);
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
public static DerivedUnitFacadeConfigurator getDerivedUnitConfigurator() {
|
|
1022
|
DerivedUnitFacadeConfigurator configurator = DerivedUnitFacadeConfigurator
|
|
1023
|
.NewInstance();
|
|
1024
|
configurator.setMoveDerivedUnitMediaToGallery(true);
|
|
1025
|
configurator.setMoveFieldObjectMediaToGallery(true);
|
|
1026
|
return configurator;
|
|
1027
|
}
|
|
1028
|
|
|
1029
|
/**
|
|
1030
|
* This method will write language properties to the config.ini located in the configuration folder
|
|
1031
|
* of the Taxonomic Ediitor. <b>This method is only used to set the default language for Taxonomic Editor.</b>
|
|
1032
|
*
|
|
1033
|
* @param setLanguage 0 is for german and 1 for english.
|
|
1034
|
* @throws IOException
|
|
1035
|
*/
|
|
1036
|
public void writePropertyToConfigFile(int setLanguage) throws IOException {
|
|
1037
|
File file = org.eclipse.core.runtime.preferences.ConfigurationScope.INSTANCE.getLocation().toFile();
|
|
1038
|
//give warning to user if the directory has no write access
|
|
1039
|
if(file == null){
|
|
1040
|
throw new IOException();
|
|
1041
|
}
|
|
1042
|
Properties properties = load(file.getAbsolutePath()+"/config.ini");
|
|
1043
|
switch(setLanguage){
|
|
1044
|
case 0:
|
|
1045
|
properties.setProperty("osgi.nl", "de");
|
|
1046
|
setStringValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "de");
|
|
1047
|
break;
|
|
1048
|
case 1:
|
|
1049
|
properties.setProperty("osgi.nl", "en");
|
|
1050
|
setStringValue(IPreferenceKeys.DEFAULT_LANGUAGE_EDITOR, "en");
|
|
1051
|
break;
|
|
1052
|
default:
|
|
1053
|
break;
|
|
1054
|
}
|
|
1055
|
save(file+"/config.ini", properties);
|
|
1056
|
}
|
|
1057
|
|
|
1058
|
/**
|
|
1059
|
* This method loads a property from a given file and returns it.
|
|
1060
|
*
|
|
1061
|
* @param filename
|
|
1062
|
* @return
|
|
1063
|
* @throws IOException
|
|
1064
|
*/
|
|
1065
|
private Properties load(String filename) throws IOException {
|
|
1066
|
FileInputStream in = new FileInputStream(filename);
|
|
1067
|
Properties prop = new Properties();
|
|
1068
|
prop.load(in);
|
|
1069
|
in.close();
|
|
1070
|
return prop;
|
|
1071
|
}
|
|
1072
|
|
|
1073
|
/**
|
|
1074
|
* This method saves a property to the specified file.
|
|
1075
|
*
|
|
1076
|
* @param filename
|
|
1077
|
* @param properties
|
|
1078
|
* @throws IOException
|
|
1079
|
*/
|
|
1080
|
private void save(String filename, Properties properties) throws IOException{
|
|
1081
|
FileOutputStream fos = new FileOutputStream(filename);
|
|
1082
|
properties.store(fos, "");
|
|
1083
|
fos.close();
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
/**
|
|
1087
|
* Saves a list of P2 Metadata Repositories as string with specified delimiters
|
|
1088
|
*
|
|
1089
|
* @param p2Repos
|
|
1090
|
*/
|
|
1091
|
public static void setP2Repositories(List<MetadataRepositoryElement> p2Repos) {
|
|
1092
|
StringBuilder sb = new StringBuilder();
|
|
1093
|
for(MetadataRepositoryElement p2Repo : p2Repos) {
|
|
1094
|
sb.append(P2_REPOSITORIES_DELIM);
|
|
1095
|
if(p2Repo.getName() == null || p2Repo.getName().isEmpty()) {
|
|
1096
|
sb.append("-");
|
|
1097
|
} else {
|
|
1098
|
sb.append(p2Repo.getName());
|
|
1099
|
}
|
|
1100
|
sb.append(P2_REPOSITORY_FIELDS_DELIM);
|
|
1101
|
sb.append(p2Repo.getLocation().toString());
|
|
1102
|
sb.append(P2_REPOSITORY_FIELDS_DELIM);
|
|
1103
|
sb.append(String.valueOf(p2Repo.isEnabled()));
|
|
1104
|
}
|
|
1105
|
getPreferenceStore().setValue(P2_REPOSITORY_LIST, sb.toString());
|
|
1106
|
}
|
|
1107
|
|
|
1108
|
|
|
1109
|
/**
|
|
1110
|
* Retrieves a list of previously saved P2 repositories
|
|
1111
|
*/
|
|
1112
|
public static List<MetadataRepositoryElement> getP2Repositories() {
|
|
1113
|
List<MetadataRepositoryElement> p2Repos = new ArrayList<MetadataRepositoryElement>();
|
|
1114
|
String p2ReposPref = getStringValue(P2_REPOSITORY_LIST, true);
|
|
1115
|
if(p2ReposPref != null && !p2ReposPref.isEmpty()) {
|
|
1116
|
StringTokenizer p2ReposPrefST = new StringTokenizer(p2ReposPref,P2_REPOSITORIES_DELIM);
|
|
1117
|
|
|
1118
|
while(p2ReposPrefST.hasMoreTokens()) {
|
|
1119
|
String p2RepoStr = p2ReposPrefST.nextToken();
|
|
1120
|
StringTokenizer p2ReposStrST = new StringTokenizer(p2RepoStr,P2_REPOSITORY_FIELDS_DELIM);
|
|
1121
|
if(p2ReposStrST.countTokens()==3) {
|
|
1122
|
String nickname = p2ReposStrST.nextToken();
|
|
1123
|
URI uri = null;
|
|
1124
|
try {
|
|
1125
|
uri = new URI(p2ReposStrST.nextToken());
|
|
1126
|
} catch (URISyntaxException e) {
|
|
1127
|
continue;
|
|
1128
|
}
|
|
1129
|
boolean enabled = Boolean.parseBoolean(p2ReposStrST.nextToken());
|
|
1130
|
MetadataRepositoryElement mre = new MetadataRepositoryElement(null, uri.getJavaUri(), true);
|
|
1131
|
mre.setNickname(nickname);
|
|
1132
|
mre.setEnabled(enabled);
|
|
1133
|
p2Repos.add(mre);
|
|
1134
|
}
|
|
1135
|
}
|
|
1136
|
}
|
|
1137
|
|
|
1138
|
return p2Repos;
|
|
1139
|
}
|
|
1140
|
|
|
1141
|
/**
|
|
1142
|
* enables/disables nested composite. <br>
|
|
1143
|
*
|
|
1144
|
* @param ctrl - Composite to be en-/disabeld
|
|
1145
|
* @param enabled - boolean
|
|
1146
|
*/
|
|
1147
|
public static void recursiveSetEnabled(Control ctrl, boolean enabled) {
|
|
1148
|
if (ctrl instanceof Composite) {
|
|
1149
|
Composite comp = (Composite) ctrl;
|
|
1150
|
for (Control c : comp.getChildren()) {
|
|
1151
|
recursiveSetEnabled(c, enabled);
|
|
1152
|
}
|
|
1153
|
} else {
|
|
1154
|
ctrl.setEnabled(enabled);
|
|
1155
|
}
|
|
1156
|
}
|
|
1157
|
|
|
1158
|
public static void setSortNodes(NavigatorOrderEnum nodesOrder) {
|
|
1159
|
if (nodesOrder == null){
|
|
1160
|
setStringValue(PreferencePredicate.TaxonNodeOrder.getKey(), null);
|
|
1161
|
}else{
|
|
1162
|
setStringValue(PreferencePredicate.TaxonNodeOrder.getKey(), nodesOrder.key);
|
|
1163
|
}
|
|
1164
|
}
|
|
1165
|
|
|
1166
|
public static NavigatorOrderEnum getSortNodes() {
|
|
1167
|
return NavigatorOrderEnum.valueOf(getStringValue(PreferencePredicate.TaxonNodeOrder.getKey()));
|
|
1168
|
}
|
|
1169
|
|
|
1170
|
public static boolean isNodesSortedNaturally() {
|
|
1171
|
NavigatorOrderEnum value = NavigatorOrderEnum.valueOf(getStringValue(PreferencePredicate.TaxonNodeOrder.getKey()));
|
|
1172
|
return value.equals(NavigatorOrderEnum.NaturalOrder);
|
|
1173
|
}
|
|
1174
|
|
|
1175
|
public static boolean isNodesSortedByName() {
|
|
1176
|
NavigatorOrderEnum value = NavigatorOrderEnum.valueOf(getStringValue(PreferencePredicate.TaxonNodeOrder.getKey()));
|
|
1177
|
return value.equals(NavigatorOrderEnum.AlphabeticalOrder);
|
|
1178
|
}
|
|
1179
|
|
|
1180
|
public static boolean isNodesSortedByNameAndRank() {
|
|
1181
|
NavigatorOrderEnum value = NavigatorOrderEnum.valueOf(getStringValue(PreferencePredicate.TaxonNodeOrder.getKey()));
|
|
1182
|
return value.equals(NavigatorOrderEnum.RankAndNameOrder);
|
|
1183
|
}
|
|
1184
|
|
|
1185
|
public static boolean isStoreNavigatorState() {
|
|
1186
|
return getBooleanValue(RESTORE_NAVIGATOR_STATE);
|
|
1187
|
}
|
|
1188
|
|
|
1189
|
public static void setStoreNavigatorState(boolean selection) {
|
|
1190
|
setBooleanValue(RESTORE_NAVIGATOR_STATE, selection);
|
|
1191
|
}
|
|
1192
|
|
|
1193
|
public static boolean isShowUpWidgetIsDisposedMessages() {
|
|
1194
|
return getBooleanValue(IS_SHOW_UP_WIDGET_IS_DISPOSED);
|
|
1195
|
}
|
|
1196
|
|
|
1197
|
public static void setShowUpWidgetIsDisposedMessages(boolean selection) {
|
|
1198
|
setBooleanValue(IS_SHOW_UP_WIDGET_IS_DISPOSED, selection);
|
|
1199
|
}
|
|
1200
|
|
|
1201
|
public static boolean isShowIdInVocabularyInChecklistEditor() {
|
|
1202
|
String area_display = getStringValue(PreferencePredicate.DisplayOfAreasInDistributionEditor.getKey());
|
|
1203
|
if (area_display.equals(TermDisplayEnum.IdInVocabulary.getKey())) {
|
|
1204
|
return true;
|
|
1205
|
}else{
|
|
1206
|
return false;
|
|
1207
|
}
|
|
1208
|
}
|
|
1209
|
public static boolean isShowSymbol1InChecklistEditor() {
|
|
1210
|
String area_display = getStringValue(PreferencePredicate.DisplayOfAreasInDistributionEditor.getKey());
|
|
1211
|
if (area_display.equals(TermDisplayEnum.Symbol1.getKey())) {
|
|
1212
|
return true;
|
|
1213
|
}else{
|
|
1214
|
return false;
|
|
1215
|
}
|
|
1216
|
}
|
|
1217
|
public static boolean isShowSymbol2InChecklistEditor() {
|
|
1218
|
String area_display = getStringValue(PreferencePredicate.DisplayOfAreasInDistributionEditor.getKey());
|
|
1219
|
if (area_display.equals(TermDisplayEnum.Symbol2.getKey())) {
|
|
1220
|
return true;
|
|
1221
|
}else{
|
|
1222
|
return false;
|
|
1223
|
}
|
|
1224
|
}
|
|
1225
|
|
|
1226
|
public static void setAreaDisplayInChecklistEditor(String selection) {
|
|
1227
|
setStringValue(PreferencePredicate.DisplayOfAreasInDistributionEditor.getKey(), selection);
|
|
1228
|
}
|
|
1229
|
|
|
1230
|
public static void setOwnDescriptionForChecklistEditor(boolean selection) {
|
|
1231
|
setBooleanValue(PreferencePredicate.OwnDescriptionForDistributionEditor.getKey(), selection);
|
|
1232
|
}
|
|
1233
|
|
|
1234
|
public static boolean isOwnDescriptionForChecklistEditor() {
|
|
1235
|
return getBooleanValue(PreferencePredicate.OwnDescriptionForDistributionEditor.getKey());
|
|
1236
|
}
|
|
1237
|
|
|
1238
|
public static TermDisplayEnum displayAreaInChecklistEditor() {
|
|
1239
|
TermDisplayEnum result;
|
|
1240
|
try{
|
|
1241
|
result = TermDisplayEnum.byKey(getStringValue(PreferencePredicate.DisplayOfAreasInDistributionEditor.getKey()));
|
|
1242
|
}catch (IllegalArgumentException e){
|
|
1243
|
result = ((TermDisplayEnum) PreferencePredicate.DisplayOfAreasInDistributionEditor.getDefaultValue());
|
|
1244
|
}
|
|
1245
|
return result;
|
|
1246
|
}
|
|
1247
|
|
|
1248
|
public static TermDisplayEnum displayStatusInChecklistEditor() {
|
|
1249
|
TermDisplayEnum result;
|
|
1250
|
try{
|
|
1251
|
result = TermDisplayEnum.byKey(getStringValue(PreferencePredicate.DisplayOfStatus.getKey()));
|
|
1252
|
}catch (IllegalArgumentException e){
|
|
1253
|
result = ((TermDisplayEnum) PreferencePredicate.DisplayOfStatus.getDefaultValue());
|
|
1254
|
}
|
|
1255
|
return result;
|
|
1256
|
}
|
|
1257
|
|
|
1258
|
public static void setDisplayStatusInChecklistEditor(String selection) {
|
|
1259
|
setStringValue(PreferencePredicate.DisplayOfStatus.getKey(), selection);
|
|
1260
|
}
|
|
1261
|
|
|
1262
|
public static boolean isShowRankInChecklistEditor() {
|
|
1263
|
return getBooleanValue(PreferencePredicate.ShowRankInDistributionEditor.getKey());
|
|
1264
|
}
|
|
1265
|
|
|
1266
|
public static void setShowRankInChecklistEditor(boolean selection) {
|
|
1267
|
setBooleanValue(PreferencePredicate.ShowRankInDistributionEditor.getKey(), selection);
|
|
1268
|
}
|
|
1269
|
|
|
1270
|
public static NameDetailsConfigurator getPreferredNameDetailsConfiguration( boolean local) {
|
|
1271
|
NameDetailsConfigurator config = new NameDetailsConfigurator();
|
|
1272
|
CdmPreferenceCache cache = CdmPreferenceCache.instance();
|
|
1273
|
CdmPreference preference = null;
|
|
1274
|
String value;
|
|
1275
|
if (!local) {
|
|
1276
|
PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.NameDetailsView);
|
|
1277
|
preference = getPreferenceFromDB(PreferencePredicate.NameDetailsView);
|
|
1278
|
if (preference == null){
|
|
1279
|
return null;
|
|
1280
|
}
|
|
1281
|
|
|
1282
|
// setBooleanValue(ALLOW_OVERRIDE_NAME_DETAILS, preference.isAllowOverride());
|
|
1283
|
value = preference.getValue();
|
|
1284
|
config.setAllowOverride(preference.isAllowOverride());
|
|
1285
|
//the preference value is build like this:
|
|
1286
|
//<section1>:true;<section2>:false....
|
|
1287
|
}else{
|
|
1288
|
value = getStringValue(PreferencePredicate.NameDetailsView.getKey(), local);
|
|
1289
|
}
|
|
1290
|
if (value!= null){
|
|
1291
|
fillNameDetailsConfigurator(config, value);
|
|
1292
|
|
|
1293
|
|
|
1294
|
}else {
|
|
1295
|
return null;
|
|
1296
|
}
|
|
1297
|
return config;
|
|
1298
|
}
|
|
1299
|
|
|
1300
|
public static void fillNameDetailsConfigurator(NameDetailsConfigurator config, String value) {
|
|
1301
|
String [] sections = value.split(";");
|
|
1302
|
Map<String, Boolean> sectionMap = new HashMap<>();
|
|
1303
|
String[] sectionValues;
|
|
1304
|
for (String sectionValue: sections){
|
|
1305
|
if (sectionValue.contains(":")){
|
|
1306
|
sectionValues = sectionValue.split(":");
|
|
1307
|
sectionMap.put(sectionValues[0], Boolean.valueOf(sectionValues[1]));
|
|
1308
|
}
|
|
1309
|
}
|
|
1310
|
for (Field field: config.getClass().getDeclaredFields()){
|
|
1311
|
try {
|
|
1312
|
config.getClass().getDeclaredField(field.getName()).set(config, getValue(sectionMap, field.getName()));
|
|
1313
|
} catch (IllegalArgumentException | IllegalAccessException | NoSuchFieldException
|
|
1314
|
| SecurityException e) {
|
|
1315
|
logger.debug(e.getMessage());
|
|
1316
|
}
|
|
1317
|
}
|
|
1318
|
}
|
|
1319
|
|
|
1320
|
public static NameDetailsConfigurator getPreferredNameDetailsConfiguration() {
|
|
1321
|
NameDetailsConfigurator config = new NameDetailsConfigurator();
|
|
1322
|
|
|
1323
|
String value;
|
|
1324
|
|
|
1325
|
value = getStringValue(PreferencePredicate.NameDetailsView.getKey(), false);
|
|
1326
|
if (value != null){
|
|
1327
|
fillNameDetailsConfigurator(config, value);
|
|
1328
|
}else {
|
|
1329
|
return null;
|
|
1330
|
}
|
|
1331
|
return config;
|
|
1332
|
}
|
|
1333
|
|
|
1334
|
public static void setPreferredNameDetailsConfiguration(NameDetailsConfigurator config, boolean local) {
|
|
1335
|
CdmPreference preference = null;
|
|
1336
|
|
|
1337
|
if (!local) {
|
|
1338
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.NameDetailsView, config.toString());
|
|
1339
|
|
|
1340
|
setPreferenceToDB(preference);
|
|
1341
|
}
|
|
1342
|
else{
|
|
1343
|
setStringValue(PreferencePredicate.NameDetailsView.getKey(), config.toString());
|
|
1344
|
}
|
|
1345
|
}
|
|
1346
|
|
|
1347
|
private static Boolean getValue(Map<String, Boolean> sectionMap, String string) {
|
|
1348
|
if (sectionMap.containsKey(string)){
|
|
1349
|
return sectionMap.get(string);
|
|
1350
|
}else{
|
|
1351
|
return true;
|
|
1352
|
}
|
|
1353
|
}
|
|
1354
|
|
|
1355
|
public static Abcd206ImportConfigurator getDBAbcdImportConfigurationPreference() {
|
|
1356
|
|
|
1357
|
Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
|
|
1358
|
ICdmRepository controller;
|
|
1359
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
1360
|
PrefKey key = CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig);
|
|
1361
|
CdmPreference preference = null;
|
|
1362
|
if (controller == null){
|
|
1363
|
return null;
|
|
1364
|
}
|
|
1365
|
preference = controller.getPreferenceService().find(key);
|
|
1366
|
if (preference == null){
|
|
1367
|
return config;
|
|
1368
|
} else{
|
|
1369
|
String configString = preference.getValue();
|
|
1370
|
extractAbcdConfiguratorFromPreferenceString(config, configString);
|
|
1371
|
}
|
|
1372
|
return config;
|
|
1373
|
}
|
|
1374
|
|
|
1375
|
public static void extractAbcdConfiguratorFromPreferenceString(Abcd206ImportConfigurator config,
|
|
1376
|
String configString) {
|
|
1377
|
if(configString != null){
|
|
1378
|
String[] configArray = configString.split(";");
|
|
1379
|
|
|
1380
|
for (String configItem: configArray){
|
|
1381
|
String[] keyValue = configItem.split(":");
|
|
1382
|
String keyString = keyValue[0];
|
|
1383
|
String valueString = null;
|
|
1384
|
if (keyValue.length>1){
|
|
1385
|
valueString = keyValue[1];
|
|
1386
|
if (keyValue.length>2){
|
|
1387
|
|
|
1388
|
for (int index = 2; index< keyValue.length; index++){
|
|
1389
|
valueString += ":"+ keyValue[index];
|
|
1390
|
}
|
|
1391
|
}
|
|
1392
|
}
|
|
1393
|
if (keyString.equals("ignoreImportOfExistingSpecimen")){
|
|
1394
|
config.setIgnoreImportOfExistingSpecimen(Boolean.valueOf(valueString));
|
|
1395
|
}else if (keyString.equals("addIndividualsAssociationsSuchAsSpecimenAndObservations")){
|
|
1396
|
config.setAddIndividualsAssociationsSuchAsSpecimenAndObservations(Boolean.valueOf(valueString));
|
|
1397
|
}else if (keyString.equals("reuseExistingTaxaWhenPossible")){
|
|
1398
|
config.setReuseExistingTaxaWhenPossible(Boolean.valueOf(valueString));
|
|
1399
|
}else if (keyString.equals("ignoreAuthorship")){
|
|
1400
|
config.setIgnoreAuthorship(Boolean.valueOf(valueString));
|
|
1401
|
}else if (keyString.equals("addMediaAsMediaSpecimen")){
|
|
1402
|
config.setAddMediaAsMediaSpecimen(Boolean.valueOf(valueString));
|
|
1403
|
}else if (keyString.equals("reuseExistingMetaData")){
|
|
1404
|
config.setReuseExistingMetaData(Boolean.valueOf(valueString));
|
|
1405
|
}else if (keyString.equals("reuseExistingDescriptiveGroups")){
|
|
1406
|
config.setReuseExistingDescriptiveGroups(Boolean.valueOf(valueString));
|
|
1407
|
}else if (keyString.equals("allowReuseOtherClassifications")){
|
|
1408
|
config.setAllowReuseOtherClassifications(Boolean.valueOf(valueString));
|
|
1409
|
}else if (keyString.equals("deduplicateReferences")){
|
|
1410
|
config.setDeduplicateReferences(Boolean.valueOf(valueString));
|
|
1411
|
}else if (keyString.equals("deduplicateClassifications")){
|
|
1412
|
config.setDeduplicateClassifications(Boolean.valueOf(valueString));
|
|
1413
|
}else if (keyString.equals("moveNewTaxaToDefaultClassification")){
|
|
1414
|
config.setMoveNewTaxaToDefaultClassification(Boolean.valueOf(valueString));
|
|
1415
|
}else if (keyString.equals("mapUnitIdToCatalogNumber")){
|
|
1416
|
config.setMapUnitIdToCatalogNumber(Boolean.valueOf(valueString));
|
|
1417
|
}else if (keyString.equals("mapUnitIdToAccessionNumber")){
|
|
1418
|
config.setMapUnitIdToAccessionNumber(Boolean.valueOf(valueString));
|
|
1419
|
}else if (keyString.equals("mapUnitIdToBarcode")){
|
|
1420
|
config.setMapUnitIdToBarcode(Boolean.valueOf(valueString));
|
|
1421
|
}else if (keyString.equals("overwriteExistingSpecimens")){
|
|
1422
|
config.setOverwriteExistingSpecimens(Boolean.valueOf(valueString));
|
|
1423
|
}else if (keyString.equals("nomenclaturalCode")){
|
|
1424
|
config.setNomenclaturalCode(NomenclaturalCode.fromString(valueString));
|
|
1425
|
}else if (keyString.equals("removeCountryFromLocalityText")){
|
|
1426
|
config.setRemoveCountryFromLocalityText(Boolean.valueOf(valueString));
|
|
1427
|
}else if (keyString.equals("getSiblings")){
|
|
1428
|
config.setGetSiblings(Boolean.valueOf(valueString));
|
|
1429
|
}else if (keyString.equals("classificationUUID")){
|
|
1430
|
config.setClassificationUuid(UUID.fromString(valueString));
|
|
1431
|
}else if (keyString.equals("classificationName")){
|
|
1432
|
config.setClassificationName(valueString);
|
|
1433
|
}else if (keyString.equals("dnaSource")){
|
|
1434
|
try{
|
|
1435
|
config.setDnaSoure(URI.create(valueString));
|
|
1436
|
}catch(Exception e){
|
|
1437
|
config.setDnaSoure(null);
|
|
1438
|
}
|
|
1439
|
}else{
|
|
1440
|
logger.debug("This key of the abcd configurator needs to be added to the transformer: " + keyString);
|
|
1441
|
}
|
|
1442
|
}
|
|
1443
|
}
|
|
1444
|
}
|
|
1445
|
|
|
1446
|
public static Abcd206ImportConfigurator getLocalAbcdImportConfigurator(){
|
|
1447
|
return getLocalAbcdImportConfigurator(true);
|
|
1448
|
}
|
|
1449
|
|
|
1450
|
public static Abcd206ImportConfigurator getLocalAbcdImportConfigurator(boolean skipCheckOverride){
|
|
1451
|
Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
|
|
1452
|
CdmPreference pref = CdmPreferenceCache.instance().get(PreferencePredicate.AbcdImportConfig.getKey());
|
|
1453
|
if (pref == null || pref.isAllowOverride()){
|
|
1454
|
String configString = PreferencesUtil.getStringValue(PreferencePredicate.AbcdImportConfig.getKey());
|
|
1455
|
if (StringUtils.isBlank(configString)){
|
|
1456
|
configString = getStringValue(PreferencePredicate.AbcdImportConfig.getKey(), skipCheckOverride);
|
|
1457
|
extractAbcdConfiguratorFromPreferenceString(config, configString);
|
|
1458
|
if (config.getNomenclaturalCode() == null){
|
|
1459
|
config.setNomenclaturalCode(getPreferredNomenclaturalCode());
|
|
1460
|
}
|
|
1461
|
}else{
|
|
1462
|
config = Abcd206ImportConfigurator.NewInstance(null, null);
|
|
1463
|
PreferencesUtil.extractAbcdConfiguratorFromPreferenceString(config, configString);
|
|
1464
|
}
|
|
1465
|
}else{
|
|
1466
|
extractAbcdConfiguratorFromPreferenceString(config, pref.getValue());
|
|
1467
|
}
|
|
1468
|
|
|
1469
|
return config;
|
|
1470
|
|
|
1471
|
}
|
|
1472
|
|
|
1473
|
public static Abcd206ImportConfigurator getLastUsedAbcdImportConfigurator(){
|
|
1474
|
Abcd206ImportConfigurator config = Abcd206ImportConfigurator.NewInstance(null,null);
|
|
1475
|
|
|
1476
|
String configString = PreferencesUtil.getStringValue(IPreferenceKeys.LAST_USED_ABCD_CONFIG, true);
|
|
1477
|
if (configString != null){
|
|
1478
|
extractAbcdConfiguratorFromPreferenceString(config, configString);
|
|
1479
|
if (config != null){
|
|
1480
|
if (config.getNomenclaturalCode() == null){
|
|
1481
|
config.setNomenclaturalCode(getPreferredNomenclaturalCode());
|
|
1482
|
}
|
|
1483
|
}
|
|
1484
|
}else{
|
|
1485
|
config = PreferencesUtil.getLocalAbcdImportConfigurator(false);
|
|
1486
|
}
|
|
1487
|
|
|
1488
|
return config;
|
|
1489
|
|
|
1490
|
}
|
|
1491
|
|
|
1492
|
public static void updateAbcdImportConfigurationPreference() {
|
|
1493
|
CdmPreferenceCache cache = CdmPreferenceCache.instance();
|
|
1494
|
|
|
1495
|
CdmPreference pref = cache.findBestMatching(CdmPreference.NewKey(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AbcdImportConfig));
|
|
1496
|
|
|
1497
|
if (!getBooleanValue(prefOverrideKey(PreferencePredicate.AbcdImportConfig.getKey())) || !pref.isAllowOverride()){
|
|
1498
|
resetToDBPreferenceAbcdCOnfigurator();
|
|
1499
|
|
|
1500
|
}
|
|
1501
|
}
|
|
1502
|
|
|
1503
|
public static void resetToDBPreferenceAbcdCOnfigurator(){
|
|
1504
|
Abcd206ImportConfigurator config = getDBAbcdImportConfigurationPreference();
|
|
1505
|
setStringValue(PreferencePredicate.AbcdImportConfig.getKey(), config.toString());
|
|
1506
|
}
|
|
1507
|
|
|
1508
|
public static boolean isSortTaxaByRankAndName() {
|
|
1509
|
return getBooleanValue(PreferencePredicate.SortTaxaByRankAndName.getKey());
|
|
1510
|
}
|
|
1511
|
|
|
1512
|
public static TermOrder getSortNamedAreasInDistributionEditor() {
|
|
1513
|
TermOrder result;
|
|
1514
|
try{
|
|
1515
|
result = TermOrder.valueOf(getStringValue(PreferencePredicate.AreasSortedInDistributionEditor.getKey()));
|
|
1516
|
}catch (IllegalArgumentException e){
|
|
1517
|
result = (TermOrder)PreferencePredicate.AreasSortedInDistributionEditor.getDefaultValue();
|
|
1518
|
}
|
|
1519
|
return result;
|
|
1520
|
}
|
|
1521
|
|
|
1522
|
public static void setSortNamedAreasInDistributionEditor(String isSortByVocabularyOrder) {
|
|
1523
|
setStringValue(PreferencePredicate.AreasSortedInDistributionEditor.getKey(), isSortByVocabularyOrder);
|
|
1524
|
}
|
|
1525
|
|
|
1526
|
public static void setLastSelectedReference(
|
|
1527
|
List<String> lastSelectedReferences) {
|
|
1528
|
|
|
1529
|
setStringValue(IPreferenceKeys.LAST_SELECTED_REFERENCES, lastSelectedReferences.toString());
|
|
1530
|
}
|
|
1531
|
|
|
1532
|
public static List<String> getLastSelectedReferences() {
|
|
1533
|
|
|
1534
|
//IPreferenceStore preferenceStore = PreferencesUtil.getPreferenceStore();
|
|
1535
|
String lastSelected = getStringValue(IPreferenceKeys.LAST_SELECTED_REFERENCES, true);
|
|
1536
|
List<String> result = new ArrayList<>();
|
|
1537
|
if (!StringUtils.isBlank(lastSelected)){
|
|
1538
|
Collections.addAll(result, lastSelected.substring(1,lastSelected.length()-1).split(", "));
|
|
1539
|
}
|
|
1540
|
return result;
|
|
1541
|
}
|
|
1542
|
|
|
1543
|
public static void setPreferredNamedAreasForDistributionEditor(
|
|
1544
|
String saveCheckedElements, String saveGrayedElements, boolean local) {
|
|
1545
|
if (local){
|
|
1546
|
setStringValue(PreferencePredicate.AvailableDistributionAreaTerms.getKey(), saveCheckedElements);
|
|
1547
|
}
|
|
1548
|
else{
|
|
1549
|
CdmPreference preference = null;
|
|
1550
|
|
|
1551
|
if (saveCheckedElements == null){
|
|
1552
|
preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaTerms);
|
|
1553
|
|
|
1554
|
if (preference == null){
|
|
1555
|
return ;
|
|
1556
|
} else{
|
|
1557
|
setStringValue(PreferencePredicate.AvailableDistributionAreaTerms.getKey(),
|
|
1558
|
saveCheckedElements);
|
|
1559
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
|
|
1560
|
setPreferenceToDB(preference);
|
|
1561
|
|
|
1562
|
}
|
|
1563
|
} else{
|
|
1564
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaTerms, saveCheckedElements);
|
|
1565
|
setPreferenceToDB(preference);
|
|
1566
|
setStringValue(PreferencePredicate.AvailableDistributionAreaTerms.getKey(),
|
|
1567
|
saveCheckedElements);
|
|
1568
|
|
|
1569
|
}
|
|
1570
|
}
|
|
1571
|
}
|
|
1572
|
|
|
1573
|
public static void setPreferredVocabulariesForDistributionEditor(String saveCheckedElements,
|
|
1574
|
boolean local, boolean isOverride) {
|
|
1575
|
if (local){
|
|
1576
|
setStringValue(PreferencePredicate.AvailableDistributionAreaVocabularies.getKey(), saveCheckedElements);
|
|
1577
|
setBooleanValue(prefOverrideKey(PreferencePredicate.AvailableDistributionAreaVocabularies.getKey()), isOverride);
|
|
1578
|
}
|
|
1579
|
else{
|
|
1580
|
CdmPreference preference = null;
|
|
1581
|
|
|
1582
|
if (saveCheckedElements == null){
|
|
1583
|
preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
|
|
1584
|
|
|
1585
|
if (preference == null){
|
|
1586
|
return ;
|
|
1587
|
} else{
|
|
1588
|
setStringValue(PreferencePredicate.AvailableDistributionAreaVocabularies.getKey(),
|
|
1589
|
saveCheckedElements);
|
|
1590
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
|
|
1591
|
preference.setAllowOverride(isOverride);
|
|
1592
|
setPreferenceToDB(preference);
|
|
1593
|
}
|
|
1594
|
} else{
|
|
1595
|
preference = CdmPreference.NewInstance(PreferenceSubject.NewTaxEditorInstance(), PreferencePredicate.AvailableDistributionAreaVocabularies, saveCheckedElements);
|
|
1596
|
preference.setAllowOverride(isOverride);
|
|
1597
|
setPreferenceToDB(preference);
|
|
1598
|
setStringValue(PreferencePredicate.AvailableDistributionAreaVocabularies.getKey(),
|
|
1599
|
saveCheckedElements);
|
|
1600
|
}
|
|
1601
|
}
|
|
1602
|
}
|
|
1603
|
|
|
1604
|
public static String getPreferredVocabulariesForDistributionEditor(boolean local) {
|
|
1605
|
if (local){
|
|
1606
|
|
|
1607
|
String pref = getStringValue(PreferencePredicate.AvailableDistributionAreaVocabularies.getKey(), local);
|
|
1608
|
return pref;
|
|
1609
|
}
|
|
1610
|
else{
|
|
1611
|
CdmPreference preference = null;
|
|
1612
|
preference = getPreferenceFromDB(PreferencePredicate.AvailableDistributionAreaVocabularies);
|
|
1613
|
if (preference == null){
|
|
1614
|
return null;
|
|
1615
|
} else{
|
|
1616
|
return preference.getValue();
|
|
1617
|
}
|
|
1618
|
}
|
|
1619
|
}
|
|
1620
|
|
|
1621
|
public static List<UUID> createUUIDListFromStringPref(String prefKey, boolean local) {
|
|
1622
|
if (prefKey == null){
|
|
1623
|
return null;
|
|
1624
|
}
|
|
1625
|
String prefValue = PreferencesUtil.getStringValue(prefKey, local);
|
|
1626
|
if (prefValue == null){
|
|
1627
|
return null;
|
|
1628
|
}
|
|
1629
|
List<UUID> uuidList = createUuidList(prefValue);
|
|
1630
|
return uuidList;
|
|
1631
|
}
|
|
1632
|
|
|
1633
|
public static List<UUID> createUuidList(String prefValue) {
|
|
1634
|
String[] stringArray = prefValue.split(";");
|
|
1635
|
List<UUID> uuidList = new ArrayList<>();
|
|
1636
|
for (String uuid: stringArray){
|
|
1637
|
if (!StringUtils.isBlank(uuid)){
|
|
1638
|
uuidList.add(UUID.fromString(uuid));
|
|
1639
|
}
|
|
1640
|
}
|
|
1641
|
return uuidList;
|
|
1642
|
}
|
|
1643
|
|
|
1644
|
public static boolean getFilterCommonNameReferences(){
|
|
1645
|
Boolean result = getBooleanValue(PreferencePredicate.CommonNameReferencesWithMarker.getKey());
|
|
1646
|
if (result == null){
|
|
1647
|
return false;
|
|
1648
|
}
|
|
1649
|
return result;
|
|
1650
|
}
|
|
1651
|
|
|
1652
|
public static void updateDBPreferences() {
|
|
1653
|
|
|
1654
|
CdmPreferenceCache cache = CdmPreferenceCache.instance();
|
|
1655
|
cache.getAllTaxEditorDBPreferences();
|
|
1656
|
|
|
1657
|
//ABCD Configurator
|
|
1658
|
|
|
1659
|
//updateAbcdImportConfigurationPreference();
|
|
1660
|
|
|
1661
|
//Name Details
|
|
1662
|
NameDetailsConfigurator config = getPreferredNameDetailsConfiguration(false);
|
|
1663
|
// if (config != null ){
|
|
1664
|
// if (!getBooleanValue(OVERRIDE_NAME_DETAILS) || !getBooleanValue(ALLOW_OVERRIDE_NAME_DETAILS)){
|
|
1665
|
// setPreferredNameDetailsConfiguration(config, false);
|
|
1666
|
// }
|
|
1667
|
// }
|
|
1668
|
|
|
1669
|
}
|
|
1670
|
|
|
1671
|
public static void setPreferencesToDB(List<CdmPreference> preferences) {
|
|
1672
|
|
|
1673
|
ICdmRepository controller;
|
|
1674
|
if(CdmStore.isActive()){
|
|
1675
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
1676
|
for (CdmPreference preference: preferences){
|
|
1677
|
if (preference.getValue() == null && preference.isAllowOverride()){
|
|
1678
|
controller.getPreferenceService().remove(preference.getKey());
|
|
1679
|
|
|
1680
|
}else{
|
|
1681
|
controller.getPreferenceService().set(preference);
|
|
1682
|
|
|
1683
|
}
|
|
1684
|
|
|
1685
|
}
|
|
1686
|
CdmPreferenceCache.instance().getAllTaxEditorDBPreferences();
|
|
1687
|
}
|
|
1688
|
}
|
|
1689
|
|
|
1690
|
/**
|
|
1691
|
* Returns whether the named preference is known.
|
|
1692
|
* @param prefKey the key of the preference
|
|
1693
|
* @return <code>true</code> if the preference is known, <code>false</code> otherwise
|
|
1694
|
*/
|
|
1695
|
public static boolean contains(String prefKey){
|
|
1696
|
return getPreferenceStore().contains(prefKey(prefKey));
|
|
1697
|
}
|
|
1698
|
|
|
1699
|
/**
|
|
1700
|
*
|
|
1701
|
*/
|
|
1702
|
public static TermTree<?> getPreferredFeatureTreeForNameDescription(boolean createNew) {
|
|
1703
|
if(preferredNameFeatureTree != null && !createNew){
|
|
1704
|
return preferredNameFeatureTree;
|
|
1705
|
}
|
|
1706
|
createPreferredFeatureTreeForNameDescription();
|
|
1707
|
return preferredNameFeatureTree;
|
|
1708
|
}
|
|
1709
|
|
|
1710
|
public static void createPreferredFeatureTreeForNameDescription() {
|
|
1711
|
|
|
1712
|
CdmPreferenceCache cache = CdmPreferenceCache.instance();
|
|
1713
|
CdmPreference pref = cache.get(PreferencePredicate.NameFeatures.getKey());
|
|
1714
|
List<Feature> terms = new ArrayList<>();
|
|
1715
|
boolean override = PreferencesUtil.getOverrideForPreference(PreferencePredicate.NameFeatures.getKey());
|
|
1716
|
|
|
1717
|
List<UUID> uuids = PreferencesUtil.createUUIDListFromStringPref(PreferencePredicate.NameFeatures.getKey(), false);
|
|
1718
|
if (uuids != null && !uuids.isEmpty()){
|
|
1719
|
terms = CdmStore.getTermManager().getTerms(uuids, Feature.class);
|
|
1720
|
}
|
|
1721
|
|
|
1722
|
if (terms.isEmpty()){
|
|
1723
|
terms.addAll(TermStore.getTerms(CdmStore.getService(IVocabularyService.class).load(VocabularyEnum.NameFeature.getUuid()), null));
|
|
1724
|
}
|
|
1725
|
terms.remove(Feature.PROTOLOGUE());
|
|
1726
|
if (terms.isEmpty()){
|
|
1727
|
preferredNameFeatureTree = TermEditorInput.getDefaultNameFeatureTree();
|
|
1728
|
}else{
|
|
1729
|
preferredNameFeatureTree = TermTree.NewInstance(terms);
|
|
1730
|
}
|
|
1731
|
}
|
|
1732
|
|
|
1733
|
public static void removeFromDB(List<CdmPreference> prefsToDelete) {
|
|
1734
|
ICdmRepository controller;
|
|
1735
|
//try{
|
|
1736
|
if(CdmStore.isActive()){
|
|
1737
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
1738
|
for (CdmPreference preference: prefsToDelete){
|
|
1739
|
controller.getPreferenceService().remove(preference.getKey());
|
|
1740
|
}
|
|
1741
|
CdmPreferenceCache.instance().getAllTaxEditorDBPreferences();
|
|
1742
|
}
|
|
1743
|
}
|
|
1744
|
|
|
1745
|
public static void removeFromDB(CdmPreference prefToDelete) {
|
|
1746
|
ICdmRepository controller;
|
|
1747
|
|
|
1748
|
if(CdmStore.isActive()){
|
|
1749
|
controller = CdmStore.getCurrentApplicationConfiguration();
|
|
1750
|
controller.getPreferenceService().remove(prefToDelete.getKey());
|
|
1751
|
|
|
1752
|
CdmPreferenceCache.instance().getAllTaxEditorDBPreferences();
|
|
1753
|
}
|
|
1754
|
}
|
|
1755
|
|
|
1756
|
public static TermTree<?> getPreferredFeatureTreeForTaxonDescription(boolean createNew) {
|
|
1757
|
if(preferredTaxonFeatureTree != null && !createNew){
|
|
1758
|
return preferredTaxonFeatureTree;
|
|
1759
|
}
|
|
1760
|
createPreferredFeatureTreeForTaxonDescription();
|
|
1761
|
return preferredTaxonFeatureTree;
|
|
1762
|
}
|
|
1763
|
|
|
1764
|
public static void createPreferredFeatureTreeForTaxonDescription() {
|
|
1765
|
|
|
1766
|
CdmPreferenceCache cache = CdmPreferenceCache.instance();
|
|
1767
|
CdmPreference pref = cache.get(PreferencePredicate.TaxonFeatures.getKey());
|
|
1768
|
List<Feature> terms = null;
|
|
1769
|
boolean override = PreferencesUtil.getOverrideForPreference(PreferencePredicate.TaxonFeatures.getKey());
|
|
1770
|
List<UUID> uuids = PreferencesUtil.createUUIDListFromStringPref(PreferencePredicate.TaxonFeatures.getKey(), false);
|
|
1771
|
if (uuids != null && !uuids.isEmpty()){
|
|
1772
|
terms = CdmStore.getTermManager().getTerms(uuids, Feature.class);
|
|
1773
|
}
|
|
1774
|
if (terms == null || terms.isEmpty()){
|
|
1775
|
terms= CdmStore.getTermManager().getPreferredTerms(TermType.Feature);
|
|
1776
|
TermVocabulary nameVocabulary = CdmStore.getService(IVocabularyService.class).load(VocabularyEnum.NameFeature.getUuid());
|
|
1777
|
Set<Feature> nameFeature = nameVocabulary.getTerms();
|
|
1778
|
terms.removeAll(nameFeature);
|
|
1779
|
|
|
1780
|
}
|
|
1781
|
|
|
1782
|
if (terms.isEmpty()){
|
|
1783
|
preferredTaxonFeatureTree = TermEditorInput.getDefaultFeatureTree();
|
|
1784
|
}else{
|
|
1785
|
preferredTaxonFeatureTree = TermTree.NewInstance(terms);
|
|
1786
|
}
|
|
1787
|
}
|
|
1788
|
|
|
1789
|
public static void setLastSelectedBiocaseProvider(String lastAccessPoint) {
|
|
1790
|
setStringValue(LAST_USED_BIOCASE_PROVIDER, lastAccessPoint);
|
|
1791
|
}
|
|
1792
|
|
|
1793
|
/**
|
|
1794
|
* @return
|
|
1795
|
*/
|
|
1796
|
public static boolean getLocalActive() {
|
|
1797
|
// TODO: this needs to be adapted!!!
|
|
1798
|
return true;
|
|
1799
|
}
|
|
1800
|
|
|
1801
|
/**
|
|
1802
|
* @return
|
|
1803
|
*/
|
|
1804
|
public static boolean showGfbioMetaData() {
|
|
1805
|
//TODO: needs to be adapted!!!
|
|
1806
|
return false;
|
|
1807
|
}
|
|
1808
|
}
|