Java tutorial
/* Copyright (C) 2015, University of Kansas Center for Research * * Specify Software Project, specify@ku.edu, Biodiversity Institute, * 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045, USA * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package edu.ku.brc.specify.utilapps; import static edu.ku.brc.helpers.XMLHelper.getAttr; import static edu.ku.brc.specify.config.init.DataBuilder.buildDarwinCoreSchema; import static edu.ku.brc.specify.config.init.DataBuilder.createAccession; import static edu.ku.brc.specify.config.init.DataBuilder.createAccessionAgent; import static edu.ku.brc.specify.config.init.DataBuilder.createAddress; import static edu.ku.brc.specify.config.init.DataBuilder.createAgent; import static edu.ku.brc.specify.config.init.DataBuilder.createAgentVariant; import static edu.ku.brc.specify.config.init.DataBuilder.createAndAddTesterToCollection; import static edu.ku.brc.specify.config.init.DataBuilder.createAttachment; import static edu.ku.brc.specify.config.init.DataBuilder.createAttributeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createAutoNumberingScheme; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectingEvent; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectingEventAttr; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectingTrip; import static edu.ku.brc.specify.config.init.DataBuilder.createCollection; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectionObject; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectionObjectAttr; import static edu.ku.brc.specify.config.init.DataBuilder.createCollectionRelType; import static edu.ku.brc.specify.config.init.DataBuilder.createCollector; import static edu.ku.brc.specify.config.init.DataBuilder.createDataType; import static edu.ku.brc.specify.config.init.DataBuilder.createDetermination; import static edu.ku.brc.specify.config.init.DataBuilder.createDiscipline; import static edu.ku.brc.specify.config.init.DataBuilder.createDivision; import static edu.ku.brc.specify.config.init.DataBuilder.createGeography; import static edu.ku.brc.specify.config.init.DataBuilder.createGeographyChildren; import static edu.ku.brc.specify.config.init.DataBuilder.createGeographyTreeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createGeographyTreeDefItem; import static edu.ku.brc.specify.config.init.DataBuilder.createGeologicTimePeriod; import static edu.ku.brc.specify.config.init.DataBuilder.createGeologicTimePeriodTreeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createGeologicTimePeriodTreeDefItem; import static edu.ku.brc.specify.config.init.DataBuilder.createGroupPerson; import static edu.ku.brc.specify.config.init.DataBuilder.createInstitution; import static edu.ku.brc.specify.config.init.DataBuilder.createJournal; import static edu.ku.brc.specify.config.init.DataBuilder.createLithoStratTreeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createLithoStratTreeDefItem; import static edu.ku.brc.specify.config.init.DataBuilder.createLocality; import static edu.ku.brc.specify.config.init.DataBuilder.createPermit; import static edu.ku.brc.specify.config.init.DataBuilder.createPickList; import static edu.ku.brc.specify.config.init.DataBuilder.createPrepType; import static edu.ku.brc.specify.config.init.DataBuilder.createPreparation; import static edu.ku.brc.specify.config.init.DataBuilder.createQuery; import static edu.ku.brc.specify.config.init.DataBuilder.createQueryField; import static edu.ku.brc.specify.config.init.DataBuilder.createReferenceWork; import static edu.ku.brc.specify.config.init.DataBuilder.createStorage; import static edu.ku.brc.specify.config.init.DataBuilder.createStorageTreeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createStorageTreeDefItem; import static edu.ku.brc.specify.config.init.DataBuilder.createTaxon; import static edu.ku.brc.specify.config.init.DataBuilder.createTaxonChildren; import static edu.ku.brc.specify.config.init.DataBuilder.createTaxonTreeDef; import static edu.ku.brc.specify.config.init.DataBuilder.createWorkbench; import static edu.ku.brc.specify.config.init.DataBuilder.createWorkbenchDataItem; import static edu.ku.brc.specify.config.init.DataBuilder.createWorkbenchMappingItem; import static edu.ku.brc.specify.config.init.DataBuilder.createWorkbenchTemplate; import static edu.ku.brc.ui.UIRegistry.getAppDataDir; import static edu.ku.brc.ui.UIRegistry.getAppDataSubDir; import static edu.ku.brc.ui.UIRegistry.getAppName; import static edu.ku.brc.ui.UIRegistry.getDefaultEmbeddedDBPath; import static edu.ku.brc.ui.UIRegistry.getDefaultMobileEmbeddedDBPath; import static edu.ku.brc.ui.UIRegistry.getDefaultWorkingPath; import static edu.ku.brc.ui.UIRegistry.getEmbeddedDBPath; import static edu.ku.brc.ui.UIRegistry.getResourceString; import static edu.ku.brc.ui.UIRegistry.getStatusBar; import static edu.ku.brc.ui.UIRegistry.getTopWindow; import static edu.ku.brc.ui.UIRegistry.setAppName; import static edu.ku.brc.ui.UIRegistry.setBaseAppDataDir; import static edu.ku.brc.ui.UIRegistry.setDefaultWorkingPath; import static edu.ku.brc.ui.UIRegistry.setEmbeddedDBPath; import static edu.ku.brc.ui.UIRegistry.setResourceLocale; import static edu.ku.brc.ui.UIRegistry.showError; import java.awt.Dimension; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; import java.math.BigDecimal; import java.sql.Connection; import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; import java.sql.Statement; import java.sql.Timestamp; import java.text.DateFormat; import java.text.NumberFormat; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Calendar; import java.util.Collections; import java.util.Comparator; import java.util.Enumeration; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.MissingResourceException; import java.util.Properties; import java.util.Random; import java.util.ResourceBundle; import java.util.Set; import java.util.Vector; import javax.swing.ImageIcon; import javax.swing.JOptionPane; import javax.swing.SwingUtilities; import javax.swing.UIManager; import javax.swing.WindowConstants; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Level; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; import org.apache.poi.hssf.usermodel.HSSFCell; import org.apache.poi.hssf.usermodel.HSSFDateUtil; import org.apache.poi.hssf.usermodel.HSSFRow; import org.apache.poi.hssf.usermodel.HSSFSheet; import org.apache.poi.hssf.usermodel.HSSFWorkbook; import org.apache.poi.poifs.filesystem.POIFSFileSystem; import org.dom4j.Element; import org.hibernate.Session; import org.hibernate.Transaction; import com.jgoodies.looks.plastic.Plastic3DLookAndFeel; import com.jgoodies.looks.plastic.PlasticLookAndFeel; import com.jgoodies.looks.plastic.theme.DesertBlue; import com.thoughtworks.xstream.XStream; import edu.ku.brc.af.auth.SecurityMgr; import edu.ku.brc.af.core.AppContextMgr; import edu.ku.brc.af.core.SchemaI18NService; import edu.ku.brc.af.core.db.BackupServiceFactory; import edu.ku.brc.af.core.db.DBFieldInfo; import edu.ku.brc.af.core.db.DBRelationshipInfo; import edu.ku.brc.af.core.db.DBTableChildIFace; import edu.ku.brc.af.core.db.DBTableIdMgr; import edu.ku.brc.af.core.db.DBTableInfo; import edu.ku.brc.af.prefs.AppPreferences; import edu.ku.brc.af.prefs.AppPrefsCache; import edu.ku.brc.af.ui.db.DatabaseLoginPanel; import edu.ku.brc.af.ui.forms.formatters.UIFieldFormatterIFace; import edu.ku.brc.af.ui.forms.formatters.UIFieldFormatterMgr; import edu.ku.brc.dbsupport.AttributeIFace; import edu.ku.brc.dbsupport.DBConnection; import edu.ku.brc.dbsupport.DBMSUserMgr; import edu.ku.brc.dbsupport.DataProviderFactory; import edu.ku.brc.dbsupport.DataProviderSessionIFace; import edu.ku.brc.dbsupport.DatabaseDriverInfo; import edu.ku.brc.dbsupport.HibernateUtil; import edu.ku.brc.helpers.Encryption; import edu.ku.brc.helpers.SwingWorker; import edu.ku.brc.helpers.XMLHelper; import edu.ku.brc.specify.Specify; import edu.ku.brc.specify.SpecifyUserTypes; import edu.ku.brc.specify.config.DisciplineType; import edu.ku.brc.specify.config.init.BldrPickList; import edu.ku.brc.specify.config.init.BldrPickListItem; import edu.ku.brc.specify.config.init.DataBuilder; import edu.ku.brc.specify.config.init.HiddenTableMgr; import edu.ku.brc.specify.config.init.TaxonLoadSetupPanel; import edu.ku.brc.specify.config.init.TreeDefRow; import edu.ku.brc.specify.conversion.BasicSQLUtils; import edu.ku.brc.specify.datamodel.Accession; import edu.ku.brc.specify.datamodel.AccessionAgent; import edu.ku.brc.specify.datamodel.Address; import edu.ku.brc.specify.datamodel.Agent; import edu.ku.brc.specify.datamodel.AgentAttachment; import edu.ku.brc.specify.datamodel.AgentVariant; import edu.ku.brc.specify.datamodel.Attachment; import edu.ku.brc.specify.datamodel.AttachmentMetadata; import edu.ku.brc.specify.datamodel.AttributeDef; import edu.ku.brc.specify.datamodel.AutoNumberingScheme; import edu.ku.brc.specify.datamodel.CollectingEvent; import edu.ku.brc.specify.datamodel.CollectingEventAttr; import edu.ku.brc.specify.datamodel.CollectingTrip; import edu.ku.brc.specify.datamodel.Collection; import edu.ku.brc.specify.datamodel.CollectionObject; import edu.ku.brc.specify.datamodel.CollectionObjectAttr; import edu.ku.brc.specify.datamodel.CollectionRelType; import edu.ku.brc.specify.datamodel.Collector; import edu.ku.brc.specify.datamodel.ConservDescription; import edu.ku.brc.specify.datamodel.ConservEvent; import edu.ku.brc.specify.datamodel.DNASequence; import edu.ku.brc.specify.datamodel.DataModelObjBase; import edu.ku.brc.specify.datamodel.DataType; import edu.ku.brc.specify.datamodel.Determination; import edu.ku.brc.specify.datamodel.Discipline; import edu.ku.brc.specify.datamodel.Division; import edu.ku.brc.specify.datamodel.Geography; import edu.ku.brc.specify.datamodel.GeographyTreeDef; import edu.ku.brc.specify.datamodel.GeographyTreeDefItem; import edu.ku.brc.specify.datamodel.GeologicTimePeriod; import edu.ku.brc.specify.datamodel.GeologicTimePeriodTreeDef; import edu.ku.brc.specify.datamodel.GeologicTimePeriodTreeDefItem; import edu.ku.brc.specify.datamodel.GroupPerson; import edu.ku.brc.specify.datamodel.Institution; import edu.ku.brc.specify.datamodel.Journal; import edu.ku.brc.specify.datamodel.LithoStrat; import edu.ku.brc.specify.datamodel.LithoStratTreeDef; import edu.ku.brc.specify.datamodel.LithoStratTreeDefItem; import edu.ku.brc.specify.datamodel.Locality; import edu.ku.brc.specify.datamodel.LocalityCitation; import edu.ku.brc.specify.datamodel.Permit; import edu.ku.brc.specify.datamodel.PickList; import edu.ku.brc.specify.datamodel.PrepType; import edu.ku.brc.specify.datamodel.Preparation; import edu.ku.brc.specify.datamodel.ReferenceWork; import edu.ku.brc.specify.datamodel.RepositoryAgreement; import edu.ku.brc.specify.datamodel.SpLocaleBase; import edu.ku.brc.specify.datamodel.SpLocaleContainer; import edu.ku.brc.specify.datamodel.SpLocaleContainerItem; import edu.ku.brc.specify.datamodel.SpLocaleItemStr; import edu.ku.brc.specify.datamodel.SpPrincipal; import edu.ku.brc.specify.datamodel.SpQuery; import edu.ku.brc.specify.datamodel.SpQueryField; import edu.ku.brc.specify.datamodel.SpecifyUser; import edu.ku.brc.specify.datamodel.Storage; import edu.ku.brc.specify.datamodel.StorageTreeDef; import edu.ku.brc.specify.datamodel.StorageTreeDefItem; import edu.ku.brc.specify.datamodel.Taxon; import edu.ku.brc.specify.datamodel.TaxonCitation; import edu.ku.brc.specify.datamodel.TaxonTreeDef; import edu.ku.brc.specify.datamodel.TaxonTreeDefItem; import edu.ku.brc.specify.datamodel.TreeDefIface; import edu.ku.brc.specify.datamodel.TreeDefItemStandardEntry; import edu.ku.brc.specify.datamodel.Treeable; import edu.ku.brc.specify.datamodel.Workbench; import edu.ku.brc.specify.datamodel.WorkbenchDataItem; import edu.ku.brc.specify.datamodel.WorkbenchRow; import edu.ku.brc.specify.datamodel.WorkbenchRowImage; import edu.ku.brc.specify.datamodel.WorkbenchTemplate; import edu.ku.brc.specify.datamodel.WorkbenchTemplateMappingItem; import edu.ku.brc.specify.dbsupport.BuildFromGeonames; import edu.ku.brc.specify.dbsupport.HibernateDataProviderSession; import edu.ku.brc.specify.dbsupport.SpecifyDeleteHelper; import edu.ku.brc.specify.tools.SpecifySchemaGenerator; import edu.ku.brc.specify.tools.schemalocale.DisciplineBasedContainer; import edu.ku.brc.specify.tools.schemalocale.SchemaLocalizerXMLHelper; import edu.ku.brc.specify.treeutils.NodeNumberer; import edu.ku.brc.specify.treeutils.TreeFactory; import edu.ku.brc.specify.treeutils.TreeHelper; import edu.ku.brc.ui.DateWrapper; import edu.ku.brc.ui.IconManager; import edu.ku.brc.ui.ProgressFrame; import edu.ku.brc.ui.UIHelper; import edu.ku.brc.ui.UIRegistry; import edu.ku.brc.ui.dnd.SimpleGlassPane; import edu.ku.brc.util.AttachmentManagerIface; import edu.ku.brc.util.AttachmentUtils; import edu.ku.brc.util.FileStoreAttachmentManager; import edu.ku.brc.util.Pair; import edu.ku.brc.util.thumbnails.Thumbnailer; /** * * @code_status Beta * * @author rods */ public class BuildSampleDatabase { private static final Logger log = Logger.getLogger(BuildSampleDatabase.class); public enum UpdateType { eBuildNew, eImport, eMerge, eLocalize } // 0 1 2 3 4 5 6 7 8 private static String[] TaxonIndexNames = { "family common name", "species author", "species source", "species guid", "species common name", "subspecies author", "subspecies source", "subspecies lsid", "subspecies common name" }; private static String[] TaxonFieldNames = { "CommonName", "Author", "Source", "GUID", "CommonName", "Author", "Source", "GUID", "CommonName" }; private static int FAMILY_COMMON_NAME = 0; private static int SPECIES_AUTHOR = 1; private static int SPECIES_SOURCE = 2; private static int SPECIES_GUID = 3; private static int SPECIES_COMMON_NAME = 4; private static int SUBSPECIES_AUTHOR = 5; private static int SUBSPECIES_SOURCE = 6; private static int SUBSPECIES_GUID = 7; private static int SUBSPECIES_COMMON_NAME = 8; private static String SHOW = "show"; private static String NAME = "name"; private static String RANK = "rank"; protected Hashtable<String, Integer> taxonExtraColsIndexes = new Hashtable<String, Integer>(); protected Hashtable<String, Integer> taxonIndexes = new Hashtable<String, Integer>(); protected static boolean debugOn = false; protected static final int TIME_THRESHOLD = 3000; protected static Hashtable<String, Boolean> fieldsToHideHash = new Hashtable<String, Boolean>(); protected static Hashtable<String, Boolean> fieldsToSkipHash = new Hashtable<String, Boolean>(); protected static List<Object> locs = null; protected Calendar calendar = Calendar.getInstance(); protected Session session; protected int steps = 0; protected ProgressFrame frame; protected Properties initPrefs = null; protected Properties backstopPrefs = null; protected SetUpBuildDlg setupDlg = null; protected boolean hideFrame = false; protected boolean doAddQueries = false; protected boolean copyToUserDir = true; protected boolean doShallowTaxonTree = false; protected List<CollectionChoice> selectedChoices = null; protected Hashtable<Class<?>, Vector<AutoNumberingScheme>> numberingSchemesHash = new Hashtable<Class<?>, Vector<AutoNumberingScheme>>(); protected Random rand = new Random(12345678L); protected Vector<Locality> globalLocalities = new Vector<Locality>(); protected Vector<Agent> globalAgents = new Vector<Agent>(); protected int stationFieldNumberCounter = 100; protected String STATION_FIELD_FORMAT = "RS%03d"; protected int NUM_LOCALTIES = 50000; protected int NUM_COLOBJS = 50000; protected boolean doHugeBotany = false; protected DataType dataType; protected StorageTreeDef stgTreeDef = null; protected int createStep = 0; protected Transaction trans = null; protected static Timestamp now = new Timestamp(System.currentTimeMillis()); protected static SimpleDateFormat dateTimeFormatter; protected static SimpleDateFormat dateFormatter; protected static String nowStr; protected LinkedList<Pair<String, Integer>> recycler = new LinkedList<Pair<String, Integer>>(); protected StringBuilder gSQLStr = new StringBuilder(); protected NumberFormat numFmt = NumberFormat.getInstance(); protected SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); protected int recCnt = 0; /** * */ public BuildSampleDatabase() { dateTimeFormatter = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss"); dateFormatter = new SimpleDateFormat("yyyy-MM-dd"); nowStr = "'" + dateTimeFormatter.format(now) + "'"; numFmt.setMinimumFractionDigits(0); numFmt.setMaximumFractionDigits(20); numFmt.setGroupingUsed(false); //gets rid of commas } /** * @return */ public Session getSession() { return session; } /** * @return */ public DataType getDataType() { return dataType; } /** * @param s */ public void setSession(final Session s) { session = s; } /** * @return */ public ProgressFrame getFrame() { return frame; } /** * @param dataObjects * @param userAgent */ protected void standardQueries(final Vector<Object> dataObjects, final Agent userAgent) { if (doAddQueries) { //Byte greaterThan = SpQueryField.OperatorType.GREATERTHAN.getOrdinal(); //Byte lessThan = SpQueryField.OperatorType.LESSTHAN.getOrdinal(); //Byte equals = SpQueryField.OperatorType.EQUALS.getOrdinal(); Byte greq = SpQueryField.OperatorType.GREATERTHANEQUALS.getOrdinal(); Byte lteq = SpQueryField.OperatorType.LESSTHANEQUALS.getOrdinal(); //Byte none = SpQueryField.SortType.NONE.getOrdinal(); Byte asc = SpQueryField.SortType.ASC.getOrdinal(); //Byte desc = SpQueryField.SortType.DESC.getOrdinal(); SpQuery query = createQuery( "CO " + AppContextMgr.getInstance().getClassObject(Collection.class).getCollectionName(), "CollectionObject", 1, AppContextMgr.getInstance().getClassObject(SpecifyUser.class), userAgent); createQueryField(query, (short) 0, "catalogNumber", "Catalog Number", false, greq, lteq, "102", "103", asc, true, "1", 1); query.setIsFavorite(true); dataObjects.add(query); } } /** * @param name the name of the scheme * @return a numbering scheme by name. */ private AutoNumberingScheme getAutoNumberingScheme(final Class<?> clazz, final String name) { Vector<AutoNumberingScheme> numberingSchemes = numberingSchemesHash.get(clazz); if (numberingSchemes != null) { for (AutoNumberingScheme ans : numberingSchemes) { if (ans.getSchemeName().equals(name)) { return ans; } } } return null; } /** * @param clazz * @param ans */ private void addAutoNumberingScheme(final Class<?> clazz, final AutoNumberingScheme ans) { Vector<AutoNumberingScheme> numberingSchemes = numberingSchemesHash.get(clazz); if (numberingSchemes == null) { numberingSchemes = new Vector<AutoNumberingScheme>(); numberingSchemesHash.put(clazz, numberingSchemes); } numberingSchemes.add(ans); } /** * */ protected void adjustLocaleFromPrefs() { String language = AppPreferences.getLocalPrefs().get("locale.lang", null); //$NON-NLS-1$ if (language != null) { String country = AppPreferences.getLocalPrefs().get("locale.country", null); //$NON-NLS-1$ String variant = AppPreferences.getLocalPrefs().get("locale.var", null); //$NON-NLS-1$ Locale prefLocale = new Locale(language, country, variant); Locale.setDefault(prefLocale); setResourceLocale(prefLocale); } try { ResourceBundle.getBundle("resources", Locale.getDefault()); //$NON-NLS-1$ } catch (MissingResourceException ex) { Locale.setDefault(Locale.ENGLISH); setResourceLocale(Locale.ENGLISH); } } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public boolean createEmptyInstitution(final Properties props, final boolean doCreateDiv, final boolean doCreateDisp, final boolean doFromWizard, final int treeDir) { AppContextMgr.getInstance().setHasContext(true); createStep = 0; if (frame != null) frame.setProcess(0, 10); if (frame != null) frame.setProcess(++createStep); Institution institution = null; //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String username = props.getProperty("usrUsername"); String password = props.getProperty("usrPassword"); startTx(); System.out.println("----- User Agent -----"); System.out.println("Userame: " + username); institution = createInstitution(props.getProperty("instName")); institution.setCode(props.getProperty("instAbbrev")); institution.setIsAccessionsGlobal((Boolean) props.get("accglobal")); Address instAddress = new Address(); instAddress.initialize(); instAddress.setAddress(props.getProperty("addr1")); instAddress.setAddress2(props.getProperty("addr2")); instAddress.setCity(props.getProperty("city")); instAddress.setCountry(props.getProperty("country")); instAddress.setState(props.getProperty("state")); instAddress.setPostalCode(props.getProperty("zip")); instAddress.setPhone1(props.getProperty("phone")); institution.setAddress(instAddress); instAddress.getInsitutions().add(institution); institution.setIsSecurityOn((Boolean) props.get("security_on")); if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", treeDir); institution.setStorageTreeDef(stgTreeDef); stgTreeDef.getInstitutions().add(institution); persist(stgTreeDef); } String storXML = props.getProperty("StorageTreeDef.treedefs"); List<Object> storages = new Vector<Object>(); createStorageDefFromXML(storages, stgTreeDef, storXML); persist(storages); String email = props.getProperty("email"); String userType = props.getProperty("userType"); String encrypted = Encryption.encrypt(password, password); SpecifyUser specifyAdminUser = DataBuilder.createAdminGroupAndUser(session, institution, null, username, email, encrypted, userType); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// dataType = createDataType("Biota"); persist(institution); persist(specifyAdminUser); persist(dataType); commitTx(); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, specifyAdminUser); AppContextMgr.getInstance().setClassObject(Institution.class, institution); if (frame != null) frame.setProcess(++createStep); if (doCreateDiv) { DisciplineType disciplineType = (DisciplineType) props.get("disciplineType"); return createEmptyDivision(institution, disciplineType, specifyAdminUser, props, doCreateDisp, doFromWizard, false) != null; } return true; } /** * @param dataType the dataType to set */ public void setDataType(DataType dataType) { this.dataType = dataType; } /** * @param institution * @param disciplineType * @param props * @return */ public Division createEmptyDivision(final Institution institution, final DisciplineType disciplineType, final SpecifyUser specifyAdminUser, final Properties props, final boolean doCreateDisp, final boolean doFromWizard, final boolean doSetProgressRange) { if (doSetProgressRange && frame != null) { frame.setProcess(0, 19); } startTx(); Division division = createDivision(institution, disciplineType.getName(), props.getProperty("divName"), props.getProperty("divAbbrev"), null); //props.getProperty("divTitle"); frame.incOverall(); persist(division); String title = props.getProperty("title", null); String firstName = props.getProperty("firstName", "Test"); String lastName = props.getProperty("lastName", "User"); String midInit = props.getProperty("middleInitial", "A"); String abbrev = props.getProperty("abbrev", ""); String email = props.getProperty("email"); //String userType = props.getProperty("userType"); /*System.out.println("----- User Agent -----"); System.out.println("Title: "+title); System.out.println("FirstName: "+firstName); System.out.println("LastName: "+lastName); System.out.println("MidInit: "+midInit); System.out.println("Abbrev: "+abbrev); System.out.println("Email: "+email); System.out.println("UserType: "+userType); */ frame.incOverall(); Agent userAgent = AppContextMgr.getInstance().getClassObject(Agent.class); Agent newUserAgent = null; boolean fromWiz = UIHelper.getProperty(props, "fromwizard", false); if (userAgent == null || (doFromWizard && fromWiz)) { userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email, division, null); } else { try { HibernateUtil.attach(specifyAdminUser, session); //HibernateUtil.attach(userAgent, session); // rods - this doesn't work 8/17/10 List<?> agentList = session.createQuery("FROM Agent WHERE id = " + userAgent.getId()).list(); Agent cloneableAgent = (Agent) agentList.get(0); newUserAgent = (Agent) cloneableAgent.clone(); Agent.initializeSets(newUserAgent); specifyAdminUser.getAgents().add(newUserAgent); newUserAgent.setSpecifyUser(specifyAdminUser); newUserAgent.setDivision(division); // Set the new Division session.saveOrUpdate(newUserAgent); session.saveOrUpdate(specifyAdminUser); userAgent = newUserAgent; } catch (CloneNotSupportedException ex) { ex.printStackTrace(); } } try { userAgent = (Agent) session.merge(userAgent); AppContextMgr.getInstance().setClassObject(Agent.class, userAgent); } catch (Exception ex) { ex.printStackTrace(); } specifyAdminUser.addReference(userAgent, "agents"); persist(specifyAdminUser); commitTx(); if (doCreateDisp) { Pair<Discipline, Collection> dc = createEmptyDisciplineAndCollection(division, props, disciplineType, userAgent, specifyAdminUser, true, false); if (dc == null) { return null; } } frame.incOverall(); return division; } /** * @param division * @param props * @param disciplineType * @param userAgent * @param specifyAdminUser * @param doCollection * @return */ public Pair<Discipline, Collection> createEmptyDisciplineAndCollection(final Division division, final Properties props, final DisciplineType disciplineType, final Agent userAgent, final SpecifyUser specifyAdminUser, final boolean doCollection, final boolean doSetProgressRange) { log.debug("In createEmptyDisciplineAndCollection - createStep: " + createStep); if (doSetProgressRange) { frame.setProcess(0, 17); } String dispName = props.getProperty("dispName"); if (StringUtils.isEmpty(dispName)) { dispName = disciplineType.getTitle(); } Object pltObj = props.get("preloadtaxon"); boolean preLoadTaxon = pltObj == null ? false : (Boolean) pltObj; String taxonXML = props.getProperty("TaxonTreeDef.treedefs"); String taxonFileName = props.getProperty("taxonfilename"); String geoXML = props.getProperty("GeographyTreeDef.treedefs"); Boolean doUserProvidedFile = (Boolean) props.get("othertaxonfile"); frame.incOverall(); Discipline discipline = createEmptyDiscipline(division, dispName, disciplineType, userAgent, preLoadTaxon, taxonFileName, doUserProvidedFile != null ? doUserProvidedFile : false, taxonXML, geoXML, props); if (discipline != null) { frame.setProcess(0, 17); frame.setProcess(++createStep); frame.setDesc("Loading Schema..."); // I18N boolean isAccGlobal = false; if (props.get("accglobal") == null) { Institution inst = AppContextMgr.getInstance().getClassObject(Institution.class); isAccGlobal = inst != null && inst.getIsAccessionsGlobal(); } else { isAccGlobal = (Boolean) props.get("accglobal"); } // The two AutoNumberingSchemes have been committed Pair<AutoNumberingScheme, AutoNumberingScheme> ansPair = localizeDisciplineSchema(division, discipline, props, isAccGlobal); // These create a new session and persist records in the Schema tables (SpLocaleContainerItem) boolean fromWiz = UIHelper.getProperty(props, "fromwizard", false); if (fromWiz) // means a new database { doShowHideTablesAndFields(null, discipline); } // Since we the Localization is at the Discipline level it is OK // to always run this here. doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setProcess(0, 17); frame.setProcess(++createStep); Collection collection = null; if (doCollection) { // Persists the Collection collection = createEmptyCollection(discipline, props.getProperty("collPrefix").toString(), props.getProperty("collName").toString(), userAgent, specifyAdminUser, ansPair.first, disciplineType.isEmbeddedCollecingEvent()); } startTx(); // Adds AutoNumberScheme to Division if (ansPair.second != null) { division.addReference(ansPair.second, "numberingSchemes"); persist(ansPair.second); persist(division); } commitTx(); buildDarwinCoreSchema(discipline); // creates own DataProviderSessionIFace log.debug("Out createEmptyDisciplineAndCollection - createStep: " + createStep); return new Pair<Discipline, Collection>(discipline, collection); } return null; } /** * @param props * @param cls * @return */ public static int getTreeDirForClass(final Properties props, final Class<?> cls) { return getTreeDirForClass(props, cls, TreeDefIface.REVERSE); } /** * @param props * @param cls * @return */ public static int getTreeDirForClass(final Properties props, final Class<?> cls, final int defVal) { String value = props.getProperty("treedir." + cls.getSimpleName()); if (value == null) return defVal; return value.equals("reverse") ? TreeDefIface.REVERSE : TreeDefIface.FORWARD; } /** * @param division * @param dispTitle * @param disciplineType * @param userAgent * @param preLoadTaxon * @param taxonFileName * @param doUserProvidedFile * @return */ public Discipline createEmptyDiscipline(final Division division, final String dispTitle, final DisciplineType disciplineType, final Agent userAgent, final boolean preLoadTaxon, final String taxonFileName, final boolean doUserProvidedFile, final String taxonDefXML, final String geoDefXML, final Properties props) { log.debug("In createEmptyDiscipline - createStep: " + createStep); startTx(); // create tree defs (later we will make the definition items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", getTreeDirForClass(props, TaxonTreeDef.class, TreeDefIface.FORWARD)); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", getTreeDirForClass(props, GeographyTreeDef.class)); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", getTreeDirForClass(props, GeologicTimePeriodTreeDef.class)); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); frame.incOverall(); Discipline discipline = createDiscipline(division, disciplineType.getName(), dispTitle, dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); persist(division); persist(discipline); persist(userAgent); //commitTx(); frame.incOverall(); //startTx(); frame.setProcess(++createStep); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// frame.setDesc("Building Trees..."); Vector<Object> taxa = new Vector<Object>(); // Create Tree Definition taxonTreeDef.setDiscipline(discipline); taxa.add(taxonTreeDef); commitTx(); frame.setProcess(++createStep); boolean isPaleo = disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.paleobotany || disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.vertpaleo || disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.invertpaleo; if (isPaleo) { startTx(); LithoStratTreeDefItem earth = createLithoStratTreeDefItem(lithoStratTreeDef, "Surface", 0, false); LithoStratTreeDefItem superGrp = createLithoStratTreeDefItem(earth, "Super Group", 100, false); LithoStratTreeDefItem lithoGrp = createLithoStratTreeDefItem(superGrp, "Litho Group", 200, false); LithoStratTreeDefItem formation = createLithoStratTreeDefItem(lithoGrp, "Formation", 300, false); LithoStratTreeDefItem member = createLithoStratTreeDefItem(formation, "Member", 400, false); LithoStratTreeDefItem bed = createLithoStratTreeDefItem(member, "Bed", 500, true); member.setIsInFullName(true); bed.setIsInFullName(true); persist(earth); // setup the root Geography record (planet Earth) LithoStrat earthNode = new LithoStrat(); earthNode.initialize(); earthNode.setName(getResourceString("Earth")); earthNode.setFullName(earthNode.getName()); earthNode.setNodeNumber(1); earthNode.setHighestChildNodeNumber(1); earthNode.setRankId(0); earthNode.setDefinition(lithoStratTreeDef); earthNode.setDefinitionItem(earth); earth.getTreeEntries().add(earthNode); persist(earthNode); commitTx(); convertChronoStratFromXLS(gtpTreeDef, userAgent); // does commits } frame.incOverall(); List<Object> geos = new Vector<Object>(); //List<Object> lithoStrats = isPaleo ? createSimpleLithoStrat(lithoStratTreeDef, false) : null; startTx(); HashSet<String> colNameHash = null; if (StringUtils.isNotEmpty(taxonFileName)) { colNameHash = getColumnNamesFromXLS(taxonFileName, doUserProvidedFile); } boolean taxonWasBuilt = createTaxonDefFromXML(taxa, colNameHash, taxonTreeDef, taxonDefXML); frame.incOverall(); log.debug(" taxonWasBuilt " + taxonWasBuilt); if (!taxonWasBuilt) { TaxonTreeDefItem ttdi = new TaxonTreeDefItem(); ttdi.initialize(); ttdi.setTreeDef(taxonTreeDef); taxonTreeDef.getTreeDefItems().add(ttdi); ttdi.setName(getResourceString("Root")); ttdi.setRankId(0); ttdi.setParent(null); ttdi.setFullNameSeparator(null); ttdi.setIsEnforced(true); ttdi.setIsInFullName(false); Taxon tx = new Taxon(); tx.initialize(); tx.setDefinition(taxonTreeDef); tx.setDefinitionItem(ttdi); ttdi.getTreeEntries().add(tx); tx.setName(getResourceString("Life")); tx.setFullName(tx.getName()); tx.setNodeNumber(1); tx.setHighestChildNodeNumber(1); persist(ttdi); persist(tx); } frame.setProcess(++createStep); frame.incOverall(); createGeographyDefFromXML(geos, geoTreeDef, geoDefXML); frame.setProcess(++createStep); persist(taxa); persist(geos); commitTx(); frame.setProcess(++createStep); frame.incOverall(); log.debug(" preLoadTaxon [" + preLoadTaxon + "]"); log.debug(" fileName [" + taxonFileName + "]"); if (preLoadTaxon && taxonFileName != null) { convertTaxonFromXLS(taxonTreeDef, taxonFileName, doUserProvidedFile); // this does a startTx() / commitTx() } frame.setProcess(++createStep); frame.incOverall(); // startTx(); // // if (lithoStrats != null) // { // persist(lithoStrats); // // } // // commitTx(); frame.setProcess(++createStep); //convertGeographyFromXLS(geoTreeDef); // this does a startTx() / commitTx() String itUsername = props.getProperty("dbUserName"); String itPassword = props.getProperty("dbPassword"); if (StringUtils.isEmpty(itUsername) || StringUtils.isEmpty(itPassword)) { frame.setVisible(false); Pair<String, String> usrPwd = DatabaseLoginPanel.getITUsernamePwd(); frame.setVisible(true); if (usrPwd != null) { itUsername = usrPwd.first; itPassword = usrPwd.second; } else { return null; } } //convertGeographyFromXLS(discipline.getGeographyTreeDef()); @SuppressWarnings("unused") Geography earth = createGeographyFromGeonames(discipline, userAgent, itUsername, itPassword); frame.setProcess(++createStep); frame.incOverall(); log.debug("Out createEmptyDiscipline - createStep: " + createStep); return discipline; } /** * @param discipline * @param collPrefix * @param collName * @param userAgent * @param specifyAdminUser * @param catNumScheme * @param isEmbeddedCE * @return */ public Collection createEmptyCollection(final Discipline discipline, final String collPrefix, final String collName, final Agent userAgent, final SpecifyUser specifyAdminUser, final AutoNumberingScheme catNumScheme, final boolean isEmbeddedCE) { log.debug("In createEmptyCollection - createStep: " + createStep); frame.setProcess(++createStep); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); frame.setDesc("Creating a Collection"); // I18N Collection collection = createCollection(collPrefix, collName, catNumScheme.getFormatName(), // Catalog Format Name catNumScheme, // Catalog Number Schema discipline, isEmbeddedCE); collection.setDiscipline(discipline); collection.getTechnicalContacts().add(userAgent); collection.getContentContacts().add(userAgent); persist(collection); persist(catNumScheme); frame.setProcess(++createStep); persist(loadPrepTypes(discipline.getType(), collection, userAgent)); /////////////////////////////////////// // Default user groups and test user /////////////////////////////////////// // create the standard user groups for this collection Map<String, SpPrincipal> groupMap = DataBuilder.createStandardGroups(session, collection); SpPrincipal userPrin = DataBuilder.createUserPrincipal(specifyAdminUser, collection); persist(userPrin); persist(specifyAdminUser); // add the administrator as a Collections Manager in this group specifyAdminUser.addUserToSpPrincipalGroup(groupMap.get(SpecifyUserTypes.UserType.Manager.toString())); // add tester //String dspAbbrev = disciplineType.getAbbrev(); //createAndAddTesterToCollection(dspAbbrev+"Tester", dspAbbrev+"tester@brc.ku.edu", dspAbbrev+"Tester", // "", dspAbbrev, "", "Tester", "", discipline, division, groupMap, SpecifyUserTypes.UserType.Manager.toString()); commitTx(); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); frame.setDesc("Creating Common PickLists..."); frame.setProcess(++createStep); createPickLists(session, null, false, collection); frame.setProcess(++createStep); frame.setDesc("Creating PickLists..."); createPickLists(session, discipline, false, collection); frame.setProcess(++createStep); log.debug("Out createEmptyCollection - createStep: " + createStep); return collection; } /** * @param props * @param propName * @param schemeName * @param tableId * @return */ public AutoNumberingScheme createAutoNumScheme(final Properties props, final String propName, final String schemeName, final int tableId) { Object numFmtObj = props.get(propName); UIFieldFormatterIFace numFormat = numFmtObj instanceof UIFieldFormatterIFace ? (UIFieldFormatterIFace) numFmtObj : null; boolean isNumFmtNumeric = false; String numFmtName = numFormat != null ? numFormat.getName() : (numFmtObj != null ? numFmtObj.toString() : null); if (numFormat != null) { isNumFmtNumeric = numFormat.isNumeric(); } else if (StringUtils.isNotEmpty(numFmtName)) { numFormat = UIFieldFormatterMgr.getInstance().getFormatter(numFmtName); if (numFormat != null) { isNumFmtNumeric = numFormat.isNumeric(); } } AutoNumberingScheme autoNumScheme = null; if (numFormat != null) { autoNumScheme = createAutoNumberingScheme(schemeName, "", numFmtName, isNumFmtNumeric, tableId); } return autoNumScheme; } /** * @param discipline * @param props * @param isAccGlobal * @return */ public Pair<AutoNumberingScheme, AutoNumberingScheme> localizeDisciplineSchema(final Division division, final Discipline discipline, final Properties props, final boolean isAccGlobal) { AutoNumberingScheme catNumScheme = createAutoNumScheme(props, "catnumfmt", "Catalog Numbering Scheme", CollectionObject.getClassTableId()); // I18N AutoNumberingScheme accNumScheme = null; // Check to see if we are creating from scratch boolean isFromScratch = props.getProperty("instName") != null; String postFix = "FROM autonumberingscheme ans INNER JOIN autonumsch_div ad ON ans.AutoNumberingSchemeID = ad.AutoNumberingSchemeID " + "INNER JOIN division d ON ad.DivisionID = d.UserGroupScopeId WHERE d.UserGroupScopeId = " + division.getId(); String sql = "SELECT COUNT(*) " + postFix; log.debug(sql); int numOfDivAns = BasicSQLUtils.getCountAsInt(sql); if (numOfDivAns > 1) { // error } // NOTE: createAutoNumScheme persists the AutoNumberingScheme if (!isAccGlobal || isFromScratch) { if (numOfDivAns == 0) { accNumScheme = createAutoNumScheme(props, "accnumfmt", "Accession Numbering Scheme", Accession.getClassTableId()); // I18N } else { sql = "SELECT ans.AutoNumberingSchemeID " + postFix; log.debug(sql); int ansId = BasicSQLUtils.getCountAsInt(sql); DataProviderSessionIFace hSession = new HibernateDataProviderSession(session); List<?> list = hSession.getDataList("FROM AutoNumberingScheme WHERE id = " + ansId); if (list != null && list.size() == 1) { accNumScheme = (AutoNumberingScheme) list.get(0); } // Do not close the session it is owned by someone else //hSession.close(); } } else { DataProviderSessionIFace hSession = new HibernateDataProviderSession(session); List<?> list = hSession .getDataList("FROM AutoNumberingScheme WHERE tableNumber = " + Accession.getClassTableId()); if (list != null && list.size() == 1) { accNumScheme = (AutoNumberingScheme) list.get(0); } // Do not close the session it is owned by someone else //hSession.close(); } startTx(); DBTableIdMgr dbMgr = new DBTableIdMgr(true); dbMgr.initialize(); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, dbMgr, catNumScheme.getFormatName(), accNumScheme != null ? accNumScheme.getFormatName() : null); DBTableIdMgr wbTableMgr = new DBTableIdMgr(false); wbTableMgr.initialize(new File(XMLHelper.getConfigDirPath("specify_workbench_datamodel.xml"))); //$NON-NLS-1$ //DataProviderSessionIFace hSession = new HibernateDataProviderSession(session); loadSchemaLocalization(discipline, SpLocaleContainer.WORKBENCH_SCHEMA, wbTableMgr, null, null, UpdateType.eBuildNew, null);//hSession); frame.setProcess(++createStep); persist(discipline); frame.setProcess(++createStep); commitTx(); // The two AutoNumberingSchemes have been persisted. return new Pair<AutoNumberingScheme, AutoNumberingScheme>(catNumScheme, accNumScheme); } /** * @param geoList * @param geoTreeDef * @param geoXML */ @SuppressWarnings("unchecked") public static void createGeographyDefFromXML(final List<Object> geoList, final GeographyTreeDef geoTreeDef, final String geoXML) { if (StringUtils.isNotEmpty(geoXML)) { XStream xstream = new XStream(); TreeDefRow.configXStream(xstream); Vector<TreeDefRow> treeDefList = (Vector<TreeDefRow>) xstream.fromXML(geoXML); GeographyTreeDefItem parent = null; for (TreeDefRow row : treeDefList) { GeographyTreeDefItem gtdi = new GeographyTreeDefItem(); gtdi.initialize(); gtdi.setTreeDef(geoTreeDef); geoTreeDef.getTreeDefItems().add(gtdi); gtdi.setName(row.getDefName()); gtdi.setTitle(row.getTitle()); gtdi.setRankId(row.getRank()); gtdi.setParent(parent); gtdi.setFullNameSeparator(row.getSeparator()); gtdi.setIsEnforced(row.isEnforced()); gtdi.setIsInFullName(row.isInFullName()); geoList.add(gtdi); if (parent != null) { parent.getChildren().add(gtdi); } parent = gtdi; } } } /** * @param taxonList * @param colNameHash * @param taxonTreeDef * @param taxonDefXML * @return */ @SuppressWarnings("unchecked") public boolean createTaxonDefFromXML(final List<Object> taxonList, final HashSet<String> colNameHash, final TaxonTreeDef taxonTreeDef, final String taxonDefXML) { if (StringUtils.isNotEmpty(taxonDefXML)) { XStream xstream = new XStream(); TreeDefRow.configXStream(xstream); Vector<TreeDefRow> treeDefList = (Vector<TreeDefRow>) xstream.fromXML(taxonDefXML); if (colNameHash != null) { Hashtable<String, TreeDefItemStandardEntry> stdTreeLevelsHash = new Hashtable<String, TreeDefItemStandardEntry>(); for (TreeDefItemStandardEntry entry : TaxonTreeDef.getStandardLevelsStatic()) { stdTreeLevelsHash.put(entry.getName().toLowerCase(), entry); } Hashtable<String, TreeDefRow> xmlTreeLevelsHash = new Hashtable<String, TreeDefRow>(); for (TreeDefRow row : treeDefList) { xmlTreeLevelsHash.put(row.getDefName().toLowerCase(), row); } for (String columnName : colNameHash) { String colName = columnName.toLowerCase(); TreeDefRow treeDefRow = xmlTreeLevelsHash.get(colName); if (treeDefRow == null) { log.debug(colName + " NOT found in XML, checking std."); TreeDefItemStandardEntry entry = stdTreeLevelsHash.get(colName); if (entry != null) { for (int i = 0; i < treeDefList.size(); i++) { if (i < treeDefList.size() && entry.getRank() < treeDefList.get(i).getRank()) { log.debug(String.format("Adding '%s' as rank %d.", colName, entry.getRank())); TreeDefRow newRow = new TreeDefRow(entry.getName(), entry.getTitle(), entry.getRank(), true, // included false, // enforced false, // is in Full Name false, // is required ","); treeDefList.insertElementAt(newRow, i); break; } } } else { //showLocalizedError("The wizard was unable to find '%s' as a standard Taxonomy level.", colName); log.debug(String.format( "The wizard was unable to find '%s' as a standard Taxonomy level.", colName)); } } else { log.debug(colName + " found in XML"); } } for (TreeDefRow row : treeDefList) { log.debug(row.getDefName() + " " + row.getTitle() + " " + row.getRank()); } } TaxonTreeDefItem ttdiRoot = null; Taxon txRoot = null; TaxonTreeDefItem parent = null; int cnt = 0; for (TreeDefRow row : treeDefList) { if (row.isIncluded() || (row.getDefName() != null && (colNameHash == null || colNameHash.contains(row.getDefName().toLowerCase())))) { TaxonTreeDefItem ttdi = new TaxonTreeDefItem(); ttdi.initialize(); ttdi.setTreeDef(taxonTreeDef); taxonTreeDef.getTreeDefItems().add(ttdi); ttdi.setName(row.getDefName()); ttdi.setTitle(row.getTitle()); ttdi.setRankId(row.getRank()); ttdi.setParent(parent); ttdi.setFullNameSeparator(row.getSeparator()); ttdi.setIsEnforced(row.isEnforced()); ttdi.setIsInFullName(row.isInFullName()); taxonList.add(ttdi); if (cnt == 0) { ttdiRoot = ttdi; Taxon tx = new Taxon(); tx.initialize(); tx.setDefinition(taxonTreeDef); tx.setDefinitionItem(ttdi); ttdi.getTreeEntries().add(tx); tx.setName(getResourceString("Life")); tx.setFullName(tx.getName()); tx.setNodeNumber(1); tx.setHighestChildNodeNumber(1); //tx.setIsAccepted(true); txRoot = tx; } if (parent != null) { parent.getChildren().add(ttdi); } parent = ttdi; cnt++; } } if (ttdiRoot != null) persist(ttdiRoot); if (txRoot != null) persist(txRoot); } return true; } /** * @param storageList * @param storageTreeDef * @param storageXML */ @SuppressWarnings("unchecked") public static void createStorageDefFromXML(final List<Object> storageList, final StorageTreeDef storageTreeDef, final String storageXML) { if (StringUtils.isNotEmpty(storageXML)) { XStream xstream = new XStream(); TreeDefRow.configXStream(xstream); Vector<TreeDefRow> treeDefList = (Vector<TreeDefRow>) xstream.fromXML(storageXML); StorageTreeDefItem parent = null; int cnt = 0; for (TreeDefRow row : treeDefList) { if (row.isIncluded()) { StorageTreeDefItem stdi = new StorageTreeDefItem(); stdi.initialize(); stdi.setTreeDef(storageTreeDef); storageTreeDef.getTreeDefItems().add(stdi); stdi.setName(row.getDefName()); stdi.setTitle(row.getTitle()); stdi.setRankId(row.getRank()); stdi.setParent(parent); stdi.setFullNameSeparator(row.getSeparator()); stdi.setIsEnforced(row.isEnforced()); stdi.setIsInFullName(row.isInFullName()); storageList.add(stdi); if (cnt == 0) { Storage stg = new Storage(); stg.initialize(); stg.setDefinition(storageTreeDef); stg.setDefinitionItem(stdi); stdi.getTreeEntries().add(stg); stg.setName(getResourceString("Site")); stg.setFullName(stg.getName()); stg.setNodeNumber(1); stg.setHighestChildNodeNumber(1); } if (parent != null) { parent.getChildren().add(stdi); } parent = stdi; cnt++; } } } } /** * Returns a list of object of a specified class. * @param cls the class * @param dataObjects the list of possible object * @return the list */ protected List<?> getObjectsOfClass(final Class<?> cls, final List<Object> dataObjects) { Vector<Object> list = new Vector<Object>(); for (Object obj : dataObjects) { if (obj.getClass() == cls) { list.add(obj); } } return list; } /** * @param dataObjects */ protected void addConservatorData(final List<Agent> agents, final List<CollectionObject> colObjs) { //startTx(); ConservDescription desc = new ConservDescription(); desc.initialize(); desc.setShortDesc("Short Description"); //desc.addReference(divs.get(0), "division"); desc.addReference(colObjs.get(0), "collectionObject"); //desc.setCollectionObject(colObjs.get(0)); //colObjs.get(0).getConservDescriptions().add(desc); ConservEvent conservEvent = new ConservEvent(); conservEvent.initialize(); conservEvent.setExamDate(Calendar.getInstance()); conservEvent.addReference(agents.get(1), "examinedByAgent"); conservEvent.addReference(agents.get(2), "treatedByAgent"); desc.addReference(conservEvent, "events"); persist(desc); } /** * @param discipline * @return */ public static BldrPickList createPickLists(final Session localSession, final Discipline discipline) { return createPickLists(localSession, discipline, false, AppContextMgr.getInstance().getClassObject(Collection.class)); } /** * @param discipline * @return */ public static BldrPickList createPickLists(final Session localSession, final Discipline discipline, final boolean doCheck, final Collection collection) { BldrPickList colMethods = null; try { Transaction trans = localSession.beginTransaction(); Hashtable<String, PickList> nameHash = doCheck ? new Hashtable<String, PickList>() : null; if (doCheck) { for (PickList pl : new Vector<PickList>(collection.getPickLists())) { if (pl.getNumItems() > 0) { nameHash.put(pl.getName(), pl); } else if (discipline == null) { log.debug("Deleting PickList: " + pl.getName()); collection.getPickLists().remove(pl); localSession.delete(pl); } } } List<BldrPickList> pickLists = DataBuilder .getBldrPickLists(discipline != null ? discipline.getType() : "common"); if (pickLists != null) { for (BldrPickList pl : pickLists) { PickList pickList; pickList = doCheck ? nameHash.get(pl.getName()) : null; if (pickList != null) { pickList.setIsSystem(true); if (pickList.getNumItems() > 0) { log.info("Skipping PickList[" + pl.getName() + "]"); continue; } } else { log.info("Creating PickList[" + pl.getName() + "]"); pickList = createPickList(pl.getName(), pl.getType(), pl.getTableName(), pl.getFieldName(), pl.getFormatter(), pl.getReadOnly(), pl.getSizeLimit(), pl.getIsSystem(), pl.getSortType(), collection); } pickList.setIsSystem(true); pickList.setCollection(collection); collection.getPickLists().add(pickList); for (BldrPickListItem item : pl.getItems()) { pickList.addItem(item.getTitle(), item.getValue(), item.getOrdinal()); } if (localSession != null) { localSession.saveOrUpdate(pickList); } if (pl.getName().equals("CollectingMethod")) { colMethods = pl; } } if (localSession != null) { localSession.saveOrUpdate(collection); } } else { log.error("No PickList XML"); } trans.commit(); localSession.flush(); } catch (Exception ex) { ex.printStackTrace(); } return colMethods; } protected CollectingEvent createFakeCollectingEvent(final List<Agent> agents, final Locality farmpond, final String method) { int year = (int) (rand.nextDouble() * 20.0) + 1990; int mon = (int) (rand.nextDouble() * 11.0) + 1; Collector collectorMeg = createCollector(agents.get(2), 1); Collector collectorRod = createCollector(agents.get(3), 2); String stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); calendar.set(year, mon, 22, 06, 12, 00); CollectingEvent ce2 = createCollectingEvent(farmpond, calendar, stationFieldNumber, new Collector[] { collectorMeg, collectorRod }); ce2.setStartDateVerbatim("22 Apr " + year + ", 6:12 AM"); calendar.set(year, mon, 22, 07, 31, 00); ce2.setEndDate(calendar); ce2.setEndDateVerbatim("22 Apr " + year + ", 7:31 AM"); ce2.setMethod(method); return ce2; } /** * @param rank * @param taxa * @return */ protected Taxon getRandomTaxon(final int rank, final List<Object> taxa) { Vector<Taxon> species = new Vector<Taxon>(); for (Object tObj : taxa) { if (tObj instanceof Taxon) { Taxon t = (Taxon) tObj; if (t.getRankId().intValue() == rank) { species.add(t); } } } int inx = (int) (rand.nextDouble() * species.size()); return species.get(inx); } /** * @param agents * @return */ protected Agent getRandomAgent(final List<Agent> agents) { int inx = (int) (rand.nextDouble() * agents.size()); return agents.get(inx); } /** * @param preps * @param agents * @param dataObjects */ protected void createLoanExamples(List<Preparation> preps, List<Agent> agents, Vector<Object> dataObjects) { /* //////////////////////////////// // loans (loan agents, shipments) //////////////////////////////// log.info("Creating loans, loan agents, and shipments"); Calendar loanDate1 = Calendar.getInstance(); loanDate1.set(2005, 03, 19); Calendar currentDueDate1 = Calendar.getInstance(); currentDueDate1.set(2005, 9, 19); Calendar originalDueDate1 = currentDueDate1; Calendar dateClosed1 = Calendar.getInstance(); dateClosed1.set(2005, 7, 4); List<LoanPreparation> loanPreps = new Vector<LoanPreparation>(); Vector<LoanReturnPreparation> returns = new Vector<LoanReturnPreparation>(); Loan closedLoan = createLoan("2007-001", loanDate1, currentDueDate1, originalDueDate1, dateClosed1, Loan.CLOSED, null); int loanPrepCnt = 0; for (int i = 0; i < 7; ++i) { Preparation prep = preps.get(rand.nextInt(preps.size())); int available = prep.getLoanAvailable(); if (available < 1 || !prep.getPrepType().getIsLoanable()) { // retry i--; continue; } int quantity = Math.min(Math.max(1, rand.nextInt(available)), available); LoanPreparation lpo = DataBuilder.createLoanPreparation(quantity, null, null, null, 0, 0, prep, closedLoan); lpo.setIsResolved(true); loanPreps.add(lpo); Calendar returnedDate = Calendar.getInstance(); returnedDate.setTime(lpo.getLoan().getLoanDate().getTime()); returnedDate.add(Calendar.DAY_OF_YEAR, 72); // make the returned date be a little while after the original loan LoanReturnPreparation lrpo = createLoanReturnPreparation(returnedDate, quantity, quantity, lpo, null, agents.get(0)); lpo.addReference(lrpo, "loanReturnPreparations"); returns.add(lrpo); prep.getLoanPreparations().add(lpo); loanPrepCnt++; if (loanPrepCnt > 3) { break; } } Calendar loanDate2 = Calendar.getInstance(); loanDate2.set(2005, 11, 24); Calendar currentDueDate2 = Calendar.getInstance(); currentDueDate2.set(2006, 5, 24); Calendar originalDueDate2 = currentDueDate2; Loan overdueLoan = createLoan("2006-002", loanDate2, currentDueDate2, originalDueDate2, null, Loan.OPEN, null); loanPrepCnt = 0; for (int i = 0; i < 5; ++i) { Preparation p = getObjectByClass(preps, Preparation.class, rand.nextInt(preps.size())); int available = p.getLoanAvailable(); if (available < 1 || !p.getPrepType().getIsLoanable()) { // retry i--; continue; } int quantity = Math.max(1, rand.nextInt(available)); LoanPreparation lpo = createLoanPreparation(quantity, null, null, null, 0, 0, p, overdueLoan); loanPreps.add(lpo); p.getLoanPreparations().add(lpo); loanPrepCnt++; if (loanPrepCnt > 3) { break; } } Calendar loanDate3 = Calendar.getInstance(); loanDate3.set(2006, 3, 21); Calendar currentDueDate3 = Calendar.getInstance(); currentDueDate3.set(2007, 3, 21); Calendar originalDueDate3 = Calendar.getInstance(); originalDueDate3.set(2006, 9, 21); Loan loan3 = createLoan("2006-003", loanDate3, currentDueDate3, originalDueDate3, null, Loan.OPEN, null); Vector<LoanPreparation> newLoanLPOs = new Vector<LoanPreparation>(); int lpoCountInNewLoan = 0; // put some LPOs in this loan that are from CollObjs that have other preps loaned out already // this algorithm (because of the randomness) can result in this loan having 0 LPOs. for( LoanPreparation lpo: loanPreps) { int available = lpo.getPreparation().getLoanAvailable(); if (available > 0) { int quantity = Math.max(1, rand.nextInt(available)); LoanPreparation newLPO = createLoanPreparation(quantity, null, null, null, 0, 0, lpo.getPreparation(), loan3); newLoanLPOs.add(newLPO); lpo.getPreparation().getLoanPreparations().add(newLPO); // stop after we put 6 LPOs in the new loan lpoCountInNewLoan++; if (lpoCountInNewLoan == 6) { break; } } } // create some LoanReturnPreparations int startIndex = returns.size(); for (int i=startIndex;i<loanPreps.size();i++) { LoanPreparation lpo = loanPreps.get(i); int quantityLoaned = lpo.getQuantity(); int quantityReturned = (i == (loanPreps.size() - 1)) ? quantityLoaned : (short)rand.nextInt(quantityLoaned); Calendar returnedDate = Calendar.getInstance(); returnedDate.setTime(lpo.getLoan().getLoanDate().getTime()); // make the returned date be a little while after the original loan returnedDate.add(Calendar.DAY_OF_YEAR, 72); LoanReturnPreparation lrpo = createLoanReturnPreparation(returnedDate, quantityReturned, quantityReturned, lpo, null, agents.get(0)); lpo.addReference(lrpo, "loanReturnPreparations"); lpo.setQuantityReturned(quantityReturned); lpo.setQuantityResolved(quantityReturned); lpo.setIsResolved(quantityLoaned == quantityReturned); returns.add(lrpo); i++; } LoanAgent loanAgent1 = createLoanAgent("loaner", closedLoan, getRandomAgent(agents)); LoanAgent loanAgent2 = createLoanAgent("loaner", overdueLoan, getRandomAgent(agents)); LoanAgent loanAgent3 = createLoanAgent("Borrower", closedLoan, getRandomAgent(agents)); LoanAgent loanAgent4 = createLoanAgent("Borrower", overdueLoan, getRandomAgent(agents)); dataObjects.add(closedLoan); dataObjects.add(overdueLoan); dataObjects.add(loan3); dataObjects.addAll(loanPreps); dataObjects.addAll(newLoanLPOs); dataObjects.addAll(returns); dataObjects.add(loanAgent1); dataObjects.add(loanAgent2); dataObjects.add(loanAgent3); dataObjects.add(loanAgent4); Calendar ship1Date = Calendar.getInstance(); ship1Date.set(2004, 03, 19); Shipment loan1Ship = createShipment(ship1Date, "2006-001", "usps", (short) 1, "1.25 kg", null, agents.get(0), agents.get(4), agents.get(0)); Calendar ship2Date = Calendar.getInstance(); ship2Date.set(2005, 11, 24); Shipment loan2Ship = createShipment(ship2Date, "2006-002", "fedex", (short) 2, "6.0 kg", null, agents.get(3), agents.get(4), agents.get(3)); loan1Ship.setLoan(closedLoan); loan2Ship.setLoan(overdueLoan); //closedLoan.setShipment(loan1Ship); //overdueLoan.setShipment(loan2Ship); closedLoan.getShipments().add(loan1Ship); overdueLoan.getShipments().add(loan2Ship); dataObjects.add(loan1Ship); dataObjects.add(loan2Ship); */ } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public List<Object> createSingleBotanyCollection(final DisciplineType disciplineType, final Institution institution, final SpecifyUser user, final CollectionChoice choice) { frame.setProcess(0, 16); frame.setDesc("Creating Botany..."); createStep = 0; startTx(); Division division = createDivision(institution, disciplineType.getName(), "Botany", "BT", "Botany"); // create tree defs (later we will make the def items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", TreeDefIface.FORWARD); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", TreeDefIface.REVERSE); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", TreeDefIface.REVERSE); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); boolean buildStorageTree = false; if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", TreeDefIface.REVERSE); institution.setStorageTreeDef(stgTreeDef); buildStorageTree = true; } lithoStratTreeDef.setRemarks("A simple super, group, formation, member, bed Litho Stratigraphy tree"); Discipline discipline = createDiscipline(division, disciplineType.getName(), disciplineType.getTitle(), dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); List<SpPrincipal> groups = new ArrayList<SpPrincipal>(); persist(institution); persist(division); persist(discipline); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, DBTableIdMgr.getInstance(), choice.getCatalogNumberingFmtName(), choice.getAccessionNumberingFmtName()); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String title = initPrefs.getProperty("useragent.title", "mr"); String firstName = initPrefs.getProperty("useragent.firstname", "Test"); String lastName = initPrefs.getProperty("useragent.lastname", "User"); String midInit = initPrefs.getProperty("useragent.midinit", "A"); String abbrev = initPrefs.getProperty("useragent.abbrev", "tu"); String email = initPrefs.getProperty("useragent.email", "testuser@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); //String password = initPrefs.getProperty("useragent.password", "rods"); System.out.println("----- User Agent -----"); System.out.println("Title: " + title); System.out.println("FirstName: " + firstName); System.out.println("LastName: " + lastName); System.out.println("MidInit: " + midInit); System.out.println("Abbrev: " + abbrev); System.out.println("Email: " + email); System.out.println("UserType: " + userType); Agent userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email); discipline.addReference(userAgent, "agents"); user.addReference(userAgent, "agents"); persist(userAgent); persist(user); frame.setProcess(++createStep); Pair<AutoNumberingScheme, AutoNumberingScheme> pairANS = createAutoNumberingSchemes(choice); AutoNumberingScheme cns = pairANS.first; AutoNumberingScheme accessionNS = pairANS.second; persist(cns); persist(accessionNS); commitTx(); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); Collection collection = createCollection("KUBOT", "Botany", choice.getCatalogNumberingFmtName(), cns, discipline); persist(collection); // create the standard user groups for this collection Map<String, SpPrincipal> groupMap = DataBuilder.createStandardGroups(session, collection); // add the administrator as a Collections Manager in this group user.addUserToSpPrincipalGroup(groupMap.get(SpecifyUserTypes.UserType.Manager.toString())); // Tester createAndAddTesterToCollection(session, "botanyuser", "botanyuser@ku.edu", "botanyuser", "mr", "Bob", "", "Botony", "", discipline, division, collection, groupMap, "Guest"); persist(discipline); AppContextMgr.getInstance().setClassObject(Collection.class, collection); persist(groups); division.addReference(accessionNS, "numberingSchemes"); persist(division); commitTx(); doShowHideTablesAndFields(null, discipline); doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setProcess(++createStep); startTx(); //DBTableIdMgr schema = new DBTableIdMgr(false); //schema.initialize(new File(XMLHelper.getConfigDirPath("specify_datamodel.xml"))); //loadSchemaLocalization(discipline, SpLocaleContainer, schema); //buildDarwinCoreSchema(discipline); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, user); user.addReference(userAgent, "agents"); persist(user); Journal journal = createJournalsAndReferenceWork(); frame.setProcess(++createStep); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// List<Object> taxa = createSimpleBotanyTaxonTree(taxonTreeDef); List<Object> geos = createSimpleGeography(geoTreeDef, true); List<Object> gtps = createSimpleGeologicTimePeriod(gtpTreeDef, true); List<Object> lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); institution.setStorageTreeDef(stgTreeDef); persist(institution); persist(journal); persist(taxa); persist(geos); persist(buildStorageTree ? createSimpleStorage(stgTreeDef) : null); persist(gtps); persist(lithoStrats); commitTx(); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); frame.setProcess(++createStep); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); frame.setDesc("Creating PickLists..."); //frame.setProcess(++createStep); createPickLists(session, null); createPickLists(session, discipline); Vector<Object> dataObjects = new Vector<Object>(); startTx(); standardQueries(dataObjects, userAgent); persist(dataObjects); dataObjects.clear(); //BldrPickList colMethods = createPickLists(); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // localities //////////////////////////////// String POINT = "Point"; String LINE = "Line"; String RECT = "Rectangle"; log.info("Creating localities"); Locality forestStream = createLocality("Unnamed forest stream pond", (Geography) geos.get(12)); forestStream.setLatLongType(POINT); forestStream.setOriginalLatLongUnit(0); forestStream.setLat1text("38.925467 deg N"); forestStream.setLatitude1(new BigDecimal(38.925467)); forestStream.setLong1text("94.984867 deg W"); forestStream.setLongitude1(new BigDecimal(-94.984867)); Locality lake = createLocality("Deep, dark lake pond", (Geography) geos.get(17)); lake.setLatLongType(RECT); lake.setOriginalLatLongUnit(1); lake.setLat1text("41.548842 deg N"); lake.setLatitude1(new BigDecimal(41.548842)); lake.setLong1text("93.732129 deg W"); lake.setLongitude1(new BigDecimal(-93.732129)); lake.setLat2text("41.642195 deg N"); lake.setLatitude2(new BigDecimal(41.642195)); lake.setLong2text("100.403180 deg W"); lake.setLongitude2(new BigDecimal(-100.403180)); Locality farmpond = createLocality("Shoal Creek at Schermerhorn Park, S of Galena at Rt. 26", (Geography) geos.get(11)); farmpond.setLatLongType(LINE); farmpond.setOriginalLatLongUnit(2); farmpond.setLat1text("41.642187 deg N"); farmpond.setLatitude1(new BigDecimal(41.642187)); farmpond.setLong1text("100.403163 deg W"); farmpond.setLongitude1(new BigDecimal(-100.403163)); farmpond.setLat2text("49.647435 deg N"); farmpond.setLatitude2(new BigDecimal(49.647435)); farmpond.setLong2text("-55.112163 deg W"); farmpond.setLongitude2(new BigDecimal(-55.112163)); persist(forestStream); persist(lake); persist(farmpond); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // agents and addresses //////////////////////////////// log.info("Creating agents and addresses"); List<Agent> agents = new Vector<Agent>(); lastName = userAgent.getLastName(); Agent steveBoyd = createAgent("mr", "Steve", "D", "Boyd", "jb", "jb@net.edu"); if (!lastName.equals("Cooper")) agents.add(createAgent("mr", "Peter", "D", "Cooper", "ds", "ds@whitehouse.gov")); if (!lastName.equals("Peck")) agents.add(createAgent("mr", "David", "H", "Peck", "rb", "beach@net.edu")); if (!lastName.equals("Appleton")) agents.add(createAgent("mrs", "Sally", "H", "Appleton", "jm", "jm@net.edu")); if (!lastName.equals("Brown")) agents.add(createAgent("mr", "Taylor", "C", "Brown", "kcs", "taylor.brown@ku.edu")); if (!lastName.equals("Boyd")) agents.add(steveBoyd); if (!lastName.equals("Thomas")) agents.add(createAgent("Mr", "James", "X", "Thomas", "dxt", "")); if (!lastName.equals("Peterson")) agents.add(createAgent("mr", "Pete", "A", "Peterson", "jb", "")); if (!lastName.equals("Guttenburg")) agents.add(createAgent("mr", "Mitch", "A", "Guttenburg", "jb", "")); if (!lastName.equals("Ford")) agents.add(createAgent("mr", "Daniel", "A", "Ford", "mas", "mas@ku.edu")); agents.add(userAgent); Agent ku = new Agent(); ku.initialize(); ku.setAbbreviation("KU"); ku.setAgentType(Agent.ORG); ku.setLastName("University of Kansas"); ku.setEmail("webadmin@ku.edu"); ku.setTimestampCreated(new Timestamp(System.currentTimeMillis())); ku.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(ku); agents.get(0).setOrganization(ku); agents.get(1).setOrganization(ku); agents.get(2).setOrganization(ku); agents.get(3).setOrganization(ku); agents.get(8).setOrganization(ku); Agent otherAgent = new Agent(); otherAgent.initialize(); otherAgent.setAbbreviation("O"); otherAgent.setAgentType(Agent.OTHER); otherAgent.setLastName("The Other Guys"); otherAgent.setEmail("other@other.com"); otherAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); otherAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(otherAgent); commitTx(); List<GroupPerson> gpList = new ArrayList<GroupPerson>(); if (true) { startTx(); Agent gm1 = createAgent("mr", "John", "A", "Lyon", "jal", "jal@group.edu"); Agent gm2 = createAgent("mr", "Dave", "D", "Jones", "ddj", "ddj@group.edu"); persist(gm1); persist(gm2); commitTx(); Agent groupAgent = new Agent(); groupAgent.initialize(); groupAgent.setAbbreviation("GRP"); groupAgent.setAgentType(Agent.GROUP); groupAgent.setLastName("The Group"); groupAgent.setEmail("group@group.com"); groupAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); groupAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(groupAgent); gpList.add(createGroupPerson(groupAgent, gm1, 0, division)); gpList.add(createGroupPerson(groupAgent, gm2, 1, division)); } startTx(); List<AgentVariant> agentVariants = new Vector<AgentVariant>(); agentVariants.add(createAgentVariant(AgentVariant.VARIANT, "James Variant #1", steveBoyd)); agentVariants.add(createAgentVariant(AgentVariant.VERNACULAR, "James VERNACULAR #1", steveBoyd)); List<Address> addrs = new Vector<Address>(); addrs.add(createAddress(agents.get(1), "1600 Pennsylvania Avenue NW", null, "Washington", "DC", "USA", "20500", 0)); addrs.add(createAddress(agents.get(1), "??? Mississippi", null, "Lawrence", "KS", "USA", "66045", 1)); addrs.add(createAddress(agents.get(2), "1 Main St", "", "Lenexa", "KS", "USA", "66071")); addrs.add(createAddress(agents.get(3), "13355 Inverness", "Bldg #3", "Lawrence", "KS", "USA", "66047")); addrs.add(createAddress(agents.get(4), "Natural History Museum", "Cromwell Rd", "London", null, "UK", "SW7 5BD")); addrs.add(createAddress(agents.get(6), "1212 Apple Street", null, "Chicago", "IL", "USA", "01010")); addrs.add(createAddress(agents.get(8), "11911 Oak Ln", null, "Orion", "KS", "USA", "66061")); addrs.add(createAddress(ku, null, null, "Lawrence", "KS", "USA", "66045")); // User Agent Address addrs.add(createAddress(userAgent, "1214 East Street", null, "Grinnell", "IA", "USA", "56060")); userAgent.setDivision(division); persist(agents); persist(agentVariants); persist(gpList); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // collecting events (collectors, collecting trip) //////////////////////////////// log.info("Creating collecting events, collectors and a collecting trip"); Collector collectorMitch = createCollector(agents.get(7), 2); Collector collectorJim = createCollector(agents.get(2), 1); calendar.set(1994, 4, 21, 11, 56, 00); String stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); CollectingEvent ce1 = createCollectingEvent(forestStream, calendar, stationFieldNumber, new Collector[] { collectorMitch, collectorJim }); ce1.setStartDateVerbatim("21 Apr 1994, 11:56 AM"); calendar.set(1994, 4, 21, 13, 03, 00); ce1.setEndDate(calendar); ce1.setEndDateVerbatim("21 Apr 1994, 1:03 PM"); ce1.setMethod("Picked"); AttributeDef cevAttrDef = createAttributeDef(AttributeIFace.FieldType.StringType, "ParkName", discipline, null);//meg added cod persist(cevAttrDef); commitTx(); startTx(); CollectingEventAttr cevAttr = createCollectingEventAttr(ce1, cevAttrDef, "Sleepy Hollow", null); Collector collectorMeg = createCollector(agents.get(2), 1); Collector collectorRod = createCollector(agents.get(3), 2); stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); calendar.set(1994, 4, 22, 06, 12, 00); CollectingEvent ce2 = createCollectingEvent(farmpond, calendar, stationFieldNumber, new Collector[] { collectorMeg, collectorRod }); ce2.setStartDateVerbatim("22 Apr 1994, 6:12 AM"); calendar.set(1994, 4, 22, 07, 31, 00); ce2.setEndDate(calendar); ce2.setEndDateVerbatim("22 Apr 1994, 7:31 AM"); ce2.setMethod("Picked"); //CollectingTrip trip = createCollectingTrip("Sample collecting trip", new CollectingEvent[]{ce1,ce2}); //dataObjects.add(trip); dataObjects.add(ce1); dataObjects.add(cevAttr); dataObjects.add(ce2); dataObjects.add(collectorMitch); dataObjects.add(collectorJim); dataObjects.add(collectorMeg); dataObjects.add(collectorRod); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); //////////////////////////////// // permit //////////////////////////////// log.info("Creating a permit"); Calendar issuedDate = Calendar.getInstance(); issuedDate.set(1993, 1, 12); Calendar startDate = Calendar.getInstance(); startDate.set(1993, 2, 1); Calendar endDate = Calendar.getInstance(); endDate.set(1993, 5, 30); Permit permit = createPermit("1991-PLAN-0001", "US Dept Wildlife", issuedDate, startDate, endDate, null); permit.setIssuedTo(ku); permit.setIssuedBy(agents.get(4)); dataObjects.add(permit); log.info("Creating a repository agreement"); RepositoryAgreement repoAg = new RepositoryAgreement(); repoAg.initialize(); repoAg.setDivision(division); repoAg.setRepositoryAgreementNumber("KU-1990-01"); repoAg.setOriginator(ku); Calendar received = Calendar.getInstance(); received.set(1992, 2, 10); repoAg.setDateReceived(received); Calendar repoEndDate = Calendar.getInstance(); received.set(2010, 2, 9); repoAg.setEndDate(repoEndDate); dataObjects.add(repoAg); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // collection objects //////////////////////////////// log.info("Creating collection objects"); List<CollectionObject> collObjs = new Vector<CollectionObject>(); Collection col = collection; Calendar[] catDates = new Calendar[8]; for (int i = 0; i < catDates.length; i++) { catDates[i] = Calendar.getInstance(); int year = 1980 + (int) (rand.nextDouble() * 20.0); catDates[i].set(year, 01, 12 + i); } String prefix = "000000"; int catNo = 100; CollectingEvent[] colEves = new CollectingEvent[8]; for (int i = 0; i < colEves.length; i++) { colEves[i] = createFakeCollectingEvent(agents, farmpond, "cut"); collObjs.add(createCollectionObject(prefix + Integer.toString(catNo), "RSC" + Integer.toString(catNo), agents.get(i), col, 1, colEves[i], catDates[i], "BuildSampleDatabase")); catNo++; } dataObjects.addAll(collObjs); for (CollectingEvent ce : colEves) { persist(ce); } persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // determinations (determination status) //////////////////////////////// log.info("Creating determinations"); List<Determination> determs = new Vector<Determination>(); Calendar recent = Calendar.getInstance(); recent.set(2005, 10, 27, 13, 44, 00); Calendar longAgo = Calendar.getInstance(); longAgo.set(1976, 01, 29, 8, 12, 00); Calendar whileBack = Calendar.getInstance(); whileBack.set(2000, 7, 4, 9, 33, 12); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(5), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(6), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(7), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.get(13).setRemarks("This determination is totally wrong. What a foolish determination."); persist(determs); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // preparations (prep types) //////////////////////////////// log.info("Creating preparations"); Vector<PrepType> prepTypesForSaving = loadPrepTypes(discipline.getType()); PrepType pressed = prepTypesForSaving.get(0); List<Preparation> preps = new Vector<Preparation>(); Calendar prepDate = Calendar.getInstance(); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(4), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(5), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(6), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(7), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(10), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(3), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(5), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(6), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(7), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); dataObjects.addAll(prepTypesForSaving); dataObjects.addAll(preps); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // accessions (accession agents) //////////////////////////////// log.info("Creating accessions and accession agents"); calendar.set(2006, 10, 27, 23, 59, 59); Accession acc1 = createAccession(division, "gift", "complete", "2000-PL-001", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); acc1.setText1("Ichthyology"); acc1.setRepositoryAgreement(repoAg); Agent donor = agents.get(4); Agent receiver = agents.get(1); Agent reviewer = agents.get(2); List<AccessionAgent> accAgents = new Vector<AccessionAgent>(); accAgents.add(createAccessionAgent("donor", donor, acc1, null)); accAgents.add(createAccessionAgent("receiver", receiver, acc1, null)); accAgents.add(createAccessionAgent("reviewer", reviewer, acc1, null)); Accession acc2 = createAccession(division, "field_work", "inprocess", "2004-PL-002", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); Agent donor2 = agents.get(5); Agent receiver2 = agents.get(3); Agent reviewer2 = agents.get(1); accAgents.add(createAccessionAgent("donor", donor2, acc2, null)); accAgents.add(createAccessionAgent("receiver", receiver2, acc2, null)); accAgents.add(createAccessionAgent("reviewer", reviewer2, acc2, null)); dataObjects.add(acc1); dataObjects.add(acc2); dataObjects.addAll(accAgents); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); createLoanExamples(preps, agents, dataObjects); frame.setProcess(++createStep); persist(dataObjects); dataObjects.clear(); persist(dataObjects); dataObjects.clear(); frame.setProcess(++createStep); commitTx(); frame.setProcess(++createStep); buildDarwinCoreSchema(discipline); // done log.info("Done creating Botany disciplineType database: " + disciplineType.getTitle()); return dataObjects; } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public List<Object> createHugeBotanyCollection(final DisciplineType disciplineType, final Institution institution, final SpecifyUser user, final CollectionChoice choice) { frame.setProcess(0, 16); frame.setDesc("Creating Botany..."); createStep = 0; startTx(); Division division = createDivision(institution, disciplineType.getName(), "Botany", "BT", "Botany"); // create tree defs (later we will make the def items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", TreeDefIface.FORWARD); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", TreeDefIface.REVERSE); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", TreeDefIface.REVERSE); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); boolean buildStorageTree = false; if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", TreeDefIface.REVERSE); institution.setStorageTreeDef(stgTreeDef); buildStorageTree = true; } lithoStratTreeDef.setRemarks("A simple super, group, formation, member, bed Litho Stratigraphy tree"); Discipline discipline = createDiscipline(division, disciplineType.getName(), disciplineType.getTitle(), dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); persist(institution); persist(division); persist(discipline); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, DBTableIdMgr.getInstance(), choice.getCatalogNumberingFmtName(), choice.getAccessionNumberingFmtName()); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String title = initPrefs.getProperty("useragent.title", "mr"); String firstName = initPrefs.getProperty("useragent.firstname", "Test"); String lastName = initPrefs.getProperty("useragent.lastname", "User"); String midInit = initPrefs.getProperty("useragent.midinit", "A"); String abbrev = initPrefs.getProperty("useragent.abbrev", "tu"); String email = initPrefs.getProperty("useragent.email", "testuser@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); System.out.println("----- User Agent -----"); System.out.println("Title: " + title); System.out.println("FirstName: " + firstName); System.out.println("LastName: " + lastName); System.out.println("MidInit: " + midInit); System.out.println("Abbrev: " + abbrev); System.out.println("Email: " + email); System.out.println("UserType: " + userType); Agent userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email); discipline.addReference(userAgent, "agents"); user.addReference(userAgent, "agents"); persist(discipline); persist(userAgent); persist(user); frame.setProcess(++createStep); Pair<AutoNumberingScheme, AutoNumberingScheme> pairANS = createAutoNumberingSchemes(choice); AutoNumberingScheme cns = pairANS.first; AutoNumberingScheme accessionNS = pairANS.second; persist(cns); persist(accessionNS); commitTx(); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); Collection collection = createCollection("KUBOT", "Botany", choice.getCatalogNumberingFmtName(), cns, discipline); persist(collection); AppContextMgr.getInstance().setClassObject(Collection.class, collection); division.addReference(accessionNS, "numberingSchemes"); persist(division); commitTx(); doShowHideTablesAndFields(null, discipline); doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setProcess(++createStep); startTx(); //DBTableIdMgr schema = new DBTableIdMgr(false); //schema.initialize(new File(XMLHelper.getConfigDirPath("specify_datamodel.xml"))); //loadSchemaLocalization(discipline, SpLocaleContainer, schema); //buildDarwinCoreSchema(discipline); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, user); user.addReference(userAgent, "agents"); persist(user); Journal journal = createJournalsAndReferenceWork(); frame.setProcess(++createStep); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// List<Object> taxa = createSimpleBotanyTaxonTree(taxonTreeDef); List<Object> geos = createSimpleGeography(geoTreeDef, true); List<Object> gtps = createSimpleGeologicTimePeriod(gtpTreeDef, true); List<Object> lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); persist(journal); persist(taxa); persist(geos); persist(buildStorageTree ? createSimpleStorage(stgTreeDef) : null); persist(gtps); persist(lithoStrats); commitTx(); frame.setProcess(++createStep); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); frame.setDesc("Creating PickLists..."); //frame.setProcess(++createStep); createPickLists(session, null); createPickLists(session, discipline); Vector<Object> dataObjects = new Vector<Object>(); startTx(); standardQueries(dataObjects, userAgent); persist(dataObjects); dataObjects.clear(); //BldrPickList colMethods = createPickLists(); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // localities //////////////////////////////// String POINT = "Point"; frame.setDesc("Creating localities"); log.info("Creating localities"); frame.setProcess(0, NUM_LOCALTIES); Vector<Locality> localities = new Vector<Locality>(); Vector<Object> evictList = new Vector<Object>(); for (int i = 0; i < NUM_LOCALTIES; i++) { Locality locality = createLocality("Unnamed forest stream pond", (Geography) geos.get(12)); locality.setLatLongType(POINT); locality.setOriginalLatLongUnit(0); locality.setLat1text("38.925467 deg N"); locality.setLatitude1(new BigDecimal(38.925467)); locality.setLong1text("94.984867 deg W"); locality.setLongitude1(new BigDecimal(-94.984867)); persist(locality); evictList.add(locality); localities.add(locality); if ((i + 1) % 10 == 0) { commitTx(); for (Object obj : evictList) { session.evict(obj); } evictList.clear(); startTx(); frame.setProcess(i); } } commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // agents and addresses //////////////////////////////// log.info("Creating agents and addresses"); List<Agent> agents = new Vector<Agent>(); lastName = userAgent.getLastName(); Agent steveBoyd = createAgent("mr", "Steve", "D", "Boyd", "jb", "jb@net.edu"); if (!lastName.equals("Cooper")) agents.add(createAgent("mr", "Peter", "D", "Cooper", "ds", "ds@whitehouse.gov")); if (!lastName.equals("Peck")) agents.add(createAgent("mr", "David", "H", "Peck", "rb", "beach@net.edu")); if (!lastName.equals("Appleton")) agents.add(createAgent("mrs", "Sally", "H", "Appleton", "jm", "jm@net.edu")); if (!lastName.equals("Brown")) agents.add(createAgent("mr", "Taylor", "C", "Brown", "kcs", "taylor.brown@ku.edu")); if (!lastName.equals("Boyd")) agents.add(steveBoyd); if (!lastName.equals("Thomas")) agents.add(createAgent("Mr", "James", "X", "Thomas", "dxt", "")); if (!lastName.equals("Peterson")) agents.add(createAgent("mr", "Pete", "A", "Peterson", "jb", "")); if (!lastName.equals("Guttenburg")) agents.add(createAgent("mr", "Mitch", "A", "Guttenburg", "jb", "")); if (!lastName.equals("Ford")) agents.add(createAgent("mr", "Daniel", "A", "Ford", "mas", "mas@ku.edu")); agents.add(userAgent); Agent ku = new Agent(); ku.initialize(); ku.setAbbreviation("KU"); ku.setAgentType(Agent.ORG); ku.setLastName("University of Kansas"); ku.setEmail("webadmin@ku.edu"); ku.setTimestampCreated(new Timestamp(System.currentTimeMillis())); ku.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(ku); agents.get(0).setOrganization(ku); agents.get(1).setOrganization(ku); agents.get(2).setOrganization(ku); agents.get(3).setOrganization(ku); agents.get(8).setOrganization(ku); Agent otherAgent = new Agent(); otherAgent.initialize(); otherAgent.setAbbreviation("O"); otherAgent.setAgentType(Agent.OTHER); otherAgent.setLastName("The Other Guys"); otherAgent.setEmail("other@other.com"); otherAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); otherAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(otherAgent); commitTx(); List<GroupPerson> gpList = new ArrayList<GroupPerson>(); if (true) { startTx(); Agent gm1 = createAgent("mr", "John", "A", "Lyon", "jal", "jal@group.edu"); Agent gm2 = createAgent("mr", "Dave", "D", "Jones", "ddj", "ddj@group.edu"); persist(gm1); persist(gm2); commitTx(); Agent groupAgent = new Agent(); groupAgent.initialize(); groupAgent.setAbbreviation("GRP"); groupAgent.setAgentType(Agent.GROUP); groupAgent.setLastName("The Group"); groupAgent.setEmail("group@group.com"); groupAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); groupAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(groupAgent); gpList.add(createGroupPerson(groupAgent, gm1, 0, division)); gpList.add(createGroupPerson(groupAgent, gm2, 1, division)); } startTx(); List<AgentVariant> agentVariants = new Vector<AgentVariant>(); agentVariants.add(createAgentVariant(AgentVariant.VARIANT, "James Variant #1", steveBoyd)); agentVariants.add(createAgentVariant(AgentVariant.VERNACULAR, "James VERNACULAR #1", steveBoyd)); List<Address> addrs = new Vector<Address>(); addrs.add(createAddress(agents.get(1), "1600 Pennsylvania Avenue NW", null, "Washington", "DC", "USA", "20500", 0)); addrs.add(createAddress(agents.get(1), "??? Mississippi", null, "Lawrence", "KS", "USA", "66045", 1)); addrs.add(createAddress(agents.get(2), "1 Main St", "", "Lenexa", "KS", "USA", "66071")); addrs.add(createAddress(agents.get(3), "13355 Inverness", "Bldg #3", "Lawrence", "KS", "USA", "66047")); addrs.add(createAddress(agents.get(4), "Natural History Museum", "Cromwell Rd", "London", null, "UK", "SW7 5BD")); addrs.add(createAddress(agents.get(6), "1212 Apple Street", null, "Chicago", "IL", "USA", "01010")); addrs.add(createAddress(agents.get(8), "11911 Oak Ln", null, "Orion", "KS", "USA", "66061")); addrs.add(createAddress(ku, null, null, "Lawrence", "KS", "USA", "66045")); // User Agent Address addrs.add(createAddress(userAgent, "1214 East Street", null, "Grinnell", "IA", "USA", "56060")); userAgent.setDivision(division); persist(agents); persist(agentVariants); persist(gpList); commitTx(); startTx(); //////////////////////////////// // Determination Status (Must be done here) //////////////////////////////// // log.info("Creating determinations status"); // current = createDeterminationStatus(discipline, "Current", "", DeterminationStatus.CURRENT); // currentAccepted = createDeterminationStatus(discipline, "Current Accepted", "", DeterminationStatus.CURRENTTOACCEPTED); // notCurrent = createDeterminationStatus(discipline, "Not current","", DeterminationStatus.NOTCURRENT); // incorrect = createDeterminationStatus(discipline, "Incorrect", "", DeterminationStatus.USERDEFINED); // oldDet = createDeterminationStatus(discipline, "Old Determination","", DeterminationStatus.OLDDETERMINATION); // persist(current); // persist(currentAccepted); // persist(notCurrent); // persist(incorrect); // persist(oldDet); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); //////////////////////////////// // collection objects //////////////////////////////// log.info("Creating collection objects"); Calendar[] catDates = new Calendar[300]; for (int i = 0; i < catDates.length; i++) { catDates[i] = Calendar.getInstance(); int year = 1980 + (int) (rand.nextDouble() * 20.0); catDates[i].set(year, 01, 12 + i); } Vector<PrepType> prepTypesForSaving = loadPrepTypes(discipline.getType()); dataObjects.addAll(prepTypesForSaving); persist(dataObjects); dataObjects.clear(); frame.setProcess(++createStep); commitTx(); PrepType pressed = prepTypesForSaving.get(0); startTx(); frame.setProcess(0, NUM_COLOBJS); evictList.clear(); frame.setDesc("Creating Collection Objects"); int catNo = 100; for (int i = 0; i < NUM_COLOBJS; i++) { int years20 = (int) (rand.nextDouble() * 20.0); int years10 = (int) (rand.nextDouble() * 10.0); int years50 = (int) (rand.nextDouble() * 50.0); Calendar recent = Calendar.getInstance(); recent.set(1950 + years20 + years10, 10, 27, 13, 44, 00); Calendar longAgo = Calendar.getInstance(); longAgo.set(1900 + years50, 01, 29, 8, 12, 00); Calendar whileBack = Calendar.getInstance(); whileBack.set(1960 + years20, 7, 4, 9, 33, 12); String catNumStr = String.format("%09d", catNo); int inx = (int) (rand.nextDouble() * localities.size()); int agentInx = (int) (rand.nextDouble() * agents.size()); int agentInx2 = (int) (rand.nextDouble() * agents.size()); int calInx = (int) (rand.nextDouble() * catDates.length); CollectingEvent ce = createFakeCollectingEvent(agents, localities.get(inx), "cut"); CollectionObject co = createCollectionObject(catNumStr, "RSC" + Integer.toString(catNo), agents.get(agentInx), collection, 1, ce, catDates[calInx], "BuildSampleDatabase"); Determination dt = createDetermination(co, getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent); Calendar prepDate = Calendar.getInstance(); Preparation prep = createPreparation(pressed, agents.get(agentInx2), co, (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate); persist(ce); persist(co); persist(dt); persist(prep); evictList.add(ce); evictList.add(co); evictList.add(dt); evictList.add(prep); if ((i + 1) % 10 == 0) { commitTx(); for (Object obj : evictList) { session.evict(obj); } evictList.clear(); startTx(); frame.setProcess(i); } catNo++; } commitTx(); frame.setProcess(++createStep); buildDarwinCoreSchema(discipline); // done log.info("Done creating Botany disciplineType database: " + disciplineType.getTitle()); return dataObjects; } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public List<Object> createSingleInvertPaleoCollection(final DisciplineType disciplineType, final Institution institution, final SpecifyUser user, final CollectionChoice choice) { frame.setProcess(0, 16); frame.setDesc("Creating " + disciplineType.getTitle() + "..."); createStep = 0; startTx(); Division division = createDivision(institution, disciplineType.getName(), disciplineType.getTitle(), "INVP", disciplineType.getTitle()); // create tree defs (later we will make the def items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", TreeDefIface.FORWARD); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", TreeDefIface.REVERSE); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", TreeDefIface.REVERSE); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); boolean buildStorageTree = false; if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", TreeDefIface.REVERSE); institution.setStorageTreeDef(stgTreeDef); buildStorageTree = true; } lithoStratTreeDef.setRemarks("A simple super, group, formation, member, bed Litho Stratigraphy tree"); Discipline discipline = createDiscipline(division, disciplineType.getName(), disciplineType.getTitle(), dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); persist(institution); persist(division); persist(discipline); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, DBTableIdMgr.getInstance(), choice.getCatalogNumberingFmtName(), choice.getAccessionNumberingFmtName()); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String title = initPrefs.getProperty("useragent.title", "mr"); String firstName = initPrefs.getProperty("useragent.firstname", "Test"); String lastName = initPrefs.getProperty("useragent.lastname", "User"); String midInit = initPrefs.getProperty("useragent.midinit", "A"); String abbrev = initPrefs.getProperty("useragent.abbrev", "tu"); String email = initPrefs.getProperty("useragent.email", "testuser@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); System.out.println("----- User Agent -----"); System.out.println("Title: " + title); System.out.println("FirstName: " + firstName); System.out.println("LastName: " + lastName); System.out.println("MidInit: " + midInit); System.out.println("Abbrev: " + abbrev); System.out.println("Email: " + email); System.out.println("UserType: " + userType); Agent userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email); discipline.addReference(userAgent, "agents"); user.addReference(userAgent, "agents"); persist(discipline); persist(userAgent); persist(user); // LithoStratTreeDefItem earth = createLithoStratTreeDefItem(lithoStratTreeDef, "Earth", 0, false); // LithoStratTreeDefItem superGrp = createLithoStratTreeDefItem(earth, "Super Group", 100, false); // LithoStratTreeDefItem lithoGrp = createLithoStratTreeDefItem(superGrp, "Litho Group", 200, false); // LithoStratTreeDefItem formation = createLithoStratTreeDefItem(lithoGrp, "Formation", 300, false); // LithoStratTreeDefItem member = createLithoStratTreeDefItem(formation, "Member", 400, false); // @SuppressWarnings("unused") // LithoStratTreeDefItem bed = createLithoStratTreeDefItem(member, "Bed", 500, true); frame.setProcess(++createStep); Pair<AutoNumberingScheme, AutoNumberingScheme> pairANS = createAutoNumberingSchemes(choice); AutoNumberingScheme cns = pairANS.first; AutoNumberingScheme accessionNS = pairANS.second; persist(cns); persist(accessionNS); //persist(earth); commitTx(); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); Collection collection = createCollection("KUIVP", disciplineType.getTitle(), choice.getCatalogNumberingFmtName(), cns, discipline); persist(collection); // create the standard user groups for this collection Map<String, SpPrincipal> groupMap = DataBuilder.createStandardGroups(session, collection); // add the administrator as a Collections Manager in this group user.addUserToSpPrincipalGroup(groupMap.get(SpecifyUserTypes.UserType.Manager.toString())); // Tester createAndAddTesterToCollection(session, "ivpuser", "InvertPaleo@ku.edu", "ivpuser", "mr", "Joe", "", "InvertPaleo", "", discipline, division, collection, groupMap, "Guest"); AppContextMgr.getInstance().setClassObject(Collection.class, collection); division.addReference(accessionNS, "numberingSchemes"); persist(division); commitTx(); doShowHideTablesAndFields(null, discipline); doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setProcess(++createStep); startTx(); //DBTableIdMgr schema = new DBTableIdMgr(false); //schema.initialize(new File(XMLHelper.getConfigDirPath("specify_datamodel.xml"))); //loadSchemaLocalization(discipline, SpLocaleContainer, schema); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, user); user.addReference(userAgent, "agents"); persist(user); Journal journal = createJournalsAndReferenceWork(); frame.setProcess(++createStep); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// List<Object> taxa = createSimpleBotanyTaxonTree(taxonTreeDef); List<Object> geos = createSimpleGeography(geoTreeDef, true); List<Object> gtps = createSimpleGeologicTimePeriod(gtpTreeDef, true); //List<Object> lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); persist(journal); persist(taxa); persist(geos); persist(buildStorageTree ? createSimpleStorage(stgTreeDef) : null); persist(gtps); //persist(lithoStrats); commitTx(); LithoStrat earthLithoStrat = convertLithoStratFromCSV(lithoStratTreeDef); if (earthLithoStrat == null) { //throw new RuntimeException("No Tree"); startTx(); List<Object> lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); persist(lithoStrats); commitTx(); } frame.setProcess(++createStep); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); frame.setDesc("Creating Common PickLists..."); //frame.setProcess(++createStep); createPickLists(session, null); frame.setDesc("Creating PickLists..."); createPickLists(session, discipline); Vector<Object> dataObjects = new Vector<Object>(); startTx(); frame.setDesc("Creating Queries..."); standardQueries(dataObjects, userAgent); persist(dataObjects); dataObjects.clear(); //BldrPickList colMethods = createPickLists(); persist(dataObjects); dataObjects.clear(); frame.setDesc("Intermediate save...."); commitTx(); frame.setDesc("Creating Localities...."); startTx(); frame.setProcess(++createStep); //////////////////////////////// // localities //////////////////////////////// String POINT = "Point"; String LINE = "Line"; String RECT = "Rectangle"; log.info("Creating localities"); Locality forestStream = createLocality("Gravel Pit", (Geography) geos.get(12)); forestStream.setLatLongType(POINT); forestStream.setOriginalLatLongUnit(0); forestStream.setLat1text("38.925467 deg N"); forestStream.setLatitude1(new BigDecimal(38.925467)); forestStream.setLong1text("94.984867 deg W"); forestStream.setLongitude1(new BigDecimal(-94.984867)); Locality lake = createLocality("Deep, dark lake pond", (Geography) geos.get(17)); lake.setLatLongType(RECT); lake.setOriginalLatLongUnit(1); lake.setLat1text("41.548842 deg N"); lake.setLatitude1(new BigDecimal(41.548842)); lake.setLong1text("93.732129 deg W"); lake.setLongitude1(new BigDecimal(-93.732129)); lake.setLat2text("41.642195 deg N"); lake.setLatitude2(new BigDecimal(41.642195)); lake.setLong2text("100.403180 deg W"); lake.setLongitude2(new BigDecimal(-100.403180)); Locality farmpond = createLocality("Shoal Creek at Schermerhorn Park, S of Galena at Rt. 26", (Geography) geos.get(11)); farmpond.setLatLongType(LINE); farmpond.setOriginalLatLongUnit(2); farmpond.setLat1text("41.642187 deg N"); farmpond.setLatitude1(new BigDecimal(41.642187)); farmpond.setLong1text("100.403163 deg W"); farmpond.setLongitude1(new BigDecimal(-100.403163)); farmpond.setLat2text("49.647435 deg N"); farmpond.setLatitude2(new BigDecimal(49.647435)); farmpond.setLong2text("-55.112163 deg W"); farmpond.setLongitude2(new BigDecimal(-55.112163)); persist(forestStream); persist(lake); persist(farmpond); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // agents and addresses //////////////////////////////// log.info("Creating agents and addresses"); List<Agent> agents = new Vector<Agent>(); lastName = userAgent.getLastName(); Agent steveBoyd = createAgent("mr", "Steve", "D", "Boyd", "jb", "jb@net.edu"); if (!lastName.equals("Cooper")) agents.add(createAgent("mr", "Peter", "D", "Cooper", "ds", "ds@whitehouse.gov")); if (!lastName.equals("Peck")) agents.add(createAgent("mr", "David", "H", "Peck", "rb", "beach@net.edu")); if (!lastName.equals("Appleton")) agents.add(createAgent("mrs", "Sally", "H", "Appleton", "jm", "jm@net.edu")); if (!lastName.equals("Brown")) agents.add(createAgent("mr", "Taylor", "C", "Brown", "kcs", "taylor.brown@ku.edu")); if (!lastName.equals("Boyd")) agents.add(steveBoyd); if (!lastName.equals("Thomas")) agents.add(createAgent("Mr", "James", "X", "Thomas", "dxt", "")); if (!lastName.equals("Peterson")) agents.add(createAgent("mr", "Pete", "A", "Peterson", "jb", "")); if (!lastName.equals("Guttenburg")) agents.add(createAgent("mr", "Mitch", "A", "Guttenburg", "jb", "")); if (!lastName.equals("Ford")) agents.add(createAgent("mr", "Daniel", "A", "Ford", "mas", "mas@ku.edu")); agents.add(userAgent); Agent ku = new Agent(); ku.initialize(); ku.setAbbreviation("KU"); ku.setAgentType(Agent.ORG); ku.setLastName("University of Kansas"); ku.setEmail("webadmin@ku.edu"); ku.setTimestampCreated(new Timestamp(System.currentTimeMillis())); ku.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(ku); agents.get(0).setOrganization(ku); agents.get(1).setOrganization(ku); agents.get(2).setOrganization(ku); agents.get(3).setOrganization(ku); agents.get(8).setOrganization(ku); Agent otherAgent = new Agent(); otherAgent.initialize(); otherAgent.setAbbreviation("O"); otherAgent.setAgentType(Agent.OTHER); otherAgent.setLastName("The Other Guys"); otherAgent.setEmail("other@other.com"); otherAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); otherAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(otherAgent); commitTx(); List<GroupPerson> gpList = new ArrayList<GroupPerson>(); if (true) { startTx(); Agent gm1 = createAgent("mr", "John", "A", "Lyon", "jal", "jal@group.edu"); Agent gm2 = createAgent("mr", "Dave", "D", "Jones", "ddj", "ddj@group.edu"); persist(gm1); persist(gm2); commitTx(); Agent groupAgent = new Agent(); groupAgent.initialize(); groupAgent.setAbbreviation("GRP"); groupAgent.setAgentType(Agent.GROUP); groupAgent.setLastName("The Group"); groupAgent.setEmail("group@group.com"); groupAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); groupAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(groupAgent); gpList.add(createGroupPerson(groupAgent, gm1, 0, division)); gpList.add(createGroupPerson(groupAgent, gm2, 1, division)); } startTx(); List<Address> addrs = new Vector<Address>(); addrs.add(createAddress(agents.get(1), "1600 Pennsylvania Avenue NW", null, "Washington", "DC", "USA", "20500", 0)); addrs.add(createAddress(agents.get(1), "??? Mississippi", null, "Lawrence", "KS", "USA", "66045", 1)); addrs.add(createAddress(agents.get(2), "1 Main St", "", "Lenexa", "KS", "USA", "66071")); addrs.add(createAddress(agents.get(3), "13355 Inverness", "Bldg #3", "Lawrence", "KS", "USA", "66047")); addrs.add(createAddress(agents.get(4), "Natural History Museum", "Cromwell Rd", "London", null, "UK", "SW7 5BD")); addrs.add(createAddress(agents.get(6), "1212 Apple Street", null, "Chicago", "IL", "USA", "01010")); addrs.add(createAddress(agents.get(8), "11911 Oak Ln", null, "Orion", "KS", "USA", "66061")); addrs.add(createAddress(ku, null, null, "Lawrence", "KS", "USA", "66045")); // User Agent Address addrs.add(createAddress(userAgent, "1214 East Street", null, "Grinnell", "IA", "USA", "56060")); userAgent.setDivision(division); persist(agents); persist(gpList); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // collecting events (collectors, collecting trip) //////////////////////////////// log.info("Creating collecting events, collectors and a collecting trip"); Collector collectorMitch = createCollector(agents.get(7), 2); Collector collectorJim = createCollector(agents.get(2), 1); String stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); calendar.set(1994, 4, 21, 11, 56, 00); CollectingEvent ce1 = createCollectingEvent(forestStream, calendar, stationFieldNumber, new Collector[] { collectorMitch, collectorJim }); ce1.setStartDateVerbatim("21 Apr 1994, 11:56 AM"); calendar.set(1994, 4, 21, 13, 03, 00); ce1.setEndDate(calendar); ce1.setEndDateVerbatim("21 Apr 1994, 1:03 PM"); ce1.setMethod("Picked"); AttributeDef cevAttrDef = createAttributeDef(AttributeIFace.FieldType.StringType, "ParkName", discipline, null);//meg added cod persist(cevAttrDef); commitTx(); startTx(); CollectingEventAttr cevAttr = createCollectingEventAttr(ce1, cevAttrDef, "Sleepy Hollow", null); Collector collectorMeg = createCollector(agents.get(2), 1); Collector collectorRod = createCollector(agents.get(3), 2); stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); calendar.set(1994, 4, 22, 06, 12, 00); CollectingEvent ce2 = createCollectingEvent(farmpond, calendar, stationFieldNumber, new Collector[] { collectorMeg, collectorRod }); ce2.setStartDateVerbatim("22 Apr 1994, 6:12 AM"); calendar.set(1994, 4, 22, 07, 31, 00); ce2.setEndDate(calendar); ce2.setEndDateVerbatim("22 Apr 1994, 7:31 AM"); ce2.setMethod("Picked"); //CollectingTrip trip = createCollectingTrip("Sample collecting trip", new CollectingEvent[]{ce1,ce2}); //dataObjects.add(trip); dataObjects.add(ce1); dataObjects.add(cevAttr); dataObjects.add(ce2); dataObjects.add(collectorMitch); dataObjects.add(collectorJim); dataObjects.add(collectorMeg); dataObjects.add(collectorRod); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); //////////////////////////////// // permit //////////////////////////////// log.info("Creating a permit"); Calendar issuedDate = Calendar.getInstance(); issuedDate.set(1993, 1, 12); Calendar startDate = Calendar.getInstance(); startDate.set(1993, 2, 1); Calendar endDate = Calendar.getInstance(); endDate.set(1993, 5, 30); Permit permit = createPermit("1980-INVRTP-0001", "US Dept Wildlife", issuedDate, startDate, endDate, null); permit.setIssuedTo(ku); permit.setIssuedBy(agents.get(4)); dataObjects.add(permit); log.info("Creating a repository agreement"); RepositoryAgreement repoAg = new RepositoryAgreement(); repoAg.initialize(); repoAg.setDivision(division); repoAg.setRepositoryAgreementNumber("KU-1979-01"); repoAg.setOriginator(ku); Calendar received = Calendar.getInstance(); received.set(1992, 2, 10); repoAg.setDateReceived(received); Calendar repoEndDate = Calendar.getInstance(); received.set(2010, 2, 9); repoAg.setEndDate(repoEndDate); dataObjects.add(repoAg); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); log.info("Creating collection objects"); List<CollectionObject> collObjs = new Vector<CollectionObject>(); Collection col = collection; Calendar[] catDates = new Calendar[8]; for (int i = 0; i < catDates.length; i++) { catDates[i] = Calendar.getInstance(); int year = 1980 + (int) (rand.nextDouble() * 20.0); catDates[i].set(year, 01, 12 + i); } String prefix = "000000"; int catNo = 100; CollectingEvent[] colEves = new CollectingEvent[8]; for (int i = 0; i < colEves.length; i++) { colEves[i] = createFakeCollectingEvent(agents, farmpond, "Dug"); collObjs.add(createCollectionObject(prefix + Integer.toString(catNo), "RSC" + Integer.toString(catNo), agents.get(i), col, 1, colEves[i], catDates[i], "BuildSampleDatabase")); catNo++; } dataObjects.addAll(collObjs); for (CollectingEvent ce : colEves) { persist(ce); } persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // determinations (determination status) //////////////////////////////// log.info("Creating determinations"); List<Determination> determs = new Vector<Determination>(); Calendar recent = Calendar.getInstance(); recent.set(2005, 10, 27, 13, 44, 00); Calendar longAgo = Calendar.getInstance(); longAgo.set(1976, 01, 29, 8, 12, 00); Calendar whileBack = Calendar.getInstance(); whileBack.set(2000, 7, 4, 9, 33, 12); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(5), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(6), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(7), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.get(13).setRemarks("This determination is totally wrong. What a foolish determination."); persist(determs); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // preparations (prep types) //////////////////////////////// log.info("Creating preparations"); Vector<PrepType> prepTypesForSaving = loadPrepTypes(discipline.getType()); PrepType pressed = prepTypesForSaving.get(0); List<Preparation> preps = new Vector<Preparation>(); Calendar prepDate = Calendar.getInstance(); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(4), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(5), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(6), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(7), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(10), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(3), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(5), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(6), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(7), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); dataObjects.addAll(prepTypesForSaving); dataObjects.addAll(preps); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // accessions (accession agents) //////////////////////////////// log.info("Creating accessions and accession agents"); calendar.set(2006, 10, 27, 23, 59, 59); Accession acc1 = createAccession(division, "gift", "complete", "2000-IP-001", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); acc1.setText1(disciplineType.getTitle()); acc1.setRepositoryAgreement(repoAg); Agent donor = agents.get(4); Agent receiver = agents.get(1); Agent reviewer = agents.get(2); List<AccessionAgent> accAgents = new Vector<AccessionAgent>(); accAgents.add(createAccessionAgent("donor", donor, acc1, null)); accAgents.add(createAccessionAgent("receiver", receiver, acc1, null)); accAgents.add(createAccessionAgent("reviewer", reviewer, acc1, null)); Accession acc2 = createAccession(division, "field_work", "inprocess", "2004-IP-002", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); Agent donor2 = agents.get(5); Agent receiver2 = agents.get(3); Agent reviewer2 = agents.get(1); accAgents.add(createAccessionAgent("donor", donor2, acc2, null)); accAgents.add(createAccessionAgent("receiver", receiver2, acc2, null)); accAgents.add(createAccessionAgent("reviewer", reviewer2, acc2, null)); dataObjects.add(acc1); dataObjects.add(acc2); dataObjects.addAll(accAgents); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); createLoanExamples(preps, agents, dataObjects); frame.setProcess(++createStep); persist(dataObjects); dataObjects.clear(); persist(dataObjects); dataObjects.clear(); frame.setProcess(++createStep); commitTx(); frame.setProcess(++createStep); buildDarwinCoreSchema(discipline); // done log.info("Done creating " + disciplineType.getTitle() + " disciplineType database: " + disciplineType.getTitle()); return dataObjects; } /** * @param treeDef * @return */ public LithoStrat convertLithoStratFromCSV(final LithoStratTreeDef treeDef) { Hashtable<String, LithoStrat> lithoStratHash = new Hashtable<String, LithoStrat>(); lithoStratHash.clear(); File file = new File("demo_files/Stratigraphy.csv"); if (!file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir"); file = XMLHelper.getConfigDir("Stratigraphy.csv"); if (!file.exists()) { file = new File("Specify/demo_files/Stratigraphy.csv"); } } if (file == null || !file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "]"); return null; } List<String> lines = null; try { lines = FileUtils.readLines(file); } catch (Exception ex) { ex.printStackTrace(); return null; } startTx(); // setup the root Geography record (planet Earth) LithoStrat earth = new LithoStrat(); earth.initialize(); earth.setName(getResourceString("Earth")); earth.setFullName(earth.getName()); earth.setNodeNumber(1); earth.setHighestChildNodeNumber(1); earth.setRankId(0); earth.setDefinition(treeDef); LithoStratTreeDefItem defItem = treeDef.getDefItemByRank(0); earth.setDefinitionItem(defItem); persist(earth); frame.setDesc("Adding Stratigraphy Objects"); frame.setProcess(0, lines.size()); int counter = 0; // for each old record, convert the record for (String line : lines) { if (counter == 0) { counter = 1; continue; // skip header line } if (counter % 100 == 0) { frame.setProcess(counter); log.info("Converted " + counter + " Stratigraphy records"); } String[] columns = StringUtils.splitPreserveAllTokens(line, ','); if (columns.length < 7) { log.error("Skipping[" + line + "]"); continue; } // grab the important data fields from the old record String superGroup = columns[2]; String lithoGroup = columns[3]; String formation = columns[4]; String member = columns[5]; String bed = columns[6]; // create a new Litho Stratigraphy object from the old data @SuppressWarnings("unused") LithoStrat newStrat = convertOldStratRecord(superGroup, lithoGroup, formation, member, bed, earth); counter++; } frame.setProcess(counter); log.info("Converted " + counter + " Stratigraphy records"); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); commitTx(); /*startTx(); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); printTree(earth, 0); saveTree(earth); commitTx();*/ log.info("Converted " + counter + " Stratigraphy records"); // set up Geography foreign key mapping for locality lithoStratHash.clear(); return earth; } /** * @param discipline * @param treeDef * @return */ public Geography createGeographyFromGeonames(final Discipline discipline, final Agent agent, final String itUsername, final String itPassword) { Geography earth = null; try { BuildFromGeonames bldGeoNames = new BuildFromGeonames(discipline.getGeographyTreeDef(), now, agent, itUsername, itPassword, frame); try { startTx(); earth = bldGeoNames.buildEarth(session); commitTx(); } catch (Exception ex) { rollbackTx(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex); return null; } //System.err.println(DBConnection.getInstance().getDatabaseName()); /*for (String nm : BasicSQLUtils.getTableNames(DBConnection.getInstance().getConnection())) { System.err.println(nm); }*/ try { if (bldGeoNames.loadGeoNamesDB(DBConnection.getInstance().getConnection().getCatalog())) // done synchronously { bldGeoNames.build(earth.getId()); } } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex); return null; } session.refresh(earth); GeographyTreeDef geoTreeDef = discipline.getGeographyTreeDef(); session.refresh(earth); frame.setDesc("Configuring Geography Tree..."); Discipline disp = AppContextMgr.getInstance().getClassObject(Discipline.class); if (disp == null) { AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); } geoTreeDef.updateAllNodes(earth, true, true); } catch (Exception ex) { ex.printStackTrace(); } return earth; } /** * @param treeDef * @return */ public Geography convertGeographyFromXLS(final GeographyTreeDef treeDef) { frame.setDesc("Building Geography Tree..."); Hashtable<String, Geography> geoHash = new Hashtable<String, Geography>(); geoHash.clear(); String fileName = "Geography.xls"; File file = XMLHelper.getConfigDir("../demo_files/" + fileName); if (!file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir"); file = XMLHelper.getConfigDir(fileName); if (!file.exists()) { file = new File("Specify/demo_files/" + fileName); } } if (file == null || !file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "]"); return null; } // setup the root Geography record (planet Earth) Geography earth = new Geography(); earth.initialize(); earth.setName(getResourceString("Earth")); earth.setFullName(earth.getName()); earth.setNodeNumber(1); earth.setHighestChildNodeNumber(1); earth.setRankId(0); earth.setDefinition(treeDef); GeographyTreeDefItem defItem = treeDef.getDefItemByRank(0); earth.setDefinitionItem(defItem); int counter = 0; try { startTx(); persist(earth); String[] cells = new String[4]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); int lastRowNum = sheet.getLastRowNum(); if (frame != null) { final int mx = lastRowNum; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setProcess(0, mx); } }); } while (rows.hasNext()) { if (counter == 0) { counter = 1; rows.next(); continue; } if (counter % 100 == 0) { if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " Geography records"); } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext() && i < 4) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString()); i++; } } // Sets nulls to unused cells for (int j = i; j < 4; j++) { cells[j] = null; } //System.out.println(); @SuppressWarnings("unused") Geography newGeo = convertGeographyRecord(cells[0], cells[1], cells[2], cells[3], earth); counter++; } } catch (Exception ex) { ex.printStackTrace(); } if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " Geography records"); frame.setDesc("Saving Geography Tree..."); frame.getProcessProgress().setIndeterminate(true); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); commitTx(); /*startTx(); TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); printTree(earth, 0); saveTree(earth); commitTx();*/ log.info("Converted " + counter + " Stratigraphy records"); // set up Geography foreign key mapping for locality geoHash.clear(); return earth; } /** * @param root */ @SuppressWarnings("unchecked") public void saveTree(Treeable<?, ?, ?> root) { persist(root); for (Treeable<?, ?, ?> child : (Set<Treeable<?, ?, ?>>) root.getChildren()) { saveTree(child); } } /** * @param root * @param level */ @SuppressWarnings("unchecked") public void printTree(final Treeable<?, ?, ?> root, int level) { for (int i = 0; i < level; i++) System.out.print(" "); System.out.println(root.getName() + " " + root.getNodeNumber() + " " + root.getHighestChildNodeNumber()); for (Treeable<?, ?, ?> child : (Set<Treeable<?, ?, ?>>) root.getChildren()) { printTree(child, level + 2); } } /** * @param superGroup * @param lithoGroup * @param formation * @param member * @param bed * @param stratRoot * @param localSession * @return */ protected LithoStrat convertOldStratRecord(String superGroup, String lithoGroup, String formation, String member, String bed, LithoStrat stratRoot) { String levelNames[] = { superGroup, lithoGroup, formation, member, bed }; int levelsToBuild = 0; for (int i = levelNames.length; i > 0; --i) { if (StringUtils.isNotEmpty(levelNames[i - 1])) { levelsToBuild = i; break; } } for (int i = 0; i < levelsToBuild; i++) { if (StringUtils.isEmpty(levelNames[i])) { levelNames[i] = "(Empty)"; } } LithoStrat prevLevelStrat = stratRoot; for (int i = 0; i < levelsToBuild; ++i) { LithoStrat newLevelStrat = buildLithoStratLevel(levelNames[i], prevLevelStrat); prevLevelStrat = newLevelStrat; } return prevLevelStrat; } /** * @param nameArg * @param parentArg * @return */ protected LithoStrat buildLithoStratLevel(final String nameArg, final LithoStrat parentArg) { String name = nameArg; if (name == null) { name = "N/A"; } // search through all of parent's children to see if one already exists with the same name Set<LithoStrat> children = parentArg.getChildren(); for (LithoStrat child : children) { if (name.equalsIgnoreCase(child.getName())) { // this parent already has a child by the given name // don't create a new one, just return this one return child; } } // we didn't find a child by the given name // we need to create a new Geography record LithoStrat newStrat = new LithoStrat(); newStrat.initialize(); newStrat.setName(name); newStrat.setParent(parentArg); parentArg.addChild(newStrat); newStrat.setDefinition(parentArg.getDefinition()); int newGeoRank = parentArg.getRankId() + 100; LithoStratTreeDefItem defItem = parentArg.getDefinition().getDefItemByRank(newGeoRank); newStrat.setDefinitionItem(defItem); newStrat.setRankId(newGeoRank); persist(newStrat); return newStrat; } /** * @param continent * @param country * @param state * @param county * @param geoRoot * @return */ protected Geography convertGeographyRecord(final String continent, final String country, final String state, final String county, final Geography geoRoot) { String levelNames[] = { continent, country, state, county }; int levelsToBuild = 0; for (int i = levelNames.length; i > 0; --i) { if (StringUtils.isNotEmpty(levelNames[i - 1])) { levelsToBuild = i; break; } } for (int i = 0; i < levelsToBuild; i++) { if (StringUtils.isEmpty(levelNames[i])) { levelNames[i] = "(Empty)"; } } Geography prevLevelGeo = geoRoot; for (int i = 0; i < levelsToBuild; ++i) { Geography newLevelGeo = buildGeographyLevel(levelNames[i], prevLevelGeo); prevLevelGeo = newLevelGeo; } return prevLevelGeo; } /** * @param nameArg * @param parentArg * @return */ protected Geography buildGeographyLevel(final String nameArg, final Geography parentArg) { String name = nameArg; if (name == null) { name = "N/A"; } // search through all of parent's children to see if one already exists with the same name Set<Geography> children = parentArg.getChildren(); for (Geography child : children) { if (name.equalsIgnoreCase(child.getName())) { // this parent already has a child by the given name // don't create a new one, just return this one return child; } } // we didn't find a child by the given name // we need to create a new Geography record Geography newGeo = new Geography(); newGeo.initialize(); newGeo.setName(name); newGeo.setParent(parentArg); parentArg.addChild(newGeo); newGeo.setDefinition(parentArg.getDefinition()); int newGeoRank = parentArg.getRankId() + 100; GeographyTreeDefItem defItem = parentArg.getDefinition().getDefItemByRank(newGeoRank); newGeo.setDefinitionItem(defItem); newGeo.setRankId(newGeoRank); persist(newGeo); return newGeo; } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public List<Object> createGenericCollection(final DisciplineType disciplineType, final Institution institution, final SpecifyUser user, final CollectionChoice choice, final String method) { frame.setProcess(0, 16); frame.setDesc("Creating " + disciplineType.getTitle() + "..."); createStep = 0; startTx(); Division division = createDivision(institution, disciplineType.getName(), disciplineType.getTitle(), disciplineType.getAbbrev(), disciplineType.getTitle()); // create tree defs (later we will make the def items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", TreeDefIface.FORWARD); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", TreeDefIface.REVERSE); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", TreeDefIface.REVERSE); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); boolean buildStorageTree = false; if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", TreeDefIface.REVERSE); institution.setStorageTreeDef(stgTreeDef); buildStorageTree = true; } Discipline discipline = createDiscipline(division, disciplineType.getName(), disciplineType.getTitle(), dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); persist(institution); persist(division); persist(discipline); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); frame.setDesc("Loading Schema..."); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, DBTableIdMgr.getInstance(), choice.getCatalogNumberingFmtName(), choice.getAccessionNumberingFmtName()); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String title = initPrefs.getProperty("useragent.title", "mr"); String firstName = initPrefs.getProperty("useragent.firstname", "Test"); String lastName = initPrefs.getProperty("useragent.lastname", "User"); String midInit = initPrefs.getProperty("useragent.midinit", "A"); String abbrev = initPrefs.getProperty("useragent.abbrev", "tu"); String email = initPrefs.getProperty("useragent.email", "testuser@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); System.out.println("----- User Agent -----"); System.out.println("Title: " + title); System.out.println("FirstName: " + firstName); System.out.println("LastName: " + lastName); System.out.println("MidInit: " + midInit); System.out.println("Abbrev: " + abbrev); System.out.println("Email: " + email); System.out.println("UserType: " + userType); Agent userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email); discipline.addReference(userAgent, "agents"); user.addReference(userAgent, "agents"); persist(discipline); persist(userAgent); persist(user); frame.setProcess(++createStep); Pair<AutoNumberingScheme, AutoNumberingScheme> pairANS = createAutoNumberingSchemes(choice); AutoNumberingScheme cns = pairANS.first; AutoNumberingScheme accessionNS = pairANS.second; persist(cns); persist(accessionNS); commitTx(); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); frame.setDesc("Creating a Collection"); Collection collection = createCollection("KU", disciplineType.getTitle(), choice.getCatalogNumberingFmtName(), cns, discipline, disciplineType.isEmbeddedCollecingEvent()); persist(collection); // create the standard user groups for this collection Map<String, SpPrincipal> groupMap = DataBuilder.createStandardGroups(session, collection); // add the administrator as a Collections Manager in this group user.addUserToSpPrincipalGroup(groupMap.get(SpecifyUserTypes.UserType.Manager.toString())); // Tester String dspAbbrev = disciplineType.getAbbrev(); createAndAddTesterToCollection(session, dspAbbrev + "Tester", dspAbbrev + "tester@brc.ku.edu", dspAbbrev + "Tester", "", dspAbbrev, "", "Tester", "", discipline, division, collection, groupMap, "Guest"); AppContextMgr.getInstance().setClassObject(Collection.class, collection); division.addReference(accessionNS, "numberingSchemes"); persist(division); commitTx(); doShowHideTablesAndFields(null, discipline); doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setProcess(++createStep); startTx(); createTaxonTreeDefFromXML(taxonTreeDef, disciplineType); persist(taxonTreeDef); //DBTableIdMgr schema = new DBTableIdMgr(false); //schema.initialize(new File(XMLHelper.getConfigDirPath("specify_datamodel.xml"))); //loadSchemaLocalization(discipline, SpLocaleContainer, schema); //buildDarwinCoreSchema(discipline); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, user); user.addReference(userAgent, "agents"); persist(user); Journal journal = createJournalsAndReferenceWork(); frame.setProcess(++createStep); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// frame.setDesc("Building Trees..."); Vector<Object> taxa = new Vector<Object>(); createTaxonTreeFromXML(taxa, taxonTreeDef, disciplineType); boolean isPaleo = disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.paleobotany || disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.vertpaleo || disciplineType.getDisciplineType() == DisciplineType.STD_DISCIPLINES.invertpaleo; if (isPaleo) { // LithoStratTreeDefItem earth = createLithoStratTreeDefItem(lithoStratTreeDef, "Earth", 0, false); // LithoStratTreeDefItem superGrp = createLithoStratTreeDefItem(earth, "Super Group", 100, false); // LithoStratTreeDefItem lithoGrp = createLithoStratTreeDefItem(superGrp, "Litho Group", 200, false); // LithoStratTreeDefItem formation = createLithoStratTreeDefItem(lithoGrp, "Formation", 300, false); // LithoStratTreeDefItem member = createLithoStratTreeDefItem(formation, "Member", 400, false); // @SuppressWarnings("unused") // LithoStratTreeDefItem bed = createLithoStratTreeDefItem(member, "Bed", 500, true); // persist(earth); } List<Object> geos = createSimpleGeography(geoTreeDef, true); List<Object> gtps = createSimpleGeologicTimePeriod(gtpTreeDef, true); List<Object> lithoStrats = isPaleo ? null : createSimpleLithoStrat(lithoStratTreeDef, true); persist(journal); persist(taxa); persist(geos); persist(buildStorageTree ? createSimpleStorage(stgTreeDef) : null); persist(gtps); if (lithoStrats != null) { persist(lithoStrats); } commitTx(); if (isPaleo) { LithoStrat earthLithoStrat = convertLithoStratFromCSV(lithoStratTreeDef);// does startTx() / commitTx if (earthLithoStrat == null) { startTx(); lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); persist(lithoStrats); commitTx(); } } frame.setProcess(++createStep); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); frame.setDesc("Creating Common PickLists..."); //frame.setProcess(++createStep); createPickLists(session, null); frame.setDesc("Creating PickLists..."); createPickLists(session, discipline); startTx(); Vector<Object> dataObjects = new Vector<Object>(); frame.setDesc("Creating Queries..."); standardQueries(dataObjects, userAgent); persist(dataObjects); dataObjects.clear(); persist(dataObjects); dataObjects.clear(); frame.setDesc("Intermediate save...."); commitTx(); frame.setDesc("Creating Localities...."); startTx(); frame.setProcess(++createStep); //////////////////////////////// // localities //////////////////////////////// String POINT = "Point"; String LINE = "Line"; String RECT = "Rectangle"; log.info("Creating localities"); frame.setDesc("Creating localities..."); Locality forestStream = createLocality("Gravel Pit", (Geography) geos.get(12)); forestStream.setLatLongType(POINT); forestStream.setOriginalLatLongUnit(0); forestStream.setLat1text("38.925467 deg N"); forestStream.setLatitude1(new BigDecimal(38.925467)); forestStream.setLong1text("94.984867 deg W"); forestStream.setLongitude1(new BigDecimal(-94.984867)); Locality lake = createLocality("Deep, dark lake pond", (Geography) geos.get(17)); lake.setLatLongType(RECT); lake.setOriginalLatLongUnit(1); lake.setLat1text("41.548842 deg N"); lake.setLatitude1(new BigDecimal(41.548842)); lake.setLong1text("93.732129 deg W"); lake.setLongitude1(new BigDecimal(-93.732129)); lake.setLat2text("41.642195 deg N"); lake.setLatitude2(new BigDecimal(41.642195)); lake.setLong2text("100.403180 deg W"); lake.setLongitude2(new BigDecimal(-100.403180)); Locality farmpond = createLocality("Shoal Creek at Schermerhorn Park, S of Galena at Rt. 26", (Geography) geos.get(11)); farmpond.setLatLongType(LINE); farmpond.setOriginalLatLongUnit(2); farmpond.setLat1text("41.642187 deg N"); farmpond.setLatitude1(new BigDecimal(41.642187)); farmpond.setLong1text("100.403163 deg W"); farmpond.setLongitude1(new BigDecimal(-100.403163)); farmpond.setLat2text("49.647435 deg N"); farmpond.setLatitude2(new BigDecimal(49.647435)); farmpond.setLong2text("-55.112163 deg W"); farmpond.setLongitude2(new BigDecimal(-55.112163)); persist(forestStream); persist(lake); persist(farmpond); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // agents and addresses //////////////////////////////// log.info("Creating agents and addresses"); frame.setDesc("Creating agents and addresses"); List<Agent> agents = new Vector<Agent>(); lastName = userAgent.getLastName(); Agent steveBoyd = createAgent("mr", "Steve", "D", "Boyd", "jb", "jb@net.edu"); if (!lastName.equals("Cooper")) agents.add(createAgent("mr", "Peter", "D", "Cooper", "ds", "ds@whitehouse.gov")); if (!lastName.equals("Peck")) agents.add(createAgent("mr", "David", "H", "Peck", "rb", "beach@net.edu")); if (!lastName.equals("Appleton")) agents.add(createAgent("mrs", "Sally", "H", "Appleton", "jm", "jm@net.edu")); if (!lastName.equals("Brown")) agents.add(createAgent("mr", "Taylor", "C", "Brown", "kcs", "taylor.brown@ku.edu")); if (!lastName.equals("Boyd")) agents.add(steveBoyd); if (!lastName.equals("Thomas")) agents.add(createAgent("Mr", "James", "X", "Thomas", "dxt", "")); if (!lastName.equals("Peterson")) agents.add(createAgent("mr", "Pete", "A", "Peterson", "jb", "")); if (!lastName.equals("Guttenburg")) agents.add(createAgent("mr", "Mitch", "A", "Guttenburg", "jb", "")); if (!lastName.equals("Ford")) agents.add(createAgent("mr", "Daniel", "A", "Ford", "mas", "mas@ku.edu")); agents.add(userAgent); Agent ku = new Agent(); ku.initialize(); ku.setAbbreviation("KU"); ku.setAgentType(Agent.ORG); ku.setLastName("University of Kansas"); ku.setEmail("webadmin@ku.edu"); ku.setTimestampCreated(new Timestamp(System.currentTimeMillis())); ku.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(ku); agents.get(0).setOrganization(ku); agents.get(1).setOrganization(ku); agents.get(2).setOrganization(ku); agents.get(3).setOrganization(ku); agents.get(8).setOrganization(ku); Agent otherAgent = new Agent(); otherAgent.initialize(); otherAgent.setAbbreviation("O"); otherAgent.setAgentType(Agent.OTHER); otherAgent.setLastName("The Other Guys"); otherAgent.setEmail("other@other.com"); otherAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); otherAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(otherAgent); commitTx(); frame.setDesc("Group Persons..."); List<GroupPerson> gpList = new ArrayList<GroupPerson>(); if (true) { startTx(); Agent gm1 = createAgent("mr", "John", "A", "Lyon", "jal", "jal@group.edu"); Agent gm2 = createAgent("mr", "Dave", "D", "Jones", "ddj", "ddj@group.edu"); persist(gm1); persist(gm2); commitTx(); Agent groupAgent = new Agent(); groupAgent.initialize(); groupAgent.setAbbreviation("GRP"); groupAgent.setAgentType(Agent.GROUP); groupAgent.setLastName("The Group"); groupAgent.setEmail("group@group.com"); groupAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); groupAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(groupAgent); gpList.add(createGroupPerson(groupAgent, gm1, 0, division)); gpList.add(createGroupPerson(groupAgent, gm2, 1, division)); } startTx(); List<Address> addrs = new Vector<Address>(); addrs.add(createAddress(agents.get(1), "1600 Pennsylvania Avenue NW", null, "Washington", "DC", "USA", "20500", 0)); addrs.add(createAddress(agents.get(1), "??? Mississippi", null, "Lawrence", "KS", "USA", "66045", 1)); addrs.add(createAddress(agents.get(2), "1 Main St", "", "Lenexa", "KS", "USA", "66071")); addrs.add(createAddress(agents.get(3), "13355 Inverness", "Bldg #3", "Lawrence", "KS", "USA", "66047")); addrs.add(createAddress(agents.get(4), "Natural History Museum", "Cromwell Rd", "London", null, "UK", "SW7 5BD")); addrs.add(createAddress(agents.get(6), "1212 Apple Street", null, "Chicago", "IL", "USA", "01010")); addrs.add(createAddress(agents.get(8), "11911 Oak Ln", null, "Orion", "KS", "USA", "66061")); addrs.add(createAddress(ku, null, null, "Lawrence", "KS", "USA", "66045")); // User Agent Address addrs.add(createAddress(userAgent, "1214 East Street", null, "Grinnell", "IA", "USA", "56060")); userAgent.setDivision(division); persist(agents); persist(gpList); commitTx(); startTx(); frame.setProcess(++createStep); frame.setDesc("Creating collecting events, collectors and a collecting trip..."); ////////////////////////////////////////////////// // collecting events (collectors, collecting trip) /////////////////////////////////////////////////// log.info("Creating collecting events, collectors and a collecting trip"); Collector collectorMitch = createCollector(agents.get(7), 2); Collector collectorJim = createCollector(agents.get(2), 1); calendar.set(1994, 4, 21, 11, 56, 00); String stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); CollectingEvent ce1 = createCollectingEvent(forestStream, calendar, stationFieldNumber, new Collector[] { collectorMitch, collectorJim }); ce1.setStartDateVerbatim("21 Apr 1994, 11:56 AM"); calendar.set(1994, 4, 21, 13, 03, 00); ce1.setEndDate(calendar); ce1.setEndDateVerbatim("21 Apr 1994, 1:03 PM"); ce1.setMethod("Picked"); AttributeDef cevAttrDef = createAttributeDef(AttributeIFace.FieldType.StringType, "ParkName", discipline, null);//meg added cod persist(cevAttrDef); commitTx(); startTx(); CollectingEventAttr cevAttr = createCollectingEventAttr(ce1, cevAttrDef, "Sleepy Hollow", null); Collector collectorMeg = createCollector(agents.get(2), 1); Collector collectorRod = createCollector(agents.get(3), 2); calendar.set(1994, 4, 22, 06, 12, 00); stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); CollectingEvent ce2 = createCollectingEvent(farmpond, calendar, stationFieldNumber, new Collector[] { collectorMeg, collectorRod }); ce2.setStartDateVerbatim("22 Apr 1994, 6:12 AM"); calendar.set(1994, 4, 22, 07, 31, 00); ce2.setEndDate(calendar); ce2.setEndDateVerbatim("22 Apr 1994, 7:31 AM"); ce2.setMethod("Picked"); //CollectingTrip trip = createCollectingTrip("Sample collecting trip", new CollectingEvent[]{ce1,ce2}); //dataObjects.add(trip); dataObjects.add(ce1); dataObjects.add(cevAttr); dataObjects.add(ce2); dataObjects.add(collectorMitch); dataObjects.add(collectorJim); dataObjects.add(collectorMeg); dataObjects.add(collectorRod); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); //////////////////////////////// // permit //////////////////////////////// log.info("Creating a permit"); frame.setDesc("Creating a permit..."); Calendar issuedDate = Calendar.getInstance(); issuedDate.set(1993, 1, 12); Calendar startDate = Calendar.getInstance(); startDate.set(1993, 2, 1); Calendar endDate = Calendar.getInstance(); endDate.set(1993, 5, 30); Permit permit = createPermit("1980-" + disciplineType.getAbbrev().substring(0, 2) + "-0001", "US Dept Wildlife", issuedDate, startDate, endDate, null); permit.setIssuedTo(ku); permit.setIssuedBy(agents.get(4)); dataObjects.add(permit); log.info("Creating a repository agreement"); RepositoryAgreement repoAg = new RepositoryAgreement(); repoAg.initialize(); repoAg.setDivision(division); repoAg.setRepositoryAgreementNumber("KU-" + disciplineType.getAbbrev() + "-01"); repoAg.setOriginator(ku); Calendar received = Calendar.getInstance(); received.set(1992, 2, 10); repoAg.setDateReceived(received); Calendar repoEndDate = Calendar.getInstance(); received.set(2010, 2, 9); repoAg.setEndDate(repoEndDate); dataObjects.add(repoAg); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // collection objects //////////////////////////////// log.info("Creating collection objects"); frame.setDesc("Creating collection objects..."); List<CollectionObject> collObjs = new Vector<CollectionObject>(); Collection col = collection; Calendar[] catDates = new Calendar[8]; for (int i = 0; i < catDates.length; i++) { catDates[i] = Calendar.getInstance(); int year = 1980 + (int) (rand.nextDouble() * 20.0); catDates[i].set(year, 01, 12 + i); } String prefix = "000000"; int catNo = 100; CollectingEvent[] colEves = new CollectingEvent[8]; for (int i = 0; i < colEves.length; i++) { colEves[i] = createFakeCollectingEvent(agents, farmpond, method); collObjs.add(createCollectionObject(prefix + Integer.toString(catNo), "RSC" + Integer.toString(catNo), agents.get(i), col, 1, colEves[i], catDates[i], "BuildSampleDatabase")); catNo++; } dataObjects.addAll(collObjs); for (CollectingEvent ce : colEves) { persist(ce); } persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // determinations (determination status) //////////////////////////////// log.info("Creating determinations"); frame.setDesc("Creating determinations..."); List<Determination> determs = new Vector<Determination>(); Calendar recent = Calendar.getInstance(); recent.set(2005, 10, 27, 13, 44, 00); Calendar longAgo = Calendar.getInstance(); longAgo.set(1976, 01, 29, 8, 12, 00); Calendar whileBack = Calendar.getInstance(); whileBack.set(2000, 7, 4, 9, 33, 12); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(5), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(6), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(7), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), true, recent)); determs.add(createDetermination(collObjs.get(0), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(1), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(2), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(3), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, whileBack)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.add(createDetermination(collObjs.get(4), getRandomAgent(agents), getRandomTaxon(TaxonTreeDef.SPECIES, taxa), false, longAgo)); determs.get(13).setRemarks("This determination is totally wrong. What a foolish determination."); persist(determs); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // preparations (prep types) //////////////////////////////// log.info("Creating preparations"); frame.setDesc("Creating preparations..."); Vector<PrepType> prepTypesForSaving = loadPrepTypes(discipline.getType()); PrepType pressed = prepTypesForSaving.get(0); List<Preparation> preps = new Vector<Preparation>(); Calendar prepDate = Calendar.getInstance(); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(4), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(5), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(6), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(7), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(10), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(2), collObjs.get(3), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(3), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(0), collObjs.get(5), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(6), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(7), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(3), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pressed, agents.get(1), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); dataObjects.addAll(prepTypesForSaving); dataObjects.addAll(preps); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); //////////////////////////////// // accessions (accession agents) //////////////////////////////// log.info("Creating accessions and accession agents"); frame.setDesc("Creating accessions..."); calendar.set(2006, 10, 27, 23, 59, 59); Accession acc1 = createAccession(division, "gift", "complete", "2000-" + disciplineType.getAbbrev().substring(0, 2) + "-001", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); acc1.setText1(disciplineType.getTitle()); acc1.setRepositoryAgreement(repoAg); Agent donor = agents.get(4); Agent receiver = agents.get(1); Agent reviewer = agents.get(2); List<AccessionAgent> accAgents = new Vector<AccessionAgent>(); accAgents.add(createAccessionAgent("donor", donor, acc1, null)); accAgents.add(createAccessionAgent("receiver", receiver, acc1, null)); accAgents.add(createAccessionAgent("reviewer", reviewer, acc1, null)); Accession acc2 = createAccession(division, "field_work", "inprocess", "2004-" + disciplineType.getAbbrev().substring(0, 2) + "-002", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); Agent donor2 = agents.get(5); Agent receiver2 = agents.get(3); Agent reviewer2 = agents.get(1); accAgents.add(createAccessionAgent("donor", donor2, acc2, null)); accAgents.add(createAccessionAgent("receiver", receiver2, acc2, null)); accAgents.add(createAccessionAgent("reviewer", reviewer2, acc2, null)); dataObjects.add(acc1); dataObjects.add(acc2); dataObjects.addAll(accAgents); persist(dataObjects); dataObjects.clear(); commitTx(); startTx(); frame.setProcess(++createStep); createLoanExamples(preps, agents, dataObjects); frame.setProcess(++createStep); persist(dataObjects); dataObjects.clear(); persist(dataObjects); dataObjects.clear(); frame.setProcess(++createStep); commitTx(); frame.setProcess(++createStep); buildDarwinCoreSchema(discipline); // done log.info("Done creating " + disciplineType.getTitle() + " disciplineType database: " + disciplineType.getTitle()); return dataObjects; } /** * @param treeDef * @param disciplineType */ @SuppressWarnings("unchecked") public void createStorageTreeDefFromXML(final Vector<Object> storageList, final File domFile, final StorageTreeDef treeDef, final boolean doAddTreeNodes) throws Exception { StorageTreeDefItem parent = null; Element root = XMLHelper.readFileToDOM4J(domFile); for (Element node : (List<Element>) root.selectNodes("/tree/treedef/level")) { String name = getAttr(node, NAME, null); int rankId = getAttr(node, RANK, 0); boolean infullname = getAttr(node, "infullname", false); boolean isEnforced = getAttr(node, "enforced", false); StorageTreeDefItem tdi = new StorageTreeDefItem(); tdi.initialize(); tdi.setName(name); tdi.setRankId(rankId); tdi.setIsEnforced(isEnforced); tdi.setIsInFullName(infullname); treeDef.getTreeDefItems().add(tdi); tdi.setParent(parent); if (parent != null) { parent.getChildren().add(tdi); } tdi.setTreeDef(treeDef); persist(tdi); parent = tdi; } createStorageTreeFromXML(storageList, root, treeDef, doAddTreeNodes); } @SuppressWarnings("unchecked") protected void createStorageTreeFromXML(final Vector<Object> storageList, final Element root, final StorageTreeDef treeDef, final boolean doAddTreeNodes) { StorageTreeDefItem rootTTD = null; Hashtable<Integer, StorageTreeDefItem> treeDefItemHash = new Hashtable<Integer, StorageTreeDefItem>(); for (StorageTreeDefItem ttdi : treeDef.getTreeDefItems()) { treeDefItemHash.put(ttdi.getRankId(), ttdi); if (ttdi.getRankId() == 0) { rootTTD = ttdi; } } Storage storage = new Storage(); storage.initialize(); storage.setRankId(0); storage.setName(getResourceString("Root")); storage.setFullName(storage.getName()); storage.setNodeNumber(1); storage.setHighestChildNodeNumber(1); storage.setDefinition(treeDef); storage.setDefinitionItem(rootTTD); rootTTD.getTreeEntries().add(storage); storage.setParent(null); persist(storage); storageList.add(storage); if (doAddTreeNodes) { for (Element node : (List<Element>) root.selectNodes("/tree/nodes/node")) { traverseTree(storageList, treeDefItemHash, treeDef, node, storage); } } TreeHelper.fixFullnameForNodeAndDescendants(storage); storage.setNodeNumber(1); fixNodeNumbersFromRoot(storage); } @SuppressWarnings("unchecked") protected void traverseTree(final Vector<Object> storageList, final Hashtable<Integer, StorageTreeDefItem> treeDefItemHash, final StorageTreeDef treeDef, final Element root, final Storage parent) { String name = getAttr(root, NAME, null); int rankId = getAttr(root, RANK, 0); Storage storage = new Storage(); storage.initialize(); storage.setRankId(rankId); storage.setName(name); storage.setFullName(name); storage.setDefinition(treeDef); storage.setDefinitionItem(treeDefItemHash.get(rankId)); storage.setParent(parent); parent.getChildren().add(storage); treeDefItemHash.get(rankId).getTreeEntries().add(storage); persist(storage); storageList.add(storage); for (Element node : (List<Element>) root.selectNodes("node")) { traverseTree(storageList, treeDefItemHash, treeDef, node, storage); } } /** * @param treeDef * @param disciplineType */ @SuppressWarnings("unchecked") protected void createTaxonTreeDefFromXML(final TaxonTreeDef treeDef, final DisciplineType disciplineType) { TaxonTreeDefItem parent = null; Element root = getDOMForDiscpline(disciplineType, "taxon_init.xml"); if (root != null) { for (Element node : (List<Element>) root.selectNodes("/tree/treedef/level")) { String name = getAttr(node, NAME, null); int rankId = getAttr(node, RANK, 0); boolean infullname = getAttr(node, "infullname", false); boolean isEnforced = getAttr(node, "enforced", false); TaxonTreeDefItem tdi = new TaxonTreeDefItem(); tdi.initialize(); tdi.setName(name); tdi.setRankId(rankId); tdi.setIsEnforced(isEnforced); tdi.setIsInFullName(infullname); treeDef.getTreeDefItems().add(tdi); tdi.setParent(parent); if (parent != null) { parent.getChildren().add(tdi); } tdi.setTreeDef(treeDef); persist(tdi); parent = tdi; } } } @SuppressWarnings("unchecked") protected void createTaxonTreeFromXML(final Vector<Object> taxonList, final TaxonTreeDef treeDef, final DisciplineType disciplineType) { TaxonTreeDefItem rootTTD = null; Hashtable<Integer, TaxonTreeDefItem> treeDefItemHash = new Hashtable<Integer, TaxonTreeDefItem>(); for (TaxonTreeDefItem ttdi : treeDef.getTreeDefItems()) { treeDefItemHash.put(ttdi.getRankId(), ttdi); if (ttdi.getRankId() == 0) { rootTTD = ttdi; } } Taxon taxon = new Taxon(); taxon.initialize(); taxon.setRankId(0); taxon.setName(getResourceString("Root")); taxon.setFullName(taxon.getName()); taxon.setNodeNumber(1); taxon.setHighestChildNodeNumber(1); taxon.setDefinition(treeDef); taxon.setDefinitionItem(rootTTD); rootTTD.getTreeEntries().add(taxon); taxon.setParent(null); persist(taxon); taxonList.add(taxon); Element root = getDOMForDiscpline(disciplineType, "taxon_init.xml"); for (Element node : (List<Element>) root.selectNodes("/tree/nodes/node")) { traverseTree(taxonList, treeDefItemHash, treeDef, node, taxon); } TreeHelper.fixFullnameForNodeAndDescendants(taxon); taxon.setNodeNumber(1); fixNodeNumbersFromRoot(taxon); } @SuppressWarnings("unchecked") protected void traverseTree(final Vector<Object> taxonList, final Hashtable<Integer, TaxonTreeDefItem> treeDefItemHash, final TaxonTreeDef treeDef, final Element root, final Taxon parent) { String name = getAttr(root, NAME, null); String common = getAttr(root, "common", null); int rankId = getAttr(root, RANK, 0); Taxon taxon = new Taxon(); taxon.initialize(); taxon.setRankId(rankId); taxon.setName(name); taxon.setFullName(name); taxon.setCommonName(common); taxon.setDefinition(treeDef); taxon.setDefinitionItem(treeDefItemHash.get(rankId)); taxon.setParent(parent); parent.getChildren().add(taxon); treeDefItemHash.get(rankId).getTreeEntries().add(taxon); persist(taxon); taxonList.add(taxon); for (Element node : (List<Element>) root.selectNodes("node")) { traverseTree(taxonList, treeDefItemHash, treeDef, node, taxon); } } protected Element getDOMForDiscpline(final DisciplineType dType, final String fileName) { return XMLHelper.readDOMFromConfigDir(dType.getFolder() + File.separator + fileName); } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public void createFishCollection(final DisciplineType disciplineType, final Institution institution, final SpecifyUser user, final CollectionChoice collChoice) { frame.setDesc("Creating Fish Collection Overhead..."); startTx(); Division division = createDivision(institution, disciplineType.getName(), "Ichthyology", "IT", "Ichthyology"); persist(division); // create tree defs (later we will make the def items and nodes) TaxonTreeDef taxonTreeDef = createTaxonTreeDef("Taxon", TreeDefIface.FORWARD); GeographyTreeDef geoTreeDef = createGeographyTreeDef("Geography", TreeDefIface.REVERSE); GeologicTimePeriodTreeDef gtpTreeDef = createGeologicTimePeriodTreeDef("Chronos Stratigraphy", TreeDefIface.REVERSE); LithoStratTreeDef lithoStratTreeDef = createLithoStratTreeDef("LithoStrat"); lithoStratTreeDef.setRemarks("A simple super, group, formation, member, bed Litho Stratigraphy tree"); boolean buildStorageTree = false; if (stgTreeDef == null) { stgTreeDef = createStorageTreeDef("Storage", TreeDefIface.REVERSE); institution.setStorageTreeDef(stgTreeDef); buildStorageTree = true; } Discipline discipline = createDiscipline(division, disciplineType.getName(), disciplineType.getTitle(), dataType, taxonTreeDef, geoTreeDef, gtpTreeDef, lithoStratTreeDef); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); persist(institution); persist(discipline); commitTx(); AppContextMgr.getInstance().setClassObject(Division.class, division); AppContextMgr.getInstance().setClassObject(Discipline.class, discipline); AppContextMgr.getInstance().setClassObject(Institution.class, institution); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String title = initPrefs.getProperty("useragent.title", "mr"); String firstName = initPrefs.getProperty("useragent.firstname", "Test"); String lastName = initPrefs.getProperty("useragent.lastname", "User"); String midInit = initPrefs.getProperty("useragent.midinit", "A"); String abbrev = initPrefs.getProperty("useragent.abbrev", "tu"); String email = initPrefs.getProperty("useragent.email", "testuser@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); System.out.println("----- User Agent -----"); System.out.println("Title: " + title); System.out.println("FirstName: " + firstName); System.out.println("LastName: " + lastName); System.out.println("MidInit: " + midInit); System.out.println("Abbrev: " + abbrev); System.out.println("Email: " + email); System.out.println("UserType: " + userType); Agent userAgent = createAgent(title, firstName, midInit, lastName, abbrev, email); userAgent.setDivision(division); discipline.addReference(userAgent, "agents"); user.addReference(userAgent, "agents"); startTx(); persist(discipline); persist(user); persist(userAgent); loadSchemaLocalization(discipline, SpLocaleContainer.CORE_SCHEMA, DBTableIdMgr.getInstance(), collChoice.getCatalogNumberingFmtName(), collChoice.getAccessionNumberingFmtName()); commitTx(); doShowHideTablesAndFields(null, discipline); doShowHideTablesAndFields(disciplineType.getName(), discipline); frame.setDesc("Creating Fish Trees..."); //////////////////////////////// // build the tree def items and nodes //////////////////////////////// Journal journal = createJournalsAndReferenceWork(); List<Object> taxa = createSimpleFishTaxonTree(taxonTreeDef, doShallowTaxonTree); List<Object> geos = createSimpleGeography(geoTreeDef, true); List<Object> gtps = createSimpleGeologicTimePeriod(gtpTreeDef, true); List<Object> lithoStrats = createSimpleLithoStrat(lithoStratTreeDef, true); startTx(); persist(journal); persist(taxa); persist(geos); persist(buildStorageTree ? createSimpleStorage(stgTreeDef) : null); persist(gtps); persist(lithoStrats); commitTx(); //frame.setProcess(++createStep); frame.setOverall(steps++); Collection voucher = null; if (isChoosen(DisciplineType.STD_DISCIPLINES.fish, false)) { voucher = createFishCollection(discipline, user, userAgent, division, journal, taxa, geos, "KUFSH", "Fish", true, false, collChoice); } frame.setOverall(steps++); Collection tissue = null; if (isChoosen(DisciplineType.STD_DISCIPLINES.fish, true)) { tissue = createFishCollection(discipline, user, userAgent, division, journal, taxa, geos, "KUTIS", "Fish Tissue", false, true, collChoice); } if (voucher != null && tissue != null) { startTx(); CollectionRelType colRelType = createCollectionRelType("Voucher Tissue", voucher, tissue); persist(colRelType); commitTx(); } buildDarwinCoreSchema(discipline); globalLocalities.clear(); } /** * @param type * @param isTissue * @return */ protected boolean isChoosen(final DisciplineType.STD_DISCIPLINES type, final boolean isTissue) { if (selectedChoices != null) { for (CollectionChoice cc : selectedChoices) { if (cc.getType() == type && cc.isTissue() == isTissue) { return true; } } } return false; } protected CollectionChoice getChoice(final DisciplineType.STD_DISCIPLINES type, final boolean isTissue) { if (selectedChoices != null) { for (CollectionChoice cc : selectedChoices) { if (cc.getType() == type && cc.isTissue() == isTissue) { return cc; } } } return null; } /** * @return returns a list of preptypes read in from preptype.xml */ protected Vector<PrepType> loadPrepTypes(final String discipline) { return loadPrepTypes(discipline, null, null); } /** * @return returns a list of preptypes read in from preptype.xml */ @SuppressWarnings("unchecked") protected Vector<PrepType> loadPrepTypes(final String discipline, final Collection collection, final Agent createdByAgent) { Vector<PrepType> prepTypes = new Vector<PrepType>(); XStream xstream = new XStream(); xstream.alias("preptype", PrepType.class); xstream.omitField(PrepType.class, "prepTypeId"); xstream.omitField(PrepType.class, "collection"); xstream.omitField(PrepType.class, "preparations"); xstream.omitField(PrepType.class, "attributeDefs"); xstream.useAttributeFor(PrepType.class, NAME); xstream.useAttributeFor(PrepType.class, "isLoanable"); xstream.aliasAttribute("isloanable", "isLoanable"); xstream.omitField(DataModelObjBase.class, "timestampCreated"); xstream.omitField(DataModelObjBase.class, "timestampModified"); xstream.omitField(DataModelObjBase.class, "lastEditedBy"); Collection colltn = collection != null ? collection : AppContextMgr.getInstance().getClassObject(Collection.class); Agent agent = createdByAgent != null ? createdByAgent : Agent.getUserAgent(); DisciplineType dType = DisciplineType.getByName(discipline); File file = XMLHelper.getConfigDir(dType.getFolder() + File.separator + "preptypes.xml"); if (file.exists()) { try { prepTypes = (Vector<PrepType>) xstream.fromXML(FileUtils.readFileToString(file)); } catch (Exception ex) { log.error(ex); } Timestamp nowTm = new Timestamp(System.currentTimeMillis()); for (PrepType pt : prepTypes) { pt.setCreatedByAgent(agent); pt.setTimestampCreated(nowTm); pt.setCollection(colltn); pt.setAttributeDefs(new HashSet<AttributeDef>()); } return prepTypes; } throw new RuntimeException("preptypes.xml is missing for discipline[" + discipline + "]"); } /** * */ protected void loadQueries() { loadQueries(XMLHelper.getConfigDirPath("common" + File.separator + "queries.xml")); String discipline = AppContextMgr.getInstance().getClassObject(Discipline.class).getType(); loadQueries(XMLHelper.getConfigDirPath(discipline + File.separator + "queries.xml")); } /** * @param path */ protected void loadQueries(final String path) { File file = new File(path); if (!file.exists()) { return; } Vector<SpQuery> queries = new Vector<SpQuery>(); try { Element root = XMLHelper.readFileToDOM4J(file); for (Object obj : root.selectNodes("/queries/query")) { Element el = (Element) obj; SpQuery query = new SpQuery(); query.initialize(); query.fromXML(el); query.setSpecifyUser(AppContextMgr.getInstance().getClassObject(SpecifyUser.class)); queries.add(query); } } catch (Exception ex) { ex.printStackTrace(); return; } // Persist out to database DataProviderSessionIFace localSession = null; try { localSession = DataProviderFactory.getInstance().createSession(); localSession.beginTransaction(); for (SpQuery query : queries) { query.setName(query.getName()); localSession.saveOrUpdate(query); } localSession.commit(); } catch (Exception ex) { edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BuildSampleDatabase.class, ex); // XXX Error dialog ex.printStackTrace(); localSession.rollback(); } finally { if (localSession != null) { localSession.close(); } } } /** * @param cc */ private Pair<AutoNumberingScheme, AutoNumberingScheme> createAutoNumberingSchemes(final CollectionChoice cc) { Pair<AutoNumberingScheme, AutoNumberingScheme> pair = new Pair<AutoNumberingScheme, AutoNumberingScheme>(); String catGroup = cc.getCatNumGroup(); if (StringUtils.isNotEmpty(catGroup)) { AutoNumberingScheme catANS = getAutoNumberingScheme(CollectionObject.class, catGroup); if (catANS == null) { catANS = createAutoNumberingScheme(catGroup, "", cc.getCatalogNumberingFmtName(), false, CollectionObject.getClassTableId()); addAutoNumberingScheme(CollectionObject.class, catANS); } pair.first = catANS; } String accGroup = cc.getAccNumGroup(); if (StringUtils.isNotEmpty(accGroup)) { AutoNumberingScheme accANS = getAutoNumberingScheme(Accession.class, accGroup); if (accANS == null) { accANS = createAutoNumberingScheme(accGroup, "", cc.getAccessionNumberingFmtName(), false, Accession.getClassTableId()); addAutoNumberingScheme(Accession.class, accANS); } pair.second = accANS; } return pair; } /** * Replace DataBuilder session with current BuildSampleDatabase session and * return old DataBuilder session so it can be later restored. * @return */ /*private Session switchDataBuilderSession() { Session oldSession = DataBuilder.getSession(); DataBuilder.setSession(session); return oldSession; }*/ /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ @SuppressWarnings("unchecked") public Collection createFishCollection(final Discipline discipline, final SpecifyUser user, final Agent userAgent, final Division division, final Journal journal, final List<Object> taxa, final List<Object> geos, final String colPrefix, final String colName, final boolean isVoucherCol, final boolean doTissues, final CollectionChoice choice) { createStep = 0; frame.setProcess(0, 15); frame.setDesc("Creating Collection " + colName); startTx(); Pair<AutoNumberingScheme, AutoNumberingScheme> pairANS = createAutoNumberingSchemes(choice); AutoNumberingScheme cns = pairANS.first; AutoNumberingScheme accessionNS = pairANS.second; persist(cns); persist(accessionNS); commitTx(); startTx(); //////////////////////////////// // Create Collection //////////////////////////////// log.info("Creating a Collection"); Collection collection = createCollection(colPrefix, colName, choice.getCatalogNumberingFmtName(), cns, discipline, false); persist(collection); AppContextMgr.getInstance().setClassObject(Collection.class, collection); division.addReference(accessionNS, "numberingSchemes"); persist(division); //////////////////////////////// // Default user groups and test user //////////////////////////////// Map<String, SpPrincipal> groupMap = DataBuilder.createStandardGroups(session, collection); // add the administrator as a Collections Manager in this group user.addUserToSpPrincipalGroup(groupMap.get(SpecifyUserTypes.UserType.Manager.toString())); persist(user); // Tester String userPrefix = (isVoucherCol) ? "" : "Tis"; createAndAddTesterToCollection(session, userPrefix + "FishTester", "fishtester@brc.ku.edu", userPrefix + "FishTester", "", "Fish", "", "Tester", "", discipline, division, collection, groupMap, "Guest"); commitTx(); //////////////////////////////// // picklists //////////////////////////////// log.info("Creating picklists"); createPickLists(session, null); BldrPickList colMethods = createPickLists(session, discipline); frame.setProcess(++createStep); startTx(); //DBTableIdMgr schema = new DBTableIdMgr(false); //schema.initialize(new File(XMLHelper.getConfigDirPath("specify_datamodel.xml"))); //loadSchemaLocalization(discipline, SpLocaleContainer, schema); //buildDarwinCoreSchema(discipline); AppContextMgr.getInstance().setClassObject(SpecifyUser.class, user); user.addReference(userAgent, "agents"); persist(user); frame.setProcess(++createStep); Vector<Object> dataObjects = new Vector<Object>(); standardQueries(dataObjects, userAgent); persist(dataObjects); dataObjects.clear(); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // localities //////////////////////////////// List<Locality> localities = new Vector<Locality>(); String POINT = "Point"; String LINE = "Line"; String RECT = "Rectangle"; Locality forestStream; Locality lake; Locality clintonLake; Locality farmpond; if (isVoucherCol) { log.info("Creating localities"); forestStream = createLocality("Unnamed forest stream pond", (Geography) geos.get(12)); localities.add(forestStream); globalLocalities.add(forestStream); forestStream.setLatLongType(POINT); forestStream.setOriginalLatLongUnit(0); forestStream.setLat1text("38.925467 deg N"); forestStream.setLatitude1(new BigDecimal(38.925467)); forestStream.setLong1text("94.984867 deg W"); forestStream.setLongitude1(new BigDecimal(-94.984867)); lake = createLocality("Deep, dark lake pond", (Geography) geos.get(17)); localities.add(lake); globalLocalities.add(lake); lake.setLatLongType(RECT); lake.setOriginalLatLongUnit(1); lake.setLat1text("41.548842 deg N"); lake.setLatitude1(new BigDecimal(41.548842)); lake.setLong1text("93.732129 deg W"); lake.setLongitude1(new BigDecimal(-93.732129)); lake.setLat2text("41.642195 deg N"); lake.setLatitude2(new BigDecimal(41.642195)); lake.setLong2text("100.403180 deg W"); lake.setLongitude2(new BigDecimal(-100.403180)); Geography douglasKS = null; for (Object o : geos) { if (o instanceof Geography) { Geography g = (Geography) o; if (g.getFullName().indexOf("Douglas") == 0) { douglasKS = g; } } } clintonLake = createLocality("Clinton Lake", douglasKS); localities.add(clintonLake); globalLocalities.add(clintonLake); farmpond = createLocality("Shoal Creek at Schermerhorn Park, S of Galena at Rt. 26", (Geography) geos.get(11)); localities.add(farmpond); globalLocalities.add(farmpond); farmpond.setLatLongType(LINE); farmpond.setOriginalLatLongUnit(2); farmpond.setLat1text("41.642187 deg N"); farmpond.setLatitude1(new BigDecimal(41.642187)); farmpond.setLong1text("100.403163 deg W"); farmpond.setLongitude1(new BigDecimal(-100.403163)); farmpond.setLat2text("49.647435 deg N"); farmpond.setLatitude2(new BigDecimal(49.647435)); farmpond.setLong2text("-55.112163 deg W"); farmpond.setLongitude2(new BigDecimal(-55.112163)); persist(forestStream); persist(lake); persist(farmpond); persist(clintonLake); } else { forestStream = globalLocalities.get(0); lake = globalLocalities.get(1); farmpond = globalLocalities.get(2); localities.addAll(globalLocalities); } frame.setProcess(++createStep); //////////////////////////////// // agents and addresses //////////////////////////////// log.info("Creating agents and addresses"); List<Agent> agents = new Vector<Agent>(); Agent johnByrn = null; Agent ku = new Agent(); if (isVoucherCol) { johnByrn = createAgent("mr", "John", "D", "Byrn", "jb", "jb@net.edu"); agents.add(createAgent("mr", "David", "D", "Smith", "ds", "ds@whitehouse.gov")); agents.add(createAgent("mr", "Robert", "H", "Burk", "rb", "beach@net.edu")); agents.add(createAgent("mrs", "Margaret", "H", "Johnson", "jm", "jm@net.edu")); agents.add(createAgent("mr", "Kip", "C", "Spencer", "kcs", "kip@ku.edu")); agents.add(johnByrn); agents.add(createAgent("sir", "Dudley", "X", "Thompson", "dxt", "")); agents.add(createAgent("mr", "Joe", "A", "Campbell", "jb", "")); agents.add(createAgent("mr", "Joe", "A", "Tester", "jb", "")); agents.add(createAgent("mr", "Mitch", "A", "Smyth", "mas", "mas@ku.edu")); agents.add(userAgent); ku.initialize(); ku.setAbbreviation("KU"); ku.setAgentType(Agent.ORG); ku.setLastName("University of Kansas"); ku.setEmail("webadmin@ku.edu"); ku.setTimestampCreated(new Timestamp(System.currentTimeMillis())); ku.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(ku); agents.get(0).setOrganization(ku); agents.get(1).setOrganization(ku); agents.get(2).setOrganization(ku); agents.get(3).setOrganization(ku); agents.get(8).setOrganization(ku); Agent otherAgent = new Agent(); otherAgent.initialize(); otherAgent.setAbbreviation("O"); otherAgent.setAgentType(Agent.OTHER); otherAgent.setLastName("The Other Guys"); otherAgent.setEmail("other@other.com"); otherAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); otherAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(otherAgent); List<GroupPerson> gpList = new ArrayList<GroupPerson>(); if (true) { startTx(); Agent gm1 = createAgent("mr", "John", "A", "Lyon", "jal", "jal@group.edu"); Agent gm2 = createAgent("mr", "Dave", "D", "Jones", "ddj", "ddj@group.edu"); persist(gm1); persist(gm2); commitTx(); //Discipline dsp = AppContextMgr.getInstance().getClassObject(Discipline.class); Agent groupAgent = new Agent(); groupAgent.initialize(); groupAgent.setAbbreviation("GRP"); groupAgent.setAgentType(Agent.GROUP); groupAgent.setLastName("The Group"); groupAgent.setEmail("group@group.com"); groupAgent.setTimestampCreated(new Timestamp(System.currentTimeMillis())); groupAgent.setDivision(AppContextMgr.getInstance().getClassObject(Division.class)); agents.add(groupAgent); gpList.add(createGroupPerson(groupAgent, gm1, 0, division)); gpList.add(createGroupPerson(groupAgent, gm2, 1, division)); } globalAgents.addAll(agents); List<AgentVariant> agentVariants = new Vector<AgentVariant>(); agentVariants.add(createAgentVariant(AgentVariant.VARIANT, "John Variant #1", johnByrn)); agentVariants.add(createAgentVariant(AgentVariant.VERNACULAR, "John VERNACULAR #1", johnByrn)); List<Address> addrs = new Vector<Address>(); addrs.add(createAddress(agents.get(1), "1600 Pennsylvania Avenue NW", null, "Washington", "DC", "USA", "20500", 0)); addrs.add(createAddress(agents.get(1), "??? Mississippi", null, "Lawrence", "KS", "USA", "66045", 1)); addrs.add(createAddress(agents.get(2), "1 Main St", "", "Lenexa", "KS", "USA", "66071")); addrs.add(createAddress(agents.get(3), "13355 Inverness", "Bldg #3", "Lawrence", "KS", "USA", "66047")); addrs.add(createAddress(agents.get(4), "Natural History Museum", "Cromwell Rd", "London", null, "UK", "SW7 5BD")); addrs.add(createAddress(agents.get(6), "1212 Apple Street", null, "Chicago", "IL", "USA", "01010")); addrs.add(createAddress(agents.get(8), "11911 Oak Ln", null, "Orion", "KS", "USA", "66061")); addrs.add(createAddress(ku, null, null, "Lawrence", "KS", "USA", "66045")); addrs.add(createAddress(userAgent, "1214 East Street", null, "Grinnell", "IA", "USA", "56060")); persist(agents); persist(agentVariants); persist(gpList); } else { agents.addAll(globalAgents); johnByrn = agents.get(4); ku = agents.get(10); } frame.setProcess(++createStep); //////////////////////////////// // collecting events (collectors, collecting trip) //////////////////////////////// log.info("Creating collecting events, collectors and a collecting trip"); Collector collectorMitch = createCollector(agents.get(8), 2); Collector collectorJim = createCollector(agents.get(1), 1); calendar.set(1993, 3, 19, 11, 56, 00); String stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); CollectingEvent ce1 = createCollectingEvent(forestStream, calendar, stationFieldNumber, new Collector[] { collectorMitch, collectorJim }); ce1.setStartDateVerbatim("19 Mar 1993, 11:56 AM"); calendar.set(1993, 3, 19, 13, 03, 00); ce1.setEndDate(calendar); ce1.setEndDateVerbatim("19 Mar 1993, 1:03 PM"); ce1.setMethod(colMethods.getItem(1).getValue()); AttributeDef cevAttrDef = createAttributeDef(AttributeIFace.FieldType.StringType, "ParkName", discipline, null);//meg added cod //startTx(); persist(cevAttrDef); //commitTx(); CollectingEventAttr cevAttr = createCollectingEventAttr(ce1, cevAttrDef, "Sleepy Hollow", null); Collector collectorMeg = createCollector(agents.get(2), 1); Collector collectorRod = createCollector(agents.get(3), 2); calendar.set(1993, 3, 20, 06, 12, 00); stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); CollectingEvent ce2 = createCollectingEvent(farmpond, calendar, stationFieldNumber, new Collector[] { collectorMeg, collectorRod }); ce2.setStartDateVerbatim("20 Mar 1993, 6:12 AM"); calendar.set(1993, 3, 20, 07, 31, 00); ce2.setEndDate(calendar); ce2.setEndDateVerbatim("20 Mar 1993, 7:31 AM"); ce2.setMethod(colMethods.getItem(2).getValue()); CollectingTrip trip = createCollectingTrip("My Collecint Trip", "Sample collecting trip", new CollectingEvent[] { ce1, ce2 }); int[] mn = { 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31 }; Vector<CollectingEvent> ceList = new Vector<CollectingEvent>(); boolean oldWay = false; if (!oldWay) { int monInx = rand.nextInt(12); int dayInx = rand.nextInt(mn[monInx]); calendar.set(1990 + rand.nextInt(15), monInx + 1, dayInx + 1, rand.nextInt(24), rand.nextInt(60), rand.nextInt(60)); stationFieldNumber = String.format(STATION_FIELD_FORMAT, stationFieldNumberCounter++); Collector collector = null; int coltrInx = rand.nextInt(4); switch (coltrInx) { case 0: collector = collectorMitch; break; case 1: collector = collectorJim; break; case 2: collector = collectorMeg; break; case 3: collector = collectorRod; break; default: collector = collectorRod; break; } Locality loc = globalLocalities.get(rand.nextInt(globalLocalities.size())); CollectingEvent ce = createCollectingEvent(loc, calendar, stationFieldNumber, new Collector[] { collector }); //ce1.setStartDateVerbatim("19 Mar 1993, 11:56 AM"); ceList.add(ce); dataObjects.add(ce); } dataObjects.add(trip); dataObjects.add(ce1); dataObjects.add(cevAttr); dataObjects.add(ce2); dataObjects.add(collectorMitch); dataObjects.add(collectorJim); dataObjects.add(collectorMeg); dataObjects.add(collectorRod); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); //////////////////////////////// // permit //////////////////////////////// log.info("Creating a permit"); Calendar issuedDate = Calendar.getInstance(); issuedDate.set(1993, 1, 12); Calendar startDate = Calendar.getInstance(); startDate.set(1993, 2, 1); Calendar endDate = Calendar.getInstance(); endDate.set(1993, 5, 30); Permit permit = createPermit("1993-FISH-0001", "US Dept Wildlife", issuedDate, startDate, endDate, null); permit.setIssuedTo(ku); permit.setIssuedBy(agents.get(4)); dataObjects.add(permit); log.info("Creating a repository agreement"); RepositoryAgreement repoAg = new RepositoryAgreement(); repoAg.initialize(); repoAg.setDivision(division); repoAg.setRepositoryAgreementNumber("KU-1992-01"); repoAg.setOriginator(ku); Calendar received = Calendar.getInstance(); received.set(1992, 2, 10); repoAg.setDateReceived(received); Calendar repoEndDate = Calendar.getInstance(); received.set(2010, 2, 9); repoAg.setEndDate(repoEndDate); dataObjects.add(repoAg); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // collection objects //////////////////////////////// log.info("Creating collection objects"); List<DNASequence> dnaObjs = new Vector<DNASequence>(); List<CollectionObject> collObjs = new Vector<CollectionObject>(); Collection col = collection; Calendar[] catDates = new Calendar[oldWay ? 8 : 50]; for (int i = 0; i < catDates.length; i++) { catDates[i] = Calendar.getInstance(); catDates[i].set(catDates[i].get(Calendar.YEAR), 01, 12 + i); } String prefix = "000000"; if (oldWay) { collObjs.add(createCollectionObject(prefix + "100", "RSC100", agents.get(0), col, 3, ce1, catDates[0], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "101", "RSC101", agents.get(0), col, 2, ce1, catDates[1], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "102", "RSC102", agents.get(1), col, 7, ce1, catDates[2], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "103", "RSC103", agents.get(1), col, 12, ce1, catDates[3], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "104", "RSC104", agents.get(2), col, 8, ce2, catDates[4], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "105", "RSC105", agents.get(2), col, 1, ce2, catDates[5], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "106", "RSC106", agents.get(2), col, 1, ce2, catDates[6], "BuildSampleDatabase")); collObjs.add(createCollectionObject(prefix + "107", "RSC107", agents.get(3), col, 1, ce2, catDates[7], "BuildSampleDatabase")); } else { for (int i = 0; i < catDates.length; i++) { Integer catNum = i + 100; int agentInx = rand.nextInt(agents.size()); CollectingEvent ce = ceList.get(rand.nextInt(ceList.size())); collObjs.add(createCollectionObject(prefix + catNum, "RSC" + catNum, agents.get(agentInx), col, rand.nextInt(12) + 1, ce, catDates[i], "BuildSampleDatabase")); } /* Comp. A : 148 Comp. G : 131 Comp. C : 199 Comp. T : 174 Ambiguous : 0 123456789012345678901234567890123456789012345678901234567890123456789012345 CCTGTATTTAGTATTTGGTGCCTGAGCAGGCATAGTCGGCACAGCCCTCAGCCTTCTGATCCGTGCCGAACTGAG CCAACCCGGTGCCCTGCTTGGCGATGATCAGATCTACAATGTTATCGTCACAGCCCACGCCTTTGTCATGATTTT CTTTATAGTAATACCCATCATAATTGGCGGATTCGGAAACTGACTGGTCCCCCTAATAATTGGGGCCCCAGACAT GGCATTTCCTCGCATGAACAATATGAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTTTTAGCCTCCTCTGG GGTAGAGGCCGGAGCCGGCACAGGGTGAACTGTTTACCCCCCACTGGCGGGAAACCTGGCCCATGCAGGAGCCTC TGTAGACCTAACCATTTTCTCCCTTCACCTGGCTGGGGTTTCGTCCATTTTGGGGGCTATTAATTTTATTACCAC CATTATTAACATGAAACCCCCCGCAGTATCCCAATATCAGACACCTCTATTTGTGTGATCTGTATTAATCACGGC CGTACTTCTCCTACTATCACTGCCAGTGCTAGCTGCAGGGATCACAATGCTCCTAACAGACCGAAATTTAAACAC CACCTTCTTTGACCCAGCCGGAGGAGGAGACCCCATCCTCTACCAACACCTA */ char[] syms = { 'A', 'C', 'T', 'G', }; for (int i = 0; i < catDates.length; i++) { int monInx = rand.nextInt(12); int dayInx = rand.nextInt(mn[monInx]); Calendar cal = Calendar.getInstance(); cal.set(2006 + rand.nextInt(3), monInx + 1, dayInx + 1, rand.nextInt(24), rand.nextInt(60), rand.nextInt(60)); DNASequence dna = new DNASequence(); dna.initialize(); //dna.setSeqDate(cal); //moved to DNASequencingRun dna.setCollectionMemberId(collObjs.get(i).getCollectionMemberId()); dna.setCollectionObject(collObjs.get(i)); //dna.setGeneName("COI5'"); int agentInx = rand.nextInt(agents.size()); dna.setCreatedByAgent(agents.get(agentInx)); dna.setSequencer(agents.get(agentInx)); StringBuilder sb = new StringBuilder(); for (int j = 0; j < ((8 * 75) + 52); j++) { sb.append(syms[rand.nextInt(syms.length)]); } dna.setGeneSequence(sb.toString()); //dna.setPcrPrimerFwd("C_VF1LFt1"); //moved to DNASequencingRun (sort of) //dna.setPcrPrimerRev("C_VR1LRt1"); //moved to DNASequencingRun (sort of) //dna.setProcessIdentifier("M13R"); //moved to DNASequencingRun (sort of) if (rand.nextInt(3) < 2) { //dna.setBarCodeIdent(String.format("NOSMF%03d-%d02", rand.nextInt(1000), i)); //moved to DNASequencingRun (sort of) Calendar submDate = (Calendar) cal.clone(); submDate.add(Calendar.DAY_OF_MONTH, 12); //dna.setSubmissionDate(submDate); } dnaObjs.add(dna); } } AttributeDef colObjAttrDef = createAttributeDef(AttributeIFace.FieldType.StringType, "MoonPhase", discipline, null);//meg added cod colObjAttrDef.setDiscipline(discipline); discipline.getAttributeDefs().add(colObjAttrDef); CollectionObjectAttr colObjAttr = createCollectionObjectAttr(collObjs.get(0), colObjAttrDef, "Full", null); dataObjects.add(colObjAttrDef); dataObjects.addAll(collObjs); dataObjects.addAll(dnaObjs); dataObjects.add(colObjAttr); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // determinations (determination status) //////////////////////////////// log.info("Creating determinations"); List<Determination> determs = new Vector<Determination>(); Calendar recent = Calendar.getInstance(); recent.set(2006, 10, 27, 13, 44, 00); Calendar longAgo = Calendar.getInstance(); longAgo.set(1976, 01, 29, 8, 12, 00); Calendar whileBack = Calendar.getInstance(); whileBack.set(2002, 7, 4, 9, 33, 12); int baseInx = 41 - (doShallowTaxonTree ? 30 : 0); if (oldWay) { determs.add(createDetermination(collObjs.get(0), agents.get(0), (Taxon) taxa.get(baseInx + 1), true, recent)); determs.add(createDetermination(collObjs.get(1), agents.get(0), (Taxon) taxa.get(baseInx + 2), true, recent)); determs.add(createDetermination(collObjs.get(2), agents.get(0), (Taxon) taxa.get(baseInx + 3), true, recent)); determs.add(createDetermination(collObjs.get(3), agents.get(0), (Taxon) taxa.get(baseInx + 4), true, recent)); determs.add(createDetermination(collObjs.get(4), agents.get(0), (Taxon) taxa.get(baseInx + 5), true, recent)); determs.add(createDetermination(collObjs.get(5), agents.get(0), (Taxon) taxa.get(baseInx + 6), true, recent)); determs.add(createDetermination(collObjs.get(6), agents.get(3), (Taxon) taxa.get(baseInx + 7), true, recent)); determs.add(createDetermination(collObjs.get(7), agents.get(4), (Taxon) taxa.get(baseInx + 8), true, recent)); determs.add( createDetermination(collObjs.get(0), agents.get(0), (Taxon) taxa.get(baseInx), false, longAgo)); determs.add(createDetermination(collObjs.get(1), agents.get(1), (Taxon) taxa.get(baseInx + 7), false, whileBack)); determs.add(createDetermination(collObjs.get(2), agents.get(1), (Taxon) taxa.get(baseInx + 9), false, whileBack)); determs.add(createDetermination(collObjs.get(3), agents.get(2), (Taxon) taxa.get(baseInx + 10), false, whileBack)); determs.add(createDetermination(collObjs.get(4), agents.get(2), (Taxon) taxa.get(baseInx + 10), false, whileBack)); determs.add(createDetermination(collObjs.get(4), agents.get(3), (Taxon) taxa.get(baseInx + 13), false, longAgo)); determs.add(createDetermination(collObjs.get(4), agents.get(4), (Taxon) taxa.get(baseInx + 12), false, longAgo)); determs.get(13).setRemarks("This determination is totally wrong. What a foolish determination."); } else { for (CollectionObject co : collObjs) { determs.add(createDetermination(co, agents.get(0), (Taxon) taxa.get(baseInx + rand.nextInt(13)), true, recent)); } } //startTx(); persist(determs); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // preparations (prep types) //////////////////////////////// log.info("Creating preparations"); Vector<PrepType> prepTypesForSaving = loadPrepTypes(discipline.getType()); Vector<PrepType> pt = new Vector<PrepType>(); if (doTissues) { pt.clear(); PrepType tissuePT = createPrepType(collection, "Tissue"); for (int i = 0; i < prepTypesForSaving.size(); i++) { pt.add(tissuePT); } prepTypesForSaving.clear(); prepTypesForSaving.add(tissuePT); } else { pt.addAll(prepTypesForSaving); } List<Preparation> preps = new Vector<Preparation>(); Calendar prepDate = Calendar.getInstance(); if (oldWay) { preps.add(createPreparation(pt.get(0), agents.get(0), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(0), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(1), collObjs.get(2), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(1), collObjs.get(3), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(2), collObjs.get(4), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(2), collObjs.get(5), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(3), collObjs.get(6), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(0), agents.get(3), collObjs.get(7), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(1), collObjs.get(0), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(1), collObjs.get(1), (Storage) locs.get(11), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(1), collObjs.get(2), (Storage) locs.get(10), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(2), collObjs.get(3), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(3), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(1), agents.get(0), collObjs.get(5), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(2), agents.get(1), collObjs.get(6), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(2), agents.get(1), collObjs.get(7), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(2), agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(3), agents.get(1), collObjs.get(0), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(3), agents.get(1), collObjs.get(1), (Storage) locs.get(7), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(3), agents.get(1), collObjs.get(2), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(3), agents.get(1), collObjs.get(3), (Storage) locs.get(8), rand.nextInt(20) + 1, prepDate)); preps.add(createPreparation(pt.get(3), agents.get(1), collObjs.get(4), (Storage) locs.get(9), rand.nextInt(20) + 1, prepDate)); } else { for (CollectionObject co : collObjs) { preps.add(createPreparation(pt.get(0), agents.get(rand.nextInt(4)), co, (Storage) locs.get(rand.nextInt(6) + 7), rand.nextInt(20) + 1, prepDate)); } } dataObjects.add(collection); dataObjects.addAll(prepTypesForSaving); dataObjects.addAll(preps); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // accessions (accession agents) //////////////////////////////// log.info("Creating accessions and accession agents"); calendar.set(2006, 10, 27, 23, 59, 59); int yr = 2000 + (int) (rand.nextDouble() * 7); Accession acc1 = createAccession(division, "gift", "complete", yr + "-IC-001", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); acc1.setText1("Ichthyology"); acc1.setRepositoryAgreement(repoAg); Agent donor = agents.get(4); Agent receiver = agents.get(1); Agent reviewer = agents.get(2); List<AccessionAgent> accAgents = new Vector<AccessionAgent>(); accAgents.add(createAccessionAgent("donor", donor, acc1, null)); accAgents.add(createAccessionAgent("receiver", receiver, acc1, null)); accAgents.add(createAccessionAgent("reviewer", reviewer, acc1, null)); Accession acc2 = createAccession(division, "field_work", "inprocess", yr + "-IC-002", DateFormat.getInstance().format(calendar.getTime()), calendar, calendar); Agent donor2 = agents.get(5); Agent receiver2 = agents.get(3); Agent reviewer2 = agents.get(1); accAgents.add(createAccessionAgent("donor", donor2, acc2, null)); accAgents.add(createAccessionAgent("receiver", receiver2, acc2, null)); accAgents.add(createAccessionAgent("reviewer", reviewer2, acc2, null)); dataObjects.add(acc1); dataObjects.add(acc2); dataObjects.addAll(accAgents); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); frame.setProcess(++createStep); createLoanExamples(preps, agents, dataObjects); frame.setProcess(++createStep); //startTx(); persist(dataObjects); //commitTx(); dataObjects.clear(); /*if (false) { TaxonCitation taxonCitation = new TaxonCitation(); taxonCitation.initialize(); Taxon taxon11 = (Taxon)taxa.get(11); taxonCitation.setTaxon(taxon11); taxonCitation.setReferenceWork(rwList.get(0)); rwList.get(0).addTaxonCitations(taxonCitation); taxon11.getTaxonCitations().add(taxonCitation); dataObjects.add(taxonCitation); LocalityCitation localityCitation = new LocalityCitation(); localityCitation.initialize(); localityCitation.setLocality(ce1.getLocality()); ce1.getLocality().getLocalityCitations().add(localityCitation); localityCitation.setReferenceWork(rwList.get(1)); rwList.get(1).addLocalityCitations(localityCitation); dataObjects.add(localityCitation); }*/ //////////////////////////////// // Workbench //////////////////////////////// // setup a template and its mapping items String name = discipline.getName() + " DataSet"; WorkbenchTemplate wbTemplate = createWorkbenchTemplate(user, name, "These are the remarks"); WorkbenchTemplateMappingItem wbtmi0 = createWorkbenchMappingItem("CollectionObject", 1, "fieldNumber", "Field Number", 25, 0, 0, wbTemplate); WorkbenchTemplateMappingItem wbtmi1 = createWorkbenchMappingItem("CollectionObject", 1, "catalogedDate", "Cataloged Date", 25, 1, 1, wbTemplate); WorkbenchTemplateMappingItem wbtmi2 = createWorkbenchMappingItem("CollectionObject", 1, "catalogNumber", "Catalog Number", 25, 2, 2, wbTemplate); WorkbenchTemplateMappingItem wbtmi3 = createWorkbenchMappingItem("CollectionObject", 1, "collectionObjectYesNo1", "Yes/No", 8, 3, 3, wbTemplate); dataObjects.add(wbTemplate); dataObjects.add(wbtmi0); dataObjects.add(wbtmi1); dataObjects.add(wbtmi2); dataObjects.add(wbtmi3); // setup a workbench based on that template Workbench workBench = createWorkbench(user, name, "These are the remarks", "field_notebook.cvs", wbTemplate); dataObjects.add(workBench); // create a bunch of rows for the workbench for (int i = 1; i <= 14; ++i) { WorkbenchRow wbRow = workBench.addRow(); WorkbenchDataItem wbdi0 = createWorkbenchDataItem(wbRow, "RS-10" + i, 0); // just to make the dates look a little random int date = (i * 547) % 31 + 1; String dateStr = "0" + Integer.toString(date); dateStr = dateStr.substring(dateStr.length() - 2); WorkbenchDataItem wbdi1 = createWorkbenchDataItem(wbRow, "03/" + dateStr + "/2007", 1); WorkbenchDataItem wbdi2 = createWorkbenchDataItem(wbRow, "CN-10" + i, 2); String boolValAsStr = null; switch (i % 3) { case 0: { boolValAsStr = "true"; break; } case 1: { boolValAsStr = "false"; break; } case 2: { boolValAsStr = ""; break; } } boolValAsStr = ""; WorkbenchDataItem wbdi3 = createWorkbenchDataItem(wbRow, boolValAsStr, 3); WorkbenchRowImage wbRowImage = null; File f = new File(getDefaultWorkingPath() + File.separator + "demo_files" + File.separator + "card" + i + (i == 2 ? ".png" : ".jpg")); if (f.exists()) { try { int imageIndex = wbRow.addImage(f); if (imageIndex > -1) { wbRowImage = wbRow.getRowImage(imageIndex); } } catch (IOException e) { String msg = getResourceString("WB_IMG_ERR_LOAD"); getStatusBar().setErrorMessage(msg, e); log.error(msg, e); } } dataObjects.add(wbRow); dataObjects.add(wbdi0); dataObjects.add(wbdi1); dataObjects.add(wbdi2); if (wbRowImage != null) { dataObjects.add(wbRowImage); } // since some of these values will be "", the data item might be null if (wbdi3 != null) { dataObjects.add(wbdi3); } } // // create a workbench that uses the old, single-image capabilities // Workbench workBench2 = createWorkbench(user, name + " (pre-conversion)", "These are the remarks", "field_notebook.cvs", wbTemplate); // dataObjects.add(workBench2); // // // create a bunch of rows for the workbench // for (int i = 1; i <= 14; ++i) // { // WorkbenchRow wbRow = workBench2.addRow(); // WorkbenchDataItem wbdi0 = createWorkbenchDataItem(wbRow, "RS-10" + i, 0); // // // just to make the dates look a little random // int date = (i*547) % 31 + 1; // String dateStr = "0" + Integer.toString(date); // dateStr = dateStr.substring(dateStr.length()-2); // WorkbenchDataItem wbdi1 = createWorkbenchDataItem(wbRow, "03/" + dateStr + "/2007", 1); // WorkbenchDataItem wbdi2 = createWorkbenchDataItem(wbRow, "CN-10" + i, 2); // // String boolValAsStr = null; // switch (i % 3) // { // case 0: // { // boolValAsStr = "true"; // break; // } // case 1: // { // boolValAsStr = "false"; // break; // } // case 2: // { // boolValAsStr = ""; // break; // } // } // boolValAsStr = ""; // WorkbenchDataItem wbdi3 = createWorkbenchDataItem(wbRow, boolValAsStr, 3); // // WorkbenchRowImage wbRowImage = null; // // File f = new File("demo_files" + File.separator + "card" + i + (i == 2 ? ".png" : ".jpg")); // if (f.exists()) // { // try // { // // NOTE: this is not scaling the images to the proper sizes. Since this is just sample DB/test code, this isn't a problem. // byte[] imageData = FileUtils.readFileToByteArray(f); // wbRow.setCardImageData(imageData); // wbRow.setCardImageFullPath(f.getAbsolutePath()); // } // catch (IOException e) // { // log.error("Unable to add card image to workbench row", e); // } // } // // dataObjects.add(wbRow); // dataObjects.add(wbdi0); // dataObjects.add(wbdi1); // dataObjects.add(wbdi2); // if (wbRowImage != null) // { // dataObjects.add(wbRowImage); // } // // // since some of these values will be "", the data item might be null // if (wbdi3 != null) // { // dataObjects.add(wbdi3); // } // } startTx(); persist(dataObjects); commitTx(); dataObjects.clear(); frame.setProcess(++createStep); //////////////////////////////// // attachments (attachment metadata) //////////////////////////////// startTx(); log.info("Creating attachments and attachment metadata"); try { String attachmentFilesLoc = getDefaultWorkingPath() + File.separator + "demo_files" + File.separator; // String bigEyeFilePath = attachmentFilesLoc + "bigeye.jpg"; // Attachment bigEye = createAttachment(bigEyeFilePath, "image/jpeg", 0); // bigEye.setLoan(closedLoan); String[] names = { "Beach", "Smyth", "Spears", "Kumin", "Bentley" }; String[] photos = { "beach.jpg", "rod.jpg", "rod.jpg", "meg.jpg", "andy.jpg" }; for (Agent agent : agents) { for (int i = 0; i < names.length; i++) { if (agent.getLastName() != null && agent.getLastName().startsWith(names[i])) { String photoPath = attachmentFilesLoc + photos[i]; File file = new File(attachmentFilesLoc + photos[i]); if (!file.exists()) { continue; } // create the attachment record Attachment photoAttachment = createAttachment(photoPath, "image/jpeg", Agent.getClassTableId()); dataObjects.add(photoAttachment); // link the attachment to the agent AgentAttachment agentAttach = new AgentAttachment(); agentAttach.initialize(); agentAttach.setAgent(agent); agentAttach.setAttachment(photoAttachment); agentAttach.setOrderIndex(0); dataObjects.add(agentAttach); // add some metadata to the attachment record AttachmentMetadata copyrightData = new AttachmentMetadata(); copyrightData.initialize(); copyrightData.setName("Copyright"); copyrightData.setValue("2008"); photoAttachment.getMetadata().add(copyrightData); copyrightData.setAttachment(photoAttachment); dataObjects.add(copyrightData); AttachmentMetadata defPhotoIndicator = new AttachmentMetadata(); defPhotoIndicator.initialize(); defPhotoIndicator.setName("Default Photo"); defPhotoIndicator.setValue("yes"); photoAttachment.getMetadata().add(defPhotoIndicator); defPhotoIndicator.setAttachment(photoAttachment); dataObjects.add(defPhotoIndicator); // store the actual file into the attachment storage system AttachmentUtils.getAttachmentManager().setStorageLocationIntoAttachment(photoAttachment, true); photoAttachment.storeFile(false); // false means do not display an error dialog } } } // String giftPdfPath = attachmentFilesLoc + "2004-18.pdf"; // Attachment giftPDF = createAttachment(giftPdfPath, "application/pdf", 0); // giftPDF.setLoan(closedLoan); // // String accessionPdfPath = attachmentFilesLoc + "Seychelles.pdf"; // Attachment accPDF = createAttachment(accessionPdfPath, "application/pdf", 0); // // TODO: change this to setAccession() // accPDF.setPermit(permit); // // String sharkVideoPath = attachmentFilesLoc + "shark5.mpg"; // Attachment sharkVideo = createAttachment(sharkVideoPath, "video/mpeg4", 0); // sharkVideo.setLoan(closedLoan); // // Attachment sharkVideo2 = createAttachment(sharkVideoPath, "video/mpeg4", 0); // sharkVideo2.setCollectingEvent(ce1); // // String beakerPath = attachmentFilesLoc + "beaker.jpg"; // Attachment beakerAsBeach = createAttachment(beakerPath, "image/jpg", 1); // beakerAsBeach.setAgent(agents.get(1)); // // dataObjects.add(bigEye); // dataObjects.add(giftPDF); // dataObjects.add(accPDF); // dataObjects.add(sharkVideo); // dataObjects.add(sharkVideo2); // dataObjects.add(beakerAsBeach); } catch (Exception e) { log.error("Could not create attachments", e); } addConservatorData(agents, collObjs); commitTx(); frame.setProcess(++createStep); if (true) { List<Taxon> taxa2 = session.createQuery("SELECT t FROM Taxon t WHERE t.name = 'Ammocrypta'").list(); List<ReferenceWork> rwList = new Vector<ReferenceWork>(); startTx(); rwList.addAll(journal.getReferenceWorks()); TaxonCitation taxonCitation = new TaxonCitation(); taxonCitation.initialize(); Taxon ammocrypta = taxa2.get(0); taxonCitation.setTaxon(ammocrypta); taxonCitation.setReferenceWork(rwList.get(0)); rwList.get(0).addTaxonCitations(taxonCitation); ammocrypta.getTaxonCitations().add(taxonCitation); dataObjects.add(taxonCitation); persist(taxonCitation); if (isVoucherCol) { Locality locality = localities.get(0); LocalityCitation localityCitation = new LocalityCitation(); localityCitation.initialize(); localityCitation.setLocality(locality); locality.getLocalityCitations().add(localityCitation); localityCitation.setReferenceWork(rwList.get(1)); rwList.get(1).addLocalityCitations(localityCitation); dataObjects.add(localityCitation); persist(localityCitation); } commitTx(); } frame.setProcess(++createStep); //SpecifyDeleteHelper.showTableCounts("EmptyDB.txt", true); return collection; } /** * Creates a single disciplineType collection. * @param disciplineName the name of the Discipline to use * @param disciplineName the disciplineType name * @return the entire list of DB object to be persisted */ public void createDisciplines(final String usernameArg, final String passwordArg) { createStep = 0; frame.setProcess(0, 4); frame.setProcess(++createStep); //////////////////////////////// // Create the really high-level stuff //////////////////////////////// String username = initPrefs.getProperty("useragent.username", usernameArg); String email = initPrefs.getProperty("useragent.email", "ku@ku.edu"); String userType = initPrefs.getProperty("useragent.usertype", SpecifyUserTypes.UserType.Manager.toString()); String password = initPrefs.getProperty("useragent.password", passwordArg); System.out.println("----- User Agent -----"); System.out.println("Userame: " + username); Institution institution = createInstitution("Natural History Museum"); startTx(); SpecifyUser specifyAdminUser = DataBuilder.createAdminGroupAndUser(session, institution, null, username, email, password, userType); dataType = createDataType("Biota"); persist(institution); persist(dataType); persist(specifyAdminUser); commitTx(); frame.setProcess(++createStep); //boolean done = false; if (isChoosen(DisciplineType.STD_DISCIPLINES.fish, false) || isChoosen(DisciplineType.STD_DISCIPLINES.fish, true)) { createFishCollection(DisciplineType.getDiscipline("fish"), institution, specifyAdminUser, getChoice(DisciplineType.STD_DISCIPLINES.fish, false)); //done = true; } frame.setOverall(steps++); if (isChoosen(DisciplineType.STD_DISCIPLINES.invertpaleo, false)) { createSingleInvertPaleoCollection(DisciplineType.getDiscipline("invertpaleo"), institution, specifyAdminUser, getChoice(DisciplineType.STD_DISCIPLINES.invertpaleo, false)); //done = true; } frame.setOverall(steps++); if (isChoosen(DisciplineType.STD_DISCIPLINES.botany, false)) { if (!doHugeBotany) { createSingleBotanyCollection(DisciplineType.getDiscipline("botany"), institution, specifyAdminUser, getChoice(DisciplineType.STD_DISCIPLINES.botany, false)); } else { createHugeBotanyCollection(DisciplineType.getDiscipline("botany"), institution, specifyAdminUser, getChoice(DisciplineType.STD_DISCIPLINES.botany, false)); } //done = true; } for (DisciplineType.STD_DISCIPLINES disp : DisciplineType.STD_DISCIPLINES.values()) { if (disp != DisciplineType.STD_DISCIPLINES.botany && disp != DisciplineType.STD_DISCIPLINES.invertpaleo && disp != DisciplineType.STD_DISCIPLINES.fish && isChoosen(disp, false)) { frame.setOverall(steps++); String method = null; switch (disp) { case herpetology: method = "trap"; break; case paleobotany: method = "dug"; break; case vertpaleo: method = "dug"; break; case bird: method = "shot"; break; case mammal: method = "trap"; break; case insect: method = "trap"; break; case invertebrate: method = "trap"; break; default: method = "XXX"; break; } DisciplineType dType = DisciplineType.getDiscipline(disp); log.debug("Building " + dType.getName()); if (XMLHelper.getConfigDir(dType.getFolder() + File.separator + "taxon_init.xml").exists()) { createGenericCollection(dType, institution, specifyAdminUser, getChoice(disp, false), method); } } } frame.setOverall(steps++); } /** * @param def * @return */ public static List<Object> createSimpleLithoStrat(final LithoStratTreeDef def, final boolean doAddTreeNodes) { log.info("createSimpleLithoStrat " + def.getName()); List<Object> newObjs = new Vector<Object>(); LithoStratTreeDefItem planet = new LithoStratTreeDefItem(); planet.initialize(); planet.setName(getResourceString("Surface")); planet.setRankId(0); planet.setIsEnforced(true); planet.setFullNameSeparator(", "); LithoStratTreeDefItem superLitho = new LithoStratTreeDefItem(); superLitho.initialize(); superLitho.setName(getResourceString("SuperLitho")); superLitho.setRankId(100); superLitho.setFullNameSeparator(", "); LithoStratTreeDefItem group = new LithoStratTreeDefItem(); group.initialize(); group.setName(getResourceString("Group")); group.setRankId(200); group.setIsInFullName(true); group.setFullNameSeparator(", "); LithoStratTreeDefItem formation = new LithoStratTreeDefItem(); formation.initialize(); formation.setName(getResourceString("Formation")); formation.setRankId(300); formation.setIsInFullName(true); formation.setFullNameSeparator(", "); LithoStratTreeDefItem member = new LithoStratTreeDefItem(); member.initialize(); member.setName(getResourceString("Member")); member.setRankId(400); member.setIsInFullName(true); member.setFullNameSeparator(", "); LithoStratTreeDefItem bed = new LithoStratTreeDefItem(); bed.initialize(); bed.setName(getResourceString("Bed")); bed.setRankId(500); bed.setIsInFullName(true); bed.setFullNameSeparator(", "); planet.setTreeDef(def); Set<LithoStratTreeDefItem> defItems = def.getTreeDefItems(); defItems.add(planet); newObjs.add(planet); if (doAddTreeNodes) { // setup parents bed.setParent(member); member.setParent(formation); formation.setParent(group); group.setParent(superLitho); superLitho.setParent(planet); // set the tree def for each tree def item superLitho.setTreeDef(def); group.setTreeDef(def); formation.setTreeDef(def); member.setTreeDef(def); bed.setTreeDef(def); defItems.add(superLitho); defItems.add(group); defItems.add(formation); defItems.add(member); defItems.add(bed); newObjs.add(superLitho); newObjs.add(group); newObjs.add(formation); newObjs.add(member); newObjs.add(bed); LithoStrat earth = new LithoStrat(); earth.initialize(); earth.setName(getResourceString("Earth")); earth.setFullName(earth.getName()); earth.setDefinition(def); earth.setDefinitionItem(planet); earth.setNodeNumber(1); earth.setHighestChildNodeNumber(1); earth.setIsAccepted(true); newObjs.add(earth); } return newObjs; } /** * @param geoTreeDef * @param doAddTreeNodes * @return */ public static List<Object> createSimpleGeography(final GeographyTreeDef geoTreeDef, final boolean doAddTreeNodes) { log.info("createSimpleGeography " + geoTreeDef.getName()); List<Object> newObjs = new Vector<Object>(); // create the geo tree def items GeographyTreeDefItem root = createGeographyTreeDefItem(null, geoTreeDef, " ", 0); root.setIsEnforced(true); GeographyTreeDefItem cont = createGeographyTreeDefItem(root, geoTreeDef, "Continent", 100); GeographyTreeDefItem country = createGeographyTreeDefItem(cont, geoTreeDef, "Country", 200); GeographyTreeDefItem state = createGeographyTreeDefItem(country, geoTreeDef, "State", 300); state.setIsInFullName(true); GeographyTreeDefItem county = createGeographyTreeDefItem(state, geoTreeDef, "County", 400); county.setIsInFullName(true); //county.setTextAfter(" Co."); // 0 newObjs.add(root); // 1 newObjs.add(cont); // 2 newObjs.add(country); // 3 newObjs.add(state); // 4 newObjs.add(county); Geography earth = null; if (doAddTreeNodes) { // Create the planet Earth. // That seems like a big task for 5 lines of code. earth = createGeography(geoTreeDef, null, "Earth", root.getRankId()); // 5 newObjs.add(earth); Geography northAmerica = createGeography(geoTreeDef, earth, "North America", cont.getRankId()); Geography us = createGeography(geoTreeDef, northAmerica, "United States", country.getRankId()); List<Geography> states = createGeographyChildren(geoTreeDef, us, new String[] { "Kansas", "Iowa", "Nebraska" }, state.getRankId()); // 6 newObjs.add(northAmerica); // 7 newObjs.add(us); // 8, 9, 10 newObjs.addAll(states); // Create Kansas and a few counties List<Geography> counties = createGeographyChildren(geoTreeDef, states.get(0), new String[] { "Cherokee", "Douglas", "Johnson", "Osage", "Sedgwick" }, county.getRankId()); // 11, 12, 13, 14 newObjs.addAll(counties); counties = createGeographyChildren(geoTreeDef, states.get(1), new String[] { "Blackhawk", "Fayette", "Polk", "Woodbury", "Johnson" }, county.getRankId()); // 15, 16, 17, 18, 19 newObjs.addAll(counties); counties = createGeographyChildren(geoTreeDef, states.get(2), new String[] { "Dakota", "Logan", "Valley", "Wheeler", "Johnson" }, county.getRankId()); // 20, 21, 22, 23, 24 newObjs.addAll(counties); } int i = 0; for (Object geo : newObjs) { if (geo instanceof Geography) { log.debug(i + " " + ((Geography) geo).getName()); } i++; } if (doAddTreeNodes) { TreeHelper.fixFullnameForNodeAndDescendants(earth); earth.setNodeNumber(1); fixNodeNumbersFromRoot(earth); } return newObjs; } /** * @param treeDef * @param doAddTreeNode * @return */ public static List<Object> createSimpleGeologicTimePeriod(final GeologicTimePeriodTreeDef treeDef, final boolean doAddTreeNode) { log.info("createSimpleGeologicTimePeriod " + treeDef.getName()); List<Object> newObjs = new Vector<Object>(); // Create a geologic time period tree definition GeologicTimePeriodTreeDefItem defItemLevel0 = createGeologicTimePeriodTreeDefItem(null, treeDef, "Level 0", 0); GeologicTimePeriodTreeDefItem defItemLevel1 = createGeologicTimePeriodTreeDefItem(defItemLevel0, treeDef, "Level 1", 100); GeologicTimePeriodTreeDefItem defItemLevel2 = createGeologicTimePeriodTreeDefItem(defItemLevel1, treeDef, "Level 2", 200); GeologicTimePeriodTreeDefItem defItemLevel3 = createGeologicTimePeriodTreeDefItem(defItemLevel2, treeDef, "Level 3", 300); newObjs.add(defItemLevel0); newObjs.add(defItemLevel1); newObjs.add(defItemLevel2); newObjs.add(defItemLevel3); defItemLevel0.setIsInFullName(false); defItemLevel1.setIsInFullName(false); defItemLevel2.setIsInFullName(true); defItemLevel3.setIsInFullName(true); // Create the defItemLevel0 GeologicTimePeriod level0 = createGeologicTimePeriod(treeDef, null, "Place Holder", 10.0f, 0.0f, defItemLevel0.getRankId()); newObjs.add(level0); if (doAddTreeNode) { GeologicTimePeriod level1 = createGeologicTimePeriod(treeDef, level0, "Some Really Big Time Period", 5.0f, 0.0f, defItemLevel1.getRankId()); GeologicTimePeriod level2 = createGeologicTimePeriod(treeDef, level1, "A Slightly Smaller Time Period", 1.74f, 0.0f, defItemLevel2.getRankId()); GeologicTimePeriod level3_1 = createGeologicTimePeriod(treeDef, level2, "Yesterday", 0.1f, 0.0f, defItemLevel3.getRankId()); GeologicTimePeriod level3_2 = createGeologicTimePeriod(treeDef, level2, "A couple of days ago", 0.2f, 0.1f, defItemLevel3.getRankId()); GeologicTimePeriod level3_3 = createGeologicTimePeriod(treeDef, level2, "Last week", 0.7f, 1.4f, defItemLevel3.getRankId()); newObjs.add(level1); newObjs.add(level2); newObjs.add(level3_1); newObjs.add(level3_2); newObjs.add(level3_3); } TreeHelper.fixFullnameForNodeAndDescendants(level0); level0.setNodeNumber(1); fixNodeNumbersFromRoot(level0); return newObjs; } public static List<Object> createSimpleStorage(final StorageTreeDef stgTreeDef) { log.info("createSimpleStorage " + stgTreeDef.getName()); locs = new Vector<Object>(); StorageTreeDefItem building = createStorageTreeDefItem(null, stgTreeDef, "building", 0); building.setIsEnforced(true); StorageTreeDefItem room = createStorageTreeDefItem(building, stgTreeDef, "room", 100); room.setIsInFullName(true); StorageTreeDefItem freezer = createStorageTreeDefItem(room, stgTreeDef, "freezer", 200); freezer.setIsInFullName(true); StorageTreeDefItem shelf = createStorageTreeDefItem(freezer, stgTreeDef, "shelf", 300); shelf.setIsInFullName(true); // Create the building Storage dyche = createStorage(stgTreeDef, null, "Dyche Hall", building.getRankId()); Storage rm606 = createStorage(stgTreeDef, dyche, "Room 606", room.getRankId()); Storage freezerA = createStorage(stgTreeDef, rm606, "Freezer A", freezer.getRankId()); Storage shelf5 = createStorage(stgTreeDef, freezerA, "Shelf 5", shelf.getRankId()); Storage shelf4 = createStorage(stgTreeDef, freezerA, "Shelf 4", shelf.getRankId()); Storage shelf3 = createStorage(stgTreeDef, freezerA, "Shelf 3", shelf.getRankId()); Storage shelf2 = createStorage(stgTreeDef, freezerA, "Shelf 2", shelf.getRankId()); Storage shelf1 = createStorage(stgTreeDef, freezerA, "Shelf 1", shelf.getRankId()); Storage rm701 = createStorage(stgTreeDef, dyche, "Room 701", room.getRankId()); Storage freezerA_701 = createStorage(stgTreeDef, rm701, "Freezer A", freezer.getRankId()); Storage shelf1_701 = createStorage(stgTreeDef, freezerA_701, "Shelf 1", shelf.getRankId()); Storage rm703 = createStorage(stgTreeDef, dyche, "Room 703", room.getRankId()); Storage freezerA_703 = createStorage(stgTreeDef, rm703, "Freezer A", freezer.getRankId()); Storage shelf1_703 = createStorage(stgTreeDef, freezerA_703, "Shelf 1", shelf.getRankId()); Storage shelf2_703 = createStorage(stgTreeDef, freezerA_703, "Shelf 2", shelf.getRankId()); Storage shelf3_703 = createStorage(stgTreeDef, freezerA_703, "Shelf 3", shelf.getRankId()); // 0 locs.add(building); // 1 locs.add(room); // 2 locs.add(freezer); // 3 locs.add(shelf); // 4 locs.add(dyche); // 5 locs.add(rm606); // 6 locs.add(freezerA); // 7 locs.add(shelf5); // 8 locs.add(shelf4); // 9 locs.add(shelf3); // 10 locs.add(shelf2); // 11 locs.add(shelf1); // 12 locs.add(rm701); // 13 locs.add(freezerA_701); // 14 locs.add(shelf1_701); // 15 locs.add(rm703); // 16 locs.add(freezerA_703); // 17 locs.add(shelf1_703); // 18 locs.add(shelf2_703); // 19 locs.add(shelf3_703); TreeHelper.fixFullnameForNodeAndDescendants(dyche); dyche.setNodeNumber(1); fixNodeNumbersFromRoot(dyche); return locs; } /** * @param taxonTreeDef * @param doShallow * @return */ public static List<Object> createSimpleFishTaxonTree(final TaxonTreeDef taxonTreeDef, final boolean doShallow) { log.info("createSimpleFishTaxonTree " + taxonTreeDef.getName()); Vector<Object> newObjs = new Vector<Object>(); Set<TaxonTreeDefItem> newItems; if (doShallow) { Object[][] taxonItems = { { TaxonTreeDef.TAXONOMY_ROOT, "Taxonomy Root", true, false }, { TaxonTreeDef.ORDER, "Order", true, false }, { TaxonTreeDef.SUBORDER, "Suborder", false, false }, { TaxonTreeDef.FAMILY, "Family", false, false }, { TaxonTreeDef.GENUS, "Genus", true, true }, { TaxonTreeDef.SPECIES, "Species", false, true }, }; newItems = TreeFactory.addStandardTaxonDefItems(taxonTreeDef, taxonItems); } else { newItems = TreeFactory.addStandardTaxonDefItems(taxonTreeDef); } newObjs.addAll(newItems); // 0 - 27 for (TaxonTreeDefItem item : newItems) { if (item.getRankId().equals(TaxonTreeDef.GENUS)) { item.setFormatToken("%G"); } else if (item.getRankId().equals(TaxonTreeDef.SPECIES)) { item.setFormatToken("%S"); } else if (item.getRankId().equals(TaxonTreeDef.SUBSPECIES)) { item.setFormatToken("%SS"); } } Taxon life = createTaxon(taxonTreeDef, null, "Life", TaxonTreeDef.TAXONOMY_ROOT); Taxon animalia = null; Taxon chordata = null; Taxon vertebrata = null; Taxon osteichthyes = null; Taxon actinopterygii = null; Taxon neopterygii = null; Taxon teleostei = null; Taxon acanthopterygii = null; if (!doShallow) { animalia = createTaxon(taxonTreeDef, life, "Animalia", TaxonTreeDef.KINGDOM); chordata = createTaxon(taxonTreeDef, animalia, "Chordata", TaxonTreeDef.PHYLUM); vertebrata = createTaxon(taxonTreeDef, chordata, "Vertebrata", TaxonTreeDef.SUBPHYLUM); osteichthyes = createTaxon(taxonTreeDef, vertebrata, "Osteichthyes", TaxonTreeDef.SUPERCLASS); actinopterygii = createTaxon(taxonTreeDef, osteichthyes, "Actinopterygii", TaxonTreeDef.CLASS); neopterygii = createTaxon(taxonTreeDef, actinopterygii, "Neopterygii", TaxonTreeDef.SUBCLASS); teleostei = createTaxon(taxonTreeDef, neopterygii, "Teleostei", TaxonTreeDef.INFRACLASS); acanthopterygii = createTaxon(taxonTreeDef, teleostei, "Acanthopterygii", TaxonTreeDef.SUPERORDER); } Taxon perciformes = createTaxon(taxonTreeDef, doShallow ? life : acanthopterygii, "Perciformes", TaxonTreeDef.ORDER); Taxon percoidei = createTaxon(taxonTreeDef, perciformes, "Percoidei", TaxonTreeDef.SUBORDER); Taxon percidae = createTaxon(taxonTreeDef, percoidei, "Percidae", TaxonTreeDef.FAMILY); Taxon ammocrypta = createTaxon(taxonTreeDef, percidae, "Ammocrypta", TaxonTreeDef.GENUS); ammocrypta.setCommonName("sand darters"); newObjs.add(life); if (!doShallow) { newObjs.add(animalia); newObjs.add(chordata); newObjs.add(vertebrata); newObjs.add(osteichthyes); newObjs.add(actinopterygii); newObjs.add(neopterygii); newObjs.add(teleostei); newObjs.add(acanthopterygii); } newObjs.add(perciformes); newObjs.add(percoidei); newObjs.add(percidae); newObjs.add(ammocrypta); // 28 - 40 String[] speciesNames = { "asprella", "beanii", "bifascia", "clara", "meridiana", "pellucida", "vivax" }; String[] commonNames = { "crystal darter", "naked sand darter", "Florida sand darter", "western sand darter", "southern sand darter", "eastern sand darter", "scaly sand darter" }; List<Object> kids = createTaxonChildren(taxonTreeDef, ammocrypta, speciesNames, commonNames, TaxonTreeDef.SPECIES); // 41 - 47 newObjs.addAll(kids); Taxon carangidae = createTaxon(taxonTreeDef, percoidei, "Carangidae", TaxonTreeDef.FAMILY); Taxon caranx = createTaxon(taxonTreeDef, carangidae, "Caranx", TaxonTreeDef.GENUS); // 48 newObjs.add(carangidae); // 49 newObjs.add(caranx); String[] speciesNames2 = { "bartholomaei", "caballus", "caninus", "crysos", "dentex", "hippos", "latus" }; String[] commonNames2 = { "yellow jack", "green jack", "Pacific crevalle jack", "blue runner", "white trevally", "crevalle jack", "horse-eye jack" }; kids = createTaxonChildren(taxonTreeDef, caranx, speciesNames2, commonNames2, TaxonTreeDef.SPECIES); // 50 - 56 newObjs.addAll(kids); int baseInx = 53 - (doShallow ? 30 : 0); // setup a couple of synonyms (and supporting nodes) Taxon fusus = createTaxon(taxonTreeDef, caranx, "fusus", TaxonTreeDef.SPECIES); fusus.setCommonName("Blue runner"); Taxon crysos = (Taxon) newObjs.get(baseInx); fusus.setAcceptedTaxon(crysos); fusus.setIsAccepted(false); Taxon carangus = createTaxon(taxonTreeDef, caranx, "carangus", TaxonTreeDef.SPECIES); carangus.setCommonName("Blacktailed trevally"); Taxon hippos = (Taxon) newObjs.get(baseInx + 2); carangus.setAcceptedTaxon(hippos); carangus.setIsAccepted(false); Taxon etheostoma = createTaxon(taxonTreeDef, percidae, "Etheostoma", TaxonTreeDef.GENUS); etheostoma.setCommonName("smoothbelly darters"); Taxon meridianum = createTaxon(taxonTreeDef, etheostoma, "meridianum", TaxonTreeDef.SPECIES); meridianum.setCommonName("southern sand darter"); Taxon merdiana = (Taxon) newObjs.get(baseInx - 8); merdiana.setAcceptedTaxon(meridianum); merdiana.setIsAccepted(false); Taxon pellucidum = createTaxon(taxonTreeDef, etheostoma, "pellucidum", TaxonTreeDef.SPECIES); pellucidum.setCommonName("eastern sand darter"); Taxon pellucida = (Taxon) newObjs.get(baseInx - 7); pellucidum.setAcceptedTaxon(pellucida); pellucidum.setIsAccepted(false); Taxon ethVivax = createTaxon(taxonTreeDef, etheostoma, "vivax", TaxonTreeDef.SPECIES); ethVivax.setCommonName("scaly sand darter"); Taxon vivax = (Taxon) newObjs.get(baseInx - 6); ethVivax.setAcceptedTaxon(vivax); ethVivax.setIsAccepted(false); Taxon beani = createTaxon(taxonTreeDef, ammocrypta, "beani", TaxonTreeDef.SPECIES); beani.setCommonName("naked sand darter"); Taxon beanii = (Taxon) newObjs.get(baseInx - 11); beani.setAcceptedTaxon(beanii); beani.setIsAccepted(false); Taxon crystallaria = createTaxon(taxonTreeDef, percidae, "Crystallaria", TaxonTreeDef.GENUS); crystallaria.setCommonName("crystal darters"); Taxon crysAsprella = createTaxon(taxonTreeDef, crystallaria, "asprella", TaxonTreeDef.SPECIES); crysAsprella.setCommonName("crystal darter"); Taxon asprella = (Taxon) newObjs.get(baseInx - 12); asprella.setAcceptedTaxon(crysAsprella); asprella.setIsAccepted(false); newObjs.add(fusus); newObjs.add(carangus); newObjs.add(etheostoma); newObjs.add(meridianum); newObjs.add(pellucidum); newObjs.add(ethVivax); newObjs.add(beani); newObjs.add(crystallaria); newObjs.add(crysAsprella); // 57 - 65 TreeHelper.fixFullnameForNodeAndDescendants(life); life.setNodeNumber(1); fixNodeNumbersFromRoot(life); return newObjs; } /** * @param taxonTreeDef * @return */ public static List<Object> createSimpleBotanyTaxonTree(final TaxonTreeDef taxonTreeDef) { log.info("createSimpleBotanyTaxonTree " + taxonTreeDef.getName()); Vector<Object> newObjs = new Vector<Object>(); Set<TaxonTreeDefItem> newItems; Object[][] taxonItems = { { TaxonTreeDef.TAXONOMY_ROOT, "Taxonomy Root", true, false }, { TaxonTreeDef.KINGDOM, "Kingdom", true, false }, { TaxonTreeDef.PHYLUM, "Division", false, false }, { TaxonTreeDef.CLASS, "Class", false, false }, { TaxonTreeDef.ORDER, "Order", false, false }, { TaxonTreeDef.FAMILY, "Family", false, false }, { TaxonTreeDef.GENUS, "Genus", true, true }, { TaxonTreeDef.SPECIES, "Species", false, true }, { TaxonTreeDef.VARIETY, "Variety", false, true }, }; newItems = TreeFactory.addStandardTaxonDefItems(taxonTreeDef, taxonItems); newObjs.addAll(newItems); // 0 - 27 for (TaxonTreeDefItem item : newItems) { if (item.getRankId().equals(TaxonTreeDef.GENUS)) { item.setFormatToken("%G"); } else if (item.getRankId().equals(TaxonTreeDef.SPECIES)) { item.setFormatToken("%S"); } else if (item.getRankId().equals(TaxonTreeDef.SUBSPECIES)) { item.setFormatToken("%SS"); } } Taxon life = createTaxon(taxonTreeDef, null, "Life", TaxonTreeDef.TAXONOMY_ROOT); Taxon Plantae = createTaxon(taxonTreeDef, life, "Plantae", TaxonTreeDef.KINGDOM); Taxon Magnoliophyta = createTaxon(taxonTreeDef, Plantae, "Magnoliophyta", TaxonTreeDef.PHYLUM); Taxon Magnoliopsida = createTaxon(taxonTreeDef, Magnoliophyta, "Magnoliopsida", TaxonTreeDef.CLASS); Taxon Sapindales = createTaxon(taxonTreeDef, Magnoliopsida, "Sapindales", TaxonTreeDef.ORDER); Taxon Sapindaceae = createTaxon(taxonTreeDef, Sapindales, "Sapindaceae", TaxonTreeDef.FAMILY); Taxon Acer = createTaxon(taxonTreeDef, Sapindaceae, "Acer", TaxonTreeDef.GENUS); newObjs.add(life); newObjs.add(Plantae); newObjs.add(Magnoliophyta); newObjs.add(Magnoliopsida); newObjs.add(Sapindales); newObjs.add(Sapindaceae); newObjs.add(Acer); String[] speciesNames = { "saccharum", "platanoides", "circinatum", "palmatum" }; String[] commonNames = { "Sugar Maple", "Norway Maple", "Vine Maple", "apanese Maple" }; List<Object> kids = createTaxonChildren(taxonTreeDef, Acer, speciesNames, commonNames, TaxonTreeDef.SPECIES); newObjs.addAll(kids); Taxon Aesculus = createTaxon(taxonTreeDef, Sapindaceae, "Aesculus", TaxonTreeDef.GENUS); newObjs.add(Aesculus); String[] speciesNames2 = { "arguta", "californica", "chinensis", "glabra" }; String[] commonNames2 = { "Texas Buckeye", "California Buckeye", "Chinese Horse-chestnut", "Ohio Buckeye" }; kids = createTaxonChildren(taxonTreeDef, Aesculus, speciesNames2, commonNames2, TaxonTreeDef.SPECIES); newObjs.addAll(kids); TreeHelper.fixFullnameForNodeAndDescendants(life); life.setNodeNumber(1); fixNodeNumbersFromRoot(life); return newObjs; } public static Journal createJournalsAndReferenceWork() { Journal journal = createJournal("Fish times", "FT"); @SuppressWarnings("unused") ReferenceWork rw = createReferenceWork((byte) 1, "Why Do Fish Have Scales?", "Fish Publishing", "NYC", "12/12/1900", "Vol 1.", "Pages 234-236", null, "112974-4532", true, journal); rw = createReferenceWork((byte) 1, "Can Fish think?", "Fish Publishing", "Chicago", "12/12/1901", "Vol 2", "Pages 1-10", null, "64543-4532", true, journal); rw = createReferenceWork((byte) 1, "The Taxon Def of Blubber Fish?", "Icthy Publishing", "SFO", "12/12/1960", "Vol 200", "Pages 10-100", null, "856433-4532", false, journal); return journal; } @SuppressWarnings("unchecked") public static int fixNodeNumbersFromRoot(Treeable<?, ?, ?> root) { int nextNodeNumber = root.getNodeNumber(); for (Treeable<?, ?, ?> child : (Set<Treeable<?, ?, ?>>) root.getChildren()) { child.setNodeNumber(++nextNodeNumber); nextNodeNumber = fixNodeNumbersFromRoot(child); } root.setHighestChildNodeNumber(nextNodeNumber); return nextNodeNumber; } public void persist(Object o) { if (session != null) { try { session.saveOrUpdate(o); } catch (Exception ex) { showError(ex.toString()); ex.printStackTrace(); throw new RuntimeException(ex); } } } public void persist(Object... objects) { for (Object o : objects) { persist(o); } } public void persist(List<?> oList) { if (oList != null) { int max = frame != null ? frame.getOrigMax() : 0; if (frame != null) frame.setProcess(0, oList.size()); int cnt = 0; for (Object o : oList) { if (frame != null) frame.setProcess(++cnt); //System.out.println("* " + cnt + " " + o.getClass().getSimpleName()); persist(o); } if (frame != null) { frame.setProcess(oList.size()); frame.setOrigMax(max); } } } public void startTx() { trans = session.beginTransaction(); } public void commitTx() { try { if (trans != null) { trans.commit(); } else { throw new RuntimeException("Transaction is null"); } trans = null; } catch (Exception ex) { rollbackTx(); trans = null; showError(ex.toString()); ex.printStackTrace(); throw new RuntimeException(ex); } } public void rollbackTx() { if (trans != null) { trans.rollback(); } else { throw new RuntimeException("Transaction is null"); } } public Object getFirstObjectByClass(List<Object> objects, Class<?> clazz) { Object ret = null; for (Object o : objects) { if (o.getClass() == clazz) { ret = o; break; } } return ret; } @SuppressWarnings("unchecked") public <T> T getObjectByClass(List<?> objects, Class<T> clazz, int index) { T ret = null; int i = -1; for (Object o : objects) { if (o.getClass() == clazz) { ++i; } if (i == index) { ret = (T) o; break; } } return ret; } /** * Returns a list of database object by class from the arg list. * @param objects the list of object (source) * @param clazz the class to use to filter * @return the new list of objects */ protected List<?> getObjectsByClass(final List<Object> objects, Class<?> clazz) { Vector<Object> rightClass = new Vector<Object>(); for (Object o : objects) { if (o.getClass() == clazz) { rightClass.add(o); } } return rightClass; } public ProgressFrame createProgressFrame(final String title) { if (frame == null) { frame = new ProgressFrame(title, "SpecifyLargeIcon"); frame.pack(); } return frame; } /** * Creates the dialog to find out what database and what database driver to use. */ public void buildSetup(final String[] args) { boolean doEmptyBuild = false; setEmbeddedDBPath(getDefaultEmbeddedDBPath()); // on the local machine if (args != null && args.length > 0) { for (String arg : args) { String[] pair = StringUtils.split(arg, "="); if (pair.length == 2) { String option = pair[0]; String value = pair[1]; if (option.equals("-Dappdir")) { setDefaultWorkingPath(value); } else if (option.equals("-Dappdatadir")) { setBaseAppDataDir(value); } else if (option.equals("-Dembeddeddbdir")) { setEmbeddedDBPath(value); } else if (option.equals("-Dmobile")) { setEmbeddedDBPath(getDefaultMobileEmbeddedDBPath()); } } } } if (StringUtils.isEmpty(getAppName())) { setAppName("Specify"); } if (hideFrame) { System.out.println("Embedded DB Path [ " + getEmbeddedDBPath() + " ]"); } // Then set this IconManager.setApplicationClass(Specify.class); IconManager.aliasImages("SpBuilder", // Source //$NON-NLS-1$ "AppIcon"); // Dest //$NON-NLS-1$ createProgressFrame("Building Specify Database"); System.setProperty(AppPreferences.factoryName, "edu.ku.brc.specify.config.AppPrefsDBIOIImpl"); // Needed by AppReferences System.setProperty("edu.ku.brc.dbsupport.DataProvider", "edu.ku.brc.specify.dbsupport.HibernateDataProvider"); // Needed By the Form System and any Data Get/Set System.setProperty(SecurityMgr.factoryName, "edu.ku.brc.af.auth.specify.SpecifySecurityMgr"); // Needed for Tree Field Names //$NON-NLS-1$ AppPrefsCache.setUseLocalOnly(true); AppPreferences localPrefs = AppPreferences.getLocalPrefs(); localPrefs.setDirPath(getAppDataDir()); localPrefs.load(); backstopPrefs = getInitializePrefs(null); String driverName = backstopPrefs.getProperty("initializer.drivername", "MySQL"); String databaseName = backstopPrefs.getProperty("initializer.databasename", "testfish"); Properties props = getInitializePrefs(databaseName); if (props.size() > 0) { initPrefs = props; } else { initPrefs = backstopPrefs; } Pair<String, String> dbUser = new Pair<String, String>( initPrefs.getProperty("initializer.dbUserName", "Specify"), initPrefs.getProperty("initializer.dbPassword", "Specify")); Pair<String, String> saUser = new Pair<String, String>( initPrefs.getProperty("initializer.saUserName", "Master"), initPrefs.getProperty("initializer.saPassword", "Master")); Pair<String, String> cmUser = new Pair<String, String>( initPrefs.getProperty("useragent.username", "testuser"), initPrefs.getProperty("useragent.password", "testuser")); if (doEmptyBuild) { /*ensureDerbyDirectory(driverName); DisciplineType disciplineType = DisciplineType.getDiscipline("fish"); DatabaseDriverInfo driverInfo = DatabaseDriverInfo.getDriver(driverName); DBConfigInfo config = new DBConfigInfo(driverInfo, "localhost", "WorkBench", "guest", "guest", "guest", "guest", "guest@ku.edu", disciplineType, "Institution", "Division"); buildEmptyDatabase(config); */ } else { setupDlg = new SetUpBuildDlg(databaseName, driverName, dbUser, saUser, cmUser, this); UIHelper.centerAndShow(setupDlg); } } /** * Starts the Build on a swing worker thread. * * @throws SQLException * @throws IOException */ protected void startBuild(final String dbName, final String driverName, final Pair<String, String> dbUser, final Pair<String, String> saUser, final Pair<String, String> cmUser, final List<CollectionChoice> selectedChoicesArg) { AppContextMgr.getInstance().setHasContext(true); // Fake that there is a Context this.selectedChoices = selectedChoicesArg; final SwingWorker worker = new SwingWorker() { @Override public Object construct() { try { build(dbName, driverName, dbUser, saUser, cmUser); } catch (Exception ex) { ex.printStackTrace(); } return null; } //Runs on the event-dispatching thread. @Override public void finished() { // do nothing // for future reference: // for that matter, there was no real reason to use SwingWorker for this since // we're not doing anything on the Swing thread in this method // we could have just used a regular Thread object // In fact, we're doing stuff in the construct method that should happen on the Swing // thread. The construct() method IS NOT run on the Swing thread. frame.setVisible(false); frame.dispose(); DBConnection.shutdown(); System.exit(0); // I didn't used to have to do this. } }; worker.start(); } /** * @param driverInfo * @param saUserName * @param saPassword * @return */ public static boolean createSpecifySAUser(final String hostName, final String itUsername, final String itPassword, final String saUsername, final String saPassword, final String databaseName) { DBMSUserMgr mgr = DBMSUserMgr.getInstance(); mgr.setHostName(hostName); boolean isOK = false; if (mgr.connectToDBMS(itUsername, itPassword, hostName)) { if (!mgr.doesUserExists(saUsername)) { isOK = mgr.createUser(saUsername, saPassword, databaseName, DBMSUserMgr.PERM_ALL_BASIC); } else { isOK = true; } } else { // No Connect Error isOK = false; } mgr.close(); return isOK; } /** * Drops, Creates and Builds the Database. * * @throws SQLException * @throws IOException */ public boolean buildEmptyDatabase(final Properties props, final boolean doFromWizard) { createProgressFrame("Building Specify Database"); final String dbName = props.getProperty("dbName"); frame.adjustProgressFrame(); frame.setTitle("Building Specify Database"); if (!hideFrame) { UIHelper.centerWindow(frame); frame.setVisible(true); ImageIcon imgIcon = IconManager.getIcon("AppIcon", IconManager.IconSize.Std16); if (imgIcon != null) { frame.setIconImage(imgIcon.getImage()); } } else { System.out.println("Building Specify Database Username[" + props.getProperty("dbUserName") + "]"); } frame.setProcessPercent(true); frame.setOverall(0, 4); frame.getCloseBtn().setVisible(false); steps = 0; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Creating Database Schema for " + dbName); frame.setOverall(steps++); } }); DatabaseDriverInfo driverInfo = (DatabaseDriverInfo) props.get("driver"); try { if (hideFrame) System.out.println("Creating schema"); String itUsername = props.getProperty("dbUserName"); String itPassword = props.getProperty("dbPassword"); boolean doBuild = true; if (doBuild) { SpecifySchemaGenerator.generateSchema(driverInfo, props.getProperty("hostName"), dbName, itUsername, itPassword); } SwingUtilities.invokeLater(new Runnable() { public void run() { frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Logging into " + dbName + "...."); frame.setOverall(steps++); } }); String connStr = driverInfo.getConnectionStr(DatabaseDriverInfo.ConnectionType.Create, props.getProperty("hostName"), dbName); if (connStr == null) { connStr = driverInfo.getConnectionStr(DatabaseDriverInfo.ConnectionType.Open, props.getProperty("hostName"), dbName); } if (!UIHelper.tryLogin(driverInfo.getDriverClassName(), driverInfo.getDialectClassName(), dbName, connStr, itUsername, itPassword)) { if (hideFrame) System.out.println("Login Failed!"); return false; } String saUserName = props.getProperty("saUserName"); // Master Username String saPassword = props.getProperty("saPassword"); // Master Password createSpecifySAUser(props.getProperty("hostName"), itUsername, itPassword, saUserName, saPassword, dbName); if (!UIHelper.tryLogin(driverInfo.getDriverClassName(), driverInfo.getDialectClassName(), dbName, connStr, saUserName, saPassword)) { if (hideFrame) System.out.println("Login Failed!"); return false; } setSession(HibernateUtil.getCurrentSession()); //DataBuilder.setSession(session); SwingUtilities.invokeLater(new Runnable() { public void run() { frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Creating database " + dbName + "...."); frame.setOverall(steps++); } }); Thumbnailer thumb = Thumbnailer.getInstance(); File thumbFile = XMLHelper.getConfigDir("thumbnail_generators.xml"); thumb.registerThumbnailers(thumbFile); thumb.setQuality(0.5f); thumb.setMaxSize(128, 128); File attLoc = getAppDataSubDir("AttachmentStorage", true); FileUtils.cleanDirectory(attLoc); AttachmentManagerIface attachMgr = new FileStoreAttachmentManager(attLoc); AttachmentUtils.setAttachmentManager(attachMgr); AttachmentUtils.setThumbnailer(thumb); if (hideFrame) System.out.println("Creating Empty Database"); createEmptyInstitution(props, true, true, doFromWizard, getTreeDirForClass(props, StorageTreeDef.class)); SwingUtilities.invokeLater(new Runnable() { public void run() { frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Saving data into " + dbName + "...."); frame.setOverall(steps++); } }); if (hideFrame) System.out.println("Persisting Data..."); HibernateUtil.getCurrentSession().close(); if (hideFrame) System.out.println("Done."); frame.setVisible(false); frame.dispose(); SpecifyDeleteHelper.showTableCounts("EmptyDB.txt", true); return true; } catch (Exception ex) { throw new RuntimeException(ex); } } /** * @param dataObjects */ protected void persistDataObjects(final List<?> dataObjects) { log.info("Persisting in-memory objects to DB"); frame.setProcess(0); frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Getting Session..."); frame.setOverall(steps++); SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setDesc("Saving data..."); frame.setOverall(steps++); } }); startTx(); persist(dataObjects); commitTx(); } /** * Drops, Creates and Builds the Database. * * @throws SQLException */ protected void build(final String dbName, final String driverName, final Pair<String, String> dbUser, final Pair<String, String> saUser, final Pair<String, String> cmUser) throws SQLException { frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); frame.pack(); Dimension size = frame.getSize(); size.width = Math.max(size.width, 500); frame.setSize(size); frame.setTitle("Building Specify Database"); if (!hideFrame) { UIHelper.centerWindow(frame); frame.setVisible(true); ImageIcon imgIcon = IconManager.getIcon("AppIcon", IconManager.IconSize.Std16); if (imgIcon != null) { frame.setIconImage(imgIcon.getImage()); } } frame.setProcessPercent(true); frame.setOverall(0, 7 + this.selectedChoices.size()); frame.getCloseBtn().setVisible(false); String databaseHost = initPrefs.getProperty("initializer.host", "localhost"); frame.setTitle("Building -> Database: " + dbName + " Driver: " + driverName + " User: " + cmUser.first); steps = 0; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.getProcessProgress().setIndeterminate(true); frame.getProcessProgress().setString(""); frame.setDesc("Creating Database Schema for " + dbName); frame.setOverall(steps++); } }); DatabaseDriverInfo driverInfo = DatabaseDriverInfo.getDriver(driverName); if (driverInfo == null) { String msg = "Couldn't find driver by name [" + driverInfo + "] in driver list."; showError(msg); throw new RuntimeException(msg); } String newConnStr = driverInfo.getConnectionStr(DatabaseDriverInfo.ConnectionType.Open, databaseHost, dbName, saUser.first, saUser.second, driverInfo.getName()); DBConnection.checkForEmbeddedDir(newConnStr); if (DBConnection.isEmbedded(newConnStr)) { try { Class.forName(driverInfo.getDriverClassName()); DBConnection testDB = DBConnection.createInstance(driverInfo.getDriverClassName(), driverInfo.getDialectClassName(), dbName, newConnStr, saUser.first, saUser.second); testDB.getConnection(); } catch (Exception ex) { ex.printStackTrace(); } DBConnection.getInstance().setDatabaseName(null); } SpecifySchemaGenerator.generateSchema(driverInfo, databaseHost, dbName, dbUser.first, dbUser.second); SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setDesc("Logging in..."); frame.setOverall(steps++); } }); if (UIHelper.tryLogin(driverInfo.getDriverClassName(), driverInfo.getDialectClassName(), dbName, driverInfo.getConnectionStr(DatabaseDriverInfo.ConnectionType.Open, databaseHost, dbName), saUser.first, saUser.second)) { createSpecifySAUser(databaseHost, dbUser.first, dbUser.second, saUser.first, saUser.second, dbName); boolean single = true; if (single) { SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setDesc("Creating data..."); frame.setOverall(steps++); } }); try { Thumbnailer thumb = Thumbnailer.getInstance(); File thumbFile = XMLHelper.getConfigDir("thumbnail_generators.xml"); thumb.registerThumbnailers(thumbFile); thumb.setQuality(0.5f); thumb.setMaxSize(128, 128); frame.setDesc("Cleaning Attachment Cache..."); frame.setOverall(steps++); File attLoc = getAppDataSubDir("AttachmentStorage", true); try { FileUtils.cleanDirectory(attLoc); } catch (IOException e) { String msg = "failed to connect to directory location to delete directory: " + attLoc; log.warn(msg); showError(msg); } AttachmentManagerIface attachMgr = new FileStoreAttachmentManager(attLoc); AttachmentUtils.setAttachmentManager(attachMgr); AttachmentUtils.setThumbnailer(thumb); // save it all to the DB setSession(HibernateUtil.getCurrentSession()); //DataBuilder.setSession(session); createDisciplines(cmUser.first, cmUser.second); attachMgr.cleanup(); frame.setDesc("Done Saving data..."); frame.setOverall(steps++); frame.setDesc("Copying Preferences..."); frame.setOverall(steps++); AppPreferences remoteProps = AppPreferences.getRemote(); for (Object key : initPrefs.keySet()) { String keyStr = (String) key; if (!keyStr.startsWith("initializer.") && !keyStr.startsWith("useragent.")) { remoteProps.put(keyStr, (String) initPrefs.get(key)); } } AppPreferences.getRemote().flush(); frame.setDesc("Build Completed."); frame.setOverall(steps++); assignPermssions(); log.info("Done"); } catch (Exception e) { e.printStackTrace(); try { rollbackTx(); log.error("Failed to persist DB objects", e); showError("Failed to persist DB objects"); return; } catch (Exception e2) { log.error( "Failed to persist DB objects. Rollback failed. DB may be in inconsistent state.", e2); showError("Failed to persist DB objects. Rollback failed."); return; } } } } else { log.error("Login failed"); showError("Login failed"); return; } System.out.println("All done"); if (frame != null) { frame.processDone(); } // Set the Schema Size into Locale Prefs String schemaKey = "schemaSize"; int schemaFileSize = 0; File schemaFile = XMLHelper.getConfigDir("specify_datamodel.xml"); if (schemaFile != null) { schemaFileSize = (int) schemaFile.length(); AppPreferences.getLocalPrefs().putInt(schemaKey, schemaFileSize); } JOptionPane.showMessageDialog(getTopWindow(), "The build completed successfully.", "Complete", JOptionPane.INFORMATION_MESSAGE); } public static void assignPermssions() { /* setSession(HibernateUtil.getCurrentSession()); SpecifyUser u = AppContextMgr.getInstance().getClassObject(SpecifyUser.class); List<?> users = HibernateUtil.getCurrentSession().createQuery("SELECT u FROM SpecifyUser u WHERE t.name = 'Ammocrypta'").list(); SpSecurtyPermissionMgr.setupTestTreePermissions(u);*/ } public static void turnOnHibernateLogging(Level level) { for (Enumeration<?> e = LogManager.getCurrentLoggers(); e.hasMoreElements();) { Logger logger = (Logger) e.nextElement(); if (StringUtils.contains(logger.getName(), "hibernate")) { logger.setLevel(level); } } } /** * Returns the Properties by database name. * @param databaseName the database * @return the properties */ public static Properties getInitializePrefs(final String databaseName) { Properties properties = new Properties(); try { String base = getDefaultWorkingPath(); File initFile = new File( base + File.separator + (databaseName != null ? (databaseName + "_") : "") + "init.prefs"); if (initFile.exists()) { properties.load(new FileInputStream(initFile)); return properties; } log.debug("Couldn't find Init Prefs [" + initFile.getAbsolutePath() + "]"); } catch (Exception ex) { edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BuildSampleDatabase.class, ex); System.err.println(ex); // XXX Error Dialog } return new Properties(); } /** * @param tableName * @param memoryItemArg * @param newItem * @param dispItem * @param hideGenericFields * @param isFish */ public static void loadLocalization(final String tableName, final SpLocaleContainerItem memoryItemArg, final SpLocaleContainerItem newItem, final SpLocaleContainerItem dispItem, final boolean hideGenericFields, final boolean isFish) { SpLocaleContainerItem memoryItem = dispItem != null ? dispItem : memoryItemArg; String itemName = memoryItem.getName(); newItem.setName(itemName); newItem.setType(memoryItem.getType()); newItem.setFormat(memoryItem.getFormat()); newItem.setIsUIFormatter(memoryItem.getIsUIFormatter()); newItem.setPickListName(memoryItem.getPickListName()); newItem.setWebLinkName(memoryItem.getWebLinkName()); newItem.setIsHidden(memoryItem.getIsHidden()); newItem.setIsRequired(memoryItem.getIsRequired()); mergeOrCreateStr(memoryItem, newItem, isFish); if (newItem.getId() == null) { setParentForItemStrs(newItem.getNames(), newItem, true); setParentForItemStrs(newItem.getDescs(), newItem, false); } } /** * @param strItems * @param item * @param isForNames * @param updateType */ protected static void setParentForItemStrs(final Set<SpLocaleItemStr> strItems, final SpLocaleContainerItem item, final boolean isForNames) { for (SpLocaleItemStr str : strItems) { if (isForNames) { str.setItemName(item); } else { str.setItemDesc(item); } } } /** * @param hash * @param baseName * @param strItems */ protected static void setParentForContainerStrs(final Set<SpLocaleItemStr> strItems, final SpLocaleContainer container, final boolean isForNames) { for (SpLocaleItemStr str : strItems) { if (isForNames) { str.setContainerName(container); } else { str.setContainerDesc(container); } } } /** * @param hash * @param baseName * @param strItems */ protected static HashMap<String, SpLocaleItemStr> makeHash(final Set<SpLocaleItemStr> strItems) { HashMap<String, SpLocaleItemStr> strHash = new HashMap<String, SpLocaleItemStr>(); for (SpLocaleItemStr nm : strItems) { strHash.put(nm.getLanguage(), nm); } return strHash; } /** * @param memBase * @param dbBase * @param session */ protected static void mergeOrCreateStr(final SpLocaleBase memBase, final SpLocaleBase dbBase, final boolean isFish) { HashMap<String, SpLocaleItemStr> namesHash = null; HashMap<String, SpLocaleItemStr> descsHash = null; if (dbBase != null && dbBase.getId() != null) { namesHash = makeHash(dbBase.getNamesSet()); descsHash = makeHash(dbBase.getDescsSet()); } for (SpLocaleItemStr nm : memBase.getNamesSet()) { String lang = nm.getLanguage(); SpLocaleItemStr str = null; if (namesHash != null) { str = namesHash.get(lang); } if (str == null) { str = new SpLocaleItemStr(); str.initialize(); } String title = nm.getText(); if (!isFish && title.equals("Collecting Event")) { title = "Collecting Information"; } else if (memBase.getName().equals("taxononly") /*&& title.equals("Taxon")*/) { title = UIRegistry.getResourceString("WB_TAXONIMPORT_ONLY"); } str.setText(title); if (debugOn) System.out.println(nm.getText()); str.setLanguage(nm.getLanguage()); str.setCountry(nm.getCountry()); str.setVariant(nm.getVariant()); if (dbBase != null && str.getId() == null) { dbBase.getNamesSet().add(str); if (dbBase instanceof SpLocaleContainer) { str.setContainerName((SpLocaleContainer) dbBase); } else { str.setItemName((SpLocaleContainerItem) dbBase); } } } for (SpLocaleItemStr desc : memBase.getDescsSet()) { String lang = desc.getLanguage(); SpLocaleItemStr str = null; if (descsHash != null) { str = descsHash.get(lang); } if (str == null) { str = new SpLocaleItemStr(); str.initialize(); } str.setText(desc.getText()); str.setLanguage(desc.getLanguage()); str.setCountry(desc.getCountry()); str.setVariant(desc.getVariant()); if (dbBase != null && str.getId() == null) { dbBase.getDescsSet().add(str); if (dbBase instanceof SpLocaleContainer) { str.setContainerDesc((SpLocaleContainer) dbBase); } else { str.setItemDesc((SpLocaleContainerItem) dbBase); } } } } /** * @param memoryContainer * @param newContainer */ private static void loadLocalization(final Integer disciplineId, final String disciplineName, final SpLocaleContainer memoryContainer, final SpLocaleContainer newContainer, final boolean hideGenericFields, final String catFmtName, final String accFmtName, final UpdateType updateType, final DataProviderSessionIFace session) { boolean isColObj = memoryContainer.getName().equals("collectionobject"); boolean isAccession = memoryContainer.getName().equals("accession"); boolean isFish = disciplineName.equals("fish"); boolean isImport = updateType == UpdateType.eImport; boolean isMerge = updateType == UpdateType.eMerge; boolean isLocalize = updateType == UpdateType.eLocalize; boolean doDBUpdate = isLocalize || isImport; if (newContainer.getId() == null) { newContainer.setName(memoryContainer.getName()); newContainer.setType(memoryContainer.getType()); newContainer.setFormat(newContainer.getFormat()); newContainer.setIsUIFormatter(newContainer.getIsUIFormatter()); newContainer.setPickListName(newContainer.getPickListName()); newContainer.setWebLinkName(newContainer.getWebLinkName()); newContainer.setIsHidden(newContainer.getIsHidden()); //debugOn = false; if (session != null) { try { session.saveOrUpdate(newContainer); } catch (Exception ex) { ex.printStackTrace(); } } } mergeOrCreateStr(memoryContainer, newContainer, isFish); if (newContainer.getId() == null) { setParentForContainerStrs(newContainer.getNames(), newContainer, true); setParentForContainerStrs(newContainer.getDescs(), newContainer, false); } if (session != null) { try { session.saveOrUpdate(newContainer); } catch (Exception ex) { ex.printStackTrace(); } } Hashtable<String, SpLocaleContainerItem> dispItemHash = new Hashtable<String, SpLocaleContainerItem>(); if (SchemaI18NService.getCurrentLocale().getLanguage().equals("en")) { if (memoryContainer instanceof DisciplineBasedContainer) { DisciplineBasedContainer dbc = (DisciplineBasedContainer) memoryContainer; Set<SpLocaleContainerItem> itemsSet = dbc.getDisciplineItems(disciplineName); for (SpLocaleContainerItem item : itemsSet) { dispItemHash.put(item.getName(), item); } } } for (SpLocaleContainerItem item : memoryContainer.getItems()) { //if (isColObj) System.err.println(item.getName()); String itemSQL = null; boolean okToCreate = true; if (isImport || isMerge || isLocalize) { String sql = String.format( " FROM splocalecontainer c INNER JOIN splocalecontaineritem ci ON c.SpLocaleContainerID = ci.SpLocaleContainerID " + "WHERE ci.Name = '%s' AND c.DisciplineID = %d AND c.SpLocaleContainerID = %d", item.getName(), disciplineId, newContainer.getId()); String fullSQL = "SELECT COUNT(*)" + sql; //if (isColObj) log.debug(fullSQL); int cnt = BasicSQLUtils.getCountAsInt(fullSQL); if (cnt > 0) { okToCreate = false; if (cnt == 1) { itemSQL = "SELECT ci.SpLocaleContainerItemID" + sql; //if (isColObj) log.debug(itemSQL); } } } if (okToCreate) { //log.debug("Adding Item: "+item.getName()); SpLocaleContainerItem newItem = new SpLocaleContainerItem(); newItem.initialize(); newContainer.getItems().add(newItem); newItem.setContainer(newContainer); SpLocaleContainerItem dispItem = dispItemHash.get(item.getName()); loadLocalization(memoryContainer.getName(), item, newItem, dispItem, hideGenericFields, isFish); if (!isLocalize) { if (isColObj && catFmtName != null && item.getName().equals("catalogNumber")) { newItem.setFormat(catFmtName); newItem.setIsUIFormatter(true); } if (isAccession && accFmtName != null && item.getName().equals("accessionNumber")) { newItem.setFormat(accFmtName); newItem.setIsUIFormatter(true); } } if (session != null) { try { session.saveOrUpdate(newItem); } catch (Exception ex) { ex.printStackTrace(); } } } else if (itemSQL != null && !isMerge) { Integer id = BasicSQLUtils.getCount(itemSQL); if (id != null) { SpLocaleContainerItem dbItem = session.get(SpLocaleContainerItem.class, id); if (!isLocalize) { //dbItem.setType(item.getType()); dbItem.setFormat(item.getFormat()); dbItem.setIsUIFormatter(item.getIsUIFormatter()); dbItem.setPickListName(item.getPickListName()); dbItem.setWebLinkName(item.getWebLinkName()); dbItem.setIsHidden(item.getIsHidden()); dbItem.setIsRequired(item.getIsRequired()); } try { if (!doDBUpdate) session.beginTransaction(); setItemStrs(dbItem, true, dbItem.getNames(), item.getNames(), session); setItemStrs(dbItem, false, dbItem.getDescs(), item.getDescs(), session); session.saveOrUpdate(dbItem); if (!doDBUpdate) session.commit(); } catch (Exception e) { if (!isImport) session.rollback(); e.printStackTrace(); } } } } } /** * @param item * @return */ private static String mkKey(final SpLocaleItemStr item) { return String.format("%s %s %s", item.getLanguage(), item.getCountry() != null ? item.getCountry() : "", item.getVariant() != null ? item.getVariant() : ""); } /** * @param dbSet * @param memSet * @param session * @throws Exception */ private static void setItemStrs(final SpLocaleContainerItem dbItem, final boolean isName, final Set<SpLocaleItemStr> dbSet, final Set<SpLocaleItemStr> memSet, final DataProviderSessionIFace session) throws Exception { HashMap<String, SpLocaleItemStr> hash = new HashMap<String, SpLocaleItemStr>(); for (SpLocaleItemStr dbItemStr : dbSet) { hash.put(mkKey(dbItemStr), dbItemStr); } for (SpLocaleItemStr memItem : memSet) { SpLocaleItemStr dbItmStr = hash.get(mkKey(memItem)); if (dbItmStr == null) { dbItmStr = new SpLocaleItemStr(); dbItmStr.initialize(); dbSet.add(dbItmStr); if (isName) { dbItmStr.setItemName(dbItem); } else { dbItmStr.setItemDesc(dbItem); } } String memText = memItem.getText(); String dbText = dbItmStr.getText(); boolean doUpdate = dbItmStr.getId() == null || (memText == null && dbText != null) || (memText != null && dbText == null) || (memText != null && dbText != null && !memText.equals(dbText)); String txt = doUpdate ? memText : dbText; if (txt == null) { txt = ""; } dbItmStr.setText(txt); dbItmStr.setLanguage(memItem.getLanguage()); dbItmStr.setCountry(memItem.getCountry()); dbItmStr.setVariant(memItem.getVariant()); if (doUpdate) session.saveOrUpdate(dbItmStr); } } /** * @param discipline * @param schemaType * @param tableMgr * @param catFmtName * @param accFmtName */ public void loadSchemaLocalization(final Discipline discipline, final Byte schemaType, final DBTableIdMgr tableMgr, final String catFmtName, final String accFmtName) { loadSchemaLocalization(discipline, schemaType, tableMgr, catFmtName, accFmtName, UpdateType.eBuildNew, null, null, null); } /** * @param discipline * @param schemaType * @param tableMgr * @param catFmtName * @param accFmtName * @param isDoingUpdate * @param externalFile * @param sessionArg */ public void loadSchemaLocalization(final Discipline discipline, final Byte schemaType, final DBTableIdMgr tableMgr, final String catFmtName, final String accFmtName, final UpdateType updateType, final DataProviderSessionIFace sessionArg) { loadSchemaLocalization(discipline, schemaType, tableMgr, catFmtName, accFmtName, updateType, null, null, sessionArg); } /** * @param discipline * @param schemaType * @param tableMgr * @param catFmtName * @param accFmtName * @param isDoingUpdate * @param externalFile * @param sessionArg */ public boolean loadSchemaLocalization(final Discipline discipline, final Byte schemaType, final DBTableIdMgr tableMgr, final String catFmtName, final String accFmtName, final UpdateType updateType, final File externalFile, final SimpleGlassPane glassPane, final DataProviderSessionIFace sessionArg) { boolean isUpdate = updateType == UpdateType.eImport || updateType == UpdateType.eMerge; boolean isLocalize = updateType == UpdateType.eLocalize; boolean isImportOrLocalize = updateType == UpdateType.eImport || updateType == UpdateType.eLocalize; HiddenTableMgr hiddenTableMgr = new HiddenTableMgr(); SchemaLocalizerXMLHelper schemaLocalizer = new SchemaLocalizerXMLHelper(schemaType, tableMgr); // NOTE: For localization 'false' is passed in if (!schemaLocalizer.loadWithExternalFile(externalFile, !isImportOrLocalize)) { return false; } boolean hideGenericFields = true; String dispName = discipline.getType().toString(); if (isLocalize) { List<Locale> availLocales = schemaLocalizer.getAvailLocales(); if (availLocales.size() > 1) { UIRegistry.displayErrorDlgLocalized("BSD.TOOMANYLOCALES"); return false; } } float progressCnt = 0.0f; float len = (float) schemaLocalizer.getSpLocaleContainers().size(); for (SpLocaleContainer table : schemaLocalizer.getSpLocaleContainers()) { progressCnt++; if (glassPane != null) { glassPane.setProgress((int) (progressCnt / len * 100.0)); } Integer spcId = null; boolean okToCreate = true; if (isUpdate || isLocalize) { String sql = String.format( " FROM splocalecontainer WHERE Name = '%s' AND SchemaType = %d AND DisciplineID = %d", table.getName(), schemaType, discipline.getId()); String fullSQL = "SELECT COUNT(*)" + sql; //log.debug(fullSQL); int cnt = BasicSQLUtils.getCountAsInt(fullSQL); if (cnt > 0) { okToCreate = false; fullSQL = "SELECT SpLocaleContainerID" + sql; //log.debug(fullSQL); spcId = BasicSQLUtils.getCount(fullSQL); } } SpLocaleContainer container = null; if (okToCreate) // && !isLocalize) { container = new SpLocaleContainer(); container.initialize(); container.setName(table.getName()); container.setType(table.getType()); container.setSchemaType(schemaType); container.setDiscipline(discipline); container.setIsHidden(hiddenTableMgr.isHidden(discipline.getType(), table.getName())); if (sessionArg != null) { try { sessionArg.saveOrUpdate(container); } catch (Exception ex) { ex.printStackTrace(); return false; } } } else { container = (SpLocaleContainer) sessionArg.getData("FROM SpLocaleContainer WHERE id = " + spcId); } loadLocalization(discipline.getId(), dispName, table, container, hideGenericFields, catFmtName, accFmtName, updateType, sessionArg); if (okToCreate) { discipline.getSpLocaleContainers().add(container); container.setDiscipline(discipline); } } return true; } /** * @param discipline * @param collection * @param userAgent * @param schemaType * @param tableMgr */ public void createPickLists(final Discipline discipline, final Collection collection, final Agent userAgent, final Byte schemaType, final DBTableIdMgr tableMgr) { SchemaLocalizerXMLHelper schemaLocalizer = new SchemaLocalizerXMLHelper(schemaType, tableMgr); // Loads and Merges the PickLists from Common and from the Discipline for (PickList pl : schemaLocalizer.getPickLists(discipline.getType())) { pl.setCreatedByAgent(userAgent); pl.setCollection(collection); persist(pl); } } /** * Make specific fields visible. * @param disciplineDirName the name of the directory for the Discipline * @param discipline the Discipline itself */ public static void doShowHideTablesAndFields(final String disciplineDirName, final Discipline discipline) { final String showFieldsFileName = "show_fields.xml"; String dirName = disciplineDirName != null ? disciplineDirName + File.separator : ""; String filePath = XMLHelper.getConfigDirPath(dirName + showFieldsFileName); File showFieldsFile = new File(filePath); if (showFieldsFile.exists()) { Connection conn = DBConnection.getInstance().getConnection(); PreparedStatement tblStmt = null; PreparedStatement fldStmt = null; try { tblStmt = conn.prepareStatement( "UPDATE splocalecontainer SET IsHidden=? WHERE DisciplineID = ? AND Name = ?"); fldStmt = conn.prepareStatement( "UPDATE splocalecontaineritem SET IsHidden=? WHERE SpLocaleContainerItemID = ?"); Element root = XMLHelper.readDOMFromConfigDir(dirName + showFieldsFileName); if (root != null) { StringBuilder sb = new StringBuilder("In show_fields.xml there were the following errors:\n"); boolean isErr = false; List<?> tables = root.selectNodes("/tables/table"); for (Iterator<?> iter = tables.iterator(); iter.hasNext();) { Element table = (Element) iter.next(); String tName = XMLHelper.getAttr(table, NAME, null); boolean isShwTbl = XMLHelper.getAttr(table, SHOW, true); String doSetTbl = XMLHelper.getAttr(table, SHOW, null); if (StringUtils.isNotEmpty(tName)) { DBTableInfo tbl = DBTableIdMgr.getInstance().getInfoByTableName(tName.toLowerCase()); if (tbl != null) { if (StringUtils.isNotEmpty(doSetTbl)) { tblStmt.setBoolean(1, !isShwTbl); tblStmt.setInt(2, discipline.getId()); tblStmt.setString(3, tName); tblStmt.executeUpdate(); } List<?> fields = table.selectNodes("field"); for (Iterator<?> fIter = fields.iterator(); fIter.hasNext();) { Element fieldEl = (Element) fIter.next(); String fName = XMLHelper.getAttr(fieldEl, NAME, null); boolean isShown = XMLHelper.getAttr(fieldEl, SHOW, true); if (StringUtils.isNotEmpty(fName)) { DBTableChildIFace childInfo = tbl.getItemByName(fName); if (childInfo != null) { String sql = String.format( "SELECT ci.SpLocaleContainerItemID FROM splocalecontainer AS c " + "INNER Join splocalecontaineritem AS ci ON c.SpLocaleContainerID = ci.SpLocaleContainerID " + "WHERE ci.Name = '%s' AND c.Name = '%s' AND c.DisciplineID = %d", fName, tName, discipline.getId()); Integer id = BasicSQLUtils.getCount(sql); if (id != null) { fldStmt.setBoolean(1, !isShown); fldStmt.setInt(2, id); fldStmt.executeUpdate(); } else { sb.append("Unable to find [" + disciplineDirName + "] for table name [" + tName + "] has bad field name[" + fName + "]\n"); } } else { sb.append("[" + disciplineDirName + "] for table name [" + tName + "] has bad field name[" + fName + "]\n"); isErr = true; } } } } else { sb.append("[" + disciplineDirName + "] has bad table name [" + tName + "]\n"); isErr = true; } } } if (isErr) { showError(sb.toString()); } } } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BuildSampleDatabase.class, ex); } finally { try { if (tblStmt != null) tblStmt.close(); if (fldStmt != null) fldStmt.close(); } catch (Exception ex) { } } } } /** * Make specific fields visible. * @param disciplineDirName the name of the directory for the Discipline * @param discipline the Discipline itself */ public static void makeFieldVisible(final String disciplineDirName, final Discipline discipline) { final String showFieldsFileName = "show_fields.xml"; String dirName = disciplineDirName != null ? disciplineDirName + File.separator : ""; String filePath = XMLHelper.getConfigDirPath(dirName + showFieldsFileName); File showFieldsFile = new File(filePath); if (showFieldsFile.exists()) { /*try { System.out.println(FileUtils.readFileToString(showFieldsFile)); } catch (IOException ex) { ex.printStackTrace(); }*/ Element root = XMLHelper.readDOMFromConfigDir(dirName + showFieldsFileName); if (root != null) { List<?> tables = root.selectNodes("/tables/table"); for (Iterator<?> iter = tables.iterator(); iter.hasNext();) { Element table = (Element) iter.next(); String tName = XMLHelper.getAttr(table, "name", null); if (StringUtils.isNotEmpty(tName)) { DBTableInfo tbl = DBTableIdMgr.getInstance().getInfoByTableName(tName.toLowerCase()); if (tbl != null) { List<?> fields = table.selectNodes("field"); for (Iterator<?> fIter = fields.iterator(); fIter.hasNext();) { Element fieldEl = (Element) fIter.next(); String fName = XMLHelper.getAttr(fieldEl, "name", null); if (StringUtils.isNotEmpty(fName)) { DBFieldInfo fld = tbl.getFieldByName(fName); DBRelationshipInfo rel = null; if (fld == null) { rel = tbl.getRelationshipByName(fName); } if (fld != null || rel != null) { setFieldVisible(tbl.getName(), fld != null ? fld.getName() : rel.getName(), discipline); } else { showError(showFieldsFileName + " in [" + disciplineDirName + "] for table name [" + tName + "] has bad field name[" + fName + "]"); } } } } else { showError(showFieldsFileName + " in [" + disciplineDirName + "] has bad table name [" + tName + "]"); } } } } } } /** * Looks up a table/field and sets it to be visible. * @param tableName the table name * @param fieldName the field name */ protected static void setFieldVisible(final String tableName, final String fieldName, final Discipline discipline) { DataProviderSessionIFace localSession = null; try { localSession = DataProviderFactory.getInstance().createSession(); String sql = "FROM SpLocaleContainer as sp INNER JOIN sp.discipline as d WHERE sp.name = '" + tableName + "' AND d.id = " + discipline.getId(); //System.err.println(sql); Object[] cols = (Object[]) localSession.getData(sql); if (cols != null && cols.length > 0) { SpLocaleContainer container = (SpLocaleContainer) cols[0]; if (container != null) { for (SpLocaleContainerItem item : container.getItems()) { //System.out.println(fieldName+" "+ item.getName()); if (item.getName().equals(fieldName)) { item.setIsHidden(false); localSession.beginTransaction(); localSession.save(item); localSession.commit(); localSession.flush(); return; } } } } else { System.err.println( "Couldn't find Table [" + tableName + "] for discipline[" + discipline.getId() + "]"); } } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BuildSampleDatabase.class, ex); } finally { if (localSession != null) { localSession.close(); } } } /** * @param args */ public static void main(final String[] args) { System.setProperty(DBMSUserMgr.factoryName, "edu.ku.brc.dbsupport.MySQLDMBSUserMgr"); try { ResourceBundle.getBundle("resources", Locale.getDefault()); //$NON-NLS-1$ } catch (MissingResourceException ex) { Locale.setDefault(Locale.ENGLISH); setResourceLocale(Locale.ENGLISH); } new HiddenTableMgr(); try { if (!System.getProperty("os.name").equals("Mac OS X")) { UIManager.setLookAndFeel(new Plastic3DLookAndFeel()); PlasticLookAndFeel.setPlasticTheme(new DesertBlue()); } } catch (Exception e) { e.printStackTrace(); } if (StringUtils.isEmpty(getAppName())) { setAppName("Specify"); } SwingUtilities.invokeLater(new Runnable() { public void run() { BuildSampleDatabase builder = new BuildSampleDatabase(); builder.buildSetup(args); } }); } /** * @param fileName * @return */ public HashSet<String> getColumnNamesFromXLS(final String fileName, final boolean doUserProvidedFile) { File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile); if (file == null) { return null; } HashSet<String> nameHash = new HashSet<String>(); try { String[] cells = new String[35]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); rows = sheet.rowIterator(); if (rows.hasNext()) { for (int i = 0; i < cells.length; i++) { cells[i] = null; } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); while (cellsIter.hasNext()) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { nameHash.add(StringUtils.trim(cell.getRichStringCellValue().getString())); } } } } catch (Exception ex) { ex.printStackTrace(); } return nameHash; } /** * @param cell * @return */ public String getXLSCellValueAsStr(final HSSFCell cell) { String value = null; // if cell is blank, set value to "" if (cell == null) { value = ""; } else { switch (cell.getCellType()) { case HSSFCell.CELL_TYPE_NUMERIC: // The best I can do at this point in the app is to guess if a // cell is a date. // Handle dates carefully while using HSSF. Excel stores all // dates as numbers, internally. // The only way to distinguish a date is by the formatting of // the cell. (If you // have ever formatted a cell containing a date in Excel, you // will know what I mean.) // Therefore, for a cell containing a date, cell.getCellType() // will return // HSSFCell.CELL_TYPE_NUMERIC. However, you can use a utility // function, // HSSFDateUtil.isCellDateFormatted(cell), to check if the cell // can be a date. // This function checks the format against a few internal // formats to decide the issue, // but by its very nature it is prone to false negatives. if (HSSFDateUtil.isCellDateFormatted(cell)) { DateWrapper scrDateFormat = AppPrefsCache.getDateWrapper("ui", "formatting", "scrdateformat"); SimpleDateFormat simpDateFmt = scrDateFormat != null && scrDateFormat.getSimpleDateFormat() != null ? scrDateFormat.getSimpleDateFormat() : sdf; value = simpDateFmt.format(cell.getDateCellValue()); } else { double numeric = cell.getNumericCellValue(); value = numFmt.format(numeric); } break; case HSSFCell.CELL_TYPE_STRING: value = cell.getRichStringCellValue().getString(); break; case HSSFCell.CELL_TYPE_BLANK: value = ""; break; case HSSFCell.CELL_TYPE_BOOLEAN: value = Boolean.toString(cell.getBooleanCellValue()); break; default: value = ""; log.error("unsuported cell type[" + cell.getCellType() + "]"); break; } } return value; } /** * @param treeDef * @param fileName * @param doUserProvidedFile * @return */ public Taxon convertTaxonFromXLS(final TaxonTreeDef treeDef, final String fileName, final boolean doUserProvidedFile) { Hashtable<String, Taxon> taxonHash = new Hashtable<String, Taxon>(); taxonHash.clear(); File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile); if (file == null) { return null; } Vector<TaxonTreeDefItem> rankedItems = new Vector<TaxonTreeDefItem>(); Hashtable<String, Boolean> colNames = new Hashtable<String, Boolean>(); for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) { colNames.put(item.getName().toLowerCase(), true); rankedItems.add(item); } Collections.sort(rankedItems, new Comparator<TaxonTreeDefItem>() { @Override public int compare(TaxonTreeDefItem o1, TaxonTreeDefItem o2) { return o1.getRankId().compareTo(o2.getRankId()); } }); Connection conn = null; Statement stmt = null; TaxonTreeDefItem rootTreeDefItem = rankedItems.get(0); Set<Taxon> rootKids = rootTreeDefItem.getTreeEntries(); Taxon root = rootKids.iterator().next(); Vector<Pair<String, Integer>> nodeList = new Vector<Pair<String, Integer>>(); Pair<String, Integer> rootNode = new Pair<String, Integer>(root.getName(), root.getId()); nodeList.add(rootNode); int counter = 0; int numDataCols = 0; try { startTx(); for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) { persist(item); } persist(root); commitTx(); String[] cells = new String[35]; String[] header = new String[35]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); int lastRowNum = sheet.getLastRowNum(); if (frame != null) { final int mx = lastRowNum; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setProcess(0, mx); } }); } conn = DBConnection.getInstance().createConnection(); //conn.setAutoCommit(false); stmt = conn.createStatement(); rows = sheet.rowIterator(); while (rows.hasNext()) { for (int i = 0; i < cells.length; i++) { cells[i] = null; } if (counter == 0) { HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext()) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = getXLSCellValueAsStr(cell); header[i] = cells[i]; i++; } } for (i = 0; i < cells.length; i++) { if (cells[i] == null) break; if (colNames.get(cells[i].toLowerCase()) != null) { numDataCols = i + 1; } else { for (String key : colNames.keySet()) { System.err.println("key[" + key + "]"); } System.err.println("Not Found: [" + cells[i].toLowerCase() + "]"); break; } } loadIndexes(cells); counter = 1; for (String hdr : header) { if (hdr == null) break; int inx = 0; for (TaxonTreeDefItem item : rankedItems) { if (hdr.equalsIgnoreCase(item.getName())) { log.debug("Header: " + hdr + " -> " + inx); taxonIndexes.put(hdr, inx); item.setIsInFullName(item.getRankId() >= TaxonTreeDef.GENUS); } else { log.debug("Header: " + hdr + " -> skipped."); } inx++; } } continue; } if (counter % 100 == 0) { if (frame != null) frame.setProcess(counter); //log.info("Converted " + counter + " of "+lastRowNum+" Taxon records"); } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext() && i < cells.length) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = getXLSCellValueAsStr(cell); i++; } } convertTaxonNodes(conn, stmt, header, cells, numDataCols, rootNode, nodeList, rankedItems, root.getDefinition().getId()); counter++; } stmt.executeUpdate( "UPDATE taxon SET IsAccepted = true WHERE IsAccepted IS NULL and AcceptedID IS NULL AND TaxonTReeDefID = " + treeDef.getId()); // Clear all GUIDs in Taxon. stmt.executeUpdate("UPDATE taxon SET GUID = NULL WHERE TaxonTreeDefID = " + treeDef.getId()); conn.close(); input.close(); if (frame != null) frame.setProcess(lastRowNum); root = (Taxon) session.createQuery("FROM Taxon WHERE id = " + root.getId()).list().get(0); } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex); } finally { try { if (stmt != null) { stmt.close(); } if (conn != null) { conn.close(); } } catch (Exception ex) { ex.printStackTrace(); } } if (frame != null) { frame.setDesc("Saving Taxon Tree..."); frame.getProcessProgress().setIndeterminate(true); } NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem> nodeNumberer = new NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem>( root.getDefinition()); nodeNumberer.doInBackground(); //startTx(); //TreeHelper.fixFullnameForNodeAndDescendants(root); //root.setNodeNumber(1); //fixNodeNumbersFromRoot(root); //commitTx(); log.info("Converted " + counter + " Taxon records"); // set up Taxon foreign key mapping for locality taxonHash.clear(); return root; } /** * @param cells */ private void loadIndexes(final String[] cells) { for (int i = FAMILY_COMMON_NAME; i <= SUBSPECIES_COMMON_NAME; i++) { for (int inx = 0; inx < cells.length; inx++) { if (cells[inx] == null) break; System.out.println(cells[inx] + " " + TaxonIndexNames[i]); if (cells[inx].equals(TaxonIndexNames[i])) { System.out.println("** " + TaxonIndexNames[i] + " -> " + inx); taxonExtraColsIndexes.put(TaxonIndexNames[i].toLowerCase(), inx); break; } } } } /** * @param conn * @param stmt * @param levelNames * @param startIndex * @param numColumns * @param parent * @param nodeList * @param rankedItems * @param txTreeDefId * @throws SQLException */ public void convertTaxonNodes(final Connection conn, final Statement stmt, final String[] header, final String[] levelNames, final int numColumns, final Pair<String, Integer> parent, final Vector<Pair<String, Integer>> nodeList, final Vector<TaxonTreeDefItem> rankedItems, final int txTreeDefId) throws SQLException { /* * kingdom phylum class order superfamily family genus species subspecies species author species source species guid species common name family common name subspecies author subspecies source subspecies lsid subspecies common name Animalia Arthropoda Insecta Orthoptera Acridoidea Acrididae Abisares depressus Uvarov 1938 orthoptera.speciesfile.org urn:lsid:catalogueoflife.org:taxon:e32007de-29c1-102b-9a4a-00304854f820:ac2008 */ String fullName = ""; for (int i = 0; i < numColumns; i++) { int inx = i + 1; if (StringUtils.isEmpty(levelNames[i])) { break; } Integer depthInx = taxonIndexes.get(header[i]); if (depthInx == null && taxonExtraColsIndexes.get(header[i]) != null) { break; } TaxonTreeDefItem ttdi = rankedItems.get(depthInx); if (ttdi.getIsInFullName()) { if (StringUtils.isNotEmpty(ttdi.getTextBefore())) { fullName += ttdi.getTextBefore(); } fullName += levelNames[i]; if (StringUtils.isNotEmpty(ttdi.getTextAfter())) { fullName += ttdi.getTextAfter(); } if (StringUtils.isNotEmpty(ttdi.getFullNameSeparator())) { fullName += ttdi.getFullNameSeparator(); } } if (inx == nodeList.size() || !levelNames[i].equals(nodeList.get(inx).first)) { for (int j = inx; j < nodeList.size(); j++) { recycler.push(nodeList.get(j)); } nodeList.setSize(inx); Pair<String, Integer> node = createTaxonNode(conn, stmt, levelNames[i], txTreeDefId, ttdi, nodeList.get(i).second, fullName.trim(), levelNames); nodeList.add(node); } } } /** * @param conn * @param stmt * @param name * @param txTreeDefId * @param tdi * @param parentId * @param fullName * @param levelNames * @return * @throws SQLException */ protected Pair<String, Integer> createTaxonNode(final Connection conn, final Statement stmt, final String name, final int txTreeDefId, final TaxonTreeDefItem tdi, final Integer parentId, final String fullName, final String[] levelNames) throws SQLException { gSQLStr.setLength(0); gSQLStr.append( "INSERT INTO taxon (Name, TaxonTreeDefID, FullName, TaxonTreeDefItemID, RankID, ParentID, TimestampCreated, Version, IsAccepted, IsHybrid"); addExtraColumns(gSQLStr, tdi.getRankId(), levelNames, true); gSQLStr.append(") VALUES ("); gSQLStr.append("\""); gSQLStr.append(name); gSQLStr.append("\","); gSQLStr.append(txTreeDefId); gSQLStr.append(","); gSQLStr.append("\""); if (StringUtils.isNotEmpty(fullName)) { gSQLStr.append(fullName); } else { gSQLStr.append(name); } gSQLStr.append("\""); gSQLStr.append(","); gSQLStr.append(tdi.getId()); gSQLStr.append(','); gSQLStr.append(tdi.getRankId()); gSQLStr.append(','); gSQLStr.append(parentId); gSQLStr.append(','); gSQLStr.append(nowStr); gSQLStr.append(",1,true,false"); addExtraColumns(gSQLStr, tdi.getRankId(), levelNames, false); gSQLStr.append(")"); //System.out.println(sb.toString()); stmt.executeUpdate(gSQLStr.toString(), Statement.RETURN_GENERATED_KEYS); Integer newId = BasicSQLUtils.getInsertedId(stmt); if (newId == null) { throw new RuntimeException("Couldn't get the Taxon's inserted ID"); } recCnt++; //System.out.println("rec: "+recCnt); if (recycler.size() > 0) { Pair<String, Integer> p = recycler.pop(); p.first = name; p.second = newId; return p; } return new Pair<String, Integer>(name, newId); } /** * @param sb * @param rankId * @param cells * @param doFieldNames */ protected void addExtraColumns(final StringBuilder sb, final int rankId, final String[] cells, final boolean doFieldNames) { switch (rankId) { case 140: // family loadTaxonFields(sb, new int[] { FAMILY_COMMON_NAME }, cells, doFieldNames); break; case 220: // Species loadTaxonFields(sb, new int[] { SPECIES_AUTHOR, SPECIES_SOURCE, SPECIES_GUID, SPECIES_COMMON_NAME }, cells, doFieldNames); break; case 230: // SubSpecies loadTaxonFields(sb, new int[] { SUBSPECIES_AUTHOR, SUBSPECIES_SOURCE, SUBSPECIES_GUID, SUBSPECIES_COMMON_NAME }, cells, doFieldNames); break; default: break; } } /** * @param taxon * @param indexes * @param cells */ private void loadTaxonFields(final StringBuilder sb, final int[] indexes, final String[] cells, final boolean doFieldNames) { for (int inx : indexes) { if (TaxonIndexNames[inx] != null) { //XXX - temporary work-around for initialization problems (bug #7204) when botany sample //taxon is loaded. Skipping block if gotten is null results in common names //(for botany) not being loaded. Integer gotten = taxonExtraColsIndexes.get(TaxonIndexNames[inx].toLowerCase()); if (gotten != null) { int index = gotten; String data = cells[index]; if (StringUtils.isNotEmpty(data)) { sb.append(","); if (doFieldNames) { sb.append(TaxonFieldNames[inx]); } else { data = StringUtils.replace(data, "'", "\\\'"); sb.append("'" + data + "'"); } } } } } } /** * @param treeDef * @return */ public GeologicTimePeriod convertChronoStratFromXLS(final GeologicTimePeriodTreeDef treeDef, final Agent userAgent) { startTx(); GeologicTimePeriodTreeDefItem root = createGeologicTimePeriodTreeDefItem(null, treeDef, "Root", 0); GeologicTimePeriodTreeDefItem era = createGeologicTimePeriodTreeDefItem(root, treeDef, "Erathem/Era", 100); GeologicTimePeriodTreeDefItem period = createGeologicTimePeriodTreeDefItem(era, treeDef, "System/Period", 200); GeologicTimePeriodTreeDefItem series = createGeologicTimePeriodTreeDefItem(period, treeDef, "Series/Epoch", 300); @SuppressWarnings("unused") GeologicTimePeriodTreeDefItem member = createGeologicTimePeriodTreeDefItem(series, treeDef, "Stage/Age", 400); persist(root); commitTx(); series.setIsInFullName(true); frame.setDesc("Building ChronoStratigraphy Tree..."); Hashtable<String, GeologicTimePeriod> chronoHash = new Hashtable<String, GeologicTimePeriod>(); chronoHash.clear(); String fileName = "chronostrat_tree.xls"; File file = XMLHelper.getConfigDir("../demo_files/" + fileName); if (!file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir"); file = XMLHelper.getConfigDir(fileName); if (!file.exists()) { file = new File("Specify/demo_files/" + fileName); } } if (file == null || !file.exists()) { log.error("Couldn't file[" + file.getAbsolutePath() + "]"); return null; } // setup the root ChronoStrat record (planet Earth) GeologicTimePeriod rootNode = new GeologicTimePeriod(); rootNode.initialize(); rootNode.setName(getResourceString("Root")); rootNode.setFullName(rootNode.getName()); rootNode.setRankId(0); rootNode.setDefinition(treeDef); rootNode.setDefinitionItem(root); rootNode.setCreatedByAgent(userAgent); int counter = 0; try { startTx(); persist(rootNode); String[] cells = new String[4]; InputStream input = new FileInputStream(file); POIFSFileSystem fs = new POIFSFileSystem(input); HSSFWorkbook workBook = new HSSFWorkbook(fs); HSSFSheet sheet = workBook.getSheetAt(0); Iterator<?> rows = sheet.rowIterator(); int lastRowNum = sheet.getLastRowNum(); if (frame != null) { final int mx = lastRowNum; SwingUtilities.invokeLater(new Runnable() { public void run() { frame.setProcess(0, mx); } }); } while (rows.hasNext()) { if (counter == 0) { counter = 1; continue; } if (counter % 100 == 0) { if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " ChronoStrat records"); } HSSFRow row = (HSSFRow) rows.next(); Iterator<?> cellsIter = row.cellIterator(); int i = 0; while (cellsIter.hasNext() && i < 4) { HSSFCell cell = (HSSFCell) cellsIter.next(); if (cell != null) { cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString()); i++; } } for (int j = i; j < 4; j++) { cells[j] = null; } //System.out.println(); @SuppressWarnings("unused") GeologicTimePeriod newGeo = convertChronoStratRecord(cells[0], cells[1], cells[2], cells[3], rootNode, userAgent); counter++; } input.close(); } catch (Exception ex) { ex.printStackTrace(); } if (frame != null) frame.setProcess(counter); log.info("Converted " + counter + " ChronoStrat records"); TreeHelper.fixFullnameForNodeAndDescendants(rootNode); rootNode.setNodeNumber(1); fixNodeNumbersFromRoot(rootNode); commitTx(); log.info("Converted " + counter + " Stratigraphy records"); // set up ChronoStrat foreign key mapping for locality chronoHash.clear(); return rootNode; } /** * @param continent * @param country * @param state * @param county * @param geoRoot * @return */ protected GeologicTimePeriod convertChronoStratRecord(final String continent, final String country, final String state, final String county, final GeologicTimePeriod geoRoot, final Agent userAgent) { String levelNames[] = { continent, country, state, county }; int levelsToBuild = 0; for (int i = levelNames.length; i > 0; --i) { if (StringUtils.isNotEmpty(levelNames[i - 1])) { levelsToBuild = i; break; } } for (int i = 0; i < levelsToBuild; i++) { if (StringUtils.isEmpty(levelNames[i])) { levelNames[i] = "(Empty)"; } } GeologicTimePeriod prevLevelGeo = geoRoot; for (int i = 0; i < levelsToBuild; ++i) { GeologicTimePeriod newLevelGeo = buildChronoStratLevel(levelNames[i], prevLevelGeo, userAgent); prevLevelGeo = newLevelGeo; } return prevLevelGeo; } /** * @param nameArg * @param parentArg * @return */ protected GeologicTimePeriod buildChronoStratLevel(final String nameArg, final GeologicTimePeriod parentArg, final Agent userAgent) { String name = nameArg; if (name == null) { name = "N/A"; } // search through all of parent's children to see if one already exists with the same name Set<GeologicTimePeriod> children = parentArg.getChildren(); for (GeologicTimePeriod child : children) { if (name.equalsIgnoreCase(child.getName())) { // this parent already has a child by the given name // don't create a new one, just return this one return child; } } // we didn't find a child by the given name // we need to create a new GeologicTimePeriod record GeologicTimePeriod newGeo = new GeologicTimePeriod(); newGeo.initialize(); newGeo.setName(name); newGeo.setParent(parentArg); parentArg.addChild(newGeo); newGeo.setDefinition(parentArg.getDefinition()); newGeo.setCreatedByAgent(userAgent); int newGeoRank = parentArg.getRankId() + 100; GeologicTimePeriodTreeDefItem defItem = parentArg.getDefinition().getDefItemByRank(newGeoRank); newGeo.setDefinitionItem(defItem); newGeo.setRankId(newGeoRank); persist(newGeo); return newGeo; } /** * @param fmt */ public static void fixNumericCatalogNumbers(final UIFieldFormatterIFace fmt) { Connection conn = DBConnection.getInstance().createConnection(); Statement stmt = null; Statement updtStmt = null; try { stmt = conn.createStatement(); updtStmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select CollectionObjectID, CatalogNumber FROM collectionobject"); while (rs.next()) { int id = rs.getInt(1); String catNum = (String) fmt.formatFromUI(rs.getString(2)); updtStmt.executeUpdate("UPDATE collectionobject SET CatalogNumber='" + catNum + "' WHERE CollectionObjectID = " + id); } rs.close(); } catch (Exception ex) { ex.printStackTrace(); } finally { try { stmt.close(); updtStmt.close(); conn.close(); } catch (Exception ex) { ex.printStackTrace(); } } } }