* Instantiate a class using the name of the class at runtime *
* * @param className * the fully qualified name of the class to instantiate * @return Instance of the requested class * @throws Exception * the class finding/creation exceptions */ public static Object createObject(String className) throws Exception { Object object = null; try { Class classDefinition = Class.forName(className); object = classDefinition.newInstance(); } catch (InstantiationException e) { throw e; } catch (IllegalAccessException e) { throw e; } catch (ClassNotFoundException e) { throw e; } return object; } /** * Generates a VBModelBean from the field names in a ResultSet. */ public static VBModelBean buildBean(ResultSetMetaData meta, ResultSet rs, String beanName) { Object bean = null; try { if (rs == null || !rs.first()) { return null; } int colCount = meta.getColumnCount(); bean = Utility.createObject(VBObjectUtils.DATA_MODEL_PACKAGE + beanName); // use DB column names to set properties for (int i=1; i<=colCount; i++) { String propName = meta.getColumnName(i); Object value = rs.getObject(i); //String value = rs.getString(i); try { if (value != null) { BeanUtils.copyProperty(bean, propName, value); } } catch (Exception ex) { log.debug("unable to set " + propName + " in bean " + beanName); } } } catch (Exception ex) { log.error("Problem building bean from DB results.", ex); } return (VBModelBean)bean; } /** ** Utility Method to check for nulls and empty String *
* * @param stringToCheck * @return Is this Empty or null? */ public static boolean isStringNullOrEmpty(String stringToCheck) { return ( stringToCheck == null || stringToCheck.equals("") ); } /** * Return true if string is not "false", "no", "O", empty or null. */ public static boolean isStringTrue(String stringToCheck) { return !(Utility.isStringNullOrEmpty(stringToCheck) || stringToCheck.equalsIgnoreCase("false") || stringToCheck.equalsIgnoreCase("no") || stringToCheck.equalsIgnoreCase("0")); } /** ** Utility Method to check for nulls and empty array. *
* * @param arrayToCheck * @return Is this Empty or null? */ public static boolean isArrayNullOrEmpty(Object[] arrayToCheck) { return arrayToCheck == null || arrayToCheck.length == 0; } /** ** Convience method to check several string for nullness or emtyness *
* * @param stringsToCheck -- Array of Strings to check * @return Are any of these Strings empty or null? */ public static boolean isAnyStringNullorEmpty( String[] stringsToCheck) { boolean result = false; for (int i = 0; i < stringsToCheck.length; i++) { if ( isStringNullOrEmpty(stringsToCheck[i]) ) { result = true; return result; } } return result; } /** ** Convience method to check several string for non nullness or non emtyness *
* * @param stringsToCheck Array ofStrings to check
* @return Are any of these Strings NOT empty or null?
*/
public static boolean isAnyStringNotNullorEmpty( String[] stringsToCheck)
{
boolean result = false;
for (int i = 0; i < stringsToCheck.length; i++)
{
if ( ! isStringNullOrEmpty(stringsToCheck[i]) )
{
result = true;
return result;
}
}
return result;
}
/**
*
* Convience method to create a simple comma separted string from an Object[].
*
Objects to convert to comma separate String
* @return String
*/
public static String arrayToCommaSeparatedString(Object[] objects)
{
return joinArray(objects, ",");
}
/**
*
* Convience method to create a simple delimetted String from
* an Object[].
*
String
* @return The delimited List as String
*/
public static String joinArray(Object[] objects, String delimiter)
{
StringBuffer sb = new StringBuffer();
for (int i=0; i < objects.length; i++)
{
sb.append(objects[i]);
if( (i +1) < objects.length )
{
sb.append(delimiter);
}
}
return sb.toString();
}
/**
* Capitalizes the first letter of a string. Leaves the rest of the Sting alone
* @param text
* @return String
*/
public static String upperCaseFirstLetter(String text)
{
String result = text.substring(0, 1).toUpperCase() + text.substring(1);
//System.out.println("Utiltiy > " +result);
return result;
}
/**
* Prints out a hashtable in an easy to read fashion
*
* @param hash -- hashtable to pretty print
*/
public static void prettyPrintHash( Hashtable hash )
{
if (hash == null) {
return;
}
log.debug(prettyPrintHash(hash, 0));
}
private static String prettyPrintHash( Hashtable hash, int indent)
{
//log.debug(indent +" -- "+hash.hashCode());
StringBuffer sb = new StringBuffer(256);
Iterator keys = hash.keySet().iterator();
while ( keys.hasNext() )
{
Object key = keys.next();
sb.append(getIdent( indent ) + key + ":");
Object value = hash.get( key );
if ( value instanceof java.util.Hashtable )
{
sb.append("\n");
sb.append( prettyPrintHash( (Hashtable) value, indent + 1));
}
else if ( value instanceof java.util.Vector )
{
Iterator it = ((Vector) value).iterator();
while ( it.hasNext())
{
Object element = it.next();
if ( element instanceof java.util.Hashtable )
{
sb.append( "--->" +((Hashtable) element).get("TableName") );
sb.append("\n");
sb.append( prettyPrintHash( (Hashtable) element, indent + 1));
}
}
}
else
{
sb.append( "\t" + value + "\n");
}
}
return sb.toString();
}
/**
* Gets current date and time using UTC Timezone.
*
* @return Date-- current Date
*/
public static java.util.Date getNow( )
{
// TODO: not tested yet
Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
return cal.getTime();
}
/**
* Gets current date in a format that can be accepted
* by the RDBMS and that is like: Aug 9, 2002
*
* @return the date in a RDBMS format
*/
public static String getCurrentDate()
{
// TODO: use getNow() when it has been tested
java.util.Date now = new java.util.Date(); //Set Date variable now to the current date and time
DateFormat med = DateFormat.getDateInstance (DateFormat.MEDIUM);
return med.format(now);
}
/**
* Convience method for get a string of tabs
*
* @param indent
* @return
*/
private static String getIdent(int indent)
{
StringBuffer sb = new StringBuffer();
for ( int i=0; i* Foreign Key don't always have the same name as the primary key of the * the the primary table, this is a utility to allow this lookup to happen. * * * Not a comprehensive lookup! *
* * @param FKName The Foriegn Key name * @return The Primary Key name that corresponds to the inputed FK name. */ public static String getPKNameFromFKName(String FKName) { // TODO: this is not comprehesive as this is only a problem // for some lookups, should be comprehensive to avoid misuse String PKname = ""; if ( FKName.equalsIgnoreCase(Plantstatus.PLANTPARENT_ID)) { PKname = Plantconcept.PKNAME; } else { PKname = FKName; } return PKname; } /** * Only certain database names need to have accessionCodes loaded * * @return boolean */ public static boolean isLoadAccessionCodeOn() { // I'm not sure what we were thinking when this code was written, // but I'm disabling it. 2/1/2005 PMA return true; /* boolean genAC = false; log.debug("Utility: databaseName = " + DATABASE_NAME); if (DATABASE_NAME.equalsIgnoreCase("vegbank") || DATABASE_NAME.equalsIgnoreCase("vegtest")) { genAC = true; } else { genAC = false; } return genAC; */ } /** * @return */ public static String getAccessionPrefix() { String accessionPrefix = ""; // This is a function of database name and host machine if ( DATABASE_NAME.equalsIgnoreCase("vegbank")) { accessionPrefix = vegbankPropFile.getString("vegbank.accession.prefix"); if (Utility.isStringNullOrEmpty(accessionPrefix)) { accessionPrefix = "VB"; } else { accessionPrefix = accessionPrefix.toUpperCase(); } } else if ( DATABASE_NAME.equalsIgnoreCase("vegtest")) { accessionPrefix = "VT"; } else { accessionPrefix = "NOTVALID"; } return accessionPrefix; } /** * Convert an inputstream to a String. Not sure how the handle encoding * so using System default for now. * * @param is * @return * @throws IOException */ public static String getStringFromInputStream(InputStream is) throws IOException { InputStreamReader reader = new InputStreamReader(is); char[] buffer = new char[4096]; StringWriter writer = new StringWriter(); int bytes_read; while ((bytes_read = reader.read(buffer)) != -1) { writer.write(buffer, 0, bytes_read); } String result = writer.toString(); return result; } /** * Convience method to Uppercase first char of a String and lower case * the rest * @param stringToCapitalize * @return */ public static String upperCaseFirstChar(String stringToCapitalize ) { StringBuffer result = new StringBuffer(); result.append( stringToCapitalize.substring(0,1).toUpperCase() ); result.append( stringToCapitalize.substring(1).toLowerCase() ); return result.toString(); } /** * Parse up an Accessioncode into its parts * * @param accessionCode Vegbank AC to be parsed. * @return code, entityname, key in aString[]
*/
public static HashMap parseAccessionCode(String accessionCode)
{
String DBCODE = "DBCODE";
String ENTITYCODE = "ENTITYCODE";
String KEYVALUE = "KEYVALUE";
String CONFIMATIONCODE = "CONFIMATIONCODE";
HashMap parsedAC = new HashMap();
// method
log.debug("Utility: accessionCode = " + accessionCode);
Pattern pattern = Pattern.compile("([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.{0,1}([^\\.]*)");
Matcher m = pattern.matcher(accessionCode);
if ( m.find() )
{
parsedAC.put("DBCODE", m.group(1) );
parsedAC.put("ENTITYCODE", m.group(2) );
parsedAC.put("KEYVALUE", m.group(3) );
parsedAC.put("CONFIMATIONCODE", m.group(4) );
}
log.debug("Parsed an AccessionCode: DBCode > '" + parsedAC.get(DBCODE) + "' ENTITYCODE > '" + parsedAC.get(ENTITYCODE) + "' KEYVALUE > '" + parsedAC.get(KEYVALUE) + "' CONFIMATIONCODE > '" + parsedAC.get(CONFIMATIONCODE) + "'" );
return parsedAC;
}
/**
* Ugly hack to test if an entityCode is a root entity or not.
*
* @param entityCode
* @return Is root entity?
*/
public static boolean isRootEntity(String entityCode)
{
boolean result = false;
if (entityCode.equalsIgnoreCase("OB") || entityCode.equalsIgnoreCase("PC")
|| entityCode.equalsIgnoreCase("CC"))
{
result = true;
}
return result;
}
/**
* Create and write a temp file in the system tmp dir (/tmp).
*
* @param in
* Reader to write out to filesystem
* @throws IOException
* @return path to temp file
*/
public static String writeTempFile(Reader in) throws IOException
{
File outputFile = File.createTempFile(Integer.toString(in.hashCode()), null);
FileWriter out = new FileWriter(outputFile);
int c;
while ((c = in.read()) != -1)
out.write(c);
out.close();
in.close();
return outputFile.getAbsolutePath();
}
/**
* Tool to save a file to the filesystem.
*
* @param in
* Reader to write out to filesystem
* @param filename
* The name of the file to write to
* @throws IOException
*/
public static void saveFile( Reader in, String filename) throws IOException
{
File outputFile = new File(filename);
if (!outputFile.exists()) {
// create the file
outputFile.createNewFile();
}
FileWriter out = new FileWriter(outputFile);
int c;
while ((c = in.read()) != -1)
out.write(c);
out.close();
in.close();
}
/**
* Tool to delete a file from the filesystem.
*
* @param filename
* The name of the file to write to
* @throws IOException
*/
public static void deleteFile(String filename) throws IOException
{
(new File(filename)).delete();
}
/**
* Serialize a file.
*
* @param fileName
* @param the Object
* @throws IOException
*/
public static void saveBinaryFile(String fileName, Object o) throws IOException {
FileOutputStream fileOut = new FileOutputStream(new File(fileName));
ObjectOutputStream objectOut = new ObjectOutputStream (fileOut);
objectOut.writeObject(o);
}
/**
* Deserialize a file.
*
* @param fileName
* @param the Object
* @throws IOException
*/
public static Object loadBinaryFile(String fileName) throws IOException {
FileInputStream fileIn = new FileInputStream(new File(fileName));
ObjectInputStream objectIn = new ObjectInputStream(fileIn);
try {
return objectIn.readObject();
} catch (Exception ex) {
log.error("couldn't load binary file " + fileName, ex);
}
return null;
}
/**
*
*/
public static String capitalize(String str) {
if (isStringNullOrEmpty(str)) {
return "";
}
return Character.toUpperCase(str.charAt(0)) +
str.toLowerCase().substring(1);
}
/**
* @return true if the value of the given string is a number
*/
public static boolean isNumeric(String s) {
if (Utility.isStringNullOrEmpty(s)) {
return false;
}
try { Long.parseLong(s); }
catch (NumberFormatException nfex) { return false; }
return true;
}
/**
* @return true if the first/only value of the given
* comma-separated list is a number
*/
public static boolean isNumericList(String csv) {
if (Utility.isStringNullOrEmpty(csv)) {
return false;
}
String value = csv;
if (csv.indexOf(',') != -1 || csv.indexOf('|') != -1) {
// a list
StringTokenizer st = new StringTokenizer(csv, ",|");
if (st.hasMoreTokens()) { value = st.nextToken(); }
}
return isNumeric(value);
}
/**
*
*/
public static void notifyAdmin(String subject, String body) {
String adminFromEmail = vegbankPropFile.getString("admin.email.from");
String adminToEmail = vegbankPropFile.getString("admin.email.to");
String server = vegbankPropFile.getString("machine_url");
if (isStringNullOrEmpty(adminFromEmail)) { adminFromEmail = "site@vegbank.org"; }
if (isStringNullOrEmpty(adminToEmail)) { adminToEmail = "dba@vegbank.org"; }
if (isStringNullOrEmpty(server)) { server = "unknown vegbank host"; }
try {
Mailer m = new Mailer();
m.sendPlain("ADMIN NOTIFICATION FROM " + server,
"SUBJECT: " + subject + "\n\n" + body, adminToEmail,
null, null, adminFromEmail);
log.info("Sent an email notification to admin re: " + subject);
} catch (MailerException mex) {
log.error("Problem notifying admin", mex);
}
}
/**
*
* @return
*/
public static boolean canAddToDatasetOnLoad(String tableName) {
if (Utility.isStringNullOrEmpty(tableName)) {
log.debug("canAddToDatasetOnLoad(): given empty string");
return false;
}
if (DS_CANDIDATES == null) {
String s = vegbankPropFile.getString("dataset.candidates");
StringTokenizer st = new StringTokenizer(s, ",");
DS_CANDIDATES = new ArrayList();
while (st.hasMoreTokens()) {
DS_CANDIDATES.add(st.nextToken().toLowerCase());
}
}
return DS_CANDIDATES.contains(tableName.toLowerCase());
}
/**
* Returns a version of the given string that is no
* longer than len chars and ends in "..." if
* any chars were abbreviated (string was long).
*/
public static String abbreviate(String src, int len) {
if (Utility.isStringNullOrEmpty(src)) {
return "";
}
if (src.length() > len) {
return src.substring(0, len-3) + "...";
} else {
return src;
}
}
/**
* Returns usr_id of authenticated user, or null if not logged in.
*/
public static Long getAuthenticatedUsrId(HttpSession session) {
return (Long)session.getAttribute(USER_KEY);
}
/**
* Returns path and parameters for last search.
*/
public static String getLastSearchURL(HttpSession session) {
String url = (String)session.getAttribute(LAST_SEARCH_URL);
if (url == null) {
url = "";
}
log.debug("GOT " + LAST_SEARCH_URL + ": " + url);
return url;
}
/**
* Saves path and parameters for last search.
*/
public static void setLastSearchURL(HttpServletRequest request) {
StringBuffer url = request.getRequestURL();
String qs = request.getQueryString();
if (qs != null) {
url.append("?").append(qs);
}
log.debug("setting " + LAST_SEARCH_URL + " to " + url.toString());
request.getSession().setAttribute(LAST_SEARCH_URL, url.toString());
}
/**
*
*/
public static String getVegBankProperty(String key) {
return vegbankPropFile.getString(key);
}
}