EDIT

// $Id$

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.common;

import java.io.BufferedReader;

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.lang.annotation.Annotation;

import java.lang.reflect.Field;

import java.lang.reflect.Modifier;

import java.net.HttpURLConnection;

import java.net.MalformedURLException;

import java.net.URI;

import java.net.URISyntaxException;

import java.net.URL;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.Map;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

/**

 * @author a.mueller

 * @author a.kohlbecker

 */

public class CdmUtils {

    private static final Logger logger = Logger.getLogger(CdmUtils.class);

    /**

     * The per user cdm folder name: ".cdmLibrary"

     */

    private static final String cdmFolderName = ".cdmLibrary";

    final static String userHome = System.getProperty("user.home");

    /**

     * The per user cdm folder "~/.cdmLibrary"

     */

    public final static File perUserCdmFolder = new File(userHome + File.separator + ".cdmLibrary" );

    static final String MUST_EXIST_FILE = "MUST-EXIST.txt";

    //folder seperator

    static String folderSeperator;

    //TODO refactor to: public static File getUserHomeDir()

    public static String getHomeDir() throws IOException{

        //TODO why do we need System.getenv("USERPROFILE")? System.getProperty("user.home") is fully sufficient!!

        String homeDirString = System.getenv("USERPROFILE") != null ? System.getenv("USERPROFILE") : System.getProperty("user.home");

        if( ! new File(homeDirString).canWrite()){

            throw new IOException("Can not write to home directory. Assumed path is: " + homeDirString);

        }

        return homeDirString;

    }

    public static File getCdmHomeDir() {

        return new File(System.getProperty("user.home")+File.separator+cdmFolderName+File.separator);

    }

	public static File getCdmSubDir(String dirName) {

		File folder = new File(System.getProperty("user.home") + File.separator

				+ cdmFolderName + File.separator + dirName + File.separator);

		// if the directory does not exist, create it

		if (!folder.exists()) {

			if (!folder.mkdir()) {

				// TODO throw some Exception

				return null;

			}

		}

		return folder;

	}

    /**

     * Returns the an InputStream for a read-only source

     * @param resourceFileName the resources path within the classpath(!)

     * @return

     * @throws IOException

     */

    public static InputStream getReadableResourceStream(String resourceFileName)

            throws IOException{

        InputStream urlStream = CdmUtils.class.getResourceAsStream("/"+ resourceFileName);

        return urlStream;

    }

    /**

     * Returns the an InputStream for a read-only source

     * @param resourceFileName the resources path within the classpath(!)

     * @return

     * @throws IOException

     */

    public static InputStreamReader getUtf8ResourceReader(String resourceFileName)

            throws IOException{

        InputStream urlStream = CdmUtils.class.getResourceAsStream("/"+ resourceFileName);

        InputStreamReader inputStreamReader = new InputStreamReader(urlStream, "UTF8");

        return inputStreamReader;

    }

    /**

     * @return

     */

    static public String getFolderSeperator(){

        if (folderSeperator == null){

            URL url = CdmUtils.class.getResource("/"+ MUST_EXIST_FILE);

            if ( url != null && ! urlIsJarOrBundle(url) ){

                folderSeperator =  File.separator;

            }else{

                folderSeperator = "/";

            }

        }

        return folderSeperator;

    }

    /**

     * @param url

     * @return

     */

    static private boolean urlIsJarOrBundle(URL url){

        return url.getProtocol().startsWith("jar") || url.getProtocol().startsWith("bundleresource");

    }

    /**

     * Returns the file name for the file in which 'clazz' is to be found (helps finding according libraries)

     * @param clazz

     * @return

     */

    static public String findLibrary(Class<?> clazz){

        String result = null;

        if (clazz != null){

            String fullPackageName = clazz.getCanonicalName();

            fullPackageName = fullPackageName.replace(".", "/");

            URL url = CdmUtils.class.getResource("/" + fullPackageName + ".class" );

            if (url != null){

                result = url.getFile();

            }else{

                result = "";

            }

            logger.debug("LibraryURL for " + clazz.getCanonicalName() + " : " + result);

        }

        return result;

    }

    static public String testMe(){

        String message = "This is a test";

        System.out.println(message);

        return message;

    }

    static public String readInputLine(String inputQuestion){

        try {

            System.out.print(inputQuestion);

            BufferedReader in = new BufferedReader( new java.io.InputStreamReader( System.in ));

            String input;

            input = in.readLine();

            return input;

        } catch (IOException e) {

            logger.warn("IOExeption");

            return null;

        }

    }

    /**

     * Returns the trimmed value string if value is not <code>null</code>.

     * Returns the empty string if value is <code>null</code>.

     * @param value

     * @return

     */

    static public String NzTrim(String value){

        return (value == null ? "" : value);

    }

    /**

     * Returns value if value is not <code>null</code>. Returns empty string if value is <code>null</code>.

     * @param value

     * @return

     */

    static public String Nz(String value){

        return (value == null ? "" : value);

    }

    /**

     * Returns value if value is not <code>null</code>. Returns defaultValue if value is <code>null</code>.

     * @param value

     * @return

     */

    static public String Nz(String value, String defaultValue){

        return (value == null ? defaultValue : value);

    }

    /**

     * Returns value if value is not <code>null</code>. Returns 0 if value is <code>null</code>.

     * @param value

     * @return

     */

    static public Integer Nz(Integer value){

        return (value == null ? 0 : value);

    }

    /**

     * Returns value if value is not <code>null</code>. Returns 0 if value is <code>null</code>.

     * @param value

     * @return

     */

    static public Long Nz(Long value){

        return (value == null ? 0 : value);

    }

    /**

     * Returns str if str is not the empty String (''). Returns null if str is empty.

     * @param str

     * @return

     */

    static public String Ne(String str){

        return ("".equals(str)? null : str);

    }

    /**

     * Returns str if str.trim() is not empty. Returns null otherwise.

     * @param str

     * @return

     */

    static public String Nb(String str){

        return (str == null || str.trim().equals("")? null : str);

    }

    /**

     * Concatenates an array of strings using the defined seperator.<BR>

     * <code>Null</code> values are interpreted as empty strings.<BR>

     * If all strings are <code>null</code> then <code>null</code> is returned.

     * @param strings

     * @param seperator

     * @return String

     */

    static public String concat(CharSequence separator, String[] strings){

        String result = "";

        boolean allNull = true;

        for (String string : strings){

            if (string != null){

                if (result.length() > 0 && string.length() > 0){

                    result += separator;

                }

                result += string;

                allNull = false;

            }

        }

        //if all strings are null result should be null, not ""

        if (allNull){

            return null;

        }else {

            return result;

        }

    }

    /**

     * Concatenates two strings, using the defined seperator.<BR>

     * <code>Null</code> values are interpreted as empty Strings.<BR>

     * If both strings are <code>null</code> then <code>null</code> is returned.

     * @see #concat(CharSequence, String[])

     * @param seperator

     * @param string1

     * @param string2

     * @return String

     */

    static public String concat(CharSequence separator, String string1, String string2){

        String[] strings = {string1, string2};

        return concat(separator, strings);

    }

	/**

	 * Returns <code>preferred</code> if not blank, else returns <code>alternative</code>.

	 * If reverse is <code>true</code> computation is

	 * the other way round (<code>alternative</code> if not blank, otherwise <code>preferred</code>).

	 * @param preferred first string

	 * @param alternative second string

	 * @param reverse reverse flag

	 * @param nzTrim if <code>true</code> the result is trimmed and <code>null</code> values are replaced by empty string.

	 * @return the preferred string

	 */

	static public String getPreferredNonEmptyString(String preferred, String alternative, boolean reverse, boolean nzTrim){

		String result;

		if (! reverse){

			result = StringUtils.isBlank(preferred) ? alternative : preferred;

		}else{

			result = StringUtils.isBlank(alternative) ? preferred : alternative;

		}

		if (nzTrim){

			result = Nz(result).trim();

		}

		return result;

	}

    /** Returns a version of the input where all contiguous

     * whitespace characters are replaced with a single

     * space. Line terminators are treated like whitespace.

     *

     * @param inputStr

     * @return

     */

    public static CharSequence removeDuplicateWhitespace(CharSequence inputStr) {

        String patternStr = "\\s+";

        String replaceStr = " ";

        Pattern pattern = Pattern.compile(patternStr);

        Matcher matcher = pattern.matcher(inputStr);

        return matcher.replaceAll(replaceStr);

    }

    /** Builds a list of strings by splitting an input string

     * with delimiters whitespace, comma, or semicolon

     * @param value

     * @return

     */

    public static ArrayList<String> buildList(String value) {

        ArrayList<String> resultList = new ArrayList<String>();

        for (String tag : value.split("[\\s,;]+")) {

            resultList.add(tag);

        }

        return resultList;

    }

    static public boolean urlExists(String strUrl, boolean withWarning){

        try {

             HttpURLConnection.setFollowRedirects(false);

              // note : you may also need

              //        HttpURLConnection.setInstanceFollowRedirects(false)

              HttpURLConnection con =

                 (HttpURLConnection) new URL(strUrl).openConnection();

              con.setRequestMethod("HEAD");

              return (con.getResponseCode() == HttpURLConnection.HTTP_OK);

        } catch (MalformedURLException e) {

            if (withWarning) {

                logger.warn(e);

            }

        } catch (IOException e) {

            //

        };

        return false;

    }

    static public URI string2Uri(String string) {

        URI uri = null;

        try {

            uri = new URI(string);

            logger.debug("uri: " + uri.toString());

        } catch (URISyntaxException ex) {

            logger.error("Problem converting string " + string + " to URI " + uri);

            return null;

        }

        return uri;

    }

    static public boolean isNumeric(String string){

        if (string == null){

            return false;

        }

        try {

            Double.valueOf(string);

            return true;

        } catch (NumberFormatException e) {

            return false;

        }

    }

    /**

     * Returns <code>true</code> if the passed string starts with an upper case letter.

     * <code>false</code> otherwise. The later includes <code>null</code> and empty strings.

     * @param string

     * @return

     */

    static public boolean isCapital(String string){

        if (isBlank(string)){

            return false;

        }else{

            Character firstChar = string.charAt(0);

            if (firstChar.equals(Character.toUpperCase(firstChar))){

                return true;

            }else{

                return false;

            }

        }

    }

    /**

     * Returns true if string is null, "" or string.trim() is ""

     * @see isNotEmpty(String string)

     * @param string

     * @return

     */

    static public boolean isBlank(String string){

        if (string == null){

            return true;

        }

        if ("".equals(string.trim())){

            return true;

        }

        return false;

    }

    /**

     * Returns <code>false</code> if string is null, "" or string.trim() is ""

     * @see isNotEmpty(String string)

     * @param string

     * @return

     */

    static public boolean isNotBlank(String string){

        return ! isBlank(string);

    }

    /**

     * @see #isBlank(String)

     * @deprecated use {@link #isBlank(String)} instead

     * @param string

     * @return

     */

    @Deprecated

    static public boolean isEmpty(String string){

        return isBlank(string);

    }

    static public boolean areBlank(String ... strings){

        for (String string : strings){

            if (! isBlank(string)){

                return false;

            }

        }

        return true;

    }

    /**

     * Tests if two objects are equal or both null. Otherwise returns false

     * @param obj1

     * @param obj2

     * @return

     */

    public static boolean nullSafeEqual(Object obj1, Object obj2) {

        if (obj1 == null && obj2 == null){

            return true;

        }

        if (obj1 == null && obj2 != null){

            return false;

        }

        return (obj1.equals(obj2));

    }

    /**

     * Returns false if string is null, "" or string.trim() is ""

     * Else true.

     * @see isBlank(String string)

     * @see #isNotBlank(String)

     * @deprecated use {@link #isNotBlank(String)} instead

     * @param string

     * @return

     */

    @Deprecated

    static public boolean isNotEmpty(String string){

        return isNotBlank(string);

    }

    /**

     * Computes all fields recursively

     * @param clazz

     * @return

     */

    public static Map<String, Field> getAllFields(Class clazz, Class highestClass, boolean includeStatic, boolean includeTransient, boolean makeAccessible, boolean includeHighestClass) {

        Map<String, Field> result = new HashMap<String, Field>();

        if ( highestClass.isAssignableFrom(clazz) && (clazz != highestClass || includeHighestClass)){

            //exclude static

            for (Field field: clazz.getDeclaredFields()){

                if (includeStatic || ! Modifier.isStatic(field.getModifiers())){

                    if (includeTransient || ! isTransient(field)){

                        field.setAccessible(makeAccessible);

                        result.put(field.getName(), field);

                    }

                }

            }

            //include superclass fields

            Class superclass = clazz.getSuperclass();

            if (superclass != null){

                result.putAll(getAllFields(superclass, highestClass, includeStatic, includeTransient, makeAccessible, includeHighestClass));

            }

        }

        return result;

    }

    /**

     * Returns true, if field has an annotation of type javax.persistence.Annotation

     * @param field

     * @return

     */

    protected static boolean isTransient(Field field) {

        for (Annotation annotation : field.getAnnotations()){

            //if (Transient.class.isAssignableFrom(annotation.annotationType())){

            if (annotation.annotationType().getSimpleName().equals("Transient")){

                return true;

            }

        }

        return false;

    }

    /**

     * Trims the string and if the string ends with a dot removes it.

     * @param string

     * @return

     */

    public static String removeTrailingDot(String string){

        if (string == null){

            return null;

        }

        if (string.trim().endsWith(".")){

            return string.substring(0, string.length() -1);

        }

        return string;

    }

    /**

     * Returns surrounding brackets "(",")". Trim the string if necessary.

     * @param text

     * @return

     */

    public static String removeBrackets(String text) {

        if (text == null){

            return null;

        }

        text = text.trim();

        if (text.matches("^\\(.*\\)$")){

            text = text.substring(1, text.length() -1);

        }

        return text;

    }

import eu.etaxonomy.cdm.common.CdmUtils;

        this.secMicroReference = CdmUtils.Nb(secMicroReference);