Metacat

/**

 *  '$RCSfile$'

 *  Copyright: 2004 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *

 *   '$Author$'

 *     '$Date$'

 * '$Revision$'

 *

 * 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., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

 */

package edu.ucsb.nceas.metacat;

import edu.ucsb.nceas.metacat.service.PropertyService;

import edu.ucsb.nceas.utilities.PropertyNotFoundException;

/**

 * @author jones

 *

 * Version represents the current version information for this Metacat instance.

 */

public class MetaCatVersion extends Version {

    public MetaCatVersion(String versionID) {

    	super(versionID);

    }

	/**

	 * Get the current version string for this metacat instance. It is currently

	 * stored in the metacat.properties file.

	 * 

	 * @return a string indicating the version of Metacat running

	 */

	public static String getVersionID() throws PropertyNotFoundException {

		String version = PropertyService.getProperty("application.metacatVersion");

		return version;

	}

    /**

	 * Get the version number in an XML document.

	 * 

	 * @return the version wrapped in an XML document

	 */

    public static String getVersionAsXml() throws PropertyNotFoundException {

        StringBuffer sb = new StringBuffer();

        sb.append("<?xml version=\"1.0\"?>");

        sb.append("<version>");

        sb.append(getVersionID());

        sb.append("</version>");

        return sb.toString();

    }

}

import edu.ucsb.nceas.metacat.shared.BaseException;

import edu.ucsb.nceas.metacat.util.ResponseUtil;

import edu.ucsb.nceas.metacat.workflow.WorkflowScheduler;

 *     queries supported by the WFS / WMS standards

 * action=shrink --

 * action=gohome --

 * action=scheduleWorkflow --

 *     delay --

 *     starttime --

 *     endtime --

 *     intervalvalue -- 

 *     intervalunit --

 *     workflowid --

 *     karid --

 *     workflowname --

 *     forwardto --

 *     qformat --

 * action=unscheduleWorkflow --

 *     workflowjobid --

 *     forwardto --

 *     qformat --

 * action=rescheduleWorkflow --

 *     workflowjobid --

 *     forwardto --

 *     qformat --

 * action=deleteScheduledWorkflow --

 *     workflowjobid --

 *     forwardto --

 *     qformat --

    public static final String XMLFORMAT = "xml";

            if (!MetacatUtil.bypassConfiguration() && !MetacatUtil.isMetacatConfigured()) {

			logMetacat.warn("Metacat (" + MetaCatVersion.getVersionID()

		if (!MetacatUtil.isMetacatConfigured()) {

			RequestUtil.forwardRequest(request, response, "/admin?action=configure");

					out.println(MetaCatVersion.getVersionAsXml());

				} else if (action.equals("gohome")) {

					// forward to the default page

					RequestUtil.forwardRequest(request, response, "/");

				} else if (action.equals("scheduleWorkflow")) {

					try {

						WorkflowScheduler.getInstance().scheduleJob(request, response, params, 

							userName, groupNames);

						return;

					} catch (BaseException be) {

						ResponseUtil.sendErrorXML(response, ResponseUtil.SCHEDULE_WORKFLOW_ERROR, be);

						return;						

					}

				} else if (action.equals("unscheduleWorkflow")) {

					try {

						WorkflowScheduler.getInstance().unScheduleJob(request, response, params, 

							userName, groupNames);

						return;

					} catch (BaseException be) {

						ResponseUtil.sendErrorXML(response, ResponseUtil.UNSCHEDULE_WORKFLOW_ERROR, be);

						return;						

					}

				} else if (action.equals("rescheduleWorkflow")) {

					try {

						WorkflowScheduler.getInstance().reScheduleJob(request, response, params, 

							userName, groupNames);

						return;

					} catch (BaseException be) {

						ResponseUtil.sendErrorXML(response, ResponseUtil.RESCHEDULE_WORKFLOW_ERROR, be);

						return;						

					}

				} else if (action.equals("getScheduledWorkflow")) {

					try {

						WorkflowScheduler.getInstance().getJobs(request, response, params, 

								userName, groupNames);				

						return;

					} catch (BaseException be) {

						ResponseUtil.sendErrorXML(response, ResponseUtil.GET_SCHEDULED_WORKFLOW_ERROR, be);

						return;						

					}

				} else if (action.equals("deleteScheduledWorkflow")) {

					try {

						WorkflowScheduler.getInstance().deleteJob(request, response, params, 

								userName, groupNames);				

						return;

					} catch (BaseException be) {

						ResponseUtil.sendErrorXML(response, ResponseUtil.DELETE_SCHEDULED_WORKFLOW_ERROR, be);

						return;						

					}

                        out, null);

                        out, null);

            docId = MetacatUtil

                    .getDocIdWithoutRevFromInlineDataID(inlineDataId);

                    String inlineDataIdWithoutRev = MetacatUtil.getInlineDataIdWithoutRev(inlineDataId);

                            qformat, out, params);

                        out, null);

                        sh.addToDeleteQue( MetacatUtil.getSmartDocId( docid[0] ) );

                        out, null);

        docId = MetacatUtil.getDocIdFromString(accessionNumber);

    dataFileId = MetacatUtil.getDocIdFromString(docIdWithRevision);

            String docId = MetacatUtil.

                               getAccessionNumberFromEcogridIdentifier(URLData);

            docId = MetacatUtil.getDocIdFromAccessionNumber(docId);

     docId = MetacatUtil.getSmartDocId(myDocid);

         docId = MetacatUtil.getDocIdFromAccessionNumber(myDocid);

		docId = MetacatUtil.getDocIdFromString(docId);

                                         MetacatUtil.

                                         getInlineDataIdWithoutRev(fileId) +

                unAccessibleIdList.put(subTreeId, MetacatUtil.

                                      getInlineDataIdWithoutRev(fileId));

            this.docid = MetacatUtil.getDocIdFromAccessionNumber(accNum);

            this.rev   = MetacatUtil.getRevisionFromAccessionNumber(accNum);

            String docIdWithoutRev = MetacatUtil.getDocIdFromAccessionNumber(accnum);

            int userSpecifyRev = MetacatUtil.getRevisionFromAccessionNumber(accnum);

            String docIdWithoutRev = MetacatUtil.getDocIdFromAccessionNumber(accnum);

            int userSpecifyRev = MetacatUtil.getRevisionFromAccessionNumber(accnum);

        String docid = MetacatUtil.getDocIdFromString(accnum);

        int rev = MetacatUtil.getVersionFromString(accnum);

                    String accessfileName = MetacatUtil

                            .getDocIdWithoutRevFromInlineDataID(fileName);

            int revision = MetacatUtil.getRevisionFromAccessionNumber(accnum);

        String docid = MetacatUtil.getDocIdFromAccessionNumber(accnum);

        int userSpecifyRev = MetacatUtil.getRevisionFromAccessionNumber(accnum);

            String docIdWithoutRev = MetacatUtil.getDocIdFromAccessionNumber(accnumber);

            int revision = MetacatUtil.getRevisionFromAccessionNumber(accnumber);

                  String aclid = MetacatUtil.getDocIdFromAccessionNumber(aclidWithRev);

                  revision = MetacatUtil.getRevisionFromAccessionNumber(aclidWithRev);

            docid = MetacatUtil.getDocIdFromString(accnumber);

            String docid = MetacatUtil.getDocIdFromAccessionNumber(accnum);

        String docId = MetacatUtil.getDocIdFromString(accNum);

            String docIdWithoutRev = MetacatUtil

                    .getDocIdFromAccessionNumber(accnum);

            String rev = MetacatUtil.getRevisionStringFromString(accnum);

        subject = MetacatUtil.getDocIdFromString(triple.getSubject());

        object = MetacatUtil.getDocIdFromString(triple.getObject());

import edu.ucsb.nceas.metacat.util.MetacatUtil;

    docIdWithoutRevision = MetacatUtil.getDocIdFromString(givenDocId);

import java.util.Stack;

import edu.ucsb.nceas.metacat.DBSAXHandler;

import edu.ucsb.nceas.metacat.NodeRecord;

import edu.ucsb.nceas.metacat.service.ServiceService;

import edu.ucsb.nceas.metacat.service.SkinPropertyService;

import edu.ucsb.nceas.metacat.shared.MetacatUtilException;

import edu.ucsb.nceas.metacat.shared.ServiceException;

import edu.ucsb.nceas.utilities.GeneralPropertyException;

import edu.ucsb.nceas.utilities.UtilException;

    private static char separator = '.';

    static {

        try {

        	separator = PropertyService.getProperty("document.accNumSeparator").charAt(0);

        } catch (PropertyNotFoundException pnfe) {

        	logMetacat.error("Could not retrieve account number separator. " 

        			+ "Separator set to '.' : " + pnfe.getMessage());

        }

    }

     * method assumes the format of the query par tof the url is an ampersand

     * Get docid from online/url string

     */

    public static String getDocIdWithRevFromOnlineURL(String url)

    {

        String docid = null;

        String DOCID = "docid";

        boolean find = false;

        char limited = '&';

        int count = 0; //keep track how many & was found

        Vector list = new Vector();// keep index number for &

        if (url == null) {

            logMetacat.info("url is null and null will be returned");

            return docid;

        }

        // the first element in list is 0

        list.add(new Integer(0));

        for (int i = 0; i < url.length(); i++) {

            if (url.charAt(i) == limited) {

                // count plus 1

                count++;

                list.add(new Integer(i));

                // get substring beween two &

                String str = url.substring(

                        ((Integer) list.elementAt(count - 1)).intValue(), i);

                logMetacat.info("substring between two & is: " + str);

                //if the subString contains docid, we got it

                if (str.indexOf(DOCID) != -1) {

                    //get index of '="

                    int start = getIndexForGivenChar(str, '=') + 1;

                    int end = str.length();

                    docid = str.substring(start, end);

                    find = true;

                }//if

            }//if

        }//for

        //if not find, we need check the subtring between the index of last &

        // and

        // the end of string

        if (!find) {

            logMetacat.info("Checking the last substring");

            String str = url.substring(((Integer) list.elementAt(count))

                    .intValue() + 1, url.length());

            logMetacat.info("Last substring is: " + str);

            if (str.indexOf(DOCID) != -1) {

                //get index of '="

                int start = getIndexForGivenChar(str, '=') + 1;

                int end = str.length();

                docid = str.substring(start, end);

                find = true;

            }//if

        }//if

        logMetacat.info("The docid from online url is:" + docid);

        return docid.trim();

    }

    /**

     * Eocgorid identifier will look like: ecogrid://knb/tao.1.1

     * The AccessionNumber tao.1.1 will be returned. If the given doesn't

     * contains ecogrid, null will be returned.

     * @param identifier String

     * @return String

     */

    public static String getAccessionNumberFromEcogridIdentifier(String identifier)

    {

      String accessionNumber = null;

      if (identifier != null && identifier.startsWith(DBSAXHandler.ECOGRID))

      {

        // find the last "/" in identifier

        int indexOfLastSlash = identifier.lastIndexOf("/");

        int start = indexOfLastSlash+1;

        int end   = identifier.length();

        accessionNumber = identifier.substring(start, end);

      }

      logMetacat.warn("The accession number from url is " +

                                 accessionNumber);

      return accessionNumber;

    }

    private static int getIndexForGivenChar(String str, char character)

    {

        int index = -1;

        // make sure str is not null

        if (str == null) {

            logMetacat.info(

                    "The given str is null and -1 will be returned");

            return index;

        }

        // got though the string

        for (int i = 0; i < str.length(); i++) {

            // find the first one then break the loop

            if (str.charAt(i) == character) {

                index = i;

                break;

            }//if

        }//for

        logMetacat.info("the index for char " + character + " is: "

                + index);

        return index;

    }

    /**

     * Utility method to get docid from a given string

     *

     * @param string, the given string should be these two format: 1) str1.str2

     *            in this case docid= str1.str2 2) str1.str2.str3, in this case

     *            docid =str1.str2

     * @param the sperator char

     */

    public static String getDocIdFromString(String str)

    {

        String docId = null;

        if (str == null) {

            logMetacat.info(

                    "The given str is null and null will be returned"

                            + " in getDocIdfromString");

            return docId;

        } //make sure docid is not null

        int dotNumber = 0;//count how many dots in given string

        int indexOfLastDot = 0;

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == separator) {

                dotNumber++;//count how many dots

                indexOfLastDot = i;//keep the last dot postion

            }

        }//for

        //The string formatt is wrong, because it has more than two or less

        // than

        //one seperator

        if (dotNumber > 2 || dotNumber < 1) {

            docId = null;

        } else if (dotNumber == 2) //the case for str1.str2.str3

        {

            docId = str.substring(0, indexOfLastDot);

        } else if (dotNumber == 1) //the case for str1.str2

        {

            docId = str;

        }

        return docId;

    }//getDocIdFromString

    /**

     * Utility method to get version number from a given string

     *

     * @param string, the given string should be these two format: 1)

     *            str1.str2(no version) version =-1; 2) str1.str2.str3, in this

     *            case version = str3; 3) other, vresion =-2

     */

    public static int getVersionFromString(String str)

            throws NumberFormatException

    {

        int version = -1;

        String versionString = null;

        int dotNumber = 0;//count how many dots in given string

        int indexOfLastDot = 0;

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == separator) {

                dotNumber++;//count how many dots

                indexOfLastDot = i;//keep the last dot postion

            }

        }//for

        //The string formatt is wrong, because it has more than two or less

        // than

        //one seperator

        if (dotNumber > 2 || dotNumber < 1) {

            version = -2;

        } else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1)))

        //the case for str1.str2.str3

        {

            versionString = str.substring((indexOfLastDot + 1), str.length());

            version = Integer.parseInt(versionString);

        } else if (dotNumber == 1) //the case for str1.str2

        {

            version = -1;

        }

        return version;

    }//getVersionFromString

    /**

     * Utility method to get version string from a given string

     *

     * @param string, the given string should be these two format: 1)

     *            str1.str2(no version) version=null; 2) str1.str2.str3, in

     *            this case version = str3; 3) other, vresion =null;

     */

    public static String getRevisionStringFromString(String str)

            throws NumberFormatException

    {

        // String to store the version

        String versionString = null;

        int dotNumber = 0;//count how many dots in given string

        int indexOfLastDot = 0;

        for (int i = 0; i < str.length(); i++) {

            if (str.charAt(i) == separator) {

                dotNumber++;//count how many dots

                indexOfLastDot = i;//keep the last dot postion

            }

        }//for

        //The string formatt is wrong, because it has more than two or less

        // than

        //one seperator

        if (dotNumber > 2 || dotNumber < 1) {

            versionString = null;

        } else if (dotNumber == 2 && (indexOfLastDot != (str.length() - 1))) {

            //the case for str1.str2.str3

            // indexOfLastDot != (str.length() -1) means get rid of str1.str2.

            versionString = str.substring((indexOfLastDot + 1), str.length());

        } else if (dotNumber == 1) //the case for str1.str2 or str1.str2.

        {

            versionString = null;

        }

        return versionString;

    }//getVersionFromString

    /**

     * This method will get docid from an AccessionNumber. There is no

     * assumption the accessnumber will be str1.str2.str3. It can be more. So

     * we think the docid will be get rid of last part

     */

    public static String getDocIdFromAccessionNumber(String accessionNumber)

    {

        String docid = null;

        if (accessionNumber == null) { return docid; }

        int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);

        docid = accessionNumber.substring(0, indexOfLastSeperator);

        logMetacat.info("after parsing accessionnumber, docid is "

                + docid);

        return docid;

    }

    /**

     * This method will get inline data id without the revision number.

     * So if inlineData.1.2 is passed as input, inlineData.2 is returned.

     */

    public static String getInlineDataIdWithoutRev(String accessionNumber)

    {

        String docid = null;

        if (accessionNumber == null) { return docid; }

        int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);

        String version = accessionNumber.substring(indexOfLastSeperator,

                                                   accessionNumber.length());

        accessionNumber = accessionNumber.substring(0, indexOfLastSeperator);

        indexOfLastSeperator = accessionNumber.lastIndexOf(separator);

        docid = accessionNumber.substring(0, indexOfLastSeperator) + version;

        logMetacat.info("after parsing accessionnumber, docid is "

                                 + docid);

        return docid;

    }

    /**

     * This method will call both getDocIdFromString and

     * getDocIdFromAccessionNumber. So first, if the string looks str1.str2,

     * the docid will be str1.str2. If the string is str1.str2.str3, the docid

     * will be str1.str2. If the string is str1.str2.str3.str4 or more, the

     * docid will be str1.str2.str3. If the string look like str1, null will be

     * returned

     *

     */

    public static String getSmartDocId(String str)

    {

        String docid = null;

        //call geDocIdFromString first.

        docid = getDocIdFromString(str);

        // If docid is null, try to call getDocIdFromAccessionNumber

        // it will handle the seperator more than2

        if (docid == null) {

            docid = getDocIdFromAccessionNumber(str);

        }

        logMetacat.info("The docid get from smart docid getor is "

                + docid);

        return docid;

    }

    /**

     * This method will get revision from an AccessionNumber. There is no

     * assumption the accessnumber will be str1.str2.str3. It can be more. So

     * we think the docid will be get rid of last part

     */

    public static int getRevisionFromAccessionNumber(String accessionNumber)

            throws NumberFormatException

    {

        String rev = null;

        int revNumber = -1;

        if (accessionNumber == null) { return revNumber; }

        int indexOfLastSeperator = accessionNumber.lastIndexOf(separator);

        rev = accessionNumber.substring(indexOfLastSeperator + 1,

                accessionNumber.length());

        revNumber = Integer.parseInt(rev);

        logMetacat.info("after parsing accessionnumber, rev is "

                + revNumber);

        return revNumber;

    }

    /**

    /**

     * Method to get docidwithrev from eml2 inline data id The eml inline data

     * id would look like eml.200.2.3

     */

    public static String getDocIdWithoutRevFromInlineDataID(String inlineDataID)

    {

        String docidWithoutRev = null;

        if (inlineDataID == null) { return docidWithoutRev; }

        char charSeperator = separator;

        int targetNumberOfSeperator = 2;// we want to know his index

        int numberOfSeperator = 0;

        for (int i = 0; i < inlineDataID.length(); i++) {

            // meet seperator, increase number of seperator

            if (inlineDataID.charAt(i) == charSeperator) {

                numberOfSeperator++;

            }

            // if number of seperator reach the target one, record the index(i)

            // and get substring and terminate the loop

            if (numberOfSeperator == targetNumberOfSeperator) {

                docidWithoutRev = inlineDataID.substring(0, i);

                break;

            }

        }

        logMetacat.info("Docid without rev from inlinedata id: "

                + docidWithoutRev);

        return docidWithoutRev;

    }

    /**

     * Revise stack change a stack to opposite order

     */

    public static Stack<NodeRecord> reviseStack(Stack<NodeRecord> stack)

    {

        Stack result = new Stack();

        // make sure the parameter is correct

        if (stack == null || stack.isEmpty()) {

            result = stack;

            return result;

        }

        while (!stack.isEmpty()) {

            Object obj = stack.pop();

            result.push(obj);

        }

        return result;

    }

	/**

	 * Reports whether metacat is fully configured.

	 * 

	 * @return a boolean that is true if all sections are configured and 

	 * false otherwise

	 */

	public static boolean isMetacatConfigured() {

		boolean metacatConfigured = false;

		try {			

			metacatConfigured = PropertyService.arePropertiesConfigured()

					&& AuthUtil.isAuthConfigured()

					&& SkinUtil.areSkinsConfigured()

					&& DatabaseUtil.isDatabaseConfigured()

					&& GeoserverUtil.isGeoserverConfigured()

					&& isBackupDirConfigured();

		} catch (MetacatUtilException ue) {

			logMetacat.error("Could not determine if metacat is configured due to utility exception: "

					+ ue.getMessage());

		} catch (PropertyNotFoundException pnfe) {

			logMetacat.error("Could not determine if metacat is configured due to property exception: "

					+ pnfe.getMessage());

		}

		return metacatConfigured;

	}

	/**

	 * Check if the application.backupDir property is populated in

	 * metacat.properties and that it points to a writable directory.

	 * 

	 * @return false if the application.backupDir property does not point to a

	 *         writable directory.

	 */

	public static boolean isBackupDirConfigured() throws MetacatUtilException, PropertyNotFoundException {

		String backupDir = PropertyService.getProperty("application.backupDir");

		if (backupDir == null || backupDir.equals("")) {

			return false;

		}		

		if (FileUtil.getFileStatus(backupDir) < FileUtil.EXISTS_READ_WRITABLE) {

			return false;

		}	

		return true;

	}

	/**

	 * Reports whether the metacat configuration utility should be run. Returns

	 * false if 

	 *   -- dev.runConfiguration=false and 

	 *   -- backup properties file exists 

	 * Note that dev.runConfiguration should only be set to false when reinstalling the 

	 * same version of the application in development.

	 * 

	 * @return a boolean that is false if dev.runConfiguration is false and the

	 *         backup properties file exists.

	 */

	public static boolean bypassConfiguration() throws MetacatUtilException, ServiceException {

		try {

			// If the system is not configured to do bypass, return false.

			if (!PropertyService.doBypass()) {

				return false;

			}

			// Get the most likely backup files.  If these cannot be found, we 

			// cannot do the configuration bypass.

			String ExternalBaseDir = SystemUtil.discoverExternalDir();

			if (ExternalBaseDir == null) {

				logMetacat.error("bypassConfiguration: Could not find backup directory.");

				// could not find backup files ... force the configuration

				return false;

			}

			String realContext = ServiceService.getRealApplicationContext();

			PropertyService.setRecommendedExternalDir(ExternalBaseDir);

			PropertyService.setProperty("application.backupDir", 

					ExternalBaseDir + FileUtil.getFS() + "." + realContext);

			// Refresh the property service and skin property service.  This will pick up 

			// the backup directory and populate backup properties in caches.

			ServiceService.refreshService("PropertyService");

			ServiceService.refreshService("SkinPropertyService");

			// Call bypassConfiguration to make sure backup properties get persisted 

			// to active properties for both main and skin properties.

			PropertyService.bypassConfiguration();

			SkinPropertyService.bypassConfiguration();

			return true;

		} catch (GeneralPropertyException gpe) {

			throw new MetacatUtilException("Property error while discovering backup directory: "

					+ gpe.getMessage());

		} catch (MetacatUtilException mue) {

			throw new MetacatUtilException("Utility error while discovering backup directory: "

					+ mue.getMessage());

		}

	}