Metacat

<%@page 

import="java.util.Iterator"%><%@page 

import="java.util.ArrayList"%><%@page 

import="edu.ucsb.nceas.utilities.OrderedMap"%><%@page 

import="java.util.List"%><%@page 

import="java.util.Enumeration"%><%@page 

import="java.sql.SQLException"%><%@page 

import="org.ecoinformatics.datamanager.transpose.DataTranspose"%><%@page 

import="au.com.bytecode.opencsv.CSVWriter"%><%@page 

import="java.io.OutputStreamWriter"%><%@page 

import="java.io.Writer"%><%@page 

import="java.sql.ResultSet"%><%@page 

import="edu.ucsb.nceas.metacat.dataquery.DataQuery"%><%@page 

import="java.io.IOException"%><%@page 

import="edu.ucsb.nceas.utilities.PropertyNotFoundException"%><%@page

import="edu.ucsb.nceas.metacat.util.SystemUtil"%><%@page 

import="java.util.Hashtable"%><%@ page 

language="java" %><%

/**

 * 

 * '$RCSfile$'

 * Copyright: 2008 Regents of the University of California and the

 *             National Center for Ecological Analysis and Synthesis

 *    '$Author: leinfelder $'

 *      '$Date: 2008-08-22 16:48:56 -0700 (Fri, 22 Aug 2008) $'

 * '$Revision: 4305 $'

 * 

 * 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

 */  

%><%

Hashtable params = getParams(request);

handleDataquery(params,response,request.getSession().getId());

%><%!

	private Hashtable getParams(HttpServletRequest request) {

		Hashtable params = new Hashtable();

		Enumeration<String> paramlist = (Enumeration<String>)request.getParameterNames();

		while (paramlist.hasMoreElements()) {

			String name = paramlist.nextElement();

			String[] value = request.getParameterValues(name);

			params.put(name, value);

		}

		return params;

	}

%><%!

	private List processResultsSet(ResultSet rs, int omitColumn, String omitColumnLabel) throws SQLException {

		List retTable = new ArrayList();

		int colCount = rs.getMetaData().getColumnCount();

		List columnHeaders = new ArrayList();

		int recordCount = 1;

		OrderedMap uniqueIds = new OrderedMap();

		while (rs.next()) {

			List row = new ArrayList();

			//get the values for this row

			for (int i = 1; i <= colCount; i++) {

				String colName = rs.getMetaData().getColumnName(i);

				String value = rs.getString(i);

				//clean up the value

				value = cleanUp(value);

				//hide the ids

				if (i == omitColumn) {

					String lookupValue = (String) uniqueIds.get(value);

					if (lookupValue == null) {

						lookupValue = recordCount + "";

					}

					uniqueIds.put(value, lookupValue);

					value = lookupValue;

					colName = omitColumnLabel;

				}

				if (recordCount == 1) {

					columnHeaders.add(colName);

				}

				row.add(value);

			}

			retTable.add(row.toArray(new String[0]));

			recordCount++;

		}

		retTable.add(0, columnHeaders.toArray(new String[0]));

		return retTable;

	}

%><%!

	private List transpose(ResultSet rs, int idCol, int pivotCol, List pivotAttributes, boolean omitIdValues) throws SQLException {

		//map keyed by id column - data

		OrderedMap table = new OrderedMap();

		//track all the data columns

		OrderedMap widestRow = new OrderedMap();

		//map keyed by the pivot column - metadata

		OrderedMap headerRows = new OrderedMap();

		//vocab columns

		String vocabNameCol = "qmetadatavocabulary";

		String vocabValueCol = "qmetadatavalue";

		//maps for the vocab lists

		OrderedMap vocabNames = new OrderedMap();

		OrderedMap vocabValues = new OrderedMap();

		//all vocab names/values

		List allVocabNames = new ArrayList();

		List allVocabValues = new ArrayList();

		boolean twoColumnMetadata = true;

		int colCount = rs.getMetaData().getColumnCount();

		String idColName = rs.getMetaData().getColumnName(idCol);

		while (rs.next()) {

			String id = rs.getString(idCol);

			String pivotValue = rs.getString(pivotCol);

			//look up the data row we are working on

			OrderedMap row = (OrderedMap) table.get(id);

			if (row == null) {

				row = new OrderedMap();

			}

			//look up the metadata row we are working on

			OrderedMap metadataRow = (OrderedMap) table.get(pivotValue);

			if (metadataRow == null) {

				metadataRow = new OrderedMap();

			}

			//get the values for this pivot

			for (int i = 1; i <= colCount; i++) {

				if (i != pivotCol) {

					String colName = rs.getMetaData().getColumnName(i);

					String value = rs.getString(i);

					//clean up the value

					value = cleanUp(value);

					//do we include this column in the pivot?

					if (pivotAttributes.contains(colName)) {

						//annotate the column name with the pivot column value if not the id column

						if (i != idCol) {

							colName = pivotValue + "_" + colName;

						}

						row.put(colName, value);

					}

					else {

						if (colName.startsWith(vocabNameCol) || colName.startsWith(vocabValueCol)) {

							//don't add it to the normal metadata

						}

						else {

							metadataRow.put(colName, value);

						}

					}

					//names

					if (colName.startsWith(vocabNameCol)) {

						List list = (List) vocabNames.get(pivotValue);

						if (list == null) {

							list = new ArrayList();

						}

						list.add(value);

						vocabNames.put(pivotValue, list);

						allVocabNames.add(value);

					}

					//values

					if (colName.startsWith(vocabValueCol)) {

						List list = (List) vocabValues.get(pivotValue);

						if (list == null) {

							list = new ArrayList();

						}

						list.add(value);

						vocabValues.put(pivotValue, list);

						allVocabValues.add(value);

					}

				}

			}

			//track the data columns - the values are junk

			widestRow.putAll(row);

			//put the row back (or maybe it's the first time)

			table.put(id, row);

			//put the metadata header back

			headerRows.put(pivotValue, metadataRow);

		}

		/** Construct the table structure for returning **/

		//now make it into a list

		List retTable = new ArrayList();

		//map keyed by metadata labels

		OrderedMap metadataHeaders = new OrderedMap();

		//do the data header - drives the other columns - based on widest entry

		List header = new ArrayList(widestRow.keySet());

		//do the metadata header rows (basically rotate them around)

		Iterator headerIter = header.iterator();

		String lastValue = "";

		while (headerIter.hasNext()) {

			String column = (String) headerIter.next();

			//get the pivotValue part of column name

			String pivotValue = column;

			try {

				pivotValue = column.substring(0, column.indexOf("_"));

			}

			catch (Exception e) {}

			//look up the row from the metadata - keyed by pivot value

			OrderedMap metadataRow = (OrderedMap) headerRows.get(pivotValue);

			if (metadataRow != null) {

				//go through the values

				Iterator metadataIter = metadataRow.keySet().iterator();

				while (metadataIter.hasNext()) {

					String key = (String) metadataIter.next();

					String value = (String) metadataRow.get(key);

					OrderedMap newMetadataRow = (OrderedMap) metadataHeaders.get(key);

					if (newMetadataRow == null) {

						newMetadataRow = new OrderedMap();

					}

					//if it's the same as the last one, just use null value

					if (lastValue.equals(pivotValue)) {

						value = null;

					} 

					newMetadataRow.put(column, value);

					metadataHeaders.put(key, newMetadataRow);

				}

			}

			lastValue = pivotValue;

		}

		//make metadata rows as list/arrays on the reteurn table

		Iterator metadataLabelIter = metadataHeaders.keySet().iterator();

		while (metadataLabelIter.hasNext()) {

			String label = (String) metadataLabelIter.next();

			OrderedMap row = (OrderedMap) metadataHeaders.get(label);

			List rowValues = new ArrayList(row.values());

			rowValues.add(0, label);

			if (twoColumnMetadata) {

				//add extra column

				rowValues.add(1, null);

			}

			retTable.add(rowValues.toArray(new String[0]));

		}

		//create the special vocab matrix rows

		List vocabTable = new ArrayList();

		List uniqueVocabs = new ArrayList();

		for (int i = 0; i < allVocabNames.size(); i++) {

			List vocabRow = new ArrayList();

			String vocabName = (String) allVocabNames.get(i);

			String vocabValue = (String) allVocabValues.get(i);

			String key = vocabName + "/" + vocabValue;

			//check if we've processed this already, skip if so

			if (uniqueVocabs.contains(key)) {

				continue;

			}

			uniqueVocabs.add(key);			

			if (twoColumnMetadata) {

				vocabRow.add(vocabName);

				vocabRow.add(vocabValue);

			}

			else {

				vocabRow.add(key);

			}

			//go through the questions now, again

			String lastPivotValue = "";

			headerIter = header.iterator();

			while (headerIter.hasNext()) {

				String column = (String) headerIter.next();

				//get the pivotValue part of column name if it exists

				String pivotValue = null;

				try {

					pivotValue = column.substring(0, column.indexOf("_"));

				}

				catch (Exception e) {}

				if (pivotValue == null) {

					continue;

				}

				//check to not duplicate values

				if (pivotValue.equals(lastPivotValue)) {

					vocabRow.add(null);

				}

				else {

					//check to see if this question has that keyword

					List names = (List) vocabNames.get(pivotValue);

					List values = (List) vocabValues.get(pivotValue);

					if (names != null && names.indexOf(vocabName) > -1 && names.indexOf(vocabName) == values.indexOf(vocabValue) ) {

						vocabRow.add("true");

					}

					else {

						vocabRow.add("false");

					}

				}

				lastPivotValue = pivotValue;

			}

			//put the row on

			vocabTable.add(vocabRow.toArray(new String[0]));

		}

		//put the vocab matrix on the table

		retTable.addAll(vocabTable);

		if (twoColumnMetadata) {

			//add column to data header row

			header.add(1, null);

		}

		//replace the "studentId" label

		int temp = header.indexOf("studentid");

		if (header.remove(temp) != null) {

			header.add(temp, "recordNum");

		}

		//put the data header row on the table

		retTable.add(header.toArray(new String[0]));

		//now the value rows in the table

		Iterator rowIter = table.values().iterator();

		int rowCount = 1;

		while (rowIter.hasNext()) {

			OrderedMap rowMap = (OrderedMap) rowIter.next();

			List row = new ArrayList();

			//iterate over the widest row's columns

			Iterator columnIter = widestRow.keySet().iterator();

			while (columnIter.hasNext()) {

				Object key = columnIter.next();

				Object value = rowMap.get(key);

				//hide the value used for Ids - just increment row

				if (key.equals(idColName) && omitIdValues) {

					value = String.valueOf(rowCount);

				}

				row.add(value);

			}

			rowCount++;

			if (twoColumnMetadata) {

				//add extra column

				row.add(1, null);

			}

			retTable.add(row.toArray(new String[0]));

		}

		return retTable;

	}

%><%!

	private String cleanUp(String value) {

		if (value != null) {

			value = value.replaceAll("\n", " ");

			value = value.replaceAll("\\s+", " ");

			value = value.replaceAll("<html>", " ");

			value = value.replaceAll("</html>", " ");

			value = value.replaceAll("<head>", " ");

			value = value.replaceAll("</head>", " ");

			value = value.replaceAll("<body>", " ");

			value = value.replaceAll("</body>", " ");

			//translate any ecogrid urls

			value = convertEcogridURL(value);

		}

		return value;

	}

%><%!

private String convertEcogridURL(String value) {

	if (value != null) {

		String prefix = "ecogrid://knb/";

		if (value.startsWith(prefix)) {

			//String docid = value.substring(prefix.length(), value.length());

			// TODO make URL

			String contextURL = "";

			try {

				contextURL = SystemUtil.getContextURL();

			}

			catch (PropertyNotFoundException pnfe) {

				//do nothing

			}

			value = value.replaceFirst(prefix, contextURL + "/metacat?action=read&docid=");

		}

	}

	return value;

}

%><%!

	private void handleDataquery(

			Hashtable<String, String[]> params,

	        HttpServletResponse response,

	        String sessionId) throws PropertyNotFoundException, IOException {

		DataQuery dq = null;

		if (sessionId != null) {

			dq = new DataQuery(sessionId);

		}

		else {

			dq = new DataQuery();

		}

		String dataqueryXML = (params.get("dataquery"))[0];

		ResultSet rs = null;

		try {

			rs = dq.executeQuery(dataqueryXML);

		} catch (Exception e) {

			//probably need to do something here

			e.printStackTrace();

			return;

		}

		//process the result set

		String qformat = "csv";

		String[] temp = params.get("qformat");

		if (temp != null && temp.length > 0) {

			qformat = temp[0];

		}

		String fileName = "query-results." + qformat;

		boolean transpose = false;

		temp = params.get("transpose");

		if (temp != null && temp.length > 0) {

			transpose = Boolean.parseBoolean(temp[0]);

		}

		int observation = 0;

		temp = params.get("observation");

		if (temp != null && temp.length > 0) {

			observation = Integer.parseInt(temp[0]);

		}

		int pivot = 0;

		temp = params.get("pivot");

		if (temp != null && temp.length > 0) {

			pivot = Integer.parseInt(temp[0]);

		}

		String[] pivotColumns = null;

		temp = params.get("pivotColumns");

		if (temp != null && temp.length > 0) {

			pivotColumns = temp;

		}

		//get the results as csv file

		if (qformat != null && qformat.equalsIgnoreCase("csv")) {

			response.setContentType("text/csv");

			//response.setContentType("application/csv");

	        response.setHeader("Content-Disposition", "attachment; filename=" + fileName);

			Writer writer = new OutputStreamWriter(response.getOutputStream());

			//CSVWriter csv = new CSVWriter(writer, CSVWriter.DEFAULT_SEPARATOR, CSVWriter.NO_QUOTE_CHARACTER);

			CSVWriter csv = new CSVWriter(writer, CSVWriter.DEFAULT_SEPARATOR, CSVWriter.DEFAULT_QUOTE_CHARACTER, CSVWriter.DEFAULT_ESCAPE_CHARACTER);

			try {

				if (transpose) {

					List pivotCols = new ArrayList();

					if (pivotColumns != null) {

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

							pivotCols.add(pivotColumns[i]);

						}

					} else {

						pivotCols.add("studentid");

						pivotCols.add("score");

						pivotCols.add("response");

						pivotCols.add("responsefile");

					}

					List transposedTable = transpose(rs, observation, pivot, pivotCols, true);

					csv.writeAll(transposedTable);

				} else {

					List processedTable = processResultsSet(rs, 3, "recordNum");

					csv.writeAll(processedTable);

				}

				csv.flush();

				response.flushBuffer();

				rs.close();

			} catch (SQLException e) {

				e.printStackTrace();

			}

			return;

		}

	}

%>