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Diffstat (limited to 'petascope/src/petascope/wcs2/server/ops/GetCoverage.java')
| -rw-r--r-- | petascope/src/petascope/wcs2/server/ops/GetCoverage.java | 529 |
1 files changed, 0 insertions, 529 deletions
diff --git a/petascope/src/petascope/wcs2/server/ops/GetCoverage.java b/petascope/src/petascope/wcs2/server/ops/GetCoverage.java deleted file mode 100644 index a6ddcff..0000000 --- a/petascope/src/petascope/wcs2/server/ops/GetCoverage.java +++ /dev/null @@ -1,529 +0,0 @@ -/* - * This file is part of rasdaman community. - * - * Rasdaman community 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 3 of the License, or - * (at your option) any later version. - * - * Rasdaman community 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 rasdaman community. If not, see <http://www.gnu.org/licenses/>. - * - * Copyright 2003, 2004, 2005, 2006, 2007, 2008, 2009 Peter Baumann / - rasdaman GmbH. - * - * For more information please see <http://www.rasdaman.org> - * or contact Peter Baumann via <baumann@rasdaman.com>. - */ -package petascope.wcs2.server.ops; - -//~--- non-JDK imports -------------------------------------------------------- -import org.apache.commons.io.IOUtils; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import org.w3c.dom.Document; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; - -import org.xml.sax.SAXException; - -import petascope.ConfigManager; - -import petascope.wcps.server.core.DbMetadataSource; -import petascope.wcps.server.core.Metadata; - -import petascope.wcs.server.exceptions.WCSException; - -//~--- JDK imports ------------------------------------------------------------ - -import java.io.IOException; - -import java.math.BigInteger; -import java.util.HashSet; -import java.util.Iterator; - -import java.util.List; -import java.util.Set; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.xpath.XPath; -import javax.xml.xpath.XPathConstants; -import javax.xml.xpath.XPathExpressionException; -import javax.xml.xpath.XPathFactory; -import org.odmg.DBag; -import org.odmg.Database; -import org.odmg.Implementation; -import org.odmg.ODMGException; -import org.odmg.OQLQuery; -import org.odmg.QueryException; -import org.odmg.Transaction; -import rasj.RasGMArray; -import rasj.RasImplementation; -import petascope.wcps.server.core.CellDomainElement; -import petascope.wcps.server.core.DomainElement; -import petascope.wcps.server.core.RangeElement; -import petascope.wcps.server.core.SDU; -import petascope.wcs.server.exceptions.InputOutputException; -import petascope.wcs.server.exceptions.InternalComponentException; -import petascope.wcs.server.exceptions.InvalidParameterValueException; -import petascope.wcs.server.exceptions.InvalidServiceConfigurationException; -import petascope.wcs.server.exceptions.NoApplicableCodeException; -import petascope.wcs.server.exceptions.WcsRuntimeException; -import petascope.wcs.server.exceptions.XmlNotValidException; -import petascope.wcs2.server.templates.WcsNamespaceContext; - -/** - * Get Coverage operation for WCS 2.0 - * - * @author Andrei Aiordachioaie - */ -public class GetCoverage implements WcsOperation { - - private static Logger LOG = LoggerFactory.getLogger(GetCoverage.class); - private DocumentBuilder builder = null; - private XPathFactory xpathFactory = XPathFactory.newInstance(); - /* Template XMLs for response types */ - private String GetCoverageResponse; - private String rangeComponentTemplate; - /* Xml request */ - private Document doc; - /* for Metadata */ - private DbMetadataSource meta; - /* The new coverage domain */ - private String lowPoint, highPoint, newAxesLabels; - - public GetCoverage(DbMetadataSource metadata) throws WCSException { - meta = metadata; - GetCoverageResponse = ConfigManager.WCS2_GET_COVERAGE_TEMPLATE; - if (GetCoverageResponse == null) { - throw new InvalidServiceConfigurationException("Could not find template file."); - } - - /* Find the RangeField template string */ - String starttag = "<gmlwcs:rangeField", endtag = "</gmlwcs:rangeField>"; - int start = GetCoverageResponse.indexOf(starttag); - int end = GetCoverageResponse.indexOf(endtag); - rangeComponentTemplate = GetCoverageResponse.substring(start, end + endtag.length()); - String newTemplate = GetCoverageResponse.substring(0, start - 1) + GetCoverageResponse.substring(end + endtag.length()); - GetCoverageResponse = newTemplate; - - /* init XML parser */ - DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); - domFactory.setNamespaceAware(true); // never forget this! - try { - builder = domFactory.newDocumentBuilder(); - } catch (Exception e) { - throw new NoApplicableCodeException("Error initializing XML parser", e); - } - } - - @Override - public String execute(String stringXml) throws WCSException { - String output; - Metadata cov; - - try { - doc = builder.parse(IOUtils.toInputStream(stringXml)); - cov = readCoverageMetadata(); - } catch (SAXException e) { - throw new XmlNotValidException("Could not parse input request.", e); - } catch (IOException e) { - throw new InputOutputException("Could not read input request", e); - } catch (XPathExpressionException e) { - throw new InternalComponentException("Invalid XPath expression", e); - } - - // Analyze input and build trim/slice info structures - String subsetting = computeRequestSubsettingLimits(cov); - String coverageName = cov.getCoverageName(); - - // Evaluate all bands and then perform string processing to get coverage data - String coverageData = buildCoverageData(cov, subsetting); - - // Build response xml document - output = buildOutputXml(coverageData, cov); - - return output; - } - - private NodeList evalXPathList(String query, Object context) throws WCSException { - try { - LOG.debug("Evaluating XPath: {}", query); - XPath xpath = xpathFactory.newXPath(); - - xpath.setNamespaceContext(new WcsNamespaceContext()); - NodeList result = (NodeList) xpath.evaluate(query, context, XPathConstants.NODESET); - - for (int i = 0; i < result.getLength(); i++) { - LOG.trace("Result {}: {}", i, result.item(i).getNodeValue()); - } - - return (NodeList) result; - } catch (XPathExpressionException e) { - LOG.error("Could not execute XPath expression '{}'", query); - - throw new WcsRuntimeException("Could not execute XPath expression", e); - } - } - - private String getCoverageName(Document doc) throws WCSException { - NodeList nodes = evalXPathList("//wcs:id/@gml:id", doc); - - if (nodes.getLength() != 1) { - LOG.error("Could not retrieve coverage name from XML document."); - - return null; - } - - return nodes.item(0).getNodeValue(); - } - - private Metadata readCoverageMetadata() throws WCSException, XPathExpressionException { - String coverageId = getCoverageName(doc); - - if (meta.existsCoverageName(coverageId)) { - try { - Metadata cov = meta.read(coverageId); - - return cov; - } catch (Exception e) { - e.printStackTrace(); - - throw new NoApplicableCodeException("Metadata for coverage '" - + coverageId + "' is not valid."); - } - } else { - throw new InvalidParameterValueException("gml:id"); - } - } - - /** Computes the domain of the new coverage, and returns a string that can be - * used to do subsetting on the original coverage. Also computes the low, high - * and the axis labels for the new coverage. - * - * @param coverage - * @return - * @throws WCSException - */ - private String computeRequestSubsettingLimits(Metadata coverage) throws WCSException { - int dims = coverage.getDimension(), i = 0; - String[] limits = new String[dims]; - BigInteger[] high = new BigInteger[dims]; - BigInteger[] low = new BigInteger[dims]; - String[] axesLabels = new String[dims]; - boolean[] sliced = new boolean[dims]; - boolean[] trimmed = new boolean[dims]; - - Iterator<CellDomainElement> it = coverage.getCellDomainIterator(); - Iterator<DomainElement> it2 = coverage.getDomainIterator(); - i = 0; - while (it.hasNext() && it2.hasNext()) { - CellDomainElement cell = it.next(); - DomainElement dom = it2.next(); - LOG.trace(cell.toString()); - LOG.trace(dom.toString()); - high[i] = cell.getHi(); - low[i] = cell.getLo(); - axesLabels[i] = dom.getName(); - limits[i] = low[i] + ":" + high[i]; - sliced[i] = false; - trimmed[i] = false; - i++; - } - - NodeList list = null; - int axisIndex; - String axis, root; - NodeList trims, slices; - - trims = evalXPathList("//wcs:trimDimension", doc); - for (i = 0; i < trims.getLength(); i++) { - Node trim = trims.item(i); - - list = evalXPathList("wcs:dimension/text()", trim); - axis = list.item(0).getNodeValue(); - axisIndex = coverage.getDomainIndexByName(axis); - if (axisIndex == -1) { - throw new InvalidParameterValueException("dimension. Explanation: Unknown axis: " + axis); - } - if (trimmed[axisIndex] || sliced[axisIndex]) { - throw new NoApplicableCodeException("Already performed one subsetting operation on axis: " + axis); - } - - list = evalXPathList("wcs:trimLow/text()", trim); - if (list.getLength() > 0) { - try { - long val = Long.parseLong(list.item(0).getNodeValue()); - low[axisIndex] = BigInteger.valueOf(val); - } catch (NumberFormatException e) { - throw new InvalidParameterValueException("trimLow. Explanation: invalid integer number: " + list.item(0).getNodeValue()); - } - } - list = evalXPathList("wcs:trimHigh/text()", trim); - if (list.getLength() > 0) { - try { - long val = Long.parseLong(list.item(0).getNodeValue()); - high[axisIndex] = BigInteger.valueOf(val); - } catch (NumberFormatException e) { - throw new InvalidParameterValueException("trimHigh. Explanation: invalid integer number: " + list.item(0).getNodeValue()); - } - } - - trimmed[axisIndex] = true; - limits[axisIndex] = low[axisIndex] + ":" + high[axisIndex]; - LOG.debug("New limits for axis {}: {}", axis, limits[axisIndex]); - } - - slices = evalXPathList("//wcs:sliceDimension", doc); - for (i = 0; i < slices.getLength(); i++) { - Node slice = slices.item(i); - - list = evalXPathList("wcs:dimension/text()", slice); - axis = list.item(0).getNodeValue(); - axisIndex = coverage.getDomainIndexByName(axis); - if (axisIndex == -1) { - throw new InvalidParameterValueException("dimension. Explanation: Unknown axis name: " + axis); - } - if (trimmed[axisIndex] || sliced[axisIndex]) { - throw new NoApplicableCodeException("Already performed one subsetting operation on axis: " + axis); - } - - list = evalXPathList("wcs:slicePoint/text()", slice); - if (list.getLength() > 0) { - try { - long point = Long.parseLong(list.item(0).getNodeValue()); - low[axisIndex] = BigInteger.valueOf(point); - } catch (NumberFormatException e) { - throw new InvalidParameterValueException("slicePoint. Explanation: invalid integer number: " + list.item(0).getNodeValue()); - } - high[axisIndex] = low[axisIndex]; - limits[axisIndex] = list.item(0).getNodeValue(); - } - - sliced[axisIndex] = true; - LOG.debug("New limits for axis {}: {}", axis, limits[axisIndex]); - } - - // Compute the lowest, highest point and the labels - lowPoint = ""; - highPoint = ""; - newAxesLabels = ""; - int first = 0; - for (i = 0; i < dims; i++) { - if (sliced[i] == false) { - if (first == 0) { - lowPoint = low[i].toString(); - highPoint = high[i].toString(); - newAxesLabels = axesLabels[i]; - first++; - } else { - lowPoint += " " + low[i]; - highPoint += " " + high[i]; - newAxesLabels += " " + axesLabels[i]; - } - } - } - - // Concatenate all limits into a single string - String result = limits[0]; - - for (i = 1; i < dims; i++) { - result += ", " + limits[i]; - } - - return result; - } - - public String executeRasqlQuery(String query) throws WCSException { - byte[] result = null; - - Implementation impl = new RasImplementation(ConfigManager.RASDAMAN_URL); - Database db = impl.newDatabase(); - - try { - db.open(ConfigManager.RASDAMAN_DATABASE, Database.OPEN_READ_ONLY); - } catch (ODMGException odmge) { - try { - db.close(); - } catch (ODMGException e) { - } - - throw new InternalComponentException("Could not connect to rasdaman server at " + ConfigManager.RASDAMAN_URL + ", database " + ConfigManager.RASDAMAN_DATABASE, odmge); - } - - Transaction tr = impl.newTransaction(); - - tr.begin(); - OQLQuery q = impl.newOQLQuery(); - DBag resultSet; - - try { - q.create(query); - resultSet = (DBag) q.execute(); - - if (resultSet != null) { - Iterator resultIterator = resultSet.iterator(); - - if (resultIterator.hasNext()) { - Object current = resultIterator.next(); - - try { - RasGMArray resultArray = (RasGMArray) current; - result = resultArray.getArray(); - } catch (ClassCastException e) { - LOG.error("result=" + current.toString()); - result = current.toString().getBytes(); - } - } - } - } catch (QueryException qe) { - tr.commit(); - - try { - db.close(); - } catch (ODMGException odmge) { - } - - throw new InternalComponentException("Could not evaluate rasdaman query: '" + query + "'. Cause: " + qe.getMessage(), qe); - } - - tr.commit(); - - try { - db.close(); - } catch (ODMGException odmge) { - } - - return new String(result); - } - - /** Creates a string with the contents of the GetCoverage response XML */ - private String buildOutputXml(String coverageData, Metadata coverage) { - String xml = GetCoverageResponse; - xml = xml.replaceAll("\\{coverageId\\}", coverage.getCoverageName() + Math.random()); - xml = xml.replaceAll("\\{gridDimension\\}", String.valueOf(coverage.getDimension())); - xml = xml.replaceAll("\\{gridId\\}", "grid-" + coverage.getCoverageName()); - // low - xml = xml.replaceAll("\\{low\\}", lowPoint); - // high - xml = xml.replaceAll("\\{high\\}", highPoint); - // axisLabels - xml = xml.replaceAll("\\{axisLabels\\}", newAxesLabels); - // coverageData - xml = xml.replaceAll("\\{coverageData\\}", coverageData); - - - - // Build the range structure - Iterator<RangeElement> it3 = coverage.getRangeIterator(); - int i = -1; - String rangeComponents = ""; - while (it3.hasNext()) { - String component = rangeComponentTemplate; - RangeElement range = it3.next(); - i++; - String rangeId = "range-" + coverage.getCoverageId() + "-" + range.getName(); - LOG.trace(range.toString()); - - component = component.replaceAll("\\{rangeFieldId\\}", rangeId); - component = component.replaceAll("\\{fieldName\\}", range.getName()); - component = component.replaceAll("\\{datatype\\}", DescribeCoverage.DATATYPE_URN_PREFIX + range.getType()); - - // Compute the null values for this range field - Set<String> nullVals = new HashSet<String>(); - Iterator<String> it = coverage.getNullSetIterator(); - while (it.hasNext()) { - List<String> nilVal = SDU.str2string(it.next()); - nullVals.add(nilVal.get(i)); - } - StringBuffer nullValsString = new StringBuffer(); - it = nullVals.iterator(); - while (it.hasNext()) { - nullValsString.append(" " + it.next()); - } - component = component.replaceAll("\\{nilValues\\}", nullValsString.toString().substring(1)); - - // And add this range field to the range structure - rangeComponents += component; - } - - xml = xml.replaceAll("\\{rangeFields\\}", rangeComponents); - xml = xml.replaceAll("\\{rangeStructureId\\}", "rangeStructure-" + coverage.getCoverageId()); - - xml = xml.replaceAll("\\{wcsSchemaUrl\\}", ConfigManager.WCS2_SCHEMA_URL); - - return xml; - } - - /** - * Retrieve the coverage data for a multi-band coverage, - * with particular subsetting parameters. - * @param coverage metadata for the coverage we want - * @param subsetting subsetting string, to be used in the RasQL query - * @return a string of space-separated values, where various bands of one - * pixel are comma-separated. For example, the string "1,2 3,4 5,6" can - * be the coverage data of a 1-by-3 coverage, with two bands - */ - private String buildCoverageData(Metadata coverage, String subsetting) throws WCSException { - String coverageName = coverage.getCoverageName(); - Iterator<RangeElement> it = coverage.getRangeIterator(); - int bandcount = 0; - while (it.hasNext()) { - it.next(); - bandcount++; - } - LOG.debug("Coverage {} has {} bands", coverageName, bandcount); - String[][] pixels = new String[bandcount][]; - String currentBand = ""; - /* For all bands of the coverage, execute a rasql query */ - for (int band = 0; band < bandcount; band++) { - LOG.trace("Processing band {}", band); - // Construct rasql query - currentBand = "." + band; - // If this is a one-band image, then band-subsetting would result in an error - if (bandcount == 1) { - currentBand = ""; - } - String rasqlQuery = "select csv(cov[" + subsetting + "]" + currentBand + ") " - + "from " + coverageName + " as cov"; - - // Execute RasQl query => coverage data - LOG.trace("Executing query {}", rasqlQuery); - String output = executeRasqlQuery(rasqlQuery); - - // Remove the curly braces from the rasql output - LOG.trace("Removing curly braces..."); - output = output.replaceAll("\\{", ""); - output = output.replaceAll("\\}", ""); - - // Tokenize the input to get the pixel values of the current band - LOG.trace("Splitting values with comma..."); - pixels[band] = output.split(","); - - LOG.trace("Done processing band {}.", band); - } - - /* Combine all bands into one single string */ - int pixelcount = pixels[0].length; - StringBuilder data = new StringBuilder(pixelcount * bandcount); - LOG.debug("Going to combine {} pixels with {} bands...", pixelcount, bandcount); - for (int pix = 0; pix < pixelcount; pix++) { - if (pixelcount > 20 && pix % (pixelcount / 20) == 0) { - LOG.debug("Processing Pixel {} of " + pixelcount + " - {}%", pix, pix * 100 / (pixelcount - 1)); - } - for (int b = 0; b < bandcount - 1; b++) { - data.append(pixels[b][pix] + ","); - } - data.append(pixels[bandcount - 1][pix]); - data.append(" "); - } - return data.substring(0, data.length() - 2); - } -} |