/** * @param sourceFile File to read from * @return List of String objects with the shas */ public static FileRequestFileContent readRequestFile(final File sourceFile) { if (!sourceFile.isFile() || !(sourceFile.length() > 0)) { return null; } Document d = null; try { d = XMLTools.parseXmlFile(sourceFile.getPath()); } catch (final Throwable t) { logger.log(Level.SEVERE, "Exception in readRequestFile, during XML parsing", t); return null; } if (d == null) { logger.log(Level.SEVERE, "Could'nt parse the request file"); return null; } final Element rootNode = d.getDocumentElement(); if (rootNode.getTagName().equals(TAG_FrostFileRequestFile) == false) { logger.severe( "Error: xml request file does not contain the root tag '" + TAG_FrostFileRequestFile + "'"); return null; } final String timeStampStr = XMLTools.getChildElementsTextValue(rootNode, TAG_timestamp); if (timeStampStr == null) { logger.severe("Error: xml file does not contain the tag '" + TAG_timestamp + "'"); return null; } final long timestamp = Long.parseLong(timeStampStr); final List<Element> nodelist = XMLTools.getChildElementsByTagName(rootNode, TAG_shaList); if (nodelist.size() != 1) { logger.severe("Error: xml request files must contain only one element '" + TAG_shaList + "'"); return null; } final Element rootShaNode = nodelist.get(0); final List<String> shaList = new LinkedList<String>(); final List<Element> xmlKeys = XMLTools.getChildElementsByTagName(rootShaNode, TAG_sha); for (final Element el : xmlKeys) { final Text txtname = (Text) el.getFirstChild(); if (txtname == null) { continue; } final String sha = txtname.getData(); shaList.add(sha); } final FileRequestFileContent content = new FileRequestFileContent(timestamp, shaList); return content; }
/** * This is just a helper function for the fromXML method. * * @param child */ public void importHelper(Node child) { if (child.getFirstChild() instanceof Text) { Text text = (Text) child.getFirstChild(); String data = text.getData(); if (child.getNodeName().equals("description")) { setDescription(data); } if (child.getNodeName().equals("refChildPattern")) { int decID = Integer.parseInt(data.substring(1)); subPatternsID.add(decID); } } }
// ## operation readReactorOutputFile(ReactionModel) public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) { // #[ operation readReactorOutputFile(ReactionModel) try { // open output file and build the DOM tree String dir = System.getProperty("RMG.workingDirectory"); String filename = "chemkin/reactorOutput.xml"; File inputFile = new File(filename); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(true); // validate the document with the DTD factory.setIgnoringElementContentWhitespace(true); // ignore whitespace DocumentBuilder builder = factory.newDocumentBuilder(); Document doc = builder.parse(inputFile); // get root element and its children Element root = doc.getDocumentElement(); NodeList rootchildren = root.getChildNodes(); // header is rootchildren.item(0) // get return message and check for successful run Element returnmessageElement = (Element) rootchildren.item(1); Text returnmessageText = (Text) returnmessageElement.getFirstChild(); String returnmessage = returnmessageText.toString(); returnmessage = returnmessage.trim(); if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) { System.out.println("External reactor model failed!"); System.out.println("Reactor model error message: " + returnmessage); System.exit(0); } // get outputvalues element and its children Element outputvaluesElement = (Element) rootchildren.item(2); NodeList children = outputvaluesElement.getChildNodes(); // get time Element timeElement = (Element) children.item(0); Text timeText = (Text) timeElement.getFirstChild(); double time = Double.parseDouble(timeText.getData()); String timeUnits = timeElement.getAttribute("units"); // get systemstate element and its children Element systemstateElement = (Element) children.item(1); NodeList states = systemstateElement.getChildNodes(); // get temperature and its units Element temperatureElement = (Element) states.item(0); String tempUnits = temperatureElement.getAttribute("units"); Text temperatureText = (Text) temperatureElement.getFirstChild(); double temp = Double.parseDouble(temperatureText.getData()); Temperature T = new Temperature(temp, tempUnits); // get pressure and its units Element pressureElement = (Element) states.item(1); String presUnits = pressureElement.getAttribute("units"); Text pressureText = (Text) pressureElement.getFirstChild(); double pres = Double.parseDouble(pressureText.getData()); Pressure P = new Pressure(pres, presUnits); // get species amounts (e.g. concentrations) ArrayList speciesIDs = new ArrayList(); ArrayList amounts = new ArrayList(); ArrayList fluxes = new ArrayList(); String amountUnits = null; String fluxUnits = null; // loop thru all the species // begin at i=2, since T and P take already the first two position of states int nSpe = (states.getLength() - 2) / 2; int index = 0; LinkedHashMap inertGas = new LinkedHashMap(); for (int i = 2; i < nSpe + 2; i++) { // get amount element and the units Element amountElement = (Element) states.item(i); amountUnits = amountElement.getAttribute("units"); Element fluxElement = (Element) states.item(i + nSpe); fluxUnits = fluxElement.getAttribute("units"); // get speciesid and store in an array list String thisSpeciesID = amountElement.getAttribute("speciesid"); // get amount (e.g. concentraion) and store in an array list Text amountText = (Text) amountElement.getFirstChild(); double thisAmount = Double.parseDouble(amountText.getData()); if (thisAmount < 0) { double aTol = ReactionModelGenerator.getAtol(); // if (Math.abs(thisAmount) < aTol) thisAmount = 0; // else throw new NegativeConcentrationException("Negative concentration in // reactorOutput.xml: " + thisSpeciesID); if (thisAmount < -100.0 * aTol) throw new NegativeConcentrationException( "Species " + thisSpeciesID + " has negative concentration: " + String.valueOf(thisAmount)); } // get amount (e.g. concentraion) and store in an array list Text fluxText = (Text) fluxElement.getFirstChild(); double thisFlux = Double.parseDouble(fluxText.getData()); if (thisSpeciesID.compareToIgnoreCase("N2") == 0 || thisSpeciesID.compareToIgnoreCase("Ne") == 0 || thisSpeciesID.compareToIgnoreCase("Ar") == 0) { inertGas.put(thisSpeciesID, new Double(thisAmount)); } else { speciesIDs.add(index, thisSpeciesID); amounts.add(index, new Double(thisAmount)); fluxes.add(index, new Double(thisFlux)); index++; } } // print results for debugging purposes /** * System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits); * System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size(); * i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); } */ ReactionTime rt = new ReactionTime(time, timeUnits); LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes); SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P); ss.inertGas = inertGas; return ss; } catch (Exception e) { System.out.println("Error reading reactor model output: " + e.getMessage()); System.exit(0); return null; } // #] }
/** * Creates nodes from index entries * * @param theIndexEntries index entries * @param theTargetDocument target document * @param theIndexEntryComparator comparator to sort the index entries. if it is null the index * entries will be unsorted * @return nodes for the target document */ private Node[] transformToNodes( final IndexEntry[] theIndexEntries, final Document theTargetDocument, final Comparator<IndexEntry> theIndexEntryComparator) { if (null != theIndexEntryComparator) { Arrays.sort(theIndexEntries, theIndexEntryComparator); } final List<Element> result = new ArrayList<Element>(); for (final IndexEntry indexEntry : theIndexEntries) { final Element indexEntryNode = createElement(theTargetDocument, "index.entry"); final Element formattedStringElement = createElement(theTargetDocument, "formatted-value"); if (indexEntry.getContents() != null) { for (final Iterator<Node> i = indexEntry.getContents().iterator(); i.hasNext(); ) { final Node child = i.next(); final Node clone = theTargetDocument.importNode(child, true); if (!i.hasNext() && clone.getNodeType() == Node.TEXT_NODE) { final Text t = (Text) clone; t.setData(t.getData().replaceAll("[\\s\\n]+$", "")); } formattedStringElement.appendChild(clone); } } else { final Text textNode = theTargetDocument.createTextNode(indexEntry.getFormattedString()); textNode.normalize(); formattedStringElement.appendChild(textNode); } indexEntryNode.appendChild(formattedStringElement); final String[] refIDs = indexEntry.getRefIDs(); for (final String refID : refIDs) { final Element referenceIDElement = createElement(theTargetDocument, "refID"); referenceIDElement.setAttribute("value", refID); indexEntryNode.appendChild(referenceIDElement); } final String val = indexEntry.getValue(); if (null != val) { indexEntryNode.setAttribute("value", val); } final String sort = indexEntry.getSortString(); if (null != sort) { indexEntryNode.setAttribute("sort-string", sort); } if (indexEntry.isStartingRange()) { indexEntryNode.setAttribute("start-range", "true"); } else if (indexEntry.isEndingRange()) { indexEntryNode.setAttribute("end-range", "true"); } if (indexEntry.isSuppressesThePageNumber()) { indexEntryNode.setAttribute("no-page", "true"); } else if (indexEntry.isRestoresPageNumber()) { indexEntryNode.setAttribute("single-page", "true"); } final IndexEntry[] childIndexEntries = indexEntry.getChildIndexEntries(); final Node[] nodes = transformToNodes(childIndexEntries, theTargetDocument, theIndexEntryComparator); for (final Node node : nodes) { indexEntryNode.appendChild(node); } final IndexEntry[] seeChildIndexEntries = indexEntry.getSeeChildIndexEntries(); if (seeChildIndexEntries != null) { final Element seeElement = createElement(theTargetDocument, "see-childs"); final Node[] seeNodes = transformToNodes(seeChildIndexEntries, theTargetDocument, theIndexEntryComparator); for (final Node node : seeNodes) { seeElement.appendChild(node); } indexEntryNode.appendChild(seeElement); } final IndexEntry[] seeAlsoChildIndexEntries = indexEntry.getSeeAlsoChildIndexEntries(); if (seeAlsoChildIndexEntries != null) { final Element seeAlsoElement = createElement(theTargetDocument, "see-also-childs"); final Node[] seeAlsoNodes = transformToNodes(seeAlsoChildIndexEntries, theTargetDocument, theIndexEntryComparator); for (final Node node : seeAlsoNodes) { seeAlsoElement.appendChild(node); } indexEntryNode.appendChild(seeAlsoElement); } result.add(indexEntryNode); } return (Node[]) result.toArray(new Node[result.size()]); }