Esempio n. 1
0
  /**
   * @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;
  }
Esempio n. 2
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 /**
  * 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);
     }
   }
 }
Esempio n. 3
0
  // ## 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;
    }

    // #]
  }
Esempio n. 4
0
  /**
   * 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()]);
  }