private boolean checkMandatoryParameters(
Repository repositoryDocument,
boolean propertyChanged,
ArrayList<Property> newPropertyList,
HashSet<String> configVariableNames) {
/*
* mandatory paramters, the ones from param that have not been covered yet.
*/
// If there was no required parameters given by WPSconfig, host and port defaults will be added
// (RServe_User and RServe_port won't be added)
if (configVariableNames.contains(RWPSConfigVariables.RSERVE_HOST.toString().toLowerCase())) {
Property host = repositoryDocument.addNewProperty();
host.setActive(true);
host.setName(RWPSConfigVariables.RSERVE_HOST.toString());
host.setStringValue(R_Config.getInstance().rServeHost);
newPropertyList.add(host);
propertyChanged = true;
}
if (configVariableNames.contains(RWPSConfigVariables.RSERVE_PORT.toString().toLowerCase())) {
Property port = repositoryDocument.addNewProperty();
port.setActive(true);
port.setName(RWPSConfigVariables.RSERVE_PORT.toString());
port.setStringValue(Integer.toString(R_Config.getInstance().rServePort));
newPropertyList.add(port);
propertyChanged = true;
}
return propertyChanged;
}
private boolean addMissingAlgorithms(
Repository repositoryDocument,
HashMap<String, Property> algorithmPropertyHash,
boolean propertyChanged,
ArrayList<Property> newPropertyList) {
// check script dir for R process files
// adjusts WPS config
String scriptDir = R_Config.getInstance().getScriptDirFullPath();
File algorithmDir = new File(scriptDir);
if (algorithmDir.isDirectory()) {
File[] scripts = algorithmDir.listFiles(new R_Config.RFileExtensionFilter());
LOGGER.debug("Loading script files from " + algorithmDir + ": " + Arrays.toString(scripts));
for (File scriptf : scripts) {
String wkn = R_Config.getInstance().FileToWkn(scriptf);
Property prop = algorithmPropertyHash.get(wkn);
// case: property is missing in wps config
if (prop == null) {
// Change Property if Algorithm is not inside process description:
prop = repositoryDocument.addNewProperty();
prop.setActive(true);
prop.setName(RWPSConfigVariables.ALGORITHM.toString());
prop.setStringValue(wkn);
newPropertyList.add(prop);
LOGGER.debug("Added new algorithm property to repo document: " + prop);
propertyChanged = true;
} else {
LOGGER.debug("Algorithm property already repo document: " + prop);
newPropertyList.add(algorithmPropertyHash.remove(wkn));
}
/*
* if(prop.getActive() && addAlgorithm){ repository.addAlgorithm(wkn); }
*/
}
}
return propertyChanged;
}
public void updateRepositoryConfiguration() {
// Retrieve repository document and properties:
String localRAlgorithmRepository_className = LocalRAlgorithmRepository.class.getCanonicalName();
Repository[] repositoryDocuments = WPSConfig.getInstance().getRegisterdAlgorithmRepositories();
Repository repositoryDocument = null;
for (Repository doc : repositoryDocuments) {
if (doc.getClassName().equals(localRAlgorithmRepository_className)) {
repositoryDocument = doc;
}
}
if (repositoryDocument == null) {
LOGGER.error("Local R Algorithm Repository is not registered");
// return;
}
Property[] oldPropertyArray = repositoryDocument.getPropertyArray();
HashMap<String, Property> algorithmPropertyHash = new HashMap<String, Property>();
boolean propertyChanged = false;
ArrayList<Property> newPropertyList = new ArrayList<Property>();
// test if host and port of rserve are available in config properties, if not, values from
// R_Config
// will be used
// retrieve set of string representations for all config variables:
HashSet<String> configVariableNames = new HashSet<String>();
for (RWPSConfigVariables var : RWPSConfigVariables.values()) {
configVariableNames.add(var.toString().toLowerCase());
}
for (Property property : oldPropertyArray) {
String pname = property.getName().toLowerCase();
// check the name and active state
if (pname.equalsIgnoreCase(RWPSConfigVariables.ALGORITHM.toString())) {
LOGGER.debug("Algorithm property: " + property);
// put id into a dictionary to check and add later:
algorithmPropertyHash.put(property.getStringValue(), property);
} else {
LOGGER.debug("NOT-algorithm property: " + property);
if (configVariableNames.contains(pname)) {
boolean success = handleConfigVariable(property);
if (!success) LOGGER.warn("Invalid config variable was omitted and deleted: " + property);
// config variable should occur only once, doubling will be omitted:
configVariableNames.remove(pname);
} else {
// valid properties which are not algorithms will be just passed to the new list
LOGGER.debug("Unprocessed property: " + property);
}
newPropertyList.add(property);
}
}
propertyChanged =
checkMandatoryParameters(
repositoryDocument, propertyChanged, newPropertyList, configVariableNames);
propertyChanged =
addMissingAlgorithms(
repositoryDocument, algorithmPropertyHash, propertyChanged, newPropertyList);
// there might be registered algorithms, which don't got a script file any more,
// those will be deleted here:
if (!algorithmPropertyHash.isEmpty()) propertyChanged = true;
propertyChanged = checkPropertyOrder(oldPropertyArray, propertyChanged);
if (propertyChanged) {
Property[] newPropertyArray = newPropertyList.toArray(new Property[0]);
// sort list of properties lexicographically:
Arrays.sort(newPropertyArray, new PropertyComparator());
repositoryDocument.setPropertyArray(newPropertyArray);
propertyChanged = true;
// write new WPSConfig if property had to be changed
WPSConfigurationDocument wpsConfigurationDocument =
WPSConfigurationDocument.Factory.newInstance();
WPSConfiguration wpsConfig = WPSConfig.getInstance().getWPSConfig();
wpsConfigurationDocument.setWPSConfiguration(wpsConfig);
// writes the new WPSConfig to a file
try {
String configurationPath = WPSConfig.getConfigPath();
File XMLFile = new File(configurationPath);
wpsConfigurationDocument.save(
XMLFile,
new org.apache.xmlbeans.XmlOptions().setUseDefaultNamespace().setSavePrettyPrint());
WPSConfig.forceInitialization(configurationPath);
LOGGER.info("WPS Config was changed.");
} catch (IOException e) {
LOGGER.error("Could not write configuration to file: " + e.getMessage());
} catch (org.apache.xmlbeans.XmlException e) {
LOGGER.error("Could not generate XML File from Data: " + e.getMessage());
}
}
}
