public List<String> getParameters() throws TaskException, MicroarrayException {
List<String> parameterStrings;
parameterStrings = new LinkedList<String>();
for (ParameterRecord parameter : operationRecord.getParameters()) {
parameterStrings.add(parameter.getValue());
}
return parameterStrings;
}
private void createOperations() {
for (OperationType operationType : sessionType.getOperation()) {
String operationSessionId = operationType.getId();
// check for unique id
if (operationRecords.containsKey(operationSessionId)) {
logger.warn("duplicate operation id: " + operationSessionId);
continue;
}
OperationRecord operationRecord = new OperationRecord();
// name id
operationRecord.setNameID(createNameID(operationType.getName()));
// category
operationRecord.setCategoryName(operationType.getCategory());
String colorString = operationType.getCategoryColor();
if (colorString != null) {
operationRecord.setCategoryColor(Color.decode(colorString));
}
// module
operationRecord.setModule(operationType.getModule());
// parameters
for (ParameterType parameterType : operationType.getParameter()) {
operationRecord.addParameter(
parameterType.getName().getId(),
parameterType.getName().getDisplayName(),
parameterType.getName().getDescription(),
parameterType.getValue());
}
// source code
String sourceCodeFileName = operationType.getSourceCodeFile();
if (sourceCodeFileName != null && !sourceCodeFileName.isEmpty()) {
String sourceCode = null;
try {
sourceCode = getSourceCode(sourceCodeFileName);
} catch (Exception e) {
logger.warn("could not load source code from " + sourceCodeFileName);
}
// might be null, is ok
operationRecord.setSourceCode(sourceCode);
}
// update names, category from the current version of the tool
OperationDefinition currentTool;
currentTool =
Session.getSession()
.getApplication()
.getOperationDefinitionBestMatch(
operationRecord.getNameID().getID(),
operationRecord.getModule(),
operationRecord.getCategoryName());
if (currentTool != null) {
operationRecord.getNameID().setDisplayName(currentTool.getDisplayName());
operationRecord.getNameID().setDescription(currentTool.getDescription());
if (currentTool.getCategory().getModule() != null) {
operationRecord.setModule(currentTool.getCategory().getModule().getModuleName());
}
operationRecord.setCategoryName(currentTool.getCategoryName());
operationRecord.setCategoryColor(currentTool.getCategory().getColor());
for (ParameterRecord parameterRecord : operationRecord.getParameters()) {
Parameter currentParameter =
currentTool.getParameter(parameterRecord.getNameID().getID());
if (currentParameter != null) {
parameterRecord.getNameID().setDisplayName(currentParameter.getDisplayName());
parameterRecord.getNameID().setDescription(currentParameter.getDescription());
}
}
}
// store the operation record
operationRecords.put(operationSessionId, operationRecord);
operationTypes.put(operationRecord, operationType);
}
}