/**
* Link OperationRecords and DataBeans by adding real input DataBean references to
* OperationRecords.
*/
private void linkInputsToOperations() {
for (OperationRecord operationRecord : operationRecords.values()) {
// get data bean ids from session data
for (InputType inputType : operationTypes.get(operationRecord).getInput()) {
String inputID = inputType.getData();
if (inputID == null) {
continue;
}
// find the data bean
DataBean inputBean = dataBeans.get(inputID);
if (inputBean == null) {
continue;
}
// skip phenodata, it is bound automatically
if (inputBean.queryFeatures("/phenodata/").exists()) {
continue;
}
// add the reference to the operation record
operationRecord.addInput(createNameID(inputType.getName()), inputBean);
}
}
}
private void deleteDataBean(DataBean bean) {
// remove from operation history
for (DataBean source : databeans()) {
// we must iterate all datas because links cannot be trusted (they might have been removed by
// user)
OperationRecord operationRecord = source.getOperationRecord();
if (operationRecord != null) {
operationRecord.removeInput(bean);
}
}
// remove links
for (Link linkType : Link.values()) {
// Remove outgoing links
for (DataBean target : bean.getLinkTargets(linkType)) {
bean.removeLink(linkType, target);
}
// Remove incoming links
for (DataBean source : bean.getLinkSources(linkType)) {
source.removeLink(linkType, bean);
}
}
// remove bean
DataFolder folder = bean.getParent();
if (folder != null) {
disconnectChild(bean, folder);
}
// remove physical file
bean.delete();
}
public static OperationRecord getUnkownOperationRecord() {
OperationRecord record = new OperationRecord();
record.setNameID(new NameID("unknown", "Unknown", "No tool information available."));
record.setCategoryName("Unknown");
record.setCategoryColor(ToolCategory.UNKNOWN_CATEGORY_COLOR);
record.setSourceCode("Source code not available.");
return record;
}
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;
}
/**
* Add links form DataBeans to the OperationRecord which created the DataBean.
*
* <p>If OperationRecord is not found, use unknown OperationRecord.
*/
private void linkOperationsToOutputs() {
for (DataBean dataBean : dataBeans.values()) {
String operationId = dataTypes.get(dataBean).getResultOf();
OperationRecord operationRecord = null;
if (operationId != null) {
operationRecord = operationRecords.get(operationId);
}
// if operation record is not found use dummy
if (operationRecord == null) {
operationRecord = OperationRecord.getUnkownOperationRecord();
}
dataBean.setOperationRecord(operationRecord);
}
}
public int getInputCount() {
return operationRecord.getInputRecords().size();
}
public Iterable<DataBean> getInputDataBeans() {
return operationRecord.getInputDataBeans();
}
public Collection<InputRecord> getInputRecords() {
return operationRecord.getInputRecords();
}
public String getFullName() {
return operationRecord.getCategoryName() + " / " + operationRecord.getNameID().getDisplayName();
}
public String getName() {
return operationRecord.getNameID().getDisplayName();
}
public String getOperationID() {
return operationRecord.getNameID().getID();
}
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);
}
}
