public boolean hasUnpositioned() {
for (ProcessNode<?, ?> node : getModelNodes()) {
if (!node.hasPos()) {
return true;
}
}
return false;
}
/**
* Normalize the process model. By default this may do nothing.
*
* @return The model (this).
*/
public M normalize(SplitFactory<? extends T, M> splitFactory) {
ensureIds();
// Make all nodes directly refer to other nodes.
for (T childNode : mProcessNodes) {
childNode.resolveRefs();
}
for (T childNode : mProcessNodes) {
// Create a copy as we are actually going to remove all successors, but need to keep the list
ArrayList<Identifiable> successors = new ArrayList<>(childNode.getSuccessors());
if (successors.size() > 1 && !(childNode instanceof Split)) {
for (Identifiable suc2 : successors) { // Remove the current node as predecessor.
ProcessNode<?, ?> suc = (ProcessNode) suc2;
suc.removePredecessor(childNode);
childNode.removeSuccessor(suc); // remove the predecessor from the current node
}
// create a new join, this should
Split<? extends T, M> newSplit = splitFactory.createSplit(asM(), successors);
childNode.addSuccessor(newSplit);
}
}
return this.asM();
}
public void ensureIds() {
Set<String> ids = new HashSet<>();
List<ProcessNode<?, ?>> unnamedNodes = new ArrayList<>();
for (ProcessNode<?, ?> node : getModelNodes()) {
String id = node.getId();
if (id == null) {
unnamedNodes.add(node);
} else {
ids.add(id);
}
}
Map<String, Integer> startCounts = new HashMap<>();
for (ProcessNode<?, ?> unnamed : unnamedNodes) {
String idBase = unnamed.getIdBase();
int startCount = getOrDefault(startCounts, idBase, 1);
for (String id = idBase + Integer.toString(startCount);
ids.contains(id);
id = idBase + Integer.toString(startCount)) {
++startCount;
}
unnamed.setId(idBase + Integer.toString(startCount));
startCounts.put(idBase, startCount + 1);
}
}
private void createGraph() {
graph = new Graph();
String[] columns = Arrays.copyOf(assayTable[0], assayTable[0].length, String[].class);
int index = 0;
ProcessNode lastProcess = null;
NodeWithComments lastMaterialOrData = null;
NodeWithComments lastSample = null;
ISAFactorValue lastFactorValue = null;
ProtocolExecutionNode lastProtocolExecutionNode = null;
List<ProtocolExecutionNode> protocolExecutionNodes = new ArrayList<ProtocolExecutionNode>();
for (String column : columns) {
if (column.matches(Date.REGEXP)) {
Date date = new Date(index, column);
if (lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.addDate(date);
}
} else if (column.matches(Performer.REGEXP)) {
Performer performer = new Performer(index, column);
if (lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.addPerformer(performer);
}
} else if (column.matches(ProtocolExecutionNode.REGEXP)) {
ProtocolExecutionNode protocolExecutionNode = new ProtocolExecutionNode(index, column);
protocolExecutionNodes.add(protocolExecutionNode);
lastProtocolExecutionNode = protocolExecutionNode;
if (lastMaterialOrData != null) {
protocolExecutionNode.setInputNode(lastMaterialOrData);
}
graph.addNode(protocolExecutionNode);
} else if (column.matches(ProcessNode.REGEXP)) {
ProcessNode processNode = new ProcessNode(index, column);
graph.addNode(processNode);
if (lastMaterialOrData != null) {
// but it could be a DataNode rather than a material node... do I need a new object?
// processNode.setInputNode(
// new MaterialNode(lastMaterialOrData.getIndex(), lastMaterialOrData.getName()));
processNode.setInputNode(lastMaterialOrData);
}
lastProcess = processNode;
if (lastProcess != null) {
lastProcess.addProtocolExecutionNodes(protocolExecutionNodes);
protocolExecutionNodes = new ArrayList<ProtocolExecutionNode>();
}
} else if (column.contains(ISADataNode.CONTAINS) && !column.contains("Comment")) {
NodeWithComments dataNode = new DataNode(index, column);
graph.addNode(dataNode);
lastMaterialOrData = dataNode;
if (lastProcess != null) {
lastProcess.setOutputNode(dataNode);
lastProcess = null;
} else if (lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.setOutputNode(dataNode);
lastProtocolExecutionNode = null;
}
if (lastMaterialOrData != null
&& lastProcess == null
&& lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.setOutputNode(dataNode);
protocolExecutionNodes = new ArrayList<ProtocolExecutionNode>();
}
} else if (column.matches(ISAMaterialAttribute.REGEXP)) {
ISAMaterialAttribute materialAttribute = new MaterialAttribute(index, column);
if (lastMaterialOrData != null && lastMaterialOrData instanceof MaterialNode) {
((MaterialNode) graph.getNode(lastMaterialOrData.getIndex()))
.addMaterialAttribute(materialAttribute);
}
} else if (column.matches(MaterialNode.REGEXP)) {
NodeWithComments materialNode = null;
if (column.matches(ISASampleNode.REGEXP)) {
materialNode = new SampleNode(index, column);
lastSample = materialNode;
} else {
materialNode = new MaterialNode(index, column);
}
// if there is a previous material node
// and no process node, add a dummy process node
if (lastMaterialOrData != null
&& lastProcess == null
&& lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.setOutputNode(materialNode);
protocolExecutionNodes = new ArrayList<ProtocolExecutionNode>();
}
graph.addNode(materialNode);
lastMaterialOrData = materialNode;
if (lastProcess != null) {
lastProcess.setOutputNode(materialNode);
lastProcess = null;
}
} else if (column.matches(ISAFactorValue.REGEXP)) {
ISAFactorValue factorValue = new FactorValue(index, column);
lastFactorValue = factorValue;
if (lastSample != null && lastSample instanceof SampleNode) {
((SampleNode) graph.getNode(lastSample.getIndex())).addFactorValue(factorValue);
}
} else if (column.matches(ISAUnit.REGEXP)) {
ISAUnit unit = new Unit(index, column);
if (lastFactorValue != null) {
lastFactorValue.setUnit(unit);
}
} else if (column.matches(ProcessParameter.REGEXP)) {
ProcessParameter parameter = new ProcessParameter(index, column);
if (lastProtocolExecutionNode != null) {
((ProcessNode) graph.getNode(lastProtocolExecutionNode.getIndex()))
.addParameter(parameter);
}
} else if (column.matches(CommentNode.REGEXP)) {
CommentNode commentNode = new CommentNode(index, column);
if (lastProcess != null
&& lastMaterialOrData != null
&& lastProtocolExecutionNode != null) {
// lastProcess greater index
if (lastProcess.getIndex() > lastMaterialOrData.getIndex()
&& lastProcess.getIndex() > lastProtocolExecutionNode.getIndex()) {
lastProcess.addComment(commentNode);
} else if (lastMaterialOrData.getIndex() > lastProcess.getIndex()
&& lastMaterialOrData.getIndex() > lastProtocolExecutionNode.getIndex()) {
lastMaterialOrData.addComment(commentNode);
} else if (lastProtocolExecutionNode.getIndex() > lastProcess.getIndex()
&& lastProtocolExecutionNode.getIndex() > lastMaterialOrData.getIndex()) {
lastProtocolExecutionNode.addComment(commentNode);
}
} else { // one of them is null
if (lastProcess != null && lastMaterialOrData != null) {
if (lastProcess.getIndex() > lastMaterialOrData.getIndex()) {
lastProcess.addComment(commentNode);
} else {
lastMaterialOrData.addComment(commentNode);
}
} else if (lastProcess != null && lastProtocolExecutionNode != null) {
if (lastProcess.getIndex() > lastProtocolExecutionNode.getIndex()) {
lastProcess.addComment(commentNode);
} else {
lastProtocolExecutionNode.addComment(commentNode);
}
} else if (lastMaterialOrData != null && lastProtocolExecutionNode != null) {
if (lastMaterialOrData.getIndex() > lastProtocolExecutionNode.getIndex()) {
lastMaterialOrData.addComment(commentNode);
} else {
lastProtocolExecutionNode.addComment(commentNode);
}
} else {
// only one is not null
if (lastMaterialOrData != null) {
lastMaterialOrData.addComment(commentNode);
} else if (lastProcess != null) {
lastProcess.addComment(commentNode);
} else if (lastProtocolExecutionNode != null) {
lastProtocolExecutionNode.addComment(commentNode);
}
}
}
}
index++;
}
}