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APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.
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package nl.uu.cs.ape.solver.solutionStructure.cwl;
import nl.uu.cs.ape.models.logic.constructs.TaxonomyPredicate;
import nl.uu.cs.ape.solver.solutionStructure.ModuleNode;
import nl.uu.cs.ape.solver.solutionStructure.SolutionWorkflow;
import nl.uu.cs.ape.solver.solutionStructure.TypeNode;
import java.util.HashMap;
import java.util.List;
import lombok.extern.slf4j.Slf4j;
/**
* Class to generate a CWL workflow structure from a given workflow solution.
*/
@Slf4j
public class AbstractCWLCreator extends CWLCreatorBase {
/**
* Maintain a list of the CWL parameter names which represent {@link TypeNode}s.
* I.e. this hashmap has TypeNode IDs as keys and their names in the CWL file as
* values.
*/
private final HashMap workflowParameters = new HashMap<>();
/**
* Instantiates a new CWL creator.
*
* @param solution The solution to represent in CWL.
*/
public AbstractCWLCreator(SolutionWorkflow solution) {
super(solution);
}
@Override
public String getCWLVersion() {
// CWL version 1.2.0-dev2 is the minimum version required for the features we
// use here.
return "v1.2.0-dev2";
}
/**
* Generates the CWL representation.
*/
@Override
protected void generateCWLRepresentation() {
// Workflow
generateWorkflowInputs();
generateWorkflowOutputs();
generateWorkflowSteps();
}
/**
* Generate the top-level inputs definition of the workflow.
*/
private void generateWorkflowInputs() {
cwlRepresentation.append("inputs:").append("\n");
// Inputs
for (TypeNode typeNode : solution.getWorkflowInputTypeStates()) {
String inputName = String.format("input_%o", workflowParameters.size() + 1);
addParameter(typeNode, inputName);
cwlRepresentation
// Name
.append(ind(1))
.append(inputName)
.append(":\n")
// Data type
.append(ind(2))
.append("type: File")
.append("\n")
// Format
.append(ind(2))
.append("format: ")
.append(typeNode.getFormat())
.append("\n");
}
}
/**
* Generate the top-level outputs definition of the workflow.
*/
private void generateWorkflowOutputs() {
cwlRepresentation.append("outputs:\n");
// Outputs
int i = 1;
for (TypeNode typeNode : solution.getWorkflowOutputTypeStates()) {
cwlRepresentation
// Name
.append(ind(1))
.append(String.format("output_%o", i))
.append(":\n")
// Data type
.append(ind(2))
.append("type: File")
.append("\n")
// Format
.append(ind(2))
.append("format: ")
.append(typeNode.getFormat())
.append("\n")
// outputSource
.append(ind(2))
.append("outputSource: ")
.append(stepName(typeNode.getCreatedByModule()))
.append("/");
// Get the id of the step run's output bound to this workflow output
// (step_name/output_name_ID)
int outId = typeNode.getCreatedByModule().getOutputTypes().get(i - 1).getAutomatonState()
.getLocalStateNumber();
cwlRepresentation
.append(generateInputOrOutputName(typeNode.getCreatedByModule(), "out", outId + 1))
.append("\n");
i++;
}
}
/**
* Generate the top-level steps of the workflow.
*/
private void generateWorkflowSteps() {
cwlRepresentation.append("steps:").append("\n");
for (ModuleNode moduleNode : solution.getModuleNodes()) {
generateStep(moduleNode);
}
}
/**
* Generate one workflow step.
*
* @param moduleNode The {@link ModuleNode} related to the step.
*/
private void generateStep(ModuleNode moduleNode) {
final int baseInd = 1;
// Name
cwlRepresentation
.append(ind(baseInd))
.append(stepName(moduleNode))
.append(":\n");
generateStepIn(moduleNode);
generateStepOut(moduleNode);
generateStepRun(moduleNode);
}
/**
* Generate the "in" section of a workflow step.
*
* @param moduleNode The {@link ModuleNode} that is the step.
*/
private void generateStepIn(ModuleNode moduleNode) {
final int baseInd = 2;
// "in" key
cwlRepresentation.append(ind(baseInd)).append("in").append(":\n");
// If there are no inputs, give an empty array as input
if (moduleNode.getInputTypes().isEmpty()) {
// Remove the last newline so the array is on the same line as "in:"
deleteLastNCharactersFromCWL(1);
cwlRepresentation
.append(" ")
.append("[]")
.append("\n");
return;
}
int i = 0;
for (TypeNode typeNode : moduleNode.getInputTypes()) {
cwlRepresentation
.append(ind(baseInd + 1))
.append(generateInputOrOutputName(moduleNode, "in", i + 1))
.append(": ")
.append(workflowParameters.get(typeNode.getNodeID()))
.append("\n");
i++;
}
}
/**
* Generate the "out" section of a workflow step.
*
* @param moduleNode The {@link ModuleNode} that is the step.
*/
private void generateStepOut(ModuleNode moduleNode) {
final int baseInd = 2;
cwlRepresentation
// "out" key
.append(ind(baseInd))
.append("out: ")
// The outputs array
.append("[");
int i = 1;
for (TypeNode typeNode : moduleNode.getOutputTypes()) {
String name = generateInputOrOutputName(moduleNode, "out", i);
addParameter(typeNode, String.format("%s/%s", stepName(moduleNode), name));
cwlRepresentation
.append(name)
.append(", ");
i++;
}
deleteLastNCharactersFromCWL(2);
cwlRepresentation.append("]").append("\n");
}
/**
* Generate the run field of a workflow step.
*
* @param moduleNode The {@link ModuleNode} related to the step.
*/
private void generateStepRun(ModuleNode moduleNode) {
final int baseInd = 2;
cwlRepresentation
// Main key
.append(ind(baseInd))
.append("run:")
.append("\n")
// Class
.append(ind(baseInd + 1))
.append("class: Operation")
.append("\n");
// Inputs
cwlRepresentation
.append(ind(baseInd + 1))
.append("inputs:")
.append("\n");
generateTypeNodes(moduleNode, moduleNode.getInputTypes(), true, baseInd + 2);
// Outputs
cwlRepresentation
.append(ind(baseInd + 1))
.append("outputs:")
.append("\n");
generateTypeNodes(moduleNode, moduleNode.getOutputTypes(), false, baseInd + 2);
// Hints and intent
generateStepHints(moduleNode, baseInd + 1);
generateStepIntent(moduleNode, baseInd + 1);
}
/**
* Generate the hints related to this step's run.
*
* @param moduleNode The {@link ModuleNode} that is the step.
* @param baseInd The indentation at which the hints should start.
*/
private void generateStepHints(ModuleNode moduleNode, int baseInd) {
cwlRepresentation
// "hints" key
.append(ind(baseInd))
.append("hints:")
.append("\n")
// "SoftwareRequirement" key
.append(ind(baseInd + 1))
.append("SoftWareRequirement:")
.append("\n")
// "packages" key
.append(ind(baseInd + 2))
.append("packages:")
.append("\n")
// The required package
.append(ind(baseInd + 3))
.append(
String.format("%s: [\"%s\"]",
moduleNode.getNodeLabel(),
moduleNode.getUsedModule().getPredicateID()))
.append("\n");
}
/**
* Generate the intent for a workflow step's run.
*
* @param moduleNode The {@link ModuleNode} that is the workflow step.
* @param baseInd The indentation level at which the intent should start.
*/
private void generateStepIntent(ModuleNode moduleNode, int baseInd) {
cwlRepresentation
.append(ind(baseInd))
.append("intent: ")
.append("[");
for (TaxonomyPredicate predicate : moduleNode.getUsedModule().getParentPredicates()) {
cwlRepresentation
.append("\"")
.append(predicate.getPredicateID())
.append("\"")
.append(", ");
}
deleteLastNCharactersFromCWL(2);
cwlRepresentation.append("]").append("\n");
}
/**
* Generate the inputs or outputs of a step's run.
*
* @param moduleNode The {@link ModuleNode} that is the workflow step.
* @param typeNodeList The {@link TypeNode}s that are either the input or output
* nodes.
* @param input Whether the type nodes are inputs. If false, they are
* consider outputs.
* @param baseInd The indentation level of the "inputs:" or "outputs:" line
* preceding this function.
*/
private void generateTypeNodes(ModuleNode moduleNode, List typeNodeList, boolean input, int baseInd) {
// If the input or output nodes are empty, give an empty array as input or
// output
if (typeNodeList.isEmpty()) {
// Remove the last newline so the array is on the same line as "inputs:"
deleteLastNCharactersFromCWL(1);
cwlRepresentation
.append(" ")
.append("[]")
.append("\n");
return;
}
int i = 0;
for (TypeNode typeNode : typeNodeList) {
// Don't include empty nodes
if (typeNode.isEmpty()) {
return;
}
i++;
cwlRepresentation
// Name
.append(ind(baseInd))
.append(generateInputOrOutputName(moduleNode, input ? "in" : "out", i))
.append(":\n")
// Data type
.append(ind(baseInd + 1))
.append("type: File")
.append("\n")
// Format
.append(ind(baseInd + 1))
.append("format: ")
.append(typeNode.getFormat())
.append("\n");
}
}
/**
* Add a parameter to the parameter hashmap.
* Will log an error to the error output if {@link TypeNode} is already known.
*
* @param typeNode The {@link TypeNode} that is the input parameter.
* @param name The name of the parameter.
*/
private void addParameter(TypeNode typeNode, String name) {
if (workflowParameters.putIfAbsent(typeNode.getNodeID(), name) != null) {
log.warn("Duplicate key \"%s\" in workflow inputs!\n", typeNode.getNodeID());
}
}
}