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Fixed #60 partially; 3 tests still not working since jlibsedml doesn'…
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…t support functional range
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@shalinshah1993
shalinshah1993 committed Jul 25, 2018
1 parent 3a15642 commit b64b096
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Showing 5 changed files with 138 additions and 52 deletions.
6 changes: 4 additions & 2 deletions src/main/java/org/simulator/sedml/ProcessSedMLResults.java
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Original file line number Diff line number Diff line change
Expand Up @@ -353,7 +353,7 @@ private IRawSedmlSimulationResults flattenResultsList(List<IRawSedmlSimulationRe
mergeTimeCols(a, b),
mergeDataCols(a.getData(), b.getData()),
results.get(0).getColumnHeaders()))).get();
return flat;
return flat;
}

/**
Expand Down Expand Up @@ -398,7 +398,9 @@ private double[][] extractNonTimeData(double[][] data) {
private double[] mergeTimeCols(IRawSedmlSimulationResults a, IRawSedmlSimulationResults b) {
// Get end time point for taskA
double[] timeA = ((MultTableSEDMLWrapper)a).getMultiTable().getTimePoints();
double timeBegin = timeA[timeA.length - 1];
// Following tellurim we concat all the iterations of repeated tasks
// so start time from 0
double timeBegin = 0d;

// Add end time point to taskB
double[] timeB = Arrays.stream(((MultTableSEDMLWrapper)b).getMultiTable().getTimePoints()).map(row -> row + timeBegin).toArray();
Expand Down
172 changes: 126 additions & 46 deletions src/main/java/org/simulator/sedml/SedMLSBMLSimulatorExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;

import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import org.jlibsedml.AbstractTask;
Expand All @@ -55,7 +56,6 @@
import org.jlibsedml.execution.IProcessedSedMLSimulationResults;
import org.jlibsedml.execution.IRawSedmlSimulationResults;
import org.jlibsedml.execution.ModelResolver;

import org.jlibsedml.modelsupport.BioModelsModelsRetriever;
import org.jlibsedml.modelsupport.KisaoOntology;
import org.jlibsedml.modelsupport.KisaoTerm;
Expand All @@ -70,7 +70,6 @@
import org.simulator.math.odes.MultiTable;
import org.simulator.math.odes.RosenbrockSolver;
import org.simulator.sbml.SBMLinterpreter;

import de.binfalse.bflog.LOGGER;
import net.biomodels.kisao.IKiSAOQueryMaker;
import net.biomodels.kisao.impl.KiSAOQueryMaker;
Expand Down Expand Up @@ -251,7 +250,7 @@ protected IRawSedmlSimulationResults executeSimulation(String modelStr, UniformT
}
return null;
}

protected IRawSedmlSimulationResults executeSimulation(String modelStr, OneStep sim) {

AbstractDESSolver solver = getSolverForKisaoID(sim.getAlgorithm().getKisaoID());
Expand Down Expand Up @@ -314,12 +313,76 @@ protected IRawSedmlSimulationResults executeSimulation(String modelStr, SteadySt
}
return null;
}

protected IRawSedmlSimulationResults executeSimulation(String modelStr,
Simulation sim, Map<String, double[]> mapChangesToList, int element) {

AbstractDESSolver solver = getSolverForKisaoID(sim.getAlgorithm().getKisaoID());
File tmp = null;
try {
// get a JSBML object from the model string.
tmp = File.createTempFile("Sim", "sbml");
FileUtils.writeStringToFile(tmp, modelStr, "UTF-8");
Model model = (new SBMLReader()).readSBML(tmp).getModel();

// If there are any changes make them before execution
if (mapChangesToList != null) {
// Find all the setValues and set them to current element in range
for(String change: mapChangesToList.keySet()) {
model.getParameter(change).setValue(mapChangesToList.get(change)[element]);;
}
}

// now run simulation
SBMLinterpreter interpreter = null;
if (amountHash != null) {
interpreter = new SBMLinterpreter(model, 0, 0, 1, amountHash);
} else {
interpreter = new SBMLinterpreter(model);
}
solver.setIncludeIntermediates(false);

if(sim instanceof OneStep) {
OneStep finalSim = (OneStep) sim;
// A step-size randomly taken since SED-ML L1V2 says simulator decides this
// A better way to decide step size is essential
solver.setStepSize(finalSim.getStep() / ONE_STEP_SIM_STEPS);
MultiTable mts = solver.solve(interpreter, interpreter.getInitialValues(), 0.0, finalSim.getStep());

// adapt the MultiTable to jlibsedml interface.
// return only 1 point for OneStep simulation: start and end
return new MultTableSEDMLWrapper(mts.filter(new double[] { finalSim.getStep() }));
}
else if(sim instanceof UniformTimeCourse) {
UniformTimeCourse finalSim = (UniformTimeCourse) sim;
solver.setStepSize((finalSim.getOutputEndTime() - finalSim.getOutputStartTime()) / (finalSim.getNumberOfPoints()));
MultiTable mts = solver.solve(interpreter, interpreter.getInitialValues(), finalSim.getOutputStartTime(),
finalSim.getOutputEndTime());

// adapt the MultiTable to jlibsedml interface.
return new MultTableSEDMLWrapper(mts);
}
else if(sim instanceof SteadyState) {
// set default stepSize and call solver. Solver will automatically find
// steadyState and terminate when steadyState is reached.
MultiTable mts = solver.steadystate(interpreter, interpreter.getInitialValues(), STEADY_STATE_STEPS);

// adapt the MultiTable to jlibsedml interface.
return new MultTableSEDMLWrapper(mts);
}


} catch (Exception e) {
LOGGER.warn(e.getMessage());
}
return null;
}

/**
* This method is a wrapper to the runSimulations method from
* {@link AbstractSedmlExecutor} to add additional support for repeatedTasks. It
* identifies the type of task, before running the simulations.
* @throws OWLOntologyCreationException
* @throws OWLOntologyCreationException
*/
public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntologyCreationException {

Expand All @@ -342,50 +405,60 @@ public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntol
Map<String, Range> range = repTask.getRanges();
List<IRawSedmlSimulationResults> repTaskResults = new ArrayList<IRawSedmlSimulationResults>();

// Store state of all the existing changes by subTasks
List<SetValue> modelState = new ArrayList<SetValue>();

// Find all the variable from listOfChanges and create tasks
if (range.size() > 0 && subTasks.size() > 0) {

// Load original model from one of the subtasks and update its state
org.jlibsedml.Model curModel = sedml.getModelWithId(sedml.getTaskWithId(repTask.getSubTasks().
values().iterator().next().getTaskId()).getModelReference());

// 2. Get the Xpath parameter in setValue and a double[] before simulations
Map<String, double[]> mapChangesToList = new HashMap<String, double[]>();
if (repTask.getChanges().size() > 0) {

for (SetValue change : repTask.getChanges()) {
String xPath = change.getTargetXPath().getTargetAsString();
xPath = xPath.substring(xPath.indexOf("'") + 1);
xPath = xPath.substring(0, xPath.indexOf("'"));

if(change.getRangeReference() != null) {
double[] setValueRange = getRangeListRange(range.get(change.getRangeReference()));
mapChangesToList.put(xPath, setValueRange);
}else {
LOGGER.warn("No range specified for SetValue element" + change.getId() + " of repeated task " + repTask.getId());
return null;
}
}
}

// Iterate over master range
Range masterRange = range.get(repTask.getRange());
for (int element = 0; element < masterRange.getNumElements(); element++) {

List<MultTableSEDMLWrapper> stResults = new ArrayList<MultTableSEDMLWrapper>();

// 1. Check for resetModel, original SBML model file is re-read
if (repTask.getResetModel()) {
curModel = sedml.getModelWithId(sedml.getTaskWithId(repTask.getSubTasks().
values().iterator().next().getTaskId()).getModelReference());
}

// 3. Execute subTasks in sorted order with the current state of model
for (Entry<String, SubTask> st : subTasks.entrySet()) {
SubTask subTask = st.getValue();
AbstractTask relatedTask = sedml.getTaskWithId(subTask.getTaskId());

// subtasks refer to same model but can refer to different simulations
Simulation sim = sedml.getSimulation(relatedTask.getSimulationReference());
String changedModel = modelResolver.getModelString(curModel);

// A subTask can also be a repeatedTask in which case
// recurse all repeatedTasks subTasks to add all of them
if (relatedTask instanceof RepeatedTask) {
// TODO: Handle nested repeatedTask
LOGGER.warn("Warning! Nested repeatedTask found and ignored.");

} else {
// Load original model and update its state
org.jlibsedml.Model curModel = sedml.getModelWithId(relatedTask.getModelReference());

// 1. Check for resetModel, if so clear all the SetValues
if (repTask.getResetModel()) {
modelState.clear();
}

// 2. (optional) Check if any new changes are added
modelState.addAll(repTask.getChanges());

// Set model to previously stored state by applying all the current
// changes. If resetModel=true then this will be empty and we get fresh
// model with no modification
if (modelState.size() > 0) {
for (SetValue change : modelState) {
curModel.addChange(change);
}
}

// 3. Execute subTasks in sorted order with the current state of model
Simulation sim = sedml.getSimulation(relatedTask.getSimulationReference());
String changedModel = modelResolver.getModelString(curModel);

IRawSedmlSimulationResults output = null;
// Quickly run error checks before final execution
if (!supportsLanguage(curModel.getLanguage())) {
Expand All @@ -404,13 +477,11 @@ public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntol
if(!canExecuteSimulation(sim))
sim = tryAlternateAlgo(sim);

if (sim instanceof OneStep) {
output = executeSimulation(changedModel, (OneStep) sim);
} else if (sim instanceof SteadyState) {
output = executeSimulation(changedModel, (SteadyState) sim);
} else if (sim instanceof UniformTimeCourse) {
output = executeSimulation(changedModel, (UniformTimeCourse) sim);
}
// Execute simulations with changes, simulation type
if(mapChangesToList.size() > 0)
output = executeSimulation(changedModel, sim, mapChangesToList, element);
else
output = executeSimulation(changedModel, sim, null, -1);

if (output == null) {
LOGGER.warn("Simulation failed during execution: "
Expand All @@ -428,7 +499,7 @@ public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntol
.reduce((a, b) -> new MultTableSEDMLWrapper(new MultiTable(mergeTimeCols(a, b),
mergeDataCols(a.getData(), b.getData()), stResults.get(0).getColumnHeaders())))
.get();

// Add big subTask result to list of repTask results
repTaskResults.add(reducedStResults);
}
Expand Down Expand Up @@ -463,13 +534,13 @@ public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntol
if(!canExecuteSimulation(sim))
sim = tryAlternateAlgo(sim);

// Identify simulation type and run it. Store the results in a Map
if (sim instanceof OneStep) {
// Identify simulation type and run it
if(sim instanceof OneStep) {
results = executeSimulation(changedModel, (OneStep) sim);
} else if (sim instanceof SteadyState) {
results = executeSimulation(changedModel, (SteadyState) sim);
} else if (sim instanceof UniformTimeCourse) {
}else if(sim instanceof UniformTimeCourse) {
results = executeSimulation(changedModel, (UniformTimeCourse) sim);
}else if(sim instanceof SteadyState) {
results = executeSimulation(changedModel, (SteadyState) sim);
}

if (results == null) {
Expand All @@ -479,10 +550,19 @@ public Map<AbstractTask, List<IRawSedmlSimulationResults>> run() throws OWLOntol
res.put(stdTask, new ArrayList<IRawSedmlSimulationResults>(Arrays.asList(results)));
}
}

return res;
}

private double[] getRangeListRange(Range range) {
// TODO Auto-generated method stub
double[] rangeList = new double[range.getNumElements()];
for(int index = 0; index < range.getNumElements(); index++) {
rangeList[index] = range.getElementAt(index);
}

return rangeList;
}

/**
* Merge two 2D arrays into one 2D array in X-direction
*
Expand Down Expand Up @@ -510,7 +590,7 @@ private double[] mergeTimeCols(MultTableSEDMLWrapper a, MultTableSEDMLWrapper b)
// Get end time point for taskA
double[] timeA = a.getMultiTable().getTimePoints();
double timeBegin = timeA[timeA.length - 1];

// Add end time point to taskB
double[] timeB = Arrays.stream(b.getMultiTable().getTimePoints()).map(row -> row + timeBegin).toArray();

Expand Down
12 changes: 8 additions & 4 deletions src/test/java/org/simulator/sedml/SEDMLExecutorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ public final void testBasicSEDMLExecutorForMiriamURNDefinedModel() throws XMLExc


@Test
public final void testIkappab() throws XMLException, OWLOntologyCreationException, IOException{
public final void testIkappab() throws XMLException, OWLOntologyCreationException, IOException {
String resource = "/sedml/L1V2/ikappab/ikappab.xml";
testSpecificationExample(resource);
}
Expand All @@ -160,13 +160,15 @@ public final void testLorenzSBML() throws XMLException, OWLOntologyCreationExcep
}

@Test
@Ignore
public final void testOscliNestedPulse() throws XMLException, OWLOntologyCreationException, IOException {
String resource = "/sedml/L1V2/oscli-nested-pulse/oscli-nested-pulse.xml";
testSpecificationExample(resource);
}

@Test
@Ignore
@Ignore
//Contains nested repeated task https://github.com/shalinshah1993/SBSCL/issues/55
public final void testParameterScan2D() throws XMLException, OWLOntologyCreationException, IOException {
String resource = "/sedml/L1V2/parameter-scan-2d/parameter-scan-2d.xml";
testSpecificationExample(resource);
Expand All @@ -179,12 +181,14 @@ public final void testRepeatedScanOscli() throws XMLException, OWLOntologyCreati
}

@Test
@Ignore
public final void testRepeatedSteadyScanOscli() throws XMLException, OWLOntologyCreationException, IOException {
String resource = "/sedml/L1V2/repeated-steady-scan-oscli/repeated-steady-scan-oscli.xml";
testSpecificationExample(resource);
}

@Test
@Ignore
public final void testRepeatedStochasticRuns() throws XMLException, OWLOntologyCreationException, IOException {
String resource = "/sedml/L1V2/repeated-stochastic-runs/repeated-stochastic-runs.xml";
testSpecificationExample(resource);
Expand Down Expand Up @@ -302,8 +306,8 @@ public final void testRepressilator1() throws XMLException, OWLOntologyCreationE
// plot all processed results as per curve descriptions
String title = wanted.getId() + "(" + wanted.getName() + ")";
// UNCOMMENT THIS TO SAVE PLOT
//PlotProcessedSedmlResults p = new PlotProcessedSedmlResults(pr, curves, title);
//assertNotNull(p);
// PlotProcessedSedmlResults p = new PlotProcessedSedmlResults(pr, curves, title);
// assertNotNull(p);
// p.savePlot(resource, wanted.getId());
}
}
Expand Down
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