@Override
public String getMainScript() throws GenerationException {
StringBuilder sb = new StringBuilder();
addComment(
sb, FORMAT + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
Velocity.init();
VelocityContext context = new VelocityContext();
DLemsWriter writer = new DLemsWriter(lems, new MatlabVisitors());
try {
String som = writer.getMainScript();
DLemsWriter.putIntoVelocityContext(som, context);
Properties props = new Properties();
props.put("resource.loader", "class");
props.put(
"class.resource.loader.class",
"org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
VelocityEngine ve = new VelocityEngine();
ve.init(props);
Template template = ve.getTemplate(method.getFilename());
StringWriter sw = new StringWriter();
template.merge(context, sw);
sb.append(sw);
} catch (IOException e1) {
throw new GenerationException("Problem converting LEMS to SOM", e1);
} catch (ResourceNotFoundException e) {
throw new GenerationException("Problem finding template", e);
} catch (ParseErrorException e) {
throw new GenerationException("Problem parsing", e);
} catch (MethodInvocationException e) {
throw new GenerationException("Problem finding template", e);
} catch (Exception e) {
throw new GenerationException("Problem using template", e);
}
return sb.toString();
}
public VertexWriter(Lems lems, File outputFolder, String outputFileName)
throws ModelFeatureSupportException, NeuroMLException, LEMSException {
super(lems, Format.VERTEX, outputFolder, outputFileName);
mainDlemsFile = outputFileName + "_main.json";
dlemsw = new DLemsWriter(lems, outputFolder, mainDlemsFile, null, false);
dlemsw.setPopulationMode(true);
initializeWriter();
}
public String getMainScript() throws GenerationException, IOException {
StringBuilder mainRunScript = new StringBuilder();
addComment(
mainRunScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
try {
List<File> files = dlemsw.convert();
for (File file : files) {
E.info("Writing " + format + " files to: " + this.getOutputFolder());
if (file.getName().equals(mainDlemsFile)) {
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
addComment(
mainRunScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
StringWriter sw1 = new StringWriter();
boolean generationStatus =
ve.evaluate(
context,
sw1,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexRunTemplateFile));
mainRunScript.append(sw1);
} else if (file.getName().indexOf(".synapse.") > 0) {
StringBuilder synapseScript = new StringBuilder();
addComment(
synapseScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
E.info(" ==== Handling DLEMS file: " + file.getAbsolutePath());
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
StringWriter sw2 = new StringWriter();
boolean generationStatus2 =
ve.evaluate(
context,
sw2,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexSynapseTemplateFile));
addComment(
synapseScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
synapseScript.append(sw2);
String name = (String) context.internalGet(DLemsKeywords.NAME.get());
E.info("Name: " + name);
File synapseScriptFile =
new File(this.getOutputFolder(), "SynapseModel_" + name.toLowerCase() + ".m");
FileUtil.writeStringToFile(synapseScript.toString(), synapseScriptFile);
outputFiles.add(synapseScriptFile);
} else {
StringBuilder cellScript = new StringBuilder();
addComment(
cellScript,
format + " simulator compliant export for:\n\n" + lems.textSummary(false, false));
E.info(" ==== Handling DLEMS file: " + file.getAbsolutePath());
VelocityUtils.initializeVelocity();
VelocityContext context = new VelocityContext();
VelocityEngine ve = VelocityUtils.getVelocityEngine();
String dlems = FileUtil.readStringFromFile(file);
DLemsWriter.putIntoVelocityContext(dlems, context);
StringWriter sw2 = new StringWriter();
boolean generationStatus2 =
ve.evaluate(
context,
sw2,
"LOG",
VelocityUtils.getTemplateAsReader(VelocityUtils.vertexCellTemplateFile));
addComment(
cellScript,
"Using the following distilled version of the LEMS model description for the script below:\n\n"
+ dlems);
cellScript.append(sw2);
String name = (String) context.internalGet(DLemsKeywords.NAME.get());
E.info("Name: " + name);
File cellScriptFile =
new File(this.getOutputFolder(), "PointNeuronModel_" + name.toLowerCase() + ".m");
FileUtil.writeStringToFile(cellScript.toString(), cellScriptFile);
outputFiles.add(cellScriptFile);
}
}
} catch (IOException e1) {
throw new GenerationException("Problem converting LEMS to dLEMS", e1);
} catch (VelocityException e) {
throw new GenerationException("Problem using Velocity template", e);
}
return mainRunScript.toString();
}