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Merge branch 'development' into feat/use-repr
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@sanjayankur31
sanjayankur31 committed Feb 15, 2024
2 parents 9511625 + 728c83f commit 2e017ee
Showing 1 changed file with 47 additions and 15 deletions.
62 changes: 47 additions & 15 deletions src/main/java/org/lemsml/export/sedml/SEDMLWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ public class SEDMLWriter extends AXMLWriter
{

public static final int SEDML_LEVEL = 1;
public static final int SEDML_VERSION = 2;
public static final int SEDML_VERSION = 3;
public static final String PREF_SEDML_SCHEMA = "https://raw.githubusercontent.com/SED-ML/sed-ml/master/schema/level"+SEDML_LEVEL+"/version"+SEDML_VERSION+"/sed-ml-L"+SEDML_LEVEL+"-V"+SEDML_VERSION+".xsd";

public static final String GLOBAL_TIME_SBML = "t";
Expand All @@ -37,6 +37,9 @@ public class SEDMLWriter extends AXMLWriter
private String inputFileName = "";
private Format modelFormat;

private final String DISPLAY_PREFIX = "DISPLAY__";
private final String OUTPUT_PREFIX = "OUTPUT__";

public SEDMLWriter(Lems lems, File outputFolder, String outputFileName, String inputFileName, Format modelFormat) throws ModelFeatureSupportException, NeuroMLException, LEMSException
{
super(lems, Format.SEDML, outputFolder, outputFileName);
Expand Down Expand Up @@ -143,26 +146,30 @@ else if(modelFormat == Format.CELLML)
endElement(main, "math");
endElement(main, "dataGenerator");

for(Component dispComp : simCpt.getAllChildren())
for(Component dispOrOutputComp : simCpt.getAllChildren())
{
if(dispComp.getTypeName().equals("Display"))
if(dispOrOutputComp.getTypeName().equals("Display") || dispOrOutputComp.getTypeName().equals("OutputFile"))
{
String dispId = dispComp.getID().replace(" ","_");
String id = dispOrOutputComp.getID().replace(" ","_");

for(Component lineComp : dispComp.getAllChildren())
for(Component lineOrColumnComp : dispOrOutputComp.getAllChildren())
{
if(lineComp.getTypeName().equals("Line"))
if(lineOrColumnComp.getTypeName().equals("Line") || lineOrColumnComp.getTypeName().equals("OutputColumn"))
{
// trace=StateMonitor(hhpop,'v',record=[0])

String quantity = lineComp.getStringValue("quantity");
String quantity = lineOrColumnComp.getStringValue("quantity");
LEMSQuantityPath lqp = new LEMSQuantityPath(quantity);
String pop = lqp.getPopulation();
String num = lqp.getPopulationIndex() + "";
String segid = lqp.getSegmentId()==0 ? "" : ("_"+lqp.getSegmentId());
String var = lqp.getVariable();

String genId = dispId + "_" + lineComp.getID().replace(" ","_");
String prefix = DISPLAY_PREFIX;
if (lineOrColumnComp.getTypeName().equals("OutputColumn"))
{
prefix = OUTPUT_PREFIX;
}

String genId = prefix + id + "_" + lineOrColumnComp.getID().replace(" ","_");
String varFull = pop + "_" + num+segid + "_" + var;

startElement(main, "dataGenerator", "id=" + genId, "name=" + genId);
Expand Down Expand Up @@ -200,16 +207,41 @@ else if(modelFormat == Format.CELLML)

startElement(main, "listOfOutputs");

for(Component dispComp : simCpt.getAllChildren())
for(Component dispOrOutputComp : simCpt.getAllChildren())
{
if(dispComp.getTypeName().equals("Display"))
if(dispOrOutputComp.getTypeName().equals("OutputFile"))
{
String reportName = dispOrOutputComp.getStringValue("fileName").replace(".dat","");
String ofId = dispOrOutputComp.getID().replace(" ","_");

startElement(main, "report", "id=" + reportName);
startElement(main, "listOfDataSets");

startEndElement(main, "dataSet", "id=time", "name=time", "dataReference=time", "label=time");

for(Component ocComp : dispOrOutputComp.getAllChildren())
{
if(ocComp.getTypeName().equals("OutputColumn"))
{
// <dataSet id="d1" name="time" dataReference="time"/>
String ocid = ocComp.getID().replace(" ","_");

String genId = OUTPUT_PREFIX + ofId + "_" + ocid;
startEndElement(main, "dataSet", "id=" + ocid, "name=" + genId, "dataReference=" + genId, "label=" + genId);
}
}
endElement(main, "listOfDataSets");

endElement(main, "report");
}
if(dispOrOutputComp.getTypeName().equals("Display"))
{
String dispId = dispComp.getID().replace(" ","_");
String dispId = dispOrOutputComp.getID().replace(" ","_");

startElement(main, "plot2D", "id=" + dispId);
startElement(main, "listOfCurves");

for(Component lineComp : dispComp.getAllChildren())
for(Component lineComp : dispOrOutputComp.getAllChildren())
{
if(lineComp.getTypeName().equals("Line"))
{
Expand All @@ -221,7 +253,7 @@ else if(modelFormat == Format.CELLML)

String lcid = lineComp.getID().replace(" ","_");

String genId = dispId + "_" + lcid;
String genId = DISPLAY_PREFIX + dispId + "_" + lcid;
// String varFull = pop+"_"+num+"_"+var;
// <curve id="curve_0" logX="false" logY="false" xDataReference="time" yDataReference="v_1" />
startEndElement(main, "curve", "id=curve_" + lcid, "logX=false", "logY=false", "xDataReference=time", "yDataReference=" + genId);
Expand Down

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