Merge pull request #115 from NeuroML/feat/sed-ml-id-fix

sedml fixes for biosimulations
NeuroML · Apr 18, 2024 · 62cfdc8 · 62cfdc8
2 parents aa62f9b + ce395cf
commit 62cfdc8
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/src/main/java/org/lemsml/export/sedml/SEDMLWriter.java b/src/main/java/org/lemsml/export/sedml/SEDMLWriter.java
@@ -170,7 +170,7 @@ else if(modelFormat == Format.CELLML)
                         }
 
                         String genId = prefix + id + "_" + lineOrColumnComp.getID().replace(" ","_");
-                        String varFull = pop + "_" + num+segid + "_" + var;
+                        String varFull = genId + "_" +  pop + "_" + num+segid + "_" + var;
 
                         startElement(main, "dataGenerator", "id=" + genId, "name=" + genId);
                         startElement(main, "listOfVariables");
@@ -212,12 +212,13 @@ else if(modelFormat == Format.CELLML)
             if(dispOrOutputComp.getTypeName().equals("OutputFile"))
             {
                 String reportName = dispOrOutputComp.getStringValue("fileName").replace(".dat","");
+                String reportId = reportName.replaceAll("[\\W]", "_");
                 String ofId = dispOrOutputComp.getID().replace(" ","_");
 
-                startElement(main, "report", "id=" + reportName);
+                startElement(main, "report", "id=" + reportId);
                 startElement(main, "listOfDataSets");
 
-                startEndElement(main, "dataSet", "id=time", "name=time", "dataReference=time", "label=time");
+                startEndElement(main, "dataSet", "id=" + reportId + "_time", "name=time", "dataReference=time", "label=time");
 
                 for(Component ocComp : dispOrOutputComp.getAllChildren())
                 {
@@ -227,7 +228,7 @@ else if(modelFormat == Format.CELLML)
                         String ocid = ocComp.getID().replace(" ","_");
 
                         String genId = OUTPUT_PREFIX + ofId + "_" + ocid;
-                        startEndElement(main, "dataSet", "id=" + ocid, "name=" + genId, "dataReference=" + genId, "label=" + genId);
+                        startEndElement(main, "dataSet", "id=" + reportId + "_" + ocid, "name=" + genId, "dataReference=" + genId, "label=" + genId);
                     }
                 }
                 endElement(main, "listOfDataSets");