Added check EXT_MORPH_BIOPHYS_CELL_MODEL, just passing on Neuron & Netne

NeuroML · Jun 4, 2024 · a335c3c · a335c3c
1 parent 528e08a
commit a335c3c
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Showing 6 changed files with 26 additions and 2 deletions.
diff --git a/src/main/java/org/neuroml/export/eden/EDENWriter.java b/src/main/java/org/neuroml/export/eden/EDENWriter.java
@@ -71,6 +71,7 @@ public void setSupportedFeatures()
 	{
 		sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.NONE);
 		sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH);

diff --git a/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java b/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java
@@ -97,6 +97,7 @@ public void setSupportedFeatures()
 	{
 		sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH);
 		sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH);

diff --git a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java
@@ -132,6 +132,7 @@ public void setSupportedFeatures()
     {
         sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);
         sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);
+        sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH);
         sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.MEDIUM);
         sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.LOW);
         sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.MEDIUM);

diff --git a/src/main/java/org/neuroml/export/utils/Utils.java b/src/main/java/org/neuroml/export/utils/Utils.java
@@ -556,7 +556,15 @@ public Sim importFile(File simFile) throws LEMSException {
 		if(run)
 		{
 			SupportLevelInfo sli = SupportLevelInfo.getSupportLevelInfo();
-			sli.checkConversionSupported(Format.LEMS, sim.getLems());
+			try 
+			{
+				sli.checkConversionSupported(Format.LEMS, sim.getLems());
+			}
+			catch (ModelFeatureSupportException mfse)
+			{
+				E.info(mfse.getMessage());
+				System.exit(-1);
+			}
 			sim.run();
 			IOUtil.saveReportAndTimesFile(sim, lemsFile);
 			E.info("Finished reading, building, running and displaying LEMS model");

diff --git a/src/main/java/org/neuroml/export/utils/support/ModelFeature.java b/src/main/java/org/neuroml/export/utils/support/ModelFeature.java
@@ -37,6 +37,7 @@ public enum ModelFeature
     NETWORK_WITH_ANALOG_CONNS_MODEL("Network model with analog/continuously communicating connections between cells"),
     ABSTRACT_CELL_MODEL("Model with abstract (non conductance based) cell(s)"), 
     COND_BASED_CELL_MODEL("Model with conductance based cell(s)"), 
+    EXT_MORPH_BIOPHYS_CELL_MODEL("Model with conductance based cell(s) with morphology and/or biophysicalProperties outside cell element"), 
     MULTICOMPARTMENTAL_CELL_MODEL("Model with multicompartmental cell(s)"), 
     CHANNEL_POPULATIONS_CELL_MODEL("Model with channel populations"), 
     CHANNEL_DENSITY_ON_SEGMENT("Model with channel density specified per segment (aot segmentGroup)"), 
@@ -106,7 +107,17 @@ private static void analyseSingleComponent(Component component, ArrayList<ModelF
 
             if(component.getComponentType().isOrExtends(NeuroMLElements.CELL_COMP_TYPE))
             {
+                if (component.quietGetChild("morphology")==null)
+                {
+                    addIfNotPresent(mfs, EXT_MORPH_BIOPHYS_CELL_MODEL);
+                }
+                if (component.quietGetChild("biophysicalProperties")==null)
+                {
+                    addIfNotPresent(mfs, EXT_MORPH_BIOPHYS_CELL_MODEL);
+                }
+
                 Cell cell = Utils.getCellFromComponent(component, lems);
+
                 if(cell.getMorphology() != null)
                 {
                     if(cell.getMorphology().getSegment().size() > 1)

diff --git a/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java b/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java
@@ -41,6 +41,7 @@ private SupportLevelInfo()
         /* Add info on formats supported in jLEMS */
         addSupportInfo(Format.LEMS, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH);
         addSupportInfo(Format.LEMS, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH);
+        addSupportInfo(Format.LEMS, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.NONE);
         addSupportInfo(Format.LEMS, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH);
         addSupportInfo(Format.LEMS, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH);
         addSupportInfo(Format.LEMS, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH);
@@ -135,11 +136,12 @@ public void checkConversionSupported(Format format, Lems lems) throws ModelFeatu
                 if(!supp.equals(SUPPORTED))
                 {
                     passed = false;
-                    report.append("Feature not supported in " + format + ": " + mf + "\n    " + myInstance.isSupported(format, mf) + "\n");
+                    report.append("Feature is not supported in " + format + ": " + mf + "\n    " + myInstance.isSupported(format, mf) + "\n");
                 }
             }
             if(!passed)
             {
+                report.insert(0, "Error! Some features of the model are not supported by that simulator.\n\n");
                 report.append("\nInfo on supported features:\n" + myInstance);
                 throw new ModelFeatureSupportException(report.toString());
             }