Dan ss results6

vcell-core/src/main/java/cbit/vcell/simdata/DataSetControllerImpl.java

@@ -2402,7 +2402,15 @@ public ODEDataBlock getODEDataBlock(VCDataIdentifier vcdID) throws DataAccessExc
 public LangevinBatchResultSet getLangevinBatchResultSet(VCDataIdentifier vcdID) throws DataAccessException {
 	if (lg.isTraceEnabled()) lg.trace("DataSetControllerImpl.getLangevinBatchResultSet()");
 	try {
-		VCData simData = getVCData(vcdID);
+		VCData vcData = getVCData(vcdID);
+		if(!(vcData instanceof SimulationData)) {
+			return null;
+		}
+		SimulationData simData = (SimulationData)vcData;
+		if(!(simData.getIsIDAData())) {
+			return null;
+		}
+
 		ODEDataInfo odeDataInfo = new ODEDataInfo(vcdID.getOwner(), vcdID.getID(),
 									simData.getDataBlockTimeStamp(ODE_DATA, 0));
 		int keepAtMost = 10000;

vcell-core/src/main/java/cbit/vcell/simdata/LangevinSolverResultSet.java

@@ -0,0 +1,74 @@
+package cbit.vcell.simdata;
+
+import cbit.vcell.solver.ode.ODESimData;
+
+import java.io.*;
+
+public class LangevinSolverResultSet implements Serializable {
+
+    private final LangevinBatchResultSet raw;
+
+    public LangevinSolverResultSet(LangevinBatchResultSet raw) {
+        this.raw = raw;
+    }
+
+//    // safe getter that returns a deep copy, but I don't think we need it
+//    public LangevinBatchResultSet getLangevinBatchResultSetSafe() {
+//        return deepCopy(raw);
+//    }
+
+    // convenience getters
+    public ODESimData getAvg() {
+        return raw == null ? null : raw.getOdeSimDataAvg();
+    }
+    public ODESimData getMin() {
+        return raw == null ? null : raw.getOdeSimDataMin();
+    }
+    public ODESimData getMax() {
+        return raw == null ? null : raw.getOdeSimDataMax();
+    }
+    public ODESimData getStd() {
+        return raw == null ? null : raw.getOdeSimDataStd();
+    }
+    public ODESimData getClusterCounts() {
+        return raw == null ? null : raw.getOdeSimDataClusterCounts();
+    }
+    public ODESimData getClusterMean() {
+        return raw == null ? null : raw.getOdeSimDataClusterMean();
+    }
+    public ODESimData getClusterOverall() {
+        return raw == null ? null : raw.getOdeSimDataClusterOverall();
+    }
+
+    // helper functions
+    public boolean isAverageDataAvailable() {
+        return getAvg() != null &&
+                getMin() != null &&
+                getMax() != null &&
+                getStd() != null;
+    }
+    public boolean isClusterDataAvailable() {
+        return getClusterCounts() != null &&
+                getClusterMean() != null &&
+                getClusterOverall() != null;
+    }
+
+    private static LangevinBatchResultSet deepCopy(LangevinBatchResultSet original) {
+        if (original == null) {
+            return null;
+        }
+        try {
+            ByteArrayOutputStream bos = new ByteArrayOutputStream();
+            ObjectOutputStream out = new ObjectOutputStream(bos);
+            out.writeObject(original);
+            out.flush();
+
+            ObjectInputStream in = new ObjectInputStream(new ByteArrayInputStream(bos.toByteArray()));
+            return (LangevinBatchResultSet) in.readObject();
+
+        } catch (ClassNotFoundException | IOException e) {
+            throw new RuntimeException("Deep copy failed", e);
+        }
+    }
+
+}

vcell-core/src/main/java/cbit/vcell/simdata/ODEDataManager.java

@@ -35,7 +35,7 @@ public class ODEDataManager implements DataManager {
 	private VCDataIdentifier vcDataIdentifier = null;
 	private ODESolverResultSet odeSolverResultSet = null;
 	private NFSimMolecularConfigurations nFSimMolecularConfigurations = null;
-	private LangevinBatchResultSet langevinBatchResultSet = null;
+	private LangevinSolverResultSet langevinSolverResultSet = null;
 	private OutputContext outputContext = null;
 
 public OutputContext getOutputContext() {
@@ -180,7 +180,11 @@ private void connect() throws DataAccessException {
 	// clone, so we can operate safely on it (adding/removing user-defined functions) - real remote data is being cached...
 	odeSolverResultSet = new ODESimData(getVCDataIdentifier(),getVCDataManager().getODEData(getVCDataIdentifier()));
 	nFSimMolecularConfigurations = getVCDataManager().getNFSimMolecularConfigurations(getVCDataIdentifier());
-//	langevinBatchResultSet = getVCDataManager().getLangevinBatchResultSet(getVCDataIdentifier());
+	LangevinBatchResultSet raw = getVCDataManager().getLangevinBatchResultSet(getVCDataIdentifier());
+	langevinSolverResultSet = new LangevinSolverResultSet(raw);		// may be null
+	if( langevinSolverResultSet.isAverageDataAvailable()) {
+		odeSolverResultSet = langevinSolverResultSet.getAvg();
+	}
 }
 
 private void addOutputFunction(AnnotatedFunction function, ODESolverResultSet odeRS) {

vcell-core/src/main/java/cbit/vcell/simdata/SimulationData.java

@@ -639,11 +639,17 @@ public synchronized File getJobFunctionsFile() throws FileNotFoundException {
 
 
 
-public synchronized boolean getIsODEData() throws DataAccessException {
-	refreshLogFile();
-	return isODEData;
-}
-
+	public synchronized boolean getIsODEData() throws DataAccessException {
+		refreshLogFile();
+		return isODEData;
+	}
+	public synchronized boolean getIsIDAData() throws DataAccessException {
+		refreshLogFile();
+		return odeIdentifier.equals(IDA_DATA_IDENTIFIER);
+	}
+	public String getDataIdentifierSafe() {
+		return new String(odeIdentifier);
+	}
 
 private long getLastModified(File pdeFile, File zipFile) throws IOException {
 	if (zipFile == null) {

vcell-core/src/test/java/cbit/vcell/simdata/LangevinResultsReadTest.java

@@ -46,6 +46,9 @@ public class LangevinResultsReadTest {
     private static File langevin_input_file;
     private static File messaging_config_file;
 
+    private static File euler_log_file;
+    private static File euler_ode_file;
+
     // results for first task in the batch, named to match single run file (ending in "_") ex: SimID_303404574_0_
     private static File ida_0_file;
     // log produced by the solver for first task in the batch, named using the normal convention ex: SimID_303404574_0_0.log
@@ -56,6 +59,8 @@ public class LangevinResultsReadTest {
     //    SimID_303404574_0_.ida
     private static File log_data_file;
 
+    // resource location of files for various test cases
+    private static String resourceBase = null;
 
     @BeforeAll
     public static void setUp() throws IOException {
@@ -71,6 +76,7 @@ public static void setUp() throws IOException {
             throw new IOException("Failed to create subdirectory: " + localSimDir.getAbsolutePath());
         }
 
+        resourceBase = "cbit/vcell/simdata/langevin/batch/";
         functions_file = copyToPrimaryDir("SimID_303404574_0_.functions");
         ida_0_file = copyToPrimaryDir("SimID_303404574_0_.ida");    // results for batch run0 (or for single run)
         log_0_file = copyToPrimaryDir("SimID_303404574_0_0.log");   // langevin-made log for run 0
@@ -87,6 +93,11 @@ public static void setUp() throws IOException {
         ida_min_file = copyToPrimaryDir("SimID_303404574_0__Min.ida");
         ida_std_file = copyToPrimaryDir("SimID_303404574_0__Std.ida");
 
+        resourceBase = "cbit/vcell/simdata/langevin/euler/";
+        euler_log_file = copyToPrimaryDir("SimID_303690651_0_.log");
+        euler_ode_file = copyToPrimaryDir("SimID_303690651_0_.ode");
+
+
 //        ida_1_File = File.createTempFile("SimID_284673710_0_", ".ida");
 //        Resources.asByteSource(Resources.getResource("cbit/vcell/simdata/SimID_284673710_0_.ida"))
 //                .copyTo(com.google.common.io.Files.asByteSink(ida_1_File));
@@ -102,7 +113,7 @@ public static void tearDown() {
 
 
     @Test
-    public void testReadData() throws IOException, DataAccessException, CacheException {
+    public void testReadDataLangevinBatch() throws IOException, DataAccessException, CacheException {
 
         String simID = "303404574";
         KeyValue key = new KeyValue(simID);
@@ -111,10 +122,13 @@ public void testReadData() throws IOException, DataAccessException, CacheExcepti
 
         VCDataIdentifier vCDataIdentifier = new VCSimulationDataIdentifier(vcSimID, 0);
         VCData vcData = new SimulationData(vCDataIdentifier, primaryDir, localSimDir, null);
+        SimulationData simData = (SimulationData)vcData;
+        String identifier = simData.getDataIdentifierSafe();
+        assertTrue(identifier.equals(SimDataConstants.IDA_DATA_IDENTIFIER), "Langevin simulation should be IDA data");
+        assertFalse(identifier.equals(SimDataConstants.ODE_DATA_IDENTIFIER), "Langevin simulation should not be ODE data");
 
         Cachetable aCacheTable = new Cachetable(10 * Cachetable.minute, 100000);
         aCacheTable.put(vCDataIdentifier, vcData);
-
         DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(aCacheTable, primaryDir, localSimDir);
 
         LangevinBatchResultSet lbrs = dataSetControllerImpl.getLangevinBatchResultSet(vCDataIdentifier);
@@ -143,6 +157,31 @@ public void testReadData() throws IOException, DataAccessException, CacheExcepti
 
     }
 
+    // we should not try to read euler results using LangevinBatchResultSet
+    @Test
+    public void testReadDataEulerBatch() throws IOException, DataAccessException, CacheException {
+
+        String simID = "303690651";
+        KeyValue key = new KeyValue(simID);
+        User usr = new User("temp",key);
+        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(key, usr);
+
+        VCDataIdentifier vCDataIdentifier = new VCSimulationDataIdentifier(vcSimID, 0);
+        VCData vcData = new SimulationData(vCDataIdentifier, primaryDir, localSimDir, null);
+        SimulationData simData = (SimulationData)vcData;
+        String identifier = simData.getDataIdentifierSafe();
+        assertFalse(identifier.equals(SimDataConstants.IDA_DATA_IDENTIFIER), "Langevin simulation should not be IDA data");
+        assertTrue(identifier.equals(SimDataConstants.ODE_DATA_IDENTIFIER), "Langevin simulation should be ODE data");
+
+        Cachetable aCacheTable = new Cachetable(10 * Cachetable.minute, 100000);
+        aCacheTable.put(vCDataIdentifier, vcData);
+        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(aCacheTable, primaryDir, localSimDir);
+
+        LangevinBatchResultSet lbrs = dataSetControllerImpl.getLangevinBatchResultSet(vCDataIdentifier);
+        assertNull(lbrs, "Result set should be null for Euler data when read as LangevinBatchResultSet");
+
+    }
+
 //    @Test
 //    public void testRead() throws IOException {
 //
@@ -167,7 +206,7 @@ private static void deleteRecursively(File file) {
 
     private static File copyToPrimaryDir(String resourceName) throws IOException {
         File out = new File(primaryDir, resourceName);
-        Resources.asByteSource(Resources.getResource("cbit/vcell/simdata/langevin/batch/" + resourceName))
+        Resources.asByteSource(Resources.getResource(resourceBase + resourceName))
                 .copyTo(com.google.common.io.Files.asByteSink(out));
         return out;
     }

vcell-core/src/test/resources/cbit/vcell/simdata/langevin/euler/SimID_303690651_0_.log

@@ -0,0 +1,3 @@
+ODEData logfile
+CompactODEData binary format version 1
+SimID_303690651_0_.ode

vcell-core/src/test/resources/cbit/vcell/simdata/langevin/euler/SimID_303690651_0__0.simtask.xml

@@ -0,0 +1,74 @@
+<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
+  <MathDescription Name="unnamed_generated">
+    <Constant Name="_F_">96485.3321</Constant>
+    <Constant Name="_F_nmol_">9.64853321E-5</Constant>
+    <Constant Name="_K_GHK_">1.0E-9</Constant>
+    <Constant Name="_N_pmol_">6.02214179E11</Constant>
+    <Constant Name="_PI_">3.141592653589793</Constant>
+    <Constant Name="_R_">8314.46261815</Constant>
+    <Constant Name="_T_">300.0</Constant>
+    <Constant Name="EmptySet_init_mole_litre_1">1.0</Constant>
+    <Constant Name="k4">180.0</Constant>
+    <Constant Name="k4prime">0.018</Constant>
+    <Constant Name="k6">1.0</Constant>
+    <Constant Name="K_millivolts_per_volt">1000.0</Constant>
+    <Constant Name="kappa">0.015</Constant>
+    <Constant Name="KMOLE">0.001660538783162726</Constant>
+    <Constant Name="Size_cell">1.0</Constant>
+    <Constant Name="u_init_mole_litre_1">0.0</Constant>
+    <Constant Name="v_init_mole_litre_1">0.0</Constant>
+    <VolumeVariable Name="u" Domain="Compartment" />
+    <VolumeVariable Name="v" Domain="Compartment" />
+    <Function Name="alpha">(k4prime / k4)</Function>
+    <Function Name="EmptySet" Domain="Compartment">(K_EmptySet_total / Size_cell)</Function>
+    <Function Name="K_EmptySet_total" Domain="Compartment">(Size_cell * EmptySet_init_mole_litre_1)</Function>
+    <Function Name="K_s_z_total" Domain="Compartment">(Size_cell * s_z_init_mole_litre_1)</Function>
+    <Function Name="LumpedJ_r0" Domain="Compartment">((k4 * (v - u) * (alpha + pow(u,2.0))) - (k6 * u))</Function>
+    <Function Name="LumpedJ_r1" Domain="Compartment">(kappa - (k6 * u))</Function>
+    <Function Name="s_z" Domain="Compartment">(K_s_z_total / Size_cell)</Function>
+    <Function Name="s_z_init_mole_litre_1" Domain="Compartment">(v_init_mole_litre_1 - u_init_mole_litre_1)</Function>
+    <CompartmentSubDomain Name="Compartment">
+      <BoundaryType Boundary="Xm" Type="Value" />
+      <BoundaryType Boundary="Xp" Type="Value" />
+      <BoundaryType Boundary="Ym" Type="Value" />
+      <BoundaryType Boundary="Yp" Type="Value" />
+      <BoundaryType Boundary="Zm" Type="Value" />
+      <BoundaryType Boundary="Zp" Type="Value" />
+      <OdeEquation Name="u" SolutionType="Unknown">
+        <Rate>(LumpedJ_r0 / Size_cell)</Rate>
+        <Initial>u_init_mole_litre_1</Initial>
+      </OdeEquation>
+      <OdeEquation Name="v" SolutionType="Unknown">
+        <Rate>(LumpedJ_r1 / Size_cell)</Rate>
+        <Initial>v_init_mole_litre_1</Initial>
+      </OdeEquation>
+    </CompartmentSubDomain>
+    <Version Name="unnamed_generated" KeyValue="164204547" BranchId="164138400" Archived="0" Date="15-Aug-2019 17:46:00" FromVersionable="false">
+      <Owner Name="danv" Identifier="26766043" />
+      <GroupAccess Type="1" />
+    </Version>
+  </MathDescription>
+  <Simulation Name="Copy of Copy of Simulation0">
+    <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Forward Euler (First Order, Fixed Time Step)">
+      <TimeBound StartTime="0.0" EndTime="100.0" />
+      <TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
+      <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
+      <OutputOptions KeepEvery="1" KeepAtMost="1000" />
+      <NumberProcessors>1</NumberProcessors>
+    </SolverTaskDescription>
+    <MathOverrides />
+    <Version Name="Copy of Copy of Simulation0" KeyValue="303690651" BranchId="303690652" Archived="0" Date="03-Feb-2026 21:49:49" FromVersionable="false">
+      <Owner Name="danv" Identifier="26766043" />
+      <GroupAccess Type="1" />
+    </Version>
+  </Simulation>
+  <Geometry Name="Compartmental1134096228" Dimension="0">
+    <Extent X="10.0" Y="10.0" Z="10.0" />
+    <Origin X="0.0" Y="0.0" Z="0.0" />
+    <SubVolume Name="Compartment" Handle="0" Type="Compartmental" KeyValue="164138398" />
+    <Version Name="Compartmental1134096228" KeyValue="164138394" BranchId="164138395" Archived="0" Date="14-Aug-2019 23:06:24" FromVersionable="false">
+      <Owner Name="danv" Identifier="26766043" />
+      <GroupAccess Type="1" />
+    </Version>
+  </Geometry>
+</SimulationTask>