use prebuilt SImID_SIMULATIONKEY_JOBINDEX_ fdata files if exists.

Author: jcschaff

vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java

@@ -12,6 +12,7 @@
 import cbit.vcell.messaging.server.SimulationTask;
 import cbit.vcell.mongodb.VCMongoMessage;
 import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.simdata.SimulationData;
 import cbit.vcell.solver.*;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
@@ -30,6 +31,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -49,24 +51,57 @@ public static void vcmlToFiniteVolumeInput(String vcml_content, String simulatio
         if (sim == null) {
             throw new IllegalArgumentException("Simulation not found: " + simulation_name);
         }
-        FieldDataIdentifierSpec[] fdiSpecs = getFieldDataIdentifierSpecs(sim, parentDir);
+        FieldDataIdentifierSpec[] fdiSpecs = getFieldDataIdentifierSpecs(sim, outputDir, parentDir);
 
         TempSimulation tempSimulation = new TempSimulation(sim, false);
         tempSimulation.setSimulationOwner(sim.getSimulationOwner());
         SimulationJob tempSimulationJob = new SimulationJob(tempSimulation, 0, fdiSpecs);
+
+        renameExistingFieldDataFiles(tempSimulation.getKey(), tempSimulationJob.getJobIndex(), outputDir);
+
         SimulationTask simTask = new SimulationTask(tempSimulationJob, 0);
         LocalFVSolverStandalone solver = new LocalFVSolverStandalone(simTask, outputDir);
         solver.initialize();
     }
 
-    private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation sim, File parentDir) throws MathException, ExpressionException {
+    private static void renameExistingFieldDataFiles(KeyValue tempSimKey, int jobId, File outputDir) {
+        File[] files = outputDir.listFiles();
+        if (files != null) {
+            for (File file : files) {
+                if (file.getName().startsWith("SimID_SIMULATIONKEY_JOBINDEX_")) {
+                    String newName = file.getName().replace("SIMULATIONKEY",tempSimKey.toString()).replace("JOBINDEX",String.valueOf(jobId));
+                    File newFile = new File(outputDir, newName);
+                    if (!file.renameTo(newFile)){
+                        throw new RuntimeException("Could not rename " + file.getName() + " to " + newFile.getAbsolutePath());
+                    }
+                }
+            }
+        }
+    }
+
+    private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation sim, File outputDir, File parentDir) throws MathException, ExpressionException {
         FieldDataIdentifierSpec[] fdiSpecs = null;
         FieldFunctionArguments[] fieldFuncArgs =  FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
         if (fieldFuncArgs != null) {
             List<FieldDataIdentifierSpec> fdiSpecList = new ArrayList<>();
             for (FieldFunctionArguments fieldFuncArg : fieldFuncArgs) {
                 if (fieldFuncArg != null) {
                     String name = fieldFuncArg.getFieldName();
+                    //
+                    // First, check if the resampled field data files are already present (e.g. if pyvcell wrote the files directly from image data)
+                    //
+                    ExternalDataIdentifier fakeExtDataId = new ExternalDataIdentifier(sim.getKey(), User.tempUser, name);
+                    String fieldDataFileName = SimulationData.createCanonicalResampleFileName(fakeExtDataId, fieldFuncArg);
+                    fieldDataFileName = fieldDataFileName.replace("SimID_" + sim.getKey().toString() + "_0_", "SimID_SIMULATIONKEY_JOBINDEX_");
+                    File preexistingFieldDataFile = new File(outputDir, fieldDataFileName);
+                    if (preexistingFieldDataFile.exists()) {
+                        fdiSpecList.add(new FieldDataIdentifierSpec(fieldFuncArg, fakeExtDataId));
+                        continue;
+                    }
+
+                    //
+                    // If not, check if the field data directory exists as a subdirectory of the parentDir - holding simulation results.
+                    //
                     File fieldDataDir = new File(parentDir, name);
                     if (!fieldDataDir.exists()) {
                         throw new IllegalArgumentException("Field data directory does not exist: " + fieldDataDir.getAbsolutePath());

vcell-native/src/main/java/org/vcell/libvcell/solvers/LocalFiniteVolumeFileWriter.java

@@ -17,6 +17,8 @@
 import cbit.vcell.solver.Simulation;
 import cbit.vcell.solvers.FiniteVolumeFileWriter;
 import org.vcell.util.DataAccessException;
+import org.vcell.util.document.ExternalDataIdentifier;
+import org.vcell.util.document.User;
 
 import java.io.File;
 import java.io.IOException;
@@ -106,7 +108,8 @@ private VariableType getVariableTypeFromFieldDataFiles(FieldDataIdentifierSpec f
             // First, look to see if the processed field data file already exists, if so, use it to determine the variable type
             //
             DataSet dataSet = new DataSet();
-            File existingFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName(fieldDataIDSpec.getExternalDataIdentifier(), ffa));
+            ExternalDataIdentifier existingFieldDataID = new ExternalDataIdentifier(this.simTask.getSimKey(), User.tempUser, ffa.getFieldName());
+            File existingFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName(existingFieldDataID, ffa));
             if (existingFieldDataFile.exists()) {
                 // field data file may already exist
                 // 1. from pyvcell writing the field data file directly into this directory for an image-based field data

vcell-native/src/test/java/org/vcell/libvcell/SolverEntrypointsTest.java

@@ -50,6 +50,23 @@ public void testSbmlToFiniteVolumeInput_vcml_instead() throws IOException {
         assertEquals("expecting SBML content, not VCML", exc.getMessage());
     }
 
+    @Test
+    public void testVcmlToFiniteVolumeInput_field_data_already_sampled() throws SolverException, ExpressionException, MappingException, IOException, XmlParseException, MathException, InterruptedException {
+        String vcmlContent = getFileContentsAsString("/FieldDataDemo.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToFiniteVolumeInput_"+UUID.randomUUID()).toFile();
+        File output_dir = new File(parent_dir, "output_dir");
+        assertEquals(0, countFiles(output_dir));
+        // prepopulate the output_dir with the resampled field data files, should use these instead.
+        extractTgz(SolverEntrypointsTest.class.getResourceAsStream("/test2_lsm_DEMO_resampled.tgz"), output_dir);
+        listFilesInDirectory(output_dir);
+        assertEquals(2, countFiles(output_dir));
+
+        String simulationName = "Simulation0";
+        vcmlToFiniteVolumeInput(vcmlContent, simulationName, parent_dir, output_dir);
+        listFilesInDirectory(output_dir);
+        assertEquals(6, countFiles(output_dir));
+    }
+
     @Test
     public void testVcmlToFiniteVolumeInput_field_data() throws SolverException, ExpressionException, MappingException, IOException, XmlParseException, MathException, InterruptedException {
         String vcmlContent = getFileContentsAsString("/FieldDataDemo.vcml");
@@ -70,7 +87,7 @@ public void testVcmlToFiniteVolumeInput_field_data() throws SolverException, Exp
     }
 
     @Test
-    public void testVcmlToFiniteVolumeInput_field_data_not_found() throws SolverException, ExpressionException, MappingException, IOException, XmlParseException, MathException, InterruptedException {
+    public void testVcmlToFiniteVolumeInput_field_data_not_found() throws IOException {
         String vcmlContent = getFileContentsAsString("/FieldDataDemo.vcml");
         File parent_dir = Files.createTempDirectory("vcmlToFiniteVolumeInput_"+UUID.randomUUID()).toFile();
         File output_dir = new File(parent_dir, "output_dir");