Merge pull request #4 from virtualcell/local-fielddata

generate FV solver input files with local field data

Author: jcschaff

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.6"
+version = "0.0.7"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <[email protected]>", "Ezequiel Valencia <[email protected]>"]
 repository = "https://github.com/virtualcell/libvcell"

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

@@ -52,7 +52,7 @@ public String toJson() {
             documentation = """
                     Converts VCML file into Finite Volume Input files.
                       vcml_content: text of VCML XML document
-                      output_dir_path: path to the output directory
+                      output_dir_path: path to the output directory (expected to be subdirectory of the workspace)
                       Returns a JSON string with success status and message"""
     )
     public static CCharPointer entrypoint_vcmlToFiniteVolumeInput(
@@ -65,7 +65,9 @@ public static CCharPointer entrypoint_vcmlToFiniteVolumeInput(
             String vcmlContentStr = CTypeConversion.toJavaString(vcml_content);
             String simulationName = CTypeConversion.toJavaString(simulation_name);
             String outputDirPathStr = CTypeConversion.toJavaString(output_dir_path);
-            vcmlToFiniteVolumeInput(vcmlContentStr, simulationName, new File(outputDirPathStr));
+            File outputDir = new File(outputDirPathStr);
+            File parentDir = outputDir.getParentFile();
+            vcmlToFiniteVolumeInput(vcmlContentStr, simulationName, parentDir, outputDir);
             returnValue = new ReturnValue(true, "Success");
         }catch (Throwable t) {
             logger.error("Error processing spatial model", t);

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

@@ -20,6 +20,7 @@ public static void main(String[] args) {
             File vcml_file = new File(args[1]);
             String vcml_sim_name = args[2];
             File output_dir = new File(args[3]);
+            File parent_dir = output_dir.getParentFile();
             logger.info("Logger logging");
             PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "none");
             PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, "none");
@@ -35,7 +36,7 @@ public static void main(String[] args) {
                 byte[] data = f_vcml.readAllBytes();
                 logger.info("Read " + data.length + " bytes from " + vcml_file.getAbsolutePath());
                 String vcml_str = new String(data);
-                vcmlToFiniteVolumeInput(vcml_str, vcml_sim_name, output_dir);
+                vcmlToFiniteVolumeInput(vcml_str, vcml_sim_name, parent_dir, output_dir);
             }
 
             // use reflection to load jsbml classes and call their default constructors

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

@@ -2,34 +2,42 @@
 
 import cbit.util.xml.VCLoggerException;
 import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.field.FieldDataIdentifierSpec;
+import cbit.vcell.field.FieldFunctionArguments;
+import cbit.vcell.field.FieldUtilities;
 import cbit.vcell.geometry.GeometrySpec;
 import cbit.vcell.mapping.MappingException;
 import cbit.vcell.mapping.SimulationContext;
+import cbit.vcell.math.MathException;
+import cbit.vcell.messaging.server.SimulationTask;
 import cbit.vcell.mongodb.VCMongoMessage;
 import cbit.vcell.parser.ExpressionException;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.SolverException;
-import cbit.vcell.solver.TimeBounds;
-import cbit.vcell.solver.UniformOutputTimeSpec;
+import cbit.vcell.solver.*;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.vcell.libvcell.solvers.LocalFVSolverStandalone;
 import org.vcell.sbml.FiniteVolumeRunUtil;
 import org.vcell.sbml.vcell.SBMLExporter;
 import org.vcell.sbml.vcell.SBMLImporter;
+import org.vcell.util.document.ExternalDataIdentifier;
+import org.vcell.util.document.KeyValue;
+import org.vcell.util.document.User;
 
 import java.beans.PropertyVetoException;
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
 
 
 public class SolverUtils {
     private static final Logger logger = LogManager.getLogger(Entrypoints.class);
 
-    public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException {
+    public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File parentDir, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException, MathException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
         if (vcml_content.substring(0, 300).contains("<sbml xmlns=\"http://www.sbml.org/sbml")) {
@@ -41,7 +49,50 @@ public static void vcmlToFiniteVolumeInput(String vcml_content, String simulatio
         if (sim == null) {
             throw new IllegalArgumentException("Simulation not found: " + simulation_name);
         }
-        FiniteVolumeRunUtil.writeInputFilesOnly(outputDir, sim);
+        FieldDataIdentifierSpec[] fdiSpecs = getFieldDataIdentifierSpecs(sim, parentDir);
+
+        TempSimulation tempSimulation = new TempSimulation(sim, false);
+        tempSimulation.setSimulationOwner(sim.getSimulationOwner());
+        SimulationJob tempSimulationJob = new SimulationJob(tempSimulation, 0, fdiSpecs);
+        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 {
+        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();
+                    File fieldDataDir = new File(parentDir, name);
+                    if (!fieldDataDir.exists()) {
+                        throw new IllegalArgumentException("Field data directory does not exist: " + fieldDataDir.getAbsolutePath());
+                    }
+                    // search fieldDataDir for files with name pattern SimID_<key>_* and extract the key
+                    KeyValue key = null;
+                    for (File f: fieldDataDir.listFiles()) {
+                        String[] filename_parts = f.getName().split("_");
+                        if (filename_parts.length < 3) {
+                            continue;
+                        }
+                        if (filename_parts[0].equals("SimID")) {
+                            key = new KeyValue(filename_parts[1]);
+                            break;
+                        }
+                    }
+                    if (key == null) {
+                        throw new IllegalArgumentException("Field data directory does not contain a file with key: " + name);
+                    }
+                    ExternalDataIdentifier extDataId = new ExternalDataIdentifier(key, User.tempUser, name);
+                    fdiSpecList.add(new FieldDataIdentifierSpec(fieldFuncArg, extDataId));
+                }
+            }
+            fdiSpecs = fdiSpecList.toArray(new FieldDataIdentifierSpec[fdiSpecList.size()]);
+        }
+        return fdiSpecs;
     }