SBML To Finite Volume Endpoint

vcell-rest/pom.xml

@@ -207,6 +207,11 @@
         </exclusion>
       </exclusions>
     </dependency>
+    <dependency>
+      <groupId>net.lingala.zip4j</groupId>
+      <artifactId>zip4j</artifactId>
+      <version>2.11.5</version>
+    </dependency>
     <dependency>
       <groupId>org.jboss.logmanager</groupId>
       <artifactId>log4j2-jboss-logmanager</artifactId>

vcell-rest/src/main/java/org/vcell/restq/handlers/SpatialResource.java

@@ -0,0 +1,84 @@
+package org.vcell.restq.handlers;
+
+import cbit.util.xml.VCLoggerException;
+import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.mapping.MappingException;
+import cbit.vcell.mapping.SimulationContext;
+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 jakarta.enterprise.context.RequestScoped;
+import jakarta.ws.rs.*;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.MediaType;
+import net.lingala.zip4j.ZipFile;
+import org.eclipse.microprofile.openapi.annotations.Operation;
+import org.jboss.resteasy.reactive.PartType;
+import org.jboss.resteasy.reactive.RestForm;
+import org.vcell.sbml.SBMLFakeSpatialBioModel;
+import org.vcell.sbml.vcell.SBMLExporter;
+import org.vcell.sbml.vcell.SBMLImporter;
+import org.w3c.www.http.HTTP;
+
+import java.beans.PropertyVetoException;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+
+@Path("/api/v1/spatial")
+@RequestScoped
+public class SpatialResource {
+    public SpatialResource() { }
+
+    @GET
+    @Path("/retrieveFiniteVolumeInputFromSpatialModel")
+    @Operation(operationId = "retrieveFiniteVolumeInputFromSpatialModel", summary = "Retrieve finite volume input from spatial model")
+    @Consumes(MediaType.MULTIPART_FORM_DATA)
+    @Produces(MediaType.APPLICATION_OCTET_STREAM)
+    public File retrieveFiniteVolumeInputFromSpatialModel(@RestForm File sbmlFile) {
+        try {
+            File workingDir = Files.createTempDirectory("vcell-").toFile();
+            File zipFile = Files.createTempFile("finite-volume", ".zip").toFile();
+            sbmlToFiniteVolumeInput(sbmlFile, workingDir);
+            ZipFile zip = new ZipFile(zipFile);
+
+            zip.addFolder(workingDir);
+            zip.close();
+
+            return zipFile;
+        }catch (Exception e){
+            throw new WebApplicationException("Error processing spatial model", HTTP.INTERNAL_SERVER_ERROR);
+        }
+    }
+
+    public record FiniteVolumeInput(
+            @RestForm @PartType(MediaType.APPLICATION_OCTET_STREAM)
+            File zipFile
+    ) { }
+
+
+
+    public static void sbmlToFiniteVolumeInput(File sbmlFile, File outputDir) throws IOException, MappingException, VCLoggerException, PropertyVetoException, SolverException, ExpressionException {
+        SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger();
+        boolean bValidateSBML = true;
+        InputStream is = new FileInputStream(sbmlFile);
+        SBMLImporter importer = new SBMLImporter(is, vcl, bValidateSBML);
+        BioModel bioModel = importer.getBioModel();
+        bioModel.updateAll(false);
+
+        final double duration = 5.0;  // endpoint arg
+        final double time_step = 0.1;  // endpoint arg
+        //final ISize meshSize = new ISize(10, 10, 10);  // future endpoint arg
+        SimulationContext simContext = bioModel.getSimulationContext(0);
+        Simulation sim = new Simulation(simContext.getMathDescription(), simContext);
+        sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0.0, duration));
+        sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(time_step));
+
+        SBMLFakeSpatialBioModel.writeInputFilesOnly(outputDir, sim);
+    }
+
+}

vcell-rest/src/test/java/org/vcell/restq/apiclient/SpacialResourceTest.java

@@ -0,0 +1,133 @@
+package org.vcell.restq.apiclient;
+
+import cbit.util.xml.VCLoggerException;
+import cbit.vcell.mapping.MappingException;
+import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.resource.PropertyLoader;
+import cbit.vcell.solver.AnnotatedFunction;
+import cbit.vcell.solver.SolverException;
+import cbit.vcell.solvers.FunctionFileGenerator;
+import io.quarkus.test.junit.QuarkusTest;
+import io.quarkus.test.keycloak.client.KeycloakTestClient;
+import jakarta.inject.Inject;
+import net.lingala.zip4j.ZipFile;
+import org.apache.commons.io.FileUtils;
+import org.eclipse.microprofile.config.inject.ConfigProperty;
+import org.jose4j.lang.JoseException;
+import org.junit.jupiter.api.*;
+import org.testcontainers.shaded.com.google.common.io.Files;
+import org.vcell.restclient.ApiClient;
+import org.vcell.restclient.ApiException;
+import org.vcell.restclient.api.SpatialResourceApi;
+import org.vcell.restq.TestEndpointUtils;
+import org.vcell.restq.config.CDIVCellConfigProvider;
+import org.vcell.restq.db.AgroalConnectionFactory;
+import org.vcell.restq.handlers.SpatialResource;
+import org.vcell.util.DataAccessException;
+
+import java.beans.PropertyVetoException;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.Arrays;
+import java.util.Scanner;
+import java.util.Vector;
+
+@QuarkusTest
+public class SpacialResourceTest {
+    @ConfigProperty(name = "quarkus.http.test-port")
+    Integer testPort;
+
+    @Inject
+    AgroalConnectionFactory agroalConnectionFactory;
+
+    KeycloakTestClient keycloakClient = new KeycloakTestClient();
+
+    private ApiClient aliceAPIClient;
+    private static String previousServerID;
+    private static String previousMongoHost;
+    private static String previousMongoPort;
+    private static String previousMongoDB;
+
+    @BeforeAll
+    public static void setupConfig(){
+        PropertyLoader.setConfigProvider(new CDIVCellConfigProvider());
+        previousServerID = PropertyLoader.getProperty(PropertyLoader.vcellServerIDProperty, null);
+        PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, "TEST2");
+
+        previousMongoDB = PropertyLoader.getProperty(PropertyLoader.mongodbDatabase, null);
+        PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, "test");
+
+        previousMongoHost = PropertyLoader.getProperty(PropertyLoader.mongodbHostInternal, null);
+        PropertyLoader.setProperty(PropertyLoader.mongodbHostInternal, "localhost");
+
+        previousMongoPort = PropertyLoader.getProperty(PropertyLoader.mongodbPortInternal, null);
+        PropertyLoader.setProperty(PropertyLoader.mongodbPortInternal, "9080");
+    }
+
+    @AfterAll
+    public static void resetConfig(){
+        if (previousServerID != null) {PropertyLoader.setProperty(PropertyLoader.vcellServerIDProperty, previousServerID);};
+        if (previousMongoHost != null) {PropertyLoader.setProperty(PropertyLoader.mongodbHostInternal, previousMongoHost);}
+        if (previousMongoDB != null) {PropertyLoader.setProperty(PropertyLoader.mongodbDatabase, previousMongoDB);}
+        if (previousMongoPort != null) {PropertyLoader.setProperty(PropertyLoader.mongodbPortInternal, previousMongoPort);}
+    }
+
+    @BeforeEach
+    public void createClients() throws JoseException {
+        aliceAPIClient = TestEndpointUtils.createAuthenticatedAPIClient(keycloakClient, testPort, TestEndpointUtils.TestOIDCUsers.alice);
+    }
+
+    @AfterEach
+    public void removeOIDCMappings() throws SQLException, DataAccessException {
+        TestEndpointUtils.removeAllMappings(agroalConnectionFactory);
+    }
+
+    // Ensure the round trip from request to resulting Zip is equivalent to a local run of input file generation
+    @Test
+    public void testSpacialSBMLResults() throws ApiException, IOException, VCLoggerException, SolverException, ExpressionException, PropertyVetoException, MappingException {
+        SpatialResourceApi spatialResourceApi = new SpatialResourceApi(aliceAPIClient);
+        File sbmlFile = TestEndpointUtils.getResourceFile("/TinySpacialProject_Application0.xml");
+
+        File zip = spatialResourceApi.retrieveFiniteVolumeInputFromSpatialModel(sbmlFile);
+        File unzipDir = Files.createTempDir();
+        File outputDir = Files.createTempDir();
+
+        SpatialResource.sbmlToFiniteVolumeInput(sbmlFile, outputDir);
+
+        ZipFile zipFile = new ZipFile(zip);
+        zipFile.extractAll(unzipDir.getAbsolutePath());
+        zipFile.close();
+
+        unzipDir = unzipDir.listFiles()[0];
+
+        for (int i = 0; i < outputDir.listFiles().length; i++) {
+            File output = outputDir.listFiles()[i];
+            File unzip = Arrays.stream(unzipDir.listFiles()).filter(
+                    f -> f.getName().split("\\.")[1].equals(output.getName().split("\\.")[1])
+            ).findFirst().orElse(null);
+            if (output.getName().split("\\.")[1].equals("functions")){
+                Vector<AnnotatedFunction> outPutAnnotated = FunctionFileGenerator.readFunctionsFile(output, "0");
+                Vector<AnnotatedFunction> unzipAnnotated = FunctionFileGenerator.readFunctionsFile(unzip, "0");
+                for (int j = 0; j < outPutAnnotated.size(); j++) {
+                    Assertions.assertTrue(outPutAnnotated.get(j).compareEqual(unzipAnnotated.get(j)));
+                }
+            } else if (output.getName().split("\\.")[1].equals("fvinput")) {
+                Scanner outputReader = new Scanner(output);
+                Scanner unzipReader = new Scanner(unzip);
+
+                while (outputReader.hasNextLine()){
+                    String outputLine = outputReader.nextLine();
+                    String unzipLine = unzipReader.nextLine();
+                    // Don't compare the file path
+                    if (!outputLine.contains("FILE")){
+                        Assertions.assertEquals(outputLine, unzipLine);
+                    }
+                }
+            } else{
+                Assertions.assertTrue(FileUtils.contentEquals(output, unzip));
+            }
+        }
+    }
+}