Support for stochastic simulation added

.gitignore

@@ -20,7 +20,7 @@ liblpsolve55j_x64.so
 jsbml.log
 
 # BiGG models
-src/test/resources/bigg/
+src/test/resources/bigg/v1.5/
 
 # sbml-test-suite
 src/test/resources/sbml-test-suite/

src/main/java/org/simulator/fba/FluxBalanceAnalysis.java

@@ -50,7 +50,10 @@
 import org.sbml.jsbml.validator.ModelOverdeterminedException;
 import org.simulator.sbml.SBMLinterpreter;
 import org.simulator.sbml.astnode.ASTNodeValue;
+import scpsolver.constraints.LinearBiggerThanEqualsConstraint;
+import scpsolver.constraints.LinearConstraint;
 import scpsolver.constraints.LinearEqualsConstraint;
+import scpsolver.constraints.LinearSmallerThanEqualsConstraint;
 import scpsolver.lpsolver.LinearProgramSolver;
 import scpsolver.lpsolver.SolverFactory;
 import scpsolver.problems.LinearProgram;
@@ -235,7 +238,7 @@ public FluxBalanceAnalysis(SBMLDocument doc)
         for (Pair<String, Double> pair : species2Reaction.get(species.getId())) {
           weights[reaction2Index.get(pair.getKey())] = pair.getValue();
         }
-        if (species2Reaction.get(species.getId()).size() > 1) {
+        if (species.isSetBoundaryCondition() && !species.getBoundaryCondition()) {
           problem.addConstraint(new LinearEqualsConstraint(weights, 0.0, "cnstrt_" + species.getId()));
         }
       }

src/test/java/org/simulator/fba/BiGGTest.java

@@ -1,6 +1,6 @@
 package org.simulator.fba;
 
-import org.junit.Ignore;
+import org.junit.Assert;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLReader;
 import org.simulator.TestUtils;
@@ -13,9 +13,10 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.*;
+import java.nio.file.Paths;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
-import java.util.zip.GZIPInputStream;
 
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
@@ -27,10 +28,24 @@
 public class BiGGTest {
 	private String resource;
     private static final Logger logger = LoggerFactory.getLogger(TestUtils.class);
+    private static final double RESULT_DEVIATION = 1E-6d;
 
+    /**
+     * HashMap for storing the reference results with key as the model names.
+     */
+    private Map<String, Double> referenceResults;
 
 	@Before
-	public void setUp(){ }
+	public void setUp() throws IOException {
+		BufferedReader reader = new BufferedReader(new FileReader(TestUtils.getPathForTestResource("/bigg/bigg_reference_solutions.csv")));
+        referenceResults = new HashMap<>();
+        String line;
+
+        while ((line = reader.readLine()) != null) {
+            String[] solution = line.split(",");
+            referenceResults.put(solution[0], Double.parseDouble(solution[1]));
+        }
+	}
 
     /**
      * Returns location of BiGG test model directory from environment variable.
@@ -51,34 +66,16 @@ public static Iterable<Object[]> data(){
 
 		// find all BiGG models (compressed .xml.gz files)
         String biggPath = getBiGGModelPath();
-        System.out.println("BiGG models path: " + biggPath);
-		return TestUtils.findResources(biggPath, ".xml.gz", filter, skip, mvnResource);
+        logger.info("BiGG models path: " + biggPath);
+		return TestUtils.findResources(biggPath, ".xml", filter, skip, mvnResource);
 	}
 
 	@Test
 	public void testFBA() throws Exception {
         logger.info("--------------------------------------------------------");
         logger.info(String.format("%s", resource));
-        System.out.println("BiGG Resource:" + resource);
-
-        if ((resource.endsWith("iAF987.xml.gz") ||
-                (resource.endsWith("iAF692.xml.gz")))) {
-            /*
-            BiGG Resource://home/mkoenig/git/sbscl-shalin/src/test/resources/bigg/v1.5/iAF987.xml.gz
-            glp_free: memory allocation error
-            Error detected in file env/alloc.c at line 72
-
-            Process finished with exit code 134 (interrupted by signal 6: SIGABRT)
-            */
-            return;
-        }
-
 
-        // read SBML
-        InputStream is = new FileInputStream(resource);
-        GZIPInputStream gzis = new GZIPInputStream(is);
-
-        SBMLDocument doc = SBMLReader.read(gzis);
+        SBMLDocument doc = SBMLReader.read(new File(resource));
         assertNotNull(doc);
 
         FluxBalanceAnalysis solver = new FluxBalanceAnalysis(doc);
@@ -90,8 +87,8 @@ public void testFBA() throws Exception {
         double[] fluxes = solver.getValues();
         assertNotNull(fluxes);
 
-        //TODO: check against reference solution
-        is.close();
+        Assert.assertEquals(objectiveValue, referenceResults.get(Paths.get(resource).getFileName().toString()), RESULT_DEVIATION);
+
 	}
 
 }

src/test/resources/bigg/bigg_reference_solutions.csv

@@ -0,0 +1,85 @@
+RECON1.xml,0
+Recon3D.xml,755.0032156
+STM_v1_0.xml,0.4778336608
+e_coli_core.xml,0.873921507
+iAB_RBC_283.xml,2.935561467
+iAF1260.xml,0.7367009389
+iAF1260b.xml,0.7367009389
+iAF692.xml,0.02678046755
+iAF987.xml,0.04732237668
+iAPECO1_1312.xml,0.9824784387
+iAT_PLT_636.xml,0
+iB21_1397.xml,0.9756145116
+iBWG_1329.xml,0.9824784387
+iCHOv1.xml,0.0323689716
+iE2348C_1286.xml,0.9824784387
+iEC042_1314.xml,0.9824784387
+iEC55989_1330.xml,0.9824784387
+iECABU_c1320.xml,0.9824784387
+iECBD_1354.xml,0.9756145116
+iECB_1328.xml,0.9824784387
+iECDH10B_1368.xml,1.037477544
+iECDH1ME8569_1439.xml,0.9824784387
+iECD_1391.xml,0.9756145116
+iECED1_1282.xml,0.9824634434
+iECH74115_1262.xml,0.9824784387
+iECIAI1_1343.xml,20.52222563
+iECIAI39_1322.xml,0.9828409641
+iECNA114_1301.xml,0.9824784387
+iECO103_1326.xml,0.9824784387
+iECO111_1330.xml,0.9824784387
+iECO26_1355.xml,0.9824784387
+iECOK1_1307.xml,0.9824784387
+iECP_1309.xml,0.9824784387
+iECS88_1305.xml,0.9824784387
+iECSE_1348.xml,0.9824784387
+iECSF_1327.xml,0.9824784387
+iECSP_1301.xml,0.9824784387
+iECUMN_1333.xml,0.9826920128
+iECW_1372.xml,0.9824784387
+iECs_1301.xml,0.9824784387
+iEKO11_1354.xml,0.9824784387
+iETEC_1333.xml,0.9824784387
+iEcDH1_1363.xml,0.9824784387
+iEcE24377_1341.xml,0.9824784387
+iEcHS_1320.xml,0.9824784387
+iEcSMS35_1347.xml,0.9824784387
+iEcolC_1368.xml,0.9824784387
+iG2583_1286.xml,0.9824784387
+iHN637.xml,0.2244545421
+iIT341.xml,0.6928126937
+iJB785.xml,0.05390186747
+iJN678.xml,0.06314983713
+iJN746.xml,1.4
+iJO1366.xml,0.9823718127
+iJR904.xml,0.9219480951
+iLB1027_lipid.xml,0.3596067078
+iLF82_1304.xml,0.9824784387
+iLJ478.xml,0.228406792
+iML1515.xml,0.8769972144
+iMM1415.xml,1.363427906
+iMM904.xml,0.2878657037
+iND750.xml,0.0973233759
+iNF517.xml,0.04263460544
+iNJ661.xml,0.05254980101
+iNRG857_1313.xml,0.9824784387
+iPC815.xml,0.2835583812
+iRC1080.xml,6.156851476
+iSB619.xml,0.1580502916
+iSBO_1134.xml,0.3998801249
+iSDY_1059.xml,0.9378903141
+iSFV_1184.xml,0.8938577496
+iSF_1195.xml,0.9145918469
+iSFxv_1172.xml,0.8940890262
+iSSON_1240.xml,0.9826450753
+iS_1188.xml,0.8570768327
+iSbBS512_1146.xml,0.9828118164
+iUMN146_1321.xml,0.9824784387
+iUMNK88_1353.xml,0.9824784387
+iUTI89_1310.xml,0.9824784387
+iWFL_1372.xml,0.9824784387
+iY75_1357.xml,0.9824784387
+iYL1228.xml,1.042637498
+iYO844.xml,0.1179663893
+iZ_1308.xml,0.9824784387
+ic_1306.xml,1.03192228

src/test/scripts/download_bigg_models.sh

@@ -15,11 +15,11 @@ TEST_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 # download and extract the bigg models for testing
 cd $TEST_DIR/../resources/bigg
-mkdir -p $TEST_DIR/../resources/bigg
-cd $TEST_DIR/../resources/bigg
 wget $BIGG_MODELS_BASE_URL/$FILE_NAME
 tar xzf $FILE_NAME
 rm $FILE_NAME
+cd $TEST_DIR/../resources/bigg/v1.5/
+gunzip *.gz
 
 # set environment variable
 export BIGG_MODELS_PATH=${TEST_DIR}/../resources/bigg/v1.5