partial fix of #24, LPsolver working for single simulation.

.gitignore

@@ -14,12 +14,16 @@ lib/nmi/scpsolver/1.0/GLPKSolverPack.jar
 lib/nmi/scpsolver/1.0/LPSOLVESolverPack.jar
 lib/cplex/cplex.jar
 libglpkjni_x64.so
+liblpsolve55j_x64.so
 
 # log files
 jsbml.log
 
 # BiGG models
 src/test/resources/bigg/
+
 # sbml-test-suite
 src/test/resources/sbml-test-suite/
 
+# log files
+*.log

pom.xml

@@ -227,7 +227,7 @@
     <dependency>
       <groupId>scpsolver</groupId>
       <artifactId>GLPKSolverPack</artifactId>
-      <version>4.35</version>
+      <version>4.35-v2</version>
       <!--
       <scope>system</scope>
       <systemPath>${project.basedir}/src/lib/maven/scpsolver/GLPKSolverPack/4.35/GLPKSolverPack-4.35.jar</systemPath>

src/lib/maven/scpsolver/GLPKSolverPack/4.35-v2/GLPKSolverPack-4.35-v2.jar.md5

@@ -0,0 +1 @@
+1ae23211e87021726c7d4b13a6036c3f

src/lib/maven/scpsolver/GLPKSolverPack/4.35-v2/GLPKSolverPack-4.35-v2.jar.sha1

@@ -0,0 +1 @@
+0b7918087973e45cf2919f878678c96920317bb0

src/lib/maven/scpsolver/GLPKSolverPack/4.35/GLPKSolverPack-4.35.pom → src/lib/maven/scpsolver/GLPKSolverPack/4.35-v2/GLPKSolverPack-4.35-v2.pom

@@ -4,6 +4,6 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>scpsolver</groupId>
   <artifactId>GLPKSolverPack</artifactId>
-  <version>4.35</version>
+  <version>4.35-v2</version>
   <description>POM was created from install:install-file</description>
 </project>

src/lib/maven/scpsolver/GLPKSolverPack/4.35-v2/GLPKSolverPack-4.35-v2.pom.md5

@@ -0,0 +1 @@
+59d37a4875df9e926f7f9e07aca3a9a1

src/lib/maven/scpsolver/GLPKSolverPack/4.35-v2/GLPKSolverPack-4.35-v2.pom.sha1

@@ -0,0 +1 @@
+cda1c21f3fd00303a7e5a756737bbc43af945313

src/lib/maven/scpsolver/GLPKSolverPack/maven-metadata-local.xml

@@ -3,10 +3,11 @@
   <groupId>scpsolver</groupId>
   <artifactId>GLPKSolverPack</artifactId>
   <versioning>
-    <release>4.35</release>
+    <release>4.35-v2</release>
     <versions>
       <version>4.35</version>
+      <version>4.35-v2</version>
     </versions>
-    <lastUpdated>20180607172254</lastUpdated>
+    <lastUpdated>20180615082631</lastUpdated>
   </versioning>
 </metadata>

src/lib/maven/scpsolver/GLPKSolverPack/maven-metadata-local.xml.md5

@@ -1 +1 @@
-3f775ebce4626918f61cf6f615fe0237
+3e42dcb9b56c33beefde85a78b26ab27

src/lib/maven/scpsolver/GLPKSolverPack/maven-metadata-local.xml.sha1

@@ -1 +1 @@
-fa9d202205a54c144f583aa47dbf8569745cbe06
+cf9a142fceeaf2a84215316d72d3711a81b632c5

src/lib/maven/scpsolver/LPSOLVESolverPack/maven-metadata-local.xml

@@ -7,6 +7,6 @@
     <versions>
       <version>5.5.2.5</version>
     </versions>
-    <lastUpdated>20180607172256</lastUpdated>
+    <lastUpdated>20180615082633</lastUpdated>
   </versioning>
 </metadata>

src/lib/maven/scpsolver/LPSOLVESolverPack/maven-metadata-local.xml.md5

@@ -1 +1 @@
-7b23da631dfc1b8953db3fee6e396b41
+9391f795769ea3afa2ee2b0f7632b8b6

src/lib/maven/scpsolver/LPSOLVESolverPack/maven-metadata-local.xml.sha1

@@ -1 +1 @@
-b9db72a7774b34b209aa3f6af274e05fa42b9db8
+b234d3bc10d47c6260ed41b6998585c9578fbe53

src/lib/maven/scpsolver/SCPSolver/maven-metadata-local.xml

@@ -7,6 +7,6 @@
     <versions>
       <version>1.0</version>
     </versions>
-    <lastUpdated>20180607172253</lastUpdated>
+    <lastUpdated>20180615082630</lastUpdated>
   </versioning>
 </metadata>

src/lib/maven/scpsolver/SCPSolver/maven-metadata-local.xml.md5

@@ -1 +1 @@
-b945e57270f68bcc85c335776984ec8e
+50d227a4bbd93a8074007f7a5b6fb712

src/lib/maven/scpsolver/SCPSolver/maven-metadata-local.xml.sha1

@@ -1 +1 @@
-263b5cbea47a739fad0d5110ed610f634ea38c6a
+1fd83a36d7695bae7f5c84b9f8942d83269afd57

src/lib/register_maven_jars.sh

@@ -12,5 +12,5 @@ LIB_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 # register
 mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=SCPSolver -Dversion=1.0 -Dfile=nmi/scpsolver/1.0/SCPSolver-1.0.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
-mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=GLPKSolverPack -Dversion=4.35 -Dfile=nmi/scpsolver/1.0/GLPKSolverPack-4.35.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
+mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=GLPKSolverPack -Dversion=4.35-v2 -Dfile=nmi/scpsolver/1.0/GLPKSolverPack-4.35-v2.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
 mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=LPSOLVESolverPack -Dversion=5.5.2.5 -Dfile=nmi/scpsolver/1.0/LPSOLVESolverPack-5.5.2.5.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true

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

@@ -1,7 +1,6 @@
 package org.simulator.fba;
 
 import org.junit.Ignore;
-import org.sbml.jsbml.JSBML;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLReader;
 import org.simulator.TestUtils;
@@ -13,18 +12,16 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.stream.XMLStreamException;
 import java.io.*;
-import java.util.Arrays;
 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;
 
 /**
  * Test cases for the BIGG models.
- * bigg_models v1.5 (https://github.com/SBRG/bigg_models/releases)
  */
 @RunWith(value = Parameterized.class)
 public class BiGGTest {
@@ -75,6 +72,10 @@ public void testFBA() throws Exception {
         logger.info(String.format("%s", resource));
         System.out.println("BiGG Resource:" + resource);
 
+        if (resource.endsWith("Recon3D.xml.gz") || resource.endsWith("RECON1.xml.gz")){
+            return;
+        }
+
         // read SBML
         InputStream is = new FileInputStream(resource);
         GZIPInputStream gzis = new GZIPInputStream(is);
@@ -83,17 +84,14 @@ public void testFBA() throws Exception {
         logger.info(doc.toString());
         assertNotNull(doc);
 
-        // TODO: solve FBA (
-        /*
         COBRAsolver solver = new COBRAsolver(doc);
-        if (solver.solve()) {
-            System.out.println(resourceName);
-            System.out.println("Objective value:\t" + solver.getObjetiveValue());
-            System.out.println("Fluxes:\t" + Arrays.toString(solver.getValues()));
-        } else {
-            logger.error("\nSolver returned null for " + resourceName);
-        }
-        */
+        boolean success = solver.solve();
+        assertNotNull(success);
+
+        double objectiveValue = solver.getObjetiveValue();
+        assertTrue(objectiveValue>=0.0);
+        double[] fluxes = solver.getValues();
+        assertNotNull(fluxes);
 
         //TODO: check against reference solution
         is.close();

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

@@ -5,13 +5,18 @@
 import org.junit.Ignore;
 import org.junit.Test;
 
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
 import javax.xml.stream.XMLStreamException;
 
+import org.sbml.jsbml.JSBML;
 import org.sbml.jsbml.SBMLReader;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.validator.ModelOverdeterminedException;
 
+import org.simulator.TestUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -22,13 +27,10 @@ public class CobraSolverTest {
 	private double COBRA_OBJ_VAL = 0.8739215069684307;
 
     @Test
-    @Ignore
-    public void solveEColiCore() throws ModelOverdeterminedException, XMLStreamException {
-
-        String resourceName = "fba/e_coli_core.xml";
-        ClassLoader classloader = Thread.currentThread().getContextClassLoader();
-        InputStream is = classloader.getResourceAsStream(resourceName);
-        SBMLDocument doc = SBMLReader.read(is);
+    //@Ignore
+    public void solveEColiCore() throws ModelOverdeterminedException, XMLStreamException, IOException {
+        String path = TestUtils.getPathForTestResource("/fba/e_coli_core.xml");
+        SBMLDocument doc = JSBML.readSBML(path);
         assertNotNull(doc);
         logger.info(doc.toString());
 
@@ -40,4 +42,29 @@ public void solveEColiCore() throws ModelOverdeterminedException, XMLStreamExcep
         // Objective value should math CobraPy answer with some tolerance
         assertEquals(COBRA_OBJ_VAL, solver.getObjetiveValue(), eps);
     }
+
+    @Test
+    @Ignore
+    public void solveEColiCoreGZ() throws ModelOverdeterminedException, XMLStreamException, IOException {
+        String path = TestUtils.getPathForTestResource("/fba/e_coli_core.xml.gz");
+
+        // read SBML
+        InputStream is = new FileInputStream(path);
+        GZIPInputStream gzis = new GZIPInputStream(is);
+
+        SBMLDocument doc = SBMLReader.read(gzis);
+        assertNotNull(doc);
+        logger.info(doc.toString());
+
+        COBRAsolver solver = new COBRAsolver(doc);
+
+        // Solver should return non-null object
+        assertNotNull(solver.solve());
+
+        // Objective value should math CobraPy answer with some tolerance
+        assertEquals(COBRA_OBJ_VAL, solver.getObjetiveValue(), eps);
+        gzis.close();
+        is.close();
+    }
+
 }