First work on #7, parametrized test for FBA

.gitignore

@@ -18,3 +18,6 @@ libglpkjni_x64.so
 # log files
 jsbml.log
 
+# BiGG models
+src/test/resources/bigg/
+

.travis.yml

@@ -3,5 +3,10 @@ language: java
 jdk:
   - oraclejdk8
 
+before_install:
+   # get BiGG models for testing
+   cd src/test
+   source ./download_bigg_models.sh
+
 script:
 - mvn clean install

INSTALL.md

@@ -11,6 +11,7 @@ http://scpsolver.org/ and add in the library folder according to the `pom.xml`.
 ### GLPK
 
 ```
+sudo apt-get install libglpk-dev
 sudo apt-get install libglpk-java
 ```
 

src/test/download_bigg_models.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#################################################
+# Download bigg models for testing
+#
+# usage:
+#  source ./download_bigg_models.sh
+#################################################
+
+TEST_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+# download and extract the bigg models for testing
+mkdir -p resources/bigg
+cd resources/bigg
+wget https://github.com/matthiaskoenig/bigg-models-fba/raw/master/models/bigg_models_v1.5.tar.gz
+tar xzvf bigg_models_v1.5.tar.gz
+rm bigg_models_v1.5.tar.gz
+
+# set environment variable
+export BIGG_MODELS_PATH=${TEST_DIR}/resources/bigg
+
+echo $BIGG_MODELS_PATH
+
+
+
+
+
+

src/test/java/org/simulator/TestUtils.java

@@ -21,38 +21,22 @@ public class TestUtils {
 
     public static String FBA_RESOURCE_PATH = "/fba";
 
-    /**
-     * Returns location of BiGG test model directory from environment variable.
-     */
-    public static String getBiGGModelPath() {
-        Map<String, String> env = System.getenv();
-        String key = "BIGG_MODELS";
-        String value = null;
-        if (env.containsKey(key)) {
-            value = env.get(key);
-            logger.info(String.format("BiGG models folder found: %s", value));
-        }
-        else {
-            logger.info(String.format("%s environment variable not set.", key));
-        }
-        return value;
-    }
-
-
     /**
      * Get an iteratable over the resources in the resourcePath.
      * <p>
      * Resources in the skip set are skipped.
      * If a filter string is given only the resources matching the filter are returned.
      */
-    public static Iterable<Object[]> findResources(String resourcePath, String extension, String filter, HashSet<String> skip) {
-
-        File currentDir = new File(System.getProperty("user.dir"));
-        // String rootPath = new File(currentDir, resourcePath).getPath();
-        String rootPath = currentDir.getAbsolutePath() + "/src/test/resources" + resourcePath;
-
-        System.out.println("curDir:" + currentDir);
-        System.out.println("rootPath:" + rootPath);
+    public static Iterable<Object[]> findResources(String resourcePath, String extension, String filter, HashSet<String> skip, Boolean mvnResource) {
+
+        String rootPath = resourcePath;
+        if (mvnResource) {
+            File currentDir = new File(System.getProperty("user.dir"));
+            System.out.println("curDir: " + currentDir);
+            // String rootPath = new File(currentDir, resourcePath).getPath();
+            rootPath = currentDir.getAbsolutePath() + "/src/test/resources" + resourcePath;
+        }
+        System.out.println("rootPath: " + rootPath);
 
         // Get SBML files for passed tests
         LinkedList<String> sbmlPaths = TestUtils.findFiles(rootPath, extension, filter, skip);

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

@@ -1,30 +1,58 @@
 package org.simulator.fba;
 
+import org.sbml.jsbml.JSBML;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLReader;
 import org.simulator.TestUtils;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
+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;
 
 /**
  * Test cases for the BIGG models.
- * bigg_models v1.4 (https://github.com/SBRG/bigg_models/releases)
- * 
- * Models were retrieved on 2017-10-10 from the available database dumps on
- * dropbox.
+ * bigg_models v1.5 (https://github.com/SBRG/bigg_models/releases)
  */
 @RunWith(value = Parameterized.class)
 public class BiGGTest {
 	private String resource;
+    private static final Logger logger = LoggerFactory.getLogger(TestUtils.class);
 
 
 	@Before
 	public void setUp(){ }
-
+
+    /**
+     * Returns location of BiGG test model directory from environment variable.
+     */
+    public static String getBiGGModelPath() {
+        Map<String, String> env = System.getenv();
+        String key = "BIGG_MODELS_PATH";
+        String version = "v1.5";
+        String value = null;
+        if (env.containsKey(key)) {
+            value = env.get(key);
+            value = value + "/" + version;
+            logger.info(String.format("BiGG models folder found: %s", value));
+        }
+        else {
+            logger.info(String.format("%s environment variable not set.", key));
+        }
+        return value;
+    }
+
 	public BiGGTest(String resource) {
 		this.resource = resource;
 	}
@@ -33,24 +61,45 @@ public BiGGTest(String resource) {
 	public static Iterable<Object[]> data(){
 		HashSet<String> skip = null;
 		String filter = null;
+		Boolean mvnResource = false;
 
-		// find all BiGG models (FIXME: work on compressed models)
+		System.out.println("Searching resources");
 
-        String bigg_path = TestUtils.getBiGGModelPath();
-		return TestUtils.findResources(bigg_path, ".xml", filter, skip);
-	}
 
-	// TODO: read cobrapy reference values for comparison
-	/**
-	@Test
-	public void testSingle() throws Exception {
-		TestUtils.testNetwork(taskMonitor, getClass().getName(), resource);
+		// find all BiGG models (compressed files)
+        String biggPath = getBiGGModelPath();
+        System.out.println("BiGG models path: " + biggPath);
+		return TestUtils.findResources(biggPath, ".xml.gz", filter, skip, mvnResource);
 	}
 
 	@Test
-    public void testSerialization() throws Exception {
-        TestUtils.testNetworkSerialization(getClass().getName(), resource);
-    }
-	*/
+	public void testFBA() throws Exception {
+        logger.info("--------------------------------------------------------");
+        logger.info(String.format("%s", resource));
+        System.out.println("BiGG Resource:" + resource);
+
+        // read SBML
+        InputStream is = new FileInputStream(resource);
+        GZIPInputStream gzis = new GZIPInputStream(is);
+
+        SBMLDocument doc = SBMLReader.read(gzis);
+        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);
+        }
+        */
+
+        //TODO: check against reference solution
+        is.close();
+	}
 
 }

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

@@ -20,6 +20,7 @@ public class CobraSolverTest {
     private static final Logger logger = LoggerFactory.getLogger(CobraSolverTest.class);
 
     @Test
+    @Ignore  // breaks on Ubuntu: https://github.com/shalinshah1993/SBSCL/issues/24
     public void solveEColiCore() throws ModelOverdeterminedException, XMLStreamException {
 
         String resourceName = "fba/e_coli_core.xml";