Merge pull request #139 from DimitriPlotnikov/master

Add Dockerfile. Refactor and improve structure.

Dockerfile

@@ -0,0 +1,54 @@
+# Pull base image.
+FROM ubuntu:16.04
+
+ENV DEBIAN_FRONTEND noninteractive
+
+# Install developer tools, alse add-re
+RUN apt-get update
+# install basics
+RUN apt-get install -y software-properties-common
+RUN apt-get install -y git
+RUN apt-get install -y wget
+RUN apt-get install -y gcc
+RUN apt-get install -y python
+RUN apt-get install -y python-dev
+
+# install oracle java
+RUN add-apt-repository -y ppa:webupd8team/java
+RUN apt-get update
+RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
+RUN apt-get install -y oracle-java8-installer
+
+WORKDIR /tmp
+RUN wget https://bootstrap.pypa.io/get-pip.py
+RUN python get-pip.py
+RUN pip install numpy
+RUN pip install mpmath
+RUN git clone https://github.com/sympy/sympy.git
+WORKDIR /tmp/sympy
+RUN python setup.py install
+WORKDIR /tmp
+
+ENV MAVEN_VERSION 3.3.9
+RUN mkdir -p /usr/share/maven
+RUN wget http://mirror.softaculous.com/apache/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz
+RUN tar -xzf apache-maven-$MAVEN_VERSION-bin.tar.gz -C /usr/share/maven --strip-components=1
+RUN ln -s /usr/share/maven/bin/mvn /usr/bin/mvn
+
+# Define commonly used JAVA_HOME variable
+ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
+ENV MAVEN_HOME /usr/share/maven
+
+# Define working directory.
+WORKDIR /data
+RUN git clone https://github.com/nest/nestml.git
+
+WORKDIR /data/nestml
+RUN mvn install
+ENV NESTML 'java -jar /data/nestml/target/nestml.jar'
+
+# Define default command.
+ENTRYPOINT ["java", "-jar", "/data/nestml/target/nestml.jar", "/nestml", "--target", "/nestml/result"]
+
+# usage from the commandlien
+# docker run -v folderWithModelsOnHost:/nestml nestml_box

src/main/java/org/nest/codegeneration/NESTCodeGenerator.java

@@ -14,7 +14,7 @@
 import org.nest.codegeneration.converters.GSLReferenceConverter;
 import org.nest.codegeneration.converters.NESTReferenceConverter;
 import org.nest.codegeneration.helpers.*;
-import org.nest.codegeneration.printers.NESTMLFunctionPrinter;
+import org.nest.codegeneration.printers.NESTFunctionPrinter;
 import org.nest.codegeneration.sympy.ODEProcessor;
 import org.nest.nestml._ast.ASTBody;
 import org.nest.nestml._ast.ASTNESTMLCompilationUnit;
@@ -270,7 +270,7 @@ private void setNeuronGenerationParameter(
     glex.setGlobalValue("simpleNeuronName", neuron.getName());
     glex.setGlobalValue("neuronSymbol", neuron.getSymbol().get());
 
-    final NESTMLFunctionPrinter functionPrinter = new NESTMLFunctionPrinter();
+    final NESTFunctionPrinter functionPrinter = new NESTFunctionPrinter();
     final NESTMLDeclarations declarations = new NESTMLDeclarations();
     glex.setGlobalValue("declarations", new NESTMLDeclarations() );
     glex.setGlobalValue("assignments", new ASTAssignments());

src/main/java/org/nest/codegeneration/helpers/ASTAssignments.java

@@ -101,6 +101,14 @@ public String printSetterName(final ASTAssignment astAssignment) {
     return "set_" + variableName;
   }
 
+  /**
+   * Returns the textual representation of the setter invocation
+   */
+  public String printLhsName(final ASTAssignment astAssignment) {
+    final String variableName = Names.getQualifiedName(astAssignment.getVariableName().getParts());
+    return variableName + "_tmp";
+  }
+
   /**
    * Returns the textual representation of the setter invocation
    */

src/main/java/org/nest/codegeneration/printers/NESTMLFunctionPrinter.java → src/main/java/org/nest/codegeneration/printers/NESTFunctionPrinter.java

@@ -28,7 +28,7 @@
  * @author plotnikov
  */
 @SuppressWarnings("unused") // class is used in templates
-public class NESTMLFunctionPrinter {
+public class NESTFunctionPrinter {
 
   public String printFunctionDeclaration(final ASTFunction astFunction) {
     checkArgument(astFunction.getEnclosingScope().isPresent(), "Function: " + astFunction.getName() + " has no scope.");
@@ -51,11 +51,13 @@ public String printFunctionDeclaration(final ASTFunction astFunction) {
     }
 
     final Optional<MethodSymbol> method = NESTMLSymbols.resolveMethod(
-        scope, astFunction.getName(), parameterNestmlTypes);
+        scope,
+        astFunction.getName(),
+        parameterNestmlTypes);
 
     final StringBuilder declaration = new StringBuilder();
     if (method.isPresent()) {
-      declaration.append("//").append(ASTNodes.printComment(astFunction));
+      declaration.append("//").append(ASTNodes.printComment(astFunction)).append("\n");
       final String returnType = new NESTML2NESTTypeConverter().convert(method.get().getReturnType()).replace(
           ".", "::");
       declaration.append(returnType);
@@ -96,7 +98,7 @@ public String printFunctionDefinition(final ASTFunction astFunction, final Strin
 
     final StringBuilder declaration = new StringBuilder();
     if (method.isPresent()) {
-      declaration.append("//").append(ASTNodes.printComment(astFunction));
+      declaration.append("//").append(ASTNodes.printComment(astFunction)).append("\n");
       final String returnType = new NESTML2NESTTypeConverter().convert(method.get().getReturnType()).replace(
           ".", "::");
       declaration.append(returnType);

src/main/java/org/nest/frontend/CLIConfigurationExecutor.java

@@ -22,7 +22,7 @@
 import java.util.List;
 import java.util.Optional;
 
-import static org.nest.utils.FileHelper.collectNESTMLModelFilenames;
+import static org.nest.utils.FilesHelper.collectNESTMLModelFilenames;
 
 /**
  * Interprets the provided configuration by collecting models and executing parsing, context

src/main/java/org/nest/frontend/NESTMLFrontend.java

@@ -10,7 +10,7 @@
 import org.apache.commons.cli.*;
 import org.nest.codegeneration.NESTCodeGenerator;
 import org.nest.nestml._symboltable.NESTMLScopeCreator;
-import org.nest.utils.FileHelper;
+import org.nest.utils.FilesHelper;
 
 import java.io.*;
 import java.nio.file.Files;
@@ -91,7 +91,7 @@ public CLIConfiguration createCLIConfiguration(String[] args) {
   }
 
   public static boolean checkEnvironment(final CLIConfiguration cliConfiguration) {
-    FileHelper.createFolders(cliConfiguration.getTargetPath());
+    FilesHelper.createFolders(cliConfiguration.getTargetPath());
     cleanUpTmpFiles(cliConfiguration);
 
     boolean isError = false;
@@ -123,14 +123,14 @@ public static boolean checkEnvironment(final CLIConfiguration cliConfiguration)
 
   private static void cleanUpTmpFiles(final CLIConfiguration cliConfiguration) {
     if (!Files.exists(cliConfiguration.getTargetPath())) {
-      FileHelper.createFolders(cliConfiguration.getTargetPath());
+      FilesHelper.createFolders(cliConfiguration.getTargetPath());
     }
     else {
-      final List<Path> tmps = FileHelper.collectFiles(
+      final List<Path> tmps = FilesHelper.collectFiles(
           cliConfiguration.getTargetPath(),
           file -> file.endsWith(".tmp"));
 
-      tmps.stream().forEach(FileHelper::deleteFile);
+      tmps.stream().forEach(FilesHelper::deleteFile);
     }
   }
 

src/main/java/org/nest/utils/FileHelper.java → src/main/java/org/nest/utils/FilesHelper.java

@@ -23,23 +23,29 @@
  *
  * @author plotnikov
  */
-public class FileHelper {
-  private static String LOG_NAME = FileHelper.class.getName();
+public class FilesHelper {
+  private static String LOG_NAME = FilesHelper.class.getName();
 
   public static List<Path> collectNESTMLModelFilenames(final Path path) {
     final PathMatcher matcher = getDefault().getPathMatcher("glob:*." + NESTMLLanguage.FILE_ENDING);
-    return FileHelper.collectFiles(path, modelFile -> matcher.matches(modelFile.getFileName()));
+    return FilesHelper.collectFiles(path, modelFile -> matcher.matches(modelFile.getFileName()));
   }
 
   public static List<Path> collectSPLModelFilenames(final Path path) {
     final PathMatcher matcher = getDefault().getPathMatcher("glob:*." + SPLLanguage.FILE_ENDING);
-    return FileHelper.collectFiles(path, modelFile -> matcher.matches(modelFile.getFileName()));
+    return FilesHelper.collectFiles(path, modelFile -> matcher.matches(modelFile.getFileName()));
   }
 
   public static void deleteFilesInFolder(final Path file) {
-    FileHelper.collectFiles(file, f -> true)
+    FilesHelper.collectFiles(file, f -> true)
         .stream()
-        .forEach(FileHelper::deleteFile);
+        .forEach(FilesHelper::deleteFile);
+  }
+
+  public static void deleteFilesInFolder(final Path file, final Predicate<Path> predicate) {
+    FilesHelper.collectFiles(file, predicate)
+            .stream()
+            .forEach(FilesHelper::deleteFile);
   }
 
   public static void deleteFile(final Path file) {

src/test/java/org/nest/base/GenerationBasedTest.java

@@ -12,7 +12,7 @@
 import org.nest.nestml._ast.ASTNESTMLCompilationUnit;
 import org.nest.nestml._cocos.NESTMLCoCoChecker;
 import org.nest.nestml._symboltable.NESTMLCoCosManager;
-import org.nest.utils.FileHelper;
+import org.nest.utils.FilesHelper;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -40,7 +40,7 @@ public abstract class GenerationBasedTest extends ModelbasedTest {
   @Before
   public void cleanUpGeneratedFolder() {
     Log.enableFailQuick(false);
-    FileHelper.deleteFilesInFolder(CODE_GEN_OUTPUT);
+    FilesHelper.deleteFilesInFolder(CODE_GEN_OUTPUT);
   }
 
   protected void invokeCodeGenerator(final String pathToModel) {
@@ -65,7 +65,7 @@ protected void generateNESTModuleCode(final List<ASTNESTMLCompilationUnit> model
     generator.generateNESTModuleCode(modelRoots, MODULE_NAME, CODE_GEN_OUTPUT);
   }
 
-  public void checkCocos(final String pathToModel) {
+  protected void checkCocos(final String pathToModel) {
     final Optional<ASTNESTMLCompilationUnit> root;
     try {
       root = parser.parse(pathToModel);

src/test/java/org/nest/codegeneration/NESTCodeGeneratorTest.java

@@ -9,6 +9,7 @@
 import org.nest.base.GenerationBasedTest;
 import org.nest.mocks.PSCMock;
 import org.nest.nestml._ast.ASTNESTMLCompilationUnit;
+import org.nest.utils.FilesHelper;
 
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -29,47 +30,42 @@ public class NESTCodeGeneratorTest extends GenerationBasedTest {
   private static final String PSC_MODEL = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
   //private static final String COND_MODEL_EXPLICIT = "src/test/resources/codegeneration/iaf_cond_alpha.nestml";
   private static final String COND_MODEL_IMPLICIT = "src/test/resources/codegeneration/iaf_cond_alpha_implicit.nestml";
+  private Path outputFolder;
 
   @Test
   public void testPSCModelWithoutOde() {
     final ASTNESTMLCompilationUnit root = parseNESTMLModel(PSC_MODEL);
     scopeCreator.runSymbolTableCreator(root);
     final NESTCodeGenerator generator = new NESTCodeGenerator(scopeCreator, pscMock);
-    generator.analyseAndGenerate(
-        root,
-        Paths.get(OUTPUT_DIRECTORY.toString(), "simple_psc"));
-    generator.generateNESTModuleCode(
-        newArrayList(root),
-        "simple_psc",
-        Paths.get(OUTPUT_DIRECTORY.toString(), "psc"));
+    outputFolder = Paths.get(OUTPUT_DIRECTORY.toString(), "simple_psc");
+
+    FilesHelper.deleteFilesInFolder(outputFolder);
+    generator.analyseAndGenerate(root, outputFolder);
+    generator.generateNESTModuleCode(newArrayList(root), "simple_psc", outputFolder);
   }
 
   @Test
   public void testPSCModelWithOde() {
     final ASTNESTMLCompilationUnit root = parseNESTMLModel(PSC_MODEL_WITH_ODE);
     scopeCreator.runSymbolTableCreator(root);
     final NESTCodeGenerator generator = new NESTCodeGenerator(scopeCreator, pscMock);
-    generator.analyseAndGenerate(
-        root,
-        Paths.get(OUTPUT_DIRECTORY.toString(), "psc"));
-    generator.generateNESTModuleCode(
-        newArrayList(root),
-        "psc",
-        Paths.get(OUTPUT_DIRECTORY.toString(), "psc"));
+    Path outputFolder = Paths.get(OUTPUT_DIRECTORY.toString(), "psc");
+
+    FilesHelper.deleteFilesInFolder(outputFolder);
+    generator.analyseAndGenerate(root, outputFolder);
+    generator.generateNESTModuleCode(newArrayList(root), "psc", outputFolder);
   }
 
   @Test
   public void testCondModelWithImplicitOdes() {
     final ASTNESTMLCompilationUnit root = parseNESTMLModel(COND_MODEL_IMPLICIT);
     scopeCreator.runSymbolTableCreator(root);
     final NESTCodeGenerator generator = new NESTCodeGenerator(scopeCreator, pscMock);
-    generator.analyseAndGenerate(
-        root,
-        Paths.get(OUTPUT_DIRECTORY.toString(), "cond"));
-    generator.generateNESTModuleCode(
-        newArrayList(root),
-        "cond",
-        Paths.get(OUTPUT_DIRECTORY.toString(), "cond"));
+    Path outputFolder = Paths.get(OUTPUT_DIRECTORY.toString(), "cond");
+
+    FilesHelper.deleteFilesInFolder(outputFolder);
+    generator.analyseAndGenerate(root, outputFolder);
+    generator.generateNESTModuleCode(newArrayList(root), "cond", outputFolder);
   }
 
 }

src/test/java/org/nest/codegeneration/sympy/ExactSolutionTransformerTest.java

@@ -27,7 +27,7 @@
  */
 public class ExactSolutionTransformerTest extends ModelbasedTest {
 
-  public static final String TARGET_TMP_MODEL_PATH = "target/tmp.nestml";
+  private static final String TARGET_TMP_MODEL_PATH = "target/tmp.nestml";
 
   private final static String P30_FILE
       = "src/test/resources/codegeneration/sympy/psc/" + SymPyScriptEvaluator.P30_FILE;
@@ -44,7 +44,7 @@ public class ExactSolutionTransformerTest extends ModelbasedTest {
   private static final String MODEL_FILE_PATH
       = "src/test/resources/codegeneration/iaf_psc_alpha.nestml";
 
-  public static final String NEURON_NAME = "iaf_psc_alpha_nestml";
+  private static final String NEURON_NAME = "iaf_psc_alpha_nestml";
 
   @Test
   public void testExactSolutionTransformation() {

src/test/java/org/nest/codegeneration/sympy/SympyScriptGeneratorTest.java

@@ -15,11 +15,9 @@
 import org.nest.ode._ast.ASTODE;
 import org.nest.symboltable.predefined.PredefinedFunctions;
 import org.nest.utils.ASTNodes;
-import org.nest.utils.FileHelper;
 
 import java.io.IOException;
 import java.io.StringReader;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Optional;
@@ -42,6 +40,7 @@ public class SympyScriptGeneratorTest extends ModelbasedTest {
       = "src/test/resources/codegeneration/iaf_cond_alpha_implicit.nestml";
 
   private static final String OUTPUT_FOLDER = "target";
+  public static final Path OUTPUT_SCRIPT_DIRECTORY = Paths.get(OUTPUT_FOLDER, "sympy");
 
   @Test
   public void generateSymPySolverForPSCModel() throws IOException {
@@ -87,8 +86,7 @@ private void generateAndCheck(final String pathToModel) throws IOException {
     nestmlScopeCreator.runSymbolTableCreator(root.get());
 
     final Optional<Path> generatedScript = generateSympyODEAnalyzer(
-        root.get().getNeurons().get(0),
-        Paths.get(OUTPUT_FOLDER, "sympy"));
+            root.get().getNeurons().get(0), OUTPUT_SCRIPT_DIRECTORY);
 
     assertTrue(generatedScript.isPresent());
   }

src/test/java/org/nest/frontend/CLICLIConfigurationExecutorTest.java

@@ -16,7 +16,7 @@
 import java.nio.file.Paths;
 import java.util.List;
 
-import static org.nest.utils.FileHelper.collectNESTMLModelFilenames;
+import static org.nest.utils.FilesHelper.collectNESTMLModelFilenames;
 
 /**
  * Mocks the codegenerator and tests executor functions.