Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/**
*
*/
package nl.uu.cs.ape.sat;
import guru.nidi.graphviz.attribute.Rank.RankDir;
import nl.uu.cs.ape.sat.configuration.tags.validation.ValidationResult;
import nl.uu.cs.ape.sat.configuration.tags.validation.ValidationResults;
import nl.uu.cs.ape.sat.constraints.ConstraintTemplate;
import nl.uu.cs.ape.sat.core.implSAT.SAT_SynthesisEngine;
import nl.uu.cs.ape.sat.core.implSAT.SATsolutionsList;
import nl.uu.cs.ape.sat.core.solutionStructure.SolutionWorkflow;
import nl.uu.cs.ape.sat.models.logic.constructs.TaxonomyPredicate;
import nl.uu.cs.ape.sat.configuration.APEConfigException;
import nl.uu.cs.ape.sat.configuration.APECoreConfig;
import nl.uu.cs.ape.sat.utils.APEDimensionsException;
import nl.uu.cs.ape.sat.utils.APEDomainSetup;
import nl.uu.cs.ape.sat.configuration.APERunConfig;
import nl.uu.cs.ape.sat.utils.APEUtils;
import nl.uu.cs.ape.sat.utils.OWLReader;
import org.json.JSONException;
import org.json.JSONObject;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import java.util.*;
import javax.imageio.ImageIO;
/**
* The {@code APE} class is the main class of the library and is supposed
* to be the main interface for working with the library.
*
* @author Vedran Kasalica
*/
public class APE {
/** Core configuration object defined from the configuration file. */
private final APECoreConfig config;
/** Object containing general APE encoding. */
private APEDomainSetup apeDomainSetup;
/**
* Create instance of the APE solver.
*
* @param configPath Path to the APE JSON configuration file. If the string is null the default './ape.config' value is assumed.
* @throws IOException Exception reading the configuration file.
* @throws OWLOntologyCreationException Exception reading the OWL file.
*/
public APE(String configPath) throws IOException, OWLOntologyCreationException {
config = new APECoreConfig(configPath);
if (config == null) {
throw new APEConfigException("Configuration failed. Error in configuration file.");
}
if (!setupDomain()) {
throw new APEConfigException("Error setting up the domain.");
}
}
/**
* Create instance of the APE solver.
*
* @param configObject The APE configuration {@link JSONObject}.
* @throws IOException Exception while reading the configuration file or the tool annotations file.
* @throws OWLOntologyCreationException Error in reading the OWL file.
*/
public APE(JSONObject configObject) throws IOException, OWLOntologyCreationException {
config = new APECoreConfig(configObject);
if (!setupDomain()) {
throw new APEConfigException("Error in setting up the domain.");
}
}
/**
* Create instance of the APE solver.
*
* @param config The APE configuration {@link APECoreConfig}.
* @throws IOException Exception while reading the configuration file or the tool annotations file.
* @throws OWLOntologyCreationException Error in reading the OWL file.
*/
public APE(APECoreConfig config) throws IOException, OWLOntologyCreationException {
this.config = config;
if (!setupDomain()) {
throw new APEConfigException("Error in setting up the domain.");
}
}
/**
* Method used to setup the domain using the configuration file and the
* corresponding annotation and constraints files.
*
* @return true if the setup was successfully performed, false otherwise.
* @throws AtomMappingsException Exception while reading the provided ontology.
* @throws IOException Error in handling a JSON file containing tool annotations.
* @throws OWLOntologyCreationException Error in reading the OWL file.
*/
private boolean setupDomain() throws APEDimensionsException, IOException, OWLOntologyCreationException {
// Variable that describes a successful execution of the method.
boolean succRun = true;
/*
* Encode the taxonomies as objects - generate the list of all types / modules
* occurring in the taxonomies defining their submodules/subtypes
*/
apeDomainSetup = new APEDomainSetup(config);
OWLReader owlReader = new OWLReader(apeDomainSetup, config.getOntologyFile());
boolean ontologyRead = owlReader.readOntology();
if (!ontologyRead) {
System.out.println("Error occurred while reading the provided ontology.");
return false;
}
// Update allModules and allTypes sets based on the module.json file
succRun &= APEUtils.readModuleJson(config.getToolAnnotationsFile(), apeDomainSetup);
succRun &= apeDomainSetup.trimTaxonomy();
// Define set of all constraint formats
apeDomainSetup.initializeConstraints();
return succRun;
}
/**
* Method that return all the supported constraint templates.
*
* @return List of {@link ConstraintTemplate} objects.
*/
public Collection getConstraintTemplates() {
return apeDomainSetup.getConstraintFactory().getConstraintTemplates();
}
/**
* The method returns the configuration file of the APE instance.
*
* @return Field {@link #config}.
*/
public APECoreConfig getConfig() {
return config;
}
/**
* Gets domain setup.
*
* @return The object that contains all crucial information about the domain (e.g. list of tools, data types, constraint factory, etc.)
*/
public APEDomainSetup getDomainSetup() {
return apeDomainSetup;
}
/**
* Function used to return all the elements of one data type dimension (e.g. all
* data types or all data formats).
*
* @param dimensionRootID ID of the data taxonomy subtree that corresponds to the list of elements that should be returned.
* @return List where each element correspond to a map that can be transformed into JSON objects.
* @throws NullPointerException the null pointer exception
*/
public List> getTaxonomyElements(String dimensionRootID) throws NullPointerException {
SortedSet elements = null;
TaxonomyPredicate root = apeDomainSetup.getAllTypes().get(dimensionRootID);
if (root != null) {
elements = apeDomainSetup.getAllTypes().getElementsFromSubTaxonomy(root);
} else {
root = apeDomainSetup.getAllModules().get(dimensionRootID);
if (root != null) {
elements = apeDomainSetup.getAllModules().getElementsFromSubTaxonomy(root);
} else {
throw new NullPointerException();
}
}
List> transformedTypes = new ArrayList>();
for (TaxonomyPredicate currType : elements) {
transformedTypes.add(currType.toMap());
}
return transformedTypes;
}
/**
* Setup a new run instance of the APE solver and run the synthesis algorithm.
*
* @param configObject Object that contains run configurations.
* @return The list of all the solutions.
* @throws IOException Error in case of not providing a proper configuration file.
*/
public SATsolutionsList runSynthesis(JSONObject configObject) throws IOException, APEConfigException {
return runSynthesis(configObject, this.getDomainSetup());
}
/**
* Setup a new run instance of the APE solver and run the synthesis algorithm.
*
* @param runConfigPath Path to the JSON that contains run configurations.
* @return The list of all the solutions.
* @throws IOException Error in case of not providing a proper configuration file.
*/
public SATsolutionsList runSynthesis(String runConfigPath) throws IOException, JSONException, APEConfigException {
String configContent = APEUtils.getFileContent(runConfigPath);
JSONObject configObject = new JSONObject(configContent);
return runSynthesis(configObject, this.getDomainSetup());
}
/**
* Setup a new run instance of the APE solver and run the synthesis algorithm.
*
* @param runConfigJson Object that contains run configurations.
* @param apeDomainSetup Domain information, including all the existing tools and types.
* @return The list of all the solutions.
* @throws IOException Error in case of not providing a proper configuration file.
* @throws JSONException Error in configuration object.
*/
private SATsolutionsList runSynthesis(JSONObject runConfigJson, APEDomainSetup apeDomainSetup) throws IOException, JSONException, APEConfigException {
apeDomainSetup.clearConstraints();
APERunConfig runConfig = new APERunConfig(runConfigJson, apeDomainSetup);
SATsolutionsList solutions = executeSynthesis(runConfig);
return solutions;
}
/**
* Run the synthesis for the given workflow specification.
* @param runConfig
*
* @return The list of all the solutions.
* @throws IOException Error in case of not providing a proper configuration file.
*/
private SATsolutionsList executeSynthesis(APERunConfig runConfig) throws IOException, JSONException {
/* List of all the solutions */
SATsolutionsList allSolutions = new SATsolutionsList(runConfig);
APEUtils.readConstraints(new File(runConfig.getConstraintsPath().toString()), apeDomainSetup);
/* Print the setup information when necessary. */
APEUtils.debugPrintout(runConfig.getDebugMode(), apeDomainSetup);
/*
* Loop over different lengths of the workflow until either, max workflow length
* or max number of solutions has been found.
*/
String globalTimerID = "globalTimer";
APEUtils.timerStart(globalTimerID, true);
int solutionLength = runConfig.getSolutionLength().getMin();
while (allSolutions.getNumberOfSolutions() < allSolutions.getMaxNumberOfSolutions()
&& solutionLength <= runConfig.getSolutionLength().getMax()) {
SAT_SynthesisEngine implSATsynthesis = new SAT_SynthesisEngine(apeDomainSetup, allSolutions, runConfig,
solutionLength);
APEUtils.printHeader(implSATsynthesis.getSolutionSize(), "Workflow discovery - length");
/* Encoding of the synthesis problem */
if (!implSATsynthesis.synthesisEncoding()) {
System.err.println("Internal error in problem encoding.");
return null;
}
/* Execution of the synthesis */
implSATsynthesis.synthesisExecution();
if ((allSolutions.getNumberOfSolutions() >= allSolutions.getMaxNumberOfSolutions() - 1)
|| solutionLength == runConfig.getSolutionLength().getMax()) {
APEUtils.timerPrintSolutions(globalTimerID, allSolutions.getNumberOfSolutions());
}
/* Increase the size of the workflow for the next depth iteration */
solutionLength++;
}
return allSolutions;
}
/**
* Validates all the tags in a configuration object.
* If {@link ValidationResults#success()} ()} returns true,
* the configuration object can be safely used to setup the
* the APE framework and create an APERunConfiguration.
*
* @param config configuration file
* @return the validation results
*/
public static ValidationResults validate(JSONObject config){
ValidationResults results = APECoreConfig.validate(config);
if(results.hasFails()){
return results;
}
try {
APE ape = new APE(config);
results.add(APERunConfig.validate(config, ape.getDomainSetup()));
} catch (IOException | OWLOntologyCreationException ignored) { }
return results;
}
/**
* Write textual "human readable" version on workflow solutions to a file.
*
* @param allSolutions Set of {@link SolutionWorkflow}.
* @return true if the writing was successfully performed, false otherwise.
* @throws IOException Exception if file not found.
*/
public static boolean writeSolutionToFile(SATsolutionsList allSolutions) throws IOException {
StringBuilder solutions2write = new StringBuilder();
for (int i = 0; i < allSolutions.size(); i++) {
solutions2write = solutions2write.append(allSolutions.get(i).getNativeSATsolution().getRelevantSolution())
.append("\n");
}
APEUtils.write2file(solutions2write.toString(), allSolutions.getRunConfiguration().getSolutionDirPath2("solutions.txt").toFile(), false);
return true;
}
/**
* Generating scripts that represent executable versions of the workflow solutions and executing them.
*
* @param allSolutions Set of {@link SolutionWorkflow}.
* @return true if the execution was successfully performed, false otherwise.
*/
public static boolean writeExecutableWorkflows(SATsolutionsList allSolutions) {
Path executionsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Executables();
Integer noExecutions = allSolutions.getRunConfiguration().getNoExecutions();
if (executionsFolder == null || noExecutions == null || noExecutions == 0 || allSolutions.isEmpty()) {
return false;
}
APEUtils.printHeader(null, "Executing first " + noExecutions + " solution");
APEUtils.timerStart("executingWorkflows", true);
final File executeDir = executionsFolder.toFile();
if(executeDir.isDirectory()) {
Arrays.stream(
executionsFolder.toFile().listFiles((dir, name) -> name.toLowerCase().startsWith("workflowSolution_")))
.forEach(File::delete);
} else {
executeDir.mkdir();
}
System.out.print("Loading");
/* Creating the requested scripts in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noExecutions).forEach(solution -> {
try {
String title = "workflowSolution_" + solution.getIndex() + ".sh";
File script = executionsFolder.resolve(title).toFile();
APEUtils.write2file(solution.getScriptExecution(), script, false);
System.out.print(".");
} catch (IOException e) {
System.err.println("Error occurred while writing a graph to the file system.");
e.printStackTrace();
}
});
APEUtils.timerPrintText("executingWorkflows", "\nWorkflows have been executed.");
return true;
}
/**
* Generate the graphical representations of the workflow solutions and write
* them to the file system. Each graph is shown in data-flow representation,
* i.e. transformation of data is in focus.
*
* @param allSolutions Set of {@link SolutionWorkflow}.
* @param orientation Orientation in which the graph will be presented.
* @return true if the generating was successfully performed, false otherwise.
* @throws IOException Exception if graph cannot be written to the file system.
*/
public static boolean writeDataFlowGraphs(SATsolutionsList allSolutions, RankDir orientation) throws IOException {
Path graphsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Figures();
Integer noGraphs = allSolutions.getRunConfiguration().getNoGraphs();
if (graphsFolder == null || noGraphs == null || noGraphs == 0 || allSolutions.isEmpty()) {
return false;
}
APEUtils.printHeader(null, "Geneating graphical representation", "of the first " + noGraphs + " workflows");
APEUtils.timerStart("drawingGraphs", true);
System.out.println();
/* Removing the existing files from the file system. */
File graphDir = graphsFolder.toFile();
if(graphDir.isDirectory()) {
Arrays.stream(graphsFolder.toFile().listFiles((dir, name) -> name.toLowerCase().startsWith("SolutionNo")))
.forEach(File::delete);
} else {
graphDir.mkdir();
}
System.out.print("Loading");
/* Creating the requested graphs in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noGraphs).forEach(solution -> {
try {
String title = "SolutionNo_" + solution.getIndex() + "_length_" + solution.getSolutionlength();
Path path = graphsFolder.resolve(title);
solution.getDataflowGraph(title, orientation).getWrite2File(path.toFile(), allSolutions.getRunConfiguration().getDebugMode());
System.out.print(".");
} catch (IOException e) {
System.err.println("Error occurred while writing a graph to the file system.");
e.printStackTrace();
}
});
APEUtils.timerPrintText("drawingGraphs", "\nGraphical files have been generated.");
return true;
}
/**
* Generate the graphical representations of the workflow solutions and write
* them to the file system. Each graph is shown in control-flow representation,
* i.e. order of the operations is in focus.
*
* @param allSolutions Set of {@link SolutionWorkflow}.
* @param orientation Orientation in which the graph will be presented.
* @return true if the generating was successfully performed, false otherwise.
* @throws IOException Exception if graphs cannot be written to the file system.
*/
public static boolean writeControlFlowGraphs(SATsolutionsList allSolutions, RankDir orientation) throws IOException {
Path graphsFolder = allSolutions.getRunConfiguration().getSolutionDirPath2Figures();
Integer noGraphs = allSolutions.getRunConfiguration().getNoGraphs();
if (graphsFolder == null || noGraphs == null || noGraphs == 0 || allSolutions.isEmpty()) {
return false;
}
APEUtils.printHeader(null, "Generating graphical representation", "of the first " + noGraphs + " workflows");
APEUtils.timerStart("drawingGraphs", true);
System.out.println();
/* Removing the existing files from the file system. */
File graphDir = graphsFolder.toFile();
if(graphDir.isDirectory()) {
Arrays.stream(graphsFolder.toFile().listFiles((dir, name) -> name.toLowerCase().startsWith("SolutionNo")))
.forEach(File::delete);
} else {
graphDir.mkdir();
}
System.out.print("Loading");
/* Creating the requested graphs in parallel. */
allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noGraphs).forEach(solution -> {
try {
String title = "SolutionNo_" + solution.getIndex() + "_length_" + solution.getSolutionlength();
Path path = graphsFolder.resolve(title);
solution.getControlflowGraph(title, orientation).getWrite2File(path.toFile(), allSolutions.getRunConfiguration().getDebugMode());
System.out.print(".");
} catch (IOException e) {
System.err.println("Error occurred while writing a graph to the file system.");
e.printStackTrace();
}
});
APEUtils.timerPrintText("drawingGraphs", "\nGraphical files have been generated.");
return true;
}
}
