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APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.
package nl.uu.cs.ape;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
import org.json.JSONException;
import org.json.JSONObject;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import guru.nidi.graphviz.attribute.Rank.RankDir;
import guru.nidi.graphviz.engine.Format;
import lombok.extern.slf4j.Slf4j;
import nl.uu.cs.ape.configuration.APEConfigException;
import nl.uu.cs.ape.configuration.APECoreConfig;
import nl.uu.cs.ape.configuration.APERunConfig;
import nl.uu.cs.ape.utils.APEFiles;
import nl.uu.cs.ape.utils.APEUtils;
import nl.uu.cs.ape.domain.BioToolsAPI;
import nl.uu.cs.ape.solver.solutionStructure.SolutionsList;
/**
* The entry point of application when the library is used in a Command Line
* Interface (CLI).
*
* @author Vedran Kasalica
*/
@Slf4j
public class LocalRun {
private static String localRepo = "/Users/vedran/git/APE_repo/APE_UseCases/";
/**
* The entry point of application when the library is used in a Command Line
* Interface (CLI).
*
* @param args APE expects at most one (1) argument: The absolute or relative
* path to the configuration file.
* @throws IOException
* @throws APEConfigException
* @throws JSONException
* @throws OWLOntologyCreationException
*/
public static void main(String[] args)
throws JSONException, APEConfigException, IOException, OWLOntologyCreationException {
exampleLocal("gmt");
// runAPE("/Users/vedran/Desktop/test.json");
// getWombatBioTools();
}
/**
* Reads the BioTools API and saves the tools in APE format in the specified
* file.
*
* @throws IOException
*/
private static void getWombatBioTools() throws IOException {
String root = "/Users/vedran/git/Workflomics_repo/domain-annotations/WombatP_tools/";
String toolNames = "tools.json";
String annotationFile = "bio.tools_new.json";
BioToolsAPI.fetchToolSet(root + toolNames, root + annotationFile);
}
private static void exampleURL(String domain) throws JSONException, APEConfigException, IOException {
Map examples = new HashMap<>();
examples.put("proteomics",
"https://raw.githubusercontent.com/Workflomics/domain-annotations/main/MassSpectometry/config.json");
runAPE(examples.get(domain));
}
private static void exampleLocal(String domain) throws JSONException, APEConfigException, IOException {
Map examples = new HashMap<>();
examples.put("proteomics",
"/Users/vedran/git/APE_repo/APE_UseCases/MassSpectometry/No1/config_original.json");
examples.put("gmt", "/Users/vedran/git/APE_repo/APE_UseCases/GeoGMT/E0/config.json");
examples.put("tmp", "/Users/vedran/Desktop/steven_example/config.json");
examples.put("wombat", "/Users/vedran/git/Workflomics_repo/domain-annotations/WombatP_tools/config_local.json");
runAPE(examples.get(domain));
}
private static JSONObject setupLocalPaths(String pathToFile) throws IOException {
File runConfigFile = APEFiles.readPathToFile(pathToFile);
String runConfigString = FileUtils.readFileToString(runConfigFile, StandardCharsets.UTF_8);
runConfigString = runConfigString.replace("./", localRepo);
return new JSONObject(runConfigString);
}
/**
* Runs the APE framework with the specified configuration file.
*
* @param pathToFile The absolute or relative path to the configuration file.
* @throws JSONException
* @throws APEConfigException
* @throws IOException
*/
public static void runAPE(String pathToFile) throws JSONException, APEConfigException, IOException {
JSONObject configurationJson = setupLocalPaths(pathToFile);
int solutionsNo = 20;
APECoreConfig coreConfig = new APECoreConfig(configurationJson);
// if (!APEUtils.isValidReadFile(path)) {
// log.error("Bad path.");
// return;
// }
APE apeFramework = null;
try {
// set up the APE framework
apeFramework = new APE(coreConfig);
} catch (APEConfigException | JSONException | IOException | OWLOntologyCreationException e) {
log.error("Error in setting up the APE framework:");
log.error(e.getMessage());
return;
}
SolutionsList solutions;
try {
APERunConfig runConfig = new APERunConfig(configurationJson, apeFramework.getDomainSetup());
if (solutionsNo > 0) {
runConfig.setMaxNoSolutions(solutionsNo);
runConfig.setNoGraphs(solutionsNo);
runConfig.setNoCWL(solutionsNo);
}
runConfig.setSolutionLength(3, 10);
// run the synthesis and retrieve the solutions
solutions = apeFramework.runSynthesis(runConfig);
} catch (APEConfigException e) {
log.error("Error in synthesis execution. APE configuration error:");
log.error(e.getMessage());
return;
} catch (JSONException e) {
log.error("Error in synthesis execution. Bad JSON formatting (APE configuration or constriants JSON). ");
log.error(e.getMessage());
return;
} catch (IOException e) {
log.error("Error in synthesis execution.");
log.error(e.getMessage());
return;
}
/*
* Writing solutions to the specified file in human readable format
*/
if (solutions.isEmpty()) {
log.info("UNSAT");
} else {
try {
APE.writeSolutionToFile(solutions);
// APE.writeDataFlowGraphs(solutions, RankDir.TOP_TO_BOTTOM);
// APE.writeControlFlowGraphs(solutions, RankDir.LEFT_TO_RIGHT);
APE.writeTavernaDesignGraphs(solutions, Format.PNG);
APE.writeTavernaDesignGraphs(solutions, Format.SVG);
// APE.writeExecutableWorkflows(solutions);
APE.writeCWLWorkflows(solutions);
// APE.writeExecutableCWLWorkflows(solutions, apeFramework.getConfig());
} catch (IOException e) {
log.error("Error in writing the solutions. to the file system.");
e.printStackTrace();
}
}
}
private static APECoreConfig generateCoreConfig(String configFilePath) throws IOException, JSONException {
File configFile = APEFiles.readPathToFile(configFilePath);
JSONObject configJson = APEFiles.readFileToJSONObject(configFile);
String ontologyURL = configJson.getString("ontology_path");
File ontology = APEFiles.readPathToFile(ontologyURL);
String ontologyPrefixIRI = configJson.getString("ontologyPrefixIRI");
String toolTaxonomyRoot = configJson.getString("toolsTaxonomyRoot");
List dataDimensionsTaxonomyRoots = APEUtils
.getListFromJsonList(configJson.getJSONArray("dataDimensionsTaxonomyRoots"), String.class);
String toolAnnotationsURL = configJson.getString("tool_annotations_path");
File toolAnnotations = APEFiles.readPathToFile(toolAnnotationsURL);
boolean strictToolAnnotations = configJson.getBoolean("strict_tool_annotations");
APECoreConfig coreConfig = new APECoreConfig(ontology, ontologyPrefixIRI, toolTaxonomyRoot,
dataDimensionsTaxonomyRoots, toolAnnotations, strictToolAnnotations);
return coreConfig;
}
}