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fix: rename classes
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@mosoriob
mosoriob committed Oct 31, 2023
1 parent d4f0b07 commit 241923b
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247 changes: 165 additions & 82 deletions src/test/java/opmw_mapper/MapperTest.java
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Original file line number Diff line number Diff line change
@@ -1,92 +1,193 @@
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package opmw_mapper;

import static org.junit.Assert.assertTrue;

import java.io.File;
import java.io.IOException;
import java.util.List;

import org.apache.jena.ontology.OntModel;
import static org.junit.Assert.*;
import org.apache.jena.sparql.function.library.e;
import org.junit.Assert;
import org.junit.Test;

import edu.isi.kcap.wings.opmm.Constants;
import edu.isi.kcap.wings.opmm.FilePublisher;
import edu.isi.kcap.wings.opmm.Mapper;
import edu.isi.kcap.wings.opmm.DataTypes.ProvenanceResponseSchema;
import edu.isi.kcap.wings.opmm.Publisher.TriplesPublisher;

/**
* This class performs different tests with different templates and executions
*
* @author Daniel Garijo
*/
public class MapperTest {
private static String webServerDirectory = "tmp/";
private static String webServerDomain = "http://localhost";
FilePublisher filePublisher = new FilePublisher(FilePublisher.Type.FILE_SYSTEM, webServerDirectory,
webServerDomain);
// Domain: it is wings domain concept: it is the name of the domain
String domain = "neuroDisk";
// exportPrefix: used by the catalog to create the URL:
// w3id.org/opmw/wings/{exportName}/{domain}#Components
// w3id.org/opmw/wings/{exportName}/{domain}#Data
String exportPrefix = "exportTest";
String exportUrl = "https://www.opmw.org/";
// catalogRepositoryDirectory: the directory where the catalog will be stored
String catalogRepositoryDirectory = "domains";
String endpointQueryURI = "https://endpoint.mint.isi.edu/provenance/query";
String endpointPostURI = "https://endpoint.mint.isi.edu/provenance/data";
String componentLibraryFilePath = "src/test/resources/neuro/components.owl";
String planFilePath = "src/test/resources/neuro/plan.owl";

@Test
public void testMapperTurtle() throws IOException {
String serialization = "TTL";
File file = new File("tmp/" + serialization);
if (!file.exists()) {
file.mkdir();
}
String targetDirectory = "tmp/" + serialization;
String executionFilePath = targetDirectory + "/execution.ttl";
String expandedTemplateFilePath = targetDirectory + "/expandedTemplate.ttl";
String abstractFilePath = targetDirectory + "/abstractTemplate.ttl";
TriplesPublisher executionTriplesPublisher = new TriplesPublisher(endpointQueryURI, endpointPostURI,
exportUrl,
exportPrefix, serialization);
TriplesPublisher catalogTriplesPublisher = new TriplesPublisher(endpointQueryURI, endpointPostURI,
Constants.CATALOG_URI,
exportPrefix, serialization);
ProvenanceResponseSchema response = Mapper.main(domain, catalogRepositoryDirectory,
componentLibraryFilePath, planFilePath, executionFilePath,
expandedTemplateFilePath, abstractFilePath,
filePublisher, executionTriplesPublisher, catalogTriplesPublisher);

assertTrue(response.getCatalog().getFilePath().contains("domains/neuroDisk"));
assertTrue(response.getCatalog().getFileUrl().contains(catalogTriplesPublisher.exportUrl));
assertTrue(response.getCatalog().getGraphUrl().contains(catalogTriplesPublisher.exportUrl));
// Test that the execution is published
assertTrue(response.getWorkflowExecution().getFilePath().contains("tmp/TTL/execution.ttl"));
assertTrue(response.getWorkflowExecution().getFileUrl().contains(executionTriplesPublisher.exportUrl));
assertTrue(response.getWorkflowExecution().getGraphUrl().contains(executionTriplesPublisher.exportUrl));
assertTrue(response.getWorkflowExpandedTemplate().getFilePath()
.contains("tmp/TTL/expandedTemplate.ttl"));
assertTrue(response.getWorkflowExpandedTemplate().getFileUrl()
.contains(executionTriplesPublisher.exportUrl));
assertTrue(response.getWorkflowExpandedTemplate().getGraphUrl()
.contains(executionTriplesPublisher.exportUrl));
assertTrue(response.getWorkflowAbstractTemplate().getFilePath()
.contains("tmp/TTL/abstractTemplate.ttl"));
assertTrue(response.getWorkflowAbstractTemplate().getFileUrl()
.contains(executionTriplesPublisher.exportUrl));
assertTrue(response.getWorkflowAbstractTemplate().getGraphUrl()
.contains(executionTriplesPublisher.exportUrl));

OntModel model = Utils.loadDirectory(targetDirectory);
validateModel(model);
}

@Test
public void testXMLTurtle() throws IOException {
String serialization = "RDF/XML";
File file = new File("tmp/" + serialization);
if (!file.exists()) {
file.mkdirs();
}
String executionFilePath = "tmp/" + serialization + "/execution.xml";
String expandedTemplateFilePath = "tmp/" + serialization + "/expandedTemplate.xml";
String abstractFilePath = "tmp/" + serialization + "/abstractTemplate.xml";
TriplesPublisher executionTriplesPublisher = new TriplesPublisher(endpointQueryURI, endpointPostURI,
exportUrl,
exportPrefix, serialization);
TriplesPublisher catalogTriplesPublisher = new TriplesPublisher(endpointQueryURI, endpointPostURI,
Constants.CATALOG_URI,
exportPrefix, serialization);
try {
Mapper.main(domain, catalogRepositoryDirectory, componentLibraryFilePath, planFilePath,
executionFilePath,
expandedTemplateFilePath, abstractFilePath,
filePublisher, executionTriplesPublisher, catalogTriplesPublisher);
} catch (Exception e) {
e.printStackTrace();
Assert.assertTrue(false);
}
List<String> entities = MockupData.metaAnalysisWorkflowExecution();
for (String entity : entities) {
Utils.checkExecutionXML(entity, executionFilePath);
}

}

/**
* Function to validate an OPMW Model. It includes a set of tests for both
* executions and templates
*
* @param m
*/
public void validateModel(OntModel m) {
// execution artifacts
System.out.println("Validating: ALL EXECUTION ARTIFACTS SHOULD BELONG TO AN ACCOUNT");
/*
* Check that artifact is connected to a:
* 1. Account
* 2. Location or value
* 3. Template artifact
* 4. Process
*/
int problems = Integer
.parseInt(Utils.getCountOf(Queries.COUNT_ARTIFACTS_WITHOUT_ACCOUNT, m, "countArt"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL EXECUTION ARTIFACTS SHOULD HAVE A LOCATION (VARIABLES) OR VALUE (PARAMETERS).");
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_ARTIFACTS_WITHOUT_LOCATION_OR_VALUE, m, "countArt"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL EXECUTION ARTIFACTS SHOULD BELONG TO A TEMPLATE VARIABLE OR PARAMETER THAT BELONGS TO A TEMPLATE.");
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_ARTIFACTS_WITHOUT_BINDING_TO_TEMPLATE_ARTIFACT, m,
"countArt"));
assertTrue(problems <= 0);
System.out.println("Validating: ALL EXECUTION ARTIFACTS SHOULD BE USED OR GENERATED BY A PROCESS.");
problems = Integer
.parseInt(Utils.getCountOf(Queries.COUNT_ARTIFACTS_WITHOUT_BINDING_TO_PROCESS, m,
"countArt"));
assertTrue(problems <= 0);
// execution processes
System.out.println("Validating: ALL EXECUTION PROCESSES SHOULD BELONG TO AN ACCOUNT.");
/**
* Check that execution process is connected to a:
* 1. Account
* 2. Artifact
* 3. Execution code
* 4. Template process
*/
problems = Integer.parseInt(Utils.getCountOf(Queries.COUNT_PROCESSES_WITHOUT_ACCOUNT, m, "countProc"));
assertTrue(problems <= 0);
System.out.println("Validating: ALL EXECUTION PROCESSES SHOULD USE OR GENERATE SOME ARTIFACT.");
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_PROCESSES_NOT_BOUND_TO_ARTIFACT, m, "countProc"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL EXECUTION PROCESSES SHOULD HAVE AN EXECUTION CODE ASSOCIATED TO THEM.");
problems = Integer.parseInt(Utils.getCountOf(Queries.COUNT_PROCESSES_WITHOUT_CODE, m, "countProc"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL EXECUTION PROCESSES SHOULD CORRESPOND TO A TEMPLATE PROCESS THAT BELONGS TO A TEMPLATE.");
problems = Integer
.parseInt(Utils.getCountOf(Queries.COUNT_PROCESSES_WITHOUT_CORRECT_TEMPLATE_BINDING, m,
"countProc"));
assertTrue(problems <= 0);
// execution accounts
System.out.println("Validating: ALL EXECUTIONS MUST BELONG TO A TEMPLATE OR EXPANDED TEMPLATE.");
/**
* Check that execution account is connected to a:
* 1. Template account
* 2. Time or status
*/
problems = Integer.parseInt(Utils.getCountOf(Queries.COUNT_EXECUTIONS_WITHOUT_TEMPLATE, m, "countAcc"));
assertTrue(problems <= 0);
System.out.println("Validating: ALL EXECUTIONS MUST HAVE AN END TIME, A START TIME AND A STATUS.");
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_EXECUTIONS_WITHOUT_TIME_OR_STATUS, m, "countAcc"));
assertTrue(problems <= 0);
// template artifacts
System.out.println("Validating: ALL TEMPLATE ARTIFCATS MUST BELONG TO A TEMPLATE.");
/**
* Check that template account is connected to a:
* 1. Template
* 2. Process
* 3. Plan
*/
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_TEMPL_ARTIFACTS_WITHOUT_TEMPLATE, m, "countArt"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL TEMPLATE ARTIFACTS MUST BE CONNECTED TO A TEMPLATE PROCESS (testing in OPMW).");
problems = Integer
.parseInt(Utils.getCountOf(Queries.COUNT_TEMPL_ARTIFACTS_WITHOUT_PROCESS_OPMW, m,
"countArt"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL TEMPLATE ARTIFACTS MUST BE CONNECTED TO A TEMPLATE PROCESS (testing in P-PLAN).");
problems = Integer
.parseInt(Utils.getCountOf(Queries.COUNT_TEMPL_ARTIFACTS_WITHOUT_PROCESS_P_PLAN, m,
"countArt"));
assertTrue(problems <= 0);
// template processes
/*
* Check that template process is connected to a:
* 1. Artifact (OPMW)
* 2. Template (OPMW)
* 3. Template (P-PLAN)
*/
System.out.println(
"Validating: ALL TEMPLATE PROCESSES MUST USE OR GENERATE A TEMPLATE ARTIFACT (test in P-PLAN).");
problems = Integer.parseInt(
Expand All @@ -103,59 +204,41 @@ public void validateModel(OntModel m) {
.parseInt(Utils.getCountOf(Queries.COUNT_TEMPL_PROCESSES_WITHOUT_TEMPLATE_PPLAN, m,
"countProc"));
assertTrue(problems <= 0);
System.out.println("Validating: ARE THERE ANY UNDECLARED WORKFLOW TEMPLATE PROCESSES?.");
/**
* Check if there are any undeclared workflow template processes
*/
problems = Integer.parseInt(Utils.getCountOf(Queries.COUNT_UNDECLARED_PROCESSES, m, "countProc"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL TEMPLATE PROCESSES MUST USE OR GENERATE A TEMPLATE ARTIFACT (test in OPMW).");
/**
* Check that all template processes must use or generate a template artifact
* (OPMW)
*/
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_TEMPL_PROCESS_WITHOUT_BINDING_TO_ARTIFACT_OPMW, m,
"countProc"));
assertTrue(problems <= 0);
System.out.println(
"Validating: ALL TEMPLATE PROCESSES MUST USE OR GENERATE A TEMPLATE ARTIFACT (test in P-PLAN).");

/**
* Check that all template processes must use or generate a template artifact
* (P-PLAN)
*/
problems = Integer.parseInt(
Utils.getCountOf(Queries.COUNT_TEMPL_PROCESS_WITHOUT_BINDING_TO_ARTIFACT_PPLAN, m,
"countProc"));
assertTrue(problems <= 0);

// expanded template (TO DO)
System.out.println("Validating: ALL EXPANDED TEMPLATE PROCESSES SHOULD LINK TO A TEMPLATE.");
// TO DO
System.out.println(
"Validating: ALL EXPANDED TEMPLATE PROCESSES SHOULD BE IMPLEMENTATIONS OF A TEMPLATE PROCESS.");
// TO DO
System.out.println("Validating: ALL EXPANDED TEMPLATE SHOULD LINK TO A TEMPLATE.");
// TO DO
System.out.println(
"Validating: ALL EXPANDED TEMPLATE VARIABLES SHOULD LINK TO A TEMPLATE VARIABLE THAT BELONG TO A TEMPLATE (AND AND EXECUTION).");
// TO DO
System.out.println(
"Validating: ALL EXPANDED PARAMETER VARIABLES SHOULD LINK TO A PARAMETER VARIABLE THAT BELONG TO A TEMPLATE (AND AND EXECUTION).");
// TO DO
// the following won't work at the moment
System.out.println(
"Validating: ALL W3ID COMPONENT CLASSES SHOULD HAVE A LABEL (OTHERWISE THEY ARE NOT CORRECTLY LINKED).");
// TO DO
// the following won't work at the moment
System.out.println(
"Validating: ALL W3ID DATA CLASSES SHOULD HAVE A LABEL (OTHERWISE THEY ARE NOT CORRECTLY LINKED).");
// TO DO

// Optional tests not included
// result+="#TEST"+(++n)+": (OPTIONAL TEST) AN ACCOUNT MAY HAVE A POINTER TO THE
// ORIGINAL LOG FILE.\n";
// result+="\t"+isTestFailed(Integer.parseInt(Utils.getCountOf(Queries.COUNT_EXECUTIONS_WITHOUT_LOG_FILE,
// m, "countAcc")))+"\n";
// result+="#TEST"+(++n)+": (OPTIONAL TEST) TEMPLATES SHOULD HAVE A VERSION
// NUMBER.\n";
// result+="\t"+isTestFailed(Integer.parseInt(Utils.getCountOf(Queries.COUNT_TEMPL_WITHOUT_VERSION_NUMBER,
// m, "countT")))+"\n";
// result+="#TEST"+(++n)+": (OPTIONAL TEST) TEMPLATES SHOULD HAVE A POINTER TO
// THE NATIVE SYSTEM TEMPLATE.\n";
// result+="\t"+isTestFailed(Integer.parseInt(Utils.getCountOf(Queries.COUNT_TEMPL_WITHOUT_NATIVE_SYS_TEMPL,
// m, "countT")))+"\n";
// TODO: Test | All expanded template processes should link to a template
// process.
// TODO: Test | All expanded template should link to a template process.
// TODO: Test | All expanded template should like to a template.
// TODO: Test | All expanded template variables should link to a template
// variable that belong to a template (and and execution).
// TODO: Test | All expanded parameter variables should link to a parameter
// variable that belong to a template (and and execution).
// TODO: Test | All w3id component classes should have a label (otherwise they
// are not correctly linked).
// TODO: Test | All w3id data classes should have a label (otherwise they are
// not correctly linked).

}

}
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