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TabularModuleTest.java
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TabularModuleTest.java
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package cz.cvut.spipes.modules;
import cz.cvut.spipes.config.ExecutionConfig;
import cz.cvut.spipes.constants.CSVW;
import cz.cvut.spipes.engine.ExecutionContext;
import cz.cvut.spipes.engine.ExecutionContextFactory;
import cz.cvut.spipes.exception.ResourceNotUniqueException;
import cz.cvut.spipes.modules.exception.SpecificationNonComplianceException;
import cz.cvut.spipes.modules.exception.TableSchemaException;
import cz.cvut.spipes.test.JenaTestUtils;
import cz.cvut.spipes.util.StreamResourceUtils;
import org.apache.jena.rdf.model.*;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.List;
import static cz.cvut.spipes.test.JenaTestUtils.assertIsomorphic;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assumptions.assumeTrue;
class TabularModuleTest extends AbstractModuleTestHelper {
private TabularModule module;
private final String DATA_PREFIX = "http://onto.fel.cvut.cz/data/";
private static final Logger LOG = LoggerFactory.getLogger(TabularModuleTest.class);
@BeforeEach
void setUp() {
module = new TabularModule();
module.setReplace(true);
module.setDelimiter('\t');
module.setQuoteCharacter('"');
module.setDataPrefix(DATA_PREFIX);
module.setOutputMode(Mode.STANDARD);
module.setInputContext(ExecutionContextFactory.createEmptyContext());
}
@Test
void executeWithSimpleTransformation() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/countries/input.tsv"))
);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/countries/plaintext-expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeWithSimpleTransformationXls() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/countries/input.xls"))
);
module.setSourceResourceFormat(ResourceFormat.XLS);
module.setProcessSpecificSheetInXLSFile(1);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/countries/excel-expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeWithSimpleTransformationXlsm() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/countries/input.xlsm"))
);
module.setSourceResourceFormat(ResourceFormat.XLSM);
module.setProcessSpecificSheetInXLSFile(1);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/countries/excel-expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeWithSimpleTransformationMergedXls() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/mergedCells/input.xls"))
);
module.setSourceResourceFormat(ResourceFormat.XLS);
module.setProcessSpecificSheetInXLSFile(1);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/mergedCells/expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeWithSimpleTransformationMergedXlsx() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/mergedCells/input.xlsx"))
);
module.setSourceResourceFormat(ResourceFormat.XLSX);
module.setProcessSpecificSheetInXLSFile(1);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/mergedCells/expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeWithSimpleTransformationMergedHTML() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/mergedCells/input.html"))
);
module.setSourceResourceFormat(ResourceFormat.HTML);
ExecutionContext outputContext = module.executeSelf();
Model expectedModel = ModelFactory.createDefaultModel().read(getFilePath("examples/mergedCells/expected-output.ttl").toString());
assertIsomorphic(outputContext.getDefaultModel(),expectedModel);
}
@Test
void executeSelfThrowSpecificationException() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/countries/input.tsv"))
);
module.setSourceResourceFormat(ResourceFormat.TSV);
module.executeSelf();
assertThrows(SpecificationNonComplianceException.class, () -> module.setDelimiter(','));
}
@Test
void executeWithDuplicateColumnsThrowsResourceNotUniqueException()
throws URISyntaxException, IOException {
module.setSourceResource(StreamResourceUtils.getStreamResource(
"http://test-file-2",
getFilePath("examples/countries/duplicate-column-input.tsv"))
);
ResourceNotUniqueException exception = assertThrows(
ResourceNotUniqueException.class,
module::executeSelf
);
String expectedMessage = "latitude";
String actualMessage = exception.getMessage();
assertTrue(actualMessage.contains(expectedMessage));
}
@Test
void checkDefaultConfigurationAgainstExemplaryModelOutput() throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(
"http://test-file",
getFilePath("examples/countries/input.tsv"))
);
ExecutionContext outputContext = module.executeSelf();
Model actualModel = outputContext.getDefaultModel();
Model expectedModel = ModelFactory.createDefaultModel()
.read(getFilePath("examples/countries/plaintext-expected-output.ttl").toString());
assertTrue(actualModel.isIsomorphicWith(expectedModel));
}
@DisplayName("Executes Tabular module with or without csvw:property.")
@ParameterizedTest(name = "{index} => message=''Test {0} (csvw:property) in the schema''")
@ValueSource(strings = {"withProperty", "withoutProperty"})
void executeSelfChecksSchemaWithoutProperty(String folderName) throws URISyntaxException, IOException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(DATA_PREFIX, getFilePath("examples/" + folderName + "/input.tsv"))
);
Model inputModel = JenaTestUtils.laodModelFromResource("/examples/" + folderName + "/input-data-schema.ttl");
module.setInputContext(ExecutionContextFactory.createContext(inputModel));
ExecutionContext outputContext = module.executeSelf();
Model actualModel = outputContext.getDefaultModel();
Model expectedModel = ModelFactory.createDefaultModel()
.read(getFilePath("examples/" + folderName + "/expected-output.ttl").toString());
assertTrue(actualModel.isIsomorphicWith(expectedModel));
}
@DisplayName("Executes Tabular module with the different number of columns in the schema.")
@ParameterizedTest(name = "{index} => message=''{0} in the schema''")
@ValueSource(strings = {"moreColumns", "lessColumns", "noColumns"})
void executeSelfThrowsException(String folderName) throws URISyntaxException, IOException {
assumeTrue(ExecutionConfig.isExitOnError());
module.setSourceResource(
StreamResourceUtils.getStreamResource(DATA_PREFIX,getFilePath("examples/" + folderName + "/input.tsv"))
);
Model inputModel = JenaTestUtils.laodModelFromResource("/examples/" + folderName + "/input-data-schema.ttl");
module.setInputContext(ExecutionContextFactory.createContext(inputModel));
assertThrows(TableSchemaException.class, () -> module.executeSelf());
}
@Test
void executeSelfWithDataSchemaNoHeaderReturnsNamedColumnsFromSchema()
throws URISyntaxException, IOException {
module.setSkipHeader(true);
module.setSourceResource(
StreamResourceUtils.getStreamResource(DATA_PREFIX,getFilePath("examples/noHeader/schemaExample/input.csv"))
);
Model inputModel = JenaTestUtils.laodModelFromResource("/examples/noHeader/schemaExample/input-data-schema.ttl");
module.setInputContext(ExecutionContextFactory.createContext(inputModel));
ExecutionContext outputContext = module.executeSelf();
String[] columns = new String[]{"col_1", "col_2", "col_3", "col_4", "col_5"};
for (int i = 2; i <= 4; i++) {
Resource resource = ResourceFactory.createResource(DATA_PREFIX + "#row-" + i);
for (String column: columns) {
Property property = ResourceFactory.createProperty(DATA_PREFIX, column);
assertTrue(outputContext.getDefaultModel().contains(resource, property));
}
}
}
@Test
void executeSelfWithNoDataSchemaNoHeaderReturnsAutonamedColumns()
throws URISyntaxException, IOException {
module.setSkipHeader(true);
module.setSourceResource(
StreamResourceUtils
.getStreamResource(DATA_PREFIX,getFilePath("examples/noHeader/noSchemaExample/input.tsv"))
);
ExecutionContext outputContext = module.executeSelf();
for (int i = 2; i <= 4; i++) {
Resource resource = ResourceFactory.createResource(DATA_PREFIX + "#row-" + i);
for (int j = 1; j <= 6; j++) {
String columnName = "column_" + j;
Property property = ResourceFactory.createProperty(DATA_PREFIX, columnName);
assertTrue(outputContext.getDefaultModel().contains(resource, property));
}
}
}
@Test
void executeSelfWithBNodesInSchema() throws IOException, URISyntaxException {
module.setSourceResource(
StreamResourceUtils.getStreamResource(DATA_PREFIX, getFilePath("examples/blankNodes/input.tsv"))
);
Model inputModel = JenaTestUtils.laodModelFromResource("/examples/blankNodes/input-data-schema.ttl");
module.setInputContext(ExecutionContextFactory.createContext(inputModel));
ExecutionContext outputContext = module.executeSelf();
Model actualModel = outputContext.getDefaultModel();
Model expectedModel = ModelFactory.createDefaultModel()
.read(getFilePath("examples/blankNodes/expected-output.ttl").toString());
assertIsomorphic(actualModel, expectedModel);
}
@Test
void executeSelfWithHTMLFileInput() throws URISyntaxException, IOException {
module.setSourceResourceFormat(ResourceFormat.HTML);
module.setSourceResource(
StreamResourceUtils.getStreamResource(DATA_PREFIX, getFilePath("examples/htmlFile/input.html"))
);
ExecutionContext outputContext = module.executeSelf();
Model actualModel = outputContext.getDefaultModel();
List<String> header = Arrays.asList("No_", "Test_1", "Test_2", "Description");
List<List<String>> rows = Arrays.asList(
Arrays.asList("1.", "123", "456", "description 1"),
Arrays.asList("2.", "789", "123", "description 2"));
header.forEach(headerValue -> assertTrue(actualModel.contains(null, CSVW.name, headerValue)));
for (List<String> row: rows){
for(int idx = 0; idx < header.size(); idx++) {
String headerValue = header.get(idx);
String rowValue = row.get(idx);
assertTrue(actualModel
.contains(null, actualModel.getProperty(DATA_PREFIX + headerValue), rowValue)
);
}
}
}
@Override
public String getModuleName() {
return "tabular";
}
public Path getFilePath(String fileName) throws URISyntaxException {
return Paths.get(getClass().getResource("/" + fileName).toURI());
}
}