Catalog dataset metadata for download

- including tests

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -17,6 +17,7 @@ package org.genesys.catalog.service.impl;
 
 import static org.genesys.catalog.model.dataset.QDataset.dataset;
 
+import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -52,6 +53,7 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.security.SecurityUtils;
+import org.genesys2.server.service.DownloadService;
 import org.genesys2.util.JPAUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
@@ -97,8 +99,13 @@ public class DatasetServiceImpl implements DatasetService {
 	@Autowired
 	private SecurityUtils securityUtils;
 
+	/** The accessions repository. */
 	@Autowired
 	private AccessionRepository accessionRepository;
+
+	/** The download service. */
+	@Autowired
+	private DownloadService downloadService;
 	
 	/** The file repository path. */
 	@Value("${file.repository.datasets.folder}")
@@ -459,7 +466,7 @@ public class DatasetServiceImpl implements DatasetService {
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	public Dataset approveDataset(final Dataset dataset) {
-		final Dataset loaded = datasetRepository.findByUuidAndVersion(dataset.getUuid(), dataset.getVersion());
+		Dataset loaded = datasetRepository.findByUuidAndVersion(dataset.getUuid(), dataset.getVersion());
 		if (loaded == null) {
 			throw new NotFoundElement("No dataset with specified uuid and version");
 		}
@@ -472,6 +479,28 @@ public class DatasetServiceImpl implements DatasetService {
 
 		loaded.setState(PublishState.PUBLISHED);
 
+		// generate file with metadata and add it to the dataset
+		try (final ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
+			downloadService.writeXlsxDatasetMetadata(loaded, bos);
+			final String fileName = "genesys_catalog_metadata.xlsx";
+			final String contentType = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet";
+			try {
+				final RepositoryFile datasetFile = repositoryService.getFile(Paths.get(datasetRepositoryPath, loaded.getUuid().toString()), fileName);
+				repositoryService.updateBytes(datasetFile, contentType, bos.toByteArray());
+			} catch (final NoSuchRepositoryFileException | InvalidRepositoryPathException e) {
+				try {
+					final RepositoryFile addedFile = repositoryService.addFile(Paths.get(datasetRepositoryPath, loaded.getUuid().toString()).toAbsolutePath(),
+							fileName, contentType, bos.toByteArray(), null);
+					loaded.getRepositoryFiles().add(addedFile);
+					loaded = lazyLoad(datasetRepository.save(loaded));
+				} catch (final InvalidRepositoryPathException | InvalidRepositoryFileDataException e1) {
+					LOG.warn("Error while adding metadata file.", e1);
+				}
+			}
+		} catch (final IOException e) {
+			LOG.warn("Error while generating metadata file.", e);
+		}
+
 		{
 			// Relax permissions on dataset files: allow USERS and ANONYMOUS to read the
 			// files

src/main/java/org/genesys2/server/service/DownloadService.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
+/*
+ * Copyright 2018 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,7 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- **/
+ */
 
 package org.genesys2.server.service;
 
@@ -21,6 +21,7 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.util.List;
 
+import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 
@@ -38,6 +39,8 @@ public interface DownloadService {
 
 	void writeXlsxDescriptor(List<Descriptor> descriptors, OutputStream outputStream) throws IOException;
 
+	void writeXlsxDatasetMetadata(Dataset dataset, OutputStream outputStream) throws IOException;
+
 	void writeCsvLastUpdated(List<Object[]> lastUpdatedStatistics, OutputStreamWriter outputStream);
 
 }

src/main/java/org/genesys2/server/service/impl/DownloadServiceImpl.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
+/*
+ * Copyright 2018 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,7 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- **/
+ */
 
 package org.genesys2.server.service.impl;
 
@@ -39,7 +39,12 @@ import org.apache.poi.xssf.streaming.SXSSFWorkbook;
 // NOTE Excel 2016 has a limit of 66,530 hyperlinks
 // import org.apache.poi.xssf.usermodel.XSSFHyperlink;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.genesys.catalog.model.dataset.AccessionIdentifier;
+import org.genesys.catalog.model.dataset.Dataset;
+import org.genesys.catalog.model.dataset.DatasetCreator;
+import org.genesys.catalog.model.dataset.DatasetLocation;
 import org.genesys.catalog.model.traits.Descriptor;
+import org.genesys.catalog.model.vocab.VocabularyTerm;
 import org.genesys2.server.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionData;
@@ -71,6 +76,7 @@ import org.springframework.transaction.annotation.Transactional;
 import com.opencsv.CSVWriter;
 
 @Service
+@Transactional(readOnly = true)
 public class DownloadServiceImpl implements DownloadService {
 
 	public static final Logger LOG = LoggerFactory.getLogger(DownloadServiceImpl.class);
@@ -131,7 +137,6 @@ public class DownloadServiceImpl implements DownloadService {
 	private HashMap<String, Method> pdciMethods;
 
 	@Override
-	@Transactional(readOnly = true)
 	public void writeXlsxMCPD(final AppliedFilters filters, final OutputStream outputStream) throws IOException {
 		XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/MCPD.xlsx"));
 
@@ -377,7 +382,127 @@ public class DownloadServiceImpl implements DownloadService {
 	}
 
 	@Override
-	@Transactional(readOnly = true)
+	public void writeXlsxDatasetMetadata(final Dataset dataset, final OutputStream outputStream) throws IOException {
+		final XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/genesys_catalog_metadata.xlsx"));
+		final SXSSFWorkbook workbook = new SXSSFWorkbook(template, -1);
+
+		final Sheet accessionsSheet = workbook.getSheet("accessions");
+		writeAccessionsMetadata(dataset.getAccessionIdentifiers(), accessionsSheet);
+		((SXSSFSheet) accessionsSheet).flushRows();
+
+		final Sheet descriptorsSheet = workbook.getSheet("descriptors");
+		writeDescriptorsMetadata(dataset.getDescriptors(), descriptorsSheet);
+		((SXSSFSheet) descriptorsSheet).flushRows();
+
+		final Sheet locationsSheet = workbook.getSheet("location_timing");
+		writeLocationsMetadata(dataset.getLocations(), locationsSheet);
+		((SXSSFSheet) locationsSheet).flushRows();
+
+		final Sheet creatorsSheet = workbook.getSheet("creators");
+		writeCreatorsMetadata(dataset.getCreators(), creatorsSheet);
+		((SXSSFSheet) creatorsSheet).flushRows();
+
+		workbook.write(outputStream);
+		workbook.dispose();
+		outputStream.flush();
+	}
+
+	private void writeDescriptorsMetadata(final List<Descriptor> descriptors, final Sheet sheet) {
+		int item = 5;
+		final String NEW_LINE = "\n";
+
+		for (final Descriptor descriptor: descriptors) {
+			item ++;
+
+			final Row nextRow = sheet.createRow(item);
+
+			createCell(nextRow, 1, descriptor.getUuid().toString());
+			createCell(nextRow, 2, descriptor.getVersion().toString());
+			createCell(nextRow, 3, descriptor.getCrop());
+			createCell(nextRow, 4, descriptor.getVersionTag());
+			createCell(nextRow, 5, descriptor.getTitle());
+			createCell(nextRow, 6, descriptor.getCategory().name());
+			createCell(nextRow, 7, descriptor.getDescription());
+			createCell(nextRow, 8, descriptor.getDataType().name());
+			createCell(nextRow, 9, descriptor.getIntegerOnly());
+			createCell(nextRow, 10, descriptor.getMinValue());
+			createCell(nextRow, 11, descriptor.getMaxValue());
+
+			final String vocabularyId = descriptor.getVocabulary() == null ? "" : descriptor.getVocabulary().getId().toString();
+			createCell(nextRow, 12, vocabularyId);
+
+			final StringBuilder codes = new StringBuilder();
+			final StringBuilder codeTitles = new StringBuilder();
+			final StringBuilder codeDescriptions = new StringBuilder();
+			for (final VocabularyTerm term: descriptor.getTerms()) {
+				codes.append(NEW_LINE).append(term.getCode());
+				codeTitles.append(NEW_LINE).append(term.getTitle());
+				String description = term.getDescription();
+				codeDescriptions.append(NEW_LINE).append(description != null ? description.replace(NEW_LINE, "; ") : "");
+			}
+			createCell(nextRow, 13, codes.toString().replaceFirst(NEW_LINE, ""));
+			createCell(nextRow, 14, codeTitles.toString().replaceFirst(NEW_LINE, ""));
+			createCell(nextRow, 15, codeDescriptions.toString().replaceFirst(NEW_LINE, ""));
+
+			createCell(nextRow, 16, descriptor.getColumnName());
+			createCell(nextRow, 17, descriptor.getUom());
+		}
+	}
+
+	private void writeLocationsMetadata(final List<DatasetLocation> locations, final Sheet sheet) {
+		int item = 5;
+		for (final DatasetLocation location: locations) {
+			item ++;
+
+			final Row nextRow = sheet.createRow(item);
+
+			createCell(nextRow, 1, location.getUuid().toString());
+			createCell(nextRow, 2, location.getVersion());
+			createCell(nextRow, 3, location.getUserCountry());
+			createCell(nextRow, 4, location.getStateProvince());
+			createCell(nextRow, 5, location.getVerbatimLocality());
+			createCell(nextRow, 6, location.getDecimalLongitude());
+			createCell(nextRow, 7, location.getDecimalLatitude());
+			createCell(nextRow, 8, location.getStartDate());
+			createCell(nextRow, 9, location.getEndDate());
+		}
+	}
+
+	private void writeCreatorsMetadata(final List<DatasetCreator> creators, final Sheet sheet) {
+		int item = 5;
+		for (final DatasetCreator creator: creators) {
+			item ++;
+
+			final Row nextRow = sheet.createRow(item);
+
+			createCell(nextRow, 1, creator.getUuid().toString());
+			createCell(nextRow, 2, creator.getVersion());
+			createCell(nextRow, 3, creator.getFullName());
+			createCell(nextRow, 4, creator.getRole().name());
+			createCell(nextRow, 5, creator.getInstitutionalAffiliation());
+			createCell(nextRow, 6, creator.getEmail());
+			createCell(nextRow, 7, creator.getPhoneNumber());
+			createCell(nextRow, 8, creator.getFax());
+			createCell(nextRow, 9, creator.getInstituteAddress());
+		}
+	}
+
+	private void writeAccessionsMetadata(final Set<AccessionIdentifier> identifiers, final Sheet sheet) {
+		int item = 5;
+		for (final AccessionIdentifier accessionIdentifier: identifiers) {
+			item ++;
+
+			final Row nextRow = sheet.createRow(item);
+
+			createCell(nextRow, 1, accessionIdentifier.getInstCode());
+			createCell(nextRow, 2, accessionIdentifier.getAcceNumb());
+			createCell(nextRow, 3, accessionIdentifier.getGenus());
+			createCell(nextRow, 4, accessionIdentifier.getSpecies());
+			createCell(nextRow, 5, accessionIdentifier.getDoi());
+		}
+	}
+
+	@Override
 	public void writeXlsxDescriptor(final List<Descriptor> descriptors, final OutputStream outputStream) throws IOException {
 		XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/DESCRIPTORS.xlsx"));
 		SXSSFWorkbook workbook = new SXSSFWorkbook(template, -1);
@@ -424,7 +549,6 @@ public class DownloadServiceImpl implements DownloadService {
 	}
 
 	@Override
-	@Transactional(readOnly = true)
 	public void writeXlsxPDCI(final AppliedFilters filters, final OutputStream outputStream) throws IOException {
 		XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/PDCI.xlsx"));
 
@@ -490,7 +614,6 @@ public class DownloadServiceImpl implements DownloadService {
 	}
 
 	@Override
-	@Transactional(readOnly = true)
 	public void writeCsvLastUpdated(final List<Object[]> lastUpdatedStatistics, final OutputStreamWriter outputStream) {
 
 		try (CSVWriter writer = new CSVWriter(outputStream, '\t', '"', '\\', "\n")) {

src/test/java/org/genesys/test/catalog/services/DatasetPublishingTest.java

@@ -24,8 +24,8 @@ import org.genesys.catalog.exceptions.NotFoundElement;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys2.server.model.PublishState;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.security.test.context.support.WithMockUser;
 import org.springframework.transaction.annotation.Transactional;
 
 public class DatasetPublishingTest extends AbstractDatasetServiceTest {
@@ -86,6 +86,7 @@ public class DatasetPublishingTest extends AbstractDatasetServiceTest {
 	}
 
 	@Test(expected = InvalidApiUsageException.class)
+	@WithMockUser(roles = "ADMINISTRATOR")
 	public void testReviewDatasetFailIfPublished() {
 		assertThat(savedDataset.getState(), is(PublishState.DRAFT));
 		final Dataset loaded = datasetRepository.findByUuid(savedDataset.getUuid());
@@ -108,8 +109,6 @@ public class DatasetPublishingTest extends AbstractDatasetServiceTest {
 		assertThat(loaded, not(nullValue()));
 	}
 
-	//FIXME Remove ignore as soon as frontend clients start supporting PublishState
-	@Ignore
 	@Test(expected = InvalidApiUsageException.class)
 	public void testApproveDatasetFailIfDrafted() {
 		assertThat(savedDataset.getState(), is(PublishState.DRAFT));
@@ -121,6 +120,7 @@ public class DatasetPublishingTest extends AbstractDatasetServiceTest {
 	}
 
 	@Test(expected = InvalidApiUsageException.class)
+	@WithMockUser(roles = "ADMINISTRATOR")
 	public void testApproveDatasetFailWhenPublished() {
 		assertThat(savedDataset.getState(), is(PublishState.DRAFT));
 		final Dataset loaded = datasetRepository.findByUuid(savedDataset.getUuid());
@@ -135,6 +135,7 @@ public class DatasetPublishingTest extends AbstractDatasetServiceTest {
 	}
 
 	@Test
+	@WithMockUser(roles = "ADMINISTRATOR")
 	public void testUnpublishDataset() {
 		assertThat(savedDataset.getState(), is(PublishState.DRAFT));
 		final Dataset loaded = datasetRepository.findByUuid(savedDataset.getUuid());