Download repository metadata for an institute

- metadata files info
- Update WiewsController
- download files metadata

pom.xml

@@ -792,7 +792,7 @@
 					</attributes>
 				</configuration>
 			</plugin>
-			<!-- <plugin>
+			 <plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>license-maven-plugin</artifactId>
 				<version>1.9</version>
@@ -815,7 +815,7 @@
 				<configuration>
 					<sortArtifactByName>true</sortArtifactByName>
 				</configuration>
-			</plugin> -->
+			</plugin>
 			<plugin>
 				<groupId>org.liquibase</groupId>
 				<artifactId>liquibase-maven-plugin</artifactId>

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

@@ -55,6 +55,8 @@ import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 
+import javax.servlet.http.HttpServletResponse;
+
 public interface GenesysService {
 
 	/**
@@ -290,4 +292,12 @@ public interface GenesysService {
 
 	Page<AccessionDetails> listAccessionsDetails(Collection<Long> accessionIds, Pageable page);
 
+	/**
+	 * Method for download files metadata
+	 * @param response response
+	 * @param repositoryPath repository path
+	 * @throws IOException
+	 */
+	void downloadFilesMetadata(HttpServletResponse response, String repositoryPath) throws IOException;
+
 }

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

+package org.genesys2.server.service.impl;
+
+import org.genesys.filerepository.model.RepositoryFile;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Service;
+
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * @author Andrey Lugovskoy.
+ */
+@Service("filesMetadataInfo")
+public class FilesMetadataInfo extends MetadataInfo<RepositoryFile> {
+
+	@Value("#{'${files.metadata.fields}'.split(',')}") private List<String> filesMetadataHeader;
+
+	@Override
+	public void downloadMetadata(List<RepositoryFile> entities, HttpServletResponse response, char separator, char quoteChar, char escapeChar, String lineEnd) throws IOException {
+		super.downloadMetadata(filesMetadataHeader, entities, response, separator, quoteChar, escapeChar, lineEnd);
+	}
+}

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

@@ -16,37 +16,16 @@
 
 package org.genesys2.server.service.impl;
 
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.stream.Collectors;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
-
-import javax.persistence.EntityManager;
-
 import com.opencsv.CSVWriter;
 import com.opencsv.ResultSetHelper;
 import com.opencsv.ResultSetHelperService;
-
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang.StringUtils;
 import org.genesys.blocks.security.SecurityContextUtil;
 import org.genesys.blocks.security.service.CustomAclService;
+import org.genesys.filerepository.model.RepositoryFile;
+import org.genesys.filerepository.service.RepositoryService;
 import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
@@ -127,6 +106,28 @@ import org.springframework.transaction.annotation.Isolation;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import javax.persistence.EntityManager;
+import javax.servlet.http.HttpServletResponse;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
+
 @Service
 @Transactional(readOnly = true)
 public class GenesysServiceImpl implements GenesysService, DatasetService {
@@ -200,6 +201,12 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Autowired
 	private GenesysFilterService filterService;
 
+	@Autowired(required = false)
+	private RepositoryService repositoryService;
+
+	@Autowired(required = false)
+	private FilesMetadataInfo filesMetadataInfo;
+
 	private List<String> availableDisplayColumns;
 
 	private List<String> defaultDisplayColumns;
@@ -290,7 +297,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public Page<AccessionDetails> listAccessionsDetails(Collection<Long> accessionIds, Pageable pageable) {
 		if (!accessionIds.isEmpty()) {
 			Page<Accession> data = accessionRepository.findById(accessionIds, pageable);
-			return new PageImpl<AccessionDetails>(getAccessionDetails(data.getContent().stream().map(a -> a.getId()).collect(Collectors.toList())), pageable, data.getTotalElements());
+			return new PageImpl<AccessionDetails>(getAccessionDetails(data.getContent().stream().map(a -> a.getId()).collect(Collectors.toList())), pageable,
+												  data.getTotalElements());
 		} else {
 			return null;
 		}
@@ -299,7 +307,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Override
 	public Accession getAccession(AccessionIdentifier3 aid3) throws NonUniqueAccessionException {
 		try {
-			Accession accession = accessionRepository.findOne(instituteRepository.findByCode(aid3.getHoldingInstitute()), aid3.getDoi(), aid3.getAccessionNumber(), aid3.getGenus());
+			Accession accession = accessionRepository
+					.findOne(instituteRepository.findByCode(aid3.getHoldingInstitute()), aid3.getDoi(), aid3.getAccessionNumber(), aid3.getGenus());
 			return lazyLoadAccession(accession);
 		} catch (IncorrectResultSizeDataAccessException e) {
 			LOG.error("Duplicate accession name instCode={} acceNumb={} genus={}", aid3.getHoldingInstitute(), aid3.getAccessionNumber(), aid3.getGenus());
@@ -881,10 +890,10 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	 * Update {@link SvalbardDeposit} data and link with Genesys accessions. The
 	 * primary key for {@link SvalbardDeposit} is the <code>sgsv_id</code> as
 	 * provided by NordGen.
-	 * 
+	 *
 	 * Any existing SGSV records are first deleted. Inserted and linked with
 	 * accessions in this method.
-	 * 
+	 *
 	 * @param svalbardDeposits
 	 * @return
 	 */
@@ -1901,4 +1910,17 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public List<Object[]> getLastUpdatedStatistics(FaoInstitute faoInstitute) {
 		return accessionRepository.lastUpdatedStatistics(faoInstitute);
 	}
+
+	/**
+	 * {@inheritDoc}
+	 *
+	 * @param response
+	 */
+	@Override
+	public void downloadFilesMetadata(HttpServletResponse response, String repositoryPath) throws IOException {
+
+		List<RepositoryFile> files = repositoryService.getFiles(repositoryPath);
+
+		filesMetadataInfo.downloadMetadata(files, response, '	', '"', '\\', "\r\n");
+	}
 }

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

+package org.genesys2.server.service.impl;
+
+import com.opencsv.CSVWriter;
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import javax.servlet.http.HttpServletResponse;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author Andrey Lugovskoy.
+ */
+public abstract class MetadataInfo<T> {
+
+	public static final Log LOG = LogFactory.getLog(MetadataInfo.class);
+
+	public abstract void downloadMetadata(List<T> entities, HttpServletResponse response, char separator, char quoteChar, char escapeChar, String lineEnd) throws IOException;
+
+	public void downloadMetadata(List<String> filesMetadataFields, List<T> entities, HttpServletResponse response, char separator, char quoteChar, char escapeChar, String lineEnd)
+			throws IOException {
+
+		try (CSVWriter writer = new CSVWriter(new BufferedWriter(new OutputStreamWriter(response.getOutputStream())), separator, quoteChar, escapeChar, lineEnd)) {
+
+			writer.writeNext(filesMetadataFields.toArray(ArrayUtils.EMPTY_STRING_ARRAY));
+
+			entities.stream().forEach(element -> {
+				List<Object> values = new ArrayList<>();
+				Class<?> aClass = element.getClass();
+				filesMetadataFields.stream().forEach(fieldName -> {
+					Field field;
+					Object value = " ";
+					try {
+						field = aClass.getField(fieldName);
+						value = field.get(element);
+					} catch (NoSuchFieldException e) {
+						try {
+							field = aClass.getSuperclass().getDeclaredField(fieldName);
+							field.setAccessible(true);
+							value = field.get(element);
+							value = value == null ? " " : value;
+						} catch (NoSuchFieldException | IllegalAccessException e1) {
+							LOG.error("Error getting value from field in " + element.getClass().getName());
+						}
+					} catch (IllegalAccessException e) {
+						LOG.error("Error getting value from field in " + element.getClass().getName());
+					}
+					values.add(value);
+				});
+				String[] stockArr = new String[values.size()];
+				stockArr = values.toArray(stockArr);
+				writer.writeNext(stockArr);
+			});
+			writer.flush();
+		}
+	}
+}

src/main/java/org/genesys2/server/servlet/controller/WiewsController.java

@@ -16,22 +16,6 @@
 
 package org.genesys2.server.servlet.controller;
 
-import java.io.EOFException;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.genesys.filerepository.InvalidRepositoryFileDataException;
 import org.genesys.filerepository.InvalidRepositoryPathException;
 import org.genesys.filerepository.NoSuchRepositoryFileException;
@@ -82,6 +66,21 @@ import org.springframework.web.servlet.HandlerMapping;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 import org.springframework.web.util.UriUtils;
 
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.EOFException;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+
 @Controller
 @Scope("request")
 @RequestMapping("/wiews")
@@ -506,8 +505,6 @@ public class WiewsController extends BaseController {
     public String uploadFile(@RequestParam MultipartFile file, @PathVariable String wiewsCode, @RequestParam String repositoryPath,
                              RedirectAttributes redirectAttributes) throws IOException {
 
-        //check user permissions
-        instituteService.getInstituteForEdit(wiewsCode);
         final String mimeType = file.getContentType();
 
         try {
@@ -610,7 +607,6 @@ public class WiewsController extends BaseController {
 		model.addAttribute("thumbnailFormat", "200x200");
 		model.addAttribute("imageGallery", imageGallery);
 		model.addAttribute("wiewsCode", wiewsCode);
-		model.addAttribute("gallerySubPath", gallerySubPath);
 
 		return MANAGE_FILES_JSP_PATH + "/gallery/details";
 	}
@@ -644,19 +640,30 @@ public class WiewsController extends BaseController {
 		}
 
 		redirectAttributes.addFlashAttribute("successMessage", "repository.gallery.successfully-updated");
-		return "redirect:/wiews/" + wiewsCode +"/files/gallery";
+		return "redirect:/wiews/" + wiewsCode + "/files/gallery";
 	}
 
 	@PostMapping(value = "{wiewsCode}/files/gallery/delete")
-	public String deleteFile(@RequestParam	String galleryPath, RedirectAttributes redirectAttributes, @PathVariable("wiewsCode") String wiewsCode) throws InvalidRepositoryPathException {
+	public String deleteFile(@RequestParam String galleryPath, RedirectAttributes redirectAttributes, @PathVariable("wiewsCode") String wiewsCode) throws InvalidRepositoryPathException {
         //check user permissions
         instituteService.getInstituteForEdit(wiewsCode);
 
-        ImageGallery imageGallery = imageGalleryService.loadImageGallery(galleryPath);
+		ImageGallery imageGallery = imageGalleryService.loadImageGallery(galleryPath);
 		imageGalleryService.removeGallery(imageGallery);
 
 		redirectAttributes.addFlashAttribute("successMessage", "repository.gallery.removed");
-		return "redirect:/wiews/" + wiewsCode +"/files/gallery";
+		return "redirect:/wiews/" + wiewsCode + "/files/gallery";
+	}
+
+	@RequestMapping(value = "{wiewsCode}/files/download/metadata")
+	public void downloadMetadata(@PathVariable("wiewsCode") String wiewsCode, HttpServletResponse response) throws IOException {
+
+		final String repositoryPath = "/wiews/" + wiewsCode;
+
+		response.setHeader("Content-Disposition", "attachment; filename=" + wiewsCode +"_files_metadata.csv ");
+
+		genesysService.downloadFilesMetadata(response, repositoryPath);
+
 	}
 
 	@InitBinder

src/main/java/org/genesys2/spring/config/ApplicationConfig.java

@@ -63,6 +63,7 @@ public class ApplicationConfig {
 
 		final List<Resource> locations = new ArrayList<>();
 		locations.add(new ClassPathResource("application.properties"));
+		locations.add(new ClassPathResource("files-metadata.properties"));
 		locations.add(new ClassPathResource("genesys.properties"));
 		final String extraConfigFile = System.getenv("config.file");
 

src/main/resources/application.properties

@@ -43,14 +43,6 @@ base.cookie-http-only=true
 # robots.txt
 robots.allow=false
 
-db.url=jdbc:mysql://localhost/genesys?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
-db.driverClassName=com.mysql.jdbc.Driver
-db.username=root
-db.password=
-db.showSql=false
-db.hbm2ddl=false
-hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
-
 google.api.key=AIzaSyBEvPuc8j5ps5GDQ3tdnTJaffKhfOdxFVc
 google.url.shortener=https://www.googleapis.com/urlshortener/v1/url
 news.menu.abbreviate.length=22

src/main/resources/content/language.properties

@@ -866,6 +866,7 @@ repository.file.dateSubmitted=Date of submission
 repository.file.lastModifiedDate=Last modified date
 
 file.upload-file=Upload file
+file.download-metadata=Download metadata
 file.upload-file.help=Select file for upload from local computer
 file.manage-files=Manage files
 

src/main/resources/content/language_ar.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=البحث في جينيسيس
 welcome.networks=الشبكات
 
 geo.country=الدولة:
+file.download-metadata=تنزيل البيانات الوصفية
+file.download-metadata=تنزيل البيانات الوصفية
 article.is.template=هو القالب:

src/main/resources/content/language_de.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=Genesys durchsuchen
 welcome.networks=Netzwerke
 
 geo.country=Land:
+file.download-metadata=Metadaten herunterladen
+file.download-metadata=Metadaten herunterladen
 article.is.template=Ist Vorlage:

src/main/resources/content/language_en.properties

@@ -13,4 +13,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #-------------------------------------------------------------------------------
-
+file.download-metadata=Download metadata

src/main/resources/content/language_es.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=Buscar en Genesys
 welcome.networks=Redes
 
 geo.country=País:
+file.download-metadata=Descargar metadatos
+file.download-metadata=Descargar metadatos
 article.is.template=Es plantilla:

src/main/resources/content/language_fa.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=جستجو در Genesys
 welcome.networks=شبکه‌ها
 
 geo.country=کشور:
+file.download-metadata=دانلود ابرداده
+file.download-metadata=دانلود ابرداده
 article.is.template=الگو است:

src/main/resources/content/language_fr.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=Recherche sur Genesys
 welcome.networks=Réseaux
 
 geo.country=Pays :
+file.download-metadata=Télécharger les métadonnées
+file.download-metadata=Télécharger les métadonnées
 article.is.template=Est-ce que le modèle:

src/main/resources/content/language_pt.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=Pesquisar no Genesys
 welcome.networks=Redes
 
 geo.country=País:
+file.download-metadata=Baixar metadados
+file.download-metadata=Baixar metadados
 article.is.template=É modelo:

src/main/resources/content/language_ru.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=Поиск по Genesys
 welcome.networks=Сети
 
 geo.country=Страна:
+file.download-metadata=Загрузить метаданные
+file.download-metadata=Загрузить метаданные
 article.is.template=Шаблон:

src/main/resources/content/language_zh.properties

@@ -858,4 +858,6 @@ welcome.search-genesys=搜索Genesys
 welcome.networks=网站
 
 geo.country=国家/地区:
+file.download-metadata=下載元數據
+file.download-metadata=下載元數據
 article.is.template=是模板

src/main/resources/files-metadata.properties

+files.metadata.fields=originalFilename,extension,title,subject,description,creator,created,license,contentType

src/main/webapp/WEB-INF/jsp/wiews/files/index.jsp

@@ -82,6 +82,13 @@
     </tbody>
 </table>
 
+<form style="padding-bottom: 5px;" action="<c:url value="/wiews/${wiewsCode}/files/download/metadata"><c:param name="${_csrf.parameterName}" value="${_csrf.token}" /></c:url>"
+      method="post" enctype="multipart/form-data" class="">
+    <input type="hidden" name="wiewsCode" value="${wiewsCode}"/>
+    <input type="hidden" name="repositoryPath" value="${currentPath}"/>
+    <button type="submit" class="btn btn-primary"><spring:message code="file.download-metadata"/></button>
+</form>
+
 <form action="<c:url value="/wiews/${wiewsCode}/upload-file"><c:param name="${_csrf.parameterName}" value="${_csrf.token}" /></c:url>"
       method="post" enctype="multipart/form-data" class="">