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Genesys Backend
Genesys Backend
Commit 96bae2b8 authored by Maxym Borodenko's avatar Maxym Borodenko
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Added new API endpoints for downloading MCPD of selected accessions; 

Updated generating methods;
parent fb418b1b
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Showing with 128 additions and 59 deletions
src/main/java/org/genesys2/server/api/v1/AccessionController.java
View file @ 96bae2b8
......@@ -486,6 +486,51 @@ public class AccessionController {
}
}
@PreAuthorize("isAuthenticated()")
@RequestMapping(value = "/download-selected", method = RequestMethod.POST, params = { "mcpd" })
public void downloadMcpdByUuids(@RequestParam(value="uuids", required = true) Set<UUID> uuids, HttpServletResponse response) throws IOException {
// Create JSON filter
AccessionFilter filter = new AccessionFilter();
filter.uuid().addAll(uuids);
final long countFiltered = accessionService.countAccessions(filter);
if (countFiltered > DOWNLOAD_LIMIT) {
throw new InvalidApiUsageException("Refusing to export more than " + DOWNLOAD_LIMIT + " entries");
}
// Write MCPD to the stream.
response.setContentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-selected-%1s.xlsx\"", System.currentTimeMillis()));
final OutputStream outputStream = response.getOutputStream();
try {
downloadService.writeXlsxMCPD(filter, outputStream, null, null);
response.flushBuffer();
} catch (EOFException e) {
LOG.warn("Download was aborted: {}", e.getMessage());
}
}
@RequestMapping(value = "/download-selected", method = RequestMethod.POST, params = { "dwca" })
public void downloadDwcaByUuids(@RequestParam(value="uuids", required = true) Set<UUID> uuids, HttpServletResponse response) throws Exception {
// Create JSON filter
AccessionFilter filter = new AccessionFilter();
filter.uuid().addAll(uuids);
final long countFiltered = accessionService.countAccessions(filter);
if (countFiltered > DOWNLOAD_LIMIT) {
throw new InvalidApiUsageException("Refusing to export more than " + DOWNLOAD_LIMIT + " entries");
}
// Write Darwin Core Archive to the stream.
response.setContentType("application/zip");
response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-selected-%1$s.zip\"", System.currentTimeMillis()));
final OutputStream outputStream = response.getOutputStream();
genesysService.writeAccessions(filter, outputStream, null, null);
response.flushBuffer();
}
@PreAuthorize("isAuthenticated()")
@RequestMapping(value = "/download", method = RequestMethod.POST, params = { "mcpd" })
public void downloadMcpd(@RequestParam(value = "f", required = false, defaultValue = "") String filterCode, @RequestParam(value="filter", required = false) AccessionFilter filter, HttpServletResponse response) throws IOException {
......@@ -505,7 +550,7 @@ public class AccessionController {
final OutputStream outputStream = response.getOutputStream();
try {
downloadService.writeXlsxMCPD(filterInfo.filter, outputStream);
downloadService.writeXlsxMCPD(filterInfo.filter, outputStream, filterInfo.filterCode, "/a/" + filterInfo.filterCode);
response.flushBuffer();
} catch (EOFException e) {
LOG.warn("Download was aborted: {}", e.getMessage());
......@@ -532,7 +577,7 @@ public class AccessionController {
final OutputStream outputStream = response.getOutputStream();
try {
downloadService.writeXlsxPDCI(filterInfo.filter, outputStream);
downloadService.writeXlsxPDCI(filterInfo.filter, outputStream, filterInfo.filterCode, "/a/" + filterInfo.filterCode);
response.flushBuffer();
} catch (EOFException e) {
LOG.warn("Download was aborted: {}", e.getMessage());
......@@ -555,7 +600,7 @@ public class AccessionController {
response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-%1$s.zip\"", filterInfo.filterCode));
final OutputStream outputStream = response.getOutputStream();
genesysService.writeAccessions(filterInfo.filter, outputStream);
genesysService.writeAccessions(filterInfo.filter, outputStream, filterInfo.filterCode, "/a/" + filterInfo.filterCode);
response.flushBuffer();
}
......
src/main/java/org/genesys2/server/api/v1/InstituteController.java
View file @ 96bae2b8
......@@ -200,7 +200,7 @@ public class InstituteController {
response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-%1$s.zip\"", faoInstitute.getCode()));
final OutputStream outputStream = response.getOutputStream();
genesysService.writeAccessions(filter, outputStream);
genesysService.writeAccessions(filter, outputStream, null, "/wiews/" + faoInstitute.getCode());
response.flushBuffer();
}
......@@ -224,7 +224,7 @@ public class InstituteController {
final OutputStream outputStream = response.getOutputStream();
try {
downloadService.writeXlsxPDCI(filter, outputStream);
downloadService.writeXlsxPDCI(filter, outputStream, null, "/wiews/" + faoInstitute.getCode());
response.flushBuffer();
} catch (EOFException e) {
LOG.warn("Download was aborted", e);
......@@ -251,7 +251,7 @@ public class InstituteController {
final OutputStream outputStream = response.getOutputStream();
try {
downloadService.writeXlsxMCPD(filter, outputStream);
downloadService.writeXlsxMCPD(filter, outputStream, null, "/wiews/" + faoInstitute.getCode());
response.flushBuffer();
} catch (EOFException e) {
LOG.warn("Download was aborted", e);
......
src/main/java/org/genesys2/server/service/DownloadService.java
View file @ 96bae2b8
......@@ -39,15 +39,15 @@ import org.genesys2.server.service.filter.AccessionFilter;
*/
public interface DownloadService {
void writeXlsxMCPD(AccessionFilter accessionFilter, OutputStream outputStream) throws IOException;
void writeXlsxMCPD(AccessionFilter accessionFilter, OutputStream outputStream, String shortFilter, String dataSource) throws IOException;
void writeXlsxMCPD(Predicate predicate, OutputStream outputStream, String filters, String dataSource) throws IOException;
void writeXlsxMCPD(Predicate predicate, OutputStream outputStream, String shortFilter, String dataSource) throws IOException;
void writeXlsxMCPD(JPQLQuery<Long> queryAccessionId, OutputStream outputStream, String filters, String dataSource) throws IOException;
void writeXlsxMCPD(JPQLQuery<Long> queryAccessionId, OutputStream outputStream, String shortFilter, String dataSource) throws IOException;
void writeXlsxMCPD(IDownloadAction action, OutputStream outputStream, String filters, String dataSource) throws IOException;
void writeXlsxMCPD(IDownloadAction action, OutputStream outputStream, String shortFilter, String dataSource) throws IOException;
void writeXlsxPDCI(AccessionFilter accessionFilter, OutputStream outputStream) throws IOException;
void writeXlsxPDCI(AccessionFilter accessionFilter, OutputStream outputStream, String shortFilter, String dataSource) throws IOException;
void writeXlsxDescriptor(List<Descriptor> descriptors, OutputStream outputStream) throws IOException;
......
src/main/java/org/genesys2/server/service/GenesysService.java
View file @ 96bae2b8
......@@ -152,7 +152,7 @@ public interface GenesysService {
long countDatasets(FaoInstitute faoInstitute);
void writeAccessions(AccessionFilter filter, OutputStream outputStream) throws Exception;
void writeAccessions(AccessionFilter filter, OutputStream outputStream, String shortFilter, String dataSource) throws Exception;
List<AccessionGeo> listAccessionsGeo(Set<Long> copy);
......
src/main/java/org/genesys2/server/service/impl/DownloadServiceImpl.java
View file @ 96bae2b8
......@@ -21,7 +21,6 @@ import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URLEncoder;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.text.MessageFormat;
......@@ -168,9 +167,6 @@ public class DownloadServiceImpl implements DownloadService {
@Autowired
private TraitService traitService;
@Value("${base.url}")
private String baseUrl;
@Value("${frontend.url}")
private String frontendUrl;
......@@ -197,9 +193,7 @@ public class DownloadServiceImpl implements DownloadService {
}
@Override
public void writeXlsxMCPD(AccessionFilter filter, OutputStream outputStream) throws IOException {
final String dataSource = baseUrl + "/explore?filter=" + filter.toString();
public void writeXlsxMCPD(AccessionFilter filter, OutputStream outputStream, String shortFilter, String dataSource) throws IOException {
if (filter.isFulltextQuery()) {
writeXlsxMCPD((action) -> {
try {
......@@ -208,14 +202,14 @@ public class DownloadServiceImpl implements DownloadService {
} catch (Exception e) {
LOG.warn("Error generating: {}", e.getMessage());
}
}, outputStream, filter.toString(), dataSource);
}, outputStream, shortFilter, dataSource);
} else {
writeXlsxMCPD(filter.buildPredicate(), outputStream, filter.toString(), dataSource);
writeXlsxMCPD(filter.buildPredicate(), outputStream, shortFilter, dataSource);
}
}
@Override
public void writeXlsxMCPD(Predicate predicate, OutputStream outputStream, String filters, String dataSource) throws IOException {
public void writeXlsxMCPD(Predicate predicate, OutputStream outputStream, String shortFilter, String dataSource) throws IOException {
PathBuilder<Accession> builder = new PathBuilderFactory().create(Accession.class);
Querydsl querydsl = new Querydsl(entityManager, builder);
JPQLQuery<Long> query = querydsl.createQuery(QAccession.accession)
......@@ -227,11 +221,11 @@ public class DownloadServiceImpl implements DownloadService {
// apply filter
query.where(predicate);
writeXlsxMCPD(query, outputStream, filters, dataSource);
writeXlsxMCPD(query, outputStream, shortFilter, dataSource);
}
@Override
public void writeXlsxMCPD(JPQLQuery<Long> queryAccessionId, OutputStream outputStream, String filters, String dataSource) throws IOException {
public void writeXlsxMCPD(JPQLQuery<Long> queryAccessionId, OutputStream outputStream, String shortFilter, String dataSource) throws IOException {
writeXlsxMCPD((action) -> {
try {
accessionProcessor.process(queryAccessionId, action, null);
......@@ -239,11 +233,11 @@ public class DownloadServiceImpl implements DownloadService {
} catch (Exception e) {
LOG.warn("Error generating: {}", e.getMessage());
}
}, outputStream, filters, dataSource);
}, outputStream, shortFilter, dataSource);
}
@Override
public void writeXlsxMCPD(IDownloadAction action, OutputStream outputStream, String filters, String dataSource) throws IOException {
public void writeXlsxMCPD(IDownloadAction action, OutputStream outputStream, String shortFilter, String dataSource) throws IOException {
XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/MCPD.xlsx"));
POIXMLProperties props = template.getProperties();
......@@ -251,7 +245,9 @@ public class DownloadServiceImpl implements DownloadService {
coreProp.setCreated(new Nullable<Date>(new Date()));
POIXMLProperties.CustomProperties custProp = props.getCustomProperties();
custProp.addProperty("Filter", filters);
if (StringUtils.isNotBlank(shortFilter)) {
custProp.addProperty("Filter", shortFilter);
}
custProp.addProperty("Genesys URL", frontendUrl);
// keep 50 rows in memory, exceeding rows will be flushed to disk
......@@ -262,23 +258,30 @@ public class DownloadServiceImpl implements DownloadService {
Sheet legal = wb.getXSSFSheet("Legal information");
Row r;
Cell c;
r = legal.createRow(0);
int row = 0;
r = legal.createRow(row++);
r.createCell(0).setCellValue("Server URL");
r.createCell(1).setCellValue(frontendUrl);
r = legal.createRow(1);
r.createCell(0).setCellValue("Filters");
r.createCell(1).setCellValue(filters);
r = legal.createRow(2);
r.createCell(0).setCellValue("Data source");
c = r.createCell(1);
c.setCellValue(dataSource);
r = legal.createRow(3);
if (StringUtils.isNotBlank(shortFilter)) {
r = legal.createRow(row++);
r.createCell(0).setCellValue("Filters");
r.createCell(1).setCellValue(shortFilter);
}
if (StringUtils.isNotBlank(dataSource)) {
r = legal.createRow(row++);
r.createCell(0).setCellValue("Data source");
c = r.createCell(1);
c.setCellValue(frontendUrl + dataSource);
}
r = legal.createRow(row++);
r.createCell(0).setCellValue("Date");
c = r.createCell(1);
c.setCellStyle(dateStyle);
c.setCellValue(new Date());
r = legal.createRow(4);
r = legal.createRow(row);
r.createCell(0).setCellValue("Attribution");
r.createCell(1).setCellValue(frontendUrl + "/content/terms");
......@@ -787,7 +790,7 @@ public class DownloadServiceImpl implements DownloadService {
}
@Override
public void writeXlsxPDCI(final AccessionFilter filter, final OutputStream outputStream) throws IOException {
public void writeXlsxPDCI(final AccessionFilter filter, final OutputStream outputStream, String shortFilter, String dataSource) throws IOException {
XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/PDCI.xlsx"));
......@@ -801,22 +804,29 @@ public class DownloadServiceImpl implements DownloadService {
Sheet legal = wb.getXSSFSheet("Legal information");
Row r;
Cell c;
r = legal.createRow(0);
int row = 0;
r = legal.createRow(row++);
r.createCell(0).setCellValue("Server URL");
updateCellUrl(r, 1, frontendUrl);
r = legal.createRow(1);
r.createCell(0).setCellValue("Filters");
r.createCell(1).setCellValue(filter.toString());
r = legal.createRow(2);
r.createCell(0).setCellValue("Data source");
updateCellUrl(r, 1, baseUrl + "/explore?filter=" + URLEncoder.encode(filter.toString(), "UTF-8"));
r = legal.createRow(3);
if (StringUtils.isNotBlank(shortFilter)) {
r = legal.createRow(row++);
r.createCell(0).setCellValue("Filters");
r.createCell(1).setCellValue(shortFilter);
}
if (StringUtils.isNotBlank(dataSource)) {
r = legal.createRow(row++);
r.createCell(0).setCellValue("Data source");
updateCellUrl(r, 1, frontendUrl + dataSource);
}
r = legal.createRow(row++);
r.createCell(0).setCellValue("Date");
c = r.createCell(1);
c.setCellStyle(dateStyle);
c.setCellValue(new Date());
r = legal.createRow(4);
r = legal.createRow(row);
r.createCell(0).setCellValue("Attribution");
updateCellUrl(r, 1, frontendUrl + "/content/terms");
......
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @ 96bae2b8
......@@ -41,6 +41,7 @@ import java.util.zip.ZipOutputStream;
import javax.persistence.EntityManager;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.genesys.blocks.security.SecurityContextUtil;
import org.genesys.blocks.security.model.AclSid;
import org.genesys.blocks.security.service.CustomAclService;
......@@ -105,6 +106,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.dao.IncorrectResultSizeDataAccessException;
import org.springframework.data.domain.Page;
......@@ -131,6 +133,9 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
public static final Logger LOG = LoggerFactory.getLogger(GenesysServiceImpl.class);
@Value("${frontend.url}")
private String frontendUrl;
@Autowired
private EntityManager entityManager;
......@@ -1072,19 +1077,23 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
@Override
// TODO FIXME Need proper term URLs
public void writeAccessions(final AccessionFilter filter, final OutputStream outputStream) throws Exception {
public void writeAccessions(final AccessionFilter filter, final OutputStream outputStream, String shortFilter, String dataSource) throws Exception {
// UTF8 is used for encoding entry names
final ZipOutputStream zos = new ZipOutputStream(outputStream);
zos.setComment("Genesys Accessions filter=" + filter);
final StringBuilder commentBuilder = new StringBuilder("Genesys Accessions");
if (StringUtils.isNotBlank(shortFilter)) {
commentBuilder.append(" ").append("filter=").append(shortFilter);
}
zos.setComment(commentBuilder.toString());
zos.flush();
// Filter information
final ZipEntry readmeEntry = new ZipEntry("README.txt");
readmeEntry.setComment("Extra iformation");
readmeEntry.setComment("Extra information");
readmeEntry.setTime(System.currentTimeMillis());
zos.putNextEntry(readmeEntry);
writeREADME(filter, zos);
writeREADME(zos, shortFilter, dataSource);
zos.closeEntry();
zos.flush();
......@@ -1206,19 +1215,24 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
outputStream.flush();
}
private void writeREADME(AccessionFilter filter, ZipOutputStream zos) throws IOException {
private void writeREADME(ZipOutputStream zos, String shortFilter, String dataSource) throws IOException {
final BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(zos));
bw.write("Date:\t");
bw.write(new Date().toString());
bw.write("\n");
bw.write("Filter:\t");
bw.write(filter.toString());
bw.write("\n");
if (StringUtils.isNotBlank(shortFilter)) {
bw.write("Filter:\t");
bw.write(shortFilter);
bw.write("\n");
}
bw.write("URL:\thttps://www.genesys-pgr.org/explore?filter=");
bw.write(filter.toString());
bw.write("\n");
if (StringUtils.isNotBlank(dataSource)) {
bw.write("URL:\t");
bw.write(frontendUrl);
bw.write(dataSource);
bw.write("\n");
}
bw.write("Attribution:\t");
bw.write("https://www.genesys-pgr.org/content/terms");
......
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