Fixed typo (dublInst->duplSite) in DWCA export, added names.csv

src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepository.java

@@ -45,4 +45,6 @@ public interface GenesysLowlevelRepository {
 	void listAccessionsColl(String code, RowCallbackHandler rowCallbackHandler);
 
 	void listMetadataAccessions(long id, RowCallbackHandler rowCallbackHandler);
+
+	void listAccessionsAlias(String code, RowCallbackHandler rowCallbackHandler);
 }

src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepositoryImpl.java

@@ -209,7 +209,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 			@Override
 			public PreparedStatement createPreparedStatement(Connection con) throws SQLException {
 				PreparedStatement stmt = con
-						.prepareStatement("select a.id, a.uuid, a.instCode, a.acceNumb, a.genus, t.species, a.orgCty, a.acqSrc, a.acqDate, a.mlsStat, a.available, a.storage, a.sampStat, a.dublInst, a.createdBy, a.createdDate, a.lastModifiedBy, a.lastModifiedDate from accession a left outer join taxonomy t on t.id=a.taxonomyId where a.instCode = ?");
+						.prepareStatement("select a.id, a.uuid, a.instCode, a.acceNumb, a.genus, t.species, a.orgCty, a.acqSrc, a.acqDate, a.mlsStat, a.available, a.storage, a.sampStat, a.duplSite, a.createdBy, a.createdDate, a.lastModifiedBy, a.lastModifiedDate from accession a left outer join taxonomy t on t.id=a.taxonomyId where a.instCode = ?");
 				stmt.setString(1, instCode);
 				// Set mysql JConnector to stream results
 				stmt.setFetchSize(Integer.MIN_VALUE);
@@ -233,6 +233,21 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 		}, rowCallbackHandler);
 	}
 
+	@Override
+	public void listAccessionsAlias(final String instCode, RowCallbackHandler rowCallbackHandler) {
+		jdbcTemplate.query(new PreparedStatementCreator() {
+			@Override
+			public PreparedStatement createPreparedStatement(Connection con) throws SQLException {
+				PreparedStatement stmt = con
+						.prepareStatement("select a.id, n.instCode, n.name, n.aliasType, n.lang, n.version from accessionalias n inner join accession a on a.id=n.accessionId where a.instCode = ?");
+				stmt.setString(1, instCode);
+				// Set mysql JConnector to stream results
+				stmt.setFetchSize(Integer.MIN_VALUE);
+				return stmt;
+			}
+		}, rowCallbackHandler);
+	}
+
 	@Override
 	public void listAccessionsColl(final String instCode, RowCallbackHandler rowCallbackHandler) {
 		jdbcTemplate.query(new PreparedStatementCreator() {

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

@@ -36,6 +36,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionAlias;
+import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.genesys2.server.model.genesys.AccessionBreeding;
 import org.genesys2.server.model.genesys.AccessionCollect;
 import org.genesys2.server.model.genesys.AccessionExchange;
@@ -661,7 +662,15 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		zos.closeEntry();
 
 		// AccessionGeo
-		ZipEntry entry = new ZipEntry("geo.csv");
+		ZipEntry entry = new ZipEntry("names.csv");
+		entry.setComment("Accession Names");
+		entry.setTime(System.currentTimeMillis());
+		zos.putNextEntry(entry);
+		writeAccessionsNames(faoInstitute, zos);
+		zos.closeEntry();
+
+		// AccessionGeo
+		entry = new ZipEntry("geo.csv");
 		entry.setComment("GIS information");
 		entry.setTime(System.currentTimeMillis());
 		zos.putNextEntry(entry);
@@ -705,6 +714,18 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		osw.write("\t<field index=\"17\" term=\"lastModifiedDate\"/>\n");
 		osw.write("</core>\n");
 
+		osw.write("<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+		osw.write("\t<files><location>");
+		osw.write("names.csv");
+		osw.write("</location></files>\n");
+		osw.write("\t<coreid index=\"0\" />\n");
+		osw.write("\t<field index=\"1\" term=\"instCode\"/>\n");
+		osw.write("\t<field index=\"2\" term=\"name\"/>\n");
+		osw.write("\t<field index=\"3\" term=\"aliasType\"/>\n");
+		osw.write("\t<field index=\"4\" term=\"lang\"/>\n");
+		osw.write("\t<field index=\"5\" term=\"version\"/>\n");
+		osw.write("</extension>\n");
+
 		osw.write("<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 		osw.write("\t<files><location>");
 		osw.write("geo.csv");
@@ -746,7 +767,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
 		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "orgCty", "acqSrc", "acqDate", "mlsStat", "available",
-				"storage", "sampStat", "dublInst", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
+				"storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
 
 		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
 
@@ -797,6 +818,42 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		csv.flush();
 	}
 
+	private void writeAccessionsNames(final FaoInstitute faoInstitute, ZipOutputStream zos) throws IOException {
+		@SuppressWarnings("resource")
+		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
+		csv.writeNext(new String[] { "genesysId", "instCode", "name", "aliasType", "lang", "version" });
+
+		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
+
+		// Write accession information
+		genesysLowlevelRepository.listAccessionsAlias(faoInstitute.getCode(), new RowCallbackHandler() {
+			int i = 0;
+
+			@Override
+			public void processRow(ResultSet rs) throws SQLException {
+				try {
+					String[] r = csvResultsetHelper.getColumnValues(rs);
+					if (r[3] != null) {
+						try {
+							AliasType aliasType = AliasType.getType(Integer.parseInt(r[3]));
+							r[3] = aliasType.name();
+						} catch (NumberFormatException e) {
+							LOG.warn(e.getMessage());
+						}
+					}
+					csv.writeNext(r);
+				} catch (IOException e) {
+					LOG.error("Reading resultset for DWCA aliases ", e);
+				}
+				if ((i++ % 5000) == 0) {
+					LOG.info("Writing alias DWCA " + faoInstitute.getCode() + " " + i);
+				}
+			}
+		});
+
+		csv.flush();
+	}
+
 	private void writeAccessionsColl(final FaoInstitute faoInstitute, ZipOutputStream zos) throws IOException {
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
@@ -909,13 +966,12 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 
 		zos.finish();
 	}
-	
 
 	private void writeDatasetCore(final Metadata metadata, ZipOutputStream zos) throws IOException {
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos), 4096), ',', '"', '\\', "\n");
 		csv.writeNext(new String[] { "coreId", "instCode", "acceNumb", "genus" });
-		
+
 		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
 
 		// Write accession information
@@ -943,7 +999,6 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		csv.flush();
 	}
 
-
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR')")