Merge branch 'genesy1-migration-to-catalog' into 'master'

Genesy1 migration to catalog

See merge request genesys-pgr/genesys-server!318

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

@@ -27,6 +27,8 @@ import java.util.UUID;
 import javax.persistence.EntityManager;
 import javax.validation.Valid;
 
+import org.apache.commons.lang3.StringUtils;
+import org.codehaus.jackson.map.ObjectMapper;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.filters.DescriptorFilter;
@@ -61,10 +63,11 @@ import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Isolation;
 import org.springframework.transaction.annotation.Transactional;
+import org.springframework.validation.annotation.Validated;
 
+import com.google.common.collect.Lists;
 import com.querydsl.core.BooleanBuilder;
 import com.querydsl.core.types.Predicate;
-import org.springframework.validation.annotation.Validated;
 
 /**
  * The Class DescriptorServiceImpl.
@@ -74,6 +77,8 @@ import org.springframework.validation.annotation.Validated;
 @Validated
 public class DescriptorServiceImpl implements DescriptorService {
 
+	private static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[] {};
+
 	/** The Constant LOG. */
 	private static final Logger LOG = LoggerFactory.getLogger(org.genesys.catalog.service.impl.DescriptorServiceImpl.class);
 
@@ -125,8 +130,33 @@ public class DescriptorServiceImpl implements DescriptorService {
 	@Override
 	@PostFilter("hasRole('ADMINISTRATOR') or filterObject.published or hasPermission(filterObject, 'READ')")
 	public List<Descriptor> searchMatchingDescriptor(final Descriptor input) {
-		final Predicate predicate = descriptor.category.in(input.getCategory()).and(descriptor.dataType.in(input.getDataType())).and(descriptor.crop.eq(input.getCrop()))
-				.and(descriptor.versionTag.eq(input.getVersionTag())).and(descriptor.title.eq(input.getTitle())).and(descriptor.key.eq(input.isKey()));
+		try {
+			input.trimStringsToNull();
+			LOG.debug("searchMatching: {}", new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(input));
+		} catch (IOException e) {
+		}
+		
+		List<Predicate> searches = Lists.newArrayList();
+		// version + title
+		searches.add(descriptor.versionTag.eq(input.getVersionTag()).and(descriptor.title.eq(input.getTitle())));
+		if (StringUtils.isNotBlank(input.getDescription())) {
+			// description
+			searches.add(descriptor.description.eq(input.getDescription()));
+		}
+		if (StringUtils.isNotBlank(input.getDescription())) {
+			// title + dataType
+			searches.add(descriptor.title.eq(input.getTitle()).and(descriptor.dataType.eq(input.getDataType())));
+		}
+		if (input.getCategory() != null) {
+			// title + category
+			searches.add(descriptor.title.eq(input.getTitle()).and(descriptor.category.eq(input.getCategory())));
+		}
+		if (StringUtils.isNotBlank(input.getUom())) {
+			// uom
+			searches.add(descriptor.dataType.eq(input.getDataType()).and(descriptor.uom.eq(input.getUom())));
+		}
+		
+		final Predicate predicate = descriptor.crop.eq(input.getCrop()).andAnyOf(searches.toArray(EMPTY_PREDICATE_ARRAY));
 		List<Descriptor> matches = new ArrayList<>();
 		descriptorRepository.findAll(predicate).forEach(match -> matches.add(lazyLoad(match)));
 		return matches;

src/main/java/org/genesys2/server/api/v0/DatasetController.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.api.v0;
 
@@ -26,17 +26,27 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.stream.Collectors;
 
 import javax.servlet.http.HttpServletResponse;
 import javax.xml.bind.ValidationException;
 
+import org.apache.commons.lang3.StringUtils;
+import org.genesys.catalog.model.traits.Descriptor;
+import org.genesys.catalog.model.traits.Descriptor.Category;
+import org.genesys.catalog.model.traits.Descriptor.DataType;
+import org.genesys.catalog.model.vocab.VocabularyTerm;
 import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.api.ModelValidationException;
 import org.genesys2.server.api.OAuth2Cleanup;
+import org.genesys2.server.api.Pagination;
 import org.genesys2.server.exception.AuthorizationException;
+import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
+import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.json.Api0Constants;
@@ -45,11 +55,15 @@ import org.genesys2.server.service.DatasetService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TraitService;
+import org.genesys2.server.service.impl.DownloadServiceImpl;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Sort.Direction;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -58,6 +72,7 @@ import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.RestController;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.google.common.collect.Lists;
 
 import io.swagger.annotations.Api;
 import net.sf.oval.ConstraintViolation;
@@ -104,6 +119,99 @@ public class DatasetController extends ApiBaseController {
 		final List<Metadata> datasets = datasetService.listMyMetadata();
 		return OAuth2Cleanup.clean(datasets);
 	}
+	
+	/**
+	 * List datasets for institute
+	 *
+	 * @param provider the originator
+	 * @param pagination the pagination
+	 * @return the page
+	 */
+	@GetMapping("/list/{wiewsCode}")
+	public Page<Metadata> listDatasets(@PathVariable("wiewsCode") String provider, Pagination pagination) {
+		return genesysService.listDatasets(provider, pagination.toPageRequest(50, Direction.ASC, "id"));
+	}
+
+	/**
+	 * List accessions.
+	 *
+	 * @param metadataId the metadata id
+	 * @param pagination the pagination
+	 * @return the page
+	 */
+	@GetMapping("/{metadataId}/accessions")
+	public Page<AccessionRef> listAccessions(@PathVariable("metadataId") long metadataId, Pagination pagination) {
+		return genesysService.listMetadataAccessionRefs(metadataId, pagination.toPageRequest(50, Direction.ASC, "a.id"));
+	}
+
+	/**
+	 * List methods.
+	 *
+	 * @param metadataId the metadata id
+	 * @return the list
+	 */
+	@GetMapping("/{metadataId}/descriptors")
+	public List<Descriptor> listMethods(@PathVariable("metadataId") long metadataId) {
+		Metadata metadata = genesysService.getMetadata(metadataId);
+		if (metadata == null) {
+			throw new NotFoundElement("No Metadata id=" + metadataId);
+		}
+		List<Method> methods = genesysService.listMethods(metadata);
+
+		return methods.stream().map(method -> {
+			Descriptor d=new Descriptor();
+			d.setColumnName(StringUtils.trimToNull(method.getFieldName()));
+			d.setTitle(StringUtils.trimToNull(method.getParameter().getTitle()));
+			d.setDescription(StringUtils.trimToNull(method.getMethod()));
+			d.setUom(StringUtils.trimToNull(method.getUnit()));
+			d.setCrop(StringUtils.trimToNull(method.getParameter().getCrop().getShortName()));
+			Category cat = Category.valueOf(DownloadServiceImpl.catalogDescriptorCategory(method.getParameter().getCategory().getName()));
+			d.setCategory(cat == null ? Category.CHARACTERIZATION : cat);
+			DataType dt = DataType.valueOf(DownloadServiceImpl.catalogDataType(method.getFieldType()));
+			d.setDataType(dt == null ? DataType.TEXT : dt);
+			d.setIntegerOnly(2 == method.getFieldType() ? Boolean.TRUE : 1 == method.getFieldType() ? Boolean.FALSE : null);
+			d.setVersionTag("genesys1");
+			if (method.isCoded()) {
+				List<VocabularyTerm> terms = Lists.newArrayList();
+				for (final TraitCode traitCode : TraitCode.parseOptions(method.getOptions())) {
+					VocabularyTerm term = new VocabularyTerm();
+					term.setCode(StringUtils.trimToNull(traitCode.getCode()));
+					term.setTitle(StringUtils.trimToNull(traitCode.getValue()));
+					terms.add(term);
+				}
+				if (terms.size() > 0) {
+					d.setTerms(terms);
+					d.setDataType(DataType.CODED);
+					d.setIntegerOnly(true);
+					
+					int minVal = Integer.MAX_VALUE;
+					int maxVal = Integer.MIN_VALUE;
+					boolean onlyInts = true, increasing = true;
+					for (VocabularyTerm term: terms) {
+						try {
+							int val = Integer.parseInt(term.getCode());
+							if (val > maxVal) {
+								maxVal = val;
+							} else {
+								increasing = false;
+							}
+							if (val < minVal) {
+								minVal = val;
+							}
+						} catch (NumberFormatException e) {
+							onlyInts = false;
+						}
+					}
+					if (onlyInts && increasing) {
+						d.setDataType(DataType.SCALE);
+						d.setMinValue((double) minVal);
+						d.setMaxValue((double) maxVal);
+					}
+				}
+			}
+			return d;
+		}).collect(Collectors.toList());
+	}
 
 	/**
 	 * Add a crop

src/main/java/org/genesys2/server/component/listener/ApplicationUpgrades.java

@@ -21,11 +21,8 @@ import org.genesys.blocks.util.ClassAclOid;
 import org.genesys.blocks.util.CurrentApplicationContext;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.persistence.PartnerRepository;
-import org.genesys.catalog.persistence.dataset.DatasetRepository;
 import org.genesys2.server.component.security.AsAdminInvoker;
 import org.genesys2.server.model.impl.FaoInstitute;
-import org.genesys2.server.persistence.SubsetRepository;
-import org.genesys2.server.persistence.kpi.ExecutionRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -58,28 +55,12 @@ public class ApplicationUpgrades implements InitializingBean {
 	 */
 	@Override
 	public void afterPropertiesSet() throws Exception {
-		kpiEnsureACL();
 		aclEnsureClassOIDs();
 		aclMakePartnersPublic();
-		aclMakeDraftsPrivate();
 	}
 	
-	@Autowired
-	private ExecutionRepository kpiExecutionRepository;
 	@Autowired
 	private CustomAclService aclService;
-	
-	protected void kpiEnsureACL() throws Exception {
-		asAdminInvoker.invoke(() -> {
-			LOG.warn("Adding ACL support to KPI Execution");
-			kpiExecutionRepository.findAll().forEach(execution -> {
-				LOG.warn("Making KPI Execution {} ACL-ready", execution.getName());
-				aclService.createOrUpdatePermissions(execution);
-			});
-			return true;
-		});
-	}
-	
 
 	private void aclEnsureClassOIDs() throws Exception {
 		asAdminInvoker.invoke(() -> {
@@ -95,7 +76,6 @@ public class ApplicationUpgrades implements InitializingBean {
 		});
 	}
 
-	
 	@Autowired
 	private PartnerRepository partnerRepository;
 	
@@ -110,29 +90,4 @@ public class ApplicationUpgrades implements InitializingBean {
 			return true;
 		});
 	}
-	
-	@Autowired
-	private DatasetRepository datasetRepository;
-	@Autowired
-	private SubsetRepository subsetRepository;
-
-	private void aclMakeDraftsPrivate() throws Exception {
-		asAdminInvoker.invoke(() -> {
-			LOG.warn("Making non-published Datasets and Subsets private, and published publicly readable");
-			
-			datasetRepository.findAll().forEach(dataset -> {
-				LOG.warn("Setting ACL for Dataset {}", dataset.getTitle());
-				aclService.makePubliclyReadable(dataset, dataset.isPublished());
-			});
-
-			subsetRepository.findAll().forEach(subset -> {
-				LOG.warn("Setting ACL for Subset {}", subset.getTitle());
-				aclService.makePubliclyReadable(subset, subset.isPublished());
-			});
-
-			LOG.warn("Datasets and Subsets are protected.");
-			return true;
-		});
-	}
-
 }

src/main/java/org/genesys2/server/mvc/WiewsController.java

@@ -288,7 +288,7 @@ public class WiewsController extends BaseController {
 			throw new ResourceNotFoundException();
 		}
 		model.addAttribute("faoInstitute", faoInstitute);
-		model.addAttribute("pagedData", genesysService.listDatasets(faoInstitute, new PageRequest(page - 1, 30)));
+		model.addAttribute("pagedData", genesysService.listDatasets(faoInstitute.getCode(), new PageRequest(page - 1, 30)));
 
 		return "/metadata/index";
 	}

src/main/java/org/genesys2/server/mvc/admin/AdminController.java

@@ -53,6 +53,8 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.persistence.FaoInstituteRepository;
 import org.genesys2.server.persistence.PDCIRepository;
+import org.genesys2.server.persistence.SubsetRepository;
+import org.genesys2.server.persistence.kpi.ExecutionRepository;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.CountryNamesUpdater;
 import org.genesys2.server.service.CropService;
@@ -545,5 +547,49 @@ public class AdminController {
 
 		return "redirect:/admin/";
 	}
+
+	@Autowired
+	private SubsetRepository subsetRepository;
+
+	@PostMapping(value = "/acl", params = { "subsets" })
+	@Transactional
+	public String aclFixSubsetAcl() throws Exception {
+
+		LOG.warn("Adding ACL for Subsets");
+		subsetRepository.findAll().forEach(subset -> {
+			LOG.warn("Setting ACL for Subset {}", subset.getTitle());
+			aclService.makePubliclyReadable(subset, subset.isPublished());
+		});
+
+		return "redirect:/admin/";
+	}
+
+	@PostMapping(value = "/acl", params = { "datasets" })
+	@Transactional
+	public String aclFixDatasetAcl() throws Exception {
+
+		LOG.warn("Adding ACL for Datasets");
+		datasetRepository.findAll().forEach(dataset -> {
+			LOG.warn("Setting ACL for Dataset {}", dataset.getTitle());
+			aclService.makePubliclyReadable(dataset, dataset.isPublished());
+		});
+
+		return "redirect:/admin/";
+	}
+	
+	@Autowired
+	private ExecutionRepository kpiExecutionRepository;
 	
+	@PostMapping(value = "/acl", params = { "kpi" })
+	@Transactional
+	public String aclFixKPIAcl() throws Exception {
+		LOG.warn("Adding ACL support to KPI Execution");
+		
+		kpiExecutionRepository.findAll().forEach(execution -> {
+			LOG.warn("Making KPI Execution {} ACL-ready", execution.getName());
+			aclService.createOrUpdatePermissions(execution);
+		});
+
+		return "redirect:/admin/";
+	}
 }

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

@@ -33,6 +33,7 @@ import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionHistoric;
 import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.AllAccnames;
 import org.genesys2.server.model.genesys.ExperimentTrait;
@@ -97,8 +98,6 @@ public interface GenesysService {
 
 	Page<Metadata> listMetadata(Pageable pageable);
 
-	Page<Metadata> listDatasets(FaoInstitute faoInstitute, Pageable pageable);
-
 	Metadata getMetadata(long metadataId);
 
 	List<Method> listMethods(Metadata metadata);
@@ -251,4 +250,8 @@ public interface GenesysService {
 
 	List<AccessionData> listActiveAndHistoric(List<UUID> accessionUuids);
 
+	Page<AccessionRef> listMetadataAccessionRefs(long metadataId, Pageable pageRequest);
+
+	Page<Metadata> listDatasets(String instCode, Pageable pageable);
+
 }

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

@@ -805,6 +805,11 @@ public class DownloadServiceImpl implements DownloadService {
 	public void writeXlsxMetadata(Metadata metadata, OutputStream outputStream) throws IOException {
 		final XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/CATALOG-DATASET.xlsx"));
 
+		template.removeSheetAt(template.getSheetIndex("creators"));
+		template.removeSheetAt(template.getSheetIndex("accessions"));
+		template.createSheet("DATA");
+		template.setSheetOrder("DATA", 0);
+		
 		final SuperSXSSFWorkbook workbook = new SuperSXSSFWorkbook(template, 50);
 		WorkbookStyles wbStyles = WorkbookStyles.create(workbook);
 
@@ -815,24 +820,26 @@ public class DownloadServiceImpl implements DownloadService {
 		String crops = metadataMethods.stream().map(method -> method.getParameter().getCrop().getShortName()).distinct().collect(Collectors.joining(";"));
 		datasetWriteMetadata(metadata, crops, datasetSheet, wbStyles);
 
-		final SuperSXSSFSheet accessionsSheet = workbook.getStreamingSheet("accessions");
-		accessionsSheet.setRowGenerator((sheet) -> {
-			genesysLowlevelRepository.listMetadataAccessions(metadata.getId(), new RowCallbackHandler() {
-				int item = 5; // data starts at 5 in the template
-
-				@Override
-				public void processRow(ResultSet rs) throws SQLException {
-					item++;
-					final Row nextRow = sheet.createRow(item);
-
-					updateCell(nextRow, 1, rs.getString(2));
-					updateCell(nextRow, 2, rs.getString(3));
-					updateCell(nextRow, 3, rs.getString(4));
-					// updateCell(nextRow, 4, accessionRef.getSpecies());
-					// updateCell(nextRow, 5, accessionRef.getDoi());
-				}
-			});
-		});
+		// final SuperSXSSFSheet accessionsSheet =
+		// workbook.getStreamingSheet("accessions");
+		// accessionsSheet.setRowGenerator((sheet) -> {
+		// genesysLowlevelRepository.listMetadataAccessions(metadata.getId(), new
+		// RowCallbackHandler() {
+		// int item = 5; // data starts at 5 in the template
+		//
+		// @Override
+		// public void processRow(ResultSet rs) throws SQLException {
+		// item++;
+		// final Row nextRow = sheet.createRow(item);
+		//
+		// updateCell(nextRow, 1, rs.getString(2));
+		// updateCell(nextRow, 2, rs.getString(3));
+		// updateCell(nextRow, 3, rs.getString(4));
+		// // updateCell(nextRow, 4, accessionRef.getSpecies());
+		// // updateCell(nextRow, 5, accessionRef.getDoi());
+		// }
+		// });
+		// });
 
 		final SuperSXSSFSheet descriptorsSheet = workbook.getStreamingSheet("descriptors");
 		descriptorsSheet.setRowGenerator((sheet) -> {
@@ -871,7 +878,7 @@ public class DownloadServiceImpl implements DownloadService {
 		// datasetWriteCreatorsSheet(dataset.getCreators(), sheet);
 		// });
 		
-		final SuperSXSSFSheet dataSheet = (SuperSXSSFSheet) workbook.createSheet("DATA");
+		final SuperSXSSFSheet dataSheet = (SuperSXSSFSheet) workbook.getStreamingSheet("DATA");
 		dataSheet.setRowGenerator((sheet) -> {
 			int item = 0;
 			SXSSFRow header = sheet.createRow(item++);
@@ -1051,7 +1058,7 @@ public class DownloadServiceImpl implements DownloadService {
 		}
 	}
 
-	private String catalogDescriptorCategory(String name) {
+	public static String catalogDescriptorCategory(String name) {
 		switch (name) {
 		case "Morphology":
 			return "CHARACTERIZATION";
@@ -1086,7 +1093,7 @@ public class DownloadServiceImpl implements DownloadService {
 		}
 	}
 
-	private String catalogDataType(int fieldType) {
+	public static String catalogDataType(int fieldType) {
 		switch (fieldType) {
 		case 0:
 			// Coded
@@ -1113,15 +1120,15 @@ public class DownloadServiceImpl implements DownloadService {
 		// 4 Title
 		updateCell(sheet.getRow(row++), col, metadata.getTitle());
 		// 5 Dataset version
-		updateCell(sheet.getRow(row++), col, "");
+		updateCell(sheet.getRow(row++), col, "genesys1");
 		// 6 Dataset description
 		updateCell(sheet.getRow(row++), col, metadata.getDescription());
 		// 7 Dataset URL
-		updateCellUrl(sheet.getRow(row++), col, "");
+		updateCellUrl(sheet.getRow(row++), col, "https://www.genesys-pgr.org/data/view/" + metadata.getId());
 		// 8 Date of registration of the dataset
 		updateCell(sheet.getRow(row++), col, metadata.getCreatedDate(), wbStyles.dateStyle);
 		// 9 License
-		updateCell(sheet.getRow(row++), col, "");
+		updateCell(sheet.getRow(row++), col, "CC-BY-NC-ND");
 		// 10 Language of the dataset
 		updateCell(sheet.getRow(row++), col, "");
 		// 11 Related resources
@@ -1133,7 +1140,7 @@ public class DownloadServiceImpl implements DownloadService {
 		 }
 
 		// 13 Dataset provider email
-		updateCellEmail(sheet.getRow(row++), col, "");
+		updateCellEmail(sheet.getRow(row++), col, "helpdesk@genesys-pgr.org");
 		// 14 Dataset provider addresss
 		updateCell(sheet.getRow(row++), col, "");
 

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

@@ -53,6 +53,7 @@ import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionHistoric;
 import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.AccessionRef;
 import org.genesys2.server.model.genesys.AccessionTrait;
 import org.genesys2.server.model.genesys.AllAccnames;
 import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
@@ -586,8 +587,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	@Override
-	public Page<Metadata> listDatasets(FaoInstitute faoInstitute, Pageable pageable) {
-		return metadataRepository.findByInstituteCode(faoInstitute.getCode(), pageable);
+	public Page<Metadata> listDatasets(String instCode, Pageable pageable) {
+		return metadataRepository.findByInstituteCode(instCode, pageable);
 	}
 
 	@Override
@@ -603,7 +604,17 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Override
 	public List<Method> listMethods(Metadata metadata) {
 		final List<Long> x = metadataMethodRepository.listMetadataMethods(metadata);
-		return x.size() == 0 ? null : methodRepository.findByIds(x);
+		if (x.size()==0) return Collections.emptyList();
+		List<Method> methods = methodRepository.findByIds(x);
+		methods.forEach(method -> { 
+			if (method.getParameter() != null) {
+				method.getParameter().getId();
+				if (method.getParameter().getCrop() != null) {
+					method.getParameter().getCrop().getId();
+				}
+			}
+		});
+		return methods;
 	}
 
 	@Override
@@ -612,6 +623,16 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		List<AccessionData> content = listAccessionData(x.getContent());
 		return new PageImpl<AccessionData>(content, pageable, x.getTotalElements());
 	}
+	
+	@Override
+	public Page<AccessionRef> listMetadataAccessionRefs(long metadataId, Pageable pageable) {
+		Page<AccessionId> x = accessionTraitRepository.listMetadataAccessions(metadataId, pageable);
+		return new PageImpl<>(x.getContent().stream().map(aid -> {
+			AccessionRef aref = new AccessionRef(accessionRepository.getOne(aid.getId()));
+			aref.setAccession(null);
+			return aref;
+		}).collect(Collectors.toList()), pageable, x.getTotalElements());
+	}
 
 	private List<AccessionData> listAccessionData(List<AccessionId> accessionIds) {
 		List<AccessionData> result = new ArrayList<AccessionData>(accessionIds.size());

src/main/webapp/WEB-INF/jsp/admin/index.jsp

@@ -192,6 +192,10 @@
   <form method="post" action="<c:url value="/admin/acl" />">
     <button type="submit" class="btn btn-default" class="btn btn-default" name="institutes" value="fix">Fix FaoInstitutes ACL</button>
     <button type="submit" class="btn btn-default" class="btn btn-default" name="repository" value="Fix">Repository ACL</button>
+    <button type="submit" class="btn btn-default" class="btn btn-default" name="kpi" value="Fix">KPI Execution ACL</button>
+    <button type="submit" class="btn btn-default" class="btn btn-default" name="datasets" value="Fix">Datasets ACL</button>
+    <button type="submit" class="btn btn-default" class="btn btn-default" name="subsets" value="Fix">Subsets ACL</button>
+
     <!-- CSRF protection -->
     <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
   </form>