DiversityTreeController.java
/*
* Copyright 2025 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.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* 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.genesys.server.api.v2.impl;
import com.google.common.collect.Sets;
import io.swagger.annotations.Api;
import org.genesys.filerepository.InvalidRepositoryFileDataException;
import org.genesys.filerepository.InvalidRepositoryPathException;
import org.genesys.server.api.ApiBaseController;
import org.genesys.server.api.FilteredPage;
import org.genesys.server.api.Pagination;
import org.genesys.server.api.v2.facade.AccessionApiService;
import org.genesys.server.api.v2.facade.DiversityTreeApiService;
import org.genesys.server.api.v2.facade.impl.DiversityTreeApiServiceImpl;
import org.genesys.server.api.v2.model.impl.AccessionDTO;
import org.genesys.server.api.v2.model.impl.DiversityTreeAccessionRefDTO;
import org.genesys.server.api.v2.model.impl.DiversityTreeDTO;
import org.genesys.server.exception.InvalidApiUsageException;
import org.genesys.server.exception.NotFoundElement;
import org.genesys.server.exception.SearchException;
import org.genesys.server.service.DiversityTreeService;
import org.genesys.server.service.ElasticsearchService;
import org.genesys.server.service.ShortFilterService;
import org.genesys.server.service.filter.AccessionFilter;
import org.genesys.server.service.filter.DiversityTreeFilter;
import org.genesys.server.service.worker.ShortFilterProcessor;
import org.genesys.spring.CSVMessageConverter;
import org.springdoc.api.annotations.ParameterObject;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Sort;
import org.springframework.http.MediaType;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.PutMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RequestPart;
import org.springframework.web.bind.annotation.RestController;
import org.springframework.web.multipart.MultipartFile;
import java.io.IOException;
import java.util.Map;
import java.util.Set;
import java.util.UUID;
@RestController("diversityTreeApi2")
@PreAuthorize("isAuthenticated()")
@RequestMapping(DiversityTreeController.CONTROLLER_URL)
@Api(tags = { "diversityTree" })
public class DiversityTreeController extends ApiBaseController {
/** The Constant CONTROLLER_URL. */
public static final String CONTROLLER_URL = ApiBaseController.APIv2_BASE + "/div-tree";
@Autowired
private DiversityTreeApiService treeApiService;
@Autowired
private DiversityTreeService treeService;
@Autowired
protected ShortFilterProcessor shortFilterProcessor;
@Autowired
private AccessionApiService accessionApiService;
/**
* Load the record by UUID
*
* @param uuid the uuid
* @return loaded record
*/
@GetMapping(value = "/{uuid}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO get(@PathVariable("uuid") final UUID uuid) {
return treeApiService.load(uuid);
}
/**
* Create a new record.
*
* @param source the source
* @return saved record
*/
@PostMapping(value = "", produces = MediaType.APPLICATION_JSON_VALUE)
public DiversityTreeDTO create(@RequestBody final DiversityTreeDTO source) {
return treeApiService.create(source);
}
/**
* Update existing record.
*
* @param source the source
* @return updated record
*/
@PutMapping(value = "", produces = MediaType.APPLICATION_JSON_VALUE)
public DiversityTreeDTO update(@RequestBody final DiversityTreeDTO source) {
return treeApiService.load(treeApiService.update(source).getUuid());
}
/**
* Remove record.
*
* @param uuid the uuid
* @param version the version
* @return removed record
*/
@DeleteMapping(value = "/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO remove(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
return treeApiService.remove(uuid, version);
}
/**
* List of records.
*
* @param page the page
* @param filter the filter
* @return the page
* @throws IOException
*/
@PostMapping(value = "/list", produces = { MediaType.APPLICATION_JSON_VALUE })
public FilteredPage<DiversityTreeDTO, DiversityTreeFilter> list(@RequestParam(name = "f", required = false) String filterCode, @ParameterObject final Pagination page,
@RequestBody(required = false) DiversityTreeFilter filter) throws IOException, SearchException {
ShortFilterService.FilterInfo<DiversityTreeFilter> filterInfo = shortFilterProcessor.processFilter(filterCode, filter, DiversityTreeFilter.class);
return new FilteredPage<>(filterInfo.filterCode, filterInfo.filter, treeApiService.list(filterInfo.filter, page.toPageRequest(MAX_PAGE_SIZE, DEFAULT_PAGE_SIZE, Sort.Direction.ASC, "id")));
}
/**
* List of records by filterCode or filter with suggestions
*
* @param page the page
* @param filterCode short filter code
* @param filter the filter
* @return the page with suggestions
* @throws IOException
*/
@PostMapping(value = "/filter", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeApiServiceImpl.DiversityTreeSuggestionPageDTO listSuggestions(@RequestParam(name = "f", required = false) String filterCode, @ParameterObject final Pagination page,
@RequestBody(required = false) DiversityTreeFilter filter) throws IOException, SearchException {
ShortFilterService.FilterInfo<DiversityTreeFilter> filterInfo = shortFilterProcessor.processFilter(filterCode, filter, DiversityTreeFilter.class);
FilteredPage<DiversityTreeDTO, DiversityTreeFilter> pageRes = new FilteredPage<>(filterInfo.filterCode, filterInfo.filter, treeApiService.list(filterInfo.filter, page.toPageRequest(MAX_PAGE_SIZE, DEFAULT_PAGE_SIZE, Sort.Direction.ASC, "id")));
Map<String, ElasticsearchService.TermResult> suggestionRes = treeService.getSuggestions(filterInfo.filter);
return DiversityTreeApiServiceImpl.DiversityTreeSuggestionPageDTO.from(pageRes, suggestionRes);
}
/**
* My trees.
*
* @param page the page
* @param filter the descriptor filter
* @return the page
* @throws IOException
*/
@PostMapping(value = "/list-mine", produces = { MediaType.APPLICATION_JSON_VALUE })
public FilteredPage<DiversityTreeDTO, DiversityTreeFilter> myTrees(@RequestParam(name = "f", required = false) String filterCode, @ParameterObject final Pagination page,
@RequestBody(required = false) DiversityTreeFilter filter) throws IOException {
ShortFilterService.FilterInfo<DiversityTreeFilter> filterInfo = shortFilterProcessor.processFilter(filterCode, filter, DiversityTreeFilter.class);
return new FilteredPage<>(filterInfo.filterCode, filterInfo.filter, treeApiService.listForCurrentUser(filterInfo.filter, page.toPageRequest(MAX_PAGE_SIZE, DEFAULT_PAGE_SIZE, Sort.Direction.DESC, "lastModifiedDate")));
}
/**
* Load AccessionRef list by tree
*
* @param uuid the uuid of tree
* @param page Pageable
* @return the page
* @throws NotFoundElement
*/
@GetMapping(value = "/accessions/{uuid}", produces = { MediaType.APPLICATION_JSON_VALUE, CSVMessageConverter.TEXT_CSV_VALUE })
public Page<DiversityTreeAccessionRefDTO> listAccessions(@PathVariable("uuid") final UUID uuid, @ParameterObject final Pagination page) throws NotFoundElement {
return treeApiService.listAccessions(uuid, page.toPageRequest(MAX_PAGE_SIZE, DEFAULT_PAGE_SIZE));
}
/**
* Load full accessions list by DiversityTree
*
* @param uuid uuid of DiversityTree
* @param page Pageable
* @return the page
* @throws NotFoundElement
*/
@GetMapping(value = "/accessions/{uuid}", produces = { MediaType.APPLICATION_JSON_VALUE, CSVMessageConverter.TEXT_CSV_VALUE }, params = { "full" })
public Page<AccessionDTO> listFullAccessions(@PathVariable("uuid") final UUID uuid, @ParameterObject final Pagination page) throws NotFoundElement, SearchException {
AccessionFilter filter = new AccessionFilter()
.diversityTrees(Sets.newHashSet(uuid));
return accessionApiService.list(filter, page.toPageRequest(MAX_PAGE_SIZE, DEFAULT_PAGE_SIZE));
}
/**
* Add accessions to diversity tree.
*
* @param uuid the uuid
* @param version the version
* @param accessionRefs the accessionRefs to be added
* @return updated record
*/
@PostMapping(value = "/add-accessions/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
@Validated
public DiversityTreeDTO addAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<DiversityTreeAccessionRefDTO> accessionRefs) {
return treeApiService.addAccessions(uuid, version, accessionRefs);
}
/**
* Set accessions to DiversityTree.
*
* @param uuid the uuid
* @param version the version
* @param accessionRefs the accessionRefs to be added
* @return updated record
*/
@PostMapping(value = "/set-accessions/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO setAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<DiversityTreeAccessionRefDTO> accessionRefs) {
return treeApiService.setAccessions(uuid, version, accessionRefs);
}
/**
* Set accessions to DiversityTree from uploaded CSV file.
*
* @param uuid the uuid
* @param version the version
* @param separator the delimiter to use for separating entries in the CSV file
* @param quotechar the character to use for quoted elements in the CSV file
* @param file the CSV file with accessionRefs to be added
* @return updated record
*/
@PostMapping(value = "/upload-accessions/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO uploadAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version,
// CSV settings
@RequestParam(required = false, defaultValue = "\t") char separator, @RequestParam(required = false, defaultValue = "\"") char quotechar,
// The file
@RequestPart(name = "file") final MultipartFile file) throws IOException {
// Permit only a CSV file
if (!file.getContentType().equalsIgnoreCase("text/csv")) {
throw new InvalidApiUsageException("Invalid file type: " + file.getContentType() + " is not permitted.");
}
return treeApiService.uploadAccessions(uuid, version, separator, quotechar, file);
}
/**
* Rematch accessions.
*
* @param uuid the uuid
* @param version the version
* @return updated record
*/
@PostMapping(value = "/rematch-accessions/{uuid},{version}")
public DiversityTreeDTO rematchAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
return treeApiService.rematchAccessions(uuid, version);
}
/**
* Publish diversity tree.
*
* @param uuid the uuid
* @param version the version
* @return published record (admin-only)
*/
@PostMapping(value = "/approve/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO approve(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
return treeApiService.approve(uuid, version);
}
/**
* Unpublish diversity tree.
*
* @param uuid the uuid
* @param version the version
* @return unpublished record
*/
@PostMapping(value = "/reject/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO reject(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
return treeApiService.reject(uuid, version);
}
/**
* Create a new version of DiversityTree based on an existing published DiversityTree.
*
* @param uuid the uuid
* @return the new version of DiversityTree
*/
@PostMapping(value = "/new-version/{uuid}")
public DiversityTreeDTO createNewVersion(@PathVariable("uuid") final UUID uuid) {
return treeApiService.createNewVersion(uuid);
}
/**
* Upload JSON file to the repository and add it to the DiversityTree
*
* @param uuid the UUID of divTree
* @param file the file to be uploaded
* @return updated tree
*/
@PostMapping(value = "/upload/{uuid}", produces = { MediaType.APPLICATION_JSON_VALUE })
public DiversityTreeDTO uploadFile(@PathVariable(name = "uuid") final UUID uuid, @RequestPart(name = "file") final MultipartFile file)
throws InvalidRepositoryPathException, InvalidRepositoryFileDataException, IOException {
return treeApiService.uploadFile(uuid, file);
}
}