GermplasmController.java

/*
 * Copyright 2023 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.gringlobal.brapi.v2.impl;

import java.util.Collection;
import java.util.Set;

import org.apache.commons.lang3.StringUtils;
import org.genesys.blocks.model.filters.StringFilter;
import org.gringlobal.brapi.BaseBrAPIController;
import org.gringlobal.brapi.BrAPIPage;
import org.gringlobal.brapi.v2.BrAPIv2Facade;
import org.gringlobal.custom.elasticsearch.SearchException;
import org.gringlobal.service.filter.AccessionFilter;
import org.springframework.beans.factory.annotation.Autowired;
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.RestController;

import uk.ac.hutton.ics.brapi.resource.base.ArrayResult;
import uk.ac.hutton.ics.brapi.resource.base.BaseResult;
import uk.ac.hutton.ics.brapi.resource.germplasm.germplasm.Germplasm;
import uk.ac.hutton.ics.brapi.resource.germplasm.germplasm.GermplasmSearch;
import uk.ac.hutton.ics.brapi.resource.germplasm.germplasm.Mcpd;

@RestController("brApi21germplasm")
@RequestMapping(BaseBrAPIController.BRAPIv2_BASE)
public class GermplasmController extends BaseBrAPIController {

	public static final String ENDPOINT_GERMPLASM = "/germplasm";

	@Autowired
	private BrAPIv2Facade brAPIv2Facade;

	@GetMapping(ENDPOINT_GERMPLASM)
	public BaseResult<ArrayResult<Germplasm>> getGermplasm(
		@RequestParam(value = "accessionNumber", required = false) String accessionNumber,
//		@RequestParam(value = "collection", required = false) String collection,
//		@RequestParam(value = "binomialName", required = false) String binomialName,
		@RequestParam(value = "genus", required = false) String genus,
		@RequestParam(value = "species", required = false) String species,
//		@RequestParam(value = "synonym", required = false) String synonym,
//		@RequestParam(value = "parentDbId", required = false) String parentDbId,
//		@RequestParam(value = "progenyDbId", required = false) String progenyDbId,
//		@RequestParam(value = "commonCropName", required = false) String commonCropName,
//		@RequestParam(value = "programDbId", required = false) String programDbId,
//		@RequestParam(value = "trialDbId", required = false) String trialDbId,
//		@RequestParam(value = "studyDbId", required = false) String studyDbId,
		@RequestParam(value = "germplasmDbId", required = false) String germplasmDbId,
		@RequestParam(value = "germplasmName", required = false) String germplasmName,
		@RequestParam(value = "germplasmPUI", required = false) String germplasmPUI,
//		@RequestParam(value = "externalReferenceId", required = false) String externalReferenceId,
//		@RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
		final BrAPIPage page
		) throws SearchException {

		var filter = new AccessionFilter();
		if (StringUtils.isNotBlank(accessionNumber)) filter.accessionNumber(Set.of(accessionNumber));
		if (StringUtils.isNotBlank(genus)) filter.taxonomySpecies().genusName(new StringFilter().eq(Set.of(genus)));
		if (StringUtils.isNotBlank(species)) filter.taxonomySpecies().speciesName().eq(Set.of(species));
		if (StringUtils.isNotBlank(germplasmDbId)) filter.id().add(Long.parseLong(germplasmDbId));
		if (StringUtils.isNotBlank(germplasmPUI)) filter.doi().add(germplasmPUI);

		var p = brAPIv2Facade.listAccessions(filter, BrAPIPage.make(page));
		return arrayResult(p);
	}

	@GetMapping(ENDPOINT_GERMPLASM + "/{germplasmDbId}")
	public BaseResult<Germplasm> getGermplasmById(@PathVariable("germplasmDbId")  long germplasmDbId) {
		return new BaseResult<>(brAPIv2Facade.getAccession(germplasmDbId), 0, 0, 0);
	}

	@GetMapping(ENDPOINT_GERMPLASM + "/{germplasmDbId}/mcpd")
	public BaseResult<Mcpd> getGermplasmMcpd(@PathVariable("germplasmDbId") long germplasmDbId) {
		return new BaseResult<>(brAPIv2Facade.getAccessionMcpd(germplasmDbId), 0, 0, 0);
	}

	/** Create new Germplasm entities on this server */
	@PostMapping(ENDPOINT_GERMPLASM)
	public BaseResult<Collection<Germplasm>> postGermplasm(@RequestBody Germplasm[] accessions) throws Exception {
		var p = brAPIv2Facade.createAccessions(accessions);
		return createResult(p, STATUS_CREATED);
	}

	/** Update germplasm */
	@PutMapping(ENDPOINT_GERMPLASM + "/{germplasmDbId}")
	public BaseResult<Germplasm> putGermplasmById(@PathVariable("germplasmDbId") long germplasmDbId, @RequestBody Germplasm accession) throws Exception {
		return new BaseResult<>(brAPIv2Facade.updateAccession(germplasmDbId, accession), STATUS_UPDATED);
	}

	@PostMapping("/search" + ENDPOINT_GERMPLASM)
	public BaseResult<ArrayResult<Germplasm>> search(@RequestBody GermplasmSearch search, final BrAPIPage page) throws Exception {
		var filter = new AccessionFilter();
		if (search.getGermplasmDbIds() != null) search.getGermplasmDbIds().stream().map(Long::parseLong).forEach(filter.id()::add);
		if (search.getAccessionNumbers() != null) search.getAccessionNumbers().stream().forEach(filter.accessionNumbers()::add);
		if (search.getGermplasmPUIs() != null) search.getGermplasmPUIs().stream().forEach(filter.doi()::add);
		if (search.getGenus() != null) filter.taxonomySpecies().taxonomyGenus().genusName().eq(Set.copyOf(search.getGenus()));
		if (search.getSpecies() != null) filter.taxonomySpecies().speciesName().eq(Set.copyOf(search.getSpecies()));
		if (search.getBinomialNames() != null) filter.taxonomySpecies().name().sw(Set.copyOf(search.getBinomialNames()));

		var p = brAPIv2Facade.listAccessions(filter, BrAPIPage.make(page));
		return arrayResult(p);
	}
}