PhenotypingController.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.List;

import org.apache.commons.lang3.StringUtils;
import org.gringlobal.brapi.BaseBrAPIController;
import org.gringlobal.brapi.BrAPIPage;
import org.gringlobal.brapi.v2.BrAPIv2Facade;
import org.gringlobal.service.filter.CropTraitFilter;
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.attribute.Trait;
import uk.ac.hutton.ics.brapi.resource.phenotyping.observation.ObservationVariable;

@RestController("brApi21phenotyping")
@RequestMapping(BaseBrAPIController.BRAPIv2_BASE)
public class PhenotypingController extends BaseBrAPIController {

	public static final String ENDPOINT_TRAITS = "/traits";
	public static final String ENDPOINT_VARIABLES = "/variables";

	@Autowired
	private BrAPIv2Facade brAPIv2Facade;

	@GetMapping(ENDPOINT_TRAITS)
	public BaseResult<ArrayResult<Trait>> getTraits(
		@RequestParam(name = "traitDbId", required = false) String traitDbId,
//		@RequestParam(name = "observationVariableDbId", required = false) String observationVariableDbId,
//		@RequestParam(name = "ontologyDbId", required = false) String ontologyDbId,
//		@RequestParam(name = "commonCropName", required = false) String commonCropName,
//		@RequestParam(name = "programDbId", required = false) String programDbId,
//		@RequestParam(name = "externalReferenceId", required = false) String externalReferenceId,
//		@RequestParam(name = "externalReferenceSource", required = false) String externalReferenceSource,
		final BrAPIPage page
		) throws Exception {

		var filter = new CropTraitFilter();
		if (StringUtils.isNotBlank(traitDbId)) filter.id().add(Long.parseLong(traitDbId));

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

	@GetMapping(ENDPOINT_TRAITS + "/{traitDbId}")
	public BaseResult<Trait> getGermplasmById(@PathVariable("traitDbId") long traitDbId) {
		return new BaseResult<>(brAPIv2Facade.getTrait(traitDbId), List.of());
	}

	/** Create new traits on this server */
	@PostMapping(ENDPOINT_TRAITS)
	public BaseResult<ArrayResult<Trait>> postGermplasm(@RequestBody Trait[] traits) throws Exception {
		var p = brAPIv2Facade.createTraits(traits);
		return arrayResult(p);
	}

	/** Update trait */
	@PutMapping(ENDPOINT_TRAITS + "/{traitDbId}")
	public BaseResult<Trait> putGermplasmById(@PathVariable("traitDbId") long traitDbId, @RequestBody Trait trait) throws Exception {
		return new BaseResult<>(brAPIv2Facade.updateTrait(traitDbId, trait), STATUS_UPDATED);
	}


	@GetMapping(ENDPOINT_VARIABLES)
	public BaseResult<ArrayResult<ObservationVariable>> getObservationVariables(
		@RequestParam(name = "observationVariableDbId", required = false) String observationVariableDbId,
//		@RequestParam("observationVariableDbId") String observationVariableDbId,
//		@RequestParam("ontologyDbId") String ontologyDbId,
//		@RequestParam("commonCropName") String commonCropName,
//		@RequestParam("programDbId") String programDbId,
//		@RequestParam("externalReferenceId") String externalReferenceId,
//		@RequestParam("externalReferenceSource") String externalReferenceSource,
		final BrAPIPage page
		) throws Exception {

		var filter = new CropTraitFilter();
		if (StringUtils.isNotBlank(observationVariableDbId)) filter.id().add(Long.parseLong(observationVariableDbId));

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

	@GetMapping(ENDPOINT_VARIABLES + "/{observationVariableDbId}")
	public BaseResult<ObservationVariable> getObservationVariableById(@PathVariable("observationVariableDbId") long observationVariableDbId) {
		return new BaseResult<>(brAPIv2Facade.getObservationVariable(observationVariableDbId), List.of());
	}

	/** Create new traits on this server */
	@PostMapping(ENDPOINT_VARIABLES)
	public BaseResult<Collection<ObservationVariable>> postObservationVariable(@RequestBody ObservationVariable[] variables) throws Exception {
		var p = brAPIv2Facade.createObservationVariables(variables);
		return new BaseResult<>(p.getContent(), STATUS_CREATED);
	}

	/** Update trait */
	@PutMapping(ENDPOINT_VARIABLES + "/{observationVariableDbId}")
	public BaseResult<ObservationVariable> putObservationVariableById(@PathVariable("observationVariableDbId") long observationVariableDbId, @RequestBody ObservationVariable variables) throws Exception {
		return new BaseResult<>(brAPIv2Facade.updateObservationVariable(observationVariableDbId, variables), STATUS_UPDATED );
	}

}