ComplexSpeciesTreeController.java

package edu.columbia.biology.controller;

import java.io.IOException;
import java.net.URLDecoder;
import java.security.Principal;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.stream.Collectors;

import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;

import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.access.AccessDeniedException;
import org.springframework.security.access.annotation.Secured;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

import edu.columbia.biology.constants.AuthoritiesSiteRoleConstants;
import edu.columbia.biology.exceptions.InvalidAdvancedSearchQueryStringException;
import edu.columbia.biology.json_model.AdvancedSearchQueryJsonModel;
import edu.columbia.biology.mapper.FitsRepositoryMapper;
import edu.columbia.biology.model.ComplexesSpeciesTree;
import edu.columbia.biology.model.FitTableInformation;
import edu.columbia.biology.processor.AdvancedSearchProcessor;
import edu.columbia.biology.processor.CellxPrincipalProcessor;
import edu.columbia.biology.processor.ComplexesSpeciesTreeProcessor;
import edu.columbia.biology.repository.FitsRepository;

/*
 * TODO: [DESIGN] Support pagination
 * - It may be hard to support pagination, searching, sorting, etc. from a derived datasource. Consider in the future. Look more into documentation
 * - Pagination can be implemented when there is a need for optimization. No need for premature optimization as of now. Perhaps we can paginate a cache!
 */
/**
 * {@link RestController} for retrieving factor-related entities
 * 
 * @author bbece
 * @see {@link RestController}
 */
@RestController
public class ComplexSpeciesTreeController {

	private static final Logger LOGGER = LoggerFactory.getLogger(ComplexSpeciesTreeController.class);

	@Autowired
	private CellxPrincipalProcessor cellxPrincipalProcessor;

	@Autowired
	private ComplexesSpeciesTreeProcessor complexSpeciesTreeProcessor;

	@Autowired
	private FitsRepository fitsRepository;

	@Autowired
	private FitsRepositoryMapper fitsRepositoryMapper;

	@Autowired
	private AdvancedSearchProcessor advancedSearchProcessor;

	@Autowired
	private ObjectMapper objectMapper;

	@Secured({ AuthoritiesSiteRoleConstants.ROLE_SITE_DEV })
	@RequestMapping(value = "/taxcomplexes/search", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrieveAdvancedSearchComplexesTreeList(Authentication authentication,
			@RequestParam(required = false) String queries)
			throws InvalidAdvancedSearchQueryStringException, IOException {
		if (authentication != null) {
			LOGGER.info("Retrieving public species complexes tree for user {}",
					cellxPrincipalProcessor.retrieveUserIdFromPrincipal(authentication));
		} else {
			LOGGER.info("Retrieving public species complexes tree for guest user");
		}

		/*
		 * Process query JSON
		 */
		AdvancedSearchQueryJsonModel advancedSearchQueryJsonModel = null;
		if (StringUtils.isNotBlank(queries)) {
			queries = URLDecoder.decode(queries, "UTF-8");
			try {
				advancedSearchQueryJsonModel = objectMapper.readValue(queries, AdvancedSearchQueryJsonModel.class);
			} catch (JsonParseException | JsonMappingException ex) {
				throw new InvalidAdvancedSearchQueryStringException(ex.getMessage());
			}
		}

		/*
		 * Retrieve universe of fits into a ComplexesSpeciesTree datatype
		 * 
		 * TODO: This should be changed to accessible fits!
		 */
		Collection<Object[]> fitResultSet = null;
		if (cellxPrincipalProcessor.isSiteAdmin(authentication)) {
			fitResultSet = fitsRepository.retrievePublicFits();
		} else {
			fitResultSet = fitsRepository.retrievePublicCuratedFits();
		}

		List<FitTableInformation> fitInformationList = null;
		if (fitResultSet.isEmpty()) {
			fitInformationList = new ArrayList<FitTableInformation>();
		} else {
			fitInformationList = fitsRepositoryMapper.retrieveAllFitsMapper(fitResultSet);
		}

		ComplexesSpeciesTree complexSpeciesTree = complexSpeciesTreeProcessor
				.constructSpeciesComplexesTreeList(fitInformationList);

		/*
		 * Perform filtering on universe of fits if requested
		 */
		if (advancedSearchQueryJsonModel != null) {
			complexSpeciesTree = advancedSearchProcessor.advancedSearchFiltering(complexSpeciesTree,
					advancedSearchQueryJsonModel);
		}

		return complexSpeciesTree;
	}

	/**
	 * Returns entire list of public factor-species combinations.
	 * TODO: 3/12/21: Deprecated?
	 * @return {@link ComplexSpeciesTree}
	 * @throws InvalidAdvancedSearchQueryStringException
	 * @throws IOException
	 */
	@Secured(AuthoritiesSiteRoleConstants.ROLE_SITE_ADMIN)
	@RequestMapping(value = "/taxcomplexes/all", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrieveAdminSpeciesComplexesTreeList(Authentication authentication,
			@RequestParam(required = false) String queries)
			throws InvalidAdvancedSearchQueryStringException, IOException {
		if (authentication != null) {
			LOGGER.info("Retrieving admin species complexes tree for user {}",
					cellxPrincipalProcessor.retrieveUserIdFromPrincipal(authentication));
		}

		/*
		 * Process query JSON
		 */
		AdvancedSearchQueryJsonModel advancedSearchQueryJsonModel = null;
		if (StringUtils.isNotBlank(queries)) {
			try {
				advancedSearchQueryJsonModel = objectMapper.readValue(queries, AdvancedSearchQueryJsonModel.class);
			} catch (JsonParseException | JsonMappingException ex) {
				throw new InvalidAdvancedSearchQueryStringException(ex.getMessage());
			}
		}

		/*
		 * Retrieve universe of fits into a ComplexesSpeciesTree datatype
		 */
		List<FitTableInformation> fitInformationList = fitsRepositoryMapper
				.retrieveAllFitsMapper(fitsRepository.retrieveAllFits());
		ComplexesSpeciesTree complexSpeciesTree = complexSpeciesTreeProcessor
				.constructSpeciesComplexesTreeList(fitInformationList);

		/*
		 * Perform filtering on universe of fits if requested
		 */
		if (advancedSearchQueryJsonModel != null) {
			complexSpeciesTree = advancedSearchProcessor.advancedSearchFiltering(complexSpeciesTree,
					advancedSearchQueryJsonModel);
		}

		return complexSpeciesTree;
	}

	/**
	 * Returns public list of public factor-species combinations.
	 * 
	 * TODO: Temporary admin secured until public launch
	 * 
	 * @return {@link ComplexSpeciesTree}
	 * @throws InvalidAdvancedSearchQueryStringException
	 * @throws IOException
	 */
	@RequestMapping(value = "/taxcomplexes/public", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrievePublicSpeciesComplexesTreeList(Authentication authentication,
			@RequestParam(required = false) String queries)
			throws InvalidAdvancedSearchQueryStringException, IOException {
		if (authentication != null) {
			LOGGER.info("Retrieving public species complexes tree for user {}",
					cellxPrincipalProcessor.retrieveUserIdFromPrincipal(authentication));
		} else {
			LOGGER.info("Retrieving public species complexes tree for guest user");
		}

		/*
		 * Process query JSON
		 */
		AdvancedSearchQueryJsonModel advancedSearchQueryJsonModel = null;
		if (StringUtils.isNotBlank(queries)) {
			try {
				advancedSearchQueryJsonModel = objectMapper.readValue(queries, AdvancedSearchQueryJsonModel.class);
			} catch (JsonParseException | JsonMappingException ex) {
				throw new InvalidAdvancedSearchQueryStringException(ex.getMessage());
			}
		}

		/*
		 * Retrieve universe of fits into a ComplexesSpeciesTree datatype
		 */
		Collection<Object[]> fitResultSet = null;
		List<FitTableInformation> fitInformationList = null;
		if (cellxPrincipalProcessor.isSiteAdmin(authentication)) {
			fitResultSet = fitsRepository.retrievePublicFits();
			fitInformationList = fitsRepositoryMapper.retrieveAllFitsMapper(fitResultSet);
		} else {
			fitResultSet = fitsRepository.retrievePublicCuratedFits();
			fitInformationList = fitsRepositoryMapper.retrieveAllFitsMapper(fitResultSet);
			fitInformationList = selectCuratedFits(fitInformationList);

		}

		ComplexesSpeciesTree complexSpeciesTree = complexSpeciesTreeProcessor
				.constructSpeciesComplexesTreeList(fitInformationList);
		/*
		 * Perform filtering on universe of fits if requested
		 */
		if (advancedSearchQueryJsonModel != null) {
			complexSpeciesTree = advancedSearchProcessor.advancedSearchFiltering(complexSpeciesTree,
					advancedSearchQueryJsonModel);
		}

		return complexSpeciesTree;
	}

	/**
	 * Returns public list of public factor-species combinations.
	 * 
	 * @return {@link ComplexSpeciesTree}
	 * @throws Exception
	 */
	@Secured({ AuthoritiesSiteRoleConstants.ROLE_SITE_DEV })
	@RequestMapping(value = "/taxcomplexes/accessible", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrieveAccessibleSpeciesComplexesTreeList(Authentication authentication,
			@RequestParam(required = false) String queries) throws Exception {
		if (authentication != null) {
			LOGGER.info("Retrieving accessible species complexes tree for user {}",
					cellxPrincipalProcessor.retrieveUserIdFromPrincipal(authentication));

			/*
			 * Process query JSON
			 */
			AdvancedSearchQueryJsonModel advancedSearchQueryJsonModel = null;
			if (StringUtils.isNotBlank(queries)) {
				try {
					advancedSearchQueryJsonModel = objectMapper.readValue(queries, AdvancedSearchQueryJsonModel.class);
				} catch (JsonParseException | JsonMappingException ex) {
					throw new InvalidAdvancedSearchQueryStringException(ex.getMessage());
				}
			}

			/*
			 * Retrieve universe of fits into a ComplexesSpeciesTree datatype
			 */
			List<FitTableInformation> fitInformationList = fitsRepositoryMapper.retrieveAllFitsMapper(fitsRepository
					.retrieveUserAccessibleFits(cellxPrincipalProcessor.retrieveUserIdFromPrincipal(authentication)));
			ComplexesSpeciesTree complexSpeciesTree = complexSpeciesTreeProcessor
					.constructSpeciesComplexesTreeList(fitInformationList);

			/*
			 * Perform filtering on universe of fits if requested
			 */
			if (advancedSearchQueryJsonModel != null) {
				complexSpeciesTree = advancedSearchProcessor.advancedSearchFiltering(complexSpeciesTree,
						advancedSearchQueryJsonModel);
			}

			return complexSpeciesTree;
		} else {
			LOGGER.info(
					"No principal/user found for the client, therefore, unable to retrieve user accessible resources");
			throw new AccessDeniedException(
					"No principal/user found for the client, therefore, unable to retrieve user accessible resources");
		}

	}

	/**
	 * Returns public list of public factor-species combinations.
	 * 
	 * @return {@link ComplexSpeciesTree}
	 */
	@Secured(AuthoritiesSiteRoleConstants.ROLE_SITE_PRIVATE)
	@RequestMapping(value = "/taxcomplexes/group/{labId}", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrieveGroupSpeciesComplexesTreeList(Principal principal,
			@PathVariable("labId") int labId) {
		throw new NotImplementedException("endpoint: /taxcomplexes/group/{labId}");
	}

	/**
	 * Returns public list of public factor-species combinations.
	 * 
	 * @return {@link ComplexSpeciesTree}
	 */
	@Secured(AuthoritiesSiteRoleConstants.ROLE_SITE_PRIVATE)
	@RequestMapping(value = "/taxcomplexes/study/{studyName}", method = RequestMethod.GET)
	public ComplexesSpeciesTree retrieveGroupSpeciesComplexesTreeList(Principal principal,
			@PathVariable("studyName") String studyName) {
		throw new NotImplementedException("endpoint: /taxcomplexes/study/{studyName}");
	}

	/**
	 * If web curation is available (not null), return that result (as override), if
	 * it is null, then return the default pipeline curation.
	 * 
	 * TODO: Need an option on front-end to remove web curation status of fit to
	 * default to the pipeline curation -> can cause potential curation bug.
	 * 
	 * @param fitInformationList
	 * @return
	 */
	private List<FitTableInformation> selectCuratedFits(List<FitTableInformation> fitInformationList) {
		return fitInformationList.stream().filter(fit -> {
			return fit.getCurated() != null ? fit.getCurated() : fit.getPipelineCurated();
		}).collect(Collectors.toList());
	}

}