ConceptCodeServiceImpl.java

package gov.samhsa.consent2share.service.valueset;

import gov.samhsa.consent2share.domain.valueset.CodeSystem;
import gov.samhsa.consent2share.domain.valueset.CodeSystemRepository;
import gov.samhsa.consent2share.domain.valueset.CodeSystemVersion;
import gov.samhsa.consent2share.domain.valueset.CodeSystemVersionRepository;
import gov.samhsa.consent2share.domain.valueset.ConceptCode;
import gov.samhsa.consent2share.domain.valueset.ConceptCodeRepository;
import gov.samhsa.consent2share.domain.valueset.ConceptCodeValueSet;
import gov.samhsa.consent2share.domain.valueset.ConceptCodeValueSetRepository;
import gov.samhsa.consent2share.domain.valueset.ValueSet;
import gov.samhsa.consent2share.domain.valueset.ValueSetRepository;
import gov.samhsa.consent2share.service.dto.ConceptCodeDto;
import gov.samhsa.consent2share.service.dto.ConceptCodeVSCSDto;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.apache.commons.lang.StringUtils;
import org.apache.poi.POIXMLException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.dao.DataIntegrityViolationException;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Sort;
import org.springframework.data.domain.Sort.Direction;
import org.springframework.data.domain.Sort.Order;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.multipart.MultipartFile;

/**
 * The Class ConceptCodeServiceImpl.
 */
public class ConceptCodeServiceImpl implements ConceptCodeService {

	/** The logger. */
	private final Logger logger = LoggerFactory.getLogger(this.getClass());

	/** The concept code page size. */
	public final int CONCEPT_CODE_PAGE_SIZE;

	/** The concept code repository. */
	private ConceptCodeRepository conceptCodeRepository;

	/** The value set repository. */
	private ValueSetRepository valueSetRepository;

	/** The code system repository. */
	CodeSystemRepository codeSystemRepository;

	/** The code system version repository. */
	CodeSystemVersionRepository codeSystemVersionRepository;

	/** The concept code value set repository. */
	ConceptCodeValueSetRepository conceptCodeValueSetRepository;

	/** The value set mgmt helper. */
	ValueSetMgmtHelper valueSetMgmtHelper;

	/**
	 * Instantiates a new concept code service impl.
	 *
	 * @param conceptCodePageSize
	 *            the concept code page size
	 * @param conceptCodeRepository
	 *            the concept code repository
	 * @param valueSetRepository
	 *            the value set repository
	 * @param codeSystemRepository
	 *            the code system repository
	 * @param codeSystemVersionRepository
	 *            the code system version repository
	 * @param conceptCodeValueSetRepository
	 *            the concept code value set repository
	 * @param valueSetMgmtHelper
	 *            the value set mgmt helper
	 */
	public ConceptCodeServiceImpl(int conceptCodePageSize,
			ConceptCodeRepository conceptCodeRepository,
			ValueSetRepository valueSetRepository,
			CodeSystemRepository codeSystemRepository,
			CodeSystemVersionRepository codeSystemVersionRepository,
			ConceptCodeValueSetRepository conceptCodeValueSetRepository,
			ValueSetMgmtHelper valueSetMgmtHelper) {
		super();
		CONCEPT_CODE_PAGE_SIZE = conceptCodePageSize;
		this.conceptCodeRepository = conceptCodeRepository;
		this.valueSetRepository = valueSetRepository;
		this.codeSystemRepository = codeSystemRepository;
		this.codeSystemVersionRepository = codeSystemVersionRepository;
		this.conceptCodeValueSetRepository = conceptCodeValueSetRepository;
		this.valueSetMgmtHelper = valueSetMgmtHelper;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#delete(java
	 * .lang.Long)
	 */
	@Override
	@Transactional(rollbackFor = ConceptCodeNotFoundException.class)
	public ConceptCodeDto delete(Long conceptCodeId)
			throws ConceptCodeNotFoundException {
		logger.debug("Deleting ConceptCode with id: " + conceptCodeId);
		ConceptCode deleted = conceptCodeRepository.findOne(conceptCodeId);
		if (deleted == null) {
			logger.debug("No ConceptCode found with an id: " + conceptCodeId);
			throw new ConceptCodeNotFoundException();
		}
		conceptCodeRepository.delete(deleted);
		return valueSetMgmtHelper.createConceptCodeDtoFromEntity(deleted);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#findById
	 * (java.lang.Long)
	 */
	@Override
	public ConceptCodeDto findById(Long id) throws ValueSetNotFoundException,
			ConceptCodeNotFoundException {
		logger.debug("Finding a ConceptCode with id: " + id);

		ConceptCode conceptCode = conceptCodeRepository.findOne(id);
		if (null == conceptCode) {
			throw new ConceptCodeNotFoundException(
					"Selected Code is not Available");
		}
		// get all value sets in the system
		ConceptCodeDto conceptCodeDto = valueSetMgmtHelper
				.createConceptCodeDtoFromEntity(conceptCode);
		conceptCodeDto.setValueSetMap(getAllValueSetsInMap());

		// get all selected value sets that are associated with this concept
		// code
		conceptCodeDto
				.setValueSetIds(getAllValueSetIdsForConceptCode(conceptCode
						.getId()));

		return conceptCodeDto;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#update(gov
	 * .samhsa.consent2share.service.dto.ConceptCodeDto)
	 */
	@Override
	@Transactional(rollbackFor = ConceptCodeNotFoundException.class)
	public ConceptCodeDto update(ConceptCodeDto updated)
			throws ConceptCodeNotFoundException, ValueSetNotFoundException {
		logger.debug("Updating ConceptCode with information" + updated);

		ConceptCode conceptCode = conceptCodeRepository
				.findOne(updated.getId());
		if (conceptCode == null) {
			logger.debug("No ConceptCode found with an id: " + updated.getId());
			throw new ConceptCodeNotFoundException();
		}

		conceptCode.update(updated.getCode(), updated.getName(),
				updated.getUserName());

		List<Long> selVsIds = updated.getValueSetIds();
		// Atleast on valueset need to be associated with a concept code
		if (null == selVsIds || selVsIds.size() <= 0) {
			throw new ValueSetNotFoundException(
					"Need to Associate atleast one valueset to the code: "
							+ updated.getCode());
		}

		// 3.Get the value sets associated to the concept code
		List<ConceptCodeValueSet> cValueSets = conceptCodeValueSetRepository
				.findAllByPkConceptCodeId(conceptCode.getId());
		if (cValueSets == null) {
			throw new ValueSetNotFoundException(
					"No Valusets associated to the given code" + conceptCode);
		}

		List<ConceptCodeValueSet> selCodeValueSets = new ArrayList<ConceptCodeValueSet>();
		List<Long> selIds = new ArrayList<Long>();

		for (ConceptCodeValueSet aCodeValueSet : cValueSets) {

			for (Long selId : selVsIds) {
				if (aCodeValueSet.getValueSet().getId().equals(selId)) {
					selCodeValueSets.add(aCodeValueSet);
					selIds.add(selId);
					break;
				}
			}

		}
		// remove the selected value sets
		cValueSets.removeAll(selCodeValueSets);
		selVsIds.removeAll(selIds);

		// delete the (existing that are not selected )association
		if (null != cValueSets && cValueSets.size() > 0)
			conceptCodeValueSetRepository.delete(cValueSets);

		// add the new associations
		List<ConceptCodeValueSet> cVSets = new ArrayList<ConceptCodeValueSet>();
		for (Long id : selVsIds) {
			ValueSet vSet = valueSetRepository.findOne(id);
			if (null == vSet) {
				throw new ValueSetNotFoundException(
						"No Valueset Found for the Selected Name");
			}
			ConceptCodeValueSet cValueSet = ConceptCodeValueSet.getBuilder(
					conceptCode, vSet).build();
			cVSets.add(cValueSet);
		}

		if (null != cVSets && cVSets.size() > 0)
			cVSets = conceptCodeValueSetRepository.save(cVSets);

		// set the selected ones back to concept code
		conceptCode.setValueSets(selCodeValueSets);

		// conceptCodeValueSetRepository.save(selCodeValueSets);
		return valueSetMgmtHelper.createConceptCodeDtoFromEntity(conceptCode);
		// return null;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#findAll()
	 */
	@Override
	public List<ConceptCodeDto> findAll() {
		logger.debug("Finding all conceptCodes");

		List<ConceptCode> conceptCodes = conceptCodeRepository.findAll();

		return valueSetMgmtHelper
				.convertConceptCodeEntitiesToDtos(conceptCodes);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#findAll()
	 */
	@Override
	public Map<String, Object> findAll(int pageNumber) {

		logger.debug("Finding all conceptCodes with paging");
		Sort sort = new Sort(new Order(Direction.ASC, "code"));
		PageRequest pageRequest = new PageRequest(pageNumber,
				CONCEPT_CODE_PAGE_SIZE, sort);

		Page<ConceptCode> pagedConceptCodes = conceptCodeRepository
				.findAll(pageRequest);
		logger.debug("Total Concept Codes: "
				+ pagedConceptCodes.getTotalElements());
		logger.debug("Total Pages: " + pagedConceptCodes.getTotalPages());

		Map<String, Object> pageResultsMap = new HashMap<String, Object>();
		pageResultsMap.put("conceptCodes", valueSetMgmtHelper
				.convertConceptCodeEntitiesToDtos(pagedConceptCodes
						.getContent()));
		pageResultsMap.put("totalNumberOfConceptCodes",
				pagedConceptCodes.getTotalElements());
		pageResultsMap.put("totalPages", pagedConceptCodes.getTotalPages());
		pageResultsMap.put("itemsPerPage", pagedConceptCodes.getSize());
		pageResultsMap.put("currentPage", pagedConceptCodes.getNumber());
		pageResultsMap.put("numberOfElements",
				pagedConceptCodes.getNumberOfElements());

		return pageResultsMap;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#findAllByCode
	 * (java.lang.String)
	 */
	@Override
	public Map<String, Object> findAllByCode(String searchTerm,
			String codeSystem, String codeSystemVersion, String valueSetName,
			int pageNumber) {
		Sort sort = new Sort(new Order(Direction.ASC, "code"));
		PageRequest pageRequest = new PageRequest(pageNumber,
				CONCEPT_CODE_PAGE_SIZE, sort);

		Page<ConceptCode> pagedConceptCodes = conceptCodeRepository
				.findAllByCodeLike("%" + searchTerm + "%", "%" + codeSystem
						+ "%", "%" + codeSystemVersion + "%", "%"
						+ valueSetName + "%", pageRequest);
		logger.debug("Total Concept Codes: "
				+ pagedConceptCodes.getTotalElements());
		logger.debug("Total Pages: " + pagedConceptCodes.getTotalPages());

		Map<String, Object> pageResultsMap = new HashMap<String, Object>();
		pageResultsMap.put("conceptCodes", valueSetMgmtHelper
				.convertConceptCodeEntitiesToDtos(pagedConceptCodes
						.getContent()));
		pageResultsMap.put("totalNumberOfConceptCodes",
				pagedConceptCodes.getTotalElements());
		pageResultsMap.put("totalPages", pagedConceptCodes.getTotalPages());
		pageResultsMap.put("itemsPerPage", pagedConceptCodes.getSize());
		pageResultsMap.put("currentPage", pagedConceptCodes.getNumber());
		pageResultsMap.put("numberOfElements",
				pagedConceptCodes.getNumberOfElements());

		return pageResultsMap;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#findAllByName
	 * (java.lang.String, java.lang.String, java.lang.String, java.lang.String,
	 * int)
	 */
	@Override
	public Map<String, Object> findAllByName(String searchTerm,
			String codeSystem, String codeSystemVersion, String valueSetName,
			int pageNumber) {
		Sort sort = new Sort(new Order(Direction.ASC, "name"));
		PageRequest pageRequest = new PageRequest(pageNumber,
				CONCEPT_CODE_PAGE_SIZE, sort);

		if (StringUtils.isEmpty(valueSetName))
			valueSetName = "%";

		Page<ConceptCode> pagedConceptCodes = conceptCodeRepository
				.findAllByName("%" + searchTerm + "%", "%" + codeSystem + "%",
						"%" + codeSystemVersion + "%", valueSetName,
						pageRequest);
		logger.debug("Total Concept Codes: "
				+ pagedConceptCodes.getTotalElements());
		logger.debug("Total Pages: " + pagedConceptCodes.getTotalPages());

		Map<String, Object> pageResultsMap = new HashMap<String, Object>();
		pageResultsMap.put("conceptCodes", valueSetMgmtHelper
				.convertConceptCodeEntitiesToDtos(pagedConceptCodes
						.getContent()));
		pageResultsMap.put("totalNumberOfConceptCodes",
				pagedConceptCodes.getTotalElements());
		pageResultsMap.put("totalPages", pagedConceptCodes.getTotalPages());
		pageResultsMap.put("itemsPerPage", pagedConceptCodes.getSize());
		pageResultsMap.put("currentPage", pagedConceptCodes.getNumber());
		pageResultsMap.put("numberOfElements",
				pagedConceptCodes.getNumberOfElements());

		return pageResultsMap;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#create()
	 */
	@Override
	public ConceptCodeVSCSDto create() throws ValueSetNotFoundException,
			CodeSystemVersionNotFoundException, CodeSystemNotFoundException {
		ConceptCodeVSCSDto conceptCodeVSCSDto = new ConceptCodeVSCSDto();

		conceptCodeVSCSDto.setValueSetsMap(getAllValueSetsInMap());

		// Get all code system versions
		List<CodeSystem> codeSystems = codeSystemRepository.findAll();

		if (codeSystems == null || codeSystems.size() == 0) {
			logger.debug("No codeSystems found in the system");
			throw new CodeSystemNotFoundException();

		}
		conceptCodeVSCSDto.setCsVersions(valueSetMgmtHelper
				.createCSVersionsDTOFormEntity(codeSystems));

		return conceptCodeVSCSDto;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * gov.samhsa.consent2share.service.valueset.ConceptCodeService#create(gov
	 * .samhsa.consent2share.service.dto.ConceptCodeDto)
	 */
	@Override
	@Transactional
	public ConceptCodeDto create(ConceptCodeDto created)
			throws ValueSetNotFoundException, CodeSystemNotFoundException,
			DuplicateConceptCodeException {

		ConceptCodeDto conceptCodeDto = new ConceptCodeDto();

		String description = (created.getDescription() != null) ? created
				.getDescription() : "";

		// STEP:1 :- Get CodeSystemVersion Object from DB
		Long codeSystemVersionId = created.getCodeSystemVersionId();

		// find code system version
		CodeSystemVersion selectedCsv = codeSystemVersionRepository
				.findOne(codeSystemVersionId);

		if (selectedCsv == null) {
			logger.debug("No Code System version found with an id: "
					+ codeSystemVersionId);
			throw new CodeSystemNotFoundException();
		}

		List<Long> selVsIds = created.getValueSetIds();

		if (null == selVsIds || selVsIds.size() <= 0) {
			throw new ValueSetNotFoundException(
					"Need to Associate atleast one valueset to the code: "
							+ created.getCode());
		}

		boolean isNewVS = false;
		int conceptCodesInserted = 0;

		// Loop through for each selected value set
		for (Long valueSetId : selVsIds) {

			// STEP:2 :-Get valueset Object from DB
			// Long valueSetId = created.getValueSetId();
			ValueSet selectedVs = valueSetRepository.findOne(valueSetId);
			if (selectedVs == null) {
				logger.debug("No valueSet found with an id: " + valueSetId);
				throw new ValueSetNotFoundException();
			}

			// STEP:3 :- Code and its association with value set save

			// Check if conceptcode already exists for the code system version
			logger.debug("Creating a new ConceptCode with information: "
					+ created);
			ConceptCode conceptCode = conceptCodeRepository
					.findByCodeAndCodeSystemVersionId(created.getCode(),
							selectedCsv.getId());
			ConceptCodeValueSet conceptCodeValueSet = ConceptCodeValueSet
					.getBuilder(conceptCode, selectedVs).build();

			if (null != conceptCode) {
				// check if association between code and valueset exists
				conceptCodeValueSet = conceptCodeValueSetRepository
						.findOne(conceptCodeValueSet.getPk());

				if (null == conceptCodeValueSet) {
					// Scenario-1 : Code Exists and Code with VS association
					// does not exists
					// build and save association
					conceptCodeValueSet = ConceptCodeValueSet.getBuilder(
							conceptCode, selectedVs).build();
					// save association
					conceptCodeValueSet = conceptCodeValueSetRepository
							.save(conceptCodeValueSet);
					isNewVS = true;
					conceptCodesInserted++;
				} else {
					// Scenario-2 : Code Exists and Code with VS association
					// exists
					logger.debug("Code and Code with VS association exists: "
							+ created);
					// isVSPresent = true;
				}

			} else {
				// Scenario-3 : Code and Code with VS association does not
				// exists

				// build conceptcode
				conceptCode = ConceptCode
						.getBuilder(created.getCode(), created.getName(),
								created.getUserName()).description(description)
						.build();

				// set code system version
				conceptCode.setCodeSystemVersion(selectedCsv);

				// Create ConceptCode_Valueset object
				conceptCodeValueSet = ConceptCodeValueSet.getBuilder(
						conceptCode, selectedVs).build();
				List<ConceptCodeValueSet> vs = new ArrayList<ConceptCodeValueSet>();
				vs.add(conceptCodeValueSet);

				// map association
				conceptCode.setValueSets(vs);
				isNewVS = true;

				// Save conceptcode
				conceptCode = conceptCodeRepository.save(conceptCode);
				conceptCodesInserted++;
			}

			conceptCodeDto = valueSetMgmtHelper
					.createConceptCodeDtoFromEntity(conceptCode);
		}
		conceptCodeDto.setConceptCodesInserted(conceptCodesInserted);

		if (!isNewVS) {
			throw new DuplicateConceptCodeException();
		}
		return conceptCodeDto;

	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gov.samhsa.consent2share.service.valueset.ConceptCodeService#
	 * conceptCodeBatchUpload
	 * (gov.samhsa.consent2share.service.dto.ConceptCodeDto,
	 * org.springframework.web.multipart.MultipartFile, java.lang.String,
	 * java.lang.String, java.lang.Long)
	 */
	@Override
	@Transactional(rollbackFor = DataIntegrityViolationException.class)
	public ConceptCodeDto conceptCodeBatchUpload(ConceptCodeDto conceptCodeDto,
			MultipartFile file, String codeSystemId, Long codeSystemVersionId,
			List<Long> valueSetIds) throws ValueSetNotFoundException,
			CodeSystemNotFoundException {

		String userName = conceptCodeDto.getUserName();

		try {
			List<ConceptCodeDto> listOfConceptCodeDtos = valueSetMgmtHelper
					.readConceptCodesFromFile(file, codeSystemId,
							codeSystemVersionId, valueSetIds, userName);

			int rowsUpdated = 0;
			// for batch upload
			List<Integer> listOfDuplicateCodes = new ArrayList<Integer>();

			// iterate rows with value set fields
			for (int i = 0; i < listOfConceptCodeDtos.size(); i++) {

				try {
					conceptCodeDto = create(listOfConceptCodeDtos.get(i));
					rowsUpdated = rowsUpdated
							+ conceptCodeDto.getConceptCodesInserted();
				} catch (DuplicateConceptCodeException e) {
					// adjusting for header row
					listOfDuplicateCodes.add(i + 2);
				}
			}
			conceptCodeDto.setConceptCodesInserted(rowsUpdated);
			conceptCodeDto.setListOfDuplicatesCodes(listOfDuplicateCodes);

		} catch (ValueSetNotFoundException ex) {
			logger.debug("Missing required field while doing batch upload: "
					+ ex.getMessage());
			conceptCodeDto.setError(true);
			conceptCodeDto.setErrorMessage(ex.getMessage());
			throw ex;
		} catch (InvalidCSVException ex) {
			conceptCodeDto.setError(true);
			conceptCodeDto.setErrorMessage(ex.getMessage());
			throw ex;
		} catch (POIXMLException ex) {
			logger.debug("Incorrect file format: " + ex.getMessage());
			conceptCodeDto.setError(true);
			conceptCodeDto
					.setErrorMessage("Incorrect file format. File should be a correct .xslx file");
		} catch (IOException ex) {
			logger.debug("Unable to open file: " + ex.getMessage());
			conceptCodeDto.setError(true);
			conceptCodeDto.setErrorMessage("Unable to open file");
		} catch (Exception ex) {
			logger.debug("Exception thrown: " + ex.getMessage());
			conceptCodeDto.setError(true);
			conceptCodeDto
					.setErrorMessage("An error occurred. Please check with administrator: "
							+ ex.getMessage());
		}
		return conceptCodeDto;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gov.samhsa.consent2share.service.valueset.ConceptCodeService#
	 * findValueSetsByCodeSystem(java.lang.String, java.lang.String)
	 */
	@Override
	public List<ValueSet> findValueSetsByCodeSystem(String codeSystem,
			String codeSystemVersion) {
		return conceptCodeRepository.findValueSetNamesFilterByCodeSystem(
				codeSystem, codeSystemVersion);
	}

	/**
	 * This setter method should be used only by unit tests.
	 *
	 * @param conceptCodeRepository
	 *            the new concept code repository
	 */
	protected void setConceptCodeRepository(
			ConceptCodeRepository conceptCodeRepository) {
		this.conceptCodeRepository = conceptCodeRepository;
	}

	/**
	 * Gets the all value sets in map.
	 *
	 * @return the all value sets in map
	 * @throws ValueSetNotFoundException
	 *             the value set not found exception
	 */
	private Map<Long, String> getAllValueSetsInMap()
			throws ValueSetNotFoundException {
		// Get all valuesets
		List<ValueSet> valueSets = valueSetRepository.findAll();

		if (valueSets == null || valueSets.size() == 0) {
			logger.debug("No Valuesets found in the system");
			throw new ValueSetNotFoundException(
					"No Value Sets Found in the system");

		}
		return valueSetMgmtHelper.convertValueSetEntitiesToMap(valueSets);
	}

	/**
	 * Gets the all value set ids for concept code.
	 *
	 * @param conceptCodeId
	 *            the concept code id
	 * @return the all value set ids for concept code
	 */
	private List<Long> getAllValueSetIdsForConceptCode(Long conceptCodeId) {
		List<ConceptCodeValueSet> cValueSets = conceptCodeValueSetRepository
				.findAllByPkConceptCodeId(conceptCodeId);
		List<Long> selValueSetIds = new ArrayList<Long>();

		for (ConceptCodeValueSet cValueSet : cValueSets) {
			selValueSetIds.add(cValueSet.getValueSet().getId());
		}
		return selValueSetIds;
	}
}