OmimRepository.java

package org.molgenis.data.annotation.core.entity.impl.omim;

import au.com.bytecode.opencsv.CSVReader;
import com.google.common.collect.Iterables;
import org.molgenis.data.Entity;
import org.molgenis.data.MolgenisDataException;
import org.molgenis.data.Query;
import org.molgenis.data.QueryRule.Operator;
import org.molgenis.data.RepositoryCapability;
import org.molgenis.data.meta.model.AttributeFactory;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.meta.model.EntityTypeFactory;
import org.molgenis.data.support.AbstractRepository;
import org.molgenis.data.support.DynamicEntity;

import java.io.*;
import java.util.*;
import java.util.stream.Stream;

import static au.com.bytecode.opencsv.CSVParser.DEFAULT_QUOTE_CHARACTER;
import static com.google.common.collect.Lists.newArrayList;
import static java.nio.charset.Charset.forName;
import static java.util.Arrays.asList;
import static java.util.Collections.emptySet;
import static org.apache.commons.lang3.StringUtils.join;
import static org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator.NAME;
import static org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator.SEPARATOR;
import static org.molgenis.data.meta.model.EntityType.AttributeRole.ROLE_ID;

public class OmimRepository extends AbstractRepository
{
	public static final String OMIM_AUTO_ID_COL_NAME = "ID";
	public static final String OMIM_PHENOTYPE_COL_NAME = "Phenotype";
	public static final String OMIM_GENE_SYMBOLS_COL_NAME = "Gene_Name";
	public static final String OMIM_MIM_NUMBER_COL_NAME = "MIMNumber";
	public static final String OMIM_CYTO_LOCATION_COL_NAME = "CytoLocation";
	public static final String OMIM_ENTRY_COL_NAME = "OmimEntry";
	public static final String OMIM_TYPE_COL_NAME = "OmimType";
	private final AttributeFactory attributeFactory;
	private final EntityTypeFactory entityTypeFactory;

	private Map<String, List<Entity>> entitiesByGeneSymbol;

	private final File file;

	public OmimRepository(File file, EntityTypeFactory entityTypeFactory, AttributeFactory attributeFactory)
	{
		this.file = file;
		this.entityTypeFactory = entityTypeFactory;
		this.attributeFactory = attributeFactory;
	}

	@Override
	public Set<RepositoryCapability> getCapabilities()
	{
		return emptySet();
	}

	@Override
	public EntityType getEntityType()
	{
		EntityType entityType = entityTypeFactory.create().setSimpleName(NAME);
		entityType.addAttribute(attributeFactory.create().setName(OMIM_GENE_SYMBOLS_COL_NAME), ROLE_ID);
		entityType.addAttribute(attributeFactory.create().setName(OMIM_PHENOTYPE_COL_NAME));
		entityType.addAttribute(attributeFactory.create().setName(OMIM_MIM_NUMBER_COL_NAME));
		entityType.addAttribute(attributeFactory.create().setName(OMIM_CYTO_LOCATION_COL_NAME));
		entityType.addAttribute(attributeFactory.create().setName(OMIM_ENTRY_COL_NAME));
		entityType.addAttribute(attributeFactory.create().setName(OMIM_TYPE_COL_NAME));
		return entityType;
	}

	@Override
	public Iterator<Entity> iterator()
	{
		return getEntities().iterator();
	}

	@Override
	public Stream<Entity> findAll(Query<Entity> q)
	{
		if (q.getRules().isEmpty())
		{
			return getEntities().stream();
		}

		if ((q.getRules().size() != 1) || (q.getRules().get(0).getOperator() != Operator.EQUALS))
		{
			throw new MolgenisDataException("The only query allowed on this Repository is gene EQUALS");
		}

		String geneSymbol = (String) q.getRules().get(0).getValue();
		List<Entity> entities = getEntitiesByGeneSymbol().get(geneSymbol);

		return entities != null ? entities.stream() : Stream.empty();
	}

	@Override
	public long count()
	{
		return Iterables.size(this);
	}

	private List<Entity> getEntities()
	{
		List<Entity> entities = new ArrayList<>();
		getEntitiesByGeneSymbol().forEach((geneSymbol, geneSymbolEntities) -> entities.addAll(geneSymbolEntities));
		return entities;
	}

	private Map<String, List<Entity>> getEntitiesByGeneSymbol()
	{
		if (entitiesByGeneSymbol == null)
		{
			Map<String, List<List<String>>> omimEntriesByGeneSymbol = new HashMap<>();
			entitiesByGeneSymbol = new LinkedHashMap<>();

			try (CSVReader csvReader = new CSVReader(new InputStreamReader(new FileInputStream(file), forName("UTF-8")),
					SEPARATOR, DEFAULT_QUOTE_CHARACTER, 1))
			{

				String[] values = csvReader.readNext();
				while (values != null)
				{
					addLineToMap(omimEntriesByGeneSymbol, values);
					values = csvReader.readNext();
				}

				for (String geneSymbol : omimEntriesByGeneSymbol.keySet())
				{
					addEntityToGeneEntityList(omimEntriesByGeneSymbol, geneSymbol);
				}
			}
			catch (IOException e)
			{
				throw new UncheckedIOException(e);
			}
		}
		return entitiesByGeneSymbol;
	}

	/**
	 * Uses the map containing the parsed OMIM map to create a list of {@link Entity}
	 *
	 * @param omimEntriesByGeneSymbol
	 * @param geneSymbol
	 */
	private void addEntityToGeneEntityList(Map<String, List<List<String>>> omimEntriesByGeneSymbol, String geneSymbol)
	{
		Entity entity = new DynamicEntity(getEntityType());
		entity.set(OMIM_GENE_SYMBOLS_COL_NAME, geneSymbol);
		entity.set(OMIM_PHENOTYPE_COL_NAME, join(omimEntriesByGeneSymbol.get(geneSymbol).get(0), ","));
		entity.set(OMIM_MIM_NUMBER_COL_NAME, join(omimEntriesByGeneSymbol.get(geneSymbol).get(1), ","));
		entity.set(OMIM_CYTO_LOCATION_COL_NAME, join(omimEntriesByGeneSymbol.get(geneSymbol).get(2), ","));
		entity.set(OMIM_TYPE_COL_NAME, join(omimEntriesByGeneSymbol.get(geneSymbol).get(3), ","));
		entity.set(OMIM_ENTRY_COL_NAME, join(omimEntriesByGeneSymbol.get(geneSymbol).get(4), ","));

		List<Entity> entities = entitiesByGeneSymbol.get(geneSymbol);
		if (entities == null)
		{
			entities = new ArrayList<>();
			entitiesByGeneSymbol.put(geneSymbol, entities);
		}
		entities.add(entity);
	}

	/*
	 * Get and parse OMIM entries.
	 * 
	 * Do not store entries without an OMIM identifier... e.g. this one: Leukemia, acute myelogenous (3)|KRAS, KRAS2,
	 * RASK2, NS, CFC2|190070|12p12.1
	 * 
	 * But do store this one: Leukemia, acute myelogenous, 601626 (3)|GMPS|600358|3q25.31
	 */
	private void addLineToMap(Map<String, List<List<String>>> omimEntriesByGeneSymbol, String[] values)
	{
		// trim mapping method field, example: (3)
		String entry = values[0];
		entry = entry.substring(0, entry.length() - 3);
		entry = entry.trim();

		// last six characters should be OMIM id
		entry = entry.substring(entry.length() - 6);
		if (entry.matches("[0-9]+"))
		{
			String disorder = values[0].substring(0, values[0].length() - 12);
			List<String> genes = asList(values[1].split(", "));
			String causalIdentifier = values[2];
			String cytogenicLocation = values[3];
			String type = values[0].substring(values[0].length() - 2, values[0].length() - 1);
			String omimEntry = entry;

			for (String geneSymbol : genes)
			{
				if (omimEntriesByGeneSymbol.containsKey(geneSymbol))
				{
					omimEntriesByGeneSymbol.get(geneSymbol).get(0).add(disorder); // first list is phenoype
					omimEntriesByGeneSymbol.get(geneSymbol).get(1).add(causalIdentifier); // second is mim number
					omimEntriesByGeneSymbol.get(geneSymbol).get(2).add(cytogenicLocation); // third is cyto location
					omimEntriesByGeneSymbol.get(geneSymbol).get(3).add(type); // fourth is type of syndrome
					omimEntriesByGeneSymbol.get(geneSymbol).get(4).add(omimEntry); // fifth is omim entry location
				}
				else
				{
					LinkedList<List<String>> mapList = new LinkedList<>();
					mapList.add(newArrayList(disorder));
					mapList.add(newArrayList(causalIdentifier));
					mapList.add(newArrayList(cytogenicLocation));
					mapList.add(newArrayList(type));
					mapList.add(newArrayList(omimEntry));
					omimEntriesByGeneSymbol.put(geneSymbol, mapList);
				}
			}
		}
	}
}