SemanticTypes.java

/*
 * #%L
 * NICTA t3as SNOMED service common classes
 * %%
 * Copyright (C) 2014 NICTA
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as
 * published by the Free Software Foundation, either version 3 of the
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 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/gpl-3.0.html>.
 * 
 * Additional permission under GNU GPL version 3 section 7
 * 
 * If you modify this Program, or any covered work, by linking or combining
 * it with H2, GWT, or JavaBeans Activation Framework (JAF) (or a
 * modified version of those libraries), containing parts covered by the
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package org.t3as.metamap;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.ImmutableSortedMap;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;

import static com.google.common.base.Charsets.UTF_8;
import static com.google.common.io.Resources.getResource;
import static com.google.common.io.Resources.readLines;

public final class SemanticTypes {

    /**
     * This has to be downloaded from the NLM MetaMap site. Last known URL was:
     * http://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt
     */
    private static final String SEMANTIC_TYPES_FILE = "SemanticTypes_2013AA.txt";
    private static final String DEFAULT_SEMANTIC_TYPES_FILE = "defaultSemanticTypes.txt";

    @SuppressWarnings("PublicStaticCollectionField")
    public static final ImmutableList<String> DEFAULT_MM_SEMANTIC_TYPES;
    @SuppressWarnings("PublicStaticCollectionField")
    public static final ImmutableMap<String, String> SEMANTIC_TYPES_CODE_TO_DESCRIPTION;

    static {
        final Map<String, String> semanticTypes = new HashMap<>();
        final Collection<String> defaultSemanticTypes = new ArrayList<>();
        try {
            defaultSemanticTypes.addAll(readLines(getResource(DEFAULT_SEMANTIC_TYPES_FILE), UTF_8));

            // load all the MetaMap Semantic Types and make a static map out of the code and descriptions
            final Collection<String> semanticTypeLines = readLines(getResource(SEMANTIC_TYPES_FILE), UTF_8);
            final Pattern PIPE = Pattern.compile("\\|");
            for (final String line : semanticTypeLines) {
                final String[] parts = PIPE.split(line);
                semanticTypes.put(parts[0], parts[2]);
            }
        }
        catch (final IOException e) {
            throw new RuntimeException("Could not load MetaMap Semantic Types: " + e.getMessage(), e);
        }

        DEFAULT_MM_SEMANTIC_TYPES = ImmutableList.copyOf(defaultSemanticTypes);
        SEMANTIC_TYPES_CODE_TO_DESCRIPTION = ImmutableSortedMap.copyOf(semanticTypes);
    }

    private SemanticTypes() {}

    /**
     * Sanitise semantic types from user input.
     * @param semanticTypes the semantic types to be sanitised
     * @return a non-null but possibly empty Collection of semantic types
     */
    public static Collection<String> sanitiseSemanticTypes(final Collection<String> semanticTypes) {
        if (semanticTypes == null) return ImmutableList.of();

        // check that each of the given types are in the map we have, otherwise throw it away
        final Set<String> s = new LinkedHashSet<>(semanticTypes);
        return s.retainAll(SEMANTIC_TYPES_CODE_TO_DESCRIPTION.keySet()) ? s : semanticTypes;
    }
}