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Protempa Framework is the core of Protempa.
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/*
 * #%L
 * Protempa Framework
 * %%
 * Copyright (C) 2012 - 2013 Emory University
 * %%
 * 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.
 * #L%
 */
package org.protempa.dest.table;

import java.io.BufferedWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.arp.javautil.string.StringUtil;
import org.protempa.KnowledgeSource;
import org.protempa.KnowledgeSourceCache;
import org.protempa.KnowledgeSourceCacheFactory;
import org.protempa.KnowledgeSourceReadException;
import org.protempa.PropositionDefinition;
import org.protempa.ProtempaUtil;
import org.protempa.dest.AbstractQueryResultsHandler;
import org.protempa.dest.QueryResultsHandlerProcessingException;
import org.protempa.dest.QueryResultsHandlerValidationFailedException;
import org.protempa.proposition.Proposition;
import org.protempa.proposition.UniqueId;

/**
 *
 * @author Andrew Post
 */
public final class TableQueryResultsHandler
        extends AbstractQueryResultsHandler {

    private final char columnDelimiter;
    private final String[] rowPropositionIds;
    private final TableColumnSpec[] columnSpecs;
    private final boolean headerWritten;
    private final BufferedWriter out;
    private final Map replace;
    private final KnowledgeSource knowledgeSource;
    private KnowledgeSourceCache ksCache;

    TableQueryResultsHandler(BufferedWriter out, char columnDelimiter,
            String[] rowPropositionIds, TableColumnSpec[] columnSpecs,
            boolean headerWritten, 
            KnowledgeSource knowledgeSource) {
        checkConstructorArgs(rowPropositionIds, columnSpecs);
        this.columnDelimiter = columnDelimiter;
        this.rowPropositionIds = rowPropositionIds.clone();
        ProtempaUtil.internAll(this.rowPropositionIds);
        this.columnSpecs = columnSpecs.clone();
        this.headerWritten = headerWritten;
        this.out = out;
        this.replace = new HashMap<>();
        this.replace.put(null, "(null)");
        this.replace.put("", "(empty)");
        this.knowledgeSource = knowledgeSource;
    }

    @Override
    public void validate() throws QueryResultsHandlerValidationFailedException {
        List invalidPropIds = new ArrayList<>();
        try {
            for (String propId : rowPropositionIds) {
                if (!knowledgeSource.hasPropositionDefinition(propId)) {
                    invalidPropIds.add(propId);
                }
            }
            if (!invalidPropIds.isEmpty()) {
                throw new QueryResultsHandlerValidationFailedException("Invalid row proposition id(s): " + StringUtils.join(invalidPropIds, ", "));
            }
            int i = 1;
            for (TableColumnSpec columnSpec : columnSpecs) {
                try {
                    columnSpec.validate(knowledgeSource);
                } catch (TableColumnSpecValidationFailedException ex) {
                    throw new QueryResultsHandlerValidationFailedException("Validation of column spec " + i + " failed", ex);
                }
                i++;
            }
        } catch (KnowledgeSourceReadException ex) {
            throw new QueryResultsHandlerValidationFailedException("Error during validation", ex);
        }
    }
    
    @Override
    public void start(Collection cache) throws QueryResultsHandlerProcessingException {
        Logger logger = Util.logger();
        if (this.headerWritten) {
            try {
                List columnNames = new ArrayList<>();
                columnNames.add("KeyId");
                for (TableColumnSpec columnSpec : this.columnSpecs) {
                    logger.log(Level.FINE, "Processing columnSpec type {0}", columnSpec.getClass().getName());
                    String[] colNames = columnSpec.columnNames(this.knowledgeSource);
                    assert colNames.length > 0 : "colNames must have length > 0";
                    for (int index = 0; index < colNames.length; index++) {
                        String colName = colNames[index];
                        if (this.replace.containsKey(colName)) {
                            colNames[index] = this.replace.get(colName);
                        }
                    }
                    if (logger.isLoggable(Level.FINE)) {
                        logger.log(Level.FINE, "Got the following columns for proposition {0}: {1}", new Object[]{StringUtils.join(this.rowPropositionIds, ", "), StringUtils.join(colNames, ", ")});
                    }
                    for (String colName : colNames) {
                        columnNames.add(colName);
                    }
                }
                StringUtil.escapeAndWriteDelimitedColumns(columnNames, this.columnDelimiter, this.out);
                this.out.newLine();
            } catch (KnowledgeSourceReadException ex1) {
                throw new QueryResultsHandlerProcessingException("Error reading knowledge source", ex1);
            } catch (IOException ex) {
                throw new QueryResultsHandlerProcessingException("Could not write header", ex);
            }
        }
        
        try {
            this.ksCache = new KnowledgeSourceCacheFactory().getInstance(this.knowledgeSource, cache, true);
        } catch (KnowledgeSourceReadException ex) {
            throw new QueryResultsHandlerProcessingException(ex);
        }
    }

    @Override
    public void handleQueryResult(String keyId, List propositions, Map> forwardDerivations, Map> backwardDerivations, Map references) throws QueryResultsHandlerProcessingException {
        int n = this.columnSpecs.length;
        Util.logger().log(Level.FINER, "Processing keyId {0}", keyId);
        for (Proposition prop : propositions) {
            if (!org.arp.javautil.arrays.Arrays.contains(this.rowPropositionIds, prop.getId())) {
                continue;
            }
            try {
                StringUtil.escapeAndWriteDelimitedColumn(keyId, this.columnDelimiter, this.out);
                if (n > 0) {
                    this.out.write(this.columnDelimiter);
                }
                for (int i = 0; i < n; i++) {
                    TableColumnSpec columnSpec = this.columnSpecs[i];
                    columnSpec.columnValues(keyId, prop, forwardDerivations, backwardDerivations, references, this.ksCache, this.replace, this.columnDelimiter, this.out);
                    if (i < n - 1) {
                        this.out.write(this.columnDelimiter);
                    } else {
                        this.out.newLine();
                    }
                }
            } catch (IOException ex) {
                throw new QueryResultsHandlerProcessingException("Could not write row" + ex);
            }
        }
    }

    private void checkConstructorArgs(String[] rowPropositionIds,
            TableColumnSpec[] columnSpecs) {
        ProtempaUtil.checkArray(rowPropositionIds, "rowPropositionIds");
        ProtempaUtil.checkArray(columnSpecs, "columnSpecs");
    }

}