annis.CSVHelper.java Source code

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Here is the source code for annis.CSVHelper.java

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/*
 * Copyright 2009-2011 Collaborative Research Centre SFB 632 
 *
 * 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.
 */
package annis;

import annis.dao.objects.AnnotatedMatch;
import annis.dao.objects.AnnotatedSpan;
import annis.model.Annotation;
import au.com.bytecode.opencsv.CSVWriter;
import com.google.common.collect.Collections2;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 *
 * @author thomas
 */
public class CSVHelper {

    private static final Logger log = LoggerFactory.getLogger(CSVHelper.class);

    public static SortedMap<Integer, SortedSet<String>> exportCSVHeader(Iterator<AnnotatedMatch> matches,
            PrintWriter w) {
        // figure out what annotations are used at each match position
        SortedMap<Integer, SortedSet<String>> columnsByNodePos = new TreeMap<>();
        while (matches.hasNext()) {
            AnnotatedMatch match = matches.next();
            for (int j = 0; j < match.size(); ++j) {
                AnnotatedSpan span = match.get(j);
                if (columnsByNodePos.get(j) == null) {
                    columnsByNodePos.put(j, new TreeSet<String>());
                }
                for (Annotation annotation : span.getAnnotations()) {
                    columnsByNodePos.get(j).add("anno_" + annotation.getQualifiedName());
                }

                for (Annotation meta : span.getMetadata()) {
                    columnsByNodePos.get(j).add("meta_" + meta.getQualifiedName());
                }

            }
        }

        CSVWriter csvWriter = new CSVWriter(w, '\t', CSVWriter.NO_QUOTE_CHARACTER, '\\');
        // print column names and data types
        int count = columnsByNodePos.keySet().size();
        ArrayList<String> headerLine = new ArrayList<>();

        for (int j = 0; j < count; ++j) {
            headerLine.add(fullColumnName(j + 1, "id"));
            headerLine.add(fullColumnName(j + 1, "span"));

            SortedSet<String> annotationNames = columnsByNodePos.get(j);
            for (String name : annotationNames) {
                headerLine.add(fullColumnName(j + 1, name));
            }
        }
        csvWriter.writeNext(headerLine.toArray(new String[headerLine.size()]));

        return columnsByNodePos;
    }

    public static void exportCSVData(Iterator<AnnotatedMatch> matches,
            SortedMap<Integer, SortedSet<String>> columnsByNodePos, PrintWriter w) {
        int count = columnsByNodePos.keySet().size();

        // print values
        while (matches.hasNext()) {
            AnnotatedMatch match = matches.next();

            List<String> line = new ArrayList<>();
            int k = 0;
            for (; k < match.size(); ++k) {
                AnnotatedSpan span = match.get(k);
                Map<String, String> valueByName = new HashMap<>();

                if (span != null) {
                    if (span.getAnnotations() != null) {
                        for (Annotation annotation : span.getAnnotations()) {
                            valueByName.put("anno_" + annotation.getQualifiedName(), annotation.getValue());
                        }
                    }
                    if (span.getMetadata() != null) {
                        for (Annotation meta : span.getMetadata()) {
                            valueByName.put("meta_" + meta.getQualifiedName(), meta.getValue());
                        }
                    }

                    line.add("" + span.getId());
                    line.add(span.getCoveredText().replace("\t", "\\t"));
                }

                for (String name : columnsByNodePos.get(k)) {
                    if (valueByName.containsKey(name)) {
                        line.add(valueByName.get(name).replace("\t", "\\t"));
                    } else {
                        line.add("'NULL'");
                    }
                }
            }
            for (int l = k; l < count; ++l) {
                line.add("'NULL'");
                for (int m = 0; m <= columnsByNodePos.get(l).size(); ++m) {
                    line.add("'NULL'");
                }
            }
            w.append(StringUtils.join(line, "\t"));
            w.append("\n");
        }
    }

    private static String fullColumnName(int i, String name) {
        return i + "_" + name;
    }
}