org.gbif.dwca.io.ArchiveFile.java Source code

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Here is the source code for org.gbif.dwca.io.ArchiveFile.java

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/*
 * Copyright 2010 Global Biodiversity Informatics Facility.
 * 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 org.gbif.dwca.io;

import org.apache.commons.lang3.StringUtils;
import org.gbif.dwc.terms.Term;
import org.gbif.dwc.terms.TermFactory;
import org.gbif.dwca.record.Record;
import org.gbif.dwca.record.RecordIterator;
import org.gbif.utils.file.csv.CSVReader;

import java.io.File;
import java.io.IOException;
import java.util.*;

/**
 * This class can be used to encapsulate information about a file contained within a Darwin Core Archive. It generally
 * represents the fileType object described in the Darwin Core Archive XSD.
 *
 * @see <a href="http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd">Darwin Core Archive XSD</a>
 */
public class ArchiveFile implements Iterable<Record> {
    private static final TermFactory TERM_FACTORY = TermFactory.instance();

    public class ArchiveFieldIndexComparator implements Comparator<ArchiveField> {

        public int compare(ArchiveField o1, ArchiveField o2) {
            if (o1.getIndex() == null && o2.getIndex() == null) {
                return 0;
            } else if (o1.getIndex() == null) {
                return -1;
            } else if (o2.getIndex() == null) {
                return 1;
            } else if (o1.getIndex().equals(o2.getIndex())) {
                return o1.getTerm().qualifiedName().compareToIgnoreCase(o2.getTerm().qualifiedName());
            } else {
                return o1.getIndex().compareTo(o2.getIndex());
            }
        }

    }

    private ArchiveField id;
    private Archive archive;
    private final LinkedList<String> locations = new LinkedList<String>();
    private String title;
    private String fieldsTerminatedBy;
    private Character fieldsEnclosedBy;
    // this is actually ignored by the CSVReader and any of \n, \r or \n\r is used
    private String linesTerminatedBy = "\n";
    private String encoding = "utf8";
    private Term rowType;
    private Integer ignoreHeaderLines = 0;

    private String dateFormat = "YYYY-MM-DD";

    private Map<Term, ArchiveField> fields = new HashMap<Term, ArchiveField>();

    public static ArchiveFile buildCsvFile() {
        ArchiveFile af = new ArchiveFile();
        af.setFieldsEnclosedBy('"');
        af.setFieldsTerminatedBy(",");
        return af;
    }

    public static ArchiveFile buildTabFile() {
        ArchiveFile af = new ArchiveFile();
        af.setFieldsEnclosedBy(null);
        af.setFieldsTerminatedBy("\t");
        return af;
    }

    public static File getLocationFileSorted(File location) {
        return new File(location.getParentFile(), location.getName() + "-sorted");
    }

    public static String getLocationSorted(String location) {
        return location + "-sorted";
    }

    public void addField(ArchiveField field) {
        fields.put(field.getTerm(), field);
    }

    public void addLocation(String location) {
        if (title == null) {
            if (location != null && location.lastIndexOf('/') > 1) {
                title = location.substring(location.lastIndexOf('/') + 1, location.length());
            } else {
                title = location;
            }
        }
        locations.add(location);
    }

    public Archive getArchive() {
        return archive;
    }

    public CSVReader getCSVReader() throws IOException {
        return org.gbif.io.CSVReaderFactory.build(this);
    }

    public String getDateFormat() {
        return dateFormat;
    }

    public String getEncoding() {
        return encoding;
    }

    public ArchiveField getField(Term term) {
        if (term == null) {
            return null;
        }
        return fields.get(term);
    }

    public ArchiveField getField(String term) {
        return getField(TERM_FACTORY.findTerm(term));
    }

    public Map<Term, ArchiveField> getFields() {
        return fields;
    }

    public Character getFieldsEnclosedBy() {
        return fieldsEnclosedBy;
    }

    public List<ArchiveField> getFieldsSorted() {
        List<ArchiveField> list = new ArrayList<ArchiveField>(fields.values());
        Collections.sort(list, new ArchiveFieldIndexComparator());
        return list;
    }

    public String getFieldsTerminatedBy() {
        return fieldsTerminatedBy;
    }

    public ArchiveField getId() {
        return id;
    }

    public Integer getIgnoreHeaderLines() {
        return ignoreHeaderLines;
    }

    public String getLinesTerminatedBy() {
        return linesTerminatedBy;
    }

    /**
     * Get the first file location.
     * TODO: check if we got more than 1 file and implement some unix concat into a single file first before sorting that
     */
    public String getLocation() {
        return locations.getFirst();
    }

    public File getLocationFile() {
        File dataFile;
        if (archive != null) {
            if (getLocation() == null) {
                // use only archive
                dataFile = archive.getLocation();
            } else if (getLocation().startsWith("/")) {
                // absolute already
                dataFile = new File(getLocation());
            } else {
                // use source file relative to archive dir
                dataFile = new File(archive.getLocation(), getLocation());
            }
        } else {
            dataFile = new File(getLocation());
        }

        return dataFile;
    }

    public List<String> getLocations() {
        return locations;
    }

    public Term getRowType() {
        return rowType;
    }

    public Set<Term> getTerms() {
        return fields.keySet();
    }

    public String getTitle() {
        return title;
    }

    public boolean hasTerm(Term term) {
        return getField(term) != null;
    }

    public boolean hasTerm(String term) {
        return getField(term) != null;
    }

    public Iterator<Record> iterator() {
        return RecordIterator.build(this, true, true);
    }

    public void setArchive(Archive archive) {
        this.archive = archive;
    }

    public void setDateFormat(String dateFormat) {
        this.dateFormat = dateFormat;
    }

    public void setEncoding(String encoding) {
        this.encoding = StringUtils.trimToNull(encoding);
    }

    public void setFieldsEnclosedBy(Character fieldsEnclosedBy) {
        this.fieldsEnclosedBy = fieldsEnclosedBy;
    }

    public void setFieldsTerminatedBy(String fieldsTerminatedBy) {
        this.fieldsTerminatedBy = StringUtils.defaultIfEmpty(fieldsTerminatedBy, null);
    }

    public void setId(ArchiveField id) {
        this.id = id;
    }

    public void setIgnoreHeaderLines(Integer ignoreHeaderLines) {
        if (ignoreHeaderLines == null || ignoreHeaderLines < 0) {
            ignoreHeaderLines = 0;
        }
        this.ignoreHeaderLines = ignoreHeaderLines;
    }

    public void setLinesTerminatedBy(String linesTerminatedBy) {
        this.linesTerminatedBy = StringUtils.defaultIfEmpty(linesTerminatedBy, null);
    }

    public void setRowType(Term rowType) {
        this.rowType = rowType;
    }
}