uk.ac.ebi.embl.api.validation.check.genomeassembly.ChromosomeFieldandValueCheck.java Source code

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Here is the source code for uk.ac.ebi.embl.api.validation.check.genomeassembly.ChromosomeFieldandValueCheck.java

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/*******************************************************************************
 * Copyright 2012 EMBL-EBI, Hinxton outstation
 * 
 * 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 uk.ac.ebi.embl.api.validation.check.genomeassembly;

import java.util.ArrayList;
import java.util.Set;
import java.util.TreeSet;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.embl.api.genomeassembly.ChromosomeRecord;
import uk.ac.ebi.embl.api.genomeassembly.GenomeAssemblyRecord;
import uk.ac.ebi.embl.api.genomeassembly.GenomeAssemblyRecord.ChromosomeDataRow;
import uk.ac.ebi.embl.api.storage.DataRow;
import uk.ac.ebi.embl.api.storage.DataSet;
import uk.ac.ebi.embl.api.validation.ValidationResult;
import uk.ac.ebi.embl.api.validation.annotation.CheckDataSet;
import uk.ac.ebi.embl.api.validation.annotation.Description;
import uk.ac.ebi.embl.api.validation.helper.Utils;

@Description("")
public class ChromosomeFieldandValueCheck extends GenomeAssemblyValidationCheck {

    @CheckDataSet("chromosome-location-keywords.tsv")
    private DataSet locationSet;
    private final static String MISSING_MANDATORY_ID = "ChromosomeFieldandValueCheck-1";
    private final static String INVALID_VALUE_ID = "ChromosomeFieldandValueCheck-2";
    private final static String INVALID_ROW_ID = "ChromosomeFieldandValueCheck-3";
    private Set<String> locations = new TreeSet<String>();
    private String object_name, chromosome_name, type, location;

    public ChromosomeFieldandValueCheck() {

    }

    public ChromosomeFieldandValueCheck(DataSet dataSet) {
        this.locationSet = dataSet;
    }

    public ValidationResult check(GenomeAssemblyRecord chromosomeRecord) {
        result = new ValidationResult();

        if (chromosomeRecord == null) {
            return result;
        }
        @SuppressWarnings("unchecked")
        ArrayList<ChromosomeDataRow> rows = (ArrayList<ChromosomeDataRow>) chromosomeRecord.getFields();

        for (DataRow dataRow : locationSet.getRows()) {
            String location = Utils.parseTSVString(dataRow.getString(0));
            locations.add(location);
        }
        for (ChromosomeDataRow row : rows) {

            object_name = row.get_object_name();
            chromosome_name = row.get_chromosome_name();
            type = row.get_type();
            location = row.get_location();
            if (!row.isValid()) {
                reportError(row.getOrigin(), INVALID_ROW_ID);
                continue;
            }
            if (object_name == null || chromosome_name == null || type == null) {
                reportError(row.getOrigin(), MISSING_MANDATORY_ID);
            }

            if (object_name != null && object_name.split(" ").length > 1) {
                reportError(row.getOrigin(), INVALID_VALUE_ID, ChromosomeRecord.OBJECT_NAME_KEYWORD, object_name);
            }
            if (chromosome_name != null && StringUtils.indexOfAny(chromosome_name.toLowerCase(),
                    ChromosomeRecord.INVALID_CHNAME_VALUES) != -1) {
                reportError(row.getOrigin(), INVALID_VALUE_ID, ChromosomeRecord.CHROMOSOME_NAME_KEYWORD,
                        chromosome_name);
            }
            if (type != null
                    && StringUtils.indexOfAny(type.toLowerCase(), ChromosomeRecord.VALID_TYPE_VALUE) == -1) {
                reportError(row.getOrigin(), INVALID_VALUE_ID, ChromosomeRecord.TYPE_KEYWORD, type);
            }

            if (location != null && !ArrayUtils.contains(locations.toArray(), location.toLowerCase())) {
                reportError(row.getOrigin(), INVALID_VALUE_ID, ChromosomeRecord.LOCATION_KEYWORD, location);
            }
        }
        return result;
    }
}