001/*
002 * Copyright 2019 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
003 *
004 * Licensed under the Apache License, Version 2.0 (the "License");
005 * you may not use this file except in compliance with the License.
006 * You may obtain a copy of the License at
007 *
008 *      http://www.apache.org/licenses/LICENSE-2.0
009 *
010 * Unless required by applicable law or agreed to in writing, software
011 * distributed under the License is distributed on an "AS IS" BASIS,
012 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
013 * See the License for the specific language governing permissions and
014 * limitations under the License.
015 */
016package de.isas.mztab2.io.validators;
017
018import de.isas.mztab2.model.Metadata;
019import de.isas.mztab2.model.MsRun;
020import de.isas.mztab2.model.Parameter;
021import java.util.LinkedList;
022import java.util.List;
023import java.util.SortedMap;
024import uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType;
025import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError;
026import uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext;
027
028/**
029 * Validates that the ms run section is present in metadata.
030 *
031 * @author nilshoffmann
032 */
033public class MsRunValidator implements RefiningValidator<Metadata> {
034
035    @Override
036    public List<MZTabError> validateRefine(Metadata metadata, MZTabParserContext parserContext) {
037        SortedMap<Integer, MsRun> runMap = parserContext.getMsRunMap();
038        List<MZTabError> errorList = new LinkedList<>();
039        for (Integer id : runMap.keySet()) {
040            if (runMap.get(id).
041                    getLocation() == null) {
042                errorList.add(new MZTabError(
043                        LogicalErrorType.NotDefineInMetadata, -1,
044                        Metadata.Properties.msRun + "[" + id + "]-" + MsRun.Properties.location));
045            }
046            List<Parameter> scanPolarity = runMap.get(id).
047                    getScanPolarity();
048            if (scanPolarity == null || scanPolarity.isEmpty()) {
049                errorList.add(new MZTabError(
050                        LogicalErrorType.NotDefineInMetadata, -1,
051                        Metadata.Properties.msRun + "[" + id + "]-" + MsRun.Properties.scanPolarity));
052            }
053
054        }
055        return errorList;
056    }
057
058}