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.Assay;
019import de.isas.mztab2.model.Metadata;
020import java.util.LinkedList;
021import java.util.List;
022import java.util.SortedMap;
023import uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType;
024import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError;
025import uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext;
026
027/**
028 * Validates that the quantification method section is present in metadata.
029 *
030 * @author nilshoffmann
031 */
032public class AssayValidator implements RefiningValidator<Metadata> {
033
034    @Override
035    public List<MZTabError> validateRefine(Metadata metadata, MZTabParserContext parserContext) {
036        SortedMap<Integer, Assay> assayMap = parserContext.getAssayMap();
037        List<MZTabError> errorList = new LinkedList<>();
038        if (assayMap.isEmpty()) {
039            errorList.add(new MZTabError(
040                    LogicalErrorType.NotDefineInMetadata, -1,
041                    Metadata.Properties.assay + ""));
042        }
043
044        for (Integer id : assayMap.keySet()) {
045            if (assayMap.get(id).
046                    getMsRunRef() == null || assayMap.get(id).
047                            getMsRunRef().isEmpty()) {
048                errorList.add(new MZTabError(
049                        LogicalErrorType.NotDefineInMetadata, -1,
050                        Metadata.Properties.assay + "[" + id + "]-" + Assay.Properties.msRunRef));
051            }
052        }
053        return errorList;
054    }
055
056}