001/*
002 * Copyright 2018 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.cvmapping;
017
018import de.isas.mztab2.model.Parameter;
019import de.isas.mztab2.validation.CvTermSelectionHandler;
020import java.util.List;
021import java.util.stream.Collectors;
022import lombok.extern.slf4j.Slf4j;
023import org.apache.commons.jxpath.Pointer;
024import org.apache.commons.lang3.tuple.Pair;
025
026/**
027 * Removes user parameters from the provided selection.
028 *
029 * @author nilshoffmann
030 */
031@Slf4j
032public class RemoveUserParams implements CvTermSelectionHandler {
033
034    @Override
035    public List<Pair<Pointer, Parameter>> handleSelection(
036        List<Pair<Pointer, Parameter>> selection) {
037        List<Pair<Pointer, Parameter>> filteredSelection = selection.
038            stream().
039            filter((pair) ->
040            {
041                if (pair.getValue().
042                    getCvAccession() == null || pair.getValue().
043                        getCvAccession().
044                        isEmpty()) {
045                    //user parameter
046                    log.debug("Removing user parameter for path " + pair.
047                        getKey().
048                        asPath() + " with value " + pair.getValue());
049                    return false;
050                }
051                return true;
052            }).
053            collect(Collectors.toList());
054        filteredSelection.forEach((pair) ->
055        {
056            Parameter p = pair.getValue();
057            if (!p.getCvAccession().
058                contains(":")) {
059                throw new RuntimeException(
060                    "Malformed cv accession '" + p.getCvAccession() + "' for " + pair.
061                    getKey().
062                    asPath() + ". Must be: <CV>:<TERMNUMBER>");
063            }
064        });
065        return filteredSelection;
066    }
067}