IdfProtocolUsageCheck.java

/*
 * Copyright 2009-2013 European Molecular Biology Laboratory
 *
 * 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.fg.annotare2.magetabcheck.checks.refs;

import uk.ac.ebi.fg.annotare2.magetabcheck.checker.annotation.Check;
import uk.ac.ebi.fg.annotare2.magetabcheck.checker.annotation.MageTabCheck;
import uk.ac.ebi.fg.annotare2.magetabcheck.checker.annotation.Visit;
import uk.ac.ebi.fg.annotare2.magetabcheck.model.idf.Protocol;
import uk.ac.ebi.fg.annotare2.magetabcheck.model.sdrf.SdrfProtocolNode;

import java.util.Set;

import static com.google.common.collect.Sets.newHashSet;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is;
import static uk.ac.ebi.fg.annotare2.magetabcheck.checker.CheckModality.WARNING;

/**
 * @author Olga Melnichuk
 */
@MageTabCheck(
        ref = "REF01",
        value = "IDF should not contain protocol definitions that are not used in SDRF",
        modality = WARNING
)
public class IdfProtocolUsageCheck {

    private final Set<String> definedProtocols = newHashSet();
    private final Set<String> usedProtocols = newHashSet();

    @Visit
    public void visit(Protocol protocol) {
        definedProtocols.add(protocol.getName().getValue());
    }

    @Visit
    public void visit(SdrfProtocolNode protocolNode) {
        Protocol protocol = protocolNode.getProtocol();
        if (protocol != null) {
            usedProtocols.add(protocol.getName().getValue());
        }
    }

    @Check
    public void check() {
        assertThat(usedProtocols, is(definedProtocols));
    }
}