CvDefinitionValidationHandler.java
- /*
- * Copyright 2018 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
- *
- * 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 de.isas.mztab2.validation;
- import de.isas.lipidomics.mztab2.validation.Validator;
- import de.isas.mztab2.cvmapping.JxPathElement;
- import de.isas.mztab2.cvmapping.SetOperations;
- import de.isas.mztab2.io.serialization.ParameterConverter;
- import de.isas.mztab2.model.CV;
- import de.isas.mztab2.model.MzTab;
- import de.isas.mztab2.model.Parameter;
- import de.isas.mztab2.model.ValidationMessage;
- import java.util.ArrayList;
- import java.util.HashSet;
- import java.util.List;
- import java.util.Map;
- import java.util.Set;
- import java.util.stream.Collectors;
- import lombok.extern.slf4j.Slf4j;
- import org.apache.commons.jxpath.JXPathContext;
- import org.apache.commons.jxpath.Pointer;
- import org.apache.commons.lang3.tuple.Pair;
- import uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType;
- import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError;
- /**
- * Validates that controlled vocabularies used by parameters are defined in the
- * metadata CV section.
- *
- * @author nilshoffmann
- */
- @Slf4j
- @lombok.Builder()
- public class CvDefinitionValidationHandler implements Validator<MzTab> {
- @Override
- public List<ValidationMessage> validate(MzTab mzTab) {
- JXPathContext context = JXPathContext.newContext(mzTab);
- return checkCvDefinitions(mzTab, context);
- }
- private List<ValidationMessage> checkCvDefinitions(MzTab mzTabFile,
- JXPathContext context) {
- Map<String, CV> cvTerms = mzTabFile.getMetadata().
- getCv().
- stream().
- collect(Collectors.toMap((key) ->
- {
- return key.getLabel();
- }, (value) ->
- {
- return value;
- }));
- List<ValidationMessage> messages = new ArrayList<>();
- List<Pair<Pointer, Parameter>> parameters = JxPathElement.
- toList(context, "//*[cvLabel!='']",
- Parameter.class);
- log.debug("Selected {} cv parameters!", parameters.size());
- Set<String> definedCvLabels = new HashSet<>(cvTerms.keySet());
- Set<String> usedCvLabels = new HashSet<>();
- parameters.stream().
- forEach((t) ->
- {
- Parameter param = t.getValue();
- log.debug("Checking parameter {}", new ParameterConverter().
- convert(param));
- if (param.getCvLabel() != null && !param.getCvLabel().
- isEmpty()) {
- usedCvLabels.add(param.getCvLabel());
- if (!cvTerms.containsKey(param.getCvLabel())) {
- log.debug(
- "Parameter {} uses undefined controlled vocabulary: {}",
- new ParameterConverter().
- convert(param), param.getCvLabel());
- MZTabError error = new MZTabError(
- CrossCheckErrorType.CvUndefinedInMetadata, -1,
- param.getCvLabel(),
- new ParameterConverter().convert(param));
- messages.add(error.toValidationMessage());
- }
- }
- });
- Set<String> unusedCvLabels = SetOperations.complement(definedCvLabels,
- usedCvLabels);
- unusedCvLabels.stream().
- forEach((cvLabel) ->
- {
- log.debug(
- "Cv with label {} is not being used by any parameters!",
- cvLabel);
- MZTabError error = new MZTabError(
- CrossCheckErrorType.CvUnused, -1,
- cvLabel);
- messages.add(error.toValidationMessage());
- });
- return messages;
- }
- }