CvParameterLookupService.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.cvmapping;
- import de.isas.mztab2.model.Parameter;
- import java.util.LinkedHashMap;
- import java.util.List;
- import java.util.Map;
- import java.util.stream.Collectors;
- import lombok.extern.slf4j.Slf4j;
- import uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient;
- import uk.ac.ebi.pride.utilities.ols.web.service.config.OLSWsConfig;
- import uk.ac.ebi.pride.utilities.ols.web.service.model.Identifier;
- /**
- * Abstraction over OLSClient to autoconvert Terms to Parameters and to allow
- * easy matching of Parameters against parent terms and their children.
- *
- * @author nilshoffmann
- */
- @Slf4j
- public class CvParameterLookupService {
- private final OLSClient client;
- private final Map<Parameter, List<Parameter>> childCache;
- private final Map<Parameter, List<Parameter>> parentCache;
- private static <K, V> Map<K, V> lruCache(final int maxSize) {
- return new LinkedHashMap<K, V>(maxSize * 4 / 3, 0.75f, true) {
- @Override
- protected boolean removeEldestEntry(Map.Entry<K, V> eldest) {
- return size() > maxSize;
- }
- };
- }
- /**
- * Create a new instance of the lookup service with default OLS configuration.
- */
- public CvParameterLookupService() {
- this(new OLSClient(new OLSWsConfig()));
- }
- /**
- * Create a new instance of the lookup service with a custom OLSClient.
- * @param client the custom OLS client
- */
- public CvParameterLookupService(OLSClient client) {
- this.client = client;
- this.childCache = lruCache(4096);
- this.parentCache = lruCache(4096);
- }
- /**
- * Create a new instance of the lookup service with a custom OLSWsConfig configuration.
- * @param config the custom configuration
- */
- public CvParameterLookupService(OLSWsConfig config) {
- this(new OLSClient(config));
- }
-
- /**
- * Clears all query result caches (parent and child).
- */
- public void clearCaches() {
- this.childCache.clear();
- this.parentCache.clear();
- }
- /**
- * Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).
- * Use at your own risk, the OLS service may terminate your connection if the response is too large or takes too long.
- * @param parameter the parameter to start from
- * @return a list of all parent parameters for the given parameter
- * @throws org.springframework.web.client.HttpClientErrorException on http related errors
- */
- public List<Parameter> resolveParents(Parameter parameter) throws org.springframework.web.client.HttpClientErrorException {
- return resolveParents(parameter, -1);
- }
- /**
- * Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).
- * @param parameter the parameter to start from
- * @param levels maximum levels to query
- * @return a list of all parent parameters for the given parameter
- * @throws org.springframework.web.client.HttpClientErrorException on http related errors
- */
- public List<Parameter> resolveParents(Parameter parameter, int levels) throws org.springframework.web.client.HttpClientErrorException {
- if (parameter.getCvAccession() == null || parameter.getCvLabel() == null) {
- throw new IllegalArgumentException(
- "Parameter must provide cvAccession and cvLabel!");
- }
- if(parentCache.containsKey(parameter)) {
- log.debug("Cache hit for parameter "+parameter+" in parent cache!");
- return parentCache.get(parameter);
- }
- Identifier ident = new Identifier(parameter.getCvAccession(),
- Identifier.IdentifierType.OBO);
- List<Parameter> parents = client.getTermParents(ident, parameter.getCvLabel(), levels).
- stream().
- map(CvMappingUtils::asParameter).
- collect(Collectors.toList());
- parentCache.put(parameter, parents);
- return parents;
- }
- /**
- * Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).
- * @param parameter the parameter to start from
- * @param levels maximum levels to query
- * @return a list of all child parameters for the given parameter
- * @throws org.springframework.web.client.HttpClientErrorException on http related errors
- */
- public List<Parameter> resolveChildren(Parameter parameter, int levels) throws org.springframework.web.client.HttpClientErrorException {
- if (parameter.getCvAccession() == null || parameter.getCvLabel() == null) {
- throw new IllegalArgumentException(
- "Parameter must provide cvAccession and cvLabel!");
- }
- if(childCache.containsKey(parameter)) {
- log.debug("Cache hit for parameter "+parameter+" in child cache!");
- return childCache.get(parameter);
- }
- Identifier ident = new Identifier(parameter.getCvAccession(),
- Identifier.IdentifierType.OBO);
- List<Parameter> children = client.getTermChildren(ident, parameter.getCvLabel(), levels).
- stream().
- map(CvMappingUtils::asParameter).
- collect(Collectors.toList());
- childCache.put(parameter, children);
- return children;
- }
- /**
- * Resolve all children of a parameter up to an arbitrary depth.
- * Use at your own risk, the OLS service may terminate your connection if the response is too large or takes too long.
- * @param parameter the parameter to start from
- * @return a list of all child parameters for the given parameter
- * @throws org.springframework.web.client.HttpClientErrorException on http related errors
- */
- public List<Parameter> resolveChildren(Parameter parameter) throws org.springframework.web.client.HttpClientErrorException {
- return resolveChildren(parameter, -1);
- }
- /**
- * Compares two parameters for their parent to child relationship. The result can be one of: IDENTICAL, if parent and potential child are the same node,
- * CHILD_OF, if potentialChild is a child of parent (at least 1 level away), or NOT_RELATED, if there is no path from child to parent.
- * @param parent the parent term to start from
- * @param potentialChild the potential child term to check against parent
- * @return the comparison result
- * @throws org.springframework.web.client.HttpClientErrorException on http related errors
- */
- public ParameterComparisonResult isChildOfOrSame(Parameter parent,
- Parameter potentialChild) throws org.springframework.web.client.HttpClientErrorException {
- if (parent.getCvAccession().
- toUpperCase().
- equals(potentialChild.getCvAccession().
- toUpperCase())) {
- return ParameterComparisonResult.IDENTICAL;
- }
- List<Parameter> parentsOf = resolveParents(potentialChild);
- boolean result = parentsOf.stream().
- anyMatch((potentialParent) ->
- {
- return CvMappingUtils.isEqualTo(potentialParent, parent);
- });
- if (result) {
- return ParameterComparisonResult.CHILD_OF;
- }
- return ParameterComparisonResult.NOT_RELATED;
- }
- }