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
*/
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
*/
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
*/
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
*/
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
* @param potentialChild
* @return the comparison result
* @throws org.springframework.web.client.HttpClientErrorException
*/
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;
}
}