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Protempa Framework is the core of Protempa.
/*
* #%L
* Protempa Framework
* %%
* Copyright (C) 2012 - 2013 Emory University
* %%
* 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.
* #L%
*/
package org.protempa.query;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.arp.javautil.arrays.Arrays;
import org.protempa.*;
import org.protempa.backend.dsb.filter.Filter;
/**
*
* @author Andrew Post
*/
public class DefaultQueryBuilder implements QueryBuilder, Serializable {
private static final long serialVersionUID = -3920993703423486485L;
private static final PropositionDefinition[] EMPTY_PROP_DEF_ARRAY
= new PropositionDefinition[0];
// Flag to control validation of proposition IDs. Should only be turned off
// for testing.
private static boolean validatePropositionIds = true;
private String[] keyIds;
private Filter filters;
private String[] propIds;
@SuppressWarnings("unchecked")
private And[] termIds;
private PropositionDefinition[] propDefs;
private String name;
private String username;
private final PropertyChangeSupport changes;
private QueryMode queryMode;
public DefaultQueryBuilder() {
this.changes = new PropertyChangeSupport(this);
this.propDefs = EMPTY_PROP_DEF_ARRAY;
this.keyIds = ArrayUtils.EMPTY_STRING_ARRAY;
this.propIds = ArrayUtils.EMPTY_STRING_ARRAY;
this.termIds = new And[0];
this.queryMode = Query.DEFAULT_QUERY_MODE;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getUsername() {
return username;
}
public void setUsername(String username) {
this.username = username;
}
public QueryMode getQueryMode() {
return queryMode;
}
public void setQueryMode(QueryMode queryMode) {
QueryMode old = this.queryMode;
if (queryMode == null) {
this.queryMode = Query.DEFAULT_QUERY_MODE;
} else {
this.queryMode = queryMode;
}
this.changes.firePropertyChange("queryMode", old, this.queryMode);
}
/**
* Gets the filters to be applied to this query.
*
* @return a {@link Filter}.
*/
public final Filter getFilters() {
return this.filters;
}
/**
* Sets the filters to apply to this query.
*
* Note that in order to serialize this query, the supplied filters must
* also implement {@link Serializable}.
*
* @param filters a {@link Filter}.
*/
public final void setFilters(Filter filters) {
Filter old = this.filters;
this.filters = filters;
this.changes.firePropertyChange("filters", old, this.filters);
}
/**
* Returns the key ids to be queried. An array of length 0 means that all
* key ids will be queried.
*
* @return a {@link String[]}. Never returns null.
*/
public final String[] getKeyIds() {
return this.keyIds.clone();
}
/**
* Sets the key ids to be queried. An array of length 0 or null
* means that all key ids will be queried.
*
* @param keyIds a {@link String[]} of key ids. If null, an
* empty {@link String[]} will be stored.
*/
public final void setKeyIds(String[] keyIds) {
if (keyIds == null) {
keyIds = ArrayUtils.EMPTY_STRING_ARRAY;
}
String[] old = this.keyIds;
this.keyIds = keyIds.clone();
this.changes.firePropertyChange("keyIds", old, this.keyIds);
}
/**
* Returns the proposition ids to be queried. An array of length 0 means
* that all proposition ids will be queried.
*
* @param propIds a {@link String[]}. Never returns null.
*/
public final String[] getPropositionIds() {
return this.propIds.clone();
}
/**
* Sets the proposition ids to be queried. An array of length 0 or
* null means that all proposition ids will be queried.
*
* @param propIds a {@link String[]} of proposition ids. If
* null, an empty {@link String[]} will be stored.
*/
public final void setPropositionIds(String[] propIds) {
String[] old = this.propIds;
if (propIds == null) {
this.propIds = ArrayUtils.EMPTY_STRING_ARRAY;
} else {
this.propIds = propIds.clone();
ProtempaUtil.internAll(this.propIds);
}
this.changes.firePropertyChange("propIds", old, this.propIds);
}
/**
* Gets the term ids to be queried in disjunctive normal form. PROTEMPA will
* navigate these terms' subsumption hierarchy, find proposition definitions
* that have been annotated with each term, and add those to the query.
* And'd term ids will only match a proposition definition if
* it is annotated with all of the specified term ids (or terms in their
* subsumption hierarchies).
*
* @return a {@link String[]} of term ids representing disjunctive normal
* form.
*/
public final And[] getTermIds() {
return this.termIds.clone();
}
/**
* Sets the term ids to be queried in disjunctive normal form. If any terms
* are specified, PROTEMPA will navigate the term's subsumption hierarchy,
* find proposition definitions that have been annotated with each term, and
* add those to the query. If and'd term ids are specified,
* proposition definitions will only match if they are annotated with all of
* the specified term ids (or terms in their subsumption hierarchies).
*
* @param termIds a {@link And[]} term ids representing disjunctive normal
* form.
*/
@SuppressWarnings("unchecked")
public final void setTermIds(And[] termIds) {
if (termIds == null) {
termIds = new And[0];
}
And[] old = this.termIds;
this.termIds = (And[]) termIds.clone();
this.changes.firePropertyChange("termIds", old, this.termIds);
}
/**
* Returns an optional set of user-specified proposition definitions.
*
* @return an array of {@link PropositionDefinition}s.
*/
public final PropositionDefinition[] getPropositionDefinitions() {
return this.propDefs.clone();
}
/**
* Returns an optional set of user-specified proposition definitions.
*
* @param propDefs an array of {@link PropositionDefinition}s.
*/
public final void setPropositionDefinitions(PropositionDefinition[] propDefs) {
if (propDefs == null) {
propDefs = EMPTY_PROP_DEF_ARRAY;
}
PropositionDefinition[] old = this.propDefs;
this.propDefs = propDefs.clone();
this.changes.firePropertyChange("propositionDefinitions", old,
this.propDefs);
}
/**
* Adds listeners for changes to this Query's properties.
*
* @param listener a {@link PropertyChangeListener}.
*/
public final void addPropertyChangeListener(PropertyChangeListener listener) {
this.changes.addPropertyChangeListener(listener);
}
/**
* Removes listeners for changes to this Query's properties.
*
* @param listener a {@link PropertyChangeListener}.
*/
public final void removePropertyChangeListener(PropertyChangeListener listener) {
this.changes.removePropertyChangeListener(listener);
}
/**
* Adds listeners for changes to the specified property.
*
* @param propertyName the name {@link String} of the property of interest.
* @param listener a {@link PropertyChangeListener}.
*/
public final void addPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
this.changes.addPropertyChangeListener(propertyName, listener);
}
/**
* Removes listeners for changes to the specified property.
*
* @param propertyName the name {@link String} of the property that is no
* longer of interest.
* @param listener a {@link PropertyChangeListener}.
*/
public final void removePropertyChangeListener(String propertyName, PropertyChangeListener listener) {
this.changes.removePropertyChangeListener(propertyName, listener);
}
@Override
public Query build(KnowledgeSource knowledgeSource, AlgorithmSource algorithmSource) throws QueryBuildException {
if (validatePropositionIds) {
Set userSpecifiedPropIds = new HashSet<>();
for (PropositionDefinition propDef : this.propDefs) {
userSpecifiedPropIds.add(propDef.getId());
}
List propIdsToTest = new ArrayList<>(propIds.length);
for (PropositionDefinition propDef : this.propDefs) {
for (String propId : propDef.getChildren()) {
if (!userSpecifiedPropIds.contains(propId)) {
propIdsToTest.add(propId);
}
}
}
for (String propId : propIds) {
if (!userSpecifiedPropIds.contains(propId)) {
propIdsToTest.add(propId);
}
}
try {
List pds = knowledgeSource.readPropositionDefinitions(propIdsToTest.toArray(new String[propIdsToTest.size()]));
List actualPropIds = new ArrayList<>(pds.size());
for (PropositionDefinition propDef : pds) {
actualPropIds.add(propDef.getId());
}
propIdsToTest.removeAll(actualPropIds);
if (!propIdsToTest.isEmpty()) {
throw new QueryBuildException("Invalid proposition ids: " + propIdsToTest);
}
} catch (KnowledgeSourceReadException ex) {
throw new QueryBuildException("Could not build query", ex);
}
}
return new Query(this.name, this.username, this.keyIds, this.filters,
this.propIds, this.termIds, this.propDefs, this.queryMode);
}
@Override
public String toString() {
return ToStringBuilder.reflectionToString(this);
}
/**
* Set the value of the flag that determined whether the build method
* validates proposition IDs.
*
* @param validatePropositionIds Proposition IDs are validated if, and only
* if, this is true. The default value for this is true.
*/
public static void setValidatePropositionIds(boolean validatePropositionIdsFlag) {
validatePropositionIds = validatePropositionIdsFlag;
}
public static boolean isValidatePropositionIds() {
return validatePropositionIds;
}
}