org.protempa.PropositionDefinitionCache Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of protempa-framework Show documentation
Show all versions of protempa-framework Show documentation
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;
import org.protempa.valueset.ValueSet;
import java.io.*;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* A collection of primitive parameter definitions, abstract parameter
* definitions, and key finding definitions. Primitive parameters are raw data
* types. Abstract Parameters are abstractions inferred from raw data. Key
* findings are aggregations of clinical data around found abstract parameters.
*
* TODO add context types.
*
* @author Andrew Post
*/
final class PropositionDefinitionCache implements Serializable {
private static final long serialVersionUID = 5988857805118255882L;
/**
* Map of abstract parameter id String objects to
* AbstractParameterDefinition objects.
*/
private Map idToAbstractionDefinitionMap;
private Map idToPropositionDefinitionMap;
private Map idToContextDefinitionMap;
private Map idToTemporalPropositionDefinitionMap;
private Map idtoValueSetMap;
PropositionDefinitionCache() {
initialize();
}
private void initialize() {
this.idToAbstractionDefinitionMap = new HashMap<>();
this.idToPropositionDefinitionMap = new HashMap<>();
this.idtoValueSetMap = new HashMap<>();
this.idToContextDefinitionMap = new HashMap<>();
this.idToTemporalPropositionDefinitionMap = new HashMap<>();
}
/**
* Overrides default serialization.
*
* @param s
* an ObjectOutputStream object.
* @throws IOException
* if serialization failed.
*/
private void writeObject(ObjectOutputStream s) throws IOException {
s.writeObject(this.idToPropositionDefinitionMap.values());
s.writeObject(this.idToAbstractionDefinitionMap.values());
s.writeObject(this.idtoValueSetMap.values());
s.writeObject(this.idToContextDefinitionMap.values());
s.writeObject(this.idToTemporalPropositionDefinitionMap.values());
}
/**
* Overrides default de-serialization.
*
* @param s
* an ObjectInputStream object.
* @throws IOException
* if de-serialization failed.
* @throws ClassNotFoundException
* if de-serialization failed.
*/
@SuppressWarnings("unchecked")
private void readObject(ObjectInputStream s) throws IOException,
ClassNotFoundException {
initialize();
Collection propositionDefinitions = (Collection) s.readObject();
Collection abstractionDefinitions = (Collection) s.readObject();
Collection valueSets = (Collection) s.readObject();
Collection contextDefinitions = (Collection) s.readObject();
Collection temporalPropositionDefinitions = (Collection) s.readObject();
if (propositionDefinitions != null) {
for (PropositionDefinition def : propositionDefinitions) {
if (def == null) {
throw new InvalidObjectException("Null primitive parameter definition; can't restore");
}
try {
addPropositionDefinition(def);
} catch (InvalidPropositionIdException ex) {
String msg = "Could not add de-serialized proposition definition " + def;
//InvalidObjectException doesn't support nested exceptions.
ProtempaUtil.logger().log(Level.SEVERE, msg, ex);
throw new InvalidObjectException(msg);
}
}
} else {
throw new InvalidObjectException("propositionDefinitions cannot be null");
}
if (abstractionDefinitions != null) {
for (AbstractionDefinition def : abstractionDefinitions) {
if (def == null) {
throw new InvalidObjectException("Null abstraction definition; can't restore");
}
try {
addAbstractionDefinition(def);
} catch (InvalidPropositionIdException ex) {
String msg = "Could not add de-serialized abstract parameter definition " + def;
//InvalidObjectException doesn't support nested exceptions.
ProtempaUtil.logger().log(Level.SEVERE, msg, ex);
throw new InvalidObjectException(msg);
}
}
} else {
throw new InvalidObjectException("abstractionDefinitions cannot be null");
}
if (valueSets != null) {
for (ValueSet valueSet : valueSets) {
if (valueSet == null) {
throw new InvalidObjectException("Null value set; can't restore");
}
try {
addValueSet(valueSet);
} catch (InvalidValueSetDefinitionException ex) {
String msg = "Could not add de-serialized value set " + valueSet;
//InvalidObjectException doesn't support nested exceptions.
ProtempaUtil.logger().log(Level.SEVERE, msg, ex);
throw new InvalidObjectException(msg);
}
}
}
if (temporalPropositionDefinitions != null) {
for (ContextDefinition def : contextDefinitions) {
if (def == null) {
throw new InvalidObjectException("Null context definition; can't restore");
}
try {
addContextDefinition(def);
} catch (InvalidPropositionIdException ex) {
String msg = "Could not add de-serialized context definition " + def;
//InvalidObjectException doesn't support nested exceptions.
ProtempaUtil.logger().log(Level.SEVERE, msg, ex);
throw new InvalidObjectException(msg);
}
}
} else {
throw new InvalidObjectException("contextDefinitions cannot be null");
}
if (temporalPropositionDefinitions != null) {
for (TemporalPropositionDefinition def : temporalPropositionDefinitions) {
if (def == null) {
throw new InvalidObjectException("Null temporalPropositionDefinition; can't restore");
}
try {
addTemporalPropositionDefinition(def);
} catch (InvalidPropositionIdException ex) {
String msg = "Could not add de-serialized temporalPropositionDefinition " + def;
//InvalidObjectException doesn't support nested exceptions.
ProtempaUtil.logger().log(Level.SEVERE, msg, ex);
throw new InvalidObjectException(msg);
}
}
} else {
throw new InvalidObjectException("temporalPropositionDefinitions cannot be null");
}
}
boolean isUniqueKnowledgeDefinitionObjectId(String id) {
return !this.idToAbstractionDefinitionMap.containsKey(id)
&& !this.idToPropositionDefinitionMap.containsKey(id);
}
boolean hasPropositionDefinition(String eventId) {
return getPropositionDefinition(eventId) != null;
}
boolean hasTemporalPropositionDefinition(String propId) {
return getTemporalPropositionDefinition(propId) != null;
}
PropositionDefinition getPropositionDefinition(String propId) {
return idToPropositionDefinitionMap.get(propId);
}
TemporalPropositionDefinition getTemporalPropositionDefinition(String propId) {
return this.idToTemporalPropositionDefinitionMap.get(propId);
}
boolean hasValueSet(String valueSetId) {
return getValueSet(valueSetId) != null;
}
ValueSet getValueSet(String valueSetId) {
return idtoValueSetMap.get(valueSetId);
}
boolean hasAbstractionDefinition(String paramId) {
return getAbstractionDefinition(paramId) != null;
}
boolean hasContextDefinition(String contextId) {
return getContextDefinition(contextId) != null;
}
AbstractionDefinition getAbstractionDefinition(String paramId) {
return idToAbstractionDefinitionMap.get(paramId);
}
ContextDefinition getContextDefinition(String contextId) {
return idToContextDefinitionMap.get(contextId);
}
void addPropositionDefinition(PropositionDefinition def) throws InvalidPropositionIdException {
assert def != null : "def cannot be null";
String id = def.getId();
if (this.idToPropositionDefinitionMap.containsKey(id)) {
throw new InvalidPropositionIdException(id);
} else {
this.idToPropositionDefinitionMap.put(id, def);
}
}
void addAbstractionDefinition(AbstractionDefinition def) throws InvalidPropositionIdException {
assert def != null : "def cannot be null";
String id = def.getId();
if (this.idToAbstractionDefinitionMap.containsKey(id)) {
throw new InvalidPropositionIdException(id);
} else {
idToAbstractionDefinitionMap.put(id, def);
}
}
void addValueSet(ValueSet valueSet) throws InvalidValueSetDefinitionException {
assert valueSet != null : "valueSet cannot be null";
String id = valueSet.getId();
if (this.idtoValueSetMap.containsKey(id)) {
throw new InvalidValueSetDefinitionException("Duplicate value set id: " + id);
} else {
this.idtoValueSetMap.put(id, valueSet);
}
}
void addContextDefinition(ContextDefinition def) throws InvalidPropositionIdException {
assert def != null : "def cannot be null";
String id = def.getId();
if (this.idToContextDefinitionMap.containsKey(id)) {
throw new InvalidPropositionIdException(id);
} else {
idToContextDefinitionMap.put(id, def);
}
}
void addTemporalPropositionDefinition(TemporalPropositionDefinition def) throws InvalidPropositionIdException {
assert def != null : "def cannot be null";
String id = def.getId();
if (this.idToTemporalPropositionDefinitionMap.containsKey(id)) {
throw new InvalidPropositionIdException(id);
} else {
idToTemporalPropositionDefinitionMap.put(id, def);
}
}
void clear() {
this.idToAbstractionDefinitionMap.clear();
this.idToPropositionDefinitionMap.clear();
this.idtoValueSetMap.clear();
this.idToContextDefinitionMap.clear();
this.idToTemporalPropositionDefinitionMap.clear();
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
return new ToStringBuilder(this).append(this.idToAbstractionDefinitionMap.values()).append(this.idToPropositionDefinitionMap.values()).toString();
}
}