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AIW i2b2 ETL is a Protempa query results handler for loading data and
abstractions into i2b2.
package edu.emory.cci.aiw.i2b2etl.dest;
/*
* #%L
* AIW i2b2 ETL
* %%
* 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%
*/
import edu.emory.cci.aiw.i2b2etl.dest.config.Concepts;
import edu.emory.cci.aiw.i2b2etl.dest.config.Configuration;
import edu.emory.cci.aiw.i2b2etl.dest.config.Data;
import edu.emory.cci.aiw.i2b2etl.dest.config.DataSpec;
import edu.emory.cci.aiw.i2b2etl.dest.config.FolderSpec;
import edu.emory.cci.aiw.i2b2etl.dest.config.Settings;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.lang3.ArrayUtils;
import org.protempa.DataSource;
import org.protempa.KnowledgeSource;
import org.protempa.KnowledgeSourceReadException;
import org.protempa.PropositionDefinition;
import org.protempa.ProtempaEventListener;
import org.protempa.ReferenceDefinition;
import org.protempa.dest.AbstractDestination;
import org.protempa.dest.GetSupportedPropositionIdsException;
import org.protempa.dest.QueryResultsHandler;
import org.protempa.dest.QueryResultsHandlerInitException;
import org.protempa.dest.Statistics;
import org.protempa.dest.StatisticsException;
import org.protempa.query.Query;
/**
*
* @author Andrew Post
*/
public final class I2b2Destination extends AbstractDestination {
private final Configuration config;
private final boolean insertSupportedPropositionIds;
/**
* Creates a new query results handler that will use the provided
* configuration file. It is the same as calling the two-argument
* constructor with inferPropositionIdsNeeded set to
* false.
*
* @param confXML an i2b2 query results handler configuration file. Cannot
* be null.
*/
public I2b2Destination(Configuration config) {
this(config, false);
}
/**
* Creates a new query results handler that will use the provided
* configuration file. This constructor, through the
* inferPropositionIdsNeeded parameter, lets you control
* whether proposition ids to be returned from the Protempa processing run
* should be inferred from the i2b2 configuration file.
*
* @param confXML an i2b2 query results handler configuration file. Cannot
* be null.
* @param inferPropositionIdsNeeded true if proposition ids to
* be returned from the Protempa processing run should include all of those
* specified in the i2b2 configuration file, false if the
* proposition ids returned should be only those specified in the Protempa
* {@link Query}.
*/
public I2b2Destination(Configuration config, boolean inferSupportedPropositionIds) {
if (config == null) {
throw new IllegalArgumentException("config cannot be null");
}
this.config = config;
this.insertSupportedPropositionIds = inferSupportedPropositionIds;
}
@Override
public QueryResultsHandler getQueryResultsHandler(Query query, DataSource dataSource, KnowledgeSource knowledgeSource, List eventListeners) throws QueryResultsHandlerInitException {
return new I2b2QueryResultsHandler(query, dataSource, knowledgeSource, this.config, eventListeners);
}
@Override
public boolean isGetStatisticsSupported() {
return true;
}
@Override
public Statistics getStatistics() throws StatisticsException {
return new I2b2Statistics(this.config);
}
@Override
public String[] getSupportedPropositionIds(DataSource dataSource, KnowledgeSource knowledgeSource) throws GetSupportedPropositionIdsException {
try {
return readPropIdsFromKnowledgeSource(dataSource, knowledgeSource);
} catch (KnowledgeSourceReadException ex) {
throw new GetSupportedPropositionIdsException(ex);
}
}
private String[] readPropIdsFromKnowledgeSource(DataSource dataSource, KnowledgeSource knowledgeSource) throws KnowledgeSourceReadException {
if (this.insertSupportedPropositionIds) {
Set result = new HashSet<>();
Settings settings = this.config.getSettings();
Data data = this.config.getData();
Concepts concepts = this.config.getConcepts();
String visitPropId = settings.getVisitDimension();
if (visitPropId != null) {
result.add(visitPropId);
PropositionDefinition visitProp = knowledgeSource.readPropositionDefinition(visitPropId);
if (visitProp == null) {
throw new KnowledgeSourceReadException("Invalid visit proposition id: " + visitPropId);
}
for (DataSpec dataSpec : data.getAll()) {
if (dataSpec.getReferenceName() != null) {
ReferenceDefinition refDef = visitProp.referenceDefinition(dataSpec.getReferenceName());
if (refDef == null) {
throw new KnowledgeSourceReadException("missing reference " + dataSpec.getReferenceName() + " for proposition definition " + visitPropId);
}
org.arp.javautil.arrays.Arrays.addAll(result, refDef.getPropositionIds());
}
}
for (FolderSpec folderSpec : concepts.getFolderSpecs()) {
for (String proposition : folderSpec.getPropositions()) {
result.add(proposition);
}
}
}
Set collectPropIdDescendantsUsingInverseIsA = knowledgeSource.collectPropIdDescendantsUsingInverseIsA(result.toArray(new String[result.size()]));
return collectPropIdDescendantsUsingInverseIsA.toArray(new String[collectPropIdDescendantsUsingInverseIsA.size()]);
} else {
return ArrayUtils.EMPTY_STRING_ARRAY;
}
}
}