org.eurekaclinical.protempa.client.json.CompoundLowLevelAbstractionJsonDeserializer Maven / Gradle / Ivy

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/*
 * #%L
 * Eureka Common
 * %%
 * 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.eurekaclinical.protempa.client.json;

import java.io.IOException;

import org.codehaus.jackson.JsonParseException;
import org.codehaus.jackson.JsonParser;
import org.codehaus.jackson.JsonProcessingException;
import org.codehaus.jackson.JsonToken;
import org.codehaus.jackson.map.DeserializationContext;
import org.codehaus.jackson.map.JsonDeserializer;
import org.protempa.Attribute;
import org.protempa.CompoundLowLevelAbstractionDefinition;
import org.protempa.CompoundLowLevelAbstractionDefinition.ValueDefinitionMatchOperator;
import org.protempa.GapFunction;
import org.protempa.PropertyDefinition;
import org.protempa.ReferenceDefinition;
import org.protempa.SourceId;
import org.protempa.ValueClassification;

public final class CompoundLowLevelAbstractionJsonDeserializer extends JsonDeserializer {

	private JsonParser parser;

	@Override
	public CompoundLowLevelAbstractionDefinition deserialize(JsonParser jp,
			DeserializationContext ctxt) throws IOException,
			JsonProcessingException {
		this.parser = jp;

		if (this.parser.getCurrentToken() == JsonToken.START_OBJECT) {
			nextToken(); // should be the id field
		}
		checkField("id");
		// now we can construct the LLA
		CompoundLowLevelAbstractionDefinition value =
				new CompoundLowLevelAbstractionDefinition(
				this.parser.readValueAs(String.class));
		value.setInDataSource(false);

		nextToken();
		checkField("displayName");
		value.setDisplayName(this.parser.readValueAs(String.class));

		nextToken();
		checkField("abbreviatedDisplayName");
		value.setAbbreviatedDisplayName(this.parser.readValueAs(String.class));

		nextToken();
		checkField("description");
		value.setDescription(this.parser.readValueAs(String.class));

		nextToken();
		checkField("inverseIsA");
		value.setInverseIsA(this.parser.readValueAs(String[].class));

		nextToken();
		checkField("properties");
		value.setPropertyDefinitions(this.parser
				.readValueAs(PropertyDefinition[].class));

		nextToken();
		checkField("references");
		value.setReferenceDefinitions(this.parser
				.readValueAs(ReferenceDefinition[].class));

		nextToken();
		checkField("sourceId");
		SourceId sourceId = this.parser.readValueAs(SourceId.class);
		value.setSourceId(sourceId);

		nextToken();
		checkField("concatenable");
		value.setConcatenable(this.parser.getBooleanValue());

		nextToken();
		checkField("inDataSource");
		value.setInDataSource(this.parser.getBooleanValue());

		nextToken();
		checkField("gapFunction");
		value.setGapFunction(this.parser.readValueAs(GapFunction.class));
		
		nextToken();
		checkField("gapFunctionBetweenValues");
		value.setGapFunctionBetweenValues(this.parser.readValueAs(GapFunction.class));

		nextToken();
		checkField("minimumNumberOfValues");
		value.setMinimumNumberOfValues(this.parser.getIntValue());

		nextToken();
		checkField("thresholdsOperator");
		value.setValueDefinitionMatchOperator(
				ValueDefinitionMatchOperator.valueOf(
				this.parser.readValueAs(String.class)));
		
		nextToken();
		checkField("context");
		value.setContextId(this.parser.readValueAs(String.class));
		
		nextToken();
		checkField("skip");
		value.setSkip(this.parser.getIntValue());

		nextToken();
		checkField("values");
		
		nextToken();
		while (parser.getCurrentToken() != JsonToken.END_OBJECT) {
			checkField("id");
			String id = this.parser.readValueAs(String.class);
			
			nextToken();
			checkField("lowLevelAbstractionId");
			String lowLevelAbstractionId = this.parser.readValueAs(String.class);
			
			nextToken();
			checkField("value");
			String lowLevelAbstractionValueDefName = this.parser.readValueAs(String.class);
			
			ValueClassification valueCls = 
					new ValueClassification(id, lowLevelAbstractionId, 
					lowLevelAbstractionValueDefName);
			value.addValueClassification(valueCls);
			
			nextToken();
		}
		
		nextToken();
		checkField("attributes");
		value.setAttributes(this.parser.readValueAs(Attribute[].class));

		nextToken();
		
		return value;
	}

	private void checkField(String field) throws JsonParseException,
			IOException {
		if (!(this.parser.getCurrentToken() == JsonToken.FIELD_NAME && field
				.equals(this.parser.getCurrentName()))) {
			fail(field);
		} else {
			nextValue();
		}
	}

	private void nextToken() throws JsonParseException, IOException {
		this.parser.nextToken();
	}

	private void nextValue() throws JsonParseException, IOException {
		this.parser.nextValue();
	}

	private void fail(String property) throws JsonProcessingException {
		throw new JsonParseException("\"" + property + "\""
				+ " not found in expected location. Found \""
				+ this.parser.getCurrentToken() + "\" instead",
				this.parser.getCurrentLocation());
	}
}