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medco-i2b2-cell/src/server/ch/epfl/lca1/medco/unlynx/UnlynxQueryResult.java
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UnlynxQueryResult.java
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package ch.epfl.lca1.medco.unlynx;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import ch.epfl.lca1.medco.util.XMLUtil;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.exceptions.I2B2XMLException;
/**
* Container class for an Unlynx query result. Given XML input extract the information.
*
* Example of such a file:
* {@code
* <medco_query_result>
* <id>query ID</id>
* <result_mode> result mode (0 or 1)</result_mode>
* <enc_result>encrypted result</enc_result>
* <error>a message error (only if error, the enc_result will be empty)</error>
* <times_ms>taks1: 44; task2: 23</times_ms>
* </medco_query_result>
* }
*/
public class UnlynxQueryResult {
/** The ID of the query. */
private String queryId;
/** The result of the query, encrypted with the querier's key, and encoded in base64. */
private String encResultB64;
/** The result mode used for the query (0 or 1). */
private int resultMode;
/** The error message if something went wrong. */
private String errorMessage;
/** The recorded execution times. */
private String timesMs;
// name of XML elements (definition)
private static String
EL_NAME_ROOT = "medco_query_result",
EL_NAME_ID = "id",
EL_NAME_RESULT_MODE = "result_mode",
EL_NAME_ENC_RESULT = "enc_result",
EL_NAME_ERROR = "error",
EL_NAME_TIMES = "times_ms";
// XML tags
private static String XML_START_TAG = "<" + EL_NAME_ROOT + ">";
private static String XML_END_TAG = "</" + EL_NAME_ROOT + ">";
/**
* Query result constructor. Parses the query and set default values of some fields.
* todo: wrong doc
* @param stdinString the XML as string to parse
* @throws I2B2XMLException in case of invalid XML
*/
public UnlynxQueryResult(String stdinString) throws I2B2XMLException {
// XXX: a bit hackish
InputStream stdin = new ByteArrayInputStream(stdinString.getBytes(StandardCharsets.UTF_8));
String resultXMLString = XMLUtil.xmlStringFromStream(stdin, XML_START_TAG, XML_END_TAG, false);
Logger.info("Parsing unlynx XML query result");
Logger.debug("XML string: " + resultXMLString);
SAXBuilder sxb = new SAXBuilder();
try {
parseDocument(sxb.build(new ByteArrayInputStream(resultXMLString.getBytes("UTF-8"))));
} catch(IOException | JDOMException e) {
throw Logger.error(new I2B2XMLException("XML parsing error", e));
}
}
/**
* Extract from a XML Document the result data.
*
* @param doc XML document
* @throws I2B2XMLException in case of invalid XML
*/
private void parseDocument(Document doc) throws I2B2XMLException {
Element root = doc.getRootElement();
// sanity check
if (!root.getName().equals(EL_NAME_ROOT)) {
throw Logger.error(new I2B2XMLException("XML not properly formed."));
}
// extract
queryId = root.getChildText(EL_NAME_ID);
encResultB64 = root.getChildText(EL_NAME_ENC_RESULT);
errorMessage = root.getChildText(EL_NAME_ERROR);
timesMs = root.getChildText(EL_NAME_TIMES);
String resultModeString = root.getChildText(EL_NAME_RESULT_MODE);
if (resultModeString != null) {
try {
resultMode = Integer.parseInt(root.getChildText(EL_NAME_RESULT_MODE));
} catch (NumberFormatException e) {
Logger.warn(e);
resultMode = -1;
}
} else {
resultMode = -1;
}
// consistency check
if (errorMessage == null && encResultB64 == null) {
throw Logger.error(new I2B2XMLException("XML message inconsistent: enc result and error are null"));
}
}
/**
* @return the query ID
*/
public String getQueryId() {
return queryId;
}
/**
* @return the result encrypted with the querier's key, encoded in base64
*/
public String getEncResultB64() {
return encResultB64;
}
/**
* @return the result mode of the query
*/
public int getResultMode() {
return resultMode;
}
/**
* @return the error message
*/
public String getErrorMessage() {
return errorMessage;
}
public String getTimes() {
return timesMs;
}
}
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