/** Returns the resourceUrl parameter from the Parameters resource. */
private String getResourceUrl(Parameters params) {
String resourceUrl = null;
final List<ParametersParameterComponent> paramList = params.getParameter();
final ParametersParameterComponent p = ParametersUtil.findByName(paramList, SEARCH_EXPR);
if (p != null) {
final Resource r = p.getResource();
if (ResourceType.Parameters.equals(r.getResourceType())) {
final Parameters searchExprParams = (Parameters) r;
final List<ParametersParameterComponent> searchExprParamList =
searchExprParams.getParameter();
final ParametersParameterComponent ppc =
ParametersUtil.findByName(searchExprParamList, RESOURCE_URL);
resourceUrl = ppc.getValue().toString();
if (resourceUrl == null) {
LOG.warn("Required parameter, resourceUrl, is missing from record-match request!");
}
}
} else {
LOG.warn("Unable to find search expression in message parameters");
}
return resourceUrl;
}
@Override
public FhirQueryAuditDataset enrichAuditDatasetFromRequest(
FhirQueryAuditDataset auditDataset, Object request, Map<String, Object> parameters) {
FhirQueryAuditDataset dataset =
super.enrichAuditDatasetFromRequest(auditDataset, request, parameters);
Parameters params = (Parameters) request;
if (params != null) {
Type sourceIdentifier =
params
.getParameter()
.stream()
.filter(ppc -> Constants.SOURCE_IDENTIFIER_NAME.equals(ppc.getName()))
.map(Parameters.ParametersParameterComponent::getValue)
.findFirst()
.orElseThrow(() -> new RuntimeException("No sourceIdentifier in PIX query"));
if (sourceIdentifier instanceof Identifier) {
Identifier identifier = (Identifier) sourceIdentifier;
dataset
.getPatientIds()
.add(String.format("%s|%s", identifier.getSystem(), identifier.getValue()));
} else if (sourceIdentifier instanceof StringType) {
StringType identifier = (StringType) sourceIdentifier;
dataset.getPatientIds().add(identifier.getValue());
} else {
dataset.getPatientIds().add(sourceIdentifier.toString());
}
}
return dataset;
}
/**
* Constructs a search URL using the information in the Parameters resource.
*
* @param params Parameters resource containing a searchExpression parameter whose value is a
* Parameters resource containing a resourceUrl parameter and other parameters that comprise
* the query expression.
* @return search url or an empty string if the url could not be formed
*/
private String buildSearchUrl(Parameters params) {
final StringBuilder searchUrl = new StringBuilder(200);
final List<ParametersParameterComponent> paramList = params.getParameter();
final ParametersParameterComponent p = ParametersUtil.findByName(paramList, SEARCH_EXPR);
if (p != null) {
final Resource r = p.getResource();
if (ResourceType.Parameters.equals(r.getResourceType())) {
final Parameters searchExprParams = (Parameters) r;
final List<ParametersParameterComponent> searchExprParamList =
searchExprParams.getParameter();
String resourceUrl = null;
final StringBuilder queryExpr = new StringBuilder(100);
// all parameters except resourceUrl contribute to the query expression
for (ParametersParameterComponent searchExprParam : searchExprParamList) {
String name = searchExprParam.getName();
try {
String value = searchExprParam.getValue().toString();
// resourceUrl is different than others
if (RESOURCE_URL.equals(name)) {
resourceUrl = value;
} else {
if (queryExpr.length() > 0) {
queryExpr.append("&");
}
queryExpr.append(name);
queryExpr.append("=");
queryExpr.append(value);
}
} catch (NullPointerException e) {
LOG.error("Null Value for search expression parameter, {}", name);
}
}
if (resourceUrl == null) {
LOG.warn("Required parameter, resourceUrl, is missing from record-match request!");
} else {
searchUrl.append(resourceUrl);
searchUrl.append("?");
searchUrl.append(queryExpr);
}
LOG.info("search Url: {}", searchUrl.toString());
}
} else {
LOG.warn("Unable to find search expression in message parameters");
}
return searchUrl.toString();
}
public void process(Bundle bundle) {
Bundle response = null;
RecordMatchResultsBuilder respBuilder;
if (BundleType.MESSAGE.equals(bundle.getType())) {
// Create a CSV data source for FRIL
final File jobDir = newRunDir(workDir);
final List<BundleEntryComponent> bundleEntries = bundle.getEntry();
try {
// The first entry is supposed to be the MessageHeader
// This will force an exception if not true.
final MessageHeader msgHdr = (MessageHeader) bundleEntries.get(0).getResource();
// This log statement keeps above from getting optimized out
LOG.trace("msg hdr id {}", msgHdr.getId());
Parameters masterQryParams = null;
Parameters queryQryParams = null;
String masterSearchUrl = null;
String querySearchUrl = null;
String masterServerBase = null;
String queryServerBase = null;
String resourceType = "Patient";
boolean isDeduplication = true;
// Find the Parameters resources that contain the search parameters
// and use those to construct search Urls
for (BundleEntryComponent entry : bundleEntries) {
Resource r = entry.getResource();
LOG.debug("Found Resource type: " + r.getResourceType().toString());
if (ResourceType.Parameters.equals(r.getResourceType())) {
Parameters params = (Parameters) r;
List<ParametersParameterComponent> paramList = params.getParameter();
// Now look for the parameter with name, resourceType.
ParametersParameterComponent p = ParametersUtil.findByName(paramList, RESOURCE_TYPE);
if (p != null) {
resourceType = p.getValue().toString();
}
// Find parameter that distinguishes between master and query sets
p = ParametersUtil.findByName(paramList, "type");
if (p != null) {
String val = p.getValue().toString();
if (val.equalsIgnoreCase(MASTER)) {
masterQryParams = params;
masterSearchUrl = buildSearchUrl(params);
masterServerBase = getServerBase(resourceType, masterQryParams);
} else if (val.equalsIgnoreCase(QUERY)) {
queryQryParams = params;
querySearchUrl = buildSearchUrl(params);
queryServerBase = getServerBase(resourceType, queryQryParams);
}
}
}
}
if (masterSearchUrl == null) {
final String errMsg =
"Required Parameter for master record set is missing, bundle: " + bundle.getId();
LOG.warn(errMsg);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
}
LoggingInterceptor loggingInterceptor = null;
if (LOG.isDebugEnabled()) {
loggingInterceptor = new LoggingInterceptor(true);
fhirRestClient.registerInterceptor(loggingInterceptor);
}
int numMasterRecs = 0;
try {
// Retrieve the data associated with the search urls
numMasterRecs = retrieveAndStoreData(masterSearchUrl, masterServerBase, jobDir, "master");
if (querySearchUrl != null) {
isDeduplication = false;
retrieveAndStoreData(querySearchUrl, queryServerBase, jobDir, "query");
}
} catch (BaseServerResponseException e) {
final String errMsg =
String.format(
"Error response from server. code: %d, %s", e.getStatusCode(), e.getMessage());
LOG.warn(errMsg);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
} catch (Exception e) {
final String errMsg = String.format("Unable to retrieve messages: %s", e.getMessage());
LOG.warn(errMsg, e);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
} finally {
if (loggingInterceptor != null) {
fhirRestClient.unregisterInterceptor(loggingInterceptor);
}
}
// if no records were returned for the master record set query
if (numMasterRecs == 0) {
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("No Records Found in Master Record Set");
response = respBuilder.build();
} else {
final File configFile = prepareMatchingRuleConfiguration(isDeduplication, jobDir);
// Perform the Match Operation
LOG.debug("About to Start FRIL w/ config {}", configFile.getAbsolutePath());
final int numMatches = findMatches(isDeduplication, configFile);
LOG.info("FRIL Number of Matches: {}", numMatches);
if (numMatches == 0) {
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("No Matches Found");
response = respBuilder.build();
} else if (numMatches > 0) {
// Find the name of the file containing duplicates from the config
// file
final File dupsFile = getDuplicatesFile(configFile);
// Ensure the duplicates file exists
if (!dupsFile.exists()) {
final String errMsg = "Unable to find duplicates file";
LOG.error(errMsg + " at " + dupsFile.getAbsolutePath());
throw new FileNotFoundException(errMsg);
}
// Construct results
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("Deduplication Complete");
respBuilder.duplicates(dupsFile);
response = respBuilder.build();
} else {
final String errMsg = "Unknown Processing Error";
LOG.error("{} bundleId: {}", errMsg, bundle.getId());
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
}
}
} catch (Exception e) {
final String errMsg = "Unexpected Error";
LOG.error("Processing bundle: {}", bundle.getId(), e);
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
try {
response = respBuilder.build();
} catch (IOException ioe) {
// only so many times we can attempt to send a response; log error
LOG.error("Unable to Send Error Response. request bundle: {}", bundle.getId(), ioe);
}
}
if (deleteJobResults) {
// Delete the Job Results folder and content
deleteFolder(jobDir);
}
} else {
final String errMsg = "Unsupported Bundle type: " + bundle.getType().toString();
LOG.info("{} msgId: {}", errMsg, bundle.getId());
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
try {
response = respBuilder.build();
} catch (IOException e) {
// only so many times we can attempt to send a response; log error
LOG.error("Unable to Send Error Response. request bundle: {}", bundle.getId());
}
}
// Send the response back to the requester
if (response != null) {
getProducer().sendBody(getProducerEndpointUri(), response);
} else {
LOG.error("Null Response for request! bundleId: {}", bundle.getId());
}
}