/**
* Invokes the given search Url and writes the results to a file in the specified job folder.
*
* @param searchUrl
* @param serverBase
* @param jobDir
* @param fileName
* @throws IOException
*/
private int retrieveAndStoreData(
String searchUrl, String serverBase, File jobDir, String fileName) throws IOException {
int numRecords = 0;
final String url = urlEncodeQueryParams(searchUrl);
LOG.info(
"retrieveAndStoreData, serverBase: {} searchUrl: {} encoded query: {}",
serverBase,
searchUrl,
url);
final ServerAuthorization serverAuthorization =
AuthorizationUtil.findServerAuthorization(serverAuthorizations, serverBase);
BearerTokenAuthInterceptor authInterceptor = null;
if (serverAuthorization != null) {
// register authorization interceptor with the client
LOG.info("assigning bearing token interceptor, {}", serverAuthorization.getAccessToken());
authInterceptor = new BearerTokenAuthInterceptor(serverAuthorization.getAccessToken());
fhirRestClient.registerInterceptor(authInterceptor);
}
try {
// Perform a search
final Bundle searchResults =
fhirRestClient.search().byUrl(url).returnBundle(Bundle.class).execute();
// Split the bundle into its component resources
final SearchResultSplitter resultSplitter = new SearchResultSplitter();
final List<Resource> resources = resultSplitter.splitBundle(searchResults);
final File dataFile = createDataSourceFile(jobDir, fileName);
writeData(dataFile, resources, serverBase, true);
numRecords = resources.size();
// retrieve other pages of search results
Bundle nextResults = searchResults;
while (nextResults.getLink(Bundle.LINK_NEXT) != null) {
nextResults = fhirRestClient.loadPage().next(nextResults).execute();
List<Resource> nextResources = resultSplitter.splitBundle(nextResults);
writeData(dataFile, nextResources, serverBase, false);
numRecords += nextResources.size();
}
} finally {
if (authInterceptor != null) {
// unregister authorization interceptor with the client
fhirRestClient.unregisterInterceptor(authInterceptor);
}
}
return numRecords;
}
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());
}
}