/** 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; }
/** * 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()); } }