Merge branch 'development' into LNK-2186

# Conflicts:
#	core/src/main/java/com/lantanagroup/link/sender/FileSystemSender.java

api/src/main/java/com/lantanagroup/link/api/MeasureEvaluator.java

@@ -46,8 +46,6 @@ private MeasureReport generateMeasureReport() {
     MeasureReport measureReport;
     String patientDataBundleId = ReportIdHelper.getPatientDataBundleId(reportContext.getMasterIdentifierValue(), patientId);
     String measureId = this.measureContext.getMeasure().getIdElement().getIdPart();
-    String start = this.criteria.getPeriodStart().substring(0, this.criteria.getPeriodStart().indexOf("."));
-    String end = this.criteria.getPeriodEnd().substring(0, this.criteria.getPeriodEnd().indexOf("."));
 
     Bundle patientBundle;
     try (Stopwatch stopwatch = this.stopwatchManager.start(Constants.TASK_RETRIEVE_PATIENT_DATA, Constants.CATEGORY_REPORT)) {
@@ -60,7 +58,7 @@ private MeasureReport generateMeasureReport() {
       Helper.dumpToFile(patientBundle, config.getDebugPath(), fileName);
     }
 
-    logger.info("Executing $evaluate-measure for measure: {}, start: {}, end: {}, patient: {}, resources: {}", measureId, start, end, patientId, patientBundle.getEntry().size());
+    logger.info("Executing $evaluate-measure for measure: {}, start: {}, end: {}, patient: {}, resources: {}", measureId, criteria.getPeriodStart(), criteria.getPeriodEnd(), patientId, patientBundle.getEntry().size());
 
     //noinspection unused
     try (Stopwatch stopwatch = this.stopwatchManager.start(Constants.TASK_MEASURE, Constants.CATEGORY_EVALUATE)) {

api/src/main/java/com/lantanagroup/link/api/auth/PreAuthTokenHeaderFilter.java

@@ -10,17 +10,17 @@
 import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.model.User;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.security.web.authentication.preauth.AbstractPreAuthenticatedProcessingFilter;
 
-import jakarta.servlet.FilterChain;
-import jakarta.servlet.ServletException;
-import jakarta.servlet.ServletRequest;
-import jakarta.servlet.ServletResponse;
-import jakarta.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
@@ -52,7 +52,7 @@ public void doFilter(ServletRequest request, ServletResponse response, FilterCha
       logger.debug("Validating the requesting IP address against the token IP address.");
       DecodedJWT jwt = JWT.decode(authHeader.substring(7));
 
-      if (!jwt.getClaim("ip").isNull() && !"0:0:0:0:0:0:0:1(0:0:0:0:0:0:0:1)".equals(ipAddress) && !jwt.getClaim("ip").asString().equals(ipAddress)) {
+      if (!jwt.getClaim("ip").isNull() && !"127.0.0.1(127.0.0.1)".equals(ipAddress) && !"0:0:0:0:0:0:0:1(0:0:0:0:0:0:0:1)".equals(ipAddress) && !jwt.getClaim("ip").asString().equals(ipAddress)) {
         throw new JWTVerificationException("IP Address does not match.");
       }
     }

api/src/main/java/com/lantanagroup/link/api/controller/GlobalReportController.java

@@ -37,25 +37,17 @@ public List<GlobalReportResponse> getReports(
     if (!startDate.isEmpty()) {
       Date date = Helper.parseFhirDate(startDate);
 
-      reports = reports.stream().filter(x -> {
-        try {
-          return Helper.parseFhirDate(x.getPeriodStart()).after(date) || Helper.parseFhirDate(x.getPeriodStart()).equals(date);
-        } catch (ParseException e) {
-          throw new RuntimeException(e);
-        }
-      }).collect(Collectors.toList());
+      reports = reports.stream().filter(x ->
+        Helper.parseFhirDate(x.getPeriodStart()).after(date) || Helper.parseFhirDate(x.getPeriodStart()).equals(date)
+      ).collect(Collectors.toList());
     }
 
     if (!endDate.isEmpty()) {
       Date date = Helper.parseFhirDate(endDate);
 
-      reports = reports.stream().filter(x -> {
-        try {
-          return Helper.parseFhirDate(x.getPeriodEnd()).before(date) || Helper.parseFhirDate(x.getPeriodStart()).equals(date);
-        } catch (ParseException e) {
-          throw new RuntimeException(e);
-        }
-      }).collect(Collectors.toList());
+      reports = reports.stream().filter(x ->
+        Helper.parseFhirDate(x.getPeriodEnd()).before(date) || Helper.parseFhirDate(x.getPeriodStart()).equals(date)
+      ).collect(Collectors.toList());
     }
 
     if (!tenantId.isEmpty()) {
@@ -66,8 +58,7 @@ public List<GlobalReportResponse> getReports(
       reports = reports.stream().filter(x -> x.getStatus().equals(ReportStatuses.valueOf(status))).collect(Collectors.toList());
     }
 
-    if(measureIds.length() > 0)
-    {
+    if (!measureIds.isEmpty()) {
       String[] ids = measureIds.split(",");
       reports = reports.stream().filter(x -> {
         HashSet<String> measureIdsSet = new HashSet<>(x.getMeasureIds());
@@ -80,7 +71,11 @@ public List<GlobalReportResponse> getReports(
       }).collect(Collectors.toList());
     }
 
-    reports = reports.stream().skip((long) (page -1) * count).limit(count).collect(Collectors.toList());
+    reports = reports
+            .stream()
+            .skip((long) (page - 1) * count)
+            .limit(count)
+            .collect(Collectors.toList());
 
     return reports;
   }

api/src/main/java/com/lantanagroup/link/api/controller/LogController.java

@@ -34,12 +34,8 @@ public LogSearchResponse getLogs(@RequestParam(required = false) String startDat
     Date startDateObj;
     Date endDateObj;
 
-    try {
-      startDateObj = Helper.parseFhirDate(startDate);
-      endDateObj = Helper.parseFhirDate(endDate);
-    } catch (ParseException ex) {
-      throw new IllegalArgumentException("Invalid date format, must be in the format yyyy-MM-dd'T'HH:mm:ss.SSSXXX or yyyy-MM-dd'T'HH:mm:ssXXX");
-    }
+    startDateObj = Helper.parseFhirDate(startDate);
+    endDateObj = Helper.parseFhirDate(endDate);
 
     List<LogMessage> logMessages = this.sharedService.findLogMessages(startDateObj, endDateObj, severity, page, content);
     LogSearchResponse res = new LogSearchResponse();

api/src/main/java/com/lantanagroup/link/api/controller/MeasureDefController.java

@@ -2,11 +2,11 @@
 
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import com.lantanagroup.link.FhirContextProvider;
-import com.lantanagroup.link.FhirDataProvider;
 import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.Helper;
 import com.lantanagroup.link.api.MeasureServiceWrapper;
 import com.lantanagroup.link.config.api.ApiConfig;
+import com.lantanagroup.link.config.api.MeasureDefConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.model.MeasureDefinition;
 import com.lantanagroup.link.db.model.MeasurePackage;
@@ -86,11 +86,12 @@ public void createOrUpdateMeasureDef(@RequestBody(required = false) Bundle bundl
       throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Either a Bundle must be specified in a JSON body of the request, or a \"measureId\" query parameter must be specified");
     }
 
-    if (StringUtils.isNotEmpty(measureId) && this.apiConfig.getMeasureDefUrls().get(measureId) == null) {
+    MeasureDefConfig foundMeasureDef = this.apiConfig.getMeasureDefinition(measureId);
+    if (StringUtils.isNotEmpty(measureId) && foundMeasureDef == null) {
       throw new ResponseStatusException(HttpStatus.NOT_FOUND, "The specified measureId is not configured with a measure definition URL");
     }
 
-    String url = StringUtils.isNotEmpty(measureId) ? this.apiConfig.getMeasureDefUrls().get(measureId) : null;
+    String url = foundMeasureDef != null ? foundMeasureDef.getDefinitionUrl() : null;
     Bundle bundle = bundleBody == null ? this.getBundleFromUrl(url) : bundleBody;
 
     if (bundle == null) {

api/src/main/java/com/lantanagroup/link/api/controller/ReportController.java

@@ -6,6 +6,7 @@
 import com.lantanagroup.link.*;
 import com.lantanagroup.link.api.ReportGenerator;
 import com.lantanagroup.link.auth.LinkCredentials;
+import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.db.model.*;
@@ -82,6 +83,10 @@ public class ReportController extends BaseController {
   @Autowired
   private ValidationService validationService;
 
+  @Autowired
+  private ApiConfig apiConfig;
+
+
   @InitBinder
   public void initBinder(WebDataBinder binder) {
     binder.setDisallowedFields(DISALLOWED_FIELDS);
@@ -275,15 +280,15 @@ public Report generateReport(
   }
 
   private void checkReportingPlan(TenantService tenantService, String periodStart, List<String> measureIds) throws ParseException, URISyntaxException, IOException {
-    if (tenantService.getConfig().getReportingPlan() == null) {
+    if (apiConfig.getReportingPlan() == null) {
       return;
     }
 
-    if (!tenantService.getConfig().getReportingPlan().isEnabled()) {
+    if (!apiConfig.getReportingPlan().isEnabled()) {
       return;
     }
 
-    if (StringUtils.isEmpty(tenantService.getConfig().getReportingPlan().getUrl())) {
+    if (StringUtils.isEmpty(apiConfig.getReportingPlan().getUrl())) {
       logger.error("Reporting plan for tenant {} is not configured with a URL", tenantService.getConfig().getId());
       throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR);
     }
@@ -293,13 +298,13 @@ private void checkReportingPlan(TenantService tenantService, String periodStart,
       throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR);
     }
 
-    ReportingPlanService reportingPlanService = new ReportingPlanService(tenantService.getConfig().getReportingPlan(), tenantService.getConfig().getCdcOrgId());
+    ReportingPlanService reportingPlanService = new ReportingPlanService(apiConfig.getReportingPlan(), tenantService.getConfig().getCdcOrgId());
 
     Date date = Helper.parseFhirDate(periodStart);
     int year = date.getYear() + 1900;
     int month = date.getMonth() + 1;
     for (String bundleId : measureIds) {
-      String planName = tenantService.getConfig().getReportingPlan().getPlanNames().get(bundleId);
+      String planName = apiConfig.getReportingPlan().getPlanNames().get(bundleId);
       if (!reportingPlanService.isReporting(planName, year, month)) {
         throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Measure not in MRP for specified year and month");
       }

api/src/main/java/com/lantanagroup/link/api/controller/TenantController.java

@@ -4,6 +4,7 @@
 import com.lantanagroup.link.api.scheduling.Scheduler;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.TenantService;
+import com.lantanagroup.link.db.model.Report;
 import com.lantanagroup.link.db.model.tenant.Tenant;
 import com.lantanagroup.link.db.model.tenant.TenantVendors;
 import com.lantanagroup.link.model.SearchTenantResponse;
@@ -49,7 +50,7 @@ public List<SearchTenantResponse> searchTenants() {
   }
 
   @GetMapping("summary")
-  public TenantSummaryResponse searchTenantSummaries(@RequestParam(required = false) String searchCriteria, @RequestParam(defaultValue = "NAME", required = false) String sort, @RequestParam(defaultValue = "1", required = false) int page, @RequestParam(defaultValue = "true", required = false) boolean sortAscend) {
+  public TenantSummaryResponse searchTenants(@RequestParam(required = false) String searchCriteria, @RequestParam(defaultValue = "NAME", required = false) String sort, @RequestParam(defaultValue = "1", required = false) int page, @RequestParam(defaultValue = "true", required = false) boolean sortAscend) {
     // validation
     int itemsPerPage = 5;
 
@@ -67,9 +68,22 @@ public TenantSummaryResponse searchTenantSummaries(@RequestParam(required = fals
         throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Invalid sort criteria. Valid values are NAME, NHSN_ORG_ID, SUBMISSION_DATE");
       }
     }
-    List<TenantSummary> tenants = this.sharedService.getTenantSummary(searchCriteria, TenantSummarySort.valueOf(sort.trim()), sortAscend).stream().collect(Collectors.toList());
 
-    List<TenantSummary> results = tenants.stream().skip(skip).limit(itemsPerPage).collect(Collectors.toList());
+    List<TenantSummary> tenants = this.sharedService.searchTenants(searchCriteria, TenantSummarySort.valueOf(sort.trim()), sortAscend);
+    List<TenantSummary> results = tenants.stream()
+            .skip(skip)
+            .limit(itemsPerPage)
+            .collect(Collectors.toList());
+
+    results.forEach(t -> {
+      TenantService tenantService = TenantService.create(this.sharedService.getTenantConfig(t.getId()));
+      Report lastReport = tenantService.findLastReport();
+
+      if (lastReport != null) {
+        t.setLastSubmissionId(lastReport.getId());
+        t.setLastSubmissionDate(String.valueOf(lastReport.getSubmittedTime()));
+      }
+    });
 
     TenantSummaryResponse response = new TenantSummaryResponse();
     response.setTotal(tenants.size());

api/src/main/java/com/lantanagroup/link/api/controller/ValidationController.java

@@ -49,7 +49,6 @@ public class ValidationController extends BaseController {
   /**
    * Validates a Bundle provided in the request body
    *
-   * @param tenantId The id of the tenant
    * @param severity The minimum severity level to report on
    * @return Returns an OperationOutcome resource that provides details about each of the issues found
    */
@@ -73,7 +72,6 @@ public OperationOutcome validate(@RequestBody Bundle bundle, @RequestParam(defau
   /**
    * Validates a Bundle provided in the request body
    *
-   * @param tenantId The id of the tenant
    * @param severity The minimum severity level to report on
    * @return Returns an OperationOutcome resource that provides details about each of the issues found
    */
@@ -92,7 +90,9 @@ public String validateSummary(@RequestBody Bundle bundle, @RequestParam(defaultV
    * @throws IOException
    */
   @GetMapping("/{tenantId}/{reportId}")
-  public OperationOutcome getValidationIssuesForReport(@PathVariable String tenantId, @PathVariable String reportId, @RequestParam(defaultValue = "INFORMATION") OperationOutcome.IssueSeverity severity, @RequestParam(required = false) String code) {
+  public OperationOutcome getValidationIssuesForReport(@PathVariable String tenantId, @PathVariable String reportId,
+                                                       @RequestParam(defaultValue = "INFORMATION") OperationOutcome.IssueSeverity severity,
+                                                       @RequestParam(required = false) String code) {
     TenantService tenantService = TenantService.create(this.sharedService, tenantId);
 
     if (tenantService == null) {

core/src/main/java/com/lantanagroup/link/ApplyConceptMaps.java

@@ -15,7 +15,6 @@
 
 public class ApplyConceptMaps {
   private static final Logger logger = LoggerFactory.getLogger(ApplyConceptMaps.class);
-  private final DefaultProfileValidationSupport validationSupport = new DefaultProfileValidationSupport(FhirContextProvider.getFhirContext());
 
   private List<com.lantanagroup.link.db.model.ConceptMap> conceptMaps;
 
@@ -27,14 +26,8 @@ public static boolean isMapped(Coding coding, String system, String code) {
             .anyMatch(mappedCoding -> mappedCoding.is(system, code));
   }
 
-  public ApplyConceptMaps() {
-    validationSupport.fetchAllStructureDefinitions();
-  }
+  public ApplyConceptMaps() {}
 
-  private FHIRPathEngine getFhirPathEngine() {
-    HapiWorkerContext workerContext = new HapiWorkerContext(FhirContextProvider.getFhirContext(), validationSupport);
-    return new FHIRPathEngine(workerContext);
-  }
 
   private void translateCoding(ConceptMap map, Coding code) {
     map.getGroup().stream().forEach((ConceptMap.ConceptMapGroupComponent group) -> {
@@ -81,7 +74,7 @@ public List<Base> filterResourcesByPathList(DomainResource resource, List<String
     List<Base> results = new ArrayList<>();
     // logger.debug(String.format("FindCodings for resource %s based on path %s", resource.getResourceType() + "/" + resource.getIdElement().getIdPart(), List.of(pathList)));
     pathList.stream().forEach(path -> {
-      results.addAll(getFhirPathEngine().evaluate(resource, path));
+      results.addAll(FhirHelper.getFhirPathEngine().evaluate(resource, path));
     });
     return results;
   }

core/src/main/java/com/lantanagroup/link/Constants.java

@@ -61,4 +61,9 @@ public class Constants {
   public static final String VALIDATION_ISSUE_TASK = "Validation";
   public static final String VALIDATION_ISSUE_CATEGORY = "Validation Issues";
   public static final String REPORT_GENERATION_TASK = "Report Generation";
+
+  //Submission file names
+  public static final String ORGANIZATION_FILE_NAME = "organization.json";
+  public static final String DEVICE_FILE_NAME = "device.json";
+  public static final String QUERY_PLAN_FILE_NAME = "query-plan.yml";
 }