IMPS-160: Alpha Billings: Location.type Concept Map Investigation Needed

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

@@ -19,6 +19,14 @@ public class ApplyConceptMaps {
 
   private List<com.lantanagroup.link.db.model.ConceptMap> conceptMaps;
 
+  public static boolean isMapped(Coding coding, String system, String code) {
+    return coding.getExtensionsByUrl(Constants.ConceptMappingExtension).stream()
+            .map(Extension::getValue)
+            .filter(value -> value instanceof Coding)
+            .map(value -> (Coding) value)
+            .anyMatch(mappedCoding -> mappedCoding.is(system, code));
+  }
+
   public ApplyConceptMaps() {
     validationSupport.fetchAllStructureDefinitions();
   }

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

@@ -32,6 +32,7 @@ public class Constants {
   public static final String OriginalElementValueExtension = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/StructureDefinition/link-original-element-value-extension";
   public static final String OriginalResourceIdExtension = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/StructureDefinition/link-original-resource-id-extension";
   public static final String BundlingFullUrlFormat = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/%s";
+  public static final String LocationAliasCodeSystem = "https://nhsnlink.org/location-alias";
 
   //Metric taskName Constants
   public static final String TASK_SUBMIT = "submit";

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

@@ -25,14 +25,16 @@ public void FixDates()
         DateTimeType end = p.getEndElement();
 
         if (start.getPrecision() == TemporalPrecisionEnum.DAY && end.getPrecision().getCalendarConstant() > TemporalPrecisionEnum.DAY.getCalendarConstant()) {
+          p.getStartElement().addExtension()
+                  .setUrl(Constants.OriginalElementValueExtension)
+                  .setValue(p.getStartElement().copy());
+
           start.setPrecision(end.getPrecision());
           start.setTimeZone(end.getTimeZone());
           start.setHour(0);
           start.setMinute(0);
           start.setSecond(0);
           start.setMillis(0);
-
-          p.setStartElement(start);
       }
 
     });

core/src/main/java/com/lantanagroup/link/events/CopyLocationAliasToType.java

@@ -1,66 +1,99 @@
 package com.lantanagroup.link.events;
 
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import com.lantanagroup.link.ApplyConceptMaps;
 import com.lantanagroup.link.Constants;
-import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.IReportGenerationDataEvent;
 import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.model.ReportContext;
 import com.lantanagroup.link.model.ReportCriteria;
+import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.r4.model.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
-import java.util.stream.Collectors;
-
+import java.util.Map;
 
 public class CopyLocationAliasToType implements IReportGenerationDataEvent {
   private static final Logger logger = LoggerFactory.getLogger(CopyLocationAliasToType.class);
 
-  @Override
-  public void execute(TenantService tenantService, Bundle bundle, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
-    //This is a specific transform to move data from a Location's alias to its type
-    //This must happen BEFORE ApplyConceptMaps as an event
-    logger.info("Called: " + CopyLocationAliasToType.class.getName());
-    for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
-      if (entry.getResource().getResourceType().equals(ResourceType.Location)) {
-        Location locationResource = (Location) entry.getResource();
-        //Check for ConceptMap extension indicating that the alias move to type and ConceptMapping has already been performed on this Location
-        List<CodeableConcept> conceptMapExtensionCheck =
-                locationResource.getType().stream().filter(t ->
-                                t.getCoding().stream().anyMatch(c ->
-                                        c.getExtension().stream().anyMatch(e ->
-                                                e.getUrl().equals(Constants.ConceptMappingExtension))))
-                        .collect(Collectors.toList());
+  private static boolean anyAliasExistsInType(Location location) {
+    return location.getType().stream()
+            .flatMap(type -> type.getCoding().stream())
+            .anyMatch(coding -> StringUtils.equals(coding.getSystem(), Constants.LocationAliasCodeSystem));
+  }
 
-        //If not already performed, continue
-        if(conceptMapExtensionCheck.size() == 0){
+  private static boolean existsInType(Location location, StringType alias) {
+    return location.getType().stream()
+            .flatMap(type -> type.getCoding().stream())
+            .anyMatch(coding -> coding.is(Constants.LocationAliasCodeSystem, alias.asStringValue())
+                    || ApplyConceptMaps.isMapped(coding, Constants.LocationAliasCodeSystem, alias.asStringValue()));
+  }
 
-          List<StringType> aliases = locationResource.getAlias();
-          List<CodeableConcept> types = locationResource.getType();
-          if (aliases.size() > 0) {
-            for (StringType alias : aliases) {
-              String value = alias.toString();
+  private static void copyToType(Location location, StringType alias) {
+    location.addType().addCoding()
+            .setSystem(Constants.LocationAliasCodeSystem)
+            .setCode(alias.asStringValue());
+  }
 
-              List<CodeableConcept> existingType = types.stream()
-                      .filter(t -> t.getCoding().stream().anyMatch(c -> c.getCode().equals(value)))
-                      .collect(Collectors.toList());
+  private final boolean iterative;
 
-              //Check for a value in alias
-              if (value != null && existingType.isEmpty()) {
-                //Add type to list of existing types
-                types.add(FhirHelper.createCodeableConcept(value, "https://nhsnlink.org/location-alias"));
-              }
-            }
+  public CopyLocationAliasToType(boolean iterative) {
+    this.iterative = iterative;
+  }
+
+  public CopyLocationAliasToType() {
+    this(false);
+  }
+
+  @Override
+  public void execute(TenantService tenantService, Bundle bundle, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
+    Map<String, Location> locationsById = new HashMap<>();
+    for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+      Resource resource = entry.getResource();
+      if (!(resource instanceof Location)) {
+        continue;
+      }
+      Location location = (Location) resource;
+      locationsById.putIfAbsent(location.getIdPart(), location);
+      if (anyAliasExistsInType(location)) {
+        continue;
+      }
+      Location ancestor = location;
+      IGenericClient client = context.getClient();
+      while (true) {
+        for (StringType alias : ancestor.getAlias()) {
+          if (!existsInType(location, alias)) {
+            copyToType(location, alias);
           }
         }
+        if (!iterative || client == null) {
+          break;
+        }
+        String ancestorId = ancestor.getPartOf()
+                .getReferenceElement()
+                .getIdPart();
+        if (ancestorId == null) {
+          break;
+        }
+        try {
+          ancestor = locationsById.computeIfAbsent(
+                  ancestorId,
+                  key -> client.read()
+                          .resource(Location.class)
+                          .withId(key)
+                          .execute());
+        } catch (Exception e) {
+          logger.error("Failed to retrieve ancestor: {}", ancestorId, e);
+          break;
+        }
       }
     }
   }
 
   @Override
-  public void execute(TenantService tenantService, List<DomainResource> data, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) throws RuntimeException {
-    throw new RuntimeException("Not yet implemented");
+  public void execute(TenantService tenantService, List<DomainResource> data, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
   }
-}
+}

core/src/main/java/com/lantanagroup/link/events/CopyLocationAliasToTypeIteratively.java

@@ -0,0 +1,7 @@
+package com.lantanagroup.link.events;
+
+public class CopyLocationAliasToTypeIteratively extends CopyLocationAliasToType {
+  public CopyLocationAliasToTypeIteratively() {
+    super(true);
+  }
+}

core/src/main/java/com/lantanagroup/link/events/CopyLocationIdentifierToType.java

@@ -1,6 +1,6 @@
 package com.lantanagroup.link.events;
 
-import com.lantanagroup.link.FhirHelper;
+import com.lantanagroup.link.ApplyConceptMaps;
 import com.lantanagroup.link.IReportGenerationDataEvent;
 import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.model.ReportContext;
@@ -9,59 +9,41 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
-import com.lantanagroup.link.Constants;
 
-/**
- * Populates the Location.type with the first value from Location.identifier
- */
 public class CopyLocationIdentifierToType implements IReportGenerationDataEvent {
-
   private static final Logger logger = LoggerFactory.getLogger(CopyLocationIdentifierToType.class);
 
+  private static boolean existsInType(Location location, Identifier identifier) {
+    return location.getType().stream()
+            .flatMap(type -> type.getCoding().stream())
+            .anyMatch(coding -> coding.is(identifier.getSystem(), identifier.getValue())
+                    || ApplyConceptMaps.isMapped(coding, identifier.getSystem(), identifier.getValue()));
+  }
+
+  private static void copyToType(Location location, Identifier identifier) {
+    location.addType().addCoding()
+            .setSystem(identifier.getSystem())
+            .setCode(identifier.getValue());
+  }
+
   @Override
   public void execute(TenantService tenantService, Bundle bundle, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
-    //This is a specific transform to move data from an extension to the type of a Location resource for UMich
-    //This must happen BEFORE ApplyConceptMaps as an event
-    logger.info("Called: " + CopyLocationIdentifierToType.class.getName());
     for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
-      if (entry.getResource().getResourceType().equals(ResourceType.Location)) {
-        Location locationResource = (Location) entry.getResource();
-        //Check for ConceptMap extension indicating that the identifier move to type and ConceptMapping has already been performed on this Location
-        List<Coding> conceptMapExtensionCheck =
-                locationResource.getType().stream().flatMap(t -> t.getCoding().stream()).filter(t ->
-                                t.getExtension().stream().anyMatch(e -> e.getUrl().equals(Constants.ConceptMappingExtension)))
-                        .collect(Collectors.toList());
-        //If not already performed, continue
-        if (conceptMapExtensionCheck.size() == 0) {
-          List<Identifier> identifiers = locationResource.getIdentifier();
-          List<CodeableConcept> types = locationResource.getType();
-          if (identifiers.size() > 0) {
-            for (Identifier identifier : identifiers) {
-              String idValue = identifier.getValue();
-              String idSystem = identifier.getSystem();
-
-              List<CodeableConcept> existingType = types.stream()
-                      .filter(t -> t.getCoding().stream().anyMatch(c -> c.getCode().equals(idValue) && c.getSystem().equals(idSystem)))
-                      .collect(Collectors.toList());
-
-              //Check for a full identifier (both system and value) and no existing type element with the values from identifier
-              if (existingType.isEmpty() && idValue != null && idSystem != null) {
-
-                //Add type to list of existing types
-                types.add(FhirHelper.createCodeableConcept(idValue, idSystem));
-              }
-            }
-          }
+      Resource resource = entry.getResource();
+      if (!(resource instanceof Location)) {
+        continue;
+      }
+      Location location = (Location) resource;
+      for (Identifier identifier : location.getIdentifier()) {
+        if (identifier.hasSystem() && !existsInType(location, identifier)) {
+          copyToType(location, identifier);
         }
       }
     }
   }
 
   @Override
-  public void execute(TenantService tenantService, List<DomainResource> data, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) throws RuntimeException {
-    throw new RuntimeException("Not yet implemented");
+  public void execute(TenantService tenantService, List<DomainResource> data, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
   }
 }

core/src/main/java/com/lantanagroup/link/events/FixPeriodDates.java

@@ -27,7 +27,6 @@ public void execute(TenantService tenantService, Bundle data, ReportCriteria cri
   }
 
   public void execute(TenantService tenantService, List<DomainResource> resourceList, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
-    throw new RuntimeException("Not Implemented yet.");
   }
 }
 

core/src/main/java/com/lantanagroup/link/events/FixResourceId.java

@@ -25,6 +25,5 @@ public void execute(TenantService tenantService, Bundle data, ReportCriteria cri
   }
 
   public void execute(TenantService tenantService, List<DomainResource> resourceList, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
-    throw new RuntimeException("Not Implemented yet.");
   }
 }

core/src/main/java/com/lantanagroup/link/events/PatientDataResourceFilter.java

@@ -159,6 +159,5 @@ public void execute(TenantService tenantService, Bundle bundle, ReportCriteria c
   @SuppressWarnings("unused")
   @Override
   public void execute(TenantService tenantService, List<DomainResource> data, ReportCriteria criteria, ReportContext context, ReportContext.MeasureContext measureContext) {
-    throw new RuntimeException("Not yet implemented");
   }
 }

core/src/main/java/com/lantanagroup/link/model/ReportContext.java

@@ -1,5 +1,6 @@
 package com.lantanagroup.link.model;
 
+import ca.uhn.fhir.rest.client.api.IGenericClient;
 import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.auth.LinkCredentials;
 import com.lantanagroup.link.db.model.PatientList;
@@ -25,6 +26,7 @@ public class ReportContext {
   private List<PatientOfInterestModel> patientsOfInterest = new ArrayList<>();
   private List<MeasureContext> measureContexts = new ArrayList<>();
   private QueryPlan queryPlan;
+  private IGenericClient client;
   private List<String> debugPatients = new ArrayList<>();
 
   public ReportContext() {

core/src/test/java/com/lantanagroup/link/PeriodDateFixerTests.java

@@ -1,10 +1,7 @@
 package com.lantanagroup.link;
 
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.DateTimeType;
-import org.hl7.fhir.r4.model.Encounter;
-import org.hl7.fhir.r4.model.Period;
+import org.hl7.fhir.r4.model.*;
 import org.junit.Assert;
 import org.junit.Test;
 
@@ -61,6 +58,11 @@ public void fixDatesTest()
     Assert.assertEquals(start, period.getStart());
     Assert.assertNotEquals(startString, period.getStartElement().asStringValue());
 
+    Assert.assertTrue(period.getStartElement().hasExtension());
+    Extension extension = period.getStartElement().getExtensionFirstRep();
+    Assert.assertEquals(Constants.OriginalElementValueExtension, extension.getUrl());
+    Assert.assertEquals("2023-05-25", extension.getValue().primitiveValue());
+
     Assert.assertEquals(end, period.getEnd());
     Assert.assertEquals(endString, period.getEndElement().asStringValue());
   }

query/src/main/java/com/lantanagroup/link/query/uscore/Query.java

@@ -60,12 +60,16 @@ public void execute(TenantService tenantService, ReportCriteria criteria, Report
     List<PatientOfInterestModel> patientsOfInterest = context.getPatientsOfInterest(queryPhase);
     if (patientsOfInterest.size() > 0) {
       try {
+        IGenericClient client = this.getFhirQueryClient(tenantService, context.getMasterIdentifierValue());
+        context.setClient(client);
         PatientScoop scoop = this.applicationContext.getBean(PatientScoop.class);
-        scoop.setFhirQueryServer(this.getFhirQueryClient(tenantService, context.getMasterIdentifierValue()));
+        scoop.setFhirQueryServer(client);
         scoop.setTenantService(tenantService);
         scoop.execute(criteria, context, patientsOfInterest, queryPhase);
       } catch (Exception ex) {
         logger.error("Error scooping data for patients", ex);
+      } finally {
+        context.setClient(null);
       }
     }
   }