App context changes

resources/src/main/java/org/cdshooks/Card.java

@@ -39,6 +39,15 @@ public String getDetail() {
   public void setDetail(String detail) {
     this.detail = detail;
   }
+
+  // Add details to what already exists
+  public void addDetail(String detail) {
+    if (this.detail == null) {
+      setDetail(detail);
+    } else {
+      this.detail = detail + "\n" + this.detail;
+    }
+  }
 
   public IndicatorEnum getIndicator() {
     return indicator;

server/src/main/java/org/hl7/davinci/endpoint/cdshooks/services/crd/CdsAbstract.java

@@ -4,9 +4,11 @@
 import org.cdshooks.*;
 import org.hl7.davinci.FhirComponentsT;
 import org.hl7.davinci.PrefetchTemplateElement;
+import org.hl7.davinci.endpoint.cdshooks.services.crd.r4.FhirRequestProcessor;
 import org.hl7.davinci.endpoint.config.YamlConfig;
 import org.hl7.davinci.endpoint.rules.CoverageRequirementRuleCriteria;
 import org.hl7.davinci.r4.crdhook.DiscoveryExtension;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -95,7 +97,7 @@ public List<PrefetchTemplateElement> getPrefetchElements() {
     }
 
     protected Link smartLinkBuilder(String patientId, String fhirBase, URL applicationBaseUrl, String questionnaireUri,
-                                  String reqResourceId, CoverageRequirementRuleCriteria criteria, boolean priorAuthRequired, String label) {
+                                    String reqResourceId, IBaseResource request, String label) {
         URI configLaunchUri = myConfig.getLaunchUrl();
         questionnaireUri = applicationBaseUrl + "/fhir/r4/" + questionnaireUri;
 
@@ -125,13 +127,9 @@ protected Link smartLinkBuilder(String patientId, String fhirBase, URL applicati
         // request is the ID of the device request or medrec (not the full URI like the
         // IG says, since it should be taken from fhirBase
 
-        String filepath = "../../getfile/" + criteria.getQueryString();
 
-        String appContext = "template=" + questionnaireUri + "&request=" + reqResourceId;
-        appContext = appContext + "&fhirpath=" + applicationBaseUrl + "/fhir/";
+        String appContext = "questionnaire=" + questionnaireUri + "&order=" + reqResourceId + "&coverage=" + FhirRequestProcessor.getCoverageFromRequest(request).getReference();
 
-        appContext = appContext + "&priorauth=" + (priorAuthRequired ? "true" : "false");
-        appContext = appContext + "&filepath=" + applicationBaseUrl + "/";
         if (myConfig.getUrlEncodeAppContext()) {
             logger.info("CdsService::smartLinkBuilder: URL encoding appcontext");
             appContext = URLEncoder.encode(appContext, StandardCharsets.UTF_8).toString();

server/src/main/java/org/hl7/davinci/endpoint/cdshooks/services/crd/CdsServiceRems.java

@@ -65,9 +65,10 @@ public CdsServiceRems(String id, Hook hook, String title, String description,
      */
     public CdsResponse handleRequest(@Valid @RequestBody requestTypeT request, URL applicationBaseUrl) {
         CdsResponse response = new CdsResponse();
+        CardBuilder cardBuilder = new CardBuilder();
         List<Coding> medications = getMedications(request);
         for (Coding medication : medications) {
-            Card card = CardBuilder.summaryCard(CardTypes.COVERAGE, "");
+            Card card = cardBuilder.summaryCard(CardTypes.COVERAGE, "");
             if (isRemsDrug(medication)) {
                 card.setSummary(String.format("%s has REMS", medication.getDisplay()));
             } else {

server/src/main/java/org/hl7/davinci/endpoint/components/CardBuilder.java

@@ -23,6 +23,8 @@
 public class CardBuilder {
   static final Logger logger = LoggerFactory.getLogger(CardBuilder.class);
 
+  public boolean deidentifiedResourcesContainPhi = false;
+
   public static class CqlResultsForCard {
     private Boolean ruleApplies;
 
@@ -77,14 +79,18 @@ public CqlResultsForCard setRequest(IBaseResource request) {
     }
   }
 
+  public void setDeidentifiedResourcesContainsPhi(boolean deidentifiedResourcesContainPhi) {
+    this.deidentifiedResourcesContainPhi = deidentifiedResourcesContainPhi;
+  }
+
   /**
    * Transforms a result from the database into a card.
    *
    * @param cardType
    * @param cqlResults
    * @return card with appropriate information
    */
-  public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, Boolean addLink) {
+  public Card transform(CardTypes cardType, CqlResultsForCard cqlResults, Boolean addLink) {
     String requestId = Utilities.getIdFromIBaseResource(cqlResults.getRequest());
     Card card = baseCard(cardType, requestId);
 
@@ -97,7 +103,7 @@ public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, B
     }
 
     card.setSummary(cqlResults.getCoverageRequirements().getSummary());
-    card.setDetail(cqlResults.getCoverageRequirements().getDetails());
+    card.addDetail(cqlResults.getCoverageRequirements().getDetails());
 
     return card;
   }
@@ -109,7 +115,7 @@ public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, B
    * @param cqlResults
    * @return card with appropriate information
    */
-  public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults) {
+  public Card transform(CardTypes cardType, CqlResultsForCard cqlResults) {
     return transform(cardType, cqlResults, true);
   }
 
@@ -121,7 +127,7 @@ public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults) {
    * @param smartAppLaunchLink smart app launch Link
    * @return card with appropriate information
    */
-  public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, Link smartAppLaunchLink) {
+  public Card transform(CardTypes cardType, CqlResultsForCard cqlResults, Link smartAppLaunchLink) {
     Card card = transform(cardType, cqlResults);
     List<Link> links = new ArrayList<Link>(card.getLinks());
     links.add(smartAppLaunchLink);
@@ -137,7 +143,7 @@ public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, L
    * @param smartAppLaunchLinks a list of links
    * @return card to be returned
    */
-  public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, List<Link> smartAppLaunchLinks) {
+  public Card transform(CardTypes cardType, CqlResultsForCard cqlResults, List<Link> smartAppLaunchLinks) {
     Card card = transform(cardType, cqlResults);
     List<Link> links = new ArrayList<Link>(card.getLinks());
     links.addAll(smartAppLaunchLinks);
@@ -152,20 +158,20 @@ public static Card transform(CardTypes cardType, CqlResultsForCard cqlResults, L
    * @param summary The desired summary for the card
    * @return valid card
    */
-  public static Card summaryCard(CardTypes cardType, String summary) {
+  public Card summaryCard(CardTypes cardType, String summary) {
     Card card = baseCard(cardType, "");
     card.setSummary(summary);
     return card;
   }
 
-  public static Card alternativeTherapyCard(AlternativeTherapy alternativeTherapy, IBaseResource resource,
+  public Card alternativeTherapyCard(AlternativeTherapy alternativeTherapy, IBaseResource resource,
                                             FhirComponentsT fhirComponents) {
     logger.info("Build Alternative Therapy Card: " + alternativeTherapy.toString());
     String requestId = Utilities.getIdFromIBaseResource(resource);
     Card card = baseCard(CardTypes.THERAPY_ALTERNATIVES_OPT, requestId);
 
     card.setSummary("Alternative Therapy Suggested");
-    card.setDetail(alternativeTherapy.getDisplay() + " (" + alternativeTherapy.getCode() + ") should be used instead.");
+    card.addDetail(alternativeTherapy.getDisplay() + " (" + alternativeTherapy.getCode() + ") should be used instead.");
 
     List<Suggestion> suggestionList = new ArrayList<>();
     Suggestion alternativeTherapySuggestion = new Suggestion();
@@ -205,17 +211,17 @@ public static Card alternativeTherapyCard(AlternativeTherapy alternativeTherapy,
     return card;
   }
 
-  public static Card drugInteractionCard(DrugInteraction drugInteraction, IBaseResource resource) {
+  public Card drugInteractionCard(DrugInteraction drugInteraction, IBaseResource resource) {
     logger.info("Build Drug Interaction Card: " + drugInteraction.getSummary());
     String requestId = Utilities.getIdFromIBaseResource(resource);
     Card card = baseCard(CardTypes.CONTRAINDICATION, requestId);
     card.setSummary(drugInteraction.getSummary());
-    card.setDetail(drugInteraction.getDetail());
+    card.addDetail(drugInteraction.getDetail());
     card.setIndicator(Card.IndicatorEnum.WARNING);
     return card;
   }
 
-  public static Card priorAuthCard(CqlResultsForCard cqlResults,
+  public Card priorAuthCard(CqlResultsForCard cqlResults,
                                    IBaseResource request,
                                    FhirComponentsT fhirComponents,
                                    String priorAuthId,
@@ -264,7 +270,7 @@ public static Card priorAuthCard(CqlResultsForCard cqlResults,
     return card;
   }
 
-  public static Suggestion createSuggestionWithResource(IBaseResource request,
+  public Suggestion createSuggestionWithResource(IBaseResource request,
                                                         IBaseResource resource,
                                                         FhirComponentsT fhirComponents,
                                                         String label,
@@ -291,7 +297,7 @@ public static Suggestion createSuggestionWithResource(IBaseResource request,
     return suggestion;
   }
 
-  public static Suggestion createSuggestionWithNote(Card card,
+  public Suggestion createSuggestionWithNote(Card card,
                                                     IBaseResource request,
                                                     FhirComponentsT fhirComponents,
                                                     String label,
@@ -394,7 +400,7 @@ public static Suggestion createSuggestionWithNote(Card card,
     return requestWithNoteSuggestion;
   }
 
-  private static Source createSource(CardTypes cardType) {
+  private Source createSource(CardTypes cardType) {
     Source source = new Source();
     source.setLabel("Da Vinci CRD Reference Implementation");
     source.setTopic(cardType.getCoding());
@@ -408,19 +414,18 @@ private static Source createSource(CardTypes cardType) {
    * @param cardType
    * @param response The response to check and add cards to
    */
-  public static void errorCardIfNonePresent(CardTypes cardType, CdsResponse response) {
+  public void errorCardIfNonePresent(CardTypes cardType, CdsResponse response) {
     if (response.getCards() == null || response.getCards().size() == 0) {
-      Card card = new Card();
+      Card card = baseCard(cardType, "");
       card.setIndicator(Card.IndicatorEnum.WARNING);
-      card.setSource(createSource(cardType));
       String msg = "Unable to process hook request from provided information.";
       card.setSummary(msg);
       response.addCard(card);
       logger.warn(msg + "; summary card sent to client");
     }
   }
 
-  private static Card baseCard(CardTypes cardType, String requestId) {
+  private Card baseCard(CardTypes cardType, String requestId) {
     Card card = new Card();
     card.setIndicator(Card.IndicatorEnum.INFO);
     card.setSource(createSource(cardType));
@@ -430,6 +435,10 @@ private static Card baseCard(CardTypes cardType, String requestId) {
       cardExtension.addAssociatedResource(requestId);
       card.setExtension(cardExtension);
     }
+
+    if (deidentifiedResourcesContainPhi) {
+      card.setDetail("Note: de-identified resources provided in request contain Protected Health Information (PHI). Please notify administrator.");
+    }
 
     return card;
   }

server/src/main/java/org/hl7/davinci/endpoint/controllers/FhirController.java

@@ -1,5 +1,6 @@
 package org.hl7.davinci.endpoint.controllers;
 
+import org.aspectj.weaver.patterns.TypePatternQuestions;
 import org.hl7.davinci.FhirResourceInfo;
 import org.hl7.davinci.endpoint.Application;
 import org.hl7.davinci.endpoint.Utils;
@@ -19,6 +20,7 @@
 import org.springframework.web.bind.annotation.*;
 
 import java.io.IOException;
+import java.util.Optional;
 import java.util.logging.Logger;
 import javax.servlet.http.HttpServletRequest;
 
@@ -28,7 +30,7 @@
  */
 @RestController
 public class FhirController {
-  private static Logger logger = Logger.getLogger(Application.class.getName());
+  private static Logger logger = Logger.getLogger(FhirController.class.getName());
 
   @Autowired
   private FileStore fileStore;
@@ -229,7 +231,23 @@ public ResponseEntity<String> submitFhirResource(HttpServletRequest request, Htt
   @PostMapping(path = "/fhir/{fhirVersion}/Questionnaire/$questionnaire-package", consumes = { MediaType.APPLICATION_JSON_VALUE, "application/fhir+json" })
   public ResponseEntity<String> questionnaireForOrderOperation(HttpServletRequest request, HttpEntity<String> entity,
                                                    @PathVariable String fhirVersion) {
+    return handleQuestionnaireOperation(request, entity, fhirVersion, null);
+  }
+
+  /**
+   * FHIR Operation to retrieve a Questionnaire and CQL files associated with a given request.
+   * @param fhirVersion (converted to uppercase)
+   * @return FHIR Bundle
+   * @throws IOException
+   */
+  @PostMapping(path = "/fhir/{fhirVersion}/Questionnaire/{questionnaireId}/$questionnaire-package", consumes = { MediaType.APPLICATION_JSON_VALUE, "application/fhir+json" })
+  public ResponseEntity<String> questionnaireForOrderOperationScoped(HttpServletRequest request, HttpEntity<String> entity,
+                                                               @PathVariable String fhirVersion, @PathVariable String questionnaireId) {
+    return handleQuestionnaireOperation(request, entity, fhirVersion, questionnaireId);
+  }
 
+  private ResponseEntity<String> handleQuestionnaireOperation(HttpServletRequest request, HttpEntity<String> entity,
+                                                              String fhirVersion, String questionnaireId) {
     fhirVersion = fhirVersion.toUpperCase();
     String baseUrl = Utils.getApplicationBaseUrl(request).toString() + "/";
 
@@ -238,15 +256,15 @@ public ResponseEntity<String> questionnaireForOrderOperation(HttpServletRequest
     String resource = null;
     if (fhirVersion.equalsIgnoreCase("R4")) {
       QuestionnairePackageOperation operation = new QuestionnairePackageOperation(fileStore, baseUrl);
-      resource = operation.execute(entity.getBody());
+      resource = operation.execute(entity.getBody(), questionnaireId);
 
       if (resource == null) {
         logger.warning("bad parameters");
         HttpStatus status = HttpStatus.BAD_REQUEST;
         MediaType contentType = MediaType.TEXT_PLAIN;
-        
+
         return ResponseEntity.status(status).contentType(contentType)
-            .body("Bad Parameters");
+                .body("Bad Parameters");
       }
 
     } else {
@@ -255,11 +273,11 @@ public ResponseEntity<String> questionnaireForOrderOperation(HttpServletRequest
       MediaType contentType = MediaType.TEXT_PLAIN;
 
       return ResponseEntity.status(status).contentType(contentType)
-          .body("Bad Request");
+              .body("Bad Request");
     }
 
     return ResponseEntity.status(HttpStatus.OK).contentType(MediaType.APPLICATION_JSON)
-          .body(resource);
+            .body(resource);
   }