#171: improve documentation in properties files

cerner-config/fhirconfig.properties

@@ -41,6 +41,6 @@ protocol.answer.no=Did NOT Follow BP Protocol
 #        e.g. with note text "Systolic: 130, Diastolic: 80", systolic-regex might be "Systolic: ([0-9]+)"
 #             with note text "BP Goal: 130/80", systolic-regex might be "([0-9]+)\\/"
 ############################################
-service-request-order.bp-goal.custom-codings=
+service-request-order.bp-goal.codings=
 service-request-order.bp-goal.note.systolic-regex=
 service-request-order.bp-goal.note.diastolic-regex=

cerner-config/fhirqueries.properties

@@ -2,10 +2,8 @@ Patient.Lookup=Patient/{id}
 Patient.Strategy=PATIENT
 Encounter.Query=
 Encounter.Strategy=PATIENT
-Observation.Category.Query=Observation?patient={subject}&category={category}
-Observation.Category.Strategy=PATIENT
-Observation.Code.Query=Observation?patient={subject}&code={code}
-Observation.Code.Strategy=PATIENT
+Observation.Query=Observation?patient={subject}&code={code}
+Observation.Strategy=PATIENT
 Condition.Query=Condition?patient={subject}&category={category}
 Condition.Strategy=PATIENT
 #Goal.Query=Goal?subject={subject}&lifecycle-status=active

epic-config/fhirconfig.properties

@@ -40,6 +40,6 @@ protocol.answer.no=Did NOT Follow BP Protocol
 #        e.g. with note text "Systolic: 130, Diastolic: 80", systolic-regex might be "Systolic: ([0-9]+)"
 #             with note text "BP Goal: 130/80", systolic-regex might be "([0-9]+)\\/"
 ############################################
-service-request-order.bp-goal.custom-codings=urn:oid:1.2.840.114350.1.13.135.2.7.2.696580|340941|COACH PATIENT REPORTED BLOOD PRESSURE
+service-request-order.bp-goal.codings=urn:oid:1.2.840.114350.1.13.135.2.7.2.696580|340941|COACH PATIENT REPORTED BLOOD PRESSURE
 service-request-order.bp-goal.note.systolic-regex=Systolic: ([0-9]+)
 service-request-order.bp-goal.note.diastolic-regex=Diastolic: ([0-9]+)

epic-config/fhirqueries.properties

@@ -2,10 +2,8 @@ Patient.Lookup=Patient/{id}
 Patient.Strategy=PATIENT
 Encounter.Query=Encounter?subject={subject}
 Encounter.Strategy=PATIENT
-Observation.Category.Query=Observation?subject={subject}&category={category}
-Observation.Category.Strategy=PATIENT
-Observation.Code.Query=Observation?subject={subject}&code={code}
-Observation.Code.Strategy=PATIENT
+Observation.Query=Observation?subject={subject}&code={code}
+Observation.Strategy=PATIENT
 Condition.Query=Condition?subject={subject}&category={category}
 Condition.Strategy=PATIENT
 Goal.Query=Goal?subject={subject}&lifecycle-status=active

epic-config/poc/fhirconfig.properties

@@ -42,6 +42,6 @@ protocol.answer.no=Did NOT Follow BP Protocol
 #        e.g. with note text "Systolic: 130, Diastolic: 80", systolic-regex might be "Systolic: ([0-9]+)"
 #             with note text "BP Goal: 130/80", systolic-regex might be "([0-9]+)\\/"
 ############################################
-service-request-order.bp-goal.custom-codings=urn:oid:1.2.840.114350.1.13.135.3.7.2.696580|340941|COACH PATIENT REPORTED BLOOD PRESSURE
+service-request-order.bp-goal.codings=urn:oid:1.2.840.114350.1.13.135.3.7.2.696580|340941|COACH PATIENT REPORTED BLOOD PRESSURE
 service-request-order.bp-goal.note.systolic-regex=Systolic: ([0-9]+)
 service-request-order.bp-goal.note.diastolic-regex=Diastolic: ([0-9]+)

logica-config/fhirconfig.properties

@@ -40,6 +40,6 @@ protocol.answer.no=Did NOT Follow BP Protocol
 #        e.g. with note text "Systolic: 130, Diastolic: 80", systolic-regex might be "Systolic: ([0-9]+)"
 #             with note text "BP Goal: 130/80", systolic-regex might be "([0-9]+)\\/"
 ############################################
-service-request-order.bp-goal.custom-codings=
+service-request-order.bp-goal.codings=
 service-request-order.bp-goal.note.systolic-regex=
 service-request-order.bp-goal.note.diastolic-regex=

logica-config/fhirqueries.properties

@@ -2,10 +2,8 @@ Patient.Lookup=Patient/{id}
 Patient.Strategy=PATIENT
 Encounter.Query=Encounter?subject={subject}
 Encounter.Strategy=PATIENT
-Observation.Category.Query=Observation?subject={subject}&category={category}
-Observation.Category.Strategy=PATIENT
-Observation.Code.Query=Observation?subject={subject}&code={code}
-Observation.Code.Strategy=PATIENT
+Observation.Query=Observation?subject={subject}&code={code}
+Observation.Strategy=PATIENT
 Condition.Query=Condition?subject={subject}&category={category}
 Condition.Strategy=PATIENT
 Goal.Query=Goal?subject={subject}&lifecycle-status=active

meld-config/fhirconfig.properties

@@ -40,6 +40,6 @@ protocol.answer.no=Did NOT Follow BP Protocol
 #        e.g. with note text "Systolic: 130, Diastolic: 80", systolic-regex might be "Systolic: ([0-9]+)"
 #             with note text "BP Goal: 130/80", systolic-regex might be "([0-9]+)\\/"
 ############################################
-service-request-order.bp-goal.custom-codings=
+service-request-order.bp-goal.codings=
 service-request-order.bp-goal.note.systolic-regex=
 service-request-order.bp-goal.note.diastolic-regex=

meld-config/fhirqueries.properties

@@ -2,10 +2,8 @@ Patient.Lookup=Patient/{id}
 Patient.Strategy=PATIENT
 Encounter.Query=Encounter?subject={subject}
 Encounter.Strategy=PATIENT
-Observation.Category.Query=Observation?subject={subject}&category={category}
-Observation.Category.Strategy=PATIENT
-Observation.Code.Query=Observation?subject={subject}&code={code}
-Observation.Code.Strategy=PATIENT
+Observation.Query=Observation?subject={subject}&code={code}
+Observation.Strategy=PATIENT
 Condition.Query=Condition?subject={subject}&category={category}
 Condition.Strategy=PATIENT
 Goal.Query=Goal?subject={subject}&lifecycle-status=active

src/main/java/edu/ohsu/cmp/coach/fhir/FhirConfigManager.java

@@ -67,7 +67,7 @@ public class FhirConfigManager {
     @Value("${protocol.answer.yes}")        private String protocolAnswerYes;
     @Value("${protocol.answer.no}")         private String protocolAnswerNo;
 
-    private List<Coding> serviceRequestOrderBPGoalCustomCodings = null;
+    private List<Coding> serviceRequestOrderBPGoalCodings = null;
     private Pattern serviceRequestOrderBPGoalNoteSystolicRegex = null;
     private Pattern serviceRequestOrderBPGoalNoteDiastolicRegex = null;
 
@@ -265,11 +265,11 @@ public List<Coding> getPulseCustomCodings() {
         return pulseCustomCodings;
     }
 
-    public List<Coding> getServiceRequestOrderBPGoalCustomCodings() {
-        if (serviceRequestOrderBPGoalCustomCodings == null) {
-            serviceRequestOrderBPGoalCustomCodings = buildCodings(env.getProperty("service-request-order.bp-goal.custom-codings"));
+    public List<Coding> getServiceRequestOrderBPGoalCodings() {
+        if (serviceRequestOrderBPGoalCodings == null) {
+            serviceRequestOrderBPGoalCodings = buildCodings(env.getProperty("service-request-order.bp-goal.codings"));
         }
-        return serviceRequestOrderBPGoalCustomCodings;
+        return serviceRequestOrderBPGoalCodings;
     }
 
     public Pattern getServiceRequestOrderBPGoalNoteSystolicRegex() {
@@ -377,10 +377,10 @@ private List<Coding> buildCodings(String s) {
      * @param s a string of the form "system|code" or "system|code|display"
      *          Coding components may be blank; if they are, those components are ignored
      *          e.g., "system" -> Coding("system", null, null)
-     *                "system|coding" -> Coding("system", "coding", null)
-     *                "system|coding|display" -> Coding("system", "coding", "display")
-     *                "|coding" -> Coding(null, "coding", null)
-     *                "|coding|display" -> Coding(null, "coding", "display")
+     *                "system|code" -> Coding("system", "code", null)
+     *                "system|code|display" -> Coding("system", "code", "display")
+     *                "|code" -> Coding(null, "code", null)
+     *                "|code|display" -> Coding(null, "code", "display")
      *                "system||display" -> Coding("system", null, "display")
      *                "||display" -> Coding(null, null, "display")
      *

src/main/java/edu/ohsu/cmp/coach/fhir/FhirQueryManager.java

@@ -11,10 +11,10 @@ public class FhirQueryManager {
     @Value("${Patient.Strategy}")               private FhirStrategy patientStrategy;
     @Value("${Encounter.Query}")                private String encounterQuery;
     @Value("${Encounter.Strategy}")             private FhirStrategy encounterStrategy;
-    @Value("${Observation.Category.Query}")     private String observationCategoryQuery;
-    @Value("${Observation.Category.Strategy}")  private FhirStrategy observationCategoryStrategy;
-    @Value("${Observation.Code.Query}")         private String observationCodeQuery;
-    @Value("${Observation.Code.Strategy}")      private FhirStrategy observationCodeStrategy;
+//    @Value("${Observation.Category.Query}")     private String observationCategoryQuery;
+//    @Value("${Observation.Category.Strategy}")  private FhirStrategy observationCategoryStrategy;
+    @Value("${Observation.Query}")              private String observationQuery;
+    @Value("${Observation.Strategy}")           private FhirStrategy observationStrategy;
     @Value("${Condition.Query}")                private String conditionQuery;
     @Value("${Condition.Strategy}")             private FhirStrategy conditionStrategy;
     @Value("${Goal.Query}")                     private String goalQuery;
@@ -46,20 +46,20 @@ public FhirStrategy getEncounterStrategy() {
         return encounterStrategy;
     }
 
-    public String getObservationCategoryQuery() {
-        return observationCategoryQuery;
-    }
-
-    public FhirStrategy getObservationCategoryStrategy() {
-        return observationCategoryStrategy;
-    }
+//    public String getObservationCategoryQuery() {
+//        return observationCategoryQuery;
+//    }
+//
+//    public FhirStrategy getObservationCategoryStrategy() {
+//        return observationCategoryStrategy;
+//    }
 
-    public String getObservationCodeQuery() {
-        return observationCodeQuery;
+    public String getObservationQuery() {
+        return observationQuery;
     }
 
-    public FhirStrategy getObservationCodeStrategy() {
-        return observationCodeStrategy;
+    public FhirStrategy getObservationStrategy() {
+        return observationStrategy;
     }
 
     public String getConditionQuery() {

src/main/java/edu/ohsu/cmp/coach/fhir/transform/BaseVendorTransformer.java

@@ -80,35 +80,35 @@ public String getEncounterQuery(String patientId, String lookbackPeriod) {
         );
     }
 
-    @Override
-    public String getObservationCategoryQuery(String patientId, String category) {
-        return getObservationCategoryQuery(patientId, category, null);
-    }
-
-    @Override
-    public String getObservationCategoryQuery(String patientId, String category, String lookbackPeriod) {
-        String observationCategoryQuery = workspace.getFhirQueryManager().getObservationCategoryQuery();
-        String query = lookbackPeriod != null ?
-                addLookbackPeriodParam(observationCategoryQuery, lookbackPeriod) :
-                observationCategoryQuery;
-
-        return buildQuery(query, params()
-                .add(TOKEN_SUBJECT, patientId)
-                .add(TOKEN_CATEGORY, category)
-        );
-    }
+//    @Override
+//    public String getObservationCategoryQuery(String patientId, String category) {
+//        return getObservationCategoryQuery(patientId, category, null);
+//    }
+//
+//    @Override
+//    public String getObservationCategoryQuery(String patientId, String category, String lookbackPeriod) {
+//        String observationCategoryQuery = workspace.getFhirQueryManager().getObservationCategoryQuery();
+//        String query = lookbackPeriod != null ?
+//                addLookbackPeriodParam(observationCategoryQuery, lookbackPeriod) :
+//                observationCategoryQuery;
+//
+//        return buildQuery(query, params()
+//                .add(TOKEN_SUBJECT, patientId)
+//                .add(TOKEN_CATEGORY, category)
+//        );
+//    }
 
     @Override
-    public String getObservationCodeQuery(String patientId, String code) {
-        return getObservationCodeQuery(patientId, code, null);
+    public String getObservationQuery(String patientId, String code) {
+        return getObservationQuery(patientId, code, null);
     }
 
     @Override
-    public String getObservationCodeQuery(String patientId, String code, String lookbackPeriod) {
-        String observationCodeQuery = workspace.getFhirQueryManager().getObservationCodeQuery();
+    public String getObservationQuery(String patientId, String code, String lookbackPeriod) {
+        String observationQuery = workspace.getFhirQueryManager().getObservationQuery();
         String query = StringUtils.isNotBlank(lookbackPeriod) ?
-                addLookbackPeriodParam(observationCodeQuery, lookbackPeriod) :
-                observationCodeQuery;
+                addLookbackPeriodParam(observationQuery, lookbackPeriod) :
+                observationQuery;
 
         return buildQuery(query, params()
                 .add(TOKEN_SUBJECT, patientId)

src/main/java/edu/ohsu/cmp/coach/fhir/transform/VendorTransformer.java

@@ -18,10 +18,10 @@ public interface VendorTransformer {
     String getPatientLookup(String id);
     String getEncounterQuery(String patientId);
     String getEncounterQuery(String patientId, String lookbackPeriod);
-    String getObservationCategoryQuery(String patientId, String category);
-    String getObservationCategoryQuery(String patientId, String category, String lookbackPeriod);
-    String getObservationCodeQuery(String patientId, String code);
-    String getObservationCodeQuery(String patientId, String code, String lookbackPeriod);
+//    String getObservationCategoryQuery(String patientId, String category);
+//    String getObservationCategoryQuery(String patientId, String category, String lookbackPeriod);
+    String getObservationQuery(String patientId, String code);
+    String getObservationQuery(String patientId, String code, String lookbackPeriod);
     String getConditionQuery(String patientId, String category);
     String getGoalQuery(String patientId);
     String getMedicationStatementQuery(String patientId);

src/main/java/edu/ohsu/cmp/coach/service/EHRService.java

@@ -132,8 +132,8 @@ public Bundle getObservations(String sessionId, String code, String lookbackPeri
         logger.info("getting Observations for session=" + sessionId + " having code(s): " + code);
         UserWorkspace workspace = userWorkspaceService.get(sessionId);
         FHIRCredentialsWithClient fcc = workspace.getFhirCredentialsWithClient();
-        return fhirService.search(fcc, workspace.getFhirQueryManager().getObservationCodeStrategy(),
-                workspace.getVendorTransformer().getObservationCodeQuery(fcc.getCredentials().getPatientId(), code, lookbackPeriod),
+        return fhirService.search(fcc, workspace.getFhirQueryManager().getObservationStrategy(),
+                workspace.getVendorTransformer().getObservationQuery(fcc.getCredentials().getPatientId(), code, lookbackPeriod),
                 new Function<ResourceWithBundle, Boolean>() {
                     @Override
                     public Boolean apply(ResourceWithBundle resourceWithBundle) {

src/main/java/edu/ohsu/cmp/coach/service/GoalService.java

@@ -84,7 +84,7 @@ public Bundle buildServiceRequestBasedBPGoals(String sessionId) {
                 if (entry.getResource() instanceof ServiceRequest) {
                     ServiceRequest sr = (ServiceRequest) entry.getResource();
                     try {
-                        if (sr.hasCode() && FhirUtil.hasCoding(sr.getCode(), fcm.getServiceRequestOrderBPGoalCustomCodings())) {
+                        if (sr.hasCode() && FhirUtil.hasCoding(sr.getCode(), fcm.getServiceRequestOrderBPGoalCodings())) {
                             Goal g = buildBPGoal(sessionId, sr);
                             if (logger.isDebugEnabled()) {
                                 logger.debug("created Goal: " + FhirUtil.toJson(g));

src/main/java/edu/ohsu/cmp/coach/util/ObservationUtil.java

@@ -51,6 +51,10 @@ public static ObservationSource getBPSource(Observation bpObservation, FhirConfi
                 ObservationSource.UNKNOWN;
     }
 
+    // todo : getPulseSource doesn't have an implementation that takes Encounter as a parameter, as getBPSource
+    //        functions above do.  This means that the PulseModel constructor doesn't make use of a fallback strategy
+    //        in the way that BloodPressureModel does, and this should be updated
+
     public static ObservationSource getPulseSource(Observation pulseObservation) {
         return FhirUtil.hasHomeSettingExtension(pulseObservation) ?
                 ObservationSource.HOME :    // this should remain generic HOME as a more specific source is unknown