issue #1777 - added tests and minor refactor

1. added simple unit tests for the new ParametersMap behavior
2. added single e2e test to SearchTest to cover the case where the
compartment inclusion criteria parameter is filtered out in the config

Also, we now add the DO_NOT_STORE extension from SearchUtil instead of
as the parameters are added to the ParametersMap

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

fhir-model/src/test/java/com/ibm/fhir/model/test/TestUtil.java

@@ -1,12 +1,11 @@
 /*
- * (C) Copyright IBM Corp. 2019, 2021
+ * (C) Copyright IBM Corp. 2019, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
 package com.ibm.fhir.model.test;
 
-import static com.ibm.fhir.model.type.String.string;
 import static org.testng.AssertJUnit.fail;
 
 import java.io.File;
@@ -117,12 +116,26 @@ public static JsonObject getRequestJsonObject(String method, String url) {
      * the specified patient via a subject attribute.
      */
     public static Observation buildPatientObservation(String patientId, String fileName) throws Exception {
-        // TODO review Reference id
         Observation observation = readLocalResource(fileName);
 
         observation = observation
             .toBuilder()
-            .subject(Reference.builder().reference(string("Patient/" + patientId)).build())
+            .subject(Reference.builder().reference("Patient/" + patientId).build())
+            .build();
+        return observation;
+    }
+
+    /**
+     * Loads an Observation resource from the specified file, then associates it with
+     * the specified patient via a subject attribute.
+     */
+    public static Observation buildPatientObservation(String patientId, String practitionerId, String fileName) throws Exception {
+        Observation observation = readLocalResource(fileName);
+
+        observation = observation
+            .toBuilder()
+            .subject(Reference.builder().reference("Patient/" + patientId).build())
+            .performer(Reference.builder().reference("Practitioner/" + practitionerId).build())
             .build();
         return observation;
     }

fhir-search/src/main/java/com/ibm/fhir/search/SearchConstants.java

@@ -18,6 +18,7 @@
 import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.model.type.Code;
 import com.ibm.fhir.model.type.Coding;
+import com.ibm.fhir.model.type.Extension;
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.search.exception.SearchExceptionUtil;
 
@@ -103,6 +104,10 @@ private SearchConstants() {
 
     public static final String IMPLICIT_SYSTEM_EXT_URL = FHIRConstants.EXT_BASE + "implicit-system";
     public static final String DO_NOT_STORE_EXT_URL = FHIRConstants.EXT_BASE + "do-not-store";
+    public static final Extension DO_NOT_STORE_EXT = Extension.builder()
+            .url(SearchConstants.DO_NOT_STORE_EXT_URL)
+            .value(true)
+            .build();
 
     // Extracted search parameter suffix for :identifier modifier
     public static final String IDENTIFIER_MODIFIER_SUFFIX = ":identifier";

fhir-search/src/main/java/com/ibm/fhir/search/parameters/ParametersMap.java

@@ -17,8 +17,6 @@
 import java.util.stream.Collectors;
 
 import com.ibm.fhir.model.resource.SearchParameter;
-import com.ibm.fhir.model.type.Extension;
-import com.ibm.fhir.search.SearchConstants;
 
 /**
  * A multi-key map that indexes a set of search parameters by SearchParameter.code and
@@ -29,11 +27,6 @@ public class ParametersMap {
 
     public static final String MISSING_EXPRESSION_WARNING = "Skipping parameter '%s' with missing expression";
 
-    public static final Extension DO_NOT_STORE = Extension.builder()
-            .url(SearchConstants.DO_NOT_STORE_EXT_URL)
-            .value(true)
-            .build();
-
     private final Map<String, SearchParameter> codeMap;
     private final Map<String, SearchParameter> canonicalMap;
 
@@ -108,10 +101,6 @@ public void insertInclusionParam(String code, SearchParameter parameter) {
             SearchParameter previous = inclusionParamMap.get(code);
             logParamConflict("inclusion criteria '" + code + "'", parameter, ParametersUtil.getCanonicalUrl(parameter), previous);
         }
-
-        parameter = parameter.toBuilder()
-                .extension(DO_NOT_STORE)
-                .build();
         inclusionParamMap.put(code, parameter);
     }
 
@@ -174,6 +163,14 @@ public Set<Entry<String, SearchParameter>> codeEntries() {
         return Collections.unmodifiableSet(codeMap.entrySet());
     }
 
+    public Collection<SearchParameter> inclusionValues() {
+        // use List to preserve order
+        return Collections.unmodifiableList(inclusionParamMap.entrySet().stream()
+                .filter(e -> !e.getKey().contains("|"))
+                .map(e -> e.getValue())
+                .collect(Collectors.toList()));
+    }
+
     /**
      * @implSpec Note that versioned search parameters will be listed twice;
      *      once with their version and once without

fhir-search/src/main/java/com/ibm/fhir/search/parameters/ParametersUtil.java

@@ -61,9 +61,10 @@ public final class ParametersUtil {
 
     // Logging:
     public static final String LOG_PARAMETERS = "Parameter is loaded -> %s";
-    public static final String LOG_HEADER = "BASE:RESOURCE_NAME:SearchParameter";
-    public static final String LOG_SIZE = "Size: %s";
-    private static final String LOG_OUTPUT = "%s|%s|%s";
+    public static final String LOG_HEADER = "ResourceType | SearchParameter.code | SearchParameter.expression\n"
+            + "'*' denotes compartment inclusion criteria parameters";
+    public static final String LOG_SIZE = "Number of resource types: %s";
+    private static final String LOG_OUTPUT = "%s | %s | %s";
 
     private static final String LEFT = "[";
     private static final String RIGHT = "]";
@@ -370,6 +371,13 @@ private static void print(PrintStream out, Map<String, ParametersMap> searchPara
                 }
                 out.println(String.format(LOG_OUTPUT, base, param.getCode().getValue(), expression));
             }
+            for(SearchParameter param : tmp.inclusionValues()) {
+                String expression = MISSING_EXPRESSION;
+                if (param.getExpression() != null) {
+                    expression = param.getExpression().getValue();
+                }
+                out.println(String.format(LOG_OUTPUT, "*" + base, param.getCode().getValue(), expression));
+            }
             out.println(SearchConstants.LOG_BOUNDARY);
         }
         out.println(SearchConstants.LOG_BOUNDARY);

fhir-search/src/main/java/com/ibm/fhir/search/util/SearchUtil.java

@@ -318,7 +318,10 @@ public static Map<SearchParameter, List<FHIRPathNode>> extractParameterValues(Re
             if (!COMPARTMENT_PARM_DEF.equals(inclusionParamName) && !parameters.containsKey(inclusionParamName)) {
                 String tenantId = FHIRRequestContext.get().getTenantId();
                 ParametersMap parametersMap = ParametersUtil.getTenantSPs(tenantId).get(resourceType.getSimpleName());
-                parameters.put(inclusionParamName, parametersMap.getInclusionParam(inclusionParamName));
+                SearchParameter inclusionParam = parametersMap.getInclusionParam(inclusionParamName).toBuilder()
+                        .extension(SearchConstants.DO_NOT_STORE_EXT)
+                        .build();
+                parameters.put(inclusionParamName, inclusionParam);
             }
         }