Introduce clinical-reasoning changes to support HEDIS measures. (#683)

* Introduce clinical-reasoning changes to support HEDIS measures.  Take the substance of the changes from the jp-cli-2 branch and ensure they work with the latest CR master with, among other things, the repository changes.  All tests pass but need to do cleanup.

* Cleanup.  Remove comments.  Remove sysouts.  Remove useless logging.  Make sure we use jdk17 idioms.   Fix Sonar issues.  Spotless.

* More Sonar.

* Add traces to debug Linux test failures.

* Add more debug info.

* Try capitalizing first letter and lowercasing the rest for fhir types and see if that works.

* Try making a case-insensitive subdirectory match.

* Use case-insensitive resolve pattern for the entire class.

* Fix path verified by unit test to use the correct spacing for all layers of directories.

* Revert to some case-sensitive FS operations in order to fix LibraryEngineTests and see how it reacts on Linux.

* Rename the "Patient" test folder to "patient".   Revert to previous file path resolves.

* Rename another patient test directory.

* Add more logging.

* Make Compartment lowercase in the IgRepository compartment.  Rename Component to IgRepositoryCompartment.  Fix path in unit test to correspond to new lowercase "patient".

* Clean up logging.  First round of ni2 refactoring.

* Finish nio2 refactoring.  Spotless.

* Spotless.

* Optimize CqlCommand code for nio2 and use of Streams to join strings.  Also, delete HedisCliTest, which seems to be used only for ad-hoc testing.

* Spotless.

* Fix Sonar issues.

* Small tweaks.

* Add testing for measure reports and txtresults files to CliTest.  Also, delete NdjsonBundleExtractor.java.

Author: lukedegruchy

.vscode/launch.json

@@ -3,5 +3,18 @@
   // Hover to view descriptions of existing attributes.
   // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
   "version": "0.2.0",
-  "configurations": []
+  "configurations": [
+    {
+        "type": "java",
+        "name": "Launch Java Program",
+        "request": "launch",
+        "mainClass": "org.opencds.cqf.fhir.cr.cli.Main",
+        "projectName": "cqf-fhir-cr-cli",
+        "args": [
+            "argfile",
+            "args.txt"
+        ],
+    }
+
+  ]
 }

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/CqlEngineOptions.java

@@ -2,6 +2,7 @@
 
 import java.util.EnumSet;
 import java.util.Set;
+import java.util.StringJoiner;
 import org.opencds.cqf.cql.engine.execution.CqlEngine;
 
 // TODO: Eventually, the cql-engine needs to expose these itself.
@@ -12,6 +13,7 @@ public class CqlEngineOptions {
     private Integer pageSize;
     private Integer maxCodesPerQuery;
     private Integer queryBatchThreshold;
+    private boolean enableHedisCompatibilityMode = false;
 
     public Set<CqlEngine.Options> getOptions() {
         return this.options;
@@ -61,9 +63,30 @@ public void setQueryBatchThreshold(Integer value) {
         this.queryBatchThreshold = value;
     }
 
+    public void setEnableHedisCompatibilityMode(boolean enableHedisCompatibilityMode) {
+        this.enableHedisCompatibilityMode = enableHedisCompatibilityMode;
+    }
+
+    public boolean isEnableHedisCompatibilityMode() {
+        return this.enableHedisCompatibilityMode;
+    }
+
     public static CqlEngineOptions defaultOptions() {
         CqlEngineOptions result = new CqlEngineOptions();
         result.options.add(CqlEngine.Options.EnableExpressionCaching);
         return result;
     }
+
+    @Override
+    public String toString() {
+        return new StringJoiner(", ", CqlEngineOptions.class.getSimpleName() + "[", "]")
+                .add("options=" + options)
+                .add("isDebugLoggingEnabled=" + isDebugLoggingEnabled)
+                .add("shouldExpandValueSets=" + shouldExpandValueSets)
+                .add("pageSize=" + pageSize)
+                .add("maxCodesPerQuery=" + maxCodesPerQuery)
+                .add("queryBatchThreshold=" + queryBatchThreshold)
+                .add("enableHedisCompatibilityMode=" + enableHedisCompatibilityMode)
+                .toString();
+    }
 }

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/RepositoryRetrieveProvider.java

@@ -5,6 +5,7 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.repository.IRepository;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -16,6 +17,7 @@
 import org.opencds.cqf.cql.engine.runtime.Interval;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
 import org.opencds.cqf.fhir.utility.iterable.BundleMappingIterable;
+import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;
 
 public class RepositoryRetrieveProvider extends BaseRetrieveProvider {
     private final IRepository repository;
@@ -54,12 +56,23 @@ public Iterable<Object> retrieve(
         this.configureProfile(config, dataType, templateId);
         this.configureDates(config, dataType, datePath, dateLowPath, dateHighPath, dateRange);
 
-        var resources = this.repository.search(bt, resourceType, config.searchParams);
+        Map<String, String> headers = headersForContext(context, contextValue);
+
+        var resources = this.repository.search(bt, resourceType, config.searchParams, headers);
 
         var iter = new BundleMappingIterable<>(repository, resources, p -> p.getResource());
         return iter.toStream().filter(config.filter).collect(Collectors.toList());
     }
 
+    // Create headers for the FHIR compartment search (e.g. X-FHIR-Compartment: Patient/123)
+    private Map<String, String> headersForContext(String context, Object contextValue) {
+        if (context == null || contextValue == null) {
+            return Collections.emptyMap();
+        }
+
+        return Map.of(IgRepository.FHIR_COMPARTMENT_HEADER, context + "/" + contextValue.toString());
+    }
+
     private void configureProfile(SearchConfig config, String dataType, String templateId) {
         var mode = this.getRetrieveSettings().getSearchParameterMode();
         switch (mode) {

cqf-fhir-cr-cli/pom.xml

@@ -72,6 +72,12 @@
             <version>3.23.0-SNAPSHOT</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.opencds.cqf.fhir</groupId>
+            <artifactId>cqf-fhir-cr</artifactId>
+            <version>3.23.0-SNAPSHOT</version>
+            <scope>compile</scope>
+        </dependency>
     </dependencies>
 
     <build>