LNK-2950: Ability to run measure eval using a command line interface

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/FileSystemInvocation.java

@@ -0,0 +1,109 @@
+package com.lantanagroup.link.measureeval;
+
+import ca.uhn.fhir.context.FhirContext;
+import com.lantanagroup.link.measureeval.services.MeasureEvaluator;
+import org.apache.commons.io.FileUtils;
+import org.hl7.fhir.r4.model.*;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This class is used to invoke measure evaluation using arbitrary artifacts on the file system for ease of testing and debugging new measures.
+ * Format: `java -jar measureeval.jar -cp com.lantanagroup.link.measureeval.FileSystemInvocation "<measure-bundle-path>" "<patient-bundle-path>" "<start>" "<end>"`
+ * Example: `java -jar measureeval.jar -cp com.lantanagroup.link.measureeval.FileSystemInvocation "C:/path/to/measure-bundle.json" "C:/path/to/patient-bundle.json" "2021-01-01" "2021-12-31"`
+ * Careful when specifying file paths to use forward-slash instead of windows' backslash, as that will cause java to interpret the backslash as an escape character and not as a path separator, leading to potentially incorrect parameter interpretation.
+ * The `start` and `end` parameters must be in a valid DateTime format from the FHIR specification.
+ * The `measure-bundle-path` can be a path to a single measure bundle file or a directory containing each of the resources needed for the measure.
+ * The `patient-bundle-path` must be a path to a single (JSON or XML) Bundle file or a directory of files containing the patient data to be used in the evaluation.
+ * The response from the operation is the MeasureReport resource being printed to the console in JSON format.
+ */
+public class FileSystemInvocation {
+    private static final FhirContext fhirContext = FhirContext.forR4Cached();
+
+    private static Bundle getBundle(String measureBundlePath) throws IOException {
+        System.out.println("Loading measure bundle from: " + measureBundlePath);
+
+        File measureBundleFile = new File(measureBundlePath);
+
+        if (!measureBundleFile.exists()) {
+            throw new IllegalArgumentException("Measure bundle file does not exist: " + measureBundlePath);
+        }
+
+        if (measureBundleFile.isFile()) {
+            String measureBundleContent = FileUtils.readFileToString(measureBundleFile);
+            if (measureBundlePath.toLowerCase().endsWith(".json")) {
+                return (Bundle) fhirContext.newJsonParser().parseResource(measureBundleContent);
+            } else if (measureBundlePath.toLowerCase().endsWith(".xml")) {
+                return (Bundle) fhirContext.newXmlParser().parseResource(measureBundleContent);
+            } else {
+                throw new IllegalArgumentException("Unsupported measure bundle file format: " + measureBundlePath);
+            }
+        } else {
+            // Parse and load each file in the directory
+            Bundle bundle = new Bundle();
+            bundle.setType(Bundle.BundleType.COLLECTION);
+
+            File[] files = measureBundleFile.listFiles();
+
+            if (files != null) {
+                List<String> loaded = new ArrayList<>();
+
+                for (File file : files) {
+                    String filePath = file.getAbsolutePath();
+                    if (file.isFile() && (filePath.endsWith(".json") || filePath.endsWith(".xml"))) {
+                        String fileName = file.getName().substring(0, file.getName().lastIndexOf('.'));
+
+                        if (loaded.contains(fileName)) {
+                            System.out.println("Skipping duplicate file: " + filePath);
+                        }
+
+                        Resource resource;
+
+                        if (filePath.endsWith(".json")) {
+                            resource = (Resource) fhirContext.newJsonParser().parseResource(FileUtils.readFileToString(file));
+                        } else {
+                            resource = (Resource) fhirContext.newXmlParser().parseResource(FileUtils.readFileToString(file));
+                        }
+
+                        bundle.addEntry(new Bundle.BundleEntryComponent().setResource(resource));
+                        loaded.add(fileName);
+                    } else {
+                        System.out.println("Skipping file: " + filePath);
+                    }
+                }
+            }
+
+            System.out.println("Loaded " + bundle.getEntry().size() + " resources from directory: " + measureBundlePath);
+
+            return bundle;
+        }
+    }
+
+    public static void main(String[] args) {
+        String measureBundlePath = args[0];
+        String patientBundlePath = args[1];
+        String start = args[2];
+        String end = args[3];
+
+        try {
+            Bundle measureBundle = getBundle(measureBundlePath);
+            Bundle patientBundle = getBundle(patientBundlePath);
+            MeasureEvaluator evaluator = MeasureEvaluator.compile(fhirContext, measureBundle);
+            Patient patient = patientBundle.getEntry().stream()
+                    .filter(e -> e.getResource() instanceof Patient)
+                    .map(e -> (Patient) e.getResource())
+                    .findFirst()
+                    .orElseThrow(() -> new IllegalArgumentException("Patient resource not found in bundle"));
+            var report = evaluator.evaluate(new DateTimeType(start), new DateTimeType(end),
+                    new StringType("Patient/" + patient.getIdElement().getIdPart()), patientBundle);
+            String json = fhirContext.newJsonParser().encodeResourceToString(report);
+            System.out.println(json);
+        } catch (Exception e) {
+            System.err.println("Error occurred while evaluating measure: " + e.getMessage());
+            e.printStackTrace();
+        }
+    }
+}