BUG FIX (Issue 537): ExtractMatBundle Non-IG Folder Structure Handling

tooling/src/main/java/org/opencds/cqf/tooling/operation/ExtractMatBundleOperation.java

@@ -6,7 +6,6 @@
 import org.opencds.cqf.tooling.Operation;
 import org.opencds.cqf.tooling.common.ThreadUtils;
 import org.opencds.cqf.tooling.utilities.BundleUtils;
-import org.opencds.cqf.tooling.utilities.LogUtils;
 import org.opencds.cqf.tooling.utilities.ResourceUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -19,9 +18,9 @@
 import java.util.ArrayList;
 import java.util.Base64;
 import java.util.List;
+import java.util.Objects;
 import java.util.concurrent.Callable;
 import java.util.concurrent.CopyOnWriteArrayList;
-import java.util.stream.Collectors;
 
 public class ExtractMatBundleOperation extends Operation {
     protected final Logger logger = LoggerFactory.getLogger(this.getClass());
@@ -60,7 +59,9 @@ public void execute(String[] args) {
             } else if (i == 0 && !args[i].equalsIgnoreCase("-ExtractMatBundle")) {
                 throw new IllegalArgumentException("Insufficient argument structure. " +
                         "Usage Example: mvn exec:java -Dexec.args=\"-ExtractMatBundle " +
-                        "/Development/ecqm-content-r4/bundles/mat/EXM124/EXM124.json -v=r4");
+                        File.separator + "Development" + File.separator + "ecqm-content-r4" +
+                        File.separator + "bundles" + File.separator +  "mat" +
+                        File.separator + "EXM124" + File.separator + "EXM124.json -v=r4");
             }
 
             //position 1 is the location of file or directory. Determine which:
@@ -135,7 +136,7 @@ public void execute(String[] args) {
             if (filesInDir != null && filesInDir.length > 0) {
                 //use recursive calls to build up task list:
                 ThreadUtils.executeTasks(processFilesInDir(filesInDir, version, suppressNarrative));
-            }else{
+            } else {
                 logger.info(ERROR_DIR_IS_EMPTY);
                 return;
             }
@@ -146,7 +147,7 @@ public void execute(String[] args) {
 
         if (!processedBundleCollection.isEmpty()) {
             logger.info("Successfully extracted " + processedBundleCollection.size() + " resource(s): \n" + String.join("\n", processedBundleCollection));
-        }else{
+        } else {
             logger.info("ExtractMatBundleOperation ended with no resources extracted!");
         }
     }
@@ -268,6 +269,22 @@ void processSingleFile(File bundleFile, String version, boolean suppressNarrativ
     }
 
 
+    private Path getParentBundleDir(String directory){
+        Path parent = Paths.get(directory);
+        // Traverse to the parent of 'bundles'
+        while (parent != null &&
+                parent.getFileName() != null &&
+                !parent.getFileName().toString().equalsIgnoreCase("bundles")) {
+            parent = parent.getParent();
+        }
+
+        // Move one level up to get the directory before 'bundles'
+        if (parent != null) {
+            return parent.getParent();
+        } else {
+            return null;
+        }
+    }
 
     /**
      * Iterates through the files and properly renames and moves them to the proper place
@@ -298,14 +315,21 @@ private void moveAndRenameFiles(String outputDir, FhirContext context, String ve
             // The extractor code names them using the resource type and ID
             // We want to name them without the resource type, use name, and if needed version
             String resourceName;
-            Path newOutputDirectory = Paths.get(outputDir.substring(0, outputDir.indexOf("bundles")), "input");
-            Path newLibraryDirectory = Paths.get(newOutputDirectory.toString(), "resources/library");
-            newLibraryDirectory.toFile().mkdirs();
+
+            // https://github.com/cqframework/cqf-tooling/issues/537
+            // if there's no bundle directory (getParentBundleDir returned null) we'll use resourceOutputDir (original outputDir):
+            Path resourceOutputDir = Paths.get(outputDir).toAbsolutePath();
+
+            Path newOutputDirectory = Paths.get(
+                    Objects.requireNonNullElse(getParentBundleDir(outputDir)
+                            , resourceOutputDir)
+                            + File.separator + "input");
+
+            Path newLibraryDirectory = Paths.get(newOutputDirectory.toString(), "resources" + File.separator + "library");
             Path newCqlDirectory = Paths.get(newOutputDirectory.toString(), "cql");
-            newCqlDirectory.toFile().mkdirs();
-            Path newMeasureDirectory = Paths.get(newOutputDirectory.toString(), "resources/measure");
-            newMeasureDirectory.toFile().mkdirs();
-            if (version == "stu3) ") {
+            Path newMeasureDirectory = Paths.get(newOutputDirectory.toString(), "resources" + File.separator + "measure");
+
+            if (version.equals(VERSION_STU3)) {
                 if (theResource instanceof org.hl7.fhir.dstu3.model.Library) {
                     org.hl7.fhir.dstu3.model.Library theLibrary = (org.hl7.fhir.dstu3.model.Library) theResource;
                     resourceName = theLibrary.getName();
@@ -329,7 +353,7 @@ private void moveAndRenameFiles(String outputDir, FhirContext context, String ve
                     // Forcing the encoding to JSON here to make everything the same in input directory
                     ResourceUtils.outputResourceByName(theResource, "json", context, newMeasureDirectory.toString(), resourceName);
                 }
-            } else if (version == VERSION_R4) {
+            } else if (version.equals(VERSION_R4)) {
                 if (theResource instanceof org.hl7.fhir.r4.model.Library) {
                     org.hl7.fhir.r4.model.Library theLibrary = (org.hl7.fhir.r4.model.Library) theResource;
                     resourceName = theLibrary.getName();
@@ -372,7 +396,13 @@ private void extractStu3CQL(org.hl7.fhir.dstu3.model.Library theLibrary, String
                 String encodedString = Base64.getEncoder().encodeToString(encodedBytes);
                 byte[] decodedBytes = Base64.getDecoder().decode(encodedString);
                 try {
-                    FileUtils.writeByteArrayToFile(new File(cqlFilename), decodedBytes);
+                    File outputFile = new File(cqlFilename);
+                    // Ensure the parent directory exists
+                    File parentDir = outputFile.getParentFile();
+                    if (parentDir != null && !parentDir.exists()) {
+                        parentDir.mkdirs();
+                    }
+                    FileUtils.writeByteArrayToFile(outputFile, decodedBytes);
                 } catch (IOException e) {
                     throw new RuntimeException(cqlFilename + ": " + e.getMessage());
                 }
@@ -395,7 +425,13 @@ private void extractR4CQL(org.hl7.fhir.r4.model.Library theLibrary, String cqlFi
                 String encodedString = Base64.getEncoder().encodeToString(encodedBytes);
                 byte[] decodedBytes = Base64.getDecoder().decode(encodedString);
                 try {
-                    FileUtils.writeByteArrayToFile(new File(cqlFilename), decodedBytes);
+                    File outputFile = new File(cqlFilename);
+                    // Ensure the parent directory exists
+                    File parentDir = outputFile.getParentFile();
+                    if (parentDir != null && !parentDir.exists()) {
+                        parentDir.mkdirs();
+                    }
+                    FileUtils.writeByteArrayToFile(outputFile, decodedBytes);
                 } catch (IOException e) {
                     throw new RuntimeException(cqlFilename + ": " + e.getMessage());
                 }

tooling/src/main/java/org/opencds/cqf/tooling/utilities/ResourceUtils.java

@@ -838,13 +838,20 @@ public static void outputResource(IBaseResource resource, String encoding, FhirC
    }
 
    public static void outputResourceByName(IBaseResource resource, String encoding, FhirContext context, String outputPath, String name) {
-      try (FileOutputStream writer = new FileOutputStream(outputPath + "/" + name + "." + encoding)) {
-         writer.write(
-                 encoding.equals("json")
-                         ? context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
-                         : context.newXmlParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
-         );
-         writer.flush();
+      try {
+         File directory = new File(outputPath);
+         if (!directory.exists()) {
+            directory.mkdirs(); // Ensure the directory exists
+         }
+
+         try (FileOutputStream writer = new FileOutputStream(outputPath + "/" + name + "." + encoding)) {
+            writer.write(
+                    encoding.equals("json")
+                            ? context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
+                            : context.newXmlParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
+            );
+            writer.flush();
+         }
       } catch (IOException e) {
          e.printStackTrace();
          throw new RuntimeException(e.getMessage());

tooling/src/test/java/org/opencds/cqf/tooling/operation/ExtractMatBundleOperationTest.java

@@ -1,23 +1,20 @@
 package org.opencds.cqf.tooling.operation;
 
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.fail;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
 import java.nio.file.Files;
 
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
+import static org.testng.Assert.*;
 
 public class ExtractMatBundleOperationTest {
 
     private ExtractMatBundleOperation operation;
 
-    @BeforeClass
+    @BeforeMethod
     public void setUp() {
         operation = new ExtractMatBundleOperation();
     }
@@ -211,9 +208,61 @@ public void run() {
         }
         File[] files = emptyDir.listFiles();
         assertNotNull(files);
-        assertEquals(16, files.length);
+        assertEquals(17, files.length);
+    }
+
+    /**
+     * In response to issue https://github.com/cqframework/cqf-tooling/issues/537
+     * The ExtractMATBundle process defaults to the location of the bundle file
+     * when no IG folder structure exists (no bundle folder found.)
+     *
+     * @throws IOException
+     */
+    @Test
+    public void TestExtractMatBundleWithNonIGStructuredDirectory() throws IOException {
+        ClassLoader classLoader = getClass().getClassLoader();
+        String resourcePath = "org/opencds/cqf/tooling/operation/ExtractMatBundle/bundles_small/";
+        URL resourceUrl = classLoader.getResource(resourcePath);
+        if (resourceUrl == null) {
+            throw new IllegalArgumentException("Resource not found: " + resourcePath);
+        }
+
+        // Create a temporary directory named "noIG" and does not include the name bundles
+        File tempDir = Files.createTempDirectory("noIG").toFile();
+        tempDir.deleteOnExit();
+
+        // Copy files from resourcePath to the temporary directory
+        File sourceDir = new File(resourceUrl.getFile());
+        if (!sourceDir.isDirectory()) {
+            throw new IllegalArgumentException("Resource path is not a directory: " + resourcePath);
+        }
+
+        //Copy our test files to the temp folder so the source location of the bundle is the temp folder
+        for (File file : sourceDir.listFiles()) {
+            File destFile = new File(tempDir, file.getName());
+            Files.copy(file.toPath(), destFile.toPath());
+        }
+
+        Thread executionThread = new Thread(() ->
+                operation.execute(new String[]{"-ExtractMATBundle", tempDir.getAbsolutePath(), "-dir"})
+        );
+
+        executionThread.start();
+        try {
+            executionThread.join();
+        } catch (InterruptedException e) {
+            throw new RuntimeException(e);
+        }
+
+        // Validate results in the temporary directory
+        File[] files = tempDir.listFiles();
+        assertNotNull(files);
+
+        //Directory should now include 1 input folder, original json bundles (6), and extracted files (16)
+        assertEquals(23, files.length);
     }
 
+
     @Test
     public void TestExtractMatBundleWithDirectoryAndSubDirectories() throws IOException {
         ClassLoader classLoader = getClass().getClassLoader();
@@ -240,7 +289,7 @@ public void run() {
         }
         File[] files = emptyDir.listFiles();
         assertNotNull(files);
-        assertEquals(41, files.length);
+        assertEquals(42, files.length);
     }
 
     @Test
@@ -265,6 +314,6 @@ public void run() {
 
         File[] files = emptyDir.listFiles();
         assertNotNull(files);
-        assertEquals(files.length, 16);
+        assertEquals(files.length, 17);
     }
 }