logic fix for library CQL in zip file, unit test, cleaning up pom and…

… add formatting utility from other projects
MeasureAuthoringTool · Jul 11, 2023 · 3c41bc1 · 3c41bc1
1 parent 3a540bb
commit 3c41bc1
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Showing 7 changed files with 200 additions and 133 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,9 +7,8 @@
 
 
 	<groupId>gov.cms.madie.packaging</groupId>
-	<artifactId>
-		packaging-utility</artifactId>
-	<version>0.2</version>
+	<artifactId>packaging-utility</artifactId>
+	<version>0.2.1-SNAPSHOT</version>
 
 	<name>packaging-utility</name>
 	<description>A
@@ -21,13 +20,9 @@
 		<java.version>17</java.version>
 		<maven.compiler.source>17</maven.compiler.source>
 		<maven.compiler.target>17</maven.compiler.target>
-
-		<junit-jupiter.version>5.7.2</junit-jupiter.version>
+		<junit-jupiter.version>5.9.3</junit-jupiter.version>
 		<slf4j.version>2.0.7</slf4j.version>
 		<hapi.fhir.r4.version>6.4.1</hapi.fhir.r4.version>
-
-
-		<junit-jupiter.version>5.7.2</junit-jupiter.version>
 		<slf4j.version>2.0.7</slf4j.version>
 
 	</properties>
@@ -69,11 +64,6 @@
 			<artifactId>hapi-fhir-structures-r4</artifactId>
 			<version>${hapi.fhir.r4.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>3.8.1</version>
-		</dependency>
 		<dependency>
 			<groupId>org.projectlombok</groupId>
 			<artifactId>lombok</artifactId>
@@ -127,12 +117,6 @@
 			<version>5.3.1</version>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.hamcrest</groupId>
-			<artifactId>hamcrest</artifactId>
-			<version>2.2</version>
-			<scope>test</scope>
-		</dependency>
 	</dependencies>
 	<build>
 		<pluginManagement><!-- lock down plugins versions to avoid using Maven
@@ -178,6 +162,30 @@
 				</plugin>
 			</plugins>
 		</pluginManagement>
+		<plugins>
+			<plugin>
+				<groupId>com.theoryinpractise</groupId>
+				<artifactId>googleformatter-maven-plugin</artifactId>
+				<version>1.7.3</version>
+				<executions>
+					<execution>
+						<id>reformat-sources</id>
+						<phase>process-sources</phase>
+						<goals>
+							<goal>format</goal>
+						</goals>
+						<configuration>
+							<includeStale>false</includeStale>
+							<style>GOOGLE</style>
+							<filterModified>false</filterModified>
+							<skip>false</skip>
+							<fixImports>false</fixImports>
+							<maxLineLength>100</maxLineLength>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
 	</build>
 
 	<reporting>

diff --git a/src/main/java/gov/cms/madie/packaging/exceptions/InternalServerException.java b/src/main/java/gov/cms/madie/packaging/exceptions/InternalServerException.java
@@ -7,8 +7,8 @@ public class InternalServerException extends RuntimeException {
   public InternalServerException(Exception ex) {
     super(ex);
   }
-  
+
   public InternalServerException(String message) {
-	  super(message);
+    super(message);
   }
 }
diff --git a/src/main/java/gov/cms/madie/packaging/utils/PackagingUtility.java b/src/main/java/gov/cms/madie/packaging/utils/PackagingUtility.java
@@ -1,11 +1,8 @@
 package gov.cms.madie.packaging.utils;
 
-
-
 import gov.cms.madie.packaging.exceptions.InternalServerException;
 
 public interface PackagingUtility {
 
-	byte[] getZipBundle(Object export, String exportFileName) throws InternalServerException;
-
+  byte[] getZipBundle(Object export, String exportFileName) throws InternalServerException;
 }
diff --git a/src/main/java/gov/cms/madie/packaging/utils/ZipUtility.java b/src/main/java/gov/cms/madie/packaging/utils/ZipUtility.java
@@ -12,11 +12,10 @@
 
 @Slf4j
 public class ZipUtility {
-
-
-  public byte[] zipEntries(Map<String, byte[]> entries, ByteArrayOutputStream baos) {    
-
-	ZipOutputStream zos = makeZos(baos);
+
+  public byte[] zipEntries(Map<String, byte[]> entries, ByteArrayOutputStream baos) {
+
+    ZipOutputStream zos = makeZos(baos);
     try {
       for (Entry<String, byte[]> reporte : entries.entrySet()) {
         ZipEntry entry = new ZipEntry(reporte.getKey());
@@ -39,7 +38,8 @@ public byte[] zipEntries(Map<String, byte[]> entries, ByteArrayOutputStream baos
     }
     return baos.toByteArray();
   }
+
   protected ZipOutputStream makeZos(ByteArrayOutputStream baos) {
-	  return new ZipOutputStream(baos) ;
-  } 
+    return new ZipOutputStream(baos);
+  }
 }
diff --git a/src/main/java/gov/cms/madie/packaging/utils/qicore411/PackagingUtilityImpl.java b/src/main/java/gov/cms/madie/packaging/utils/qicore411/PackagingUtilityImpl.java
@@ -32,31 +32,29 @@ public PackagingUtilityImpl() {
   private static final String TEXT_CQL = "text/cql";
   private static final String CQL_DIRECTORY = "cql/";
   private static final String RESOURCES_DIRECTORY = "resources/";
+
   @Override
   public byte[] getZipBundle(Object o, String exportFileName) throws InternalServerException {
-	  if (o instanceof Export) {
-		  Export export = (Export)o;
-		  String measureBundle = export.getMeasureBundleJson();
-	    IParser jsonParser = context.newJsonParser();
-
-	    org.hl7.fhir.r4.model.Bundle bundle =
-	        (org.hl7.fhir.r4.model.Bundle) jsonParser.parseResource(measureBundle);
-	    return getZipBundle(bundle, exportFileName) ; 
-	  }
-	  else if (o instanceof Bundle) {
-		  Bundle bundle = (Bundle)o;
-		  return getZipBundle(bundle, exportFileName) ; 
-	  }
-	  else throw new InternalServerException("Calling gicore411.PackagingUtilityImpl with invalid object");
-
+    if (o instanceof Export) {
+      Export export = (Export) o;
+      String measureBundle = export.getMeasureBundleJson();
+      IParser jsonParser = context.newJsonParser();
+
+      org.hl7.fhir.r4.model.Bundle bundle =
+          (org.hl7.fhir.r4.model.Bundle) jsonParser.parseResource(measureBundle);
+      return getZipBundle(bundle, exportFileName);
+    } else if (o instanceof Bundle) {
+      Bundle bundle = (Bundle) o;
+      return getZipBundle(bundle, exportFileName);
+    } else
+      throw new InternalServerException(
+          "Calling gicore411.PackagingUtilityImpl with invalid object");
   }
 
   private byte[] getZipBundle(Bundle bundle, String exportFileName) throws InternalServerException {
 
-
     IParser jsonParser = context.newJsonParser();
     IParser xmlParser = context.newXmlParser();
-
 
     if (bundle == null) {
       return null;
@@ -97,9 +95,7 @@ private byte[] zipEntries(
     for (CqlLibrary library : cqlLibraries) {
       String filePath =
           CQL_DIRECTORY + library.getCqlLibraryName() + "-" + library.getVersion() + ".cql";
-      String data = library.getCql();
-
-      entries.put(filePath, xmlBytes);
+      entries.put(filePath, library.getCql().getBytes());
     }
     // add Library Resources to Export
     List<Library> libraries = getLibraryResources(bundle);

diff --git a/src/test/java/gov/cms/madie/measure/utilities/qicore411/PackagingUtilityImplTest.java b/src/test/java/gov/cms/madie/measure/utilities/qicore411/PackagingUtilityImplTest.java
@@ -1,9 +1,11 @@
 package gov.cms.madie.measure.utilities.qicore411;
 
+import static org.hamcrest.MatcherAssert.assertThat;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.fail;
 
+import org.apache.commons.io.FilenameUtils;
 import org.hl7.fhir.r4.model.Bundle;
 import org.junit.jupiter.api.Test;
 
@@ -14,9 +16,17 @@
 import gov.cms.madie.packaging.utils.PackagingUtility;
 import gov.cms.madie.packaging.utils.qicore411.PackagingUtilityImpl;
 
+import java.io.*;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import static org.hamcrest.CoreMatchers.is;
+
 class PackagingUtilityImplTest {
 
- @Test
+  @Test
   void testGetZipExport() {
     PackagingUtility utility = new PackagingUtilityImpl();
     Export export = new Export();
@@ -31,22 +41,90 @@ void testGetZipExport() {
 
     assertNotNull(results);
   }
-  
+
   @Test
   void testGetZipBundle_Error() {
-    PackagingUtility utility = new PackagingUtilityImpl();    
-    Bundle bundle = new Bundle();    
+    PackagingUtility utility = new PackagingUtilityImpl();
+    Bundle bundle = new Bundle();
     assertThrows(InternalServerException.class, () -> utility.getZipBundle(bundle, "widget"));
   }
-  
+
   @Test
   void testGetZipBundle() {
     PackagingUtility utility = new PackagingUtilityImpl();
-    
+
     final String json = gov.cms.madie.packaging.utils.JsonBits.BUNDLE;
     Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, json);
-
     assertNotNull(utility.getZipBundle(bundle, "widget"));
-
+  }
+
+  @Test
+  void testGetZipBundleWithLibraries() throws IOException {
+    PackagingUtility utility = new PackagingUtilityImpl();
+
+    final String bundleJson = gov.cms.madie.packaging.utils.JsonBits.BUNDLE;
+    Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, bundleJson);
+    byte[] widgets = utility.getZipBundle(bundle, "widget");
+    assertNotNull(widgets);
+
+    // Make some assertions on the contents of the zip
+    // Doing this in-memory to prevent writing to file system on build servers..this may need to
+    // change
+    // in the future if the test bundle is too large
+    Map<String, String> zipContents = new HashMap<>();
+
+    try (var zipInputStream = new ZipInputStream(new ByteArrayInputStream(widgets))) {
+      ZipEntry entry;
+      byte[] buffer = new byte[2048];
+
+      while ((entry = zipInputStream.getNextEntry()) != null) {
+        int size;
+        String filename = FilenameUtils.getName(entry.getName());
+        var byteArrayOutputStream = new ByteArrayOutputStream();
+        while ((size = zipInputStream.read(buffer)) > 0) {
+          byteArrayOutputStream.write(buffer, 0, size);
+        }
+
+        String fileContents = byteArrayOutputStream.toString();
+        byteArrayOutputStream.flush();
+        zipInputStream.closeEntry();
+        zipContents.put(filename, fileContents);
+      }
+
+      zipInputStream.closeEntry();
+    }
+
+    assertThat(zipContents.containsKey("widget.xml"), is(true));
+    assertThat(
+        zipContents.get("widget.xml").startsWith("<Bundle xmlns=\"http://hl7.org/fhir\">"),
+        is(true));
+
+    assertThat(zipContents.containsKey("TestCreateNewLibrary-1.0.000.xml"), is(true));
+    assertThat(
+        zipContents
+            .get("TestCreateNewLibrary-1.0.000.xml")
+            .startsWith("<Library xmlns=\"http://hl7.org/fhir\">"),
+        is(true));
+
+    assertThat(zipContents.containsKey("widget.json"), is(true));
+    assertThat(
+        zipContents.get("widget.json").startsWith("{\n  \"resourceType\": \"Bundle\""), is(true));
+
+    assertThat(zipContents.containsKey("widget.html"), is(true));
+    assertThat(zipContents.get("widget.html").startsWith("<!DOCTYPE html>"), is(true));
+
+    assertThat(zipContents.containsKey("TestCreateNewLibrary-1.0.000.cql"), is(true));
+    assertThat(
+        zipContents
+            .get("TestCreateNewLibrary-1.0.000.cql")
+            .startsWith("library TestCreateNewLibrary version '1.0.000'"),
+        is(true));
+
+    assertThat(zipContents.containsKey("TestCreateNewLibrary-1.0.000.json"), is(true));
+    assertThat(
+        zipContents
+            .get("TestCreateNewLibrary-1.0.000.json")
+            .startsWith("{\n  \"resourceType\": \"Library\","),
+        is(true));
   }
 }