Merge pull request #9 from dcm4che/dev

Shadow the gradle plugin and relocate dependencies

README.MD

@@ -25,7 +25,7 @@ repositories {
 
 ```groovy
 dependencies {
-    implementation 'org.dcm4che:dcm4che-typeddicom-lib-std:0.5.3'
+    implementation 'org.dcm4che:dcm4che-typeddicom-lib-std:0.5.4'
 }
 ```
 
@@ -41,7 +41,7 @@ repositories {
 
 ```kotlin
 dependencies {
-    implementation("org.dcm4che:dcm4che-typeddicom-lib-std:0.5.3")
+    implementation("org.dcm4che:dcm4che-typeddicom-lib-std:0.5.4")
 }
 ```
 
@@ -60,7 +60,7 @@ dependencies {
 <dependency>
     <groupId>org.dcm4che</groupId>
     <artifactId>dcm4che-typeddicom</artifactId>
-    <version>0.5.3</version>
+    <version>0.5.4</version>
 </dependency>
 ```
 ### Use private tags with the gradle plugin
@@ -78,7 +78,7 @@ buildscript {
 
 plugins {
     id 'java-library'
-    id 'org.dcm4che.typeddicom-java-generator' version '0.5.3'
+    id 'org.dcm4che.typeddicom-java-generator' version '0.5.4'
 }
 
 generateTypeddicomJavaSources {
@@ -99,7 +99,7 @@ buildscript {
 
 plugins {
     id("java-library")
-    id("org.dcm4che.typeddicom-java-generator") version "0.5.3"
+    id("org.dcm4che.typeddicom-java-generator") version "0.5.4"
 }
 
 generateTypeddicomJavaSources {

dcm4che-typeddicom-generator/dcm4che-typeddicom-java-generator-gradleplugin/build.gradle.kts

@@ -1,5 +1,8 @@
+import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
+
 plugins {
     id("com.gradle.plugin-publish") version "1.1.0"
+    id("com.github.johnrengelman.shadow") version "8.1.1"
     id("org.dcm4che.typeddicom-xml-parser")
     id("org.dcm4che.typeddicom-publisher")
 }
@@ -45,6 +48,12 @@ java {
     targetCompatibility = JavaVersion.VERSION_11
 }
 
+tasks.named<ShadowJar>("shadowJar") {
+    isEnableRelocation = true
+    relocate("org.dcm4che.typeddicom.generator.gradleplugin", "org.dcm4che.typeddicom.generator.gradleplugin")
+    archiveClassifier.set("")
+}
+
 tasks.withType<Jar> {
     exclude("dicom-standard-xml/")
 }

dcm4che-typeddicom-generator/dcm4che-typeddicom-java-generator-lib/src/main/resources/templates/Module.java.mustache

@@ -1,6 +1,7 @@
 // Auto generated
 package org.dcm4che.typeddicom.modules;
 
+import org.dcm4che.typeddicom.AttributesWrapper;
 import org.dcm4che.typeddicom.AbstractAttributesWrapper;
 {{#value.contains}}
 import org.dcm4che.typeddicom.dataelements.{{.}};
@@ -13,7 +14,7 @@ import org.dcm4che3.data.Attributes;
  * @see <a href="{{value.href}}">DICOM Standard Part 3 - {{value.name}}</a>
  *
  */
-public interface {{key}} extends {{{value.implementsHolderInterfaces}}} {
+public interface {{key}} extends AttributesWrapper, {{{value.implementsHolderInterfaces}}} {
     public static {{key}} wrap(Attributes attributes) {
         return new SimpleWrapper(attributes);
     }

dcm4che-typeddicom-lib/dcm4che-typeddicom-lib-std/src/test/java/SimpleTests.java

@@ -1,10 +1,9 @@
+import org.dcm4che.typeddicom.AttributesWrapper;
 import org.dcm4che.typeddicom.UniversalAttributesWrapper;
-import org.dcm4che.typeddicom.dataelements.DisplayedAreaSelectionSequence;
-import org.dcm4che.typeddicom.dataelements.PixelAspectRatio;
-import org.dcm4che.typeddicom.dataelements.ReferencedImageSequence;
-import org.dcm4che.typeddicom.dataelements.ReferencedSeriesSequence;
+import org.dcm4che.typeddicom.dataelements.*;
 import org.dcm4che.typeddicom.iods.CRImageIOD;
 import org.dcm4che.typeddicom.iods.GrayscaleSoftcopyPresentationStateIOD;
+import org.dcm4che.typeddicom.modules.ImagePixelModule;
 import org.dcm4che3.data.Attributes;
 import org.dcm4che3.data.Sequence;
 import org.dcm4che3.data.Tag;
@@ -15,9 +14,9 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.util.Arrays;
 
-import static org.junit.jupiter.api.Assertions.assertArrayEquals;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.*;
 
 class SimpleTests {
     public static final String HPStateTag_CREATOR = "AGFA-AG_HPState";
@@ -162,4 +161,50 @@ void callingBuildOnHolderBuilderReturnsAValidObjectContainingTheAttribute() {
                 .setPixelAspectRatio().asInts(ratio);
         assertArrayEquals(ratio, pixelAspectRatioHolderBuilder.build().getPixelAspectRatio().getInts());
     }
+
+    @Test
+    void afterAddingAnUnknownTag_theMethodGetUnknownTagReturnsThisTag() {
+        Attributes attributes = new Attributes();
+        int tag = 0x0000_0001;
+        attributes.setString(tag, VR.ST, "Test");
+        PixelAspectRatio.Holder pixelAspectRatioHolder = PixelAspectRatio.Holder.wrap(attributes);
+        int[] unknownAttributeTags = pixelAspectRatioHolder.getUnknownAttributeTags();
+        assertArrayEquals(new int[]{tag}, unknownAttributeTags);
+    }
+
+    @Test
+    void aHolderOnlyContainsItsTagInTheArrayOfKnownTags() {
+        PixelAspectRatio.Holder pixelAspectRatioHolder = PixelAspectRatio.Holder.builder().build();
+        int[] knownAttributeTags = pixelAspectRatioHolder.getKnownAttributeTags();
+        assertArrayEquals(new int[]{PixelAspectRatio.TAG}, knownAttributeTags);
+    }
+
+    @Test
+    void aModuleContainsItsTagsInTheArrayOfKnownTags() {
+        ImagePixelModule imagePixelModule = ImagePixelModule.wrap(new Attributes());
+        assertThatAttributesWrappersKnownAttributesContainTheseTags(imagePixelModule,
+                PixelAspectRatio.TAG,
+                SamplesPerPixel.TAG,
+                Columns.TAG,
+                Rows.TAG);
+    }
+
+    @Test
+    void anIodContainsItsTagsInTheArrayOfKnownTags() {
+        CRImageIOD crImageIod = CRImageIOD.builder().build();
+        assertThatAttributesWrappersKnownAttributesContainTheseTags(crImageIod,
+                PixelAspectRatio.TAG,
+                SamplesPerPixel.TAG,
+                Columns.TAG,
+                Rows.TAG,
+                PatientName.TAG,
+                PatientID.TAG);
+    }
+
+    void assertThatAttributesWrappersKnownAttributesContainTheseTags(AttributesWrapper attributesWrapper, int... tags) {
+        int[] knownAttributeTags = attributesWrapper.getKnownAttributeTags();
+        for (int tag : tags) {
+            assertTrue(Arrays.stream(knownAttributeTags).anyMatch((knownTag -> knownTag == tag)), "Expected " + tag + " in the array of knownTags.");
+        }
+    }
 }

dcm4che-typeddicom-publisher/src/main/java/org/dcm4che/typeddicom/publisher/TypeddicomPublisherPlugin.java

@@ -17,7 +17,7 @@
 
 public class TypeddicomPublisherPlugin implements Plugin<Project> {
     private static final String TYPEDDICOM_GROUP = "org.dcm4che";
-    private static final String TYPEDDICOM_VERSION = "0.5.3";
+    private static final String TYPEDDICOM_VERSION = "0.5.4";
 
     private static final String STANDARD_PUBLICATION_NAME = "mavenJava";
     private static final String GRADLE_PLUGIN_PUBLICATION_NAME = "pluginMaven";

dcm4che-typeddicom-skeleton/src/main/java/org/dcm4che/typeddicom/AttributesWrapper.java

@@ -4,6 +4,11 @@
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
+import java.util.Arrays;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
 
 public interface AttributesWrapper {
     static <T extends AttributesWrapper> T wrap(Attributes attributes, Class<T> wrapperClass) {
@@ -16,6 +21,33 @@ static <T extends AttributesWrapper> T wrap(Attributes attributes, Class<T> wrap
         }
     }
 
+    static IntStream getKnownAttributeTags(Class<? extends AttributesWrapper> attributesWrapperClass) {
+        return getImplementedDataElementHolders(attributesWrapperClass)
+                .map(Class::getDeclaringClass)
+                .mapToInt(clazz -> {
+                    try {
+                        return clazz.getField("TAG").getInt(null);
+                    } catch (IllegalAccessException | NoSuchFieldException e) {
+                        throw new RuntimeException(e);
+                    }
+                });
+    }
+
+    @SuppressWarnings({
+            "unchecked", // It's okay we are checking the type by reflection
+            "java:S1872", // We want a simple name comparison and no instanceof because there are multiple nested classes with that name
+    })
+    static Stream<Class<? extends AttributesWrapper>> getImplementedDataElementHolders(Class<? extends AttributesWrapper> clazz) {
+        if ("Holder".equals(clazz.getSimpleName())) {
+            return Stream.of(clazz);
+        } else {
+            return Arrays.stream(clazz.getInterfaces())
+                    .filter(AttributesWrapper.class::isAssignableFrom)
+                    .map(parent -> (Class<? extends AttributesWrapper>) parent)
+                    .flatMap(AttributesWrapper::getImplementedDataElementHolders);
+        }
+    }
+
     /**
      * Get the wrapped Attributes.
      *
@@ -44,4 +76,16 @@ default <T extends AttributesWrapper> T copy(Class<T> wrapperClass) {
     default boolean isEmpty() {
         return getAttributes().isEmpty();
     }
+
+    default int[] getUnknownAttributeTags() {
+        Set<Integer> knownAttributeTags = getKnownAttributeTags(this.getClass())
+                .boxed()
+                .collect(Collectors.toUnmodifiableSet());
+        return Arrays.stream(this.getAttributes().tags())
+                .filter(tag -> !knownAttributeTags.contains(tag)).toArray();
+    }
+
+    default int[] getKnownAttributeTags() {
+        return getKnownAttributeTags(this.getClass()).toArray();
+    }
 }