Update sample plugin (sdk 3.4.1) (#19)

* Update project manifest and dependencies (sdk 3.4.1)

- update project version to 3.1.0 (minor bump)
- update dicoogle-sdk to 3.4.1 (latest SDK)
- update build dependency maven-compiler-plugin to the latest version
- update license-maven-plugin to v2.9

* Update ghactions CI workflow

- update actions/checkout to v4
- update actions/setup-java to v4
- use temurin for the JDK distro

* Fix URI creation logic at RSIQuery

- URIs always use forward slashes regardless of platform OS

* Use maven-shade-plugin instead of maven-assembly-plugin

- better practice

* Update README

- Update URLs
- Ask user to have Java 8 or 11 installed
- Suggest to use `mvn package` instead of `mvn install`
- Update the resulting jar file name
- Refer to Dicoogle learning pack
- Suggest adding dicoogle-plugin-sample to the list of DIM providers
- Tweak formatting a bit

* Remove JsonWebService, extend RSIWebResource instead

* Remove unused imports

* Fix reported scheme of RSIStorage

- scheme should not include the "://" part

* Refactor RSIStorage

- do not use raw types
- save byte arrays instead of dangling output streams

* Update webplugin

- Instead of hello world,
  provide Dicoogle Health Check, the tutorial webplugin
- use parcel to build the plugin

Author: Enet4

.github/workflows/maven.yml

@@ -19,11 +19,11 @@ jobs:
         java-version: ['8', '11']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Java (JDK ${{ matrix.java-version }})
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
-        distribution: 'zulu'
+        distribution: 'temurin'
         java-version: ${{ matrix.java-version }}
         cache: 'maven'
     - name: Build with Maven

README.md

@@ -9,8 +9,8 @@ Getting Started
 
 ### Installing and running Dicoogle
 
-1. Go to http://www.dicoogle.com/downloads
-2. Download version 2 (or later) of Dicoogle
+1. Make sure that you have Java installed in your system. Versions 8 and 11 are known to work.
+1. Go to https://www.dicoogle.com/downloads and get version 3 of Dicoogle
 3. Extract your contents to its own directory (e.g. "~/dicoogle" or "C:\dicoogle", depending on the platform).
 4. Run Dicoogle with: sh DicoogleClient.sh (OSX / Linux) or DicoogleClient.bat (Windows).
 5. You should see your web browser opening the Dicoogle user interface. Is it running? You're ok!
@@ -21,33 +21,39 @@ Maven is required in order to build the project. An IDE with Maven support such
 
 1. Clone the git repository at https://github.com/bioinformatics-ua/dicoogle-plugin-sample.git
 
-2. Go to the project's base directory in a command line and run `mvn install`. Alternatively, open
-   the Maven project of the plugin with your IDE, then force it to build your project.
+2. Go to the project's base directory in a command line and run `mvn package`.
+   Alternatively, open the Maven project of the plugin with your IDE, then force it to build your project.
 
-3. If the building task is successful, you will have a new jar with dependencies in the target
-   folder (target/dicoogle-plugin-sample-2.0-jar-with-dependencies.jar).
+3. If the building task is successful, you will have a new shaded jar (with the necessary dependencies)
+   in the `target` folder (e.g. `target/dicoogle-plugin-sample-3.1.0.jar`)
 
 ### Developing your own plugin based on this sample
 
-The first class to look into is RSIPluginSet. It is the main entry point for everything else.
+The first class to look into is [`RSIPluginSet`][pluginset].
+It is the main entry point for everything else.
 Once modified to suit your needs, build the plugin again and re-deploy it to Dicoogle (see below).
 
+Be sure to consult the [Dicoogle Learning Pack][learningpack] for more information.
+
+[pluginset]: src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIPluginSet.java
+[learningpack]: https://bioinformatics-ua.github.io/dicoogle-learning-pack/docs/developing-plugins/
+
 ### Using your plugin
 
-1. Copy your plugin's package with dependencies (target/dicoogle-plugin-sample-2.0-jar-with-dependencies.jar)
+1. Copy your plugin's built jar (`target/dicoogle-plugin-sample-3.1.0.jar`)
    to the "Plugins" folder inside the root folder of Dicoogle.
 
 2. Run Dicoogle. The plugin will be automatically included.
 
 Available content
 -----------------
 
-- _RSIIndexer_ : a sample indexer, only logs the DIM contents of files
-- _RSIStorage_ : a sample storage service, keeps files in memory buffers
-- _RSIQuery_ : a sample query provider, returns random data on request
-- _RSIJettyPlugin_ : a sample plugin for providing web services, holds `RSIWebService`
-- _RSIWebService_ : a sample web service in the form of a servlet, serves a web page and a few other services
-- _RSIRestPlugin_ : a sample Restlet server resource, provides dummy data
+- `RSIIndexer` : a sample indexer, only logs the DIM contents of files
+- `RSIStorage` : a sample storage service, keeps files in memory buffers
+- `RSIQuery` : a sample query provider, returns random data on request
+- `RSIJettyPlugin` : a sample plugin for providing web services, holds `RSIWebService`
+- `RSIWebService` : a sample web service in the form of a servlet, serves a web page and a few other services
+- `RSIRestPlugin` : a sample Restlet server resource, provides dummy data
 - Sample HTML5 content and consuming web service: helps you to build a web app
 
 Web service plugin sample and Web App: 
@@ -62,6 +68,23 @@ To test the webservice plugin, you may open your browser and navigate to these U
 You may also use the built-in Dicoogle services for testing other plugins:
 
 - GET `http://localhost:8080/search?query=test&provider=dicoogle-plugin-sample` to test the query provider
+  - Note: You will need to record `dicoogle-plugin-sample`
+    as a DIM provider first. In `confs/server.xml`,
+    add the query provider in `config/archive/dim-providers`
+    like this:
+    ```xml
+    <config>
+      <!-- ... -->
+      <archive>
+        <!-- ... -->
+        <dim-providers>
+          <dim-provider>dicoogle-plugin-sample</dim-provider>
+        </dim-providers>
+        <!-- ... -->
+    ```
+    Then restart Dicoogle.
+    Remember to remove the provider from the list after testing
+    if you do not want to keep it.
 - POST `http://localhost:8080/management/tasks/index?plugin=dicoogle-plugin-sample&uri=<file:/path/to/DICOM/dir>` to test the indexer
 
 Platforms
@@ -73,5 +96,5 @@ Dicoogle has been tested in:
 - Linux
 - Mac OS X
 
-For more information, please visit http://www.dicoogle.com
+For more information, please visit https://www.dicoogle.com
 

pom.xml

@@ -4,14 +4,14 @@
     <groupId>pt.ua.dicoogle.demo</groupId>
     <artifactId>dicoogle-plugin-sample</artifactId>
     <name>dicoogle-plugin-sample</name>
-    <version>3.0.0</version>
+    <version>3.1.0</version>
     <packaging>jar</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
         <!-- Dicoogle SDK version here -->
-        <dicoogle.version>3.2.2</dicoogle.version>
+        <dicoogle.version>3.4.1</dicoogle.version>
 
         <!-- Jetty server version here -->        
         <jetty.version>9.0.3.v20130506</jetty.version>
@@ -24,7 +24,7 @@
                 <directory>src/main/resources/html5/</directory>
             </resource>
             <resource>
-                <directory>src/main/resources/webplugin-sample</directory>
+                <directory>src/main/resources/webplugin-sample/dist</directory>
                 <targetPath>WebPlugins/webplugin-sample</targetPath>
                 <filtering>false</filtering>
                 <includes>
@@ -38,37 +38,46 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>1.8</source>
                     <target>1.8</target>
                 </configuration>
             </plugin>
             <plugin>
-                <artifactId>maven-assembly-plugin</artifactId>
-                <configuration>
-                    <descriptorRefs>
-                        <descriptorRef>jar-with-dependencies</descriptorRef>
-                    </descriptorRefs>
-                    <archive>
-                    </archive>
-                </configuration>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.6.0</version>
                 <executions>
                     <execution>
-                        <id>make-assembly</id>
                         <phase>package</phase>
                         <goals>
-                            <goal>single</goal>
+                            <goal>shade</goal>
                         </goals>
+                        <configuration>
+                            <filters>
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>**/*.SF</exclude>
+                                        <exclude>**/*.DSA</exclude>
+                                        <exclude>**/*.RSA</exclude>
+                                        <exclude>**/module-info.class</exclude>
+                                        <exclude>**/module-info.java</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                            <minimizeJar>true</minimizeJar>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>
             <plugin>
                 <groupId>com.mycila</groupId>
                 <artifactId>license-maven-plugin</artifactId>
-                <version>2.4</version>
+                <version>2.9</version>
                 <configuration>
-                    <header>./short-license.txt</header>
+                    <header>short-license.txt</header>
                     <includes>
                         <include>**/*.java</include>
                     </includes>
@@ -140,7 +149,5 @@
             <artifactId>jetty-webapp</artifactId>
             <version>${jetty.version}</version>
         </dependency>
-
-
     </dependencies>
 </project>

src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/JsonWebService.java

@@ -19,7 +19,6 @@
 package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample;
 
 import java.net.URL;
-import javax.servlet.http.HttpServlet;
 import org.eclipse.jetty.server.handler.HandlerList;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;

src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIJettyPlugin.java

@@ -19,7 +19,6 @@
 
 package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample;
 
-import java.io.File;
 import java.net.URI;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -61,7 +60,7 @@ private SearchResult generateSearchResult()
         map.put("SeriesDate","20150120");
 
         SearchResult r = new SearchResult(
-                URI.create("file:" + File.separatorChar + UUID.randomUUID().toString() ), 1, map);
+                URI.create("file://" + UUID.randomUUID().toString() ), 1, map);
         return r;
     }
 

src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java

@@ -28,8 +28,7 @@
 import pt.ua.dicoogle.sdk.StorageInputStream;
 import pt.ua.dicoogle.sdk.StorageInterface;
 import pt.ua.dicoogle.sdk.settings.ConfigurationHolder;
-import java.util.ArrayList;
-import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
@@ -45,13 +44,13 @@
 public class RSIStorage implements StorageInterface {
     private static final Logger logger = LoggerFactory.getLogger(RSIStorage.class);
 
-    private final Map<String, ByteArrayOutputStream> mem = new HashMap<>();
+    private final Map<String, byte[]> mem = new HashMap<>();
     private boolean enabled = true;
     private ConfigurationHolder settings;
 
     @Override
     public String getScheme() {
-        return "mem://";
+        return "mem";
     }
 
     @Override
@@ -67,7 +66,6 @@ public Iterable<StorageInputStream> at(final URI location, Object... objects) {
 
             @Override
             public Iterator<StorageInputStream> iterator() {
-                Collection c2 = new ArrayList<>();
                 StorageInputStream s = new StorageInputStream() {
 
                     @Override
@@ -77,18 +75,17 @@ public URI getURI() {
 
                     @Override
                     public InputStream getInputStream() throws IOException {
-                        ByteArrayOutputStream bos = mem.get(location.toString());
-                        ByteArrayInputStream bin = new ByteArrayInputStream(bos.toByteArray());
+                        byte[] data = mem.get(location.toString());
+                        ByteArrayInputStream bin = new ByteArrayInputStream(data);
                         return bin;
                     }
 
                     @Override
                     public long getSize() throws IOException {
-                        return mem.get(location.toString()).size();
+                        return mem.get(location.toString()).length;
                     }
                 };
-                c2.add(s);
-                return c2.iterator();
+                return Collections.singletonList(s).iterator();
             }
         };
         return c;
@@ -97,16 +94,14 @@ public long getSize() throws IOException {
     @Override
     public URI store(DicomObject dicomObject, Object... objects) {
         ByteArrayOutputStream bos = new ByteArrayOutputStream();
-        DicomOutputStream dos = new DicomOutputStream(bos);
-        try {
+        try (DicomOutputStream dos = new DicomOutputStream(bos)) {
             dos.writeDicomFile(dicomObject);
         } catch (IOException ex) {
             logger.warn("Failed to store object", ex);
         }
-        bos.toByteArray();
         URI uri = URI.create("mem://" + UUID.randomUUID().toString());
-        mem.put(uri.toString(), bos);
-        
+        mem.put(uri.toString(), bos.toByteArray());
+
         return uri;
     }