Merge pull request #3 from Enet4/new/dicoogle3

Migrate to Dicoogle 3

Author: Enet4

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>pt.ua.dicoogle</groupId>
     <artifactId>nifti</artifactId>
-    <version>1.0-SNAPSHOT</version>
+    <version>2.0.0</version>
     <packaging>jar</packaging>
     <name>dicoogle-nifti</name>
     <description>NIFTI-1 file convertion and storage for Dicoogle</description>
@@ -12,10 +12,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
         <!-- Dicoogle SDK version here -->
-        <dicoogle.version>2.4.0</dicoogle.version>
-
-        <!-- Jetty server version here -->
-        <jetty.version>9.0.3.v20130506</jetty.version>
+        <dicoogle.version>3.0.2</dicoogle.version>
     </properties>
 
     <build>
@@ -75,34 +72,34 @@
         <repository>
             <id>maven-restlet</id>
             <name>Public online Restlet repository</name>
-            <url>http://maven.restlet.org</url>
+            <url>https://maven.restlet.org</url>
         </repository>
         <repository>
             <id>mavencentral</id>
-            <url>http://repo1.maven.org/maven2/</url>
+            <url>https://repo1.maven.org/maven2/</url>
             <snapshots>
                 <enabled>true</enabled>
             </snapshots>
         </repository>
         <repository>
             <id>dcm4che</id>
-            <url>http://www.dcm4che.org/maven2/</url>
+            <url>https://www.dcm4che.org/maven2/</url>
             <snapshots>
                 <enabled>true</enabled>
             </snapshots>
         </repository>
 
         <repository>
             <id>mi</id>
-            <url>http://bioinformatics.ua.pt/maven/content/repositories/mi</url>
+            <url>https://bioinformatics.ua.pt/maven/content/repositories/mi</url>
             <snapshots>
                 <enabled>false</enabled>
             </snapshots>
         </repository>
 
         <repository>
             <id>mi-snapshots</id>
-            <url>http://bioinformatics.ua.pt/maven/content/repositories/mi-snapshots</url>
+            <url>https://bioinformatics.ua.pt/maven/content/repositories/mi-snapshots</url>
             <snapshots>
                 <enabled>true</enabled>
             </snapshots>

src/main/java/pt/ua/dicoogle/nifti/NIFTIPluginSet.java

@@ -23,16 +23,11 @@
 import java.util.Collection;
 import java.util.Collections;
 import net.xeoh.plugins.base.annotations.PluginImplementation;
-import org.restlet.resource.ServerResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import pt.ua.dicoogle.nifti.config.NIFTIPluginSettings;
-import pt.ua.dicoogle.sdk.GraphicalInterface;
-import pt.ua.dicoogle.sdk.IndexerInterface;
 import pt.ua.dicoogle.sdk.JettyPluginInterface;
 import pt.ua.dicoogle.sdk.PluginSet;
-import pt.ua.dicoogle.sdk.QueryInterface;
-import pt.ua.dicoogle.sdk.StorageInterface;
 import pt.ua.dicoogle.sdk.settings.ConfigurationHolder;
 
 /** The main plugin set.
@@ -60,16 +55,6 @@ public NIFTIPluginSet() throws IOException {
 
         logger.info("NIFTI Plugin Set is ready");
     }
-
-    @Override
-    public Collection<IndexerInterface> getIndexPlugins() {
-        return Collections.EMPTY_LIST;
-    }
-
-    @Override
-    public Collection<QueryInterface> getQueryPlugins() {
-        return Collections.EMPTY_LIST;
-    }
 
     /** This method is used to retrieve a name for identifying the plugin set. Keep it as a constant value.
      * 
@@ -80,11 +65,6 @@ public String getName() {
         return "NIFTI";
     }
 
-    @Override
-    public Collection<ServerResource> getRestPlugins() {
-        return Collections.EMPTY_LIST;
-    }
-
     @Override
     public Collection<JettyPluginInterface> getJettyPlugins() {
         return Collections.singleton(this.jettyWeb);
@@ -95,11 +75,6 @@ public void shutdown() {
         logger.info("NIFTI plugin is shutting down");
     }
 
-    @Override
-    public Collection<StorageInterface> getStoragePlugins() {
-        return Collections.EMPTY_LIST;
-    }
-
     @Override
     public void setSettings(ConfigurationHolder xmlSettings) {
         this.settings = xmlSettings;
@@ -110,10 +85,4 @@ public void setSettings(ConfigurationHolder xmlSettings) {
     public ConfigurationHolder getSettings() {
         return this.settings;
     }
-
-    @Override
-    public Collection<GraphicalInterface> getGraphicalPlugins() {
-        // Graphical plugins are deprecated. Do not use or provide any.
-        return Collections.EMPTY_LIST;
-    }
 }

src/main/java/pt/ua/dicoogle/nifti/ws/NIFTIConvertWebServlet.java

@@ -28,7 +28,6 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ForkJoinPool;
 import java.util.function.UnaryOperator;
-import java.util.logging.Level;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import java.util.zip.GZIPInputStream;
@@ -38,7 +37,6 @@
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.Part;
 import net.sf.json.JSONObject;
-import org.apache.commons.lang3.tuple.Pair;
 import org.dcm4che2.data.DicomObject;
 import org.dcm4che2.data.Tag;
 import org.dcm4che2.data.VR;
@@ -77,7 +75,9 @@ public NiftiFileEntry(String name, S inputStream) {
     @Override
     protected void doGet(HttpServletRequest req, HttpServletResponse response)
                     throws ServletException, IOException {
-        response.setStatus(418, "I'm a teapot");
+        response.setStatus(405);
+        response.setHeader("Content-Type", "text/plain; charset=UTF-8");
+        response.getWriter().println("⚠ Please use POST to upload nifti files");
     }
 
     @Override
@@ -92,7 +92,7 @@ protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws S
 
         Stream<NiftiFileEntry<InputStream>> niftiObjects;
         int nFiles;
-        resp.setContentType("application/json");
+        resp.setContentType("application/json; charset=UTF-8");
         if (req.getContentType() == null) {
             JSONObject reply = new JSONObject();
             reply.put("error", "no content");

src/main/java/pt/ua/dicoogle/nifti/ws/NIFTIServletPlugin.java

@@ -22,8 +22,6 @@
 import org.eclipse.jetty.server.handler.HandlerList;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import pt.ua.dicoogle.sdk.JettyPluginInterface;
 import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface;
@@ -35,13 +33,10 @@
  * @author Luís A. Bastião Silva - <bastiao@ua.pt>
  */
 public class NIFTIServletPlugin implements JettyPluginInterface, PlatformCommunicatorInterface {
-    private static final Logger logger = LoggerFactory.getLogger(NIFTIServletPlugin.class);
-    
     private static final String NIFTI_FILE_PATH = System.getProperty("java.io.tmpdir");
 
     private boolean enabled;
     private ConfigurationHolder settings;
-    private DicooglePlatformInterface platform;
     private final NIFTIConvertWebServlet wsConvert;
 
     public NIFTIServletPlugin() {
@@ -51,7 +46,6 @@ public NIFTIServletPlugin() {
 
     @Override
     public void setPlatformProxy(DicooglePlatformInterface pi) {
-        this.platform = pi;
         // since web service is not a plugin interface, the platform interface must be provided manually
         this.wsConvert.setPlatformProxy(pi);
     }
@@ -101,20 +95,8 @@ public HandlerList getJettyHandlers() {
         convertServletHolder.getRegistration().setMultipartConfig(new MultipartConfigElement(NIFTI_FILE_PATH));
         handler.addServlet(convertServletHolder, "/convert");
 
-//        URL url = NIFTIServletPlugin.class.getResource("/WEBAPP");
-//        logger.debug("Retrieving web app from \"{}\"", url);
-//        String directoryToServeAssets = url.toString();
-//        
-//        final WebAppContext webpages = new WebAppContext(directoryToServeAssets, "/dashboardSample");
-//        webpages.setInitParameter("org.eclipse.jetty.servlet.Default.dirAllowed", "true"); // disables directory listing
-//        webpages.setInitParameter("useFileMappedBuffer", "false");
-//        webpages.setInitParameter("cacheControl", "max-age=0, public");
-//
-//        webpages.setWelcomeFiles(new String[]{"index.html"});
-
         HandlerList l = new HandlerList();
         l.addHandler(handler);
-        //l.addHandler(webpages);
 
         return l;
     }