completely restore the Bioengine

pom.xml

@@ -126,5 +126,10 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.msgpack</groupId>
+			<artifactId>jackson-dataformat-msgpack</artifactId>
+			<version>0.9.5</version>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/io/bioimage/modelrunner/bioimageio/BioimageioRepo.java

@@ -23,7 +23,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -39,6 +38,7 @@
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
 
+import io.bioimage.modelrunner.bioimageio.bioengine.BioEngineAvailableModels;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
 import io.bioimage.modelrunner.bioimageio.download.DownloadModel;
 import io.bioimage.modelrunner.bioimageio.download.DownloadTracker;
@@ -340,6 +340,18 @@ public static List<String> getModelNicknames(){
 		return modelNicknames;
 	}
 
+	/**
+	 * Check whether a model is available on the Bioengine or not by providing its id
+	 * @param id
+	 * 	id of the model of interest
+	 * @return true if it is available or false otherwise
+	 * @throws IOException if there is no connection to the internet or the
+	 * 	JSOn with the information cannot be accessed: https://raw.githubusercontent.com/bioimage-io/bioengine-model-runner/gh-pages/manifest.bioengine.json
+	 */
+	public static boolean isModelOnTheBioengineById(String id) throws IOException {
+		return BioEngineAvailableModels.isModelSupportedInBioengine(id);
+	}
+
 	/**
 	 * Return the {@link ModelDescriptor} for the model defined by the modelID
 	 * (field 'id' in the rdf.yaml) introduced as a parameter.

src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptor.java

@@ -37,6 +37,7 @@
 
 import javax.xml.bind.ValidationException;
 
+import io.bioimage.modelrunner.bioimageio.BioimageioRepo;
 import io.bioimage.modelrunner.bioimageio.description.weights.ModelWeight;
 import io.bioimage.modelrunner.utils.Log;
 import io.bioimage.modelrunner.utils.YAMLUtils;
@@ -326,7 +327,7 @@ private void addBioEngine() throws ValidationException {
 			return;
 	    }
     	try {
-			supportBioengine = false;// BioimageioRepo.isModelOnTheBioengineById(modelID);
+			supportBioengine =  BioimageioRepo.isModelOnTheBioengineById(modelID);
 		} catch (Exception e) {
 			e.printStackTrace();
 		}

src/main/java/io/bioimage/modelrunner/engine/EngineLoader.java

@@ -33,6 +33,7 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 
+import io.bioimage.modelrunner.bioimageio.bioengine.BioengineInterface;
 import io.bioimage.modelrunner.exceptions.LoadEngineException;
 import io.bioimage.modelrunner.versionmanagement.DeepLearningVersion;
 
@@ -127,6 +128,7 @@ private EngineLoader( ClassLoader classloader, EngineInfo engineInfo ) throws Lo
 		this.engine = engineInfo.getFramework();
 		this.bioengine = engineInfo.isBioengine();
 		if (engineInfo.isBioengine()) {
+			this.engineInstance = new BioengineInterface();
 			return;
 		}
 		this.enginePath = engineInfo.getDeepLearningVersionJarsDirectory();

src/main/java/io/bioimage/modelrunner/model/Model.java

@@ -32,6 +32,8 @@
 
 import javax.xml.bind.ValidationException;
 
+import io.bioimage.modelrunner.bioimageio.bioengine.BioEngineAvailableModels;
+import io.bioimage.modelrunner.bioimageio.bioengine.BioengineInterface;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
 import io.bioimage.modelrunner.bioimageio.description.weights.WeightFormat;
 import io.bioimage.modelrunner.engine.DeepLearningEngineInterface;
@@ -381,6 +383,35 @@ public static Model createDeepLearningModel( String modelFolder, String modelSou
 		return new Model( engineInfo, modelFolder, modelSource, classLoader );
 	}
 
+	/**
+	 * Load a model from the bioimage.io directly on the Bioengine. 
+	 * Only the path to the model folder that contains the rdf.yaml is needed.
+	 * To load a model on the bioengine we need to specify the server where our instance
+	 * of the Bioengine is hosted.
+	 * @param bmzModelFolder
+	 * 	folder where the bioimage.io model is located (parent folder of the rdf.yaml file)
+	 * @param serverURL
+	 * 	url where the wanted insance of the bioengine is hosted
+	 * @return a model ready to be loaded
+	 * @throws Exception if there is any error creating the model (no rdf.yaml file,
+	 *  or the url does not exist) or if the model is not supported on the Bioengine.
+	 *  To check the models supported on the Bioengine, visit: https://raw.githubusercontent.com/bioimage-io/bioengine-model-runner/gh-pages/manifest.bioengine.yaml
+	 */
+	public static Model createBioimageioModelForBioengine(String bmzModelFolder, String serverURL) throws Exception {
+		if (new File(bmzModelFolder, Constants.RDF_FNAME).isFile() == false)
+			throw new IOException("A Bioimage.io model folder should contain its corresponding rdf.yaml file.");
+		ModelDescriptor descriptor = 
+				ModelDescriptor.readFromLocalFile(bmzModelFolder + File.separator + Constants.RDF_FNAME, false);
+		boolean valid = BioEngineAvailableModels.isModelSupportedInBioengine(descriptor.getModelID());
+		if (!valid)
+			throw new IllegalArgumentException("The selected model is currently not supported by the Bioegine. "
+					+ "To check the list of supported models please visit: " + BioEngineAvailableModels.getBioengineJson());
+		EngineInfo info = EngineInfo.defineBioengine(serverURL);
+		Model model =  Model.createDeepLearningModel(bmzModelFolder, null, info);
+		model.bioengine = true;
+		return model;
+	}
+
 	/**
 	 * Sets the classloader containing the Deep Learning engine
 	 * 
@@ -411,6 +442,8 @@ public void loadModel() throws LoadModelException
 		DeepLearningEngineInterface engineInstance = engineClassLoader.getEngineInstance();
 		engineClassLoader.setEngineClassLoader();
 		engineInstance.loadModel( modelFolder, modelSource );
+		if (engineClassLoader.isBioengine())
+			((BioengineInterface) engineInstance).addServer(engineInfo.getServer());
 		engineClassLoader.setBaseClassLoader();
 	}