bring back Bioengine

src/main/java/io/bioimage/modelrunner/bioimageio/bioengine/BioEngineAvailableModels.java

@@ -0,0 +1,220 @@
+/*-
+ * #%L
+ * Use deep learning frameworks from Java in an agnostic and isolated way.
+ * %%
+ * Copyright (C) 2022 - 2023 Institut Pasteur and BioImage.IO developers.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package io.bioimage.modelrunner.bioimageio.bioengine;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javax.net.ssl.HttpsURLConnection;
+
+import io.bioimage.modelrunner.utils.Constants;
+
+import com.google.gson.Gson;
+import com.google.gson.internal.LinkedTreeMap;
+
+/**
+ * Class to handle the JSON file that contains the information about the 
+ * models supported by the Bioengine. The model is located at: 
+ * https://raw.githubusercontent.com/bioimage-io/bioengine-model-runner/gh-pages/manifest.bioengine.json
+ * @author Carlos Garcia Lopez de Haro
+ *
+ */
+public class BioEngineAvailableModels {
+
+	/**
+	 * Collection of models available at the bioengine
+	 */
+	private ArrayList<LinkedTreeMap<String, String>> collection;
+	/**
+	 * Logs for the CI of the Bioengine
+	 */
+	private ArrayList<String> conversion_logs;
+	/**
+	 * Description of the file
+	 */
+	private String description;
+	/**
+	 * Format version
+	 */
+	private String format_version;
+	/**
+	 * Name of the file
+	 */
+	private String name;
+	/**
+	 * Tags fo the file
+	 */
+	private ArrayList<String> tags;
+	/***
+	 * Type of the file
+	 */
+	private String type;
+	/**
+	 * Version of the file
+	 */
+	private String version;
+
+	/**
+	 * URL of the Json file containing the bioengine compatible models json
+	 */
+	final private static String BIOENGINE_COMPATIBLE_JSON = 
+			"https://raw.githubusercontent.com/bioimage-io/bioengine-model-runner/gh-pages/manifest.bioengine.json";
+	/**
+	 * Key for the ID of the models supported by the bioengine in the collections object
+	 */
+	final private static String ID_KEY = "id";
+
+	private static BioEngineAvailableModels BAM;
+	/**
+	 * Address of the first public server that hosts a bioengine instance
+	 */
+	public static final String PUBLIC_BIOENGINE_SERVER = "https://ai.imjoy.io";
+
+	/**
+	 * Method that parses the json file that contains all the supported models by the BioEngine
+	 * @return obejct containing the spported models by the bioengine
+	 * @throws IOException if the bioengine website cannot 
+	 * be accessed or if there is any error parsing the json
+	 */
+	public static BioEngineAvailableModels load() throws IOException
+    {
+		HttpsURLConnection con;
+		try {
+			URL url = new URL(BIOENGINE_COMPATIBLE_JSON);
+			con = (HttpsURLConnection) url.openConnection();
+		} catch (IOException ex) {
+			throw new IOException("Unable to access the following link: " + BIOENGINE_COMPATIBLE_JSON
+					+ System.lineSeparator() + "Please, check your Internet connection. If the site does "
+					+ "not exist, please report it at : " + Constants.ISSUES_LINK);
+		}
+		try (InputStream inputStream = con.getInputStream();
+			InputStreamReader inpStreamReader = new InputStreamReader(inputStream);
+		    BufferedReader br = new BufferedReader(inpStreamReader);){
+	        Gson g = new Gson();
+	        return g.fromJson(br, BioEngineAvailableModels.class); 
+		} catch (IOException ex) {
+			throw new IOException("Unable to parse JSON that contains BioEngine compatible models at: "
+					+ System.lineSeparator() + BIOENGINE_COMPATIBLE_JSON + System.lineSeparator()
+					+ ex.getCause().toString());
+		}
+    }
+
+	/**
+	 * Creates empty BioEngineAvailableModels object that works with all its methods.
+	 * Created to avoid errors caused by {@link NullPointerException}
+	 * @return
+	 */
+	private static BioEngineAvailableModels createEmptyObject() {
+		BioEngineAvailableModels availableModels = new BioEngineAvailableModels();
+		availableModels.collection = new ArrayList<LinkedTreeMap<String, String>>();
+		availableModels.conversion_logs = new ArrayList<String>();
+		return availableModels;
+	}
+
+	/**
+	 * Method that returns a list of the IDs corresponding to the models that are supported by 
+	 * the bioengine
+	 * @return a list of the IDs supported by the bioengine
+	 */
+	public List<String> getListOfSupportedIDs() {
+		return collection.stream().map(x -> x.get(ID_KEY)).collect(Collectors.toList());
+	}
+
+	/**
+	 * Method that finds whether a model is supported by the Bioengine by looking if its
+	 * model ID is spedified in the JSON file that contains all valid models
+	 * @param modelID
+	 * 	ID of the model of interest
+	 * @return true if supported, false otherwise
+	 */
+	public boolean isModelSupportedByBioengine(String modelID) {
+		LinkedTreeMap<String, String> isFound = collection.stream()
+				.filter(x -> modelID.startsWith(x.get(ID_KEY)+ "/")).findFirst().orElse(null);
+		if (isFound == null)
+			return false;
+		return true;
+	}
+
+	/**
+	 * Static method that finds whether a model is supported by the Bioengine by looking if its
+	 * model ID is spedified in the JSON file that contains all valid models.
+	 * This method only recovers the file that contains the information of the models
+	 * supported by the Bioengine the first time. In order to retrieve the file each
+	 * time, do the following:
+	 * 	BioEngineAvailableModels bam =  BioEngineAvailableModels.load();
+	 * 	String id = "model/ID":
+	 * 	boolean supported = bam.isModelSupportedByBioengine(id);
+	 * @param modelID
+	 * 	ID of the model of interest
+	 * @return true if supported, false otherwise
+	 */
+	public static boolean isModelSupportedInBioengine(String modelID) {
+		if (BAM == null) {
+			try {
+				BAM =  BioEngineAvailableModels.load();
+			} catch (IOException ex) {
+				BAM = createEmptyObject();
+			}
+		}
+		return BAM.isModelSupportedByBioengine(modelID);
+	}
+
+	public ArrayList<LinkedTreeMap<String, String>> getCollection() {
+		return this.collection;
+	}
+
+	public String getType() {
+		return this.type;
+	}
+
+	public ArrayList<String> getConversionLogs() {
+		return this.conversion_logs;
+	}
+
+	public ArrayList<String> getTags() {
+		return this.tags;
+	}
+
+	public String getName() {
+		return this.name;
+	}
+
+	public String getFormatVersion() {
+		return this.format_version;
+	}
+
+	public String getVersion() {
+		return this.version;
+	}
+
+	public String getDescription() {
+		return this.description;
+	}
+
+	public static String getBioengineJson() {
+		return BIOENGINE_COMPATIBLE_JSON;
+	}
+}