add custom exception to read rdf.yaml file

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

@@ -35,9 +35,8 @@
 import java.util.Map.Entry;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.ValidationException;
-
 import io.bioimage.modelrunner.bioimageio.BioimageioRepo;
+import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.bioimageio.description.weights.ModelWeight;
 import io.bioimage.modelrunner.utils.Log;
 import io.bioimage.modelrunner.utils.YAMLUtils;
@@ -101,9 +100,9 @@ private ModelDescriptor()
      * @param modelFile
      *        Model descriptor file.
      * @return The instance of the model descriptor.
-     * @throws ValidationException if any of the parameters in the rdf.yaml file does not make fit the constraints
+     * @throws ModelSpecsException if any of the parameters in the rdf.yaml file does not make fit the constraints
      */
-    public static ModelDescriptor readFromLocalFile(String modelFile) throws ValidationException
+    public static ModelDescriptor readFromLocalFile(String modelFile) throws ModelSpecsException
     {
     	return readFromLocalFile(modelFile, true);
     }
@@ -116,9 +115,9 @@ public static ModelDescriptor readFromLocalFile(String modelFile) throws Validat
      * @param verbose
      * 	whether to print the path to the file and the time to the console or not
      * @return The instance of the model descriptor.
-     * @throws ValidationException if any of the parameters in the rdf.yaml file does not make fit the constraints,
+     * @throws ModelSpecsException if any of the parameters in the rdf.yaml file does not make fit the constraints,
      */
-    public static ModelDescriptor readFromLocalFile(String modelFile, boolean verbose) throws ValidationException
+    public static ModelDescriptor readFromLocalFile(String modelFile, boolean verbose) throws ModelSpecsException
     {
     	// Get the date to be able to log with the time
     	if (verbose)
@@ -127,7 +126,7 @@ public static ModelDescriptor readFromLocalFile(String modelFile, boolean verbos
     	try {
         	yamlElements = YAMLUtils.load(modelFile);
         } catch (IOException ex) {
-        	throw new ValidationException("", ex);
+        	throw new IllegalStateException("", ex);
         }
         yamlElements.put(fromLocalKey, true);
         yamlElements.put(modelPathKey, new File(modelFile).getParent());
@@ -140,9 +139,9 @@ public static ModelDescriptor readFromLocalFile(String modelFile, boolean verbos
      * @param yamlText
      *        text read from a yaml file that contains an rdf.yaml file
      * @return The instance of the model descriptor.
-     * @throws ValidationException if any of the parameters in the rdf.yaml file does not make fit the constraints
+     * @throws ModelSpecsException if any of the parameters in the rdf.yaml file does not make fit the constraints
      */
-    public static ModelDescriptor readFromYamlTextString(String yamlText) throws ValidationException
+    public static ModelDescriptor readFromYamlTextString(String yamlText) throws ModelSpecsException
     {
     	return readFromYamlTextString(yamlText, true);
     }
@@ -155,9 +154,9 @@ public static ModelDescriptor readFromYamlTextString(String yamlText) throws Val
      * @param verbose
      * 	whether to print info about the rdf.yaml that is being read or not
      * @return The instance of the model descriptor.
-     * @throws ValidationException if any of the parameters in the rdf.yaml file does not make fit the constraints
+     * @throws ModelSpecsException if any of the parameters in the rdf.yaml file does not make fit the constraints
      */
-    public static ModelDescriptor readFromYamlTextString(String yamlText, boolean verbose) throws ValidationException
+    public static ModelDescriptor readFromYamlTextString(String yamlText, boolean verbose) throws ModelSpecsException
     {
     	// Convert the String of text that contains the yaml file into Map
     	Map<String,Object> yamlElements = YAMLUtils.loadFromString(yamlText);
@@ -178,9 +177,9 @@ public static ModelDescriptor readFromYamlTextString(String yamlText, boolean ve
      * @param yamlElements
      * 	map with the information read from a yaml file
      * @return a {@link ModelDescriptor} with the info of a Bioimage.io model
-     * @throws ValidationException if any of the parameters in the rdf.yaml file does not make fit the constraints
+     * @throws ModelSpecsException if any of the parameters in the rdf.yaml file does not make fit the constraints
      */
-    private static ModelDescriptor buildModelDescription(Map<String, Object> yamlElements) throws ValidationException
+    private static ModelDescriptor buildModelDescription(Map<String, Object> yamlElements) throws ModelSpecsException
     {
         ModelDescriptor modelDescription = new ModelDescriptor();
 
@@ -299,7 +298,7 @@ private static ModelDescriptor buildModelDescription(Map<String, Object> yamlEle
             }
             catch (IOException e)
             {
-                throw new ValidationException("Invalid model element: " + field + "->" + e.getMessage());
+                throw new ModelSpecsException("Invalid model element: " + field + "->" + e.getMessage());
             }
         }
 
@@ -313,9 +312,9 @@ private static ModelDescriptor buildModelDescription(Map<String, Object> yamlEle
      * Every model in the bioimage.io can be run in the BioEngine as long as it is in the
      * collections repo: 
      * https://github.com/bioimage-io/collection-bioimage-io/blob/e77fec7fa4d92d90c25e11331a7d19f14b9dc2cf/rdfs/10.5281/zenodo.6200999/6224243/rdf.yaml
-     * @throws MalformedURLException servers do not correspond to an actual url
+     * @throws ModelSpecsException servers do not correspond to an actual url
      */
-    private void addBioEngine() throws ValidationException {
+    private void addBioEngine() throws ModelSpecsException {
 		// TODO decide what to do with servers. Probably need permissions / Implement authentication
     	if (getName().equals("cellpose-python")) {
     		supportBioengine = true;
@@ -517,7 +516,7 @@ private static List<Badge> buildBadgeElements(List<?> coverElements)
     }
 
     @SuppressWarnings("unchecked")
-    private static List<TensorSpec> buildInputTensors(List<?> list) throws ValidationException
+    private static List<TensorSpec> buildInputTensors(List<?> list) throws ModelSpecsException
     {
     	if (!(list instanceof List<?>))
     		return null;
@@ -545,7 +544,7 @@ public void setInputTensors(List<TensorSpec> inputTensors) {
     }
 
     @SuppressWarnings("unchecked")
-    private static List<TensorSpec> buildOutputTensors(List<?> list) throws ValidationException
+    private static List<TensorSpec> buildOutputTensors(List<?> list) throws ModelSpecsException
     {
     	if (!(list instanceof List<?>))
     		return null;

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

@@ -24,8 +24,7 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.xml.bind.ValidationException;
-
+import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.utils.YAMLUtils;
 
 /**
@@ -59,10 +58,10 @@ public class ShapeSpec
      * @param input
      *        True if it is an input shape. False if it's an output shape descriptor.
      * @return The shape specification instance.
-     * @throws ValidationException if any of the rdf.yaml does not comply the requirements
+     * @throws ModelSpecsException if any of the rdf.yaml does not comply the requirements
      */
     @SuppressWarnings("unchecked")
-    public static ShapeSpec build(Object shapeElem, boolean input) throws ValidationException
+    public static ShapeSpec build(Object shapeElem, boolean input) throws ModelSpecsException
     {
         ShapeSpec shape = new ShapeSpec();
         shape.input = input;
@@ -174,12 +173,12 @@ public float[] getScale()
      * always be divisible by 0.5
      * @param offset
      * 	the output offset
-     * @throws ValidationException if the offset is not divisible by 0.5
+     * @throws ParseException if the offset is not divisible by 0.5
      */
-    public void setOffset(float[] offset) throws ValidationException  {
+    public void setOffset(float[] offset) throws ModelSpecsException  {
     	for (float ff : offset) {
     		if (ff % 0.5 != 0) {
-    			throw new ValidationException("Invalid output specifications. "
+    			throw new ModelSpecsException("Invalid output specifications. "
     					+ "Every output offset should be divisible by 0.5");
     		}
     	}

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

@@ -25,8 +25,7 @@
 import java.util.Map;
 import java.util.stream.IntStream;
 
-import javax.xml.bind.ValidationException;
-
+import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.tiling.PatchGridCalculator;
 import io.bioimage.modelrunner.utils.YAMLUtils;
 
@@ -112,10 +111,10 @@ public class TensorSpec {
      * @param input
      *        Whether it is an input (true) or an output (false) tensor.
      * @return The tensor specification instance.
-     * @throws ValidationException if any of the fields does not fulfill the requirements
+     * @throws ModelSpecsException if any of the fields does not fulfill the requirements
      */
     @SuppressWarnings("unchecked")
-    public static TensorSpec build(Map<String, Object> tensorSpecMap, boolean input) throws ValidationException
+    public static TensorSpec build(Map<String, Object> tensorSpecMap, boolean input) throws ModelSpecsException
     {
         TensorSpec tensor = new TensorSpec();
         tensor.name = (String) tensorSpecMap.get("name");

src/main/java/io/bioimage/modelrunner/bioimageio/description/exceptions/ModelSpecsException.java

@@ -0,0 +1,39 @@
+/*-
+ * #%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.description.exceptions;
+
+/**
+ * A exception to be launched when there is any error reading the Bioimage.io rdf.yaml file
+ * 
+ * @author Carlos Garcia Lopez de Haro
+ */
+public class ModelSpecsException extends Exception
+{
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Constructor for every exception related to reading the Bioimage.io rdf.yaml specs file
+	 * @param message
+	 * 	the message that wants to be passed as the exception info.
+	 */
+	public ModelSpecsException(String message) {
+        super(message);
+    }
+}

src/main/java/io/bioimage/modelrunner/engine/installation/EngineInstall.java

@@ -36,10 +36,9 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.ValidationException;
-
 import io.bioimage.modelrunner.bioimageio.BioimageioRepo;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
+import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.bioimageio.description.weights.WeightFormat;
 import io.bioimage.modelrunner.bioimageio.download.DownloadTracker;
 import io.bioimage.modelrunner.bioimageio.download.DownloadTracker.TwoParameterConsumer;
@@ -960,10 +959,10 @@ public static boolean installEnginesForModelByNameinDir(String modelName, String
 	 * @return true if at least one DL engine of the model weights defined in the rdf.yaml is
 	 * 	successfully installed
 	 * @throws FileNotFoundException if the rdf.yaml specs file does not exist
-	 * @throws ValidationException if there is any error with the rdf.yaml file
+	 * @throws ModelSpecsException if there is any error with the rdf.yaml file
 	 * @throws IOException if there is any error creating the folder for the engine or downloading the jar files
 	 */
-	public static boolean installEnginesForModelInFolder(String modelFolder) throws FileNotFoundException, ValidationException, IOException {
+	public static boolean installEnginesForModelInFolder(String modelFolder) throws FileNotFoundException, ModelSpecsException, IOException {
 		return installEnginesinDirForModelInFolder(modelFolder, InstalledEngines.getEnginesDir(), null);
 	}
 
@@ -982,11 +981,11 @@ public static boolean installEnginesForModelInFolder(String modelFolder) throws
 	 * @return true if at least one DL engine of the model weights defined in the rdf.yaml is
 	 * 	successfully installed
 	 * @throws FileNotFoundException if the rdf.yaml specs file does not exist
-	 * @throws ValidationException if there is any error with the rdf.yaml file
+	 * @throws ModelSpecsException if there is any error with the rdf.yaml file
 	 * @throws IOException if there is any error creating the folder for the engine or downloading the jar files
 	 */
 	public static boolean installEnginesForModelInFolder(String modelFolder, 
-			DownloadTracker.TwoParameterConsumer<String, Double> consumer) throws FileNotFoundException, ValidationException, IOException {
+			DownloadTracker.TwoParameterConsumer<String, Double> consumer) throws FileNotFoundException, ModelSpecsException, IOException {
 		return installEnginesinDirForModelInFolder(modelFolder, InstalledEngines.getEnginesDir(), consumer);
 	}
 
@@ -1004,10 +1003,10 @@ public static boolean installEnginesForModelInFolder(String modelFolder,
 	 * @return true if at least one DL engine of the model weights defined in the rdf.yaml is
 	 * 	successfully installed
 	 * @throws FileNotFoundException if the rdf.yaml specs file does not exist
-	 * @throws ValidationException if there is any error with the rdf.yaml file
+	 * @throws ModelSpecsException if there is any error with the rdf.yaml file
 	 * @throws IOException if there is any error creating the folder for the engine or downloading the jar files
 	 */
-	public static boolean installEnginesinDirForModelInFolder(String modelFolder, String enginesDir) throws FileNotFoundException, ValidationException, IOException {
+	public static boolean installEnginesinDirForModelInFolder(String modelFolder, String enginesDir) throws FileNotFoundException, ModelSpecsException, IOException {
 		return installEnginesinDirForModelInFolder(modelFolder, enginesDir, null);
 	}
 
@@ -1027,12 +1026,12 @@ public static boolean installEnginesinDirForModelInFolder(String modelFolder, St
 	 * @return true if at least one DL engine of the model weights defined in the rdf.yaml is
 	 * 	successfully installed
 	 * @throws FileNotFoundException if the rdf.yaml specs file does not exist
-	 * @throws ValidationException if there is any error with the rdf.yaml file
+	 * @throws ModelSpecsException if there is any error with the rdf.yaml file
 	 * @throws IOException if there is any error creating the folder for the engine or downloading the jar files
 	 */
 	public static boolean installEnginesinDirForModelInFolder(String modelFolder, String enginesDir, 
 			DownloadTracker.TwoParameterConsumer<String, Double> consumer) 
-					throws FileNotFoundException, ValidationException, IOException {
+					throws FileNotFoundException, ModelSpecsException, IOException {
 		if (new File(modelFolder, "rdf.yaml").isFile() == false)
 			throw new FileNotFoundException("A Bioimage.io model folder should contain its corresponding rdf.yaml file.");
 		ModelDescriptor descriptor =