make modeldescriptor reader more robust

bioimage-io · Oct 9, 2024 · 8f43fce · 8f43fce
1 parent 09c579c
commit 8f43fce
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Showing 3 changed files with 41 additions and 10 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptor.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptor.java
@@ -70,6 +70,11 @@ public interface ModelDescriptor {
      */
     public String getModelID();
 
+    /**
+     * @return The ID of this model.
+     */
+    public String getNickname();
+
     /**
      * @return The creation timestamp of this model.
      */

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV04.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV04.java
@@ -47,7 +47,6 @@ public class ModelDescriptorV04 implements ModelDescriptor
 {
     private String format_version;
     private String name;
-    private String nickname;
     private String timestamp;
     private String description;
     private String type;
@@ -121,10 +120,6 @@ protected static ModelDescriptorV04 buildModelDescription(Map<String, Object> ya
                     case "description":
                         modelDescription.description = (String) fieldElement;
                         break;
-                    case "id":
-                    	modelDescription.newModelID = findID(yamlElements);
-                    	modelDescription.modelID = findOldID(yamlElements);
-                        break;
                     case "authors":
                         modelDescription.authors = buildAuthorElements((List<?>) fieldElement);
                         break;
@@ -195,12 +190,11 @@ protected static ModelDescriptorV04 buildModelDescription(Map<String, Object> ya
                 throw new ModelSpecsException("Invalid model element: " + field + "->" + e.getMessage());
             }
         }
+    	modelDescription.newModelID = findID(yamlElements);
+    	modelDescription.modelID = findOldID(yamlElements);
 
         modelDescription.addSampleAndTestImages(yamlElements);
 
-        Object bio = modelDescription.config.getSpecMap().get("bioimageio");
-        if ((bio != null) && (bio instanceof Map))
-        	modelDescription.nickname = (String) (((Map<String, Object>) bio).get("nickname"));
         modelDescription.addBioEngine();
         if (modelDescription.localModelPath == null)
         	return modelDescription;
@@ -284,6 +278,13 @@ private static String findOldID(Map<String, Object> yamlElements) {
     		Map<String, Object> configMap = (Map<String, Object>) yamlElements.get("config");
     		if (configMap.get("_conceptdoi") != null && configMap.get("_conceptdoi") instanceof String) {
     			return (String) configMap.get("_conceptdoi");
+    		} else if (configMap.get("_id") != null && configMap.get("_id") instanceof String) {
+        		String id = (String) configMap.get("_id");
+        		if (id.length() - id.replace("/", "").length() >= 2 
+        				&& id.substring(id.indexOf("/") + 1).indexOf("/") - id.indexOf("/") > 2 )
+        			return id.substring(0, id.indexOf("/") + id.substring(id.indexOf("/") + 1).indexOf("/") + 1);
+        		else
+        			return id;
     		}
     	}
     	if (yamlElements.get("id") != null && yamlElements.get("id") instanceof String) {
@@ -518,7 +519,7 @@ public String getName()
      */
     public String getNickname()
     {
-        return nickname;
+        return this.newModelID;
     }
 
     /**

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV05.java
@@ -152,7 +152,7 @@ protected void buildModelDescription() throws ModelSpecsException
                         // TODO createAttachments();
                         break;
                     case "covers":
-                    	// TODO createCovers();
+                    	covers = castListStrings(yamlElements.get(field));
                         break;
                     case "inputs":
                     	input_tensors = buildInputTensors((List<?>) yamlElements.get(field));
@@ -182,12 +182,29 @@ protected void buildModelDescription() throws ModelSpecsException
                 throw new ModelSpecsException("Invalid model element: " + field + "->" + e.getMessage());
             }
         }
+        if (modelID == null) {
+        	modelID = findID(yamlElements);
+        }
         addBioEngine();
         if (localModelPath == null)
         	return;
     	// TODO SpecialModels.checkSpecialModels(null);
     }
 
+    @SuppressWarnings("unchecked")
+	private static String findID(Map<String, Object> yamlElements) {
+
+    	if (yamlElements.get("config") != null && yamlElements.get("config") instanceof Map) {
+    		Map<String, Object> configMap = (Map<String, Object>) yamlElements.get("config");
+    		if (configMap.get("bioimageio") != null && configMap.get("bioimageio") instanceof Map) {
+    			Map<String, Object> bioimageMap = (Map<String, Object>) configMap.get("bioimageio");
+    			if (bioimageMap.get("nickname") != null)
+    				return (String) bioimageMap.get("nickname");
+    		}
+    	}
+    	return (String) yamlElements.get("id");
+    }
+
     /**
      * Every model in the bioimage.io can be run in the BioEngine as long as it is in the
      * collections repo: 
@@ -380,6 +397,14 @@ public String getModelID()
         return modelID;
     }
 
+    /**
+     * @return The nickname of this model, for v0.5 is the same as the id.
+     */
+    public String getNickname()
+    {
+        return modelID;
+    }
+
     /**
      * @return The creation timestamp of this model.
      */