correct arising errors

bioimage-io · Aug 5, 2024 · 2accea9 · 2accea9
1 parent 9586f37
commit 2accea9
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Showing 3 changed files with 19 additions and 4 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/BioimageioRepo.java b/src/main/java/io/bioimage/modelrunner/bioimageio/BioimageioRepo.java
@@ -178,6 +178,7 @@ public Map<Path, ModelDescriptor> listAllModels(boolean verbose) {
 				ModelDescriptor descriptor = ModelDescriptorFactory.readFromYamlTextString(stringRDF);
 				models.put(Paths.get(url), descriptor);
 			} catch (Exception ex) {
+				ex.printStackTrace();
 				// TODO Maybe add some error message? This should be responsibility of the BioImage.io user
 				// Only display error message if there was an error creating
 				// the descriptor from the yaml file

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV04.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV04.java
@@ -22,7 +22,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.net.URL;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -118,7 +117,7 @@ protected static ModelDescriptorV04 buildModelDescription(Map<String, Object> ya
                         modelDescription.description = (String) fieldElement;
                         break;
                     case "id":
-                        modelDescription.modelID = (String) fieldElement;
+                    	modelDescription.modelID = findID(yamlElements);
                         break;
                     case "authors":
                         modelDescription.authors = buildAuthorElements((List<?>) fieldElement);
@@ -264,6 +263,19 @@ private void addBioEngine() throws ModelSpecsException {
 		}
     }
 
+    private static String findID(Map<String, Object> yamlElements) {
+
+    	if (yamlElements.get("config") instanceof Map) {
+    		Map<String, Object> configMap = (Map<String, Object>) yamlElements.get("config");
+    		if (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");
+    }
+
     /**
      * MAke sure that an object that is supposed to be a List<String>
      * is actually a List<String>
@@ -440,6 +452,7 @@ private void calculateTotalInputHalo() {
 						if (inAx == null || inAx.getHalo() > axHalo) return;
 						inAx.halo = axHalo;
 					});
+					return;
 				}
 
 				double axScale = ax.getScale();

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV05.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV05.java
@@ -147,10 +147,10 @@ protected void buildModelDescription() throws ModelSpecsException
                     	// TODO createCovers();
                         break;
                     case "inputs":
-                    	buildInputTensors((List<?>) yamlElements.get(field));
+                    	input_tensors = buildInputTensors((List<?>) yamlElements.get(field));
                         break;
                     case "outputs":
-                        buildOutputTensors((List<?>) yamlElements.get(field));
+                        output_tensors = buildOutputTensors((List<?>) yamlElements.get(field));
                         calculateTotalInputHalo();
                         break;
                     case "config":
@@ -324,6 +324,7 @@ private void calculateTotalInputHalo() {
 						if (inAx == null || inAx.getHalo() > axHalo) return;
 						inAx.halo = axHalo;
 					});
+					return;
 				}
 
 				double axScale = ax.getScale();