handle zenodo shit

bioimage-io · Oct 31, 2023 · 290e5f7 · 290e5f7
1 parent ec14b9d
commit 290e5f7
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Showing 6 changed files with 72 additions and 8 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/KerasWeights.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/KerasWeights.java
@@ -20,11 +20,15 @@
 package io.bioimage.modelrunner.bioimageio.description.weights;
 
 import java.io.File;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import io.bioimage.modelrunner.utils.CommonUtils;
+import io.bioimage.modelrunner.utils.Constants;
+
 /**
  * Class that contains the information for Keras weights.
  * For more information about the parameters go to:
@@ -276,7 +280,15 @@ public void setArchitectureSha256(Object architectureSha256) {
 	public String getSourceFileName() {
 		if (source == null)
 			return source;
-		return new File(source).getName();
+		try {
+			return CommonUtils.getFileNameFromURLString(source);
+		} catch (MalformedURLException e) {
+			if (source.startsWith(Constants.ZENODO_DOMAIN) && source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+				return new File(source.substring(0, 
+						source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length())).getName();
+			else
+				return new File(source).getName();
+		}
 	}
 
 	boolean gpu = false;

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/OnnxWeights.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/OnnxWeights.java
@@ -20,11 +20,14 @@
 package io.bioimage.modelrunner.bioimageio.description.weights;
 
 import java.io.File;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import io.bioimage.modelrunner.utils.CommonUtils;
+import io.bioimage.modelrunner.utils.Constants;
 import io.bioimage.modelrunner.versionmanagement.SupportedVersions;
 
 /**
@@ -295,7 +298,15 @@ public void setArchitectureSha256(Object architectureSha256) {
 	public String getSourceFileName() {
 		if (source == null)
 			return source;
-		return new File(source).getName();
+		try {
+			return CommonUtils.getFileNameFromURLString(source);
+		} catch (MalformedURLException e) {
+			if (source.startsWith(Constants.ZENODO_DOMAIN) && source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+				return new File(source.substring(0, 
+						source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length())).getName();
+			else
+				return new File(source).getName();
+		}
 	}
 
 	/**

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/PytorchWeights.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/PytorchWeights.java
@@ -20,11 +20,15 @@
 package io.bioimage.modelrunner.bioimageio.description.weights;
 
 import java.io.File;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import io.bioimage.modelrunner.utils.CommonUtils;
+import io.bioimage.modelrunner.utils.Constants;
+
 /**
  * Class that contains the information for Pytorch state dic weights.
  * For more information about the parameters go to:
@@ -151,7 +155,13 @@ public void setSha256(Object s) {
 	 * {@inheritDoc}
 	 */
 	public String getSource() {
-		return source;
+		if (source != null && 
+				source.startsWith(Constants.ZENODO_DOMAIN) 
+				&& source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+			return source.substring(0, 
+					source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length());
+		else
+			return source;
 	}
 
 	/**
@@ -276,7 +286,15 @@ public void setArchitectureSha256(Object architectureSha256) {
 	public String getSourceFileName() {
 		if (source == null)
 			return source;
-		return new File(source).getName();
+		try {
+			return CommonUtils.getFileNameFromURLString(source);
+		} catch (MalformedURLException e) {
+			if (source.startsWith(Constants.ZENODO_DOMAIN) && source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+				return new File(source.substring(0, 
+						source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length())).getName();
+			else
+				return new File(source).getName();
+		}
 	}
 
 	boolean gpu = false;

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/TfJsWeights.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/TfJsWeights.java
@@ -20,11 +20,15 @@
 package io.bioimage.modelrunner.bioimageio.description.weights;
 
 import java.io.File;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import io.bioimage.modelrunner.utils.CommonUtils;
+import io.bioimage.modelrunner.utils.Constants;
+
 /**
  * Class that contains the information for Tensorflow Javascript weights.
  * For more information about the parameters go to:
@@ -276,7 +280,15 @@ public void setArchitectureSha256(Object architectureSha256) {
 	public String getSourceFileName() {
 		if (source == null)
 			return source;
-		return new File(source).getName();
+		try {
+			return CommonUtils.getFileNameFromURLString(source);
+		} catch (MalformedURLException e) {
+			if (source.startsWith(Constants.ZENODO_DOMAIN) && source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+				return new File(source.substring(0, 
+						source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length())).getName();
+			else
+				return new File(source).getName();
+		}
 	}
 
 	boolean gpu = false;

diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/TorchscriptWeights.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/weights/TorchscriptWeights.java
@@ -20,11 +20,14 @@
 package io.bioimage.modelrunner.bioimageio.description.weights;
 
 import java.io.File;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import io.bioimage.modelrunner.utils.CommonUtils;
+import io.bioimage.modelrunner.utils.Constants;
 import io.bioimage.modelrunner.versionmanagement.SupportedVersions;
 
 /**
@@ -297,7 +300,15 @@ public void setArchitectureSha256(Object architectureSha256) {
 	public String getSourceFileName() {
 		if (source == null)
 			return source;
-		return new File(source).getName();
+		try {
+			return CommonUtils.getFileNameFromURLString(source);
+		} catch (MalformedURLException e) {
+			if (source.startsWith(Constants.ZENODO_DOMAIN) && source.endsWith(Constants.ZENODO_ANNOYING_SUFFIX))
+				return new File(source.substring(0, 
+						source.length() - Constants.ZENODO_ANNOYING_SUFFIX.length())).getName();
+			else
+				return new File(source).getName();
+		}
 	}
 
 	/**

diff --git a/src/main/java/io/bioimage/modelrunner/model/Model.java b/src/main/java/io/bioimage/modelrunner/model/Model.java
@@ -677,9 +677,9 @@ void doTiling(List<Tensor<R>> inputTensors, List<Tensor<T>> outputTensors,
 		int[] tilesPerAxis = inTileSpecs.values().stream().findFirst().get().getPatchGridSize();
 		int nTiles = 1;
 		for (int i : tilesPerAxis) nTiles *= i;
-		tileCounter.acceptTotal(new Long(nTiles));
+		tileCounter.acceptTotal(Long.valueOf(nTiles));
 		for (int j = 0; j < nTiles; j ++) {
-			tileCounter.acceptProgress(new Long(j));
+			tileCounter.acceptProgress(Long.valueOf(j));
 			int tileCount = j + 0;
 			List<Tensor<?>> inputTileList = IntStream.range(0, inputTensors.size()).mapToObj(i -> {
 				if (!inputTensors.get(i).isImage())