Generate ChEMBL Predictions


This is a companion discussion topic for the original entry at https://kni.me/w/f1wguQAF_quMkdj9

Hello. I’m looking for help running this workflow, please. I would also appreciate any pointers to debugging techniques for this sort of problem.

I can’t get the “ONNX to Tensorflow” node to execute correctly. I’ve tried various versions of Python and Tensorflow and am now at 3.7.9 and 2.10.0. I’m running Windows 10-64 with no GPU.

I get an error on the node which just says “Execute failed: ‘input’”

I see the following in the log:

2022-11-08 19:23:07,367 : INFO : Thread-41 : PythonKernel : ONNX to TensorFlow Network Converter : 0:2 : To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-11-08 19:23:07,678 : ERROR : KNIME-Worker-14-ONNX to TensorFlow Network Converter 0:2 : Node : ONNX to TensorFlow Network Converter : 0:2 : Execute failed: ‘input’
org.knime.dl.tensorflow.core.convert.DLNetworkConversionException: ‘input’
at org.knime.dl.onnx.core.convert.tf.ONNXTFNetworkConverter.getSpecificConversionException(ONNXTFNetworkConverter.java:247)
at org.knime.dl.onnx.core.convert.tf.ONNXTFNetworkConverter.convertNetworkInternal(ONNXTFNetworkConverter.java:156)
at org.knime.dl.onnx.core.convert.tf.ONNXTFNetworkConverter.convertNetworkInternal(ONNXTFNetworkConverter.java:1)
at org.knime.dl.tensorflow.core.convert.TFAbstractNetworkConverter.convertNetwork(TFAbstractNetworkConverter.java:108)
at org.knime.dl.tensorflow.base.nodes.converter.TFAbstractConverterNodeModel.execute(TFAbstractConverterNodeModel.java:160)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:549)
at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1267)
at org.knime.core.node.Node.execute(Node.java:1041)
at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:559)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:201)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:117)
at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:367)
at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:221)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)
Caused by: org.knime.python2.kernel.PythonIOException: ‘input’
Traceback (most recent call last):
File “”, line 8, in
File “”, line 8, in
KeyError: ‘input’

at org.knime.python2.kernel.Python2KernelBackend.executeCommand(Python2KernelBackend.java:1278)
at org.knime.python2.kernel.Python2KernelBackend.execute(Python2KernelBackend.java:1234)
at org.knime.python2.kernel.Python2KernelBackend.lambda$9(Python2KernelBackend.java:1240)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)

Blockquote