Hi,
I am an author of a knime Python node. We have been using this node in our laboratory for a while without issues, but, having been installed on a Mac with an intel processor we have got an error.
The code for the node is (GitHub - sergsb/KNIME-standardizer)
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/at.ac.univie.pharminfo.univiestand_0.1.1.202306071257/src/main/python/univiestand_extension.py”, line 127, in configure
input_schema = input_schema.append(knext.Column(Chem.rdchem.Mol, “Standardized Molecules (UNIVIE)”))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/schema.py”, line 597, in init
raise TypeError(
TypeError: (“Could not create column with type <class ‘rdkit.Chem.rdchem.Mol’>, please use a supported column type”, TypeError("\n Could not find registered KNIME extension type for Python logical type <class ‘rdkit.Chem.rdchem.Mol’>. \n Call knime.api.schema.LogicalType.supported_value_types() to get a list of supported types and use one of these.\n ", TypeError(“The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.”)))
2024-03-04 07:54:19,657 : ERROR : main : : Node : Standardizer : 4:4 : Configure failed (PythonNodeRuntimeException): (“Could not create column with type <class ‘rdkit.Chem.rdchem.Mol’>, please use a supported column type”, TypeError("\n Could not find registered KNIME extension type for Python logical type <class ‘rdkit.Chem.rdchem.Mol’>. \n Call knime.api.schema.LogicalType.supported_value_types() to get a list of supported types and use one of these.\n “, TypeError(“The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.”)))
org.knime.python3.nodes.PythonNodeRuntimeException: (“Could not create column with type <class ‘rdkit.Chem.rdchem.Mol’>, please use a supported column type”, TypeError(”\n Could not find registered KNIME extension type for Python logical type <class ‘rdkit.Chem.rdchem.Mol’>. \n Call knime.api.schema.LogicalType.supported_value_types() to get a list of supported types and use one of these.\n ", TypeError(“The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.”)))
at org.knime.python3.nodes.CloseablePythonNodeProxy$FailureState.throwIfFailure(CloseablePythonNodeProxy.java:475)
at org.knime.python3.nodes.CloseablePythonNodeProxy.configure(CloseablePythonNodeProxy.java:402)
at org.knime.python3.nodes.DelegatingNodeModel.lambda$2(DelegatingNodeModel.java:130)
at org.knime.python3.nodes.DelegatingNodeModel.runWithProxy(DelegatingNodeModel.java:204)
at org.knime.python3.nodes.DelegatingNodeModel.configure(DelegatingNodeModel.java:128)
at org.knime.core.node.NodeModel.configureModel(NodeModel.java:1078)
at org.knime.core.node.Node.invokeNodeModelConfigure(Node.java:2007)
at org.knime.core.node.Node.configure(Node.java:1943)
at org.knime.core.node.workflow.NativeNodeContainer.performConfigure(NativeNodeContainer.java:566)
at org.knime.core.node.workflow.SingleNodeContainer.callNodeConfigure(SingleNodeContainer.java:315)
at org.knime.core.node.workflow.SingleNodeContainer.configure(SingleNodeContainer.java:200)
at org.knime.core.node.workflow.WorkflowManager.configureSingleNodeContainer(WorkflowManager.java:6540)
at org.knime.core.node.workflow.WorkflowManager.configureNodeAndPortSuccessors(WorkflowManager.java:6699)
at org.knime.core.node.workflow.WorkflowManager.configureNodeAndSuccessors(WorkflowManager.java:6642)
at org.knime.core.node.workflow.WorkflowManager.resetAndConfigureNodeAndSuccessors(WorkflowManager.java:5321)
at org.knime.core.node.workflow.WorkflowManager.resetAndConfigureNode(WorkflowManager.java:5242)
at org.knime.core.node.workflow.WorkflowManager.addConnection(WorkflowManager.java:1309)
at org.knime.core.node.workflow.WorkflowManager.addConnection(WorkflowManager.java:1225)
at org.knime.core.ui.wrapper.WorkflowManagerWrapper.addConnection(WorkflowManagerWrapper.java:223)
at org.knime.workbench.editor2.commands.CreateConnectionCommand.lambda$2(CreateConnectionCommand.java:404)
at org.knime.workbench.ui.async.AsyncUtil.wfmAsyncSwitchRethrow(AsyncUtil.java:200)
at org.knime.workbench.editor2.commands.CreateConnectionCommand.createConnection(CreateConnectionCommand.java:404)
at org.knime.workbench.editor2.commands.CreateConnectionCommand.execute(CreateConnectionCommand.java:331)
at org.eclipse.gef.commands.CommandStack.execute(CommandStack.java:228)
at org.eclipse.gef.tools.AbstractTool.executeCommand(AbstractTool.java:425)
at org.eclipse.gef.tools.AbstractTool.executeCurrentCommand(AbstractTool.java:438)
at org.eclipse.gef.tools.AbstractConnectionCreationTool.handleCreateConnection(AbstractConnectionCreationTool.java:256)
at org.eclipse.gef.tools.ConnectionDragCreationTool.handleButtonUp(ConnectionDragCreationTool.java:63)
at org.eclipse.gef.tools.AbstractTool.mouseUp(AbstractTool.java:1200)
at org.eclipse.gef.tools.SelectionTool.mouseUp(SelectionTool.java:574)
at org.eclipse.gef.EditDomain.mouseUp(EditDomain.java:301)
at org.eclipse.gef.ui.parts.DomainEventDispatcher.dispatchMouseReleased(DomainEventDispatcher.java:380)
at org.eclipse.draw2d.LightweightSystem$EventHandler.mouseUp(LightweightSystem.java:548)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:224)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:89)
at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4604)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1524)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1547)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1532)
at org.eclipse.swt.widgets.Widget.notifyListeners(Widget.java:1325)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4390)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3966)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1155)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:338)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1046)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:155)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:644)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:338)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:551)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:156)
at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:191)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:136)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:402)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:255)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:659)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:596)
at org.eclipse.equinox.launcher.Main.run(Main.java:1467)
2024-03-04 07:54:35,112 : ERROR : main : : CloseablePythonNodeProxyFactory : Standardizer : 4:4 : py4j.clientserver:There was an exception while executing the Python Proxy on the Python Side.
Traceback (most recent call last):
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/schema.py”, line 501, in logical
bundle = kt.get_value_factory_bundle_for_python_type(value_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/types.py”, line 328, in get_value_factory_bundle_for_python_type
raise TypeError(
TypeError: The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/at.ac.univie.pharminfo.univiestand.channel.bin.macosx.x86_64_0.1.1.202306071257/env/lib/python3.11/site-packages/py4j/clientserver.py”, line 617, in _call_proxy
return_value = getattr(self.pool[obj_id], method)(*params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/_node_backend_launcher.py”, line 361, in getDialogRepresentation
“schema”: kp.extract_schema(self._node, extension_version, inputs),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 163, in extract_schema
“properties”: {“model”: _extract_schema(obj, extension_version, specs)},
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 171, in _extract_schema
properties[name] = param_obj._extract_schema(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 1336, in _extract_schema
properties[name] = param_obj._extract_schema(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 878, in _extract_schema
values = _filter_columns(specs, self._port_index, self._column_filter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 965, in _filter_columns
filtered = [_const(column.name) for column in spec if column_filter(column)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3.nodes_4.7.3.v202305081333/src/main/python/knime/extension/parameter.py”, line 965, in
filtered = [_const(column.name) for column in spec if column_filter(column)]
^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/at.ac.univie.pharminfo.univiestand_0.1.1.202306071257/src/main/python/univiestand_extension.py”, line 15, in is_mol
return column.ktype == knext.logical(Chem.Mol)
^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/schema.py”, line 511, in logical
raise TypeError(
TypeError: ("\n Could not find registered KNIME extension type for Python logical type <class ‘rdkit.Chem.rdchem.Mol’>. \n Call knime.api.schema.LogicalType.supported_value_types() to get a list of supported types and use one of these.\n ", TypeError(“The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.”))
2024-03-04 07:54:35,495 : ERROR : main : : CEFNodeView : : : TypeError: Cannot read properties of undefined (reading ‘schema’) (source: http://org.knime.js.pagebuilder/org/knime/core/knime-pagebuilder2-ap.js; line: 7)
2024-03-04 07:57:40,445 : WARN : main : : Node : Sorter : 3:3 : No selected columns to sort
2024-03-04 08:00:40,049 : WARN : main : : CloseablePythonNodeProxy : Standardizer : 3:4 : Traceback (most recent call last):
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/schema.py”, line 501, in logical
bundle = kt.get_value_factory_bundle_for_python_type(value_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/Applications/KNIME 4.7.7.app/Contents/Eclipse/plugins/org.knime.python3_4.7.3.v202305081333/src/main/python/knime/api/types.py”, line 328, in get_value_factory_bundle_for_python_type
raise TypeError(
TypeError: The python type <class ‘rdkit.Chem.rdchem.Mol’> is not compatible with any registered Python value factory.
What can be the reason for this error?
2 posts - 2 participants