Hi knime community, I am a novice at knime and am currently facing some issues. I would like to request your assistance in resolving my issues with running knime inside my python notebook. I am currently trying 2 approaches, both of which are not working so far. Seeking help from experts please. I am trying to use this workflow that I downloaded: GitHub - kmansouri/QSAR-ready: Standardization workflow for QSAR-ready chemical structures pre-treatment. See "release" tab for the latest version and sample files! . It works when I run it inside knime itself, but I am trying to see if I can run it inside python notebooks. I would like to seek your assistance in solving these errors. Thank you in advance! I have detailed the 2 methods below. Best, Marcus In the first approach, I ran pip install for knime and I am trying to run the workflow in this way, however I am not sure how to run the command. df_ld50.head() df_ld50 = pd.read_csv(r"C:\Users\TechD\Documents\Marcus\screening\src\data\raw\knime\knime_input_rat_oral_ld50.csv") # Initialize workflow with knime.Workflow(knime_workflow_path) as wf: wf.data_table_inputs[0] = df_ld50[] wf.execute() if len(wf.data_table_outputs) == 0: raise ValueError("The workflow does not have any output ports. Please add an output port to the workflow.") # Retrieve output data from the first output port output_table = wf.data_table_outputs[0] print(output_table) Here is what the dataframe looks like and here are the errors I encountered: [image][image] In the second approach, I tried running the subprocess. However it appears that no matter what I try, the input file path is not the file I specify. Please see the highlighted part in the screenshot below command = [ executable_path, "-reset", "-nosplash", "-nosave", "-application", "org.knime.product.KNIME_BATCH_APPLICATION", f"-workflowDir={knime_workflow_path}", f'-workflow.variable=cmd_input,{input_file_path},String' ] result = subprocess.run(command, capture_output=True, text=True) # Check for errors if result.returncode != 0: print("KNIME workflow execution failed.") print("STDOUT:", result.stdout) print("STDERR:", result.stderr) else: print("KNIME workflow executed successfully.") print("Output:", result.stdout) [image]

knime workflow errors in python

mlauber71 October 1, 2024, 8:43pm 2

@MCHR_CHR you can run knime from Jupyter notebooks

1 Like