Hi @potts,
Thank you for your reply. I ave opened an issue as you mentioned in the comment:https://github.com/knime/knimepy/issues/25. And of course I would be happy to help in the testing phase.
I have another problem now, with the same workflow and python script.
When I am passing a big input from a csv file (2 rows and 2000 columns) instead of a small input (2 rows and 10 columns) I am getting following error in the saved workflow:
“No such file or URL: C:\Users\z639760\AppData\Local\Temp\tmpoyy6_xco\input_3.json”
Code:
import pandas as pd
import knime
#knime workflow information
knime.executable_path = "D:/Documents/knime_4.1.2/knime.exe"
workspace = "D:/knime-workspace-4"
workflow = "Test/python_knime"
#input data to knime
interesting_targets = {'target_chembl_id':["CHEMBL1","CHEMBL21","CHEMBL12"]}
df = pd.read_csv("C:/Users/uname/Documents//Data/sample_data.csv", sep=",", encoding = "ISO-8859-1")
#knime workflow execution
with knime.Workflow(workflow_path=workflow,workspace_path=workspace) as wf:
wf.data_table_inputs[0] = df
wf.save_after_execution = True
wf.execute()
#knime workflow output
print(wf.data_table_outputs)
Full error message in python:
ERROR:root:captured stdout: CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
Install location:
file:/d:/Documents/knime_4.1.2/
Configuration file:
file:/d:/Documents/knime_4.1.2/configuration/config.ini loaded
Configuration location:
file:/d:/Documents/knime_4.1.2/configuration/
Framework located:
file:/d:/Documents/knime_4.1.2/plugins/org.eclipse.osgi_3.12.100.v20180210-1608.jar
Loading extension: reference:file:javax.transaction_1.1.1.v201105210645.jar
eclipse.properties not found
Loading extension: reference:file:org.eclipse.osgi.compatibility.state_1.1.0.v20170516-1513.jar
eclipse.properties not found
Framework classpath:
file:/d:/Documents/knime_4.1.2/plugins/org.eclipse.osgi_3.12.100.v20180210-1608.jar
file:/d:/Documents/knime_4.1.2/plugins/
file:/d:/Documents/knime_4.1.2/plugins/javax.transaction_1.1.1.v201105210645.jar
file:/d:/Documents/knime_4.1.2/plugins/org.eclipse.osgi.compatibility.state_1.1.0.v20170516-1513.jar
Debug options:
file:/C:/Users/z639760/Documents/KNIME/Python/.options not found
Time to load bundles: 11
Starting application: 1212
WARN main Node No such file or URL: C:\Users\z639760\AppData\Local\Temp\tmpoyy6_xco\input_3.json
WARN main Node The file "C:\Users\z639760\AppData\Local\Temp\tmpbdsdsw5l\input_3.json" could not be resolved to json
Start VM: -server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UnsyncloadClass
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Xmx24576m
-Dorg.eclipse.swt.browser.IEVersion=11001
-Dsun.awt.noerasebackground=true
-Dequinox.statechange.timeout=30000
-Djava.class.path=D:/Documents/knime_4.1.2/\plugins/org.eclipse.equinox.launcher_1.4.0.v20161219-1356.jar
-os win32
-ws win32
-arch x86_64
-launcher D:/Documents/knime_4.1.2/knime.exe
-name Knime
--launcher.library D:/Documents/knime_4.1.2/\plugins/org.eclipse.equinox.launcher.win32.win32.x86_64_1.1.551.v20171108-1834\eclipse_1630.dll
-startup D:/Documents/knime_4.1.2/\plugins/org.eclipse.equinox.launcher_1.4.0.v20161219-1356.jar
--launcher.overrideVmargs
-debug
-application org.knime.product.KNIME_BATCH_APPLICATION
-data C:\Users\z639760\AppData\Local\Temp\tmpbdsdsw5l\knime_data
-workflowDir=D:\knime-workspace-4\Test\python_knime
-option=3,inputPathOrUrl,C:\Users\z639760\AppData\Local\Temp\tmpbdsdsw5l\input_3.json,String
-option=4,outputPathOrUrl,C:\Users\z639760\AppData\Local\Temp\tmpbdsdsw5l\output_4.json,String
-vm D:/Documents/knime_4.1.2/\plugins/org.knime.binary.jre.win32.x86_64_1.8.0.202-b08/jre/bin\server\jvm.dll
-vmargs
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UnsyncloadClass
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Xmx24576m
-Dorg.eclipse.swt.browser.IEVersion=11001
-Dsun.awt.noerasebackground=true
-Dequinox.statechange.timeout=30000
-Djava.class.path=D:/Documents/knime_4.1.2/\plugins/org.eclipse.equinox.launcher_1.4.0.v20161219-1356.jar
ERROR:root:captured stderr: Oct 12, 2020 5:03:52 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http (280) [org.apache.cxf.transport.http.HTTPTransportFactory, org.apache.cxf.transport.http.HTTPWSDLExtensionLoader, org.apache.cxf.transport.http.policy.HTTPClientAssertionBuilder, org.apache.cxf.transport.http.policy.HTTPServerAssertionBuilder, org.apache.cxf.transport.http.policy.NoOpPolicyInterceptorProvider]
Oct 12, 2020 5:03:52 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (281) [org.apache.cxf.transport.http.HTTPConduitFactory, org.apache.cxf.transport.ConduitInitiator]
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Oct 12, 2020 5:04:12 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 280
Oct 12, 2020 5:04:12 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 281
Traceback (most recent call last):
File "<ipython-input-54-9c07be34ec76>", line 1, in <module>
runfile('C:/Users/z639760/Documents/KNIME/Python/knime_python.py', wdir='C:/Users/z639760/Documents/KNIME/Python')
File "C:\Users\z639760\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 786, in runfile
execfile(filename, namespace)
File "C:\Users\z639760\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/z639760/Documents/KNIME/Python/knime_python.py", line 27, in <module>
wf.execute()
File "C:\Users\z639760\AppData\Local\Continuum\anaconda3\lib\site-packages\knime.py", line 384, in execute
output_as_pandas_dataframes=output_as_pandas_dataframes,
File "C:\Users\z639760\AppData\Local\Continuum\anaconda3\lib\site-packages\knime.py", line 272, in run_workflow_using_multiple_service_tables
raise ChildProcessError("Output from KNIME not found")
ChildProcessError: Output from KNIME not found