Monday, 25 January 2016

CPython Scripting in Pentaho Data Integration

Using the approach developed for integrating Python into Weka, Pentaho Data Integration (PDI) now has a new step that can be used to leverage the Python programming language (and its extensive package-based support for scientific computing) as part of a data integration pipeline. The step has been released to the community from Pentaho Labs and can be installed directly from PDI via the marketplace.


Python is becoming a serious contender to R when it comes to programming language choice for data scientists. In fact, many folks are leveraging the strengths of both languages when developing solutions. With that in mind, it is clear that data scientists and predictive application developers can boost productivity by leveraging the PDI + Python combo. As we all know, data preparation consumes the bulk of time in a typical predictive project. That data prep can typically be achieved more quickly in PDI, compared to developing code from scratch, thanks to its intuitive graphical development environment and extensive library of connectors and processing steps. Instead of having to write (and rewrite) code to connect to source systems (such as relational databases, NoSQL databases, Hadoop filesystems and so forth), and to join/filter/blend data etc., PDI allows the developer to focus their coding efforts on the cool data science-oriented algorithms.

CPython Script Executor

As the name suggests, the new step uses the C implementation of the Python programming language. While there are JVM-based solutions available - such as Jython - that allow a more tightly integrated experience when executing in the JVM, these do not facilitate the use of many high-powered Python libraries for scientific computing, due to the fact that such libraries include highly optimised components that are written in C or Fortran. In order to gain access to such libraries, the PDI step launches, and communicates with, a micro-service running in the C Python environment. Communication is done over plain sockets and messages are stored in JSON structures. Datasets are transmitted as CSV and the very fast routines for reading and writing CSV from the pandas Python package are leveraged.

The step itself offers maximum flexibility when it comes to dealing with data. It can act as a start point/data source in PDI (thus allowing the developer the freedom to source data directly via their Python code if so desired), or it can accept data from an upstream step and push it into the Python environment. In the latter case, the user can opt to send all incoming rows to Python in one hit, send fixed sized batches of rows, or send rows one-at-a-time. In any of these cases the data sent is considered a dataset, gets stored in a user-specified variable in Python, and the user's Python script is invoked. In the "all data" case, there is also the option to apply reservoir sampling to down-sample to a fixed size before sending the data to Python. The pandas DataFrame is used as the data structure for datasets transferred into Python.



A python script can be specified via the built-in editor, or loaded from a file dynamically at runtime. There are two scenarios for getting output from the Python environment to pass on to downstream PDI steps for further processing. The first (primary) scenario is when there is a single variable to retrieve from Python and it is a pandas DataFrame. In this case, the columns of the data frame become output fields from the step. In the second scenario, one or more non-data frame variables may be specified. In this case, their values are assumed to be textual (or can be represented as text) or contain image data (in which case they are retrieved from Python as binary PNG data). Each variable is output in a separate PDI field.


Requirements

The CPython Script Executor step will work with PDI >= 5.0. Of course, it requires Python to be installed and the python executable to be in your PATH environment variable. The step has been tested with Python 2.7 and 3.x and, at a minimum, needs the pandas, matplotlib and numpy libraries to be installed. For Windows users in particular, I'd recommend installing the excellent Anaconda python distribution. This includes the entire SciPy stack (including pandas and scikit-learn) along with lots of other libraries.

Example

The example transformation shown in the following screenshot can be obtained from here.

The example uses Fisher's classic iris data. The first python step (at the top) simply computes some quartiles for the numeric columns in the iris data. This is output from the step as a pandas DataFrame, where each row corresponds to one of the quartiles computed (25th, 50th and 75th), and each column holds the value for one of the numeric fields in the iris data. The second python step from the top uses the scikit-learn decomposition routine to compute a principal components analysis on the iris data and then transforms the iris data into the PCA space, which is then the output of the step. The third python step from the top uses the matplotlib library and plotting routines from the pandas library to compute some visualisations of the iris data (scatter plot matrix, Andrew's curves, parallel coordinates and rad-viz). These are then extracted as binary PNG data from the python environment and saved to files in the same directory as the transformation was loaded from. The two python steps at the bottom of the transformation learn a decision tree model and then use that model to score the iris data respectively. The model is saved (from the python environment) to the directory that the transformation was loaded from.


Conclusion

The new PDI CPython Script Executor step opens up the power of Python to the PDI developer and data scientist. It joins the R Script Executor and Weka machine learning steps in PDI as part of an expanding array of advanced statistical and predictive tools that can be leveraged within data integration processes.

171 comments:

  1. Great stuff. Thanks for sharing this!
    Question: Is it possible to pass a JSON string instead of a CSV?

    ReplyDelete
  2. Kettle rows are transferred as CSV and materialised as a pandas data frame on the Python side. If your json strings are stored as quoted kettle fields (escaping is probably necessary for quotes in the json itself) then I guess it should be possible to just pull the values out of the rows of the frame on the Python side.

    We could, in a future release, add an option to the row-by-row mode to simply assign the value of each field in the Kettle row to a separate variable in Python.

    Cheers,
    Mark.

    ReplyDelete
  3. I keep getting the error as at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.executeScript(CPythonScriptExecutor.java:446)

    Any suggestions ?

    I am using Anaconda python.

    ReplyDelete
  4. I assume that you have the Anaconda bin directory in your PATH? Is Anaconda installed system-wide, or in your home directory? Some people have reported problems with a system-wide installation - something to do with file permissions preventing Anaconda from writing data.

    Is there a stack trace available on the console or in the PDI logs?

    Cheers,
    Mark.

    ReplyDelete
  5. Hi Mark!
    Thanks a lot for wonderful job.
    It is amazing opportunity ti incorporate pure Python script inside PDI.
    I use PDI 7.0 Community Edition on iOS X and Ubuntu.
    But sometimes I got a error after saving and trying to open CPythonExecutor step.
    "Enable to open dialog for this step"
    Argument cannot be null
    java.lang.IllegalArgumentException: Argument cannot be null
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.SWT.error(Unknown Source)
    at org.eclipse.swt.widgets.Widget.error(Unknown Source)
    at org.eclipse.swt.widgets.Text.setText(Unknown Source)
    at org.pentaho.di.ui.core.widget.TextVar.setText(TextVar.java:210)
    at org.pentaho.di.ui.trans.steps.cpythonscriptexecutor.CPythonScriptExecutorDialog.getData(CPythonScriptExecutorDialog.java:886)
    at org.pentaho.di.ui.trans.steps.cpythonscriptexecutor.CPythonScriptExecutorDialog.open(CPythonScriptExecutorDialog.java:249)
    at org.pentaho.di.ui.spoon.delegates.SpoonStepsDelegate.editStep(SpoonStepsDelegate.java:127)
    at org.pentaho.di.ui.spoon.Spoon.editStep(Spoon.java:8789)
    at org.pentaho.di.ui.spoon.trans.TransGraph.editStep(TransGraph.java:3179)
    at org.pentaho.di.ui.spoon.trans.TransGraph.mouseDoubleClick(TransGraph.java:775)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(Unknown Source)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.notifyListeners(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.pentaho.di.ui.spoon.Spoon.readAndDispatch(Spoon.java:1359)
    at org.pentaho.di.ui.spoon.Spoon.waitForDispose(Spoon.java:7990)
    at org.pentaho.di.ui.spoon.Spoon.start(Spoon.java:9290)
    at org.pentaho.di.ui.spoon.Spoon.main(Spoon.java:685)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.pentaho.commons.launcher.Launcher.main(Launcher.java:92)

    ReplyDelete
    Replies
    1. Konstantin, I ran into that as well. I've submitted a fix to that to the pentaho-labs repo, but the commit that fixed it is here if you need it in the meantime:

      https://github.com/CodeSolid/pentaho-cpython-plugin/commit/0e2e9dc32cbd0759429ab17b45983cb6a57916c8

      Delete
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    ReplyDelete
  7. Hi
    Thanks for making this available. I'm using the CPython Scripting tab in the Explorer interface. I have loaded a csv file into Explorer and this is transferred as a py_data dataframe into the CPython tab and I can inspect the data. However, if I make changes to the dataframe, adding another column for instance, how do I update the data loaded into Explorer? I have tried to write out a csv file so I can load it in again, but this fails with an error. I wonder if you have an example?

    Thanks again,
    Mark.

    ReplyDelete
  8. Hi Mark,

    I have a script which decodes a URL , I just need to feed the input URL to it. Can you help me please
    below is the script
    #!python

    import sys
    import re
    import urllib.parse
    import html.parser

    def main():
    rewrittenurl = sys.argv[1]
    match = re.search(r'https://urldefense.proofpoint.com/(v[0-9])/', rewrittenurl)
    if match:
    if match.group(1) == 'v1':
    decodev1(rewrittenurl)
    elif match.group(1) == 'v2':
    decodev2(rewrittenurl)
    else:
    print('Unrecognized version in: ', rewrittenurl)

    else:
    print('No valid URL found in input: ', rewrittenurl)

    def decodev1 (rewrittenurl):
    match = re.search(r'u=(.+?)&k=',rewrittenurl)
    if match:
    urlencodedurl = match.group(1)
    htmlencodedurl = urllib.parse.unquote(urlencodedurl)
    url = html.parser.HTMLParser().unescape(htmlencodedurl)
    print(url)
    else:
    print('Error parsing URL')

    def decodev2 (rewrittenurl):
    match = re.search(r'u=(.+?)&[dc]=',rewrittenurl)
    if match:
    specialencodedurl = match.group(1)
    trans = str.maketrans('-_', '%/')
    urlencodedurl = specialencodedurl.translate(trans)
    htmlencodedurl = urllib.parse.unquote(urlencodedurl)
    url = html.parser.HTMLParser().unescape(htmlencodedurl)
    print(url)
    else:
    print('Error parsing URL')

    if __name__ == '__main__':
    main()
    I need to give rewrittenurl variable the output of my previous step in pentaho.(which is coming from a select values having field name S3link.
    Thanks

    ReplyDelete
  9. Hello

    I am using this step in Kettle and would like to test the use of Script in Python using this step by step of pandas / pivot table. But I'm not getting the same results.

    I used the example, I got some values, but in some cases I have a number format problem.

    I would like to know if there is something I have to change for the pivot table to work .... as the example in
    Http://pbpython.com/pandas-pivot-table-explained.html

    ReplyDelete
  10. can anyone give the exact steps to configure cpython in kettle

    ReplyDelete
    Replies
    1. It should be fairly straightforward. I recommend installing the Anaconda python distribution, because this comes with the few dependencies that are required for the step to operate. Beyond this, all that is necessary is that the python executable is in your PATH environment variable. Note that if you are using OS X you will need to start Spoon via a console using the spoon.sh script so that the PATH variable is picked up (I have not found a reliable way of specifying environment variables in the Info.plist file in an Mac application bundle yet).

      Another thing to watch out for is permissions on the python side. Some people have reported problems when their Anaconda distribution is installed system-wide. Python occasionally needs to write files and there can be problems unless you are running with elevated privileges. The best thing to do is to install Anaconda locally in your home directory.

      Cheers,
      Mark.

      Delete
  11. One annoying thing with the plugin is when the python side tries to ship a unicode string back and a Message Size io exception occurs. At this point (at least in Windows and Spoon) subsequent attempts to run the CPython step fail with a java.io socket exception and I have to restart Spoon to continue to work. This isn't a bug since when the dataframe is properly constructed with ASCII only it works fine. Not sure if that socket can be disposed of somehow. I haven't checked but I get the feeling there is a python process left spinning in limbo.

    ReplyDelete
    Replies
    1. There's a bug in the call to taskkill on Windows -- I've submitted a fix for it. So the restart may be be addressed by that fix for you. Not sure about the Message Size IOException however.

      Delete
  12. Yes, the micro server and the PDI side of things requires UTF-8. I'll have to return to the code at some stage and see if it is possible to recover from a catastrophic failure, kill any orphaned python process and establish a new socket.

    Cheers,
    Mark.

    ReplyDelete
  13. Hi Mark,

    thanks a lot for the great plugin. I am having trouble executing a ktr with a cpython step in it on a remote (headless server).

    Executing the ktr locally in PDI (spoon) is working fine, but one I use a remote server as run configuration it is complaining about missing plugin. The server is a headless linux box without the client tools. Is it possible to run a Cpython ktr on such an environment and where do I have to install the plugin?

    Thanks
    Christoph

    ReplyDelete
  14. Hi Christoph,

    What sort of server is this? Carte or BA server? I don't have a 7.x install at hand at the moment, only an old 6.1 version. Within that version of the BA server plugins for PDI can be installed in

    suite/server/data-integration-server/pentaho-solutions/system/kettle/plugins/

    Cheers,
    Mark.

    ReplyDelete
    Replies
    1. Hi Mark,

      thanks a lot for your reply. After copying the plugin into the right folder the server is not complaining about a missing plugin anymore. But I get a java null pointer exception without a lot more information:

      2017-10-20 07:11:06,417 INFO [org.pentaho.di] 2017/10/20 07:11:06 - 170817_Python_Test - Dispatching started for transformation [170817_Python_Test]
      2017-10-20 07:11:07,042 ERROR [org.pentaho.di] 2017/10/20 07:11:07 - CPython Script Executor.0 - ERROR (version 7.1.0.0-12, build 1 from 2017-05-16 17.18.02 by buildguy) : Unexpected error
      2017-10-20 07:11:07,043 ERROR [org.pentaho.di] 2017/10/20 07:11:07 - CPython Script Executor.0 - ERROR (version 7.1.0.0-12, build 1 from 2017-05-16 17.18.02 by buildguy) : java.lang.NullPointerException
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.python.PythonSession.executeScript(PythonSession.java:479)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.executeScript(CPythonScriptExecutor.java:446)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.executeScriptAndProcessResult(CPythonScriptExecutor.java:349)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.processBatch(CPythonScriptExecutor.java:338)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.processRow(CPythonScriptExecutor.java:243)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at org.pentaho.di.trans.step.RunThread.run(RunThread.java:62)
      2017/10/20 07:11:07 - CPython Script Executor.0 - at java.lang.Thread.run(Thread.java:748)

      python 3.5 is installed and added to the path system variable. The necessary packages are installed as well.
      Any hint what might be wrong?

      Cheers
      Christoph

      Delete
  15. Are you sure that the PATH environment variable is available to PDI running on the server (and contains the entry to python)? Perhaps create a simple transformation that prints the contents of PATH to a text file so that you can check.

    Cheers,
    Mark.

    ReplyDelete
  16. Hi Mark,

    I have checked it again and all prerequisists seem to be fullfilled. I have executed a simple job on the remote server with a shell step and the following script:

    echo $PATH
    which python
    python --version

    And here is the corresponding pentaho log on the server:

    2017-10-24 12:44:27,099 INFO [org.pentaho.di] 2017/10/24 12:44:27 - RepositoriesMeta - Reading repositories XML file: /pentaho/.kettle/repositories.xml
    2017-10-24 12:44:27,100 INFO [org.pentaho.di] 2017/10/24 12:44:27 - PurRepository - Creating repository meta store interface
    2017-10-24 12:44:27,104 INFO [org.pentaho.di] 2017/10/24 12:44:27 - PurRepository - Connected to the enterprise repository
    2017-10-24 12:44:27,104 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Connected to AWS Pentaho Repo as admin
    2017-10-24 12:44:27,172 INFO [org.pentaho.di] 2017/10/24 12:44:27 - PurRepository - Creating repository meta store interface
    2017-10-24 12:44:27,173 INFO [org.pentaho.di] 2017/10/24 12:44:27 - PurRepository - Connected to the enterprise repository
    2017-10-24 12:44:27,218 INFO [org.pentaho.di] 2017/10/24 12:44:27 - my_shell_test - Start of job execution
    2017-10-24 12:44:27,238 INFO [org.pentaho.di] 2017/10/24 12:44:27 - my_shell_test - Starting entry [Shell]
    2017-10-24 12:44:27,245 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Shell - Running on platform : Linux
    2017-10-24 12:44:27,255 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Shell - Executing command : /pentaho/server/pentaho-server/tomcat/temp/kettle_123c6e0a-b8b9-11e7-af93-19d8b78f0f78shell
    2017-10-24 12:44:27,258 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Shell - (stdout) /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin
    2017-10-24 12:44:27,258 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Shell - (stdout) /usr/bin/python
    2017-10-24 12:44:27,259 INFO [org.pentaho.di] 2017/10/24 12:44:27 - Shell - (stdout) Python 3.5.2
    2017-10-24 12:44:27,269 INFO [org.pentaho.di] 2017/10/24 12:44:27 - my_shell_test - Finished job entry [Shell] (result=[true])
    2017-10-24 12:44:27,270 INFO [org.pentaho.di] 2017/10/24 12:44:27 - my_shell_test - Job execution finished

    The PATH environment variable can be resolved and contains /usr/bin where python is located and the python --version shows the version 3.5.2 I have installed.

    But the simple python script:
    # python script
    import pandas as pd

    X=15

    Generates a null pointer exception. Any ideas on how to debug that problem?

    Cheers
    Christoph

    ReplyDelete
  17. Hmm. The next question would be is python on the server setup the same as on your desktop machine? I.e. does it have the required python packages installed that the PDI plugin requires - pandas, numpy, matplotlib etc.? If you ssh to the server and run the transformation from the data integration installation using the pan command line tool does it work?

    Cheers,
    Mark.

    ReplyDelete
    Replies
    1. Hi Mark,

      thank you very much for your support! I had not been aware of the matplotlib requirement. I had installed python using anaconda locally on my laptop, but not on the server.

      You probably could update the blog post requirements section to include numpy and matplotlib as mandatory.

      Thanks again for your great plugin and support. It´s really appreciated.

      Cheers
      Christoph

      Delete
    2. Hi Chris,

      Good point :-) I've updated the requirements section. I'm glad to hear that it worked on the server in the end.

      Cheers,
      Mark.

      Delete
  18. Thank you Mark, you built the bridge that was missing on PDI

    ReplyDelete
  19. Hello Mark,


    What I did so far:
    - The transformation is running under root privileges (PDI5.3 Ubuntu16.04)
    - Python 2 and 3 are both on PATH
    - All dependencies were installed for both
    - The pyCheck.py and pyServer.py were extracted from .jar file and manually tested on python 2 and 3
    - command: "# python /var/pyCheck.py" (OK ExitStatus:0 Zero dependency errors)
    - command: "# python /var/pyServer.py" (OK ExitStatus:1 Zero dependency errors)
    - The same 2 commands above, was executed under a .kjb, inside 2 "ExecuteAShellScript" steps (No Dependency errors, either)
    - The most recent github's CPythonScriptExecutor was downloaded and compiled.
    - Even the simplest python code (eg: whatever=1+1) generates error

    The stacktrace is always the same:
    ERROR (version 5.3.0.0-213, build 1 from 2015-02-02_12-17-08 by buildguy) : Unexpected error
    ERROR (version 5.3.0.0-213, build 1 from 2015-02-02_12-17-08 by buildguy) : java.lang.NullPointerException
    at org.pentaho.python.PythonSession.rowsToPythonDataFrame(PythonSession.java:409)
    at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.rowsToPyDataFrame(CPythonScriptExecutor.java:458)
    at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.processBatch(CPythonScriptExecutor.java:276)
    at org.pentaho.di.trans.steps.cpythonscriptexecutor.CPythonScriptExecutor.processRow(CPythonScriptExecutor.java:243)
    at org.pentaho.di.trans.step.RunThread.run(RunThread.java:62)
    at java.lang.Thread.run(Thread.java:748)
    Finished processing (I=0, O=0, R=1, W=0, U=0, E=1)

    I've spent all day long trying to get this step running and I have no idea of what else can be done. I really appreciate any tip that would help to trackdown why this NPE is occurring.


    Thank you

    ReplyDelete
  20. Hi margenn,

    Was this running the example transformation from the github project? And I assume that you set the PATH from a terminal, and started PDI from spoon.sh? NPEs are almost always associated with an environment that is not configured correctly.

    Cheers,
    Mark.

    ReplyDelete
  21. Hi Mark,

    Thank a lot for this plugin. On a windows machine everything works fine (Pentaho 8.0), but on my AWS linux machine for some reason it won't work properly(also Pentaho 8.0).
    The OS is Ubuntu 16.04 with python3.6.3 (including matplotlib 2.1.1,numpy 1.13.3,pandas 0.21.1 and sklearn 0.19.1). Pentaho is running with root permissions.

    I get the following error:
    2018/01/29 09:30:47 - CPython Script Executor - Was unable to start python server
    2018/01/29 09:30:47 - CPython Script Executor - ERROR (version 8.0.0.0-28, build 8.0.0.0-28 from 2017-11-05 07.27.50 by buildguy) : org.pentaho.di.core.exception.KettleException:
    2018/01/29 09:30:47 - CPython Script Executor - java.io.IOException: Was unable to start python server
    2018/01/29 09:30:47 - CPython Script Executor - Was unable to start python server

    I've spent some time trying to get the CPython Script Executor step running but at this moment I have no idea what might be wrong. It seems like it is some kind of JAVA motivated Error. Have I missed anything crutial for the setup?

    Cheers,
    Matthias

    ReplyDelete
  22. Hi Matthias,

    There is also a dependency on scipy. Since sklearn depends on this, I always assumed that pip would install it too when sklearn is installed - not so I found out just recently :-)

    Anyhow, try installing scipy. Other dependencies (which you should have already) include: io (python 3), StringIO (python 2), math, traceback, socket, struct, os. json, base64, and pickle.

    I always use Anaconda python, which has everything and the kitchen sink out of the box.

    Cheers,
    Mark.

    ReplyDelete
  23. Hi Mark,
    Thank you for your answer. I checked all of those dependencies and there all installed and up to date. I also tried to use Anaconda python (as recommended) but unfortunately I still get the following error:

    2018/01/31 15:04:31 - CPython Script Executor.0 - ERROR (version 8.0.0.0-28, build 8.0.0.0-28 from 2017-11-05 07.27.50 by buildguy) :
    2018/01/31 15:04:31 - CPython Script Executor.0 - java.io.IOException: Was unable to start python server
    2018/01/31 15:04:31 - CPython Script Executor.0 - Was unable to start python server
    2018/01/31 15:04:31 - CPython Script Executor.0 - ERROR (version 8.0.0.0-28, build 8.0.0.0-28 from 2017-11-05 07.27.50 by buildguy) : org.pentaho.di.core.exception.KettleException:
    2018/01/31 15:04:31 - CPython Script Executor.0 - java.io.IOException: Was unable to start python server
    2018/01/31 15:04:31 - CPython Script Executor.0 - Was unable to start python server


    Cheers,
    Matthias

    ReplyDelete
    Replies
    1. Try "yum install PyQt4 tkinter".

      Delete
    2. I reinstalled pyqt4 and tkinter but unfortunately it didnt help. There remains the java.io.IOException: Was unable to start python server

      Delete
    3. One of our support guys had a similar issue under Ubuntu. He was able to get the step working after executing:

      sudo apt-get install python3-tk

      Cheers,
      Mark.

      Delete
    4. Hi, did you manage to fix this, I'm struggling with the same issue

      Delete
  24. Hi Mark, thank you for the plugin.
    I'm using PDI 8.0 CE on Windows X. When I try to connect the Cpython step with another I get the following error:
    java.lang.ClassCastException: java.base/java.lang.String cannot be cast to org.pentaho.di.trans.step.StepMeta
    at org.pentaho.di.trans.step.StepMeta.equals(StepMeta.java:537)
    at org.pentaho.di.ui.spoon.trans.TransGraph.mouseDoubleClick(TransGraph.java:801)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(Unknown Source)
    at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
    at org.pentaho.di.ui.spoon.Spoon.readAndDispatch(Spoon.java:1366)
    at org.pentaho.di.ui.spoon.Spoon.waitForDispose(Spoon.java:7984)
    at org.pentaho.di.ui.spoon.Spoon.start(Spoon.java:9245)
    at org.pentaho.di.ui.spoon.Spoon.main(Spoon.java:692)
    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.pentaho.commons.launcher.Launcher.main(Launcher.java:92)

    what went wrong?
    Cheers,
    Guido

    ReplyDelete
  25. Very strange! I've never seen this error before, and can't reproduce it using my copy of PDI 8. Do you have the latest version of the CPython step (v1.4) installed from the marketplace?

    Cheers,
    Mark.

    ReplyDelete
    Replies
    1. I have the latest version, I have downloaded it from the marketplace because my spoon version does not show the marketplace button. When I try to connect the Cpython step to the previous step the program says that no input are recived from the Cpython step.

      Delete
  26. This comment has been removed by the author.

    ReplyDelete
  27. Hi Mark,

    I have same problem, but OS is Linux Redhat 7, PDI 8 and Pentaho Server 8, python 2.7 (all library in requirement) and communication fail:

    2018-04-11 18:42:42,961 ERROR [org.pentaho.di] 2018/04/11 18:42:42 - CPython Script Executor.0 - ERROR (version 8.0.0.0-28, build 8.0.0.0-28 from 2017-11-05 07.27.50 by buildguy) : org.pentaho.di.core.exception.KettleException:
    2018/04/11 18:42:42 - CPython Script Executor.0 - java.io.IOException: Was unable to start python server
    2018/04/11 18:42:42 - CPython Script Executor.0 - Was unable to start python server


    In Windows execute success!!

    Any help on problem?

    Thanks,
    Yerko.

    ReplyDelete
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  29. Mark, I'm getting a ` java.lang.ArrayIndexOutOfBoundsException` when the dataframe I pass back is empty (edge case), is it not ok to pass empty dataframes into the stream?

    Thanks - brez

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  33. Dear Mark,

    I discovered that, when using CPython Scripting in Pentaho, the values in the data tables(frames) entering Python codes at a Cpython Pentaho step, differ totally from output of the step's previous step. For example, a 200,000 rows table flows into Cpython step, but only 200 rows came into the Python codes. (Because I placed Python codes for writing output to my PC within the Cpython scritps, therefore I can see the values of the variables in Cpython. )
    Besides, the values in each column within the 100 row table, differ from the output of the previous step. For instance, various string values in the original data table, become "value1", "value2", etc.
    The reason I care about how Cpython communicates with Pentaho is that, the Cpython generates totally different results from the results generated from pure Python codes.
    Besides, I am not able to get output from Cpython Pentaho steps which flow into following steps-- I can only generate output via Python codes within Cpython scripts. From Pentaho step metrics interface, I see only inflow into Cpython but no outflow. And Cpython step is pending with no finishing status.

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  41. Hi Mark,
    i install CPython Executor via marketplace on pdi-ce-8.2 on ubuntu 18. I install via pip all the libraries. When i launch pyTest1(the example you describe) from Spoon it gave me those errors:
    CPython Script Executor 2.0 - There was a problem initializing the python environment:
    CPython Script Executor 2.0 - Library "scipy" is not available
    CPython Script Executor 2.0 - Library "sklearn" is not available
    CPython Script Executor 2.0 - Library "matplotlib" is not avail.
    CPython Script Executor 2.0 - Library "numpy" is not available
    CPython Script Executor 2.0 - Library "pandas" is not available

    There is a way to solve this issue?
    thank you

    ReplyDelete
  42. Hi Mark
    Ive installed Pentaho and used it to create transformations with success, but after I've used Cpython script executor I get the following error
    2019/05/07 11:40:59 - CPython Script Executor.0 - ERROR (version 8.2.0.0-342, build 8.2.0.0-342 from 2018-11-14 10.30.55 by buildguy) :
    2019/05/07 11:40:59 - CPython Script Executor.0 - java.io.IOException: Was unable to start python server
    2019/05/07 11:40:59 - CPython Script Executor.0 - Was unable to start python server.
    Can you please guide?

    ReplyDelete
    Replies
    1. I've installed Numpy and matplotlib and all the dependencies as well. Thanks in advance

      Delete
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  47. I am getting the below error, when am trying to run

    CPython Script Executor.0 - ERROR (version 8.1.0.0-365, build 8.1.0.0-365 from 2018-04-30 09.42.24 by buildguy) :
    2019/07/29 14:40:08 - CPython Script Executor.0 - There was a problem initializing the python environment:

    Library "sklearn" is not available
    2019/07/29 14:40:08 - CPython Script Executor.0 - ERROR (version 8.1.0.0-365, build 8.1.0.0-365 from 2018-04-30 09.42.24 by buildguy) : org.pentaho.di.core.exception.KettleException:
    2019/07/29 14:40:08 - CPython Script Executor.0 - There was a problem initializing the python environment:

    Library "sklearn" is not available

    ReplyDelete
  48. i am able to import all required packages on local set up, i am new to pentaho but i have been working on python, so i am sure this is not a python set up issue.
    >>> from scipy.fftpack import fft

    >>> import scipy.integrate

    >>> from scipy import interpolate

    >>> from sklearn import datasets

    >>> from sklearn import metrics

    >>> import scipy

    >>> import numpy

    >>> import pandas

    >>> from scipy.constants import pi

    >>> from spicy.fftpack import fft



    I am getting the below error, when am trying to run

    CPython Script Executor.0 - ERROR (version 8.1.0.0-365, build 8.1.0.0-365 from 2018-04-30 09.42.24 by buildguy) :
    2019/07/29 14:40:08 - CPython Script Executor.0 - There was a problem initializing the python environment:

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    2019/07/29 14:40:08 - CPython Script Executor.0 - ERROR (version 8.1.0.0-365, build 8.1.0.0-365 from 2018-04-30 09.42.24 by buildguy) : org.pentaho.di.core.exception.KettleException:
    2019/07/29 14:40:08 - CPython Script Executor.0 - There was a problem initializing the python environment:

    Library "sklearn" is not available

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