Nodes failing after update to v4.5

KNIME Analytics Platform
1

Hi,

I am a newbie so please bear with me. I recently updated to v4.5 from v4.3 and tried to run a workflow that was working in v4.3. When I tried to run it in v4.5 I had a few complaints due to missing nodes, so I installed the necessary nodes. Then, it ran fine until some nodes failed (they were not those freshly installed), and I got these messages; please note that I tried to execute 2 different nodes separately to see whether I kept on having issues - although the failure affected one at a time:
Joiner (#442)/port_1/data.zip": invalid entry size (expected 4264289790 but got 529220091 bytes)
Cell Replacer (#47)/port_1/data.zip": Unexpected end of ZLIB input stream

I do not want to reset the whole workflow, because I cannot lose what was already processed. I have no idea what to do to fix this, and what is the cause. I am working on Ubuntu 20.04.

I would greatly appreciate some help!
Thanks in advance,
Luca

2

For my experience, KNIME updates in Windows are backward compatible. Not sure for Ubuntu.

3

(Do you have the old 4.3 version available to see if it successfully loads?)

Generally, KNIME is backward compatible. Workflows created with older versions of KNIME (e.g. 4.3) will load in newer versions in KNIME (e.g. 4.5) [unless there is a bug]

Messages like invalid entry size (expected 4264289790 but got 529220091 bytes) Cell Replacer (#47)/port_1/data.zip sound as if the files are corrupted.

Can you send the output of these commands?

  • file "<path-to-workflow>/Cell Replacer (#47)/port_1/data.zip"
  • unzip -t "<path-to-workflow>/Cell Replacer (#47)/port_1/data.zip"
  • cat "<path-to-workflow>/workflow.knime" | grep -A5 tableBackend
  • cat "<path-to-workflow>/workflow.knime" | grep version

– Bernd

2 Likes
4

Thanks Bernd. I had no issues on knime4.3, the workflow was originally created within that version.
Here are the outputs when using v4.5:

  • file "<path-to-workflow>/Cell Replacer (#47)/port_1/data.zip"
    Cell Replacer (#47)/port_1/data.zip: Zip archive data, at least v2.0 to extract

  • unzip -t "<path-to-workflow>/Cell Replacer (#47)/port_1/data.zip"
    Archive: Cell Replacer (#47)/port_1/data.zip
    testing: data.bin
    error: invalid compressed data to inflate
    testing: meta.xml OK
    At least one error was detected in Cell Replacer (#47)/port_1/data.zip.

  • cat "<path-to-workflow>/workflow.knime" | grep -A5 tableBackend
    (no output)

  • cat "<path-to-workflow>/workflow.knime" | grep version

<?xml version="1.0" encoding="UTF-8"?> 
<entry key="version" type="xstring" value="4.1.0"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
        <entry key="annotation-version" type="xint" value="20151123"/>
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I fear the data file is corrupted somehow. The file is detected to be a zip file (and it should be) but there are errors in the zip. I’m not sure if that’s related to 4.3 → 4.5 (because it’s a low level zip error, not a format incompatibility).

Apologies. I think you will need to reset the workflow up to that point and re-run.

6

Thanks Bernd. After resetting the workflow, it gave the desired output with no other issue/error. I think what happened was that the workflow in v4.3 had crashed (likely for RAM issues) before I decided to upgrade to v4.5. I realize now it was an important detail, my apologies for not mentioning that earlier - it just did not occur to me. My guess is that something must have happened during the zipping process at the time of the crash that caused the issues. Thanks again.

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