kaleido and internet access

[fergsc]

Hi,

I am trying to use NanoPlot to generate distribution plots in png/jpg format.
Having read #281 & #266 it appears that in order to generate such figures an internet connection is required. Is this ture?

When running on my institutions HPC we dont have internet access in the standard queues.

Thanks.

[wdecoster]

As I don't have a problem with internet access I haven't been able to replicate that issue - did you run into errors?

[fergsc]

Not an error as such, NanoPlot fails to produce png files for graphs. Having the png files makes sharing results easy and the plots look much better than if taken with a screenshot from the html dynamic plots.

[chienchi]

Problem Description

When running NanoPlot v1.40.2 on my institution’s HPC system (no internet access computer node), attempts to export figures as PDF fail with a “Failed to serialize document: Uncaught” error.

The error does not occur when running the same NanoPlot workflow on a head node with internet access.

Python version: 3.8.11 (default, Aug 3 2021, 15:09:35) [GCC 7.5.0]

plotly version: 5.24.1

kaleido version: 0.2.1

Workaround

I edited plot.py in NanoPlotter to fall back to write_image if scope.transform raises an exception.

This allows PDF (and other static formats) to be generated, bypassing the serialization failures.

Before

def save_static(self, figformat):
        scope = PlotlyScope()
        with open(self.path.replace("html", figformat), "wb") as f:
            f.write(scope.transform(self.fig, format=figformat))
            logging.info(
                f"Saved {self.path.replace('.html', '')}  as {figformat} (or png for --legacy)"
            )

After

def save_static(self, figformat):
        try:
            scope = PlotlyScope()
            with open(self.path.replace("html", figformat), "wb") as f:
                f.write(scope.transform(self.fig, format=figformat))
            logging.info(f"Saved {self.path.replace('.html', '')} as {figformat} (PlotlyScope)")
        except Exception as e:
            logging.warning(f"scope.transform failed: {e}. Falling back to write_image.")
            self.fig.write_image(self.path.replace("html", figformat))
            logging.info(f"Saved {self.path.replace('.html', '')} as {figformat} (write_image fallback)")

[wdecoster]

Ah, sounds like a nice fix. And that then solved it on computer nodes without internet, producing appropriate quality static images? Would you want to submit a PR for this fix?

[chienchi]

I just noticed that the latest version, 1.46.1, now uses Plotly’s write_image feature. Upgrading NanoPlot to the latest version should resolve the issue.

However, for users who encounter similar problems with older versions and are unable to upgrade, The workaround that may help.