How to process files after using FileInput function

I’m trying to modify an existing program I have such that it allows the user to select a file, which some python code then processes and some nice plots result. However, I’m really stuck on getting the input from the FileInput reader into a dataframe. My inputs are in relatively standardized xls and xlsx files, but I can’t figure out how I can put them in a dataframe as pd.read_excel expects a link to the file.

Here is the simple code I’m using to try and test my function, I’m sure I’m missing something simple but I’ve spent a fair bit of time trying to figure this out an am not making much headway.

from bokeh.io import curdoc
from bokeh.models.widgets import FileInput
from pybase64 import b64decode
import pandas as pd


def upload_fit_data(attr, old, new):
    print("fit data upload succeeded")
    print(file_input.value)
    print(type(new))
    decoded = b64decode(new)
    #print("Decoded: ", decoded)
    xls = pd.read_excel(decoded)
    print(xls)
    #f = open(decoded, "r")
    #contents = f.read()
    #print(contents)
file_input = FileInput(accept=".csv,.json,.txt,.pdf,.xls")
file_input.on_change('value', upload_fit_data)

doc=curdoc()
doc.add_root(file_input)

Hi mylesmoose!

This one was tough! I feel like I ought to start out by saying that this is really more a pandas/python issue than a Bokeh issue, but I was intrigued by it and went down the rabbithole anyway.

Here’s what I got to work:

from bokeh.io import curdoc
from bokeh.models.widgets import FileInput
from pybase64 import b64decode
import pandas as pd
import io


def upload_fit_data(attr, old, new):
    print("fit data upload succeeded")

    decoded = b64decode(new)
    f = io.BytesIO(decoded)
    new_df = pd.read_excel(f)
    print(new_df)

file_input = FileInput(accept=".csv,.json,.txt,.pdf,.xls")
file_input.on_change('value', upload_fit_data)

doc=curdoc()
doc.add_root(file_input)

The turning point was finding this buried SO answer that mentioned that xlrd (the engine doing the conversion for the read_excel function) is apparently mis-documented, and rather than wanting a string, it really wants bytes.

Good luck! By the way, if you end up with a working example, we’d love to see it-- keep in touch!

Works great! Thanks!

New bokeh user here. This was incredibly helpful ! My relatively simple use-case was to have the user select a file using FileInput widget and plot the contents of select columns on a scatter plot.

Is there a way to tell if the file uploading is completed before we actually proceed with the data?

When you receive the change signal on the backend, it will already arrive with all the data. So the upload would be complete. Same with the frontend - you receive the event already with the data.