Exception: REPORT BUG: error calculating text offset

[andreas-wilm]

Describe the bug

When exporting samples with the newish export(..., include_metadata=True) we sometimes experience Exception: REPORT BUG: error calculating text offset.

Code To Reproduce

We take one big FCS files and split it into multiple smaller ones. Every now and then we get the above error. I pickled two affected (sub)samples for a reproducible minimal working example.

In [1]: import pickle
In [2]: import flowkit as fk

In [3]: with open("SDBB030_210_ATVQGQNLK.pkl", 'rb') as fh:
    ...:     sample = pickle.load(fh)
In [4]: sample
Out[4]: Sample(v3.1, None, 60 channels, 6 events)
In [5]: sample.export(export_fcs, source='raw', include_metadata=True)
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-28-4a3b1964e193> in <module>
----> 1 sample.export(export_fcs, source='raw', include_metadata=True)

~/miniconda3/envs/tetdecon-test/lib/python3.9/site-packages/flowkit/_models/sample.py in export(self, filename, source, exclude_neg_scatter, exclude_flagged, exclude_normal, subsample, include_metadata, directory)
   1102             fh = open(output_path, 'wb')
   1103
-> 1104             flowio.create_fcs(
   1105                 fh,
   1106                 events.flatten().tolist(),

~/miniconda3/envs/tetdecon-test/lib/python3.9/site-packages/flowio/create_fcs.py in create_fcs(file_handle, event_data, channel_names, opt_channel_names, metadata_dict)
    312     # verify the final BEGINDATA value == text start position + length of the text string
    313     if text_start + len(text_string) != int(text['BEGINDATA']):
--> 314         raise Exception("REPORT BUG: error calculating text offset")
    315
    316     #

Exception: REPORT BUG: error calculating text offset

Expected behavior

Exporting should work (as it does in most cases)

Desktop (please complete the following information):

Reproduced in multiple OS

• OS: Mac OS 12.3.1
• Python version 3.9.12
• FlowKit version 0.9.0

Additional context

Happy to provide pkl files with affected samples via PM.

[whitews]

Hey Andreas,

Yep, send me an example and I'll try to figure out what's going on. I put that tripwire exception in there b/c I suspected there may be additional edge cases where the offset needs to be adjusted.

[whitews]

Andreas,

I think I've fixed this in FlowIO. Can you try uninstalling FlowIO and clone the latest master branch of FlowIO to replace it (should be version 1.0.1b0)?

[andreas-wilm]

Works! Wonderful. Thanks so much for the prompt fix.