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[Indigo] Indexing of a substantial quantity of molecules instigates the indexing process for the entire file. #1425

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bodyangug opened this issue Dec 6, 2023 · 2 comments · Fixed by #1742
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Bug Export to SDF Bucket: Export to SDF related issues

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@bodyangug
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Steps to Reproduce

  1. Arrange a considerable sized sdf file
  2. Invoke the iteradeSDF function with the prepared file
  3. Wait until an exception surfaces

Expected behavior
It is anticipated that the entire file should be processed without any exceptions.

Actual behavior
An exception is encountered with one molecule, effectively halting the indexing process for the subsequent content in the file.

Attachments
Example of error:
image

Indigo/Bingo version
Indigo version: 1.14.0-rc.1.0

Aditional Context
I've created the test, which reproduces that behavior - link
The way to run that test:

  1. using docker at the tests folder run prepeared container with the next command: docker-compose up -d
  2. run the test at tests.py file.
@khyurri
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khyurri commented Feb 28, 2024

This issue is fixed on #1742

To skip all errors when helpers.iterate_sdf is used, you need to pass error_handler.

For example:

from bingo_elastic.elastic import ElasticRepository, IndexName
from bingo_elastic.model import helpers, record

sdf = helpers.iterate_sdf("data/big_test.sdf", error_handler=record.skip_errors)
ElasticRepository(
    IndexName.BINGO_CUSTOM, host="localhost", port=9200
).index_records(sdf)

@AlexeyGirin
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Fixed as per @AlexanderSavelyev report

@AlexeyGirin AlexeyGirin added the Export to SDF Bucket: Export to SDF related issues label May 3, 2024
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Labels
Bug Export to SDF Bucket: Export to SDF related issues
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