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Add sorting and pagination to bingo-elastic #1826

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khyurri opened this issue Mar 15, 2024 · 3 comments
Open

Add sorting and pagination to bingo-elastic #1826

khyurri opened this issue Mar 15, 2024 · 3 comments
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@khyurri
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khyurri commented Mar 15, 2024

Background
Currently, users can only access a limited count of compounds (up to 10,000 by default) from ElasticSearch. We need to incorporate sorting and pagination functionality into the bingo-elastic driver. This will allow users to receive more than 10,000 compounds from the index.

Solution
ElasticSearch offers a pagination feature (PIT). Visit https://www.elastic.co/guide/en/elasticsearch/reference/current/paginate-search-results.html to learn more.
We need to incorporate both the Java and Python functionality to enable transparent use of PIT, thus eliminating the need for user-level management. Therefore, if a user sets a sorting parameter, the bingo-elastic driver will automatically continue fetching documents until the limit is reached.
Importantly, after implementing this change, the limit option should be optional. This will allow users to download the entire index if they choose to do so.

@khyurri
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khyurri commented Mar 15, 2024

In progress PR for Python: #1712

@khyurri khyurri self-assigned this Mar 15, 2024
uladkaminski added a commit to uladkaminski/Indigo that referenced this issue Mar 15, 2024
@uladkaminski
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Java changes PR: #1827

@uladkaminski
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Additional Java changes PR: #1880

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