Remove explicit reference to xref partition and use declarative parti…

[afg1]

The database has for a long time had a partitioning scheme on the xref table based on inheritance and a big trigger function. This made adding new databases to RNAcentral more painful than it needed to be.

This PR accompanies structural changes in the database to enable declarative partitioning, and get rid of most of the manual modification of the trigger function that was previously required.

The only change in the code was one reference to a specific partiton, which we can get rid of by adding a couple more conditions to the query that were implicit by using the partition.

This whole change pending a test import into the test database, and testing website deployment from there before I synchronise the changes in the PRO database, hence draft PR

[gemini-code-assist]

Summary of Changes

Hello @afg1, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request streamlines the database's xref table management by moving towards declarative partitioning, replacing an older, more cumbersome inheritance-based system. The primary code change involves updating a query to remove a direct reference to a specific database partition, instead incorporating the necessary filtering conditions directly into the query. This modification simplifies future database integrations and maintenance by decoupling the application code from specific partition names.

Highlights

• Database Partitioning Scheme Update: The pull request facilitates a transition from an inheritance-based database partitioning scheme for the xref table, which relied on triggers, to a more modern declarative partitioning approach. This change aims to simplify the process of adding new databases to RNAcentral.
• Code Simplification: A specific, hardcoded reference to an xref partition (xref_p11_not_deleted) has been removed from the query logic. This makes the code more flexible and less dependent on the underlying physical partition names.
• Explicit Query Conditions: To maintain the correct data filtering after removing the explicit partition reference, the query now includes explicit WHERE clauses (xref.dbid == 11 and xref.deleted == "N"). These conditions were previously implicit in the use of the specific partition.

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[gemini-code-assist]

Code Review

This pull request updates the database query logic to use declarative partitioning for the xref table, instead of referencing a specific partition. The changes correctly replace the hardcoded partition table with the main xref table and add the necessary conditions (dbid and deleted) to the WHERE clause. My review includes a couple of suggestions to improve code style and maintainability, specifically regarding import ordering and the use of magic numbers.

[gemini-code-assist]

According to PEP 8, imports should be sorted alphabetically within their groups. The previous order of these third-party imports was alphabetical. Please restore the alphabetical order to improve code readability and consistency.

Suggested change

	import psycopg2
	import psycopg2.extras
	from bs4 import BeautifulSoup
	from bs4 import BeautifulSoup
	import psycopg2
	import psycopg2.extras

References

1. PEP 8, the style guide for Python code, recommends that imports should be sorted alphabetically. Specifically, within each grouping (standard library, third-party, local), imports should be sorted. ^(link)

[gemini-code-assist]

These hardcoded values 11 and 'N' are magic numbers. To improve readability and maintainability, it's better to define them as named constants at the module level. For example:

# At the top of the file
RIBOVISION_DBID = 11
NOT_DELETED = 'N'

Then you can use these constants in the query, making the code more self-documenting.

References

1. Avoid using magic numbers. Define them as named constants to improve code readability and maintainability. This makes the code self-documenting and easier to update if the values change.