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Make mikado compatible with Sqlalchemy 1.4.0 and following #388

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lucventurini opened this issue Mar 17, 2021 · 3 comments · Fixed by #419
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Make mikado compatible with Sqlalchemy 1.4.0 and following #388

lucventurini opened this issue Mar 17, 2021 · 3 comments · Fixed by #419
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@ljyanesm @lucventurini
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EI-Internal enhancement
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2.2.x

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lucventurini commented Mar 17, 2021 •
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Version 2.2.1 introduces a pin for https://github.com/kvesteri/sqlalchemy-utils as it is incompatible with SQLAlchemy 1.4.0 and newer.

This pin should be removed as soon as sqlalchemy-utils is updated with a patch introducing the compatibility.
@lucventurini lucventurini added this to the 2.2.x milestone Mar 17, 2021
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lucventurini commented Mar 17, 2021 •
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Please note that the bioconda/bioconda-recipes meta.yaml file will also need to be updated, removing the pin, once sqlalchemy-utils is updated.

@lucventurini lucventurini changed the title Remove the pin for SQLAlchemy [IN PROGRESS] Make mikado compatible with Sqlalchemy 1.4.0 and following Mar 18, 2021
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Update: I have revised the release notes for SQLA 1.4.0 and ... Mikado will need lots of work to be made compatible. Many constructs that are used in the code have been deprecated (session.query, baked queries to name two).

This would require dedicated work.

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Update: sqlalchemy-utils now supports SQLA 1.4+, from 0.37 (present in PyPI but not Conda).
The pin on sqlalchemy can now be removed if sqlalchemy-utils is enforced to 0.37 and later.

ljyanesm added a commit that referenced this issue Aug 5, 2021
@ljyanesm
Update sqlalchemy version
8ae1201 
- Updates implicitly converted scalar queries in orf and junctions.
- Removes "threadlocal" strategy from the engine connection parameters in xml_serialiser.py as this is not supported.

Fixes #388
@lucventurini lucventurini mentioned this issue Aug 20, 2021
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Solve performance issues affecting extra-dense superloci in ONT runs. EI-CoreBioinformatics/mikado
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@ljyanesm @lucventurini